8,097 Matching Annotations
  1. Jun 2026
    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript entitled "Essential function reflected in the phylodynamics of a multigene family - the pir genes of malaria parasites" by Jackson and colleagues investigates the global phylogeny of pir genes across 14 Plasmodium species and one Hepatocystis species. The authors also focus on the functional characterization of the conserved ortholog pirC1 and claim that pirC1 is not the founder of the family and that it plays an essential role in blood-stage growth.

      Strengths:

      Overall, the manuscript is well written and interesting, as it combines comparative genomics and evolutionary analysis with functional experiments. The phylogenetic analysis is rigorous and represents a major strength of the manuscript.

      Weaknesses:

      The general conclusions regarding the potential function of this gene family are not fully supported by the data presented. The manuscript moves too quickly from growth phenotype and localization studies to a specific mechanistic model. The discussion argues that PIRC1 may be involved in nutrient acquisition, host sensing, or metabolic support, but the data provided do not directly support these functions, and the manuscript in its present form remains speculative. Although the manuscript includes some experimental results, it lacks direct mechanistic validation of the specific functions of the pir genes, including pirC1. In its current form, the study does not yet establish a definitive role for pirC1 in metabolic processes.

      The reviewer is correct that there is no definitive proof for the function of the PIRC1 protein. We speculate that this protein is involved in a metabolic process based on mutant phenotype – small, poorly developed parasites that do not produce the same amount of DNA as wildtype parasites (and hence likely fewer merozoites). That this occurs in an in vitro culture of Plasmodium knowlesi rules out a role in the interaction with the host organism, such as sequestration or facilitating passage through the spleen. The localization of the protein outside of the parasite is consistent with a role in nutrient uptake, but we agree that additional experiments are required to determine the role of the protein definitively. We aim to look at the differences in the transcriptome and the metabolome to gain more insight into the pirC1 phenotype; this should reveal metabolic deficiencies in the mutant parasite.

      Reviewer #2 (Public review):

      Summary:

      This is an extensive study using phylogenetic comparison across multiple plasmodium species to gain new insights in relation to their evolutionary pathways and the potential function of pir. In addition to establishing a framework to identify related orthologues across species as well as expanding paralogues families within a species, the work also focuses on understanding loss and gain of different PIRs and how this indicates a relative lack of functional constraints and essentiality for most members of the gene family.

      The authors provide evidence that at least pirC has a conserved function and plays an important role in parasite growth in multiple species.

      While this study represents a significant effort and does provide interesting new insights that would help our understanding of this complex gene family in the future, it has a number of limitations.

      Strengths:

      Extensive and thorough phylogenetic analysis that is supported by some biological validation. Provides an indication that the PIR gene family has limited biological constraints and evolved independently across different species, leading to rapid expansion and deletion of orthologous groups. Identified pirC as a functional and important member of the family that is conserved across the species.

      Weaknesses:

      The phylogenetic tree is based on a truncated sequence that focuses on the more conserved parts of the pir sequence. This could potentially lead to missing the key functional drivers of evolution. The biological validation of the role of pirC has some inconsistencies that need to be addressed.

      The reviewer is correct. We do not use the repetitive parts of the pir gene sequences for the phylogeny. We define these as the ‘distal variable’ and ‘proximal’ domains of the protein in Fig. S1, results text and supplementary results. We remove these parts from the alignment because they are only nominally homologous (they cannot be aligned) and so break the basic assumption of phylogenetic analysis. Amino acid repeats evolve quickly and are homoplasic (their similarities do not reflect ancestry) so omitting them is correct and makes the phylogeny more reliable. While these features do not contribute to the phylogenetic estimate, we propose in the results text and Fig. S3, in agreement with the reviewer, that they are an important demonstration of how pirs have differentiated and what is different between the subfamilies. The reviewer is also correct that we have considered the whole gene sequence when comparing Alphafold predictions and in selection analyses of closely related sequences (in these cases, the repeat sequences can be aligned).

      A structural prediction for the sequence used in the alignment would mostly reflect the distal conserved domain but would be misleading because the alignment combines conserved regions that are not physically attached in reality. We will clarify these points.

      Reviewer #3 (Public review):

      This paper aims to classify, from an evolutionary perspective, the multigene family PIR found in malaria parasites infecting rodents and Old World monkeys, and to link this classification to functional diversification. The authors also hypothesize that PIR members conserved across species play important roles in parasite survival, and seek to clarify their functions.

      To achieve these aims, the authors comprehensively analyze the evolution of PIR genes using genomic and transcriptomic information from many malaria parasite species. They focus on PIRC1, a member conserved across species, and attempt to clarify its function in rodent and simian malaria parasites by examining the phenotypes of parasites in which the corresponding genetic locus has been disrupted. They also attempt to determine its localization using PIRC1 tagged with an epitope sequence. However, although the locus-disrupted parasites appear to show an approximately 50% reduction in growth rate, this effect seems to be overestimated. Another weakness is that the cause of the reduced growth rate has not been clarified. The localization analysis also remains insufficiently conclusive.

      Therefore, I consider that the first half of the paper, consisting of the bioinformatics analyses, achieves the objective of comprehensively summarizing PIR and may become a reference paper for discussing the evolution and function of the PIR gene family. On the other hand, regarding the function of PIRC1, no clear conclusion can be drawn from the results presented, and several additional experiments are necessary.

      My major comments are as follows.

      (1) The claim that the failure of eight disruption attempts indicates that pirC1 is essential is too strong.

      Lines 319-321: The authors argue that a total of eight failed attempts to disrupt the pirC1 locus using two different construct designs suggest that pirC1 is essential in P. berghei. However, the failure of these attempts could also reflect technical issues with the construct design itself, such as the length of the homologous regions used for recombination, which are approximately 650 bp. Therefore, it is an overstatement to conclude that "pirC1 is essential for P. berghei blood-stage growth." Given that parasites with disruption of the corresponding locus could be obtained in both P. chabaudi and P. knowlesi, a more appropriate statement would be that "pirC1 is important for P. berghei blood-stage growth."

      It is correct that we cannot rule out that the inability to delete the pirC1 gene is Plasmodium berghei is unrelated to an essential function. We are happy to change the text to the suggested description.

      (2) The data on the mCherry-expressing P. berghei line shown in Supplementary Figure 11 are insufficient.

      (a) Panel C: Southern blot analysis

      To conclusively identify the lower band in panel C as chromosome 1, additional probes specific to genes located on chromosomes 1 and 2 would be required. In addition, a parental parasite control should also be included. The Southern blot image of the parental parasite should show only a single band at the higher position, with no band at the lower position. Probes specific to chromosomes 1 and 2 would help demonstrate that the lower band corresponds to chromosome 1, rather than chromosome 2.

      To this end, the authors could describe the result as follows:

      "In the parental parasite, only a single band corresponding to chromosome 7 was detected, indicating that the smaller chromosome was genetically modified. The size of the lower band detected with the dhfr probe was identical to that of the band detected with the control chromosome 1 probe, but distinct from that detected with the chromosome 2 probe, indicating that chromosome 1 was modified."

      That said, this chromosome-level Southern blot analysis is not sufficient to demonstrate that the target PBANKA_0100500 locus was specifically modified. The authors should provide more direct evidence showing that the PBANKA_0100500 locus, rather than another genomic locus, was modified. For example, Southern blot analysis after restriction enzyme digestion would provide more definitive evidence. Diagnostic PCR may also provide more specific evidence.

      Although we are confident that the parasites has been modified in the expected way, we are planning to generate PCR data confirming that the mCherry tag is correctly integrated into PBANKA_010050.

      (b) Panel D: Flow cytometry analysis

      To allow a more accurate interpretation of the percentage of mCherry-positive cells, flow cytometry data for the parental parasite line should also be presented.

      We will repeat the flow cytometry experiments and include a wildtype strain in the analysis.

      (3) There are unclear points in the PCR results shown in Supplementary Figure 12.

      Supplementary Figure 12: In panel B, a PCR product should also be amplified from dPCHAS_0101200 using the P1-P3 primer pair. Why is this band absent? The authors should provide the uncropped electrophoresis image so that the larger band can be seen. In addition, if labels 1 and 2 indicate independent clones, this should be stated in the figure legend.

      We will gladly supply the full, uncropped electrophoresis image and we will clarify what the numbers indicate in the legend.

      (4) The growth rates of P. chabaudi and P. knowlesi parasites with disruption of the PIRC1 gene locus should be quantitatively analyzed.

      The growth rates of P. chabaudi and P. knowlesi are described only qualitatively, but they should be evaluated quantitatively. In Figure 4A, the parasitemia of wild-type P. chabaudi increases from approximately 6.1% on day 6 to approximately 15.6% on day 8, corresponding to a 3.8-fold increase. However, because parasite growth may already be affected by immune-mediated suppression at this stage, this value should be regarded as a minimum estimate. In contrast, the mutant increases from approximately 3.2% on day 8 to approximately 6.8% on day 10, corresponding to a 2.1-fold increase. Based on these values, the daily growth rate of the mutant appears to be reduced to at least approximately 56% of that of the wild type. Similarly, from the growth curve of P. knowlesi in Fig. 5A, the DMSO-treated group appears to increase approximately two-fold per day, whereas the rapamycin-treated group increases only approximately one-fold per day. Thus, P. knowlesi also appears to show an approximately 50% reduction in growth rate. Taken together, both P. chabaudi and P. knowlesi appear to reproducibly show an approximately 50% reduction in growth capacity. A reduction of this magnitude is difficult to describe as a "severe growth defect"; a more appropriate wording would be simply that the parasites "showed a growth defect." In addition, the terms "a severe growth defect" and "essential" appear to be overstated throughout the manuscript, and the wording should be toned down. Finally, I recommend presenting Figure 4A and Figure 5A on a logarithmic scale so that the trend in growth rates can be more intuitively appreciated from the graphs.

      It should be possible to determine the growth rate of the wildtype and mutant P. knowlesi parasites. In addition, we can change the text to reflect that although there is a growth phenotype in the two species in which we obtained mutants, the parasites do have the capacity to replicate. Note that in the case of P. knowlesi, the parasites numbers in vitro do not increase, hence any additional factors that decrease the growth rate, such as immune system and spleen, will lower the reproductive rate further and render the mutant parasite unable to proliferate.

      (5) The evidence that disruption of the PIRC1 gene locus in P. knowlesi does not affect erythrocyte invasion is weak.

      The authors describe that "the developmental cycle of the parasites lacking PIRCl is slightly longer than that of parasites that produce PIRCl (line 383-384)," and appear to support this interpretation with data showing that "mutant parasites are significantly smaller than wild-type parasites (line 414)" and that "the DNA content in ML10-arrested parasites lacking PIRCl is lower than that of DMSO-treated parasites (line 417-418)" at 24 hours after invasion. However, a slightly longer developmental cycle alone does not seem sufficient to explain a 50% growth reduction.

      I think the erythrocyte invasion capacity has not been quantitatively evaluated, and therefore, the evidence supporting the conclusion that the phenotype of P. knowlesi parasites with disruption of the PIRC1 gene locus is unrelated to erythrocyte invasion is weak. The authors should assess invasion efficiency using purified merozoites. For P. chabaudi, it should also be possible to apply an in vitro or in vivo erythrocyte invasion assay similar to that used for other rodent malaria parasites, and this should be evaluated as well.

      We can further investigate the invasion phenotype of the mutant P. knowlesi parasites. The presence of a clear phenotype during the intraerythrocytic stage indicates that the protein also has a role after invasion, but we agree that determining the effect on invasion directly will be useful.

      Alternatively, the reduced DNA content in ML10-arrested parasites lacking PIRC1 (lines 416-417) could suggest that the number of merozoites formed per schizont may be reduced. To clarify this point, the authors should assess whether the number of merozoites per schizont is altered in P. knowlesi (and P. chabaudi parasites lacking PIRC1).

      We aim to count merozoites and the level of invasion, which will allow us to determine the reproductive rate of the mutant parasites.

      (7) The authors propose the possibility that PIRC1 expressed in merozoites is released after invasion; however, the evidence that PIRC1 localizes to intracellular organelles is weak.

      Line 333: "a peripheral pattern around the parasite" is indicative of parasite plasma membrane, PV, or PVM. ", indicative of a parasitophorous vacuole (PV) or parasitophorous vacuole membrane (PVM) location" should be amended to ", indicative of parasite plasma membrane, a parasitophorous vacuole (PV) or parasitophorous vacuole membrane (PVM) location". In the Figure S14 image, red signals are uniformly detected from the merozoites formed in the schizont stage parasite (not really microorganelle patterns), but not from the PVM surrounding the schizont, suggesting parasite plasma membrane localization, not PVM. I agree that the signal is detected from the compartments extending into the iRBC cytosol, which may be difficult to explain if it is located on the parasite plasma membrane, but how frequently were such images seen?

      To determine the localization of the protein in the merozoite, we will image P. knowlesi merozoites.

      Figure 4D. In the images of liver-stage schizonts, AMA1 does not appear to localize to the micronemes in mature merozoites, suggesting this image is an immature schizont. Although PIRC1 appears to be expressed in liver-stage schizonts, it is difficult to clearly determine whether it localizes to intracellular organelles or to the parasite plasma membrane.

      This is a valuable comment. It is difficult to impossible to determine the exact localization of the protein at this stage, irrespective of the exact stage of the parasite. It is clear from the images is that the protein is not secreted at this stage. The main aim of the experiment was to determine whether the protein is produced by the parasite during the liver stage, which the results confirm.

      To clarify the above points, the authors should examine whether PIRC1 is detected in intracellular organelles or around the merozoites by analyzing its localization in purified merozoites.

      This we aim to do.

    1. Author response:

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

      eLife Assessment

      This valuable manuscript presents an open-source and low-cost acoustic system for quantifying biting and chewing in mice. The approach is carefully validated against human observers, demonstrating strong methodological reliability and enabling high-resolution analysis of feeding microstructure. The tool has broad relevance for studies of appetite circuits and pharmacological interventions. An important contribution is the identification of previously unrecognized "meal-related" neurons in the lateral hypothalamus, providing novel biological insight into solid food consumption. While the support for the methodological advances is compelling and robust, some circuit-level conclusions are preliminary or incomplete, relying on small pilot samples and manual classification, and should be interpreted with caution. This paper will be of interest to those interested in ingestive behavior and/or the hypothalamus.

      We thank the reviewers for their careful reading and constructive comments, which have substantially strengthened the manuscript. In the revised version, we have addressed every suggestion and introduced the following major additions: New experiments. We added one additional Vglut2 mouse to the calcium imaging cohort, achieving 386 neurons (Figure 8), and three naive Vgat mice with unilateral DREADD injections (Supplementary Fig. 5-1). New analyses. We performed ROC analyses on all feeding- and licking-related responses of n = 79 LH GABAergic and n = 386 LH glutamatergic neurons (Figures 7D-F and 8D-F). We also characterized the robustness of the Crunchometer to additive white-noise injection (Supplementary Fig. 1-2). New supplementary material. Three new supplementary figures have been added in total (Supplementary Figs. 1-2, 5-1, and 6-1). Supplementary Fig. 6-1 provides instructions for building a 1-Hz pulse generator that blinks an LED in synchrony with the video. Software improvements. We upgraded the original MATLAB scripts to an App GUI version, migrated the full codebase from MATLAB to Python, and packaged it as fully standalone executables for macOS (Apple Silicon) and Windows both of which run without a MATLAB license.

      Our point-by-point responses to the reviewers' comments are in red below. Deletions are omitted for brevity. We hope that the revisions fully address the points raised and render the manuscript suitable for publication.

      Public Reviews:

      Reviewer #1 (Public review):

      This is an interesting and valuable paper by Gil-Lievana, Arroyo et al. that presents an open-source method (the "Crunchometer") for quantifying biting and chewing behavior in mice using audio detection. The work addresses an important and unmet need in the field: quantitative measures of feeding behavior with solid foods, since most prior approaches have been limited to liquids. The authors make a clear and compelling case for why this problem is important, and I fully agree with their motivation.

      The system is carefully validated against human-scored video data and is shown to be at least as accurate, and in some cases more accurate, than human observers. This is a major strength of the study. I also particularly appreciate the demonstration of the technology in the context of LHA circuitry, which nicely illustrates its utility and importance for mechanistic studies of feeding. I also appreciate the ability to readily time-lock neural data to individual crunches. Overall, the manuscript is well-executed and represents a useful contribution to the field.

      We thank you for your appreciation of the Crunchometer and its alignment with ephys:

      To further facilitate alignment with neuronal activity, we have now also included a schematic diagram of the pulse generator used to blink an LED in synchronization with the video (see the new Supplementary Fig. 6-1).

      The comments I have are largely minor and should be straightforward to address:

      (1) The authors should report sample sizes for all mouse cohorts, either alongside the statistics or in the figure legends for mean data.

      We apologize for this oversight. We have now included all sample sizes in the figure captions.

      (2) Clarification is needed as to whether crunch detection fidelity is influenced by the hardness or softness of the food. The focus here is on standard pellets, with some additional high-fat pellet data, but it would be useful to know how generalizable the method is across different textures.

      We thank the reviewer for this important observation. Because the Crunchometer depends on bites generating an audible acoustic signal, food hardness directly impacts detection fidelity. Hard, brittle foods are readily detected, whereas soft foods such as jelly, pudding, or peanut butter are unlikely to produce a reliably detectable signal. This is a genuine scope limitation of the method, and we now make it explicit in the manuscript (see below).

      Regarding the two diets used in our study, Chow and HFD pellets differ only slightly in consistency, with HFD being marginally softer. These differences proved too subtle to separate acoustically: the intensity (dB) and spectral content of bites on the two diets were closely overlapping. Accordingly, when we trained an SVM on audio features alone, it could not reliably discriminate Chow from HFD bites.

      Importantly, the Crunchometer does not need to resolve food identity from sound, because audio and video play complementary roles in the system: the acoustic channel confirms that a bite occurred, while the mouse's position within the food-specific ROI determines which food was consumed. This division of labor is what allows per-diet attribution despite acoustically similar pellets.

      We have added to the Result section:

      “The Crunchometer, therefore, does not need to infer food identity acoustically: audio confirms that a bite occurred, and the mouse's position within a food-specific ROI identifies which food was consumed. This design enables per-diet attribution even for pellets with indistinguishable crunch signatures.”

      We fully agree with the reviewer that the study of solid-food consumption should not be restricted to standard murine diets. Foods with naturalistic textures, for example, the Granny Smith apple, chocolate, and salted peanuts used by O'Connell et al. (2025), span a much wider range of hardness and elasticity than Chow vs. HFD, and would likely generate more clearly differentiated acoustic signatures. We hypothesize that the Crunchometer could generalize to such foods to the extent that each food produces a clear and distinct acoustic pattern, and even where acoustic signatures overlap, ROI-based spatial attribution would continue to resolve food identity as long as each food is presented at a separate, trackable location.

      To make this scope explicit for readers, we have added the following clarification to the Behavioral Protocol section:

      "Our study is limited to the acoustic detection of standard Chow and HFD pellets, both of which exhibit a firm, brittle consistency. Future work should evaluate the fidelity of the Crunchometer across a broader range of food textures, encompassing varying degrees of hardness and elasticity, as explored by O'Connell et al. (2025)."

      (3) The authors should comment on how susceptible the Crunchometer is to background noise. For example, how well does it perform in the presence of white noise, experimenter movement, or other task-related sounds?

      We thank the reviewer for this valuable comment. The Crunchometer performs reliably in controlled, low-noise environments, but like any acoustic detection system, it is vulnerable to interference from sounds whose spectral content overlaps with the bite-related frequency band (500–950 Hz). To quantify this vulnerability, we stress-tested both the threshold-based and SVM-based detection methods by adding white noise to the original audio recordings at progressively decreasing amplitudes and measuring how detection performance degraded as the signal-to-noise ratio decreased. We found that the threshold-based method was more robust to white-noise contamination than the SVM-based method, maintaining acceptable detection performance at lower SNR values before degrading [see the new Supplementary Fig. 1-2].

      First, the white noise amplitude is generated as follows:

      Where L<sub>𝑛𝑜𝑖𝑠𝑒</sub> is the desired amplitude of the White Noise in dB. Then, the audio signal was range-normalized to its absolute maximum value, and the white noise was added with its desired amplitude, as shown by the following formula:

      (4) Chemogenetic activation of LHA GABAergic neurons is used. DREADD-based activation may strongly drive these neurons in a way that is not directly comparable to optogenetic or more physiological manipulations. While I do not think additional experiments are required, it would strengthen the discussion to briefly acknowledge this limitation.

      We thank the Reviewer for this thoughtful observation, which we agree with. Chemogenetic activation of LHA GABAergic neurons via DREADDs does not reproduce the physiological firing dynamics of these neurons along several dimensions: it imposes a sustained, tonic drive lasting hours after CNO administration; it likely produces firing rates above the endogenous range; and it lacks the fine temporal structure, phasic bursts, behaviorally- phased locked activity that these neurons exhibit during natural feeding episodes.

      We recognize, however, that this limitation is not unique to chemogenetics. Optogenetic approaches likewise fail to reproduce endogenous activity, as they impose synchronous, high-frequency activation patterns on a single cell type that are unlikely to occur under physiological conditions. Moreover, as we previously described in a phenomenon our laboratory termed optoception (Luis-Islas et al., 2022), optogenetic stimulation can itself generate signals perceptible to the animal, adding a further interpretive caveat. Thus, both techniques depart from physiological activity.

      For these reasons, we interpret our findings as evidence that activation of LHA GABAergic neurons is sufficient to drive the observed behavioral effects, without claiming that the endogenous firing pattern encodes these behaviors in the same manner or with the same dynamics imposed by our manipulation. We have now added a brief statement to the Discussion acknowledging this limitation explicitly:

      “A methodological consideration is that chemogenetic activation via DREADDs imposes a sustained, supra-physiological drive that does not reproduce the temporal structure of endogenous LHA GABAergic activity during feeding; optogenetic manipulations share analogous limitations (see optoception; Luis-Islas et al., 2022). Our findings, therefore, establish that activation of this neuronal population is sufficient to produce uncontrolled feeding and gnawing, without implying that its endogenous firing encodes them in the same manner.”

      Reviewer #2 (Public review):

      Summary:

      This manuscript introduces the Crunchometer, a low-cost, open-source acoustic platform for monitoring the microstructure of solid food intake in mice. The Crunchometer is designed to overcome the limitations of existing methods for studying feeding behavior in rodents. The goal was to provide a tool that could precisely capture the microstructure of solid food intake, something often overlooked in favor of liquid-based assays, while being affordable, scalable, and compatible with neural recording techniques. By doing so, the authors aimed to enable detailed analysis of how physiological states, drugs, and specific neural circuits shape naturalistic feeding behaviors.

      Strengths:

      The study's strengths lie in its clear innovation, methodological rigor in validation against human annotation, and demonstration of broad utility across behavioral and neuroscience paradigms. The approach addresses a significant methodological gap in the field by moving beyond liquid-based feeding assays and provides an accessible tool for precisely dissecting ingestive behavior. The system is validated across multiple contexts, including physiological state (fed vs. fasted), pharmacological manipulation (semaglutide), and circuit-level interventions (chemogenetic activation of LH neurons), and is further shown to integrate seamlessly with both electrophysiology and calcium imaging.

      (1) Introduces a low-cost, open-source acoustic tool for measuring solid food intake, filling a critical gap left by expensive and proprietary systems.

      (2) Makes the method easily adoptable across labs with detailed setup instructions and shared benchmark datasets.

      (3) Provides high temporal precision for detecting bite events compared to human observers.

      (4) Successfully distinguishes feeding microstructure (bites, bouts, IBIs, gnawing vs.

      consumption) with greater objectivity than manual annotation.

      (5) Demonstrates compatibility with electrophysiology and calcium imaging, enabling fine-scale alignment of neural activity with feeding behavior.

      (6) Effectively discriminates between fed vs. fasted states, validating physiological sensitivity.

      (7) Captures the pharmacological effects of semaglutide, although this is really just reduced feeding and associated readouts (bouts, latency, etc).

      (8) Has potential to distinguish consummatory vs. non-consummatory behaviors (e.g., food spillage, gnawing); however, the current SVM model struggles to separate biting from gnawing due to similar acoustic profiles, and manual validation is still required.

      (9) Provides potential for closed-loop experiments.

      Weaknesses:

      Several limitations temper the strength of the conclusions: the supervised classifier still requires manual correction for gnawing, generalizability across different setups is limited, and the neuroscience findings, particularly calcium imaging of GABAergic and glutamatergic neurons, are based on small pilot samples. These issues do not undermine the value of the tool, but mean that the neural circuit findings should be interpreted as preliminary.

      We sincerely thank the Reviewer for the careful and generous reading of our manuscript, and particularly for recognizing the methodological gap that the Crunchometer seeks to fill. We appreciate the acknowledgment that the tool's validation spans physiological, pharmacological, and circuit-level contexts, and that its integration with electrophysiology and calcium imaging was considered seamless. The Reviewer has also accurately identified the three main limitations of the current version of the platform, which we address in turn below:

      (1) The supervised SVM classifier still requires manual correction for gnawing.

      We agree with the Reviewer. The acoustic signatures of biting (consummatory) and gnawing (non-consummatory manipulation of the pellet) share overlapping linear spectrotemporal features that our SVM exploits for discrimination. This overlap reflects a genuine biomechanical similarity (both involve incisor contact with the pellet surface) rather than a shortcoming of the classifier per se. In ongoing work toward Crunchometer 2.0, we are addressing these limitations. The Crunchometer 2.0 will incorporate more sophisticated deep learning algorithms, such as ResNet, to better exploit non-linear features. Also, we are currently collecting a larger database of bite, gnawing, and environmental noise sounds across different setups, microphones, and conditions to build a more robust dataset for training new AI algorithms that can discriminate between gnawing and biting and generalize more robustly across microphones and behavioral setups. This effort will also be important for developing a closed-loop version of the Crunchometer to detect bites in real time and trigger an actuator (e.g., a laser). But we agree that, for the present manuscript, gnawing classification remains the weakest link in the pipeline.

      Nevertheless, we think that having a human in the loop is an advantage (not a disadvantage) of the equipment, as it improves the quality of database curation. No matter how sophisticated future algorithms become, human intervention will remain essential. To this end, we have now developed a human-validation GUI that further facilitates human revision of snippets through an intuitive, easy workflow, reducing human effort (Author response image 1).

      Author response image 1.

      The visual validator GUI allows a human to verify and reclassify snippets into the correct category in a friendly interface.

      (1) Generalizability across different setups is limited.

      This is a fair concern and one we have taken seriously, as noted above, and one we have already recognized. The acoustic signal captured by the Crunchometer is inherently sensitive to the geometry and material of the box, microphone placement, the ambient noise floor of the vivarium or experimental room, and the hardness of the specific pellet batch. To mitigate this, we have 1) released the full hardware specifications and bill of materials so that other laboratories can reproduce the acquisition geometry, and 2) provided the benchmark dataset and trained classifier weights so that groups using comparable setups can deploy the tool directly. We have already acknowledged that the SVM does not always generalize across setups. In this regard, we have now shown that the threshold method is more resistant to white-noise contamination (see new Supplementary Fig. 1–2) and, in our experience in the lab, it performs robustly across multiple setups and conditions we have tested. More importantly, improved algorithms are currently under development in our laboratory.

      (1) Some neuroscience findings (calcium imaging of GABAergic vs. glutamatergic neurons) are based on small pilot samples (n=2 mice per condition), limiting generalizability.

      (3) The neuroscience findings (calcium imaging of GABAergic and glutamatergic LH neurons) are based on small pilot samples.

      The Reviewer is correct, and we appreciate the comment. As noted in the manuscript, we explicitly state in the Results and Discussion that these findings are presented as preliminary. As the Reviewer noted, these findings do not undermine the value of the Crunchometer; we fully agree. The calcium imaging experiments were designed as a proof-of-concept to demonstrate that the temporal precision of the Crunchometer is sufficient to align neural activity with individual bite events, rather than as a definitive circuit-level characterization of LH GABAergic and glutamatergic populations during feeding. Nevertheless, we have now increased the number of Vglut2 mice by 1, bringing the total number of glutamatergic neurons to 386. We have now also performed a formal quantification of all the experiments recorded in Vgat (n=2, three sessions, 79 neurons) and Vglut2 (n=3, 6 sessions, 386 neurons). This new formal analysis uncovers neurons selectively tuned to liquid, solid, and both food types. A fully powered characterization of these two populations is underway in our laboratory, once funding arrives in the lab, and will be reported in a dedicated follow-up study.

      (2) Chemogenetic and pharmacological experiments used small cohorts, raising statistical power concerns.

      The chemogenetic experiments were conducted with a modest sample size (n = 4 bilaterally infected mice). Nevertheless, the data revealed a robust, reproducible behavioral effect consistent across all four subjects. The primary aim of this study was to illustrate the potential utility of the Crunchometer using complementary experimental approaches, including chemogenetic activation of GABAergic neurons in the lateral hypothalamic area (LHA). To further address this concern, we have now included three additional transgenic mice with unilateral infections and obtained results comparable to those of the bilateral condition. These new data are presented in a new supplementary figure comparing unilateral and bilateral infections (Supplementary Fig. 5-1). Notably, chemogenetic activation of LHA GABAergic neurons promoted eating-related consummatory behaviors to a similar extent under both unilateral and bilateral DREADD activation. Accordingly, we have now added the following text to the Results section:

      “Notably, unilateral DREADD infections in other naïve n=3 Vgat-cre mice yielded results comparable to bilateral infections. While the effect size was slightly reduced with unilateral administration, the difference between the two delivery methods was not statistically significant (Supplementary Fig. 5-1)”

      (3) Correlation with actual food intake is modest and sometimes less accurate than human observers.

      We agree that this result highlights the complexity of feeding behavior, influenced by factors such as hoarding and spillage. The threshold method detects feeding behavior solely based on the magnitude of bite-related sounds (e.g., when the mouse bites the pellet close to the microphone), whereas human observers incorporate additional visual information to infer feeding behavior even in the absence of detectable chewing sounds, introducing variability in detection criteria. Although the number of bouts identified by the Threshold method was comparable to those annotated by human observers, the estimated duration (Bout Size) of those detections differed. This discrepancy likely reflects some inconsistency in the detection criteria among human observers and delays in identifying the onset. Moreover, instances of mice chewing pellets without consuming them (i.e., spillage) were observed. These events were often misclassified as feeding bouts, resulting in false positives for both the threshold method and human observers.

      (4) Sensitive to hoarding behavior, which can reduce detection accuracy and requires manual correction for misclassifications (e.g., tail movements, non-food noises). However, these limitations are discussed and not ignored.

      We thank the reviewer for this constructive comment and for acknowledging that we explicitly discuss these limitations rather than overlook them. Indeed, gnawing and hoarding behaviors (together with tail movements and non-food noises) are factors that can reduce the accuracy of feeding detection. Even using the Crunchometer, an accurate measurement of solid-food consumption therefore remains challenging, which further supports the inclusion of a human-in-the-loop step to ensure a high-quality, well-curated database. Accordingly, we have added the following sentence to the Result section:

      "This human validation was essential for ensuring the high fidelity of our behavioral database and mitigating the inherent limitations of automated classification."

      Conclusion:

      Overall, this is an exciting and impactful methodological advance that will likely be widely adopted in the field. I recommend minor revisions to clarify the limits of classifier generalizability, better contextualize the small-sample neuroscience findings as pilot data, and discuss future directions (e.g., real-time closed-loop applications).

      We thank you for your constructive comments.

      Reviewer #3 (Public review):

      Summary:

      The manuscript provides detailed information on the construction of open-source systems to monitor ingestive behavior with low-cost equipment. Overall, this is a welcome addition to the arsenal of equipment that could be used to make measurements. The authors show interesting applications with data that reveal important neurophysiological properties of neurons in the lateral hypothalamus. The identification of previously unknown "meal-related" neurons in the LH highlights the utility of the device and is a novel insight that should spark further investigation on the LH. This manuscript and videos provide a wealth of useful information that should be a must-read for anyone in the ingestive behavior or hypothalamus fields.

      A scholarly introduction to the history and utility of various ways feeding is measured in rodents is provided. One point - the microstructure of eating solid food - has been studied extensively (for one of many studies, see https://doi.org/10.1371/journal.pone.0246569 ). However, I agree that the crunchometer will allow for more people to access recordings during food intake and temporally lock consummatory behavior to neural activity.

      Apologize for this oversight. This is indeed an important reference for the microstructure of eating solid food in a social context. We have now included it in the Introduction of this reference “Food intake in social contexts is a more ethologically valid model, in which radio-frequency identification (RFID) transponders enable the simultaneous assessment of feeding behavior across multiple mice in a single box (Rathod and Fulvio, 2021)”

      Questions on results:

      (1) It is unclear why 10% sucrose solution was used as a liquid instead of water, given that the study is focusing on the solid food source.

      One motivation for using sucrose rather than water alone was to create a highly palatable environment and to test whether mice would prefer palatable liquid sucrose over HFD. However, the choice of liquid stimulus will ultimately depend on the end user and the specific experimental conditions of each lab implementing the Crunchometer. Future versions of the apparatus could also incorporate multiple sippers to deliver several tastants alongside solid food.

      (2) It is unclear how essential the human verification is in the pipeline - results for Figure 1 keep referring to the verification as essential. Is that dispensable once the ML algorithms have been trained?

      Human validation, also referred to as a human-in-the-loop approach, is a deliberate design feature of the Crunchometer rather than a limitation (also see answer to Reviewer 2). The outputs of machine-learning algorithms, no matter how accurate, require expert corroboration to confirm or reject the specific behaviors under study, particularly when the behavioral repertoire is as heterogeneous as feeding (which encompasses sniffing, gnawing, biting, hoarding, and manipulating the food item). For this reason, we view human oversight as a safeguard for scientific rigor that remains valuable even as more advanced algorithms (e.g., deep learning and convolutional neural networks) are incorporated into future versions of the pipeline. As noted above, we have implemented a graphical user interface (GUI) that enables batch sorting and rapid inspection of multiple snippets (using a photographic montage view strategy), substantially reducing manual curation time.

      (3) The ability to extrapolate food quantity consumed is limited, with high variability. This limitation does not undercut the utility of the crunchometer, but should be highlighted as one of the parameters that are not suitable for this system. This limitation should be added to the limitations section.

      We thank the reviewer for this constructive observation. We fully agree that, although the Crunchometer reliably detects feeding events and their temporal microstructure (bouts, meals, and latencies), extrapolating absolute food quantity consumed from acoustic signals is indirect and carries substantial variability and should not be the primary readout for studies that require precise gravimetric measurements. As recommended, we have now explicitly listed this limitation in the Limitations section of the Discussion:

      "While the Crunchometer provides accurate temporal detection of bites and feeding microstructure, the estimation of absolute food mass consumed from bite-related acoustic signals shows considerable variability across trials and subjects. This limitation arises from individual differences in gnawing patterns, food fragmentation, and hoarding behavior. Accordingly, the Crunchometer is best suited for analyses of feeding dynamics and behavioral microstructure, whereas studies requiring precise quantification of ingested mass should complement the system with direct gravimetric measurements for example, real-time weighing of feeders."

      (4) The ability to discriminate between gnawing and consummatory behavior is a strength (Figure 5), and these findings are important. However, it is unclear what can be made of mice that have 'gnawing' behavior in the fasted state (like in Figure 3). It seems they would need to be eliminated from the analysis with this tool?

      We apologize for this misunderstanding. We have now more clearly indicated in Figure 3A that the cumulative feeding time reflects only Chow and HFD feeding bouts, excluding gnawing.

      We now state: “The lower panel shows the cumulative feeding time (only for Chow and HFD pellets, gnawing is excluded) over a two-hour session for the fed (green) and fasted (purple) groups (n = 6 mice).”

      Under normal physiological conditions, gnawing is an infrequent behavior in rodents. In our study, however, its frequency increased in the fasted state a change possibly attributable to heightened stress. This behavior was further exacerbated by chemogenetic manipulation, driving it to non-physiological levels.

      (5) Why is there a post-semaglutide fed group and not a fasted group in Figure 4? It seems both would have been interesting, as one could expect an effect on feeding even 24h after semaglutide treatment. This would help parse the preference better because the animals eat such a small amount of semaglutide, that it is hard to compare to the fasted condition with saline treatment.

      We thank the reviewer for this insightful suggestion. It would have been interesting to include a fasted post-semaglutide group, as it could provide relevant information about the lasting effect of an acute administration of semaglutide. However, we decided not to include this additional experimental condition because the semaglutide fasted mice displayed a markedly reduced food intake during the experimental session. An additional post-semaglutide fasted session would have required a prolonged food restriction (at least 24 hours), which we consider an unnecessarily stressful condition for the mice. Therefore, we decided to feed the mice once the experiment was completed. Nevertheless, we believe that comparing the food intake (grams) between the fed group shown in Figure 3C and the post-semaglutide fed group reported in Figure 4D provides insight into the lasting effect of semaglutide. The comparison reveals a remarkable reduction of food intake in the post-sem fed mice relative to the fed group, suggesting that the acute administration of semaglutide suppresses the feeding behavior for up to 24 hours.

      (6) The identification of 'meal-related' neurons in the LH is another strength of the manuscript. Although there is currently insufficient data, could similar recordings be used to give a neurophysiological definition of a 'meal' duration/size? Typically, these were somewhat arbitrarily defined behaviorally. Having a neural correlate to a 'meal' would be a powerful tool for understanding how meals are involved in overall caloric intake.

      We thank the reviewer for this insightful suggestion. We agree that the traditional behavioral criteria for defining meals, typically derived from log-survivor analyses of inter-pellet or inter-lick intervals, are operationally useful but ultimately arbitrary, and that a neurophysiologically grounded definition would be a valuable complement for the field.

      Our current dataset was not designed to formally establish such a definition, and we want to be cautious about the logic of the problem: validating a neural criterion solely against the behavioral one it would replace is circular. A genuinely neural definition of a meal would need to be anchored to independent criteria, for example, its ability to predict the latency and size of the subsequent meal, its correspondence with post-prandial satiety markers, or its response to anorectic agents such as GLP-1 receptor agonists. This is a methodologically nontrivial undertaking that we believe deserves a dedicated follow-up study.

      As preliminary evidence that such a problem is tractable, we note that the meal-related LH neurons identified here display sustained activity with onset and offset dynamics that broadly parallel the behaviorally defined meal boundaries (Figure 6), suggesting that meal structure is reliably encoded at the population level. A related approach, using neural activity to segment ingestive behavior at finer temporal scales, has been successful in our previous work on licking microstructure in the nucleus accumbens (Tellez, et al. 2012), and we consider the present findings a natural extension of that line of research to the larger meal timescale.

      (7) The conclusion in the title of Figure 8 is premature, given the pilot nature and small number of neurons and mice sampled.

      We appreciate this comment and agree with the reviewer. Accordingly, we have performed additional experiments on the Vglut2 glutamatergic population, in some cases using three-plane recordings, which substantially increased the yield to 386 glutamatergic neurons. As the reviewer anticipated, we observed a broad diversity of response profiles in this population, including neurons selective for liquid licking, for solid food intake, and for both food types. We also formally quantified these responses using ROC analysis, applying the same procedure to the Vgat GABAergic neurons (n = 79). These new findings have been incorporated into the revised manuscript (Results and Discussion). We thank the reviewer for prompting this extension of the analysis (see Manuscript).

      Conclusion:

      Overall, this report on the Crunchometer is well done and provides a valuable tool for all who study food intake and the behaviors around food intake. Clarification or answers to the points above will only further the utility and understanding of the tool for the research community. I am excited to see the future utility of this tool in emerging research.

      We sincerely thank the Reviewer for these kind and encouraging words, and for the constructive feedback provided throughout the review. The clarifications and additional analyses prompted by these comments have substantially improved the manuscript, and we share the Reviewer's enthusiasm about the potential of the Crunchometer to contribute to future research on feeding behavior.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) The authors have done a phenomenal job with the Introduction, highlighting the need for this tool, citing the history of feeding measurement systems and their relative strengths and weaknesses.

      Thank you for your comment; we greatly appreciate your positive feedback.

      (2) A limitation of Automated Pellet Dispensers is the possibility that the animals fail to consume the pellet after it has been retrieved from and registered by the device, potentially constraining accuracy.

      We address this issue in the Introduction, specifically, we wrote:

      “Current methods to monitor feeding behavior could be classified into four different classes…3) Automated Pellet Dispensers: Often integrated into operant conditioning chambers, these devices provide a controlled way of delivering food pellets. While devices like the open-source Feeding Experimentation Device (FED3) (Ali and Kravitz, 2018; Matikainen-Ankney et al., 2021), a pellet dispenser, are useful for measuring reinforcement, they alter the natural feeding patterns of mice, for example, requiring a simple action, such as a nose-poke can reduce overeating and weight gain in mice (Barrett et al., 2025). A further limitation is that FED3 may overestimate consumption if an animal retrieves and registers a pellet without actually consuming it. A significant strength of this method is its ability to enable closed-loop optogenetic stimulation concurrent with neuronal recordings.”

      (3) I really appreciate the data in Figure 2G, where they displayed the results of an "outlier" animal, as behavior is extremely variable, and it's useful to see how this system deals with the variability of the subjects. This is again highlighted by mouse number 5 in Figure 3A, which exhibited profound gnawing behavior.

      We thank the reviewer for this positive comment. Our decision to include the outlier animal in Fig. 2G and to report the atypical gnawing behavior of mouse 5 in Fig. 3A reflects a deliberate commitment to documenting inter-individual variability, which we consider a core strength rather than a limitation of behavioral work. We believe that such cases are particularly informative for evaluating the robustness of automated monitoring systems under behavioral-lab conditions.

      (4) It would be useful to know if the mice had prior exposure to HFD, as I found it surprising that many animals consumed the chow at all, sometimes completely ignoring the HFD (fasted mouse 3). I only ask because in our experience, mice with constant exposure to both HFD and chow predominantly, if not always, consume the HFD over chow. This could have something to do with the way the food substrates are presented in this chamber.

      We thank the reviewer for this point. Mice in this experiment did receive prior exposure to both Chow and HFD during the habituation phase, with at least two 30-min sessions in the experimental chamber with both diets available (no video was collected at this stage). The Chow and HFD feeders were identical in geometry, position, and accessibility, so we do not consider either environmental novelty or spatial bias to be the main driver of the pattern. Rather, we interpret the strong chow preference of fasted mouse 3 as a case of residual neophobia toward the HFD pellet. Since performing these experiments, we have refined our habituation protocol: pre-exposing animals to a single HFD pellet in their home cage, a familiar and safe environment, prior to any chamber session, greatly mitigates HFD neophobia in our hands. Familiarity with the novel food in a safe context thus appears to be the critical factor, rather than the duration of exposure in the experimental chamber. We have added this refinement to the Methods as a recommendation for future users of the Crunchometer.

      “Behavioral protocol. All mice were habituated to the Crunchometer for 2 days before the recording session. Each habituation session lasted 30 minutes, during which two food pellets were placed in the chamber: one standard Chow pellet (LabDiet 5008) and one highly palatable high-fat diet (HFD) pellet (Research Diet, D12451). As a practical note, we recommend allowing the HFD to equilibrate to room temperature before the experiment and pre-exposing mice to a single HFD pellet in their home cage to attenuate neophobia prior to testing.”

      (5) The authors claim saline or semaglutide was administered immediately before the start of the behavioral experiment, but given the time it takes for this drug to blunt appetite, I was somewhat surprised it led to such a rapid decrease in both chow and HFD intake. Could the authors comment on this? How quickly do these animals experience the malaise associated with these drugs? Also, this dose seems to be on the very high side, so I imagine it's making the animals feel quite sick and is probably a big reason why the effects last so long into the post-sem measurements. Was bodyweight tracked across this treatment? I'm not so convinced that sema treatment led to a loss of strong HFD preference, as the chow intake was already very low to begin with, and as mentioned above, it looks like the drug just led to a cessation of all intake. I'd just tamp down this claim of preference switch. It clearly reduced intake of both substrates, it's just harder to detect for the chow because it was already so low to begin with.

      Thank you for these comments. We agree with the Reviewer and have toned down the claim regarding a switch in HFD/chow preference. In the revised Results section, we now explicitly acknowledge that further characterization is needed using chronic semaglutide treatment. Specifically, we added the following sentence:

      "Future studies should use the Crunchometer to characterize changes in HFD/chow preference during 24-h monitoring under chronic semaglutide treatment."

      In addition, we administered a single subcutaneous dose of semaglutide at 30 nmol/kg (0.123 mg/kg), following the protocol described by Zhang et al. (2023). In their study, pharmacokinetic analyses showed that plasma concentrations, measured by an ELISA assay that immunoreacts with both growth differentiation factor 15 (GDF15) and the intact N-terminal region of glucagon-like peptide-1 (GLP-1), increased shortly after administration of the 30 nmol/kg dose in C57BL/6 mice. Peak plasma concentration (Cmax = 43.1 nmol/L) was reached at 6.7 hours (Tmax), and levels returned to baseline by 24 hours post-administration, indicating complete drug clearance. Although this dose is relatively high, it was intentionally selected to produce a robust acute response from a single administration, as our objective was to assess the drug’s effects within a short, 2-hour observational window. Under these conditions, we observed a rapid reduction in food intake immediately following the onset of Crunchometer recording. While we do not exclude the possibility that these effects could be more pronounced over longer observation periods or with chronic dosing regimens, our study was strictly limited to a single acute exposure.

      Although semaglutide is known to suppress food intake through multiple mechanisms, including stress and malaise measured by Conditioned Taste Aversion and release of stress hormones (Teixidor-Deulofeu et al., 2025), we do not believe that discomfort or malaise played a significant role in our study. While the mice did reduce their food intake during semaglutide administration, this reduction persisted for at least 24 hours after the final dose—at which point the drug was no longer present—suggesting a satiety-driven effect rather than one mediated by aversion. In this sense, previous studies have demonstrated that semaglutide continues to suppress food intake even when the aversive pathway mediated by Area Postrema GLP1R neurons is inhibited. Although blocking this pathway reduces flavour aversion, the anorexic effect remains, indicating that suppression of intake can be driven by satiety independently of nausea or malaise (Huang et al., 2024). In summary, although we selected a relatively high dose to ensure a detectable acute effect within our experimental window, this choice was grounded in previously published data, and our findings are consistent with established mechanisms of action for semaglutide.

      Additionally, body weight data have now been included in Figure 4D. We observed a similar body weight loss of approximately 5% on the first day of drug administration, consistent with the findings reported by Zhang et al. (2023).

      (6) The authors demonstrate that CNO administration prompted significant increase in liquid sugar intake in the last panel of Figure 5F as a confirmation that LH GABAergic neurons are implicated in processing reward, however given the above results it seems likely that these mice will drink anything including water (when not thirsty, thus in a non-rewarding scenario) or possibly aversive agents like quinine.

      This is an interesting question, and we agree with the Reviewer. The original discovery by Jennings and Stuber showed that optogenetic activation of these GABAergic neurons induces voracious feeding and that Vgat mice kept licking for liquid rewards in an appetitive task (Jennings et al., 2015). We also acknowledge that prior work has shown LH GABAergic neuron activation can drive consumption of non-caloric and biologically irrelevant stimuli, including wood gnawing, water, or saccharin (Navarro et al., 2016). However, several lines of evidence support a role in reward/palatability processing rather than purely indiscriminate consumption. Our own lab (Garcia et al., 2021) showed that activation of LH Vgat+ neurons increased quinine intake only during water deprivation; in sated animals, activation failed to promote quinine intake. Instead, these neurons promoted overconsumption of sucrose when available, leading us to conclude that LH Vgat+ neurons increase the drive to consume the nearest food, but this drive is potentiated by the palatability of the tastant. In non-human primates, LH GABA activation drives goal-directed eating predominantly for palatable food (Ha et al., 2024), supporting a reward-related function across species. Together, these findings indicate that while LH GABAergic activation does broadly promote consumption, the selectivity toward palatable stimuli observed in Figure 5F is consistent with a reward-related function.

    1. Author response:

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

      eLife Statement

      This valuable study characterizes the emergence of the membrane-associated periodic cytoskeleton (MPS) in the axons of human motor neurons derived from induced pluripotent stem cells. Super-resolution imaging of beta-II spectrin provides convincing evidence for the patterned assembly of spectrin-poor gaps and spectrin-rich MPS in the medial region of the axons and its enhancement by the kinase inhibitor staurosporine. The data advocates against gap formation by cytoskeleton disassembly in a continuous MPS. Instead, a continuous MPS may result from nascent MPS patches and their maturation, a model that would benefit from live imaging for validation.

      (R1) We thank the reviewers and editor for their constructive and thoughtful feedback. We are pleased the reviewers found our evidence to be convincing and that our study provides a valuable framework for understanding the complex dynamics of MPS assembly.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Ever since the surprising discovery of the membrane-associated Periodic Skeleton (MPS) in axons, a significant body of published work has been aimed at trying to understand its assembly mechanism and function. Despite this, we still lack a mechanistic understanding of how this amazing structure is assembled in neuronal cells. In this article, the authors report a "gap-and-patch" pattern of labelled spectrin in iPSC-derived human motor neurons grown in culture. The mid-sections of these axons exhibit patches with reasonably well-organized MPS that are separated by gaps lacking any detectable MPS and having low spectrin content. Further, they report that the intensity modulation of spectrin is correlated with intensity modulations of tubulin as well. However, neurofilament fluorescence does not show any correlation. Using DIC imaging, the authors show that often the axonal diameter remains uniform across segments, showing a patch-gap pattern. Gaps are seen more abundantly in the midsection of the axon, with the proximal section showing continuous MPS and the distal segment showing continuous spectrin fluorescence but no organized MPS. The authors show that spectrin degradation by caspase/calpain is not responsible for gap formation, and the patches are nascent MPS domains. The gap and patch pattern increases with days in culture and can be enhanced by treating the cells using the general kinase inhibitor staurosporine. Treatment with the actin depolymerizing agent Latrunculin A reduces gap formation. The reasons for the last two observations are not well understood/explained.

      (R2) We thank the reviewer for the detailed and accurate description of the data shown and its relevance to further our understanding of MPS assembly mechanism and function.

      Strengths:

      The claims made in the paper are supported by extensive imaging work and quantification of MPS. Overall, the paper is well written and the findings are interesting. Although much of the reported data are from axons treated with staurosporine, this may be a convenient system to investigate the dynamics of MPS assembly, which is still an open question.

      (R3) We thank the reviewer for the positive comments on the manuscript and the convenience of the experimental system developed to further study the dynamics of MPS assembly. We hope others turn into motor neurons to explore cortical cytoskeleton biology and hopefully shed light into their susceptibility in various degenerative diseases.

      Weaknesses:

      Much of the analysis is on staurosporine-treated cells, and the effects of this treatment can be broad. The increase in patch-gap pattern with days in culture is intriguing, and the reason for this needs to be checked carefully. It would have been nice to have live cell data on the evolution of the patch and gap pattern using a GFP tag on spectrin. The evolution of individual patches and possible coalescence of patches can be observed even with confocal microscopy if live cell super-resolution observation is difficult.

      (R4) Because staurosporine may hit various kinases relevant to the phenomenon under study we did not elaborate too deeply on the likely targets in the discussion. We have, however, included the possibility that the relevant kinase in this matter could be PKC, in light of the new study published while our manuscript was under revision (Heller et al., 2025) (see second last paragraph in the Discussion section). Staurosporine represented a convenient initial approach that allowed us to find the phenomenon, and we are now conducting new studies dissecting the molecular pathways involved. However, the extent of such studies lies beyond the scope of the present report.

      See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      Some more comments:

      (1) Axons can undergo transient beading or regularly spaced varicosity formation during media change if changes in osmolarity or chemical composition occur. Such shape modulations can induce cytoskeletal modulations as well (the authors report modulations in microtubule fluorescence). The authors mention axonal enlargements in some instances. Although they present DIC images to argue that the axons showing gaps are often tubular, possible beading artefacts need to be checked. Beading can be transient and can be checked by doing media changes while observing the axons on a microscope.

      (R5) As we acknowledge this possibility, we believe that, even if they occurred, they could not contribute to our observations of gaps-and-patches phenomenon since this latter subsisted long (hours and days) after any gross manipulation of media. Moreover fixed samples, when observed under DIC, confocal or STED did not evidence such beadings. We do refer to a characteristic local enlargement that was very localized and very low in numbers (see Fig.1C and E, and Suppl. Fig1C and E), so we don't believe these are transient, and do not resemble the structure referred to as beading. Structurally, beading is essentially different since it appears in rows of consecutive “beads” in long stretches, where round, small enlargements of axonal caliber are arranged in a consecutive manner, resembling pearls on a string. As mentioned by the reviewer, the beading phenomena can occur transiently when drastically changing media osmolarity (rarely done in cell culture manipulations) or non-tranciently when axons are undergoing degeneration. Indeed, to prevent gross changes in osmolarity, our routine fixation is a 4% PFA and 4% sucrose in PBS. In any case, we did not observe signs of beading in the cultures used for this study.

      (2) Why do microtubules appear patchy? One would imagine the microtubule lengths to be greater than the patch size and hence to be more uniform.

      (R6) Our stainings are for tubulin protein isoforms beta-III and alpha-II. That is, they would label microtubules, but free tubulin as well. Hence we don't think this is evidence for “patchy microtubules”. The slight decrease in intensity for tubulin within gaps is indeed something to investigate, and can indicate that tubulin prefers to accumulate within patches.

      (3) Why do axons with gaps increase with days in culture? If patches are nascent MPS that progressively grow, one would have expected fewer gaps with increasing days in culture. Is this indicative of some sort of degeneration of axons?

      (R7) We agree with the apparent discrepancy. However, one has to take into account that these axons are still elongating even at 2 weeks in culture and beyond. Hence, at any time point, there is a new axonal compartment recently added, and hence, with low βII-spectrin and no organized MPS. Also, the dynamical evolution of the gaps-and-patches structure has to take into account the rate of βII-spectrin supply and transport. If supply is somehow lower than a given threshold, it is expected that there will be more gaps, given the new, more distant parts of the axons have a lower supply of βII-spectrin. To explore this formally, we are working on simulations of these multifactorial dynamic systems to better understand this, that together with key experimental observations would enhance our understanding into our model of MPS assembly in growing axons. However, findings for this project will be the subject of another manuscript.

      (4) It is surprising that Latrunculin A reduces gap formation induced by staurosporine (also seems to increase MPS correlation) while it decreases actin filament content. How can this be understood? If the idea is to block actin dynamics, have the authors tried using Jasplakinolide to stabilize the filaments?

      (R8) The results with the co-treatment with Latrunculin A and Staurosporine are indeed intriguing, and provide clear evidence that the gap-and-patch pattern arises from local assembly of the MPS, requiring newly formed actin filaments. On the other hand, the fact that F-actin within the pre-formed MPS seems unaffected is not surprising. There are many different populations of F-actin in axons (i.e. MPS rings, longitudinal filaments, actin patches, actin trails), all of which have a different rate of monomer turnover. Latrunculin A affects filaments indirectly. The target of Latrunculin A is not actin filaments, but free monomers. Monomer sequestration ultimately affects actin filaments: filaments are constantly exchanging monomers, but, devoid of free monomers, filaments get shorter and eventually disappear. The drastic decrease in global F-actin in LatA-treated axons reflects that. The fact that F-actin in the MPS is preserved shows that these filaments are stable -if they are not losing monomers in the time frame of the treatment, the filament remains unaffected. This subject is extensively covered in the 8th paragraph of the Discussion section.

      We have not used Jasplakinolide. The expected outcome will not mimic that of Latrunculin A since Jasplakinolide has a different mechanism of action (i.e. it binds -and stabilizes- the actin filament).

      (5) The authors speculate that the patches are formed by the condensation of free spectrins, which then leaves the immediate neighborhood depleted of these proteins. This is an interesting hypothesis, and exploring this in live cells using spectrin-GFP constructs will greatly strengthen the article. Will the patch-gap regions evolve into continuous MPS? If so, do these patches expand with time as new spectrin and actin are recruited and merge with neighboring patches, or can the entire patch "diffuse" and coalesce with neighboring patches, thus expanding the MPS region?

      (R9) We agree with the reviewer's interpretation. A virtue of our experimental model and our interpretations of the observations in fixed cells is that it gives rise to informative questions such as the ones posed by the reviewer. See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Gazal et al. describe the presence of unique gaps and patches of BetaII-spectrin in medial sections of long human motor neuron axons. BII-spectrin, along with Alpha-spectrin, forms horizontal linkers between 180nm spaced F-actin rings in axons. These F-actin rings, along with the spectrin linkers, form membrane periodic structures (MPS) which are critical for the maintenance of the integrity, size, and function of axons. The primary goal of the authors was to address whether long motor axons, particularly those carrying familial mutations associated with the neurodegenerative disorder ALS, show defects in gaps and patches of BetaII-spectrin, ultimately leading to degradation of these neurons.

      (R10) We thank the reviewer for the detailed and accurate description of the data shown.

      Strengths:

      The experiments are well-designed, and the authors have used the right methods and cutting-edge techniques to address the questions in this manuscript. The use of human motor neurons and the use of motor neurons with different familial ALS mutations is a strength. The use of isogenic controls is a positive. The induction of gaps and patches by the kinase inhibitor staurosporine and their rescue by Latrunculin A is novel and well-executed. The use of biochemical assays to explore the role of calpains is appropriate and well-designed. The use of STED imaging to define the periodicity of MPS in the gaps and patches of spectrin is a strength.

      (R11) We thank the reviewer for the positive comments on the manuscript, the techniques used and the proposed model.

      Weaknesses:

      The primary weakness is the lack of rigorous evaluation to validate the proposed model of spectrin capture from the gaps into adjacent patches by the use of photobleaching and live imaging. Another point is the lack of investigation into how gaps and patches change in axons carrying the familial ALS mutations as they age, since 2 weeks is not a time point when neurodegeneration is expected to start.

      (R12) See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      We don't discard the notion that axons carrying familial ALS mutations will show defects in MPS formation and/or stability when observed at longer culture times, or under culture conditions that promote neuronal aging (Guix et al., 2021). Thus, we continue to work with these cells, but the goal of such project lies well beyond the primary message of the present manuscript, as we discuss in the second paragraph of the Discussion section.

      Reviewer #3 (Public review):

      Summary:

      Gazal et al present convincing evidence supporting a new model of MPS formation where a gap-and-patch MPS pattern coalesces laterally to give rise to a lattice covering the entire axon shaft.

      Strengths:

      (1) This is a very interesting study that supports a change in paradigm in the model of MPS lattice formation.

      (2) Knowledge on MPS organization is mainly derived from studies using rat hippocampal neurons. In the current manuscript, Gazal et al use human IPS-derived motor neurons, a highly relevant neuron type, to further the current knowledge on MPS biology.

      (3) The quality of the images provided, specifically of those involving super-resolution, is of a high standard. This adequately supports the conclusions of the authors.

      (R13) We thank the reviewer for the positive comments on the manuscript, the techniques used and the proposed model.

      Weaknesses:

      (1) The main concern raised by the manuscript is the assumption that staudosporine-induced gap and patch formation recapitulates the physiological assembly of gaps and patches of betaII-spectrin.

      (R14) Along the project, various gaps-and-patches parameters were measured in different conditions and stainings. In all these examinations the only parameter that changed considerably was their abundance. While this suggests that the gaps-and-patches features are comparable between control and staurosporine-treated cells, we acknowledge as a general caution regarding negative data—that subtle qualitative differences cannot be entirely ruled out. We have now emphasized this possibility in the 9th paragraph of the Discussion section.

      (2) One technical challenge that limits a more compelling support of the new model of MPS formation is that fixed neurons are imaged, which precludes the observation of patch coalescence.

      (R15) See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      Recommendations for the authors:

      Reviewing Editor Comments:

      The reviewers all agree that the work would strongly benefit from live imaging to assess the maturation dynamics of the gap/patch pattern.

      (R16) Reviewers agreed that some of the conclusions of our manuscript would benefit from live imaging for validation. Various anticipated technical and biological challenges made these approaches not to be conducted for this initial study on human motor neurons. Just to mention the most important, from previous work of our labs, these cells themselves are difficult to transfect at 2 weeks in culture. Also, ectopically expression of tagged βII-spectrin escapes normal expression control and it has been noticed that ectopic expression yields to protein localization that does not necessarily reflect the endogenous distribution, or that produces cellular responses that precludes the observation of the phenomena under study. These difficulties in studying over-expressed tagged βII-spectrin have been reported in the field, with mentions that the analysed axons were those expressing “low levels of the construct” (Boyer et al., 2026; Zhong et al., 2014; Zhou et al., 2022). Taking this into account, we did not anticipate that, for the goals of the present project, live-imaging was to be included. However, given the positive comments and reception of our conclusions, we sought to try to perform this challenging and risky approach. To that end, we used a C-terminus tagged mouse βII-spectrin-GreenLantern plasmid to transfect our cells (a kind gift from Dr. Subjohit Roy, UCSD, USA). After 3 rounds of differentiating cells and trying various combinations of plasmid quantity, lipofectimine-to-DNA ratios and times of transfection (amongst other parameters), we have got an extremely low efficiency of transfection, and the few expressing neurons showed a distribution of βII-spectrin-GreenLantern that did not match our observations of immunolocalization of endogenous βII-spectrin. Taking all these into account, the present version of the manuscript will not include live-cell imaging on expressed tagged βII-spectrin. Given that reviewers found that some statements in the initial submission would have been better supported by live-imaging, we made changes in the manuscript so as to acknowledge the limitations of concluding dynamic mechanisms from fixed samples (see for example last sentences on 5th paragraph of the Discussion section). Having said so, we hope to be able, in the future, to overcome these experimental challenges and be able to establish live-imaging of βII-spectrin in neurons. For example, to avoid unregulated transgene expression, Heller and colleagues recently generated a βII- spectrin-mNeonGreen conditional knock-in (cKI) mice, consisting of a LoxP- flanked alternative final exon of endogenous βII-spectrin with a C- terminal mNeonGreen fusion that is expressed upon Cre expression (Heller et al., 2025). The implementation and further development of such approaches will be very helpful in new studies on the dynamics of βII-spectrin and the MPS as a whole. However, the scale of work needed to accomplish those approaches represent stand-alone projects.

      Reviewer #1 (Recommendations for the authors):

      In the section "The MPS is absent in beta-II spectrin gaps, the authors mention that the presence of MPS in patches suggests that the axons are not undergoing degeneration. I don't think this is a good criterion to use, despite the citations they take support from.

      (R17) We agree with the reviewer's suggestion: in virtue of the unlikely connection between the cited developmental axon degeneration process in sensory neurons and the possible axon degeneration of long term cultures of human-iPSCs-derived motor neurons studied here, we have eliminated the sentence of reference

      The authors show that degradation by proteases does not happen in their case. In this regard, they may want to discuss the recent article by Heller et al, Science 2025 (https://doi.org/10.1126/science.adn6712) and Hofmann et al, Sci. Rep., 2022 (https://doi.org/10.1038/s41598-022-18562-5)

      (R18) By western blot analysis, we did not see evident changes in proteolysis-derived fragments. However it is likely that even when finding phenotypes with protease inhibitors, protein fragments accumulation is below the sensitivity of western blots. We were expecting gross changes observable by western blot in the case proteolysis explained gap formation.

      Calpain and Caspase activity has been shown to be relevant in different aspects of MPS biology. To the works cited by the reviewer, now one has to add the very recent work by Fei and colleagues (Fei et al., 2026). We have modified part of the Discussion section to analyse our results in this broader context.

      Briefly, Hofmann and colleagues found that acute treatment with calpain inhibitors right before axotomy lead to an increase in percentage of periodic βII-spectrin (referred by authors as “periodicity”) in the regenerated axons in a 2-hour period. Interestingly, the βII-spectrin patches they describe at distal portions did not increase in number, but they increased in size. This indicates that in the particular situation of axonal regeneration calpain activity puts a brake into MPS formation within patches. This invited us to re-examine our own protease inhibition experiments, and measured patch length in this. The new results are shown in Supplementary Fig. 6 and and further analysed in the Discussion section. In summary, our changes were much less notable than the ones found in regenerating axons, but follow the same trend: protease inhibitors made patches longer.

      On the other hand, Heller and colleagues found in live-imaging studies that calpain activity contributes to the steady-state dynamics of βII-spectrin exchange in a mature MPS lattice. More recently, Fei and colleagues found that caspase or calpain inhibition does not change the steady-state organization of a mature MPS lattice when observing treated axons after fixation samples. Fei and colleagues find a relevant role for calpains whenever massive endocytosis (of any kind) is engaged experimentally. Interestingly, all these studies, including ours, examined calpains roles in MPS in different scenarios. When looked in detail, we don’t believe that these are contradictory results among them, and a complete picture of calpains (and caspases) roles in MPS assembly, growth, maintenance and remodeling will have to take into account all the above mentioned results, including ours. All these analyses are now included in the Discussion section.

      Minor comments:

      (1) "Recently, it was proposed that this continuous MPS organization arises from the coalescence of discontinuous "patches" of incomplete MPS units that originate in the distal axon and migrate proximally (Zhong et al. 2014)." Please check the citation. Should it be Hoffman et al. 2022?

      (R19) The reviewer is correct. The proper citation has now been included.

      (2) Is there an established link between ALS and spectrin? I would suggest decreasing the emphasis on this as no clear conclusions are achieved.

      (R20) As stated in the text, the study of ALS mutations is justified from two aspects: one aspect is that there are several tubulin and other cytoskeletal proteins whose mutations are linked to ALS (Castellanos-Montiel et al., 2020) and microtubules dynamics has been shown to affect the cortical skeleton (Qu et al., 2017). Second, since human motor neurons are affected in ALS, we thought that a complete characterization of the βII-spectrin cortical cytoskeleton in these cells should include ALS-related mutations. We have now included an a basic MPS description in TDP43 and SOD1 mutation (Suppl. Fig. 5).

      The aspect of ALS-related mutations only occupies two short paragraphs in the main text and some panels in Supplementary information. To follow the suggestions by the Reviewer, we have downplayed the relative relevance of these results in the text, without compromising the amount of data we show.

      (3) There is a typo in the approximate symbol used for 150 kDa in the section where calpain and caspase activity is reported.

      (R21) Typo corrected.

      (4) Please add the Latrunculin concentration used in the main text, as it makes it easier for the reader.

      (R22) Done.

      (5) In the Discussion, paragraph starting with "We further showed ...", there is a typo where Zhong et al is cited.

      (R23) Corrected.

      (6) Supplementary Figure 1B: attachment instead of 'atachment'.

      (R24) Corrected.

      (7) Include DIVs or time in the schematic. It is easier for the reader to understand.

      (R25) We have now included time references in schematics of Suppl. Fig1B.

      (8) Supplementary Figure 1C

      Unable to distinguish βII-spectrin and βIII-tubulin in the merged image. Separate figure panels will help.

      (R26) The merged images in the reconstructions are merely to better show the tracing individual axons at such low magnification. Relevant portions with only βII-spectrin channels are shown in C1 and C2. Separated individual channels are shown elsewhere across the manuscript.

      (9) Supplementary Figure 4D

      Why is there so much cleavage product for αII-spectrin across DMSO and treatment? It varied over batches as well. Doesn't this mean that αII-spectrin is going through more proteolytic cleavage? Why?

      (R27) The amount of cleavage product for αII-spectrin is not a surprise to us. For instance, although calpains and caspases can potentially process both α- and β-spectrin, in in vivo scenarios where calpain activity is triggered there are much more fragments of α-spectrin being produced (Czogalla & Sikorski, 2005). On the other hand, our staining of cleaved-αII-spectrin by the SNTF antibody by immunofluorescence (Fig4C) parallels the findings by western blot -high levels of cleaved-αII-spectrin across treatments. A similar strong staining using this antibody has been recently shown in the intact axon (Heller et al., 2025). It will be interesting in the future to address if these fragments have any biological significance beyond being mere byproducts of αII-spectrin processing.

      Reviewer #2 (Recommendations for the authors):

      Suggestions for improving the quality of the manuscript:

      (1) Live imaging in combination with FRAP assays will help define whether the capture of spectrin from gaps into patches is true. Fixed neurons only provide static information and may not reflect real-time physiological effects.

      (R28) See R16 regarding possible live-imaging experiments using tagged βII-spectrin constructs.

      (2) Could the presence of F-actin trails in axons facilitate the formation of patches? Will the use of formin/Arp2/3 inhibitors rescue the effect of staurosporine, similar to Latrunculin A?

      (R29) Very interesting suggestion. It is likely that different pools of F-actin contribute to the dynamic of MPS formation, and actin trails are definitely worth investigating in this context.

      (3) Figure 8 lacks a latrunculin A treated condition? Why is this not present?

      (R30) The quantification of that treatment was excluded for space and readability. We have now included the values of group LatA + DMSO in Fig8Cand D and rearranged the whole figure.

      (4) Does neuronal stimulation have any effect (KCl treatment) on gaps and patches?

      (R31) Very interesting suggestion. Unfortunately, we have not examined whereas neuronal stimulation affects any parameter of the gaps-and-patches structure.

      (5) Please check the manuscript for typos and reference insertion points in the text. More than a couple were noted.

      (R32) We have corrected typos.

      Reviewer #3 (Recommendations for the authors):

      This is a very interesting study that supports a change in paradigm in the model of MPS lattice formation.

      (1) One major concern is the assumption that staudosporine-induced gap and patch formation recapitulates the physiological assembly of gaps and patches of betaII-spectrin, solely based on their morphological similarity. This should be further discussed in the manuscript. Further analysis of additional cytoskeleton components, including microtubules in staurosporine-treated neurons, could also be provided.

      (R33) See R14.

      (2) In Figure 1E, betaIII-tubulin and NF-H seem to accumulate in betaII-spectrin-rich axonal enlargements. If these are patches, how do you reconcile this finding with Figure 2C-D, where NF-M and alphaII-tubulin are not specifically enriched in betaII-spectrin patches?

      (R34) We actually show that axonal enlargements and patches are structurally unrelated, in many aspects. We mention these axonal enlargements as a way to perform an exhaustive characterization of all βII-spectrin features found in these axons.

      (3) One technical challenge that limits a more compelling support of the new model of MPS formation is that fixed neurons are imaged, which precludes the observation of patch coalescence. This should be further discussed in the revised version of the manuscript.

      (R35) The limitation of the experimental approach is now further discussed (see for example last sentences on 5th paragraph of the Discussion section).

      (4) On a more general note, the title of some of the Results sub-sections could be revised to convey the findings of those sub-sections and not the Methods that were used (example: "Quantitave and Qualitative analyses of betII-spectrin distribution....").

      (R36) According to the suggestion, we have changed the title of this subsection.

      References

      Boyer, N. P., Sharma, R., Wiesner, T., Parperis, C., Delamare, A., Pelletier, F., Jullien, N., Bhatt, A. M., Parra-Rivas, L. A., Kearney, P. J., Shavarebi, F., Leterrier, C., & Roy, S. (2026). Spectrin condensates provide a nidus for assembling the axonal membrane-associated periodic skeleton. iScience, 29(1), 114454. https://doi.org/10.1016/j.isci.2025.114454

      Castellanos-Montiel, M. J., Chaineau, M., & Durcan, T. M. (2020). The Neglected Genes of ALS: Cytoskeletal Dynamics Impact Synaptic Degeneration in ALS. Frontiers in Cellular Neuroscience, 14, 594975. https://doi.org/10.3389/fncel.2020.594975

      Czogalla, A., & Sikorski, A. F. (2005). Spectrin and calpain: A “target” and a “sniper” in the pathology of neuronal cells. Cellular and Molecular Life Sciences: CMLS, 62(17), 1913–1924. https://doi.org/10.1007/s00018-005-5097-0

      Guix, F. X., Capitán, A. M., Casadomé-Perales, Á., Palomares-Pérez, I., López Del Castillo, I., Miguel, V., Goedeke, L., Martín, M. G., Lamas, S., Peinado, H., Fernández-Hernando, C., & Dotti, C. G. (2021). Increased exosome secretion in neurons aging in vitro by NPC1-mediated endosomal cholesterol buildup. Life Science Alliance, 4(8), e202101055. https://doi.org/10.26508/lsa.202101055

      Heller, E., Kurup, N., & Zhuang, X. (2025). The membrane skeleton is constitutively remodeled in neurons by calcium signaling. Science (New York, N.Y.), 389(6760), eadn6712. https://doi.org/10.1126/science.adn6712

      Qu, Y., Hahn, I., Webb, S. E. D., Pearce, S. P., & Prokop, A. (2017). Periodic actin structures in neuronal axons are required to maintain microtubules. Molecular Biology of the Cell, 28(2), 296–308. https://doi.org/10.1091/mbc.E16-10-0727

      Zhong, G., He, J., Zhou, R., Lorenzo, D., Babcock, H. P., Bennett, V., & Zhuang, X. (2014). Developmental mechanism of the periodic membrane skeleton in axons. eLife, 3, e04581. https://doi.org/10.7554/eLife.04581

      Zhou, R., Han, B., Nowak, R., Lu, Y., Heller, E., Xia, C., Chishti, A. H., Fowler, V. M., & Zhuang, X. (2022). Proteomic and functional analyses of the periodic membrane skeleton in neurons. Nature Communications, 13(1), 3196. https://doi.org/10.1038/s41467-022-30720-x

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      The manuscript by Butler et al. explores a novel physiological role for connexin 32 (Cx32) hemichannels in Schwann cells at peripheral nerves. Building on the authors' prior work on CO<sub>2</sub> - sensitive gating of connexins, this study proposes that mitochondrial CO<sub>2</sub> production dependent on neuronal activity promotes the opening of Cx32 hemichannels in the paranode, which in turn modulates neuronal activity by reducing conduction velocity. This hypothesis is addressed using a multifaceted approach that includes immunofluorescence microscopy, dye uptake assays, calcium imaging, computational modeling, and extracellular recordings in isolated sciatic nerves.

      Among the strengths of the study are the interdisciplinary integration of imaging, in silico approaches, and functional data. Also, this study proposes a new mechanism with profound physiological relevance. Specifically, Butler et al. provide new insights into glial modulation of electrical conduction in sensory/motor myelinated nerves.

      In the current state, the study has some limitations. The evidence linking Cx32 to the observed dye uptake and conduction velocity changes relies primarily on pharmacological inhibition with carbenoxolone, which lacks specificity. The imaging data show overlapping marker signals that preclude the anatomical distinction between nodes and paranodes. FITC uptake, while convincing to test Cx32 hemichannel gating, lacks spatial-temporal information and validation of distribution and localization to viable intracellular compartments. Moreover, while the findings are intriguing, functional proof that Cx32 regulates conduction velocity through ATP release or other downstream effects remains incomplete. Further work using targeted genetic tools, live-tissue imaging, and additional controls would strengthen the mechanistic conclusions.

      Overall, the manuscript offers compelling preliminary evidence that supports a new role for Cx32 in peripheral nerve physiology and raises important questions for future investigation.

      We thank the reviewer for their comments and agree that the evidence for involvement of Cx32 is indirect. We have now used viral expression of Cx32<sup>DN</sup> in SCs to remove CO<sub>2</sub> sensitivity from the endogenous Cx32 to strengthen this link. We have reviewed our presentation of the morphology in terms of the node/paranode/juxtaparanode distribution and adjusted accordingly. We have added new data using GCaMP transduced into Schwann cells that provides the live-tissue imaging that the reviewer requests.

      Reviewer #2 (Public review):

      Summary:

      This article aims to demonstrate that local production of CO<sub>2</sub> at the axonal node opens Cx32 hemichannels in the Schwann cell paranode, and that CO<sub>2</sub> diffuses through the AQP1 channel to reach Cx32 and trigger its opening. The authors also present evidence supporting a physiological role for this regulatory mechanism. They propose that CO<sub>2</sub>-dependent Cx32 activation mediates activity-dependent Ca<sup>2+</sup> influx into the paranode, and by increasing the leak current across the myelin sheath, it contributes to a slowing of action potential conduction velocity.

      The study presents a very interesting and novel mechanism for the physiological regulation of Cx32 hemichannels. The findings are relevant to the field, and the methods and results are of good quality, with some improvements in interpretation and explanation required, and some minor experimental suggestions.

      Strengths:

      The article is solid in terms of the novelty of the findings and relevance for the physiology of myelinated axons. In addition, it is of major interest for the Connexin field because it explores a physiological way to open Cx32 hemichannels. The experiments are well elaborated, and most of them are sufficient for the main points described by the authors. The finding that nervous activity will trigger the mechanism of hemichannel opening by CO2 is probably the most relevant biological mechanism derived from this article.

      Weaknesses:

      Throughout the manuscript, the authors interpret their findings as if the described mechanism specifically occurs in the node and paranode regions. However, there is no direct evidence identifying the precise site of CO<sub>2</sub> production or the activation site of Cx32 hemichannels. Therefore, statements such as the one in the title ("activity-dependent CO<sub>2</sub> production in the axonal node opens Cx32 in the Schwann cell paranode") should be reconsidered or removed, as they may be misleading and are not essential to the interpretation of the data. In addition, the participation of aquaporin AQP1 as the main conduit for CO2 diffusion through the plasma membrane could have another interpretation.

      We thank the reviewer for their comments and agree that we do not have direct evidence for the site of CO<sub>2</sub> production or the site of activation of Cx32 hemichannels. This direct evidence is extremely difficult to obtain, and we therefore depend on indirect arguments. Mitochondria represent the major source of CO<sub>2</sub>, and their distribution will therefore indicate where CO<sub>2</sub> is likely to be produced. We agree that this is not essential to the interpretation of the data and have adjusted the text as recommended. We have added a section to the Discussion to consider this point in more detail. The reviewer alludes to a reported interaction between AQP1 and NaV1.8 as a possible alternative interpretation. We can confidently rule this out as the AQP1 blocker has no effect on the compound action potential.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Main comments:

      (1) While the imaging system used in this study is technically capable of resolving nodes and paranodes, interpretation depends critically on marker specificity and tissue orientation. In some figures, markers such as Caspr or KCNA2 appear to partially overlap with KCNQ2 or the putative axonal node, which could reflect biological proximity but may also result from incomplete spatial separation in the z-dimension or the curvature of teased fibers. Similarly, Cx32 immunoreactivity or FITC signal is occasionally seen within nodal gaps, raising questions about how accurately this data supports the author's hypothesis. Additionally, while the authors claim that AQP1 is localized in nodes, the data suggest the opposite. Clarifying these patterns using fluorescence intensity line scans or additional nodal markers such as Nav1.6 or Ankyrin G would help distinguish overlapping signals from true domain-specific localization and reinforce the spatial conclusions of the study.

      We have changed our presentation of the localisation studies. We have concentrated on colocalization of Cx32 and AQP1 (now Fig 2) and moved the other studies to supplements to this figure. While we have retained the same images of Cx32 and AQP1 localisation, we have emphasized that these are SIM images and thus higher resolution than conventional LSM images, and also from a single optical plane. We have also clarified that the colocalization studies are restricted to analysis of the node/paranode regions.

      (2) To strengthen the conclusion that Cx32 specifically mediates the observed dye uptake, additional data or an alternative approach would be valuable. One feasible, though technically demanding, strategy would be the use of AAV-mediated delivery of Cx32-targeting shRNA directly into the sciatic nerve, ideally under a Schwann cell-specific promoter. This approach could achieve localized, cell-type-specific knockdown of Cx32 within a relevant time frame. Alternatively, the authors are encouraged to consider using additional pharmacological inhibitors to exclude the contribution of other conduction pathways, such as pannexin channels. These complementary strategies would reduce the interpretive ambiguity associated with non-specific blockade.

      We agree that this is desirable and have used Cx32<sup>DN</sup> under the control of the Mpz promoter (delivered by AAV via intranerval injection). This approach has several advantages -the Cx32<sup>DN</sup> subunit coassembles with endogenous Cx32<sup>WT</sup> and the heteromeric assemblies lack CO<sub>2</sub> sensitivity (first shown in Butler & Dale, 2023; and this strategy used with Cx26 to demonstrate its role in the control of breathing van de Wiel, 2020). This is a new figure (Fig 9). We have included supplemental figures with Fig 9 to document the coassembly of Cx32<sup>DN</sup> with Cx32<sup>WT</sup> by FRET.

      These new data test a very specific hypothesis: that CO<sub>2</sub> binding to Cx32 is responsible for the CO<sub>2</sub> sensitivity of the nerve. We find by comparing transduced and non-transduced fibres in the same nerve that Cx32<sup>DN</sup> essentially abolishes activity dependent loading of FITC into the Schwann cells.

      (3) Related to FITC experiments: Assuming the hypothesis of the authors is correct and CO2 release is restricted to the node, one should expect that if the major source of CO2 is in the nodal mitochondria, the hemichannels adjacent to the node will open first, assuming the spatial-temporal diffusion of CO2. To demonstrate this point, I would strongly suggest performing tissue imaging with real-time dye uptake. This approach should capture the FITC wave starting from the Cx32 channel opening in the paranode, as expected. Visualization of uptake in fixed and sectioned tissue is not the ideal approach to detect functional hemichannel opening in intact, viable cells, and at this point, they do not demonstrate that the uptake occurs in the node. From my perspective, if real-time experiments using isolated axons are feasible, it would make this paper more solid.

      The suggested method is not practical as the FITC in solution will be fluorescent and thus obscure the entry of FITC into the paranode. We have however expressed GCaMP8 under the control of the Mpz promoter, and this is expressed at paranodes and gives a CO<sub>2</sub> and activity-dependent Ca<sup>2+</sup> signal at the paranode. This gives a real time measure of the effect of CO<sub>2</sub> on the nerve. The GCaMP8 signal is enhanced by AZ and blocked by TC AQP1-1 (see below).

      (4) In Figure 5, Supplement 1, the authors present data using GRAB-ATP to suggest that Cx31.3 hemichannels do not release ATP under CO<sub>2</sub> stimulation. However, control experiments with GRAB-ATP alone (without Cx31.3 expression) are not shown, and parallel conditions with Cx32-expressing cells are lacking. Including these controls would strengthen the manuscript. Finally, testing the permeability of Cx31.3 to FITC directly, using the same conditions as in the main experiments, would clarify whether the discrepancy reflects differences in molecular permselectivity or CO<sub>2</sub> sensitivity.

      Figure 5 supplement 1, does show GRAB<sub>ATP</sub> alone without Cx31.3 expression (in the box plot). However, we have now added raw traces for this to the figure in panel B. CO<sub>2</sub>-dependent and voltage dependent ATP release via Cx32 has been previously shown in two papers (Butler & Dale 2023, Frontiers Cell Neurosci; Lovatt et al 2025, J Biol Chem). The Cx32<sup>DN</sup> result (above) further eliminates any contribution of Cx31.3.

      (5) Suggestion: It would be valuable to explore whether the proposed mechanism is conserved across both motor and sensory neurons, as this would broaden its physiological relevance. Since the sciatic nerve contains both fiber types, selective analysis or comparative data could clarify whether hemichannel activity is differentially regulated or restricted to a specific neuronal subtype.

      This is a great idea, but well beyond the scope of this paper. In an ex vivo preparation it would be very difficult to selectively stimulate the sensory vs motor fibres.

      Suggestions to improve data presentation and other minor comments:

      (1) Reduce/reorganize the figures to make the paper straightforward. For example, (a) immunofluorescence data showing the CO2 signaling machinery could be represented in one single figure; (b) Figure 1 could include all the findings and keep it as a final figure to summarize what the authors claim.

      We thank the reviewer for these suggestions. We prefer to keep Fig 1 up front to have our hypothesis clear for the reader to assist their interpretation as they go through the paper. We have altered the balance of figure supplements and main figures that document the immunolocalisation studies to concentrate on the main areas of novelty (AQP1 and Cx32 colocalisation and CA localisation).

      (2) The following phrase in the Results section is incomplete: "There was colocalization between Cx32 and CytC in the Schwann cell paranode, and (Fig 2, mean; 95% confidence interval, M1: 0.314; 0.198, 0.431 and M2: 0.261; 0.165, 0.357)."

      We have corrected this

      Additionally, the three values for M1 and M2 should be clearly defined and contextualized. In the current state, I couldn't understand them.

      The three values are mean and lower and upper 95% confidence limit:

      M1: mean 0.314; 95% CI, 0.198 to 0.431

      We have now made this clearer in the text.

      (3) It is unclear whether the authors calculate Manders' coefficients across the whole image or selectively at the node/paranode. Clarifying this would help interpret the specificity of co-localization claims.

      The Manders’ coefficients were selectively calculated at the node/paranode and we have amended the text to clarify this.

      (4) It is possible that mislocalization of CytC and SFXN1 could reflect antibody unspecificity or post-isolation alterations in protein distribution (e.g., apoptosis or stress). The authors briefly discussed this observation, but it could be a good idea to consider the use of an additional antibody to validate mitochondria localization.

      Apoptosis or stress is unlikely as the isolated nerves were fixed immediately after isolation with little dissection prior to fixation.

      The SFXN1 antibody was validated by Fowler et al 2013, and IP-HTMS confirmed SFXN1 as an interacting partner with Cx32. In this paper they also described SFXN1 as being present at the plasma membrane, the speculation being that it was taken there by Cx32.

      We think this is probably a valid result and we have further cited the Fowler et al 2013 paper in our discussion of this point.

      (5) Figure 4: The legend states: "Arrow heads indicate the node, and arrows depict the outer myelin." However, no arrows are visible in the figure. Please check.

      Corrected.

      (6) Figure 5: Keep consistency: Include in panel N that trpa1 inhibitor is in the presence of 70mmHg PCO2, as indicated for cbx in the same panel.

      Done

      (7) Figure 5 Supplement 1: Normalization using 1 concentration of ATP could not be appropriate if the sensor-dependent signal is not linear. If possible, authors should make a concentration-response curve and fit the data using the appropriate equation.

      Over the range we are measuring ATP (low µM) GRAB<sub>ATP</sub> is approximately linear to allow a single point calibration -we documented this in Butler and Dale 2023. This is also shown in the original paper describing GRAB<sub>ATP</sub> (Wu et al 2022 Neuron). We have clarified this point in the methods by referring to these papers.

      (8) Figure 6: The increase in FITC signal could represent a basal uptake over time. Authors should clarify the magnitude/rate of the basal uptake. Another option is showing a picture of the uptake using the control frequency at a time of 10 min. Legend: It is not clear in panel C if this picture corresponds to frequency stimulation. If so, it would be beneficial to specify the time.

      Could dye loading in this Fig simply be time dependent rather than stimulation dependent? Our data show that this is not the case -the dye loading controls of Fig 5A were exposed to FITC for 10 mins at 35 mmHg PCO<sub>2</sub> -very little loading is apparent. We now explicitly make this point in the text. Our use of Cx32<sup>DN</sup> also eliminates this explanation, by demonstrating the necessity of CO<sub>2</sub> binding to Cx32 for dye loading to occur.

      As there is no panel C in this figure, we assume the referee means panel B and have added the frequency of stimulation and time duration used to achieve the loading.

      (9) Please revise the legend of Figure 7. It seems to refer to a previous version of the manuscript's figure.

      Thanks for pointing this out. We omitted giving a letter to one of the panels and we have corrected this so that legend and figure now correspond.

      (10) Figures 10 and 11. Please consider including a bright field image or indicating with an arrow where the node and/or paranode is located.

      The old Fig 11 has been omitted. The old Fig 11 is now Fig 10. Unfortunately, we cannot add a bright field image as we did not save these in this experiment.

      (11) Figure 11. The authors could consider doing this experiment in the presence of Cx32 blockers to strengthen their conclusion.

      We have decided to remove this figure as it the information it contains is shown in the new GCaMP8 figure (Fig 12).

      (12) Figure 12: Calcium signal increases in different areas beyond the ROI. Not clear that the calcium signal is restricted to the node, as shown in previous figures. Please clarify if the preparation is different.

      We agree that this is a limitation – there is a lot of out of focus light due to Fluo4 being membrane permeable and loading many fibres within the nerve (potentially both axon and Schwann cell). Importantly, this phenomenon occurs in the in-focus ROI (for which we show BF image).

      As we think this is basically a limitation of using Fluo4-AM, we have now produced better data using GCaMP8 under the Mpz promoter (new Fig 12). This expresses at the paranode and in far fewer fibres so the resolution of the recordings is better. We have added these new data into the main body of the paper and relegated the Fluo4 data as a figure supplement to Fig 12 that provides independent supporting information.

      (13) Figure 13: Please indicate the stimulation frequency. The authors could consider attaching Figure 7 Supplement 1 to this figure to make the manuscript straightforward.

      Frequency now indicated.

      With regard to the original Figure 7 supplement 1 -thanks for this suggestion. After consideration, we have split this up and attached it as figure supplements to the relevant figures (Figure 6 and Figure 8). We have added equivalent data to Fig 7 (effect of H<sub>2</sub>O<sub>2</sub>). We think this simplifies presentation for the readers.

      (14) Figure 7 Supplement 1 and Figure 8 Supplements: Please indicate trace colors in panel A of these figures. Also, correct the spelling issue in the legend of Figure 8 Supplement 1 (for panel B).

      Corrected

      (15) Statistical clarifications: The authors should specify which experimental groups were included in some statistical analysis where p-values are reported, but the information about which groups are compared is missing.

      Corrected

      Reviewer #2 (Recommendations for the authors):

      (1) Localization of CO<sub>2</sub> production and Cx32 activation

      Throughout the manuscript, the authors interpret their findings as if the described mechanism specifically occurs in the node and paranode regions. However, there is no direct evidence identifying the precise site of CO<sub>2</sub> production or the activation site of Cx32 hemichannels. Therefore, statements such as the one in the title ("activity-dependent CO<sub>2</sub> production in the axonal node opens Cx32 in the Schwann cell paranode") should be reconsidered or removed, as they may be misleading and are not essential to the interpretation of the data.

      We agree that we have not shown this -and now exercise more caution in the description of the results and discuss this point.

      (2) Figures 2 and 3 - Cx32, mitochondria, and AQP1 localization

      In Figures 2 and 3, it is difficult to clearly discern the localization of Cx32, mitochondria, and AQP1 in the nodal and paranodal regions. The addition of zoomed-in images and 3D reconstructions (or at least orthogonal views) would greatly help clarify whether these components are indeed localized to the axon or Schwann cell, and whether they are specifically enriched in nodal or paranodal domains. As currently presented, the images suggest that all components of this "triad" are broadly distributed within the cells, not restricted to, nor particularly enriched in, nodal or paranodal areas. This observation further supports the concern raised in point 1.

      We have revised our presentation of the localisation more clearly and added a section to the discussion to consider this point more fully. We now explicitly mention that these are SIM images and in a single optical plane, therefore colocalization is genuine. We have also clarified that the calculation of Manders’ coefficients was performed only at the node/paranode regions. However, we accept that these components are distributed more widely than the node/paranode.

      (3) Figure 5 - Clarify legend labels

      In the graph shown in Figure 5, the legend would benefit from more descriptive labeling of the experimental groups. For clarity, indicate that FCCP was applied alone, and that HCO30031 was co-applied with high PCO<sub>2</sub>, to simplify interpretation for the reader.

      Corrected

      (4) Additional experiment to block mitochondrial CO<sub>2</sub> production

      An experiment should be added to completely or significantly inhibit mitochondrial CO<sub>2</sub> production, for example, by combining FCCP treatment with a TCA cycle inhibitor such as fluoroacetate. This would more directly demonstrate that CO<sub>2</sub> generation is required for hemichannel opening during FCCP treatment. It is important to control for this because FCCP can increase ROS production as a result of compensatory metabolic activity (i.e., increased NADH/FADH<sub>2</sub> generation). Since Cx32 hemichannels are known to be modulated by ROS, and can also regulate mitochondrial ROS production, it is crucial to distinguish the role of CO<sub>2</sub> from that of ROS in these experiments.

      Thanks for this great comment, as it gave us the idea of linking activity-dependent (rather than FCCP-evoked) gating of Cx32 to the TCA cycle and, as the reviewer says, CO<sub>2</sub> generation more directly. As fluoroacetate is only effective at inhibiting the TCA cycle in glial cells, we used H<sub>2</sub>O<sub>2</sub> at 50 µM which is highly effective at blocking aconitase in neurons (Tretter & Adam-Vizi, 2000). This greatly reduced FITC dye loading in response to activity. We now include these data in the paper (Fig 7).

      We note that our new data with Cx32<sup>DN</sup> further establishes the link to CO<sub>2</sub> as opposed to ROS.

      Furthermore, to complement the experiments involving carbonic anhydrase (CA) manipulation, additional controls or mechanistic validation may be necessary to support the conclusions drawn.

      We think that our use of Cx32<sup>DN</sup> greatly strengthens our conclusions that CO<sub>2</sub> is the messenger from the axon that gates Cx32 in the paranode.

      (5) AQP1 and Na<sup>+</sup> channel interaction - alternative interpretation

      It has been reported that AQP1 interacts with voltage-gated Na<sup>+</sup> channels, influencing action potential generation. For example, in AQP1 knockout mice, current injection-evoked action potentials show a reduced peak inward current, suggesting impaired Nav1.8 function (Zhang et al., J. Biol. Chem., 2010; doi: 10.1074/jbc.M109.090233). This raises the possibility that the observed effects of AQP1 inhibition (e.g., with TC AQP1-1) could also result from altered Na<sup>+</sup> channel activity, not just impaired CO<sub>2</sub> transport. I suggest that this alternative interpretation be acknowledged and discussed, as the current data do not rule it out.

      While constitutive KO of AQP1 does alter action potential generation in DRGs and an interaction between AQP1 and Nav1.8 has been documented, we do not think that this is a viable alternative interpretation of our data. We have measured the CAP during all our manipulations including the use of TC AQP1-1, and its amplitude is unaltered (see Fig 8 fig supplement 1 and Fig 13D). Our data therefore shows that, in the context of our experiments, application of the AQP1 blocker, TC AQP1-1, does not alter Na<sup>+</sup> channel activity. The difference between our data and the evidence from AQP1 knock-out may arise from the nature of an acute application of an antagonist (short term effect without changing protein expression) and constitutive knock out, which is likely to have longer term effects. We have added some discussion to address this point (last few lines, Page 9).

      (6) Figures 11A and 12C - Add heat map calibration

      In Figures 11A and 12C, the changes in Ca<sup>2+</sup> signals are difficult to interpret. In some areas, color changes appear to occur outside of cellular structures. I recommend including a heat map calibration scale for both figures to facilitate the interpretation of the signal intensity and localization.

      We agree that these data are limited by the technique used, and as mentioned above we now have GCaMP8 data that has better resolution and strengthens our conclusions.

    1. Intrapersonal communication can be defined as communication with one’s self, and that may include self-talk, acts of imagination and visualization, and even recall and memory (McLean, 2005).

      This definition explains that intrapersonal communication is the communication we have with ourselves. It includes our inner thoughts, self-talk, memories, and mental visualization. This type of communication is important because it influences how we think, make decisions, solve problems, and understand our experiences before communicating with others.

    2. Intrapersonal communication can be defined as communication with one’s self, and that may include self-talk, acts of imagination and visualization, and even recall and memory (McLean, 2005).

      The communication we have with ourselves. Takes place in our own mind. It includes the thoughts that run through our minds, the way we talk to ourselves, imagine different situations, and think back to past experiences.

    1. Author response:

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

      eLife Assessment

      This important study builds on previous work from the same authors to present a conceptually distinct workflow for cryo-EM reconstruction that uses 2D template matching to enable highresolution structure determination of small (sub-50 kDa) protein targets. The paper describes how density for small-molecule ligands bound to such targets can be reconstructed without these ligands being present in the template. However, the evidence described for the claim that this technique “significantly” improves the alignment of the reconstruction of small complexes is incomplete. The authors could better evaluate the effects of model bias on the reconstructed densities.

      We have addressed both concerns. Regarding the claim that 2DTM “significantly” improves alignment, the most direct evidence is the controlled comparison in Fig. 3: using the same particle stack and the same reconstruction software (RELION), 2DTM-derived orientations yield a 3.1 Å reconstruction whereas RELION auto-refinement of the same particles yields 3.7 Å. Because the orientations are the only variable, this comparison directly demonstrates that 2DTM produces more accurate alignments.

      We further evaluated RELION auto-refinement with initial low-pass filters of 3, 5, 10, and 15 Å (Fig. 3c); the final resolution remained between 3.7 and 4.0 Å across all conditions, indicating that the achievable resolution difference reflects a fundamental distinction between the two approaches. 2DTM directly leverages high-resolution signal in the template during alignment, which is particularly advantageous for small particles.

      To assess whether this improvement extends beyond the ligand pocket, we constructed a composite omit map (Fig. 5) assembled from 36 reconstructions, each generated using a template with a different subset of residues deleted. The composite shows that density can be recovered at distributed locations across the kinase, including peripheral and surface-exposed regions further away from the alignment center. Recovery varies across sites, with some regions exhibiting weaker or fragmented density, consistent with local differences in structural heterogeneity and residual alignment error. Together, these results indicate that the orientation estimates support global density recovery rather than being confined to the ligand-binding region.

      Regarding model bias, we have strengthened both the quantitative and visual analyses. Specifically, we have (i) updated the template-bias metric Ω in Fig. 4, (ii) added grouped occupancy refinement showing that omitted residues 222–227 refine to 0.55–0.80 (mean 0.72), ATP to 0.61, and Mn to 0.28, while template-included control residues 150–155 remain near 1.0 (0.88–1.00; mean 0.96), and (iii) completed the composite omit map described above. Together, these results provide consistent evidence that densities corresponding to omitted regions are not driven by the template and can be recovered from the data, while template-included regions show some, albeit limited evidence of overfitting, as expected.

      Reviewer #1 (Public review):

      Summary:

      This paper describes an application of the high-resolution cryo-EM 2D template matching technique to sub-50kDa complexes. The paper describes how density for ligands can be reconstructed without having to process cryo-EM data through the conventional single particle analysis pipelines.

      Strengths:

      This paper contributes additional data (alongside other papers by the same authors) to convey the message that high-resolution 2D template matching is a powerful alternative for cryo-EM structure determination. The described application to ligand density reconstruction, without the need for extensive refinements, will be of interest to the pharmaceutical industry, where often multiple structures of the same protein in complex with different ligands are solved as part of their drug development pipelines. Improved insights into which particles contribute to the best ligand density are also highly valuable and transferable to other applications of the same technique.

      Weaknesses:

      Although the convenient visualisation of small molecules bound to protein targets of a known structure would be relevant for the pharmaceutical industry, the evidence described for the claim that this technique “significantly” improves alignment of reconstruction of small complexes is incomplete. The authors are encouraged to better evaluate the effects of model bias on the reconstructed densities in a revised paper.

      We thank the reviewer for these constructive comments. We have updated the template-bias metric Ω in Fig. 4 and added two further quantitative controls: grouped occupancy refinement of omitted residues and a composite omit map spanning the entire protein. Full details are provided in our responses to Comments 1 and 2 below.

      Reviewer #1 (Recommendations for the authors):

      Main Comments

      (1) For the 1ATP structure: Q-scores for deleted residues/ligands are worse than the Q-scores for residues in the template. This means that the reconstructed map must suffer from template bias. Another indication of this bias is that the density for the ATP (and the omitted residues) appears to be weaker than the density for the residues in the template (although this is not easy to assess from the figures). The authors should perform additional experiments to quantify this bias.

      (a) One option could be to do what the X-ray crystallographers call an OMIT map, and omit allresidues, a few at a time, from the template in multiple 2DTM runs. They could then assemble a density map from all the omitted residues together and measure the resolution of the omit map against the known template by FSC.

      (b) Another insightful experiment would be to take the various 2DTM reconstructed maps describedin the paper and perform a refinement of the atom occupancies of all residues in the structure. Residues included in the template should refine to values close to 1. In the absence of bias, the occupancies of the omitted residues should be 1 too; if the reconstructed map were completely biased, those occupancies would refine to 0. Therefore, the refined occupancies of omitted residues could perhaps serve as a measure for the amount of bias in the reconstructed map.

      We thank the reviewer for these detailed and constructive suggestions. We agree that the lower Q-scores for omitted regions indicate weaker density and that template bias exists at residues that are included in the template. To quantify this more directly, we corrected the template-bias metrics at the omitted region (mask from the full–omit template difference) in Fig. 4.

      Following the reviewer’s suggestion, we performed Phenix real-space grouped occupancy refinement against the omit reconstruction using the docked full model. The results are shown in Table. S2. We refined occupancies for the omitted residues (chain E 222–227), ATP, Mn, and template-included control residues (chain E 150–155), while excluding waters. The omitted residues refined to occupancies of 0.55–0.80 (mean 0.72), ATP to 0.61, and Mn to 0.28, whereas the control residues remained near 1.0 (0.88–1.00; mean 0.96). These results indicate substantial recovery of density in the omitted regions, but also some degree of bias.

      The substantially lower refined occupancy of Mn<sup>2+</sup> may reflect genuine partial occupancy in the dataset. While compact features can be especially sensitive to residual alignment error, we cannot conclude from the present analysis that alignment effects alone account for the weak Mn<sup>2+</sup> density.

      Finally, we have constructed a composite omit map to assess density recovery across the protein. We generated 36 omit templates, each deleting ∼10 non-overlapping residues scattered across the structure (including peripheral and surface-exposed regions). For each template, an independent 2DTM search and reconstruction was performed. Local density patches were extracted within 3 Å of the omitted atoms (with neighboring residues excluded as described in Methods) and assembled into a composite map (Fig. 5). The composite map shows that density can be recovered at distributed locations across the protein and is not restricted to the central binding pocket. Recovery is variable across sites, with some regions exhibiting weaker or fragmented density, consistent with local differences in signal-to-noise, structural heterogeneity, and residual alignment error.

      (2) The claim that 2DTM leads to “Improved” reconstruction (title) and “alignment and reconstruction [...] can be significantly improved” (abstract) is not supported by the data presented in the paper. The smallest single particle structure to resolutions sufficient for de novo atomic modelling is currently the ACA2 complex, with an ordered mass of less than 40 kDa, which was reconstructed using Blush regularisation in RELION. This paper should be referenced, and statements about single particle analysis (SPA) not working for sub-50 kDa complexes should be toned down. In general, I would say that 2DTM and SPA are not competing techniques, and the paper would be better if it focused on the intrinsic advantages of 2DTM (like ease-of-use for screening of pharmaceutical compounds) and useful findings described that make 2DTM better, e.g., excluding thick ice.

      We thank the reviewer for this important perspective and have added the Blush regularization reference Kimanius et al. (2024) to the revised manuscript, noting that the 40 kDa Aca2–RNA complex was reconstructed to 2.5 Å resolution using this approach (at L451). Furthermore, Blush regularization could be applied to reconstructions derived from 2DTM-based particle stacks, and a combination of both approaches may yield further improvements.

      We agree that 2DTM and SPA are complementary rather than competing techniques and have revised the manuscript to reflect this. We have also toned down claims in the abstract, which now states that 2DTM “reconstructed a previously intractable ∼43 kDa kinase complex and improved the density of its ligand-binding site” rather than making broad claims about SPA limitations. In the discussion, we now describe 2DTM as broadening possibilities for structural studies of targets “that have remained difficult to reconstruct” rather than implying they are impossible by SPA.

      Regarding the intrinsic advantages of 2DTM: beyond ligand screening, the composite omit map (Fig. 5, described in Comment 1) demonstrates that 2DTM-derived orientations support density recovery throughout the entire protein, including peripheral and surface-exposed residues, using roughly an order of magnitude fewer particles than conventional SPA workflows.

      (3) Given the uncertainties about the amount of template bias in the reconstructed 2DTM densities, I have trouble interpreting the predictions in Table 1. Where would the 1ATP structure lie in Figure 8? How much bias would there be in a 2DTM reconstruction at SNR n = SNR s? Could the authors perform tests on simulated data to confirm these predictions? At the point of SNR n = SNR s, how would a 2DTM reconstruction look, and what would refined occupancies for deleted residues be?

      (This may reflect a misunderstanding on my part, but I don’t really see how the SNR n = SNR s is completely dependent on the number of orientations searched (through Equation 1). In Figure 8, is the full search in a 4k x 4k micrograph, or inside a particle box? And what are the relevant search ranges? Perhaps as a consequence of this misunderstanding, I do not understand how one would decide on the amount of noise in the simulated data for these tests.)

      We thank the reviewer for this important question and agree that this point needed clearer explanation. In our framework, is the expected alignment-noise level from maximizing many cross correlations, where N<sub>s</sub> is the total number of sampled hypotheses in the 5D search (in-plane angle, out of-plane angles, and x, y shifts), not only the number of orientations. Thus, the relevant search is the per-particle alignment search window (full or constrained), not a full 4k×4k micrograph area.

      At SNR<sub>n</sub> = SNR<sub>s</sub>, the true-match and noise-maxima levels are at a threshold; one could imagine if SNR<sub>s</sub> is only slightly larger than SNR<sub>n</sub>, the correct pose is favored on average, so with sufficiently large particle numbers real omitted-region density should accumulate, but with residual pose errors that attenuate high-frequency amplitudes (effectively a large positive B-factor). In that regime, sharpening (negative-B correction) can improve visibility once signal is accumulated. Therefore, we expect partial recovery rather than fully unbiased recovery at this threshold, with omitted-region occupancies remaining between 0 and 1 and below template-included controls (consistent with our measured values), and improving as SNR<sub>s</sub> − SNR<sub>n</sub> and particle number increase. Simulations at this exact threshold would require a very large particle number to achieve sufficient statistics, and we leave this to future work. We have added this clarification to the Supporting Information.

      (4) The strong (> 5 sigma!!) and ubiquitous difference densities in Figure 9A imply that the authors have a serious problem with their forward model, which could explain some of the effects of model bias discussed above. I recommend they investigate these differences in detail. It would be good to see negative and positive densities in different colours to understand these differences better. The text speaks about incomplete capture of the solvent background, but the difference densities appear to be of much higher spatial frequencies than those typical for background/solvent effects (e.g., 15-20A). It may thus also be helpful to analyse these differences in Fourier space.

      We thank the reviewer for this important point. In our previous analysis, we did not incorporate an appropriate protein mask when generating the difference map, which contributed to widespread residual densities. We have now regenerated the map using the program diffmap.exe (https: //grigoriefflab.umassmed.edu/diffmap) with a protein soft mask and moved it to the Supplementary Information (Fig. Figure 1—figure supplement 4, contour SD = 20). With this controlled setup, the strongest coherent residual densities localize to the omitted ATP pocket and residues 222–227, consistent with recovery of omitted features. We have revised the figure/text accordingly and clarified that remaining diffuse residuals are likely due to forward-model mismatch (including solvent/background representation). We also added to the manuscript that improved template generation may be achieved by incorporating recent methods that learn environment-aware scattering factors directly from experimental cryo-EM maps.

      Other Comments

      (1) P.1: Alongside reference 2, a reference to the 1.2 Å apoferritin structure from the Stark group should be included.

      We have added the reference at L30.

      (2) P.2: “commond line tool”

      We have corrected the typo.

      (3) P.2-3: Robust reconstruction of the ATP binding pocket: Auto-refinements in RELION without alignments do not exist, and corresponding statements need to be removed from the manuscript. If one wants to skip alignments, then there is no refinement left to be done. In that case, one should just perform a reconstruction of the 2 halves (e.g., using relion reconstruct) and then run a standard RELION postprocessing.

      We agree with the reviewer and have revised the manuscript accordingly. Technically, RELION’s relion refine with the --skip align flag runs an iterative loop that re-estimates the per-particle noise model (spectral noise σ<sup>2</sup>) and computes the gold-standard FSC between half-maps, but it does not modify the particle orientations or translations. As the reviewer correctly points out, this is effectively a 3D reconstruction followed by postprocessing, not a refinement. We have updated the text to replace “skip-alignment auto-refinement” with “3D reconstruction without angular refinement” to accurately reflect what was performed.

      (4) P.3: What are “first-quadrant p-values” and “three-quadrant p-values”?

      We apologize for the ambiguity and now define these terms explicitly in the revised text (with citation to the p-value paper). After transforming z-score and SNR to probit coordinates, “first-quadrant” (1Q) p-values use only candidate points with both coordinates > 0 (i.e., both probit-zscore and probitSNR are positive). “Three-quadrant” (3Q) p-values include candidates where at least one coordinate is > 0 (equivalently, all points except the quadrant where both are < 0).

      (5) P.5: In Equation (2), it is unclear what Q means from the main text. Would it be better to leave Equation (2) for the Appendix, and only show Equation (3) in the main text?

      Thank you for this suggestion. We kept Equation (2) in the main text to preserve the continuity of the derivation, but we now define Q(k,N<sub>i</sub>) explicitly at first use as the normalized exposure-weighting transfer function (following Grant 2015). The detailed derivation and assumptions remain in the Supporting Information.

      (6) P.6: “Remaining gaps”: this section considers differences between 200 keV and 300 keV electron beam energies. The main practical effect for cryo-EM data sets is that the current detectors are designed for detecting 300 keV electrons, and their DQE is thus a lot worse at 200 keV. The entire paper doesn’t mention detectors. Perhaps because they are assumed to be perfect, but it is still far from the case.

      Also, why were defocus searches not performed if the thickness of micrographs was up to 1500 A?

      The conclusion of this section states “Considering all these factors...”, but it then claims standard single particle analysis still remains an outstanding challenge. This concluding statement makes no sense, as this whole section was about 2DTM.

      Thank you for this comment. We agree and have revised the text to make these points explicit. First, we now state clearly that detector response (DQE) is generally more favorable at 300 keV than at 200 keV, which contributes to the experimental–theoretical gap. Second, we clarify why we did not perform a defocus search in 2DTM: after CTF/thickness filtering, the retained micrographs are predominantly in the thin-ice regime, so expected defocus spread is smaller, while adding a defocus dimension substantially increases computational cost. We also tested downstream refinement (including CTF/beam-tilt related refinement in cisTEM) and did not observe measurable improvement for this dataset (data not included in the manuscript). Finally, we revised the concluding sentence in this subsection to refer specifically to 2DTM-based alignment limits rather than standard SPA, so the section scope is now consistent.

      (7) P.7: Data-driven refinement of AlphaFold3 models: it might be worth pointing out that removing residues a few at a time from AF3 models and checking their reconstructed density by 2DTM would come at a considerable computational cost.

      We agree. We have demonstrated residue-level omission validation using the X-ray template via a composite omit map (Fig. 5), confirming that the approach is feasible. We have updated the Discussion to reflect this: extending the composite omit approach to AlphaFold3-based templates remains computationally expensive — each omission design requires an independent 2DTM search and downstream reconstruction — and we present this as an important direction for future work.

      (8) Figure 1: What is “full FSC” and what is “particle FSC”?

      Thank you for pointing this out. We have clarified the terminology in the figure legend and text using cisTEM and Frealign definitions (Grant et al., 2018). What was previously labeled “Full FSC” is now referred to as the uncorrected FSC (FSC<sub>uncor</sub>), computed within a generous mask. “Particle FSC” denotes the solvent-corrected FSC, obtained from FSC<sub>uncor</sub> using the mask-volume correction factor f as described in the cisTEM/Frealign framework (Grant et al., 2018).

      (9) Figure 3: Why were particles in class 5 discarded? The 2DTM approaches described in this paper are all about carefully selecting good particles, yet now the authors use standard 3D classification to throw away another 156 particles. This seems to be an arbitrary choice. How different would the results have been if these had been included in the reconstruction? Alternatively, did these few particles have any 2DTM metrics that would justify their exclusion?

      We thank the reviewer for raising this point. Class 5 contained only 156 particles (∼2% of the dataset). While the 2DTM p-value and SNR metrics provide principled criteria for particle selection, they are not perfect, and a small number of suboptimal particles may still pass these filters. To address the reviewer’s concern, we repeated the reconstruction including all five classes. The resulting map achieved a resolution of 3.7 Å, identical to the reconstruction without class 5, confirming that including these particles does not affect the results. We have clarified this point in the manuscript.

      (10) Figure 4C: What are the negative sample thicknesses here? Why use an inset?

      The negative sample thickness values are artifacts of the CTF-based thickness estimation algorithm in ctffind5. This algorithm fits oscillations in the 1-D power spectrum arising from the interaction between the CTF and the specimen’s finite thickness (a sinc-modulated envelope). When the ice is very thin or the power spectrum is noisy, the optimizer can converge to a physically meaningless negative value. Of the 2,488 total micrographs across both sessions (after CTF score filtering, 2,314 retained), 136 (∼5.9%) returned negative thickness estimates. We have revised Figure 1—figure supplement 1c (previously Figure 4c) to show only the physically meaningful positive thickness values without the inset, which gives a clearer view of the unimodal distribution peaked near 350–400 Å.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Zhang et al describe a method for cryo-EM reconstruction of small (sub50kDa) complexes using 2D template matching. This presents an alternative, complementary path for high-resolution structure determination when there is a prior atomic model for alignment. Importantly, regions of the atomic model can be deleted to avoid bias in reconstructing the structure of these regions, serving as an important mechanism of validation.

      The manuscript focuses its analysis on a recently published dataset of the 40kDa kinase complex deposited to EMPIAR. The original processing workflow produced a medium resolution structure of the kinase (GSFSC ∼4.3 Å, though features of the map indicate ∼6-7 Å resolution); at this resolution, the binding pocket and ligand were not resolved in the original published map. With 2DTM, the authors produce a much higher resolution structure, showing clear density for the ATP binding pocket and the bound ATP molecule. With careful curation of the particle images using statistically derived 2DTM p-values, a high-resolution 2DTM structure was reconstructed from just 8k particles (2.6 Å non-gold standard FSC; ligand Q-score of 0.6), in contrast to the 74k particles from the original publication. This aligns with recent trends that fewer, higher-quality particles can produce a higher-quality structure. The authors perform a detailed analysis of some of the design choices of the method (e.g., p-value cutoff for particle filtering; how large a region of the template to delete).

      Overall, the workflow is a conceptually elegant alternative to the traditional bottom-up reconstruction pipeline. The authors demonstrate that the p-values from 2DTM correlations provide a principled way to filter/curate which particle images to extract, and the results are impressive. There are only a few minor recommendations that I could make for improvement.

      We appreciate the positive assessment. In response to the bias-related concerns raised elsewhere, we have: (i) updated the template-bias metric Ω reported in Fig. 4, (ii) added grouped occupancy refinement showing that omitted residues 222–227 refine to a mean occupancy of 0.72 while template-included control residues remain near 1.0, and (iii) assembled a composite omit map (Fig. 5) from 36 partial-deletion reconstructions spanning the entire protein. These additions are described in the revised Results and in the rebuttal below.

      Reviewer #2 (Recommendations for the authors):

      (1) On page 3, “Finally, by comparing Figure 2a and b, we observed that deleting IP20 strongly reduced signal at several residues.” Looking at Figure 2a and 2b, it was unclear which residues they were referring to.

      We have revised the text to explicitly list the affected residues. In the updated Figure 2, we now label the omitted residues with the lowest backbone Q-scores in the structural views (column 2) and include per-residue backbone Q-score plots (column 4), making the comparison between panels (a) and (b) quantitative. For example, when IP20 is additionally deleted (Fig. 2b), residues Phe54, Gly55, Lys72, Glu127, Glu170, and Asp184 all fall below a backbone Q-score of 0.5, compared with only Ser53 and Glu127 in the within-3 Å deletion alone (Fig. 2a).

      (2) Figure 1a. Both the published density map and the text “Template” are gray, but the 2DTM template density map is yellow.

      Thank you for catching this inconsistency. We have updated Figure 1a so that the 2DTM template density is now rendered in gray, consistent with the X-ray crystal structure (PDB) coloring. The published single-particle map is shown in wheat and the 2DTM reconstruction in blue, providing a clear three-way color distinction.

      (3) Figure 1b. I would recommend the x-axis label of “spatial frequency” instead of “resolution” (which is overloaded). Furthermore, the fact that this is not a GSFSC should be clearly labeled in the figure to prevent confusion with a standard GSFSC.

      We agree with both suggestions. The x-axis has been relabeled “Spatial Frequency (1/Å)” in the revised figure. We have also added a note in the figure caption stating that these FSC curves are not gold-standard FSCs, as the reconstruction uses orientations determined by template matching rather than independent half-set refinement.

      (4) Figure 2: The usage of the negative sign in the labels “-3 Å”, “-5 Å” to indicate within a given radius is a bit confusing. “Within 3 Å”, perhaps?

      Thank you for this suggestion. We have changed the labels in Figure 2 from “−3 Å” and “−5.5 Å” to “Within 3 Å” and “Within 5.5 Å.” We have also added a fourth column to Figure 2 showing per-residue backbone Q-scores for each deletion experiment, with omitted residues distinguished by color and marker shape. The residues with the lowest backbone Q-scores among the omitted set are circled in red and correspond to the labeled residues in the structural views.

      (5) Figure 4c: Why does the sample thickness histogram go to negative values (-20,000 A)?

      As noted in our response to Reviewer 1, the negative thickness values are artifacts of the ctffind5 thickness estimation, which fits a sinc-modulated envelope to the 1-D power spectrum. For micrographs with very thin ice or noisy power spectra, the fit can converge to unphysical negative values. These account for ∼5.9% of micrographs. We have revised Figure 1—figure supplement 1 (originally Fig. 4c) to display only positive thickness values, removing the inset and providing a clearer histogram.

      (6) Figured 4d: Should the label be “(Before Filtering)” instead of After?

      Yes, thank you for catching this. The original Figure 4d was mislabeled—it showed particle counts before filtering but was titled “After Filtering.” We have corrected the labels: Figure 1—figure supplement 1d (originally Fig. 4d) now reads “Before Filtering” and Figure 1—figure supplement 1e (originally Fig. 4e) reads “After Filtering.”

      (7) Supplementary Note 1: Please provide units for d, p, D, and k max in equation S4 and the preceding text.

      We have added units to the text preceding Eq. S4: d = 1/k<sub>max</sub> is the high-resolution alignment limit (Å), k<sub>max</sub> is the maximum spatial frequency (Å <sup>−1</sup>), p = d/2 is the ideal pixel size (Å/pixel), and D is the particle diameter (Å).

      (8) What does the map-model FSC look like with the template as the model vs. the AF3 structure as the model?

      We have computed the map–model FSC for both the X-ray crystallographic template (PDB 1ATP) and the AlphaFold3-predicted template against their respective 2DTM reconstructions (Fig. Figure 6—figure supplement 1). Both curves cross the FSC = 0.143 threshold at ∼2.3 Å. We note that the map–model FSC in this context should be interpreted with caution, because the vast majority of the structure lies outside the omitted region and is present in the template, so template bias in those regions will dominate the map–model FSC and obscure differences in the small omitted region.

      Reviewer #3 (Public review):

      Summary:

      Due to the low SNR of cryo-EM micrographs necessitated by radiation damage, determining the structure of proteins smaller than 50 kDa is exceedingly challenging, such that only a handful have been solved to date. This work aims to improve the reconstruction of small proteins in single-particle cryo-EM by using high-resolution 2D template matching, an algorithm previously used to locate and align macromolecules in situ, to align and reconstruct small proteins. This approach uses an existing macromolecular structure, either experimentally determined or predicted by AlphaFold, to simulate a noise-free 3D reference and generates whitened projections, crucially including high-spatial-frequency information, to align particles by the orientation with maximal cross-correlation. They demonstrate the success of this approach by generating a 3D reconstruction from an existing dataset of a 41.3 kDa protein kinase that had previously evaded attempts at high-resolution structure determination. To alleviate concerns that this is purely from template bias, they demonstrate clear density at two regions that were not present in the template: 6 residues in an alpha helix and an ATP in the ligand binding pocket. The latter is particularly important for its implications in determining structures of ligand-bound proteins for drug discovery. Additionally, the authors provide an update to the classic calculation in Henderson 1995 to predict the minimum molecular mass of a protein that can be solved by single-particle cryo-EM.

      Strengths:

      I am in no doubt that this technique can be used to gain valuable insights into the structures of small proteins, and this is an important advancement for the field. The ability to determine the structure of ligands in a binding site is particularly important, and this paper provides a method of doing that which outperforms traditional single-particle cryo-EM processing workflows.

      The claim that using high-spatial frequency information is essential for aligning small proteins is a valuable insight. A recent pre-print published at a similar time to this manuscript used high-resolution information in standard ab-initio reconstruction to generate a high-resolution reconstruction from the same dataset, supporting the claims made in the manuscript.

      The theoretical section outlined in the appendix is also theoretically sound. It uses the same logic as Henderson, but applies more up-to-date knowledge, such as incorporating dose-weighting and altering the cross-correlation-based noise estimation. This update is valuable for understanding factors preventing us from reaching the theoretical limit.

      Weaknesses:

      Given that this technique creates template bias, only parts of the reconstruction not in the template can be trusted, unlike standard single-particle processing, where the independent half-maps from separate, ab initio templates are used to generate a 3D reconstruction. Although, in principle, one could perform the search many times such that every residue has been omitted in at least one search, this will be extremely computationally intensive and was not demonstrated in this manuscript. It is therefore currently only realistically applicable when only a small portion of the sub-50 kDa protein is of interest.

      The applicability of this technique to more than a single target was also not demonstrated, and there are concerns that it may not work effectively in many cases. The authors note in the results that “the ATP density was consistently recovered more robustly than nearby residues” and speculate that this may be because misalignments disproportionately blur peripheral residues. Since the region of interest in a structure is not necessarily in the center, this may need further investigation. The implications of this statement may also be unclear to the reader. For example, can this issue be minimized by having the region of interest centered in the simulated volume?

      In Figure 3, the authors demonstrate that it is not solely improved particle filtering and a noise-free reference that improves alignment, but that the high spatial frequency information is important. This information is very valuable since it can be applied to other, more standard methods. However, this key figure is not as clear or convincing as it could be. The FSC curves are possibly misleading, since the reduced resolution could be explained by reduced template bias when auto-refining with a map initially low-pass filtered to 10 A. Moreover, although the helix reconstruction does look slightly better using the 2DTM angles, the improvement in density for ATP in the binding pocket is not clear. A qualitative argument only clear in one out of two cases is not as convincing as a quantitative metric across more examples.

      We address these concerns in three ways: (i) we quantify template bias using Phenix real-space grouped occupancy refinement: omitted residues 222–227 refine to occupancies of 0.55–0.80 (mean 0.72) and ATP to 0.61, while template-included control residues 150–155 remain near 1.0 (mean 0.96), confirming that recovered density is genuine rather than a template artifact; (ii) we have now completed a composite omit-map experiment (Fig. 5), in which 36 partial-deletion templates, each omitting ∼10 non-overlapping residues, were used to perform independent 2DTM searches and reconstructions; local density patches from all 36 reconstructions were assembled into a composite map showing density recovery at distributed locations across the protein, including peripheral and surface-exposed regions, although recovery is variable across sites; and (iii) we have expanded the discussion to clarify that, while the primary scope of this work is omitted-region validation for the ligand-binding site, the composite omit-map result demonstrates that the approach generalizes beyond the central pocket.

      Reviewer #3 (Recommendations for the authors):

      In addition to the comments on the public review, I have some more specific suggestions that could improve the manuscript.

      (1) Another recent pre-print posted on BioRxiv shortly before this manuscript (Kim et al. Highresolution ab initio reconstruction enables cryo-EM structure determination of small particles) determined a high-resolution structure of the same protein from the same dataset, as well as determining the structures of other small proteins. Since both manuscripts rely on high-spatial frequency information, I think that the paper strengthens the claims in this manuscript and should be cited.

      We thank the reviewer for this suggestion. We agree that the recent preprint by Kim et al. strengthens the relevance of high-spatial-frequency information for small-particle cryo-EM reconstruction. We have now added this work to the revised manuscript and included a brief discussion comparing its ab initio strategy with our 2DTM-based approach.

      (2) The claim in the abstract that “we were able to reconstruct previously intractable targets under 50 kDa and improve the density of the ligand-binding sites in the reconstructions” should be altered to make it clear that this is only a single previously intractable target.

      We agree. The revised abstract now reads “. . . we reconstructed a previously intractable ∼43 kDa kinase complex and improved the density of its ligand-binding site” making clear that a single target is demonstrated in this work.

      (3) Q-scores in the manuscript were sometimes used to quantify the improvement in map to model fit for the ATP binding pocket, but never for the 6 residues of the alpha helix. They were also not reported in every case for the ATP-binding pocket. This could lead a reader to think it is only being reported when the Q-score matches the expectation. For transparency, I would suggest either using Q-scores in every comparison or in no cases and simply relying on the qualitative result.

      We agree with the reviewer. In the revised manuscript, we now report Q-scores consistently for both ATP and residues 222–227 across all conditions: individual residue Q-scores for the omitted residues 222–227 in Fig. 1 are reported in the main text and figure caption; per-residue backbone Q-score plots for all deletion experiments in Fig. 2 are shown as the fourth column of each panel; Fig. 3 (RELION reconstruction) does not include Q-scores as the focus is on orientation accuracy rather than map-model fit; and average Q-scores for all four particle selection conditions in Fig. 4 are listed in Figure 4—source data 1.

      (4) The sigma values used for viewing the maps should also be stated in several figures, particularly Figure 3 and Figure 6.

      We have added contour levels (σ) to the captions of Fig. 3 and Fig. 4 (originally Fig. 6) in the revised manuscript.

      (5) I have a slight concern about how well this method applies away from the region centered in the alignment. If parts on the periphery of the structure are removed, do these also reconstruct? Is it required that the omitted region be centered in the simulation of the 3D volume for each alignment? If so, this should be clearly stated.

      2DTM determines particle orientations by matching the full projected template to the image, so alignment is driven by the global structure rather than a localized region. As a result, the recovered orientations define the reconstruction throughout the entire particle, not only near the center. The omitted region does not need to be centered in the template volume. Any region of the protein can be omitted and its density evaluated after reconstruction.

      To directly test whether peripheral regions are recovered in the same manner as central ones, we performed a composite omit-map experiment. We generated 36 omit templates, each deleting ∼10 non-overlapping residues distributed across the entire protein, including peripheral and surface-exposed regions. For each template, an independent 2DTM search and reconstruction was performed. Local density patches corresponding to the omitted regions were then extracted and assembled into a composite map (Fig. 5). The resulting map shows density at distributed locations across the protein, indicating that density recovery is not restricted to regions near the alignment center and that peripheral regions can be reconstructed under the same alignment framework, although the quality of recovery varies across sites.

      (6) I was confused by the difference between the FSCs in Figure 1 and Figure 3. I understand Figure 1 is from cisTEM and Figure 3 from RELION, but I expected the unmasked FSC and full FSC to be similar. Do the authors have any insights into why there is such a large difference? I would also consider removing the FSCs in Figure 3, since the reduced resolution may only be due to reduced template bias, meaning including this may be misleading.

      Thank you for raising this point. The apparent discrepancy arises from multiple differences between the two figures: different FSC definitions, different half-maps (reconstructed with different software and slightly different particle sets), and different masks.

      In cisTEM (Fig. 1), two FSC curves are reported: the uncorrected FSC (FSC<sub>uncor</sub>), measured within a spherical mask, and the “Particle FSC”, which applies an analytical solvent-fraction correction (Grant et al., 2018) to account for solvent dilution within the mask. The Particle FSC crossed the 0.143 threshold at ∼2.6 Å, whereas FSC<sub>uncor</sub> crossed at ∼3.0 Å. In Fig. 3, RELION postprocess applied phase-randomization correction with a soft mask, yielding ∼3.1 Å. However, the Fig. 3 FSC was computed on different half-maps (RELION skip-alignment reconstruction of 7,197 particles after 3D classification) with a different mask.

      To directly compare the two packages, we computed the FSC on the same cisTEM half-maps using both methods (Figure 3—figure supplement 1). The cisTEM Particle FSC (spherical mask + solvent correction) gave ∼2.6 Å, while RELION image handler with a tight 3D protein mask gave ∼2.7 Å. These two approaches converge to a similar resolution through different mechanisms: cisTEM compensates for a generous spherical mask using the solvent-fraction correction, while RELION uses a tight mask that excludes most solvent directly. This confirms that when the same half-maps are used, the two packages give consistent results and the apparent discrepancy between Figs. 1 and 3 is primarily due to differences in the reconstruction and particle set, not the FSC calculation.

      We agree with the reviewer that the FSC values in Figure 3 should be interpreted with caution. In this case, the particle orientations are not independently refined but are instead inherited from the 2DTM alignment, so the two half-maps are not strictly independent. We have added clarifying language in the revised manuscript to make this point explicit (Fig. 1 caption).

      (7) I would also like to see how RELION auto-refinement performs with different low-pass filtering. This could strengthen the argument that high-resolution information is necessary from the start to successfully align small particles.

      We thank the constructive suggestion from the reviewer. We performed RELION auto-refinement on the same 7,197-particle stack using different initial low-pass filter resolutions (--ini high) of 3, 5, 10, and 15 Å. The resulting post-processed resolutions were:

      Author response table 1.

      The results show that varying the initial low-pass filter has minimal effect on the final resolution. This is expected because RELION uses a gold-standard, maximum-likelihood framework in which the resolution used for alignment is determined iteratively from the data via a probability distribution, rather than being fixed by the initial reference. After the first iteration, the reference is updated from the data, and higher-resolution information is incorporated only to the extent supported by the definition of the current reconstruction. Consequently, differences in the initial low-pass filter have limited impact on the final refinement outcome.

      This behavior contrasts with 2DTM, where alignment is performed by direct cross-correlation against a fixed template. In this case, high-resolution features in the template contribute directly to the scoring function and can improve alignment accuracy.

      To directly test the importance of high-resolution information for 2DTM alignment, we performed an additional experiment in which 2DTM was run on bin4x images (2.234 Å/pixel), and the detected particle coordinates were used to extract particles from the corresponding bin2x images (1.117 Å/pixel) for reconstruction. Despite using the same bin2x images for reconstruction, the bin4x-aligned particles yielded a map in which ATP density was lost and backbone density for residues 222–227 was visibly degraded compared to the bin2x-aligned reconstruction (Fig. Figure 1—figure supplement 3). This demonstrates that access to high-spatial-frequency information during template matching is critical for accurate alignment of small particles.

      (8) The caption in Figure 3 should be more descriptive about what is being shown in each panel.

      We have substantially expanded the Figure 3 caption. It now describes each panel explicitly: (a) 3D classification results with particle counts, percentages, and per-class resolutions; (b) side-by-side comparison of reconstructions using 2DTM orientations versus RELION auto-refine, including full maps, zoomed binding-pocket views with the atomic model overlaid, orientation distributions, and FSC curves with reported resolutions; and (c) a table of RELION auto-refinement resolution as a function of the initial low-pass filter setting. We also added a new panel (c) showing that including all five classes yields the same 3.7 Å resolution, addressing the concern about Class 5 exclusion.

      (9) Figures 4 and 5 may be better suited as supplementary figures.

      We agree. Figures 4 and 5 have been moved to the Supplementary Information in the revised manuscript.

      (10) In Figure 4c, it is difficult to understand why the thickness distribution plot goes negative, especially to such a high magnitude as 1.5 microns.

      We agree this was confusing. The negative values are fitting artifacts from ctffind5’s thickness estimation, which fits a sinc-modulated envelope to the power spectrum. When the ice is very thin or the spectrum is noisy, the optimizer can converge to unphysical negative values (affecting ∼5.9% of micrographs). We have revised Figure 1—figure supplement 1c (previously Figure 4c) to show only positive thickness values, which now clearly displays the unimodal distribution peaked at 350–400 Å.

      (11) In Figure 5d, the micrograph looks a lot like a cross-grating grid used for calibration instead of crystalline ice or a fractured film.

      We agree. We have updated the caption for Figure 1—figure supplement 2d (originally Figure 5d) to read “Cross-grating calibration grid”

      (12) Figure 6 was very surprising to me if I am interpreting it correctly. It is not stated in the caption what omega is, but I am assuming it is a measurement of template bias. It is very surprising that the template bias drops when using more particles by reducing the p-value from 8.0 to 7.0. This goes against what I understood from Lucas et al. 2023, so I am curious as to why this is the case.

      We thank the reviewer for this question and apologize for the unclear presentation. We have revised Fig. 4 (previously Figure 6) and its caption to define Ω explicitly and updated the Ω values. We also identified that the mask used in the original computation was too loose; the revised mask is now constrained to the omitted region only (ATP, Mn<sup>2+</sup>, and residues 222–227), derived from the difference between the full and omit templates and shown in Figure 4—figure supplement 1. Ω is adapted from the template-bias metric introduced in (Lucas et al., 2023) and measures how much of the density in the omitted region is attributable to using the full template rather than the omit template. Specifically, for each particle selection condition we reconstruct two maps using orientations and particles derived from independent 2DTM searches with the full and omit templates (V<sub>full</sub> and V<sub>omit</sub>, respectively). Ω is the fractional reduction in density within the omission mask: . In the revised Fig. 4, Ω increases from 46% (p-value = 8.0) to 48% (p-value = 7.0), consistent with the expectation that including more, lower-quality particles increases the relative contribution of the template to the reconstruction. The Ω values are 48% for the SNR = 7.5 and 53% for the tilt conditions.

      (13) It would be useful if the in-house Python script used to calculate template bias could be made publicly available.

      We agree. The template-bias calculation (measure-template-bias) is now included in the publicly available Python package at https://github.com/kekexinz/2DTM_postprocess_tool, and can also be accessed in the official cisTEM repository at https://github.com/timothygrant80/cisTEM. The package also contains the extract-particles and filter-particles tools described in the Methods section.

      (14) The p-value used is said to be a three-quadrant p-value instead of a one-quadrant p-value. Although I assume this is simply replacing an ‘and’ statement with an ‘or’ statement, the exact difference could be made clearer to the reader.

      We have now defined these terms explicitly in the revised Methods. After probit transformation of z-score and SNR, the first-quadrant (1Q) p-value requires both values to be > 0 (logical AND), whereas the three-quadrant (3Q) p-value requires at least one to be > 0 (logical OR). The 3Q criterion is therefore looser, retaining more candidates—which is beneficial for small targets that may score well on one metric but not both.

      (15) I was, perhaps naively, surprised that z-scores could not be used. It was my understanding that by removing the rotationally invariant component from the cross-correlation, the z-score would down-weight low-resolution information compared to the cross-correlation. Given that the manuscript suggests low-resolution alignment can cause getting stuck in local minima, this is surprising to me. The authors note it led to the rejection of most particles; were there simply too many false positives when a lower threshold was used?

      The reviewer is correct that subtracting the angular mean removes the rotationally invariant component of the cross-correlation. However, the resulting z-score primarily measures how strongly a specific orientation stands out relative to other orientations. In other words, it reflects the orientation discriminability (closely related to Fisher information) rather than the absolute correlation strength. For small particles the cross correlation often varies only weakly across orientations, so CC<sub>max</sub>− CC<sub>avg</sub> remains small even when the absolute correlation is significant. As a result, using the z-score alone as a selection criterion led to the rejection of many true particles.

      Theoretical Section Improvements

      (a) The discussion on beam-induced motion could be improved by separating it into initial motion (e.g., cryo-crinkling, buckling) that can be eliminated through grid design, and pseudo-Brownian motion, which cannot. Pseudo-Brownian motion will become much more significant for small proteins (based on reference 5, for a 10 kDa protein, this would be a MSD of ∼0.1 A 2/e−/A 2, or a B-factor of over 2 A 2/e−/A 2), and Bayesian Polishing is unlikely to correct this perfectly, given that it imposes a smoothness of motion between nearby particles. The impact of not correcting for this could be quantified more explicitly.

      We thank the reviewer for this helpful suggestion. As noted, pseudo-Brownian motion of particles within irradiated ice introduces stochastic displacements that accumulate with dose and are expected to be more significant for small particles. Based on the analysis in (Mcmullan et al., 2015), and scaling with particle size, this effect can be aproximated as a dose-dependent mean-squared displacement (MSD) of ∼0.1 Å<sup>2</sup> per (e<sup>−</sup>/Å<sup>2</sup>) for a ∼10 kDa particle. Over a typical total exposure of 40–60 e<sup>−</sup>/Å<sup>2</sup>, this corresponds to an accumulated RMS displacement of ∼2–2.5 Å, sufficient to attenuate high-resolution signal.

      In practice, such motion acts as an additional high-frequency attenuation in Fourier space, analogous to an envelope function, reducing the coherent signal available for template matching. While Bayesian polishing can partially correct beam-induced motion, it assumes spatially smooth trajectories between nearby particles and therefore may not fully compensate for stochastic, particle-specific motion.

      Within the theoretical framework presented here, this effect can be interpreted as an additional frequency-dependent damping of the signal (B-factor). Its primary consequence would be to reduce the effective signal-to-noise ratio at high spatial frequencies and therefore shift the detectable molecular-weight limit somewhat upward, without altering the structure of the derivation. We have added text in the manuscript to clarify this point and to indicate the expected magnitude of this effect.

      (b) The inclusion of inelastic scattering assumes an energy filter is being used, and this should be clearly stated.

      We have added this clarification in the inelastic scattering paragraph of the Supplementary Information.

      (c) The reasons for not including other factors, such as DQE and the temporal and spatial coherence envelope functions, could be stated.

      We have added a note in the dose-weighting section clarifying that these instrument-dependent attenuation factors were not explicitly included, and that they could be incorporated as additional frequency-dependent weighting terms without changing the structure of the derivation.

      (d) The flexibility and heterogeneity in protein structures, especially at high spatial frequencies, must also be a reason for a gap from experiment to theory, but this is not clearly stated.

      We agree. We have added a statement in the “Remaining gaps” section noting that structural flexibility and conformational heterogeneity act as an additional envelope that attenuates high-resolution signal relative to the rigid-particle model assumed in our derivation.

      Additional Minor Comments

      (15) It is noted in the discussion that 2DTM-based single-particle alignment simplifies the processing pipeline. Although true, I think stating the computation time would be useful for the reader.

      We have added computation times to the Discussion. For a typical single-particle dataset of ∼2,000 micrographs (5k × 4k pixels), a 2DTM search without defocus refinement completes in approximately one day on 64 NVIDIA A6000 GPUs. Once particles are located with their orientations and positions, a single 3D reconstruction is sufficient without further refinement, eliminating the iterative 2D classification, ab initio modeling, 3D classification and refinement steps of a conventional pipeline.

      (16) There are some formatting issues with e−/A 2, sometimes losing the minus sign.

      Thank you for catching this. We have corrected all instances to consistently use e<sup>−</sup>/Å<sup>2</sup> throughout the manuscript.

    1. Author response:

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

      In response to the reviewers’ comments, we have made revisions to the manuscript. Specifically, we have:

      (1) Increased the sample size in the whole-brain imaging and demixed principal component analysis (dPCA) analyses presented in Figures 1 and 3, strengthening the statistical support for our conclusions;

      (2) Revised the presentation of Figure 3B to clarify that the displayed dPC1 traces were scaled for visualization purposes only (dPC1 / max(dPC1)), rather than normalized for quantitative comparison across animals;

      (3) Expanded the main text and supplementary figures to provide more intuitive explanations and geometric illustrations of dPCA and hyperbolic space analysis, and clarified the interpretation of correlation matrices and principal-angle analyses to improve readability;

      (4) Substantially expanded the sections on Bayesian multidimensional scaling and hyperbolic embedding, including additional methodological details and validation analyses to strengthen the computational framework and its interpretation;

      (5) Expanded the Discussion to incorporate recent studies and discuss potential mechanisms underlying DRN 5-HT-mediated motor suppression.

      We believe that these revisions have substantially strengthened the manuscript and addressed the major concerns raised during peer review.

      Reviewer #1 (Public review):

      The wide-ranging serotonergic projections emerging from the Dorsal Raphe nucleus (DRN) are suggestive of a central role in regulating brain-wide activity and behavioural states. DRN activity has been associated with diverse functions, ranging from mood, motivation and pain regulation to sleep and cognitive flexibility. Its far-reaching connectivity made it challenging to assess the brain-wide effect of its activation, especially during behaviour.

      The present study by Qi et al. addresses these challenges by combining state-of-the-art tracking microscopy with the whole-brain accessibility of the larval zebrafish model. To investigate the effect of DRN activation, the authors leveraged the Tg(tph2:ChrimsonR) line to optogenetically activate tph2-positive neurons in the DRN, while monitoring changes in brain-wide activity, locomotion and auditory-stimuli evoked responses.

      Optogenetic activation had a suppressing effect on locomotion, which the authors distinguished from inducing sleep by the maintenance of posture and its sleep disturbing effect of nighttime stimulations. Further, the authors report a distinct effect of DRN activation on motor-related, but not auditoryrelated neuronal subspaces, identified by demixed principal component analysis.

      In addition, rather than affecting all motor-correlated neurons similarly, tph2+ DRN-mediated suppression focused on neurons encoding high-amplitude or turning motion.

      In summary, the work of Qi et al. provides solid evidence for a predominant role of the DRN in wake-state motor suppression by aptly combining the vast data-acquisition possibilities of the larval zebrafish model with computational methods to extract relevant information.

      The brain-wide scope of the analysis is a key strength, reducing bias, confirming the involvement of known motor and auditory regions, and providing a valuable dataset for future analyses.

      While the results well support the conclusion of the authors, certain biological and technical aspects demand discussion.

      We thank you for the positive and thoughtful evaluation of our work. We also appreciate your constructive comments on the biological and technical aspects of the study. We have carefully considered these concerns and addressed them point-by-point below, with corresponding revisions to the manuscript.

      Reviewer #1 (Recommendations for the authors):

      (1) Further samples required:

      Figure 1D relies on n=3 with lots of variability; the author should add more Ns to illustrate their point (typically 10-15 fish used per study to show reliability across fish).

      Figure 3 also relies only on 5 fish in each condition; the authors should increase to 10-15 to show variability.

      Thank you for this valuable suggestion. To address this concern, we have increased the sample size in the revised manuscript. Specifically, the number of animals in Figure 1D has been increased from n = 3 to n = 5, and additional statistical analyses have been included to strengthen the quantitative support for our conclusions. Note that the error bars are plotted as standard deviation (SD), which may make the variability appear larger. In Figure 3, the number of animals was also increased from n = 5 to n = 8.

      In addition, our findings are consistent with previous work showing a strong association between elevated dorsal raphe nucleus (DRN) activity and reduced locomotion in zebrafish [1, 2, 3]. Importantly, across animals, the variance explained by the dPCA components and the rapid modulation of whole-brain state remain highly consistent, supporting the robustness and reproducibility of our observations.

      Given this increased sample size together with consistency across animals and convergence with prior studies, we believe the current dataset provides sufficient statistical and biological support for our conclusions.

      (2) Further steps to be added to the analysis to fully support the claim:

      It appears that the individual brains are registered and individually clustered into areas by combining highly-correlated nearby neurons.

      dPCA is then computed for individual brains. Evidence for our interpretation of individual dPCA spaces:

      (1) Figure 3A depicts separate dPCs for different fish.

      (2) Line 488–489 describes normalization of the value range of dPCs to compare across fish, which implies separate dPCs.

      While the authors normalize the projections onto the principal components, the dPCA spaces remain individual, as does the meaning of their components. It is thus questionable how to conclude from data across fish in a rigorous manner.

      Instead, we recommend that the authors build voxels for each individual’s brain and calculate dPCA across all brains, not individual ones, so that components could become truly comparable across the brains of given individuals.

      We thank the reviewer for this important comment. We would like to clarify that our analysis does not aim to construct a shared dPCA space across animals or to quantitatively compare dPC scores between individuals. In this analysis, dPCA was performed separately for each fish to capture the dominant low-dimensional population dynamics within each individual brain.

      The purpose of Figure 2 is to demonstrate that DRN activation induces a rapid and robust transition in whole-brain activity, rather than to define a common population subspace across animals.

      We also attempted to register and pool data across animals for a joint analysis, as suggested by the reviewer. However, our dataset includes zebrafish at slightly different developmental stages (6–12 dpf). Although the behavioral effects of DRN activation (including motor suppression and global brain-state modulation) were robust across this age range, developmental differences introduced substantial anatomical variability in brain size and morphology, which reduced registration accuracy and made voxel-wise correspondence across animals unreliable.

      We realize that our previous description of “normalization” may have caused confusion. To clarify, the dPC1 traces shown in Figure 2 were only scaled for visualization by dividing each fish’s projection by its maximum value (dPC1 / max(dPC1)), so that trajectories from different fish could be displayed on the same axis. This scaling does not alter the underlying dPCA space, does not constitute normalization for cross-animal comparison, and was not used for any quantitative analysis.

      Importantly, despite being computed independently for each fish, we observed a consistent temporal pattern across animals: DRN activation was reliably accompanied by a rapid transition captured by dPC1 in each individual fish. We have revised the Methods and corresponding text in the manuscript to make this distinction explicit and avoid ambiguity.

      Reviewer #2 (Public review):

      Summary:

      The authors examine the effects of activating the dorsal raphe nucleus serotonergic system using a combination of calcium imaging and optogenetics in freely moving larval zebrafish. Their findings show that optogenetic stimulation induces a state of behavioral quiescence.

      They further investigate whether this state corresponds to sleep or reduced motor activity. Analyses of posture and sleep-related paradigms indicate that serotonergic activation primarily suppresses motor output rather than promoting sleep. Notably, this suppression appears to be bout type-dependent, with stronger effects on neurons associated with larger tail amplitudes and turning angles.

      In addition, auditory stimulation experiments reveal no significant impact of serotonin on sound encoding.

      We thank the reviewer for the careful and thoughtful summary of our work.

      Strengths:

      The study combines advanced experimental techniques with state-of-the-art analytical methods, enabling precise and compelling insights into the role of serotonergic modulation. The experiments and analyses are well aligned with the questions being addressed, and the results appear robust and reliable.

      Moreover, the implementation of experiments that combine calcium imaging and optogenetics in freely moving animals is technically challenging and appears well justified in the context of the research questions.

      We thank you for the positive assessment of our work and for recognizing the technical and analytical strengths of our experimental approach.

      We address the reviewer’s specific comments in detail below.

      Weaknesses:

      While the analytical techniques employed are sophisticated and appear to be appropriately applied, their presentation makes the manuscript difficult to follow. Although the explanations are provided in the Methods section, including more guidance in the main text, such as how to interpret each analytical approach and what outcomes would be expected under different scenarios, would help readers who are less familiar with these techniques.

      Providing this context would better guide the reader in navigating the figures, broaden the accessibility of the work, and ultimately increase its impact.

      We thank you for this important suggestion. To improve clarity and accessibility, we have revised the main text to provide more intuitive explanations of both demixed principal component analysis (dPCA) and hyperbolic space analysis, with additional emphasis on how to interpret their outputs and what different outcomes imply biologically.

      Additionally, we have included new supplementary figures (Figure S2 and Figure S6) with geometric illustrations and simplified examples to provide a more visual and conceptual understanding of these methods. We hope these revisions make the analytical framework easier to follow and improve the accessibility and impact of the manuscript.

      While the authors discuss different quiescent states mediated by serotonin reported in previous studies, their interpretation is limited to stating that “a common feature shared by these distinct behavioral states is a pronounced reduction in movement,” and consequently proposing that activation of dorsal raphe nucleus is not sufficient to specify a particular behavioral state, but rather plays a primary role in driving motor suppression.

      In my view, a more thorough attempt to determine whether the observed state corresponds to any of the previously described forms of quiescence, or represents a subset or variant of them, would strengthen the manuscript. This would help better integrate the findings with the existing literature.

      For example, given that the authors have access to whole-brain activity data, it would be valuable to examine and discuss whether there are shared patterns of activation with previously reported quiescent states.

      Thank you for the insightful suggestion. To address this, we compared our whole-brain activity patterns with key neural signatures reported in previously characterized zebrafish quiescent states.

      A recent study reported that exposure to conspecific alarm substance (CAS) induces a quiescent but vigilant state associated with elevated DRN 5-HT activity and low-frequency synchronized forebrain activity [3]. In our dataset, although DRN 5-HT activation similarly induced robust locomotor suppression, we did not detect comparable low-frequency synchronized forebrain dynamics during the stimulation period. These results suggest that while DRN 5-HT activation is sufficient to induce motor suppression, it does not recapitulate the full neural signature of CAS-induced vigilant quiescence. We have incorporated this comparison and its interpretation into the Discussion section of the revised manuscript.

      Following the termination of optogenetic stimulation, we observed a gradual recovery of locomotory speed, consistent with the behavior in an earlier study [3], although our recovery was much faster. Interestingly, whole brain imaging also revealed a transient increase in forebrain activity. This elevated forebrain activity gradually returned to baseline as locomotor activity recovered. In accordance with the reviewer’s suggestion, we propose that these forebrain dynamics represent a common motif that facilitates the transition out of the DRN-induced quiescent state (Author response image 1.).

      The manuscript largely avoids discussing the mechanisms underlying the observed motor suppression. For instance, is this effect driven directly by serotonin release onto target neurons? Is it mediated by glial activity, as suggested in other studies? Are additional neuromodulatory systems being recruited?

      While addressing these questions may require substantial further work, potentially beyond the scope of the present study, the availability of whole-brain data provides an opportunity to at least explore or

      Author response image 1.

      Forebrain activity increases following termination of DRN optogenetic stimulation. (A) Following the termination of optogenetic stimulation of DRN 5-HT neurons, locomotor speed in Tg(tph2:ChrimsonR) zebrafish gradually recovered and returned to control levels. (B) Neural activity in forebrain regions showed a transient increase immediately after stimulation offset and gradually returned to baseline as locomotor activity recovered. discuss these possibilities. In particular, it would be interesting to examine the recruitment of regions not directly stimulated but known to be associated with other neuromodulatory systems or promoting glial activation (e.g., the locus coeruleus).

      We thank you for this important suggestion. In the revised Discussion, we now frame our findings in relation to several candidate mechanisms.

      Our results are most consistent with a direct neuromodulatory action of serotonin on downstream motor-related circuits. This is supported by the known projection patterns of DRN 5-HT neurons [4], which target midbrain and hindbrain regions involved in motor control, as well as by prior serotonin imaging studies showing elevated 5-HT levels in hindbrain regions during low-motor states, where inhibitory HTR1-family receptors are enriched [5]. In addition, recent voltage imaging studies have shown that DRN serotonergic neurons are embedded within a broader motor-state-dependent circuit, in which they are dynamically regulated by local GABAergic inputs [6]. We have incorporated a discussion of these potential mechanisms into the revised Discussion.

      Reviewer #2 (Recommendations for the authors):

      (1) Lines 91-97 page 2.

      “dPCA separates neural population activity into components tied to specific experimental variables, allowing us to isolate DRN-dependent changes (Methods). Components associated with DRN activation explained significantly more variance in Tg(tph2:ChrimsonR) zebrafish than in controls (Fig. 3A), indicating a strong serotonergic impact on brain-wide neural activity. The small stimulation-related variance in controls likely reflected visual responses to laser.”

      Directly stimulated neurons are not included, as stated in the Methods, but I think it would be better to mention this explicitly in the main text.

      We thank you for this helpful suggestion. We agree that explicitly stating this point in the main text improves clarity. In our analysis, neurons directly stimulated by the laser were excluded (as described in the Methods) to ensure that the identified components reflect whole brain responses rather than direct optogenetic activation. We have now added a clarifying sentence in the Results section to make this explicit.

      (2) Lines 113 - 115 page 3.

      “To examine how DRN 5-HT neuron activation affects sensorimotor processing (Fig. 4C), we next recorded whole-brain neural activity in head-fixed, tail-free larvae embedded in agarose to capture transient calcium signals with minimal motion artifacts.”

      Lines 117-119 page 3.

      “Because head-fixed larvae rarely enter natural sleep, we applied 1 mM mepyramine, a sleep-promoting antihistamine, to induce a sleep-like state (41), which markedly changed auditory responses (Fig. 4E, Fig. S2C)”

      Why not perform these experiments in freely moving fish instead? To what extent do movements in freely moving animals affect segmentation? Is it actually problematic to apply dPCA in that case? You used it in the previous section.

      We thank the reviewer for raising this important point. In principle, freely moving preparations would provide a more natural behavioral context. However, reliable application of dPCA requires stable neuron identification and accurate trial alignment across time, both of which are substantially compromised in freely moving larvae due to motion-induced imaging noise and segmentation errors.

      In our hands, whole-brain calcium imaging in freely moving fish introduces significant variability in segmentation and signal extraction, which in turn leads to unstable and noisy low-dimensional decompositions, preventing robust estimation of task-related components. By contrast, the head-fixed preparation enables consistent neuron tracking and precise alignment to sensory stimuli, which are critical for dPCA.

      We have now clarified in the manuscript that all dPCA analyses were performed on head-fixed animals.

      (3) Line 117 page 3.

      Why do you use cosine similarity? Are the results different when using other metrics?

      I can see the matrix, but what exactly are you looking for in it to support the claim ”DRN activation preserved the structure of the auditory population code”? I think explaining some of these concepts more clearly, or at least providing expectations or interpretations for the different metrics and analyses, would make the manuscript easier to follow.

      We thank you for this question. Cosine similarity is widely used to quantify similarity between population activity patterns because it captures relative activity across neurons while ignoring overall gain.

      In our analysis, each trial is a population activity vector, and the cosine similarity matrix encodes pairwise relationships between these vectors. We assess preservation of the auditory population code by testing whether this similarity structure (i.e., the geometry of population responses) remains consistent across conditions. We have expanded the text to clarify how these matrices are constructed and interpreted.

      In addition, we computed alternative similarity measures based on Pearson correlation, which is equivalent to the cosine similarity of two vectors after they have been centered (subtracting the mean of each vector) (Author response image 2A). We further quantified pairwise trial distances using the Euclidean chord distance on the unit hypersphere, defined as

      D<sub>ij</sub> = √2(1−C<sub>ij</sub>), where C<sub>ij</sub> is Pearson correlation; smaller distances indicate higher similarity (Author response image 2B). Both alternative measures yielded qualitatively consistent results, showing that DRN 5-HT neuron activation preserves the similarity structure across trials.

      (4) Figure 4D.

      If “significant alignment between DRN activation and motor-related neural subspaces, with the sound related subspace being nearly orthogonal” is correct, shouldn’t there be some visible overlap between blue and red, and little to no overlap with yellow? This is not easy to see. Perhaps plotting all three in a single panel would help.

      We thank you for this helpful suggestion. We would like to clarify that the “alignment” we refer to is defined in terms of the angle between neural subspaces, rather than the spatial overlap of neurons. In other words, significant alignment indicates that the corresponding population activity patterns occupy similar directions in a high-dimensional activity space.

      As a result, even statistically significant aligned subspaces (see further exposition below) do not necessarily involve overlapping sets of neurons with large PC weights. This distinction is important because subspace geometry is defined at the population level and cannot be directly inferred from spatial overlap in low-dimensional visualizations. In addition, the visualization shown in Fig. 4D highlights only brain regions containing neurons with relatively high weights for illustrative purposes.

      We also note that the current visualization is based on a maximum intensity projection of a 3D volume, which can create the appearance of overlap in two dimensions even when the underlying neurons are spatially segregated in three dimensions. To provide a clearer spatial reference, we have re-plotted the three subspaces in a three-dimensional representation.

      (5) Figure 4F.

      Do the arrows represent the values for each combination? This is not clear to me. Perhaps it could be clarified in the paragraph. Most of the values, including those being compared, are around 87 plus minus 2 degrees, i.e., mostly orthogonal. Does this imply no overlap between patterns (again, this is hard to see in Figure 4D)? The values are different from the null model but still close to orthogonal. The phrase “significant alignment between DRN activation and motor-related neural subspaces” could be interpreted as strong alignment, but the values do not seem to support that, do they?

      Author response image 2.

      Alternative similarity measures reveal preserved trial-to-trial similarity structure. (A) Trial-by-trial similarity matrix quantified using Pearson correlation. Higher correlation indicates greater similarity between trials (B) Pairwise trial distances quantified using the Euclidean chord distance on the unit hypersphere (D<sub>ij</sub> = √2(1−C<sub>ij</sub>)), where smaller distances indicate greater similarity between trials.

      Author response image 3.

      Three-dimensional visualization of DRN activation-, motor-, and sound-related subspaces. Threedimensional rendering of the high-weight neurons in the DRN 5-HT activation, motor-related, and sound-related subspaces. Colors are consistent with Figure 4D.

      We thank the reviewer for this important clarification.

      We agree that the phrase “alignment” could be interpreted as implying strong spatial overlap in the anatomical space, which is not what we intend to convey. In our analysis, “alignment” refers to a statistically significant deviation from a null distribution.

      In high-dimensional spaces, random vectors are expected to be nearly orthogonal, with angles tightly concentrated around 90°. To demonstrate this phenomenon, we conducted simulations using random vectors over a range of dimensionalities (100–10,000 dimensions) and observed that the expected angle distribution over 1000 trials becomes progressively more concentrated around 90° as the dimensionality increases (Author response image 4). Therefore, even modest deviations from 90° reflect a systematic bias and indicate structured overlap beyond chance. So, “significantly aligned” means the motor–DRN angle is significantly less than the random baseline, and “significantly orthogonal” for sound–DRN means the angle is significantly closer to 90° than the random baseline. We will revise the text to clarify this point and avoid potential misinterpretation.

      Regarding Figure 4D, we agree that the meaning of the arrows was not sufficiently clear. The arrows represent the mean angle, computed across all fish, between the DRN 5-HT activation subspace and the motor-related subspace (left), and between the DRN 5-HT activation subspace and the sound-related subspace (right). We will update the figure legend to explicitly define these elements.

      Author response image 4.

      Random vectors become increasingly orthogonal in high-dimensional spaces. Simulated distributions of pairwise angles between random vectors across different dimensionalities (100–10,000 dimensions; 1000 repetitions per dimensionality). As dimensionality increases, the angle distribution becomes increasingly concentrated around 90°.

      (6) Lines 125 - 126 page 5.

      “After detecting bouts, we computed each bout’s direction and amplitude and classified them into 12 types.”

      It would be interesting to see how the distribution of bouts looks in the direction-amplitude space, in order to better visualize the 12 bout types (perhaps using different colors). It might also be useful to include examples of the 12 bout types in the supplementary material.

      We thank you for this helpful suggestion. To better visualize the distribution of bouts and the definition of the 12 bout types, we have added a new supplementary figure showing the distribution of all bouts in the direction–amplitude space, with each bout color-coded according to its assigned category, consistent with the scheme used in the main text.

      We further quantified the frequency of each bout type across the dataset, which comprises 1,493 bouts from 7 animals. Among these, 4 animals exhibited all 12 bout types and were therefore included in subsequent regression analyses that require complete coverage of all categories.

      In addition, we have included examples of representative bout types in the supplementary material. These additions improve the clarity and interpretability of the bout classification scheme.

      (7) Lines 131 - 133 page 5.

      “Some neurons exhibited activity related to all bout types with similar amplitudes, yielding low coefficient variability, whereas others responded selectively to specific bout types - typically those with larger tail amplitudes and turning angles - exhibiting higher variability in regression coefficients (Fig. 5B).”

      I would appreciate some quantification of “typically.”

      We thank you for this suggestion. Fig. 5B (bottom) shows a neuron with large variability in regression coefficients across bout types, quantified by the coefficient of variation (CV). Bout types with large amplitudes and turning angles (e.g., type 12) have larger regression coefficients than others. We will remove “typically” from the text.

      (8) Lines 546 - 547 page 15.

      “Fish whose baseline tail movements were insufficient to cover all 12 bout types were excluded from further analysis.”

      It would be useful to report the number or proportion of animals that did not exhibit all 12 bout types. Which types of bouts are less frequently observed?

      Thank you for this helpful suggestion. In the full dataset (n = 7 fish), 4 animals exhibited all 12 bout types. We have now added a supplementary figure showing the occurrence probability of each bout type across all animals.

      (9) Line 147 page 5.

      Honestly, the Bayesian multi-dimensional scaling is difficult to follow, and it is not clear what new insight it provides. I assume that ”hyperbolic geometry indicates complex hierarchical organization” is the main point, but its meaning in this context is not sufficiently explained. This paragraph would benefit from being rewritten for clarity or potentially removed if it does not contribute essential information.

      We appreciate your insightful comments. In response, we have substantially expanded the section on Bayesian multidimensional scaling. First, we now provide an intuitive exposition (see Figure S6) of hyperbolic geometry and multidimensional scaling, clarifying why this framework constitutes a powerful approach for uncovering the geometric and functional organization of neuronal populations. Second, we show that multidimensional scaling in a curved hyperbolic space more accurately captures the correlation structure among neurons than embeddings in a flat Euclidean space. Third, and most notably, we find that the inferred curvature of the hyperbolic embedding space tightly scales with the degree of quiescence: fish in which dorsal raphe nucleus (DRN) stimulation nearly abolished locomotor activity exhibit the largest curvatures (new Figure 5F). Collectively, these computational analysis indicate that the curvature of the embedding space serves as a quantitative signature of the quiescent state.

      References

      (1) J. C. Marques, M. Li, D. Schaak, D. N. Robson, J. M. Li, Internal state dynamics shape brainwide activity and foraging behaviour. Nature 577, 239–243 (2020).

      (2) V. Choudhary, C. R. Heller, S. Aimon, L. de Sardenberg Schmid, D. N. Robson, J. M. Li, Neural and behavioral organization of rapid eye movement sleep in zebrafish. bioRxiv pp. 2023–08 (2023).

      (3) Y. Zhao, C.-X. Huang, Y. Gu, Y. Zhao, W. Ren, Y. Wang, J. Chen, N. N. Guan, J. Song, Serotonergic modulation of vigilance states in zebrafish and mice. Nature Communications 15, 2596 (2024).

      (4) Z. Song, C.-X. Huang, H. Zhang, C. Ye, N. Guan, J. Song, Integrated single-cell atlases unveil the operation principles of whole-brain 5-ht neuronal subsystems. Science Advances 11, eadv8128 (2025).

      (5) R. Haruvi, R. Barbara, I. Shainer, A. Rosenberg, L. Moshe, D. Malamud, J. Toledano, D. Braun, H. Baier, T. Kawashima, Global and compartmentalized serotonergic control of sensorimotor integration underlying motor adaptation. BioRxiv pp. 2024–09 (2024).

      (6) T. Kawashima, Z. Wei, R. Haruvi, I. Shainer, S. Narayan, H. Baier, M. B. Ahrens, Voltage imaging reveals circuit computations in the raphe underlying serotonin-mediated motor vigor learning. Neuron (2025).

    1. Author response:

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

      eLife Assessment

      Tropical single-island endemic bird populations are particularly vulnerable to climate change. The authors investigate genetic evidence of how such species dealt with climate changes in the past as a possible predictor for how they will respond to change in the future, which could provide an important example for the fields of conservation genetics and island biogeography. The authors' integration of genomics and habitat modeling is commendable, but we find that the support for their conclusions is incomplete: at times, the results presented appear to contradict each other, the authors do not fully account for key variables, and the limited taxonomic scope may cause problematic biases for the conclusion.

      We thank the editors for supporting the premise of this study and highlighting the importance of the study approach. Based on the lacuna identified by the editors and the reviewers, we have modified the manuscript and details of the same are given below. We believe that these revisions have now substantially improved the flow and scope of the manuscript and have addressed the concerns raised by the reviewers.

      Reviewer #1 (Public review):

      Summary:

      The authors combine PSMC and habitat modeling to try to connect habitat change during the Last Glacial Period to changes in Ne.

      Strengths:

      Observing how tropical single-island endemic bird species responded to habitat change in the past may help inform conservation interventions for these particularly vulnerable species. The combination of genomics and habitat modeling is a good idea - this sort of interdisciplinary thinking is what is needed to tackle these complex questions. Additionally, the use of PSMC makes it possible to perform this analysis on poorly-studied species with only a single genome available.

      Room for Improvement:

      Why coalescent Ne is a better predictor of extinction risk than current genomic diversity, or current Ne, isn't explicitly explained. PSMC in particular has many caveats, and some are not acknowledged or adequately addressed by the authors. For example, the authors note that population structure is a confounding factor with PSMC, but that it is not a problem in this instance. They do not provide compelling evidence for why this would be the case, they simply state that the species studied are all single-island endemics. However, single-island endemic species are not necessarily panmictic; this is even less likely to be true for species studied here that inhabit a large geographic area (ie, Australian species). Differing PSMC parameters may also impact results: the differences between passerines and non-passerines were one of their main results, but they do not provide any analysis to show that this difference was not driven by the different mutation rates used for the two groups.

      Parameters for many steps are not described, and choices that are described (such as the PSMC parameters) are not always fully explained. It is unclear why all data was mapped to the autosomes rather than removing reads that map to the sex chromosomes first. Using all the data, the reads belonging to the sex chromosomes could potentially map to other areas of the genome. It does not seem like a mapping quality filter was used, so these potential spurious alignments would not have been removed prior to analysis.

      There are points where the results are described in ways that appear to potentially differ from the supplementary figures. The authors state that even for species where PSMC results differed between models, "trends of Ne increase or decrease from the LIG to LGM were robust across all three PSMC models considered." The figures in the supplement for Pachycephala philippinensis, Rhynochetos jubatus, and Zosterops hypoxanthus appear to potentially contradict this statement, but it is difficult to tell, as the time period observed is not clearly marked on the graphs. How this robustness of trends was determined is not explained, leaving the precision of the analysis unclear.

      Table 1 also includes some information that contradicts what is in the Supplementary Tables, leading to a lack of clarity. Centropus unirufus, Chaetorhynchus papuensis, and Cnemophilus loriae are not included in Supplementary Table 4. Table 1 says Eulacestoma nigropectus, Paradisaea rubra, and Parotia lawesii did not undergo PSMC analysis, but Supplementary Table 4 says PSMC and modeling trends matched for these species. Table 1 says Rhagologus leucostigma underwent both PSMC and climate modeling, but Supplementary Table 4 says "NA" as if it was missing one of these analyses.

      Additionally, some of the results appear to contradict each other. For example, they show that there is no impact of habitat change in larger-bodied species, but also that larger-bodied species saw a decrease in Ne during the LGP. In another example, they state that when a species saw an increase in habitat during the LGP, they also had an increase in Ne. However, they also state that this was not the case for non-passerines.

      Ecosystems are highly complex; there may also be other variables influencing past demographic change other than those explored here. Results should be interpreted with caution.

      We thank the reviewer for their comments, which has helped us in improving the scope of the manuscript while also removing errors in the supporting information. We have improved the section of the manuscript which addressed the drawbacks of PSMC in our revised version. Details and rational for parameter choice are now included in the revised manuscript.

      We performed additional PSMC analyses for a subset of the samples (n = 5), wherein the scaffolds mapping to the sex chromosome were removed only after mapping the reads. We compared the new approach suggested by the reviewer to our original approach and no differences in the PSMC pattern were observed, highlighting the robustness of the results (Supplementary Information Fig. S3).

      Additionally, we have included multiple box-plot and tables in the revised manuscript that helps with interpreting the changes in effective population size. The details of the revisions are presented below in the “Recommendations for the authors” section. We believe that these changes have improved the scope of the manuscript and removed any redundancies and conflicts.

      Reviewer #2 (Public review):

      Summary and strengths:

      In this manuscript, Karjee and colleagues used coalescent-based effective population size reconstruction (PSMC) from single genomes to understand past population trends in island birds and related this to life history traits and glacial patterns. This concept is fairly new, as there are still relatively few multiple PSMC synthesis studies. I also thought that the focus on island endemics was unique and adds value to this paper. I enjoyed seeing a paper focused on South East Asia and think that this could help contribute to our knowledge of the important biodiversity within this region.

      Major weaknesses:

      My biggest concern with this paper is that the analyses are limited to 20-30 species, and significant taxonomic bias is present (there are multiple species of passerine but only 1-2 representatives of other groups). While this is not an issue alone, many of the life history traits or geographical traits are conflated with phylogenetic diversity (e.g., there are no large-bodied passerines). Thus, it is my opinion that the impact of these drivers of past population size is conflated and cannot be disentangled with the current data. The authors themselves state that the core hypothesis surrounding Ne and habitat availability is not supported by their entire dataset (only seen in Passerines). This was not clear enough in the abstract, and conclusions cannot be drawn here as the impact of taxonomy cannot be separated from data richness, traits, etc. The PSMC analysis was done according to the most recent recommendations, and this part of the manuscript is fairly robust. However, in several places, it is incorrectly stated that the PSMC measures or can infer genetic diversity; PSMC only infers past effective population size. It cannot measure genetic diversity in the past. I cannot review the habitat reconstruction modelling as I am a conservation genomics specialist.

      Appraisal:

      I am not convinced about the findings within the paper. I do not think that the results are sufficiently supported at this time, largely due to the conflation of taxonomy with other variables. As this type of comparison is new, I do think that there is a chance for reasonable impact on the field of genomics and island biogeography if the manuscript's constraints are addressed. I do not see scope for impact on conservation at this time and find the conclusions in the abstract regarding conservation relevance to be unfounded.

      We thank the reviewer for highlighting the unique and robust analytical approaches we have taken in this study. We agree with the reviewer that our sample size currently is small. However, we do observe a robust correlation between habitat fluctuation and change in effective population size. Further, the study also highlights the predicament of tropical island endemics, which are currently understudied and future studies are necessary to safeguard the biodiversity. We have highlighted this while also addressing the concerns in the revised version of the manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Overall:

      This starts with a great premise - looking at how tropical single-island endemic bird species dealt with climate changes in the past may be a predictor of how they will respond to change in the future. Since these species are at high risk of extinction in the face of climate change, tailored approaches to conservation are a good idea. While the premise is solid, I have some questions and recommendations. At times while reading, I did feel a bit confused, which may be due to the fact that this isn't my exact area of expertise. However, if I'm confused, that means a reader from a general audience is also likely to be confused. Some results appear to be conflicting, some claims about data seem possibly inaccurate, and some major limitations are not acknowledged or fully addressed.

      Below I've noted areas that I feel could benefit from revisions. That being said, I liked the integration of habitat modeling and genomics! These sorts of multifaceted approaches are necessary when it comes to unraveling the complex dynamics involved in ecology and evolution.

      Crucial Issues to Address:

      (1) Line 75: With the lower sea levels and habitat change, you say animals can disperse across barriers of land and sea. When it comes to these single-island endemics, were they always confined to a single island? Is there no possibility of introgression with ancient populations of birds on other islands during these periods?

      We thank the reviewers for identifying the potential artifact in effective population size estimates that may occur due to hybridization/introgression. Most of our species belong to small and oligotypic families as has been addressed in the discussion section already, making them likely to be newly arisen lineages rather than refugial ones. There is scant information available in the literature on where the species in our dataset originated from, and further species-specific studies are required to identify signatures of hybridization/introgression. However, we have included this caveat in the revised version of the manuscript (line numbers: 73-78 and 303–305).

      (2) Lines 149-151 "However, in these species as well, trends of Ne increase or decrease from the LIG to LGM were robust across all three PSMC models considered." Please double-check this claim. Some of your figures in the supplement appear to contradict this. In particular, Pachycephala philippinensis, Rhynochetos jubatus, and Zosterops hypoxanthus appear to differ a bit in the time frame described, but it is difficult to tell-I would recommend adding some shading on the graphs to indicate the time period observed. If there was a way you determined this that is more precise than eyeballing the figures like I did, this should also be explained.

      We thank the reviewer for this comment and have reworded the sentence by cross verifying with the PSMC graphs. In addition, we have calculated the precise values of effective population size at the Last Interglacial (LIG) and Last Glacial Maximum (LGM) for each species using custom scripts and used these to evaluate whether the change in Ne during the Last Glacial Period (LGP) was significantly different for the three PSMC settings used. A table depicting these effective population size changes from LIG to LGM are also included in the revised version of the manuscript (Supplementary table S4; line numbers: 145­-156 and 345-357).

      (3) Lines 280-292: Issues with PSMC that are not acknowledged here are my largest concern. The situation being investigated does not necessarily meet all the assumptions PSMC makes (ie, neutral evolution and panmixia), which should be explained in this section. I'll point out the two issues I think should be acknowledged and addressed: First, selection is a confounding factor with PSMC, which is not mentioned here. While that's likely not an issue due to the size of the genome, this is still something that should be stated and explained. Second, the following statement is what I take the most issue with: "Population structure is thus a confounding factor. However, this is unlikely to be a problem given that all our species are single-island endemics". This needs justification. You state that in the past, islands could be connected (see my first comment regarding line 75), so it seems unlikely that 1) migration between past populations on other islands never happened, and 2) there is no population structure *on* the island.

      We thank the reviewer and have modified the PSMC caveats section of the revised version of the manuscript (line numbers: 289-307).

      (4) Line 310: Mapping all the data to the autosomes seems inappropriate to me. The sex chromosome reads could potentially map to other areas of the genome. Unless this information was accidentally left out of the methods section, it doesn't seem like any mapping quality filter was used, so spurious alignments aren't being removed. To remove sex chromosome data, I would instead align data to the whole genome, remove all reads that map to the sex chromosomes, and then map the remaining reads to the autosomes.

      As mentioned earlier, for a subset of the species (n =5), we directly mapped raw reads files onto the genome and then called SNPs on only autosomal regions using the SAMtools mpileup-bcftools pipeline, after which we performed PSMC as above (Supplementary Information Fig. S3). We did not observe and significant difference between the two approaches. Further, only high-quality mapped reads were used for SNP calling as mentioned in the previous version of the manuscript (line numbers: 338-343; Supplementary Information Fig. S3).

      (4) Table 1 includes some information that contradicts what is in the Supplementary Tables: Centropus unirufus, Chaetorhynchus papuensis and Cnemophilus loriae are not included in Supplementary Table 4. Table 1 says Eulacestoma nigropectus, Paradisaea rubra, and Parotia lawesii did not undergo PSMC analysis, but Supplementary Table 4 says PSMC and modeling trends matched for these species. "Pseudorectes ferrugineus" and "Rhynochetos jubatus" are spelled differently in Supplementary Table 4. Table 1 says Rhagologus leucostigma underwent both PSMC and climate modeling, but Supplementary Table 4 says "NA" as if it was missing one of these analyses.

      We thank the reviewer for identifying the errors and we have corrected for these in the revised version of the manuscript. Please see the detailed changes for these comments outlined below

      Centropus unirufus, Chaetorhynchus papuensis and Cnemophilus loriae are not included in Supplementary Table S4 (Now Supplementary table S2): we have added these species to the revised table S2.

      Table 1 says Eulacestoma nigropectus, Paradisaea rubra, and Parotia lawesii did not undergo PSMC analysis, but Supplementary Table 4 says PSMC and modeling trends matched for these species: The genomes for these samples were obtained from museums and exhibited high error rates. Hence, we excluded these samples from further analysis. However, the supplementary table S2 was not updated, and we have corrected this error in the revised version of the manuscript.

      "Pseudorectes ferrugineus" and "Rhynochetos jubatus" are spelled differently in Supplementary Table 4 (Now table S2): we have corrected the typographical error in the revised manuscript.

      Table 1 says Rhagologus leucostigma underwent both PSMC and climate modeling, but Supplementary Table 4 (Now table S2) says "NA" as if it was missing one of these analyses: This was a typographical error, and we have updated it to “mismatch”.

      Major Issues to Address:

      (1) Lines 97-99: "Information on tropical, single-island endemics' demographic responses to past climate change can inform conservation efforts, owing to the genomic signatures that predispose a species to extinction". This needs more explanation. For example, why couldn't we just look at these genomic signatures instead of recreating demographic responses? I'm not sure I fully understand what you mean here.

      We thank the reviewer for this comment and have modified the introduction to highlight the importance of demographic history in predicting species extinction. Comparison of genomic diversity and demographic history of over 200 mammalian genomes, highlights the importance of demographic history in predicting species endangerment and extinction risk (Wilder et al., 2023) (line numbers: 99-104).

      (2) Line 181-182: Whether or not a species was a passerine was an important predictor of Ne only in combination with the change in habitat from LIG to LGM". This is a major finding, but "respond positively to habitat change" (line 183) is a bit ambiguous. Were they responding to habitat expansion? Habitat contraction? Increase in rainfall? What is the change happening? Not all habitat changes are equal.

      We thank the reviewer for this comment and have modified this section for clarity in the revised results and discussion section of the manuscript. We observed a positive correlation between effective population size and availability of suitable habitat. Further, we observed precipitation of the warmest quarter to be the largest contributing bioclimatic variable for all but one Caribbean species (line numbers: 172-­191; 196-211).

      (3) Line 184-185: "The interaction between habitat change and body mass (β = 10.05, 95% CI: [-0.3, 24.41) suggests that there is no impact of habitat change in larger species." Doesn't this contradict the earlier finding of larger-bodied species seeing a decrease in Ne? Or do you mean the decrease in Ne was not due to habitat change?

      We have edited this section for clarity. With the inclusion of additional species, we observed a significant positive relationship between body size and effective population size (line number: 191-193).

      (4) Lines 206-207: "Our results also reveal that both passerine and non-passerine island endemics have entered the Holocene with low genetic diversity." How does this align with the statement that passerines responded positively to habitat change?

      The observation that passerines respond positively to habitat change is based on a systematic analysis of the last glacial period. However, a close look at the entire species’ demographic history reveals the often the Ne is at the lowest following the LGM, and coinciding with the advent of Holocene, the current interglacial. We have therefore modified the sentence in the revised version of the manuscript (line numbers: 213-214).

      (5) Line 215: If we already know flightless birds and endemics are particularly prone to extinction, what is the benefit of this study? Be clear about how your method can be used in a way that is better than what people are already doing. It would be good to explicitly explain why coalescent Ne is a better predictor of extinction risk than current genomic diversity or current Ne.

      We thank the reviewer for this comment and have modified this section in the revised version of the manuscript (line numbers: 221-224).

      (6) Line 259-261: "Habitat change in the LGP was positively associated with Ne fluctuations (Figure 3, β = 9.45), that is, species which showed an increase in habitat in the LGP also showed a concurrent increase in Ne." Is this true in all instances? I thought you found it had no effect for some, or did I misunderstand?

      We thank the reviewers for pointing this out. Species which showed an increase in habitat in the LGP did not always show a concurrent increase in Ne. Our results instead reflect an overall trend and this is clarified in the revised version of the manuscript (line numbers: 268-269).

      Lines 328-330: Could the different mutation rates used for passerines and non-passerines be driving the differences found between the two groups?

      The difference in the mutation rate is low and using the passerine specific mutation rate for non-passerines only shifts the PSMC graph slightly. As our analysis is considering the change in Ne across the LGP, this shift is minimal and does not affect the overall results.

      How are you connecting the demographic changes to species traits? I'm a bit confused about that, so I think some further explanation would be beneficial.

      We have modified the discussion to highlight the role of species traits in shaping the species response to habitat modification and ultimately the change in effective population size. We have included this in the revised version of the manuscript (line numbers: 437­-439).

      Minor Issues to Address:

      (1) Lines 165-168: "Habitat change was poorly associated with change in Ne for the 20 species for which both PSMC and ENM analyses were possible (Cramer's V = 0.15). However, passerine species only showed a strong association (Cramer's V = 0.96), while non-passerines showed a weak negative association (Cramer's V = -0.15)." This is phrased in a way that is a bit confusing. I'd consider rephrasing for clarity.

      We have modified this section in the revised version of the manuscript (line numbers: 167­-170).

      (2) Line 177: The confidence interval says "16.27, -2.61". I think it's supposed to be -16.27?

      We have corrected the typographical error in the revised version of the manuscript.

      (3) Line 185-187: "Finally, the random intercept for Country (sd (Intercept)) showed a marginal positive influence (β = 0.85, 95% CI: [0.04, 2.24])". What does this mean? This needs further explanation.

      We modified this sentence in the revised version of the manuscript (line number: 189-191).

      (4) Line 204: landbridge is misspelled as "landbride".

      We have fixed the typographical error.

      (5) Line 310: What were your Trimmomatic parameters?

      We have included the parameters used for Trimmomatic in the revised version of the manuscript (line numbers: 324-326).

      (6) Line 311: What were your bwa parameters?

      We used default parameters for bwa alignment and this is included in the revised version of the manuscript (line numbers: 328-329).

      (7) Line 322-324: Why did you choose those specific parameters for PSMC? Splitting up the first time window makes sense (as shown in Hilgers 2025), but why did you choose t=5, r=1, and 84 atomic time intervals? Did you choose these parameters independently, or did you decide to use them because they were used by Nadachowska-Brzyska et al? Either way, that information is important to state.

      The parameter selection followed the suggestions based on both Hilgers et al. 2025 and Nadachowska-Brzyska et al. 2016. The information is included in the revised version of the manuscript (line numbers: 345-350).

      (8) Lines 325-326: What did you use for bootstrapping? If not Psmcfa, why?

      We have used “splitfa” to generate files for bootstrap analysis and have included this information in the revised version of the manuscript (line numbers: 350-351).

      (9) Lines 350-354: Please explain the reasoning behind using the different resolution and worldclim for Amazona guildingii.

      Based on the reviewer’s comment, we have re-run the habitat model with the same resolution for Amazona guildingii and include this in the revised version of the manuscript.

      (10) Line 412-413: "For the response variable i.e., the change in Ne, a Bernoulli distribution with a logit link because it is a binary response variable." I think this sentence might be missing some words.

      We have fixed the typographical error in the revised version of the manuscript (line numbers: 444-445).

      (11) Figure 1 is difficult to read, especially the top left panel. I would consider presenting this differently.

      We have supplemented Figure 1 with boxplots of effective population size values estimated during the Last Interglacial and the Last Glacial Maximum which should aid in clarity.

      Reviewer #2 (Recommendations for the authors):

      The authors state that they intentionally chose to remove several avian species that would be suitable for this analysis, because they were subject to larger studies elsewhere. This seems like an unnecessary constraint, and it is my opinion that the authors need to add this data in. I am not aware of what species were excluded, but I hope this will increase the non-passerine proportion of their dataset to help them robustly address their questions. An alternative solution would be for the authors to only include passerines, but this will come at the expense of statistical power with the current dataset and so would also require an increase in sample size. Overall, I recommend including more non-passerine species with traits similar to your passerine species.

      This was a typographical error from the previous versions of the manuscript arising from the fact that we excluded museum species from our samples. We have modified this sentence in the revised version of the manuscript as well as included one new species (Melanocharis versteri) in our study panel (line number: 311-314).

      It was not clear how or if PSMC bootstrapping was included in the comparisons across species, i.e. how did you include bootstrapping when you turned PSMC into a response variable within your statistical analysis? Failing to account for it would introduce measurement error into the data, and I would suggest that the authors explore how to incorporate this.

      We thank the reviewer for this comment and have calculated the precise values of effective population size during the LIG and the LGM using custom scripts to generate boxplots. These boxplots were used to investigate if effective population size values were significantly different during the LGP for all three PSMC parameter settings. Non-significant results were treated as “no change” in effective population size for further statistical analyses. The bootstrap values were used for this analysis, in addition to circumventing the issue of selection on the genome.

      I would also like to see a greater discussion on what aspects of the PSMC curve were used for comparisons and the limitations therein. These cross-species comparisons are still relatively new, and I think they will add value to this paper.

      In our study, the change in Ne from LIG to LGM is considered. We have elaborated this in the revised version of the manuscript. Addition analysis, depicting the changes in Ne as box plots were also included to help understand the fluctuations in Ne.

      Lines 164-168, which refer to your core hypothesis, are really unclear. What was actually found here? Please rephrase.

      We have rephrased the sentence for clarity in the revised version of the manuscript (line numbers: 169­-172).

      PSMC measures effective population size, not genetic diversity. Please change throughout.

      Based on the reviewer’s comment we have changed this in the revised version of the manuscript.

      I was surprised to see some references to conservation within the abstract of the paper. It is important that this is also included in the discussion so that the authors ensure their logic is accessible to managers. It would also be good to discuss the risks of using PSMC to inform conservation from just one genome, as I see these being quite high.

      We thank the reviewer for this comment and have included both pros and cons of using PSMC in the revised version of the manuscript (line numbers: 229-237).

      As this paper is based on public reference genomes, it is best practice that the original notes or reference genome papers are cited to acknowledge the data holders.

      We thank the reviewer for this comment and have included a supplementary table (Supplementary Table S7) acknowledging all the data holders.

    1. Reviewer #2 (Public review):

      Summary:

      This paper presents results interpreted to indicate that sequences upstream of stop codons capable of base-pairing with the 3' end of 18S rRNA prolong the dwell time of 80S ribosomes at stop codons in a manner impeded by Rps26 in the 40S subunit exit channel, which leads to the proper completion of termination and ribosome recycling and prevents spurious translation of 3'UTR sequences by one or more unconventional mechanisms.

      Strengths:

      The standard 80S and selective eRF1 80S ribosome profiling data obtained using EZRA-Seq are of high quality, allowing the authors to detect an enrichment for purine-rich sequences upstream of stop codons at sites where termination is relatively slow and ribosomal complexes are paused with eRF1 still engaged in the A site.

      Weaknesses:

      There are many weaknesses in the experimental design and interpretation of results that undermine several of the final conclusions of the study described in the abstract, as described in detail below.

      (1) It's not indicated how far upstream of the stop codon the sequences were searched to find the enriched motifs in Figs. 1C and 2D. If it's further upstream of -15 then the sequence would generally not be found in the exit channel of a terminating ribosome positioned with the stop codon in the A site in the manner expected from their final model of mRNA:18S rRNA pairing. (This would be analogous to the occurrence of the Shine-Dalgarno within 15 nt of the initiation codon for most mRNAs in E. coli.) They could have depicted nucleotide percentages at each nucleotide from -1 to -15 for the high and low pause stop codons to better facilitate consideration of their proposed mechanism of termination pausing involving the 3' end of 18S rRNA.

      (2) lines 234-242: Their reporter data in Fig. 4B suggest that only the presence of GGG triplets at any location in the 9 nt substantially prevents downstream translation. If their interpretation about these G-rich sequences promoting termination by forming G-quadruplexes is correct, then this would have little to do with the purine-rich motifs identified by the profiling experiments (and their proposed function in base-pairing with rRNA), as the purine-rich motifs do not feature GG bases (as shown in Fig. 2D in particular). The authors point out that the MPRA can sample sequence space not represented in living cells. While true, this doesn't change the fact that it failed identify sequences conforming to the purine rich motifs found by the profiling experiments and identified instead sequences capable of forming G-quadruplexes that may well function by a different mechanism than that employed in cells. The authors cannot persist in claiming that the MPRA results confirm the findings of the profiling experiments regarding the purine-rich motif. Also, the claim of enrichment for C-rich sequences in the MPRA results is not compelling as only 3 of the 11 triplets showing the smallest M/P ratios contain more than 1 C and three of them contain no Cs. Also, there was no evidence for depletion of C's upstream of the stop codons with low pause scores from the ribosome profiling data in Fig. 1, so it's inaccurate to claim "mirroring" of results from the ribosome profiling and MPRA data on this point as well.

      (3) lines 256-260: I still contend that the different results shown in Fig. 4E for the C-rich and GA-rich sequences are not compelling as results for only a single sequence of each type are shown, which might not be typical of the entire class. In fact, the GA-rich sequence has two GG's and could form a G-quadruplex, whereas the GA-rich motifs identified by ribosome profiling and eRF1-seq do not exhibit consecutive GGs, such that the single G-rich sequence chosen for analysis might function by G-quadruplex mediated stalling rather than base-pairing with the 3' end of 18S rRNA, as they actually suggested in their rebuttal. Even the second GA-rich sequence analyzed in Fig. S3G has two GGs. Thus, while the results in Fig. 4 provide support for the notion that C-rich sequences preceding the stop codon promote stop codon read-through, it's important to note that no evidence was obtained by ribosome-profiling in Fig. 1 that the increased 3'UTR translation seen for low-pause stop codons is associated with C-rich sequences. It's unclear why they would be unable to observe this in the manner they document for the eRF1-Seq data in Fig. 2D for the three C-rich triplets enriched at stop codons lacking eRF1 peaks.<br /> - lines 278-282: These differences are quite small and could arise from the different sequences of the GFP-HiBit fusion proteins, as observed in Fig. 4C (top two control constructs), precluding mechanistic interpretations.

      (4) Notwithstanding their claim in the rebuttal, I still find no definition of the GA-rich and C-rich mRNAs described in Fig. 5C in the Methods or legends, nor whether the compilation is restricted to -15 from the stop codons. In addition, if expression of the mutant 18S rRNA is sufficient to alter the height of the termination peaks as shown in Fig. 5C and to alter reporter expression in Fig. 5D, I see no reason why they cannot carry out the pause score/motif enrichment of Fig. 1C to determine if they see the expected diminished enrichment for the GA-motif shown there on expressing the mutant 18S vs. the WT 18S control strain. If not, this would undermine their interpretation of the results in Figs. 5C-D as favoring base-pairing between the 3' end of 18S rRNA and sequences upstream of the stop codon.

      (5) I still find a significant shortcoming in their failure to analyze the 18S rRNA 3' end biochemically to show that the expected ~15% with the mutant sequence. Stating simply that they followed a previous protocol is not sufficient to document their success in this notoriously challenging experimental approach.

      (6) lines 382-384: The level of the control protein RACK1 is diminished in testis polysomes, and it's unclear that the ratio of Rps26:RACK1 is actually lower in testis polysomes in the manner claimed.

      (7) lines 414-427: I still contend that the authors should have quantified the ratio of the stop codon peak to the adjacent coding sequences in Figures 7E to establish that Rps26 OE decreased the stop codon peaks selectively on the GA-rich cohort of mRNAs. In addition, they still have not explained why the C-rich reporter behaves like the GA-rich reporter in Fig. 7F in showing reduced HiBiT expression on Rps26 OE when it should be unaffected. As such, the reporter data do not support the conclusion reached from the data in Fig. 7E.

      (8) Notwithstanding their rebuttal I still contend that the failure to measure Rps26 association with 80S ribsoomes or polysomes and show that it is depleted by the shRNA knockdown and increased by Rps26 OE is a significant shortcoming, especially since their interpretation of the OE data depends on the occurrence of 40S subunits lacking Rps26 in unstressed WT cells, which seems improbable based on the prior work on yeast.

      (9) Overall, examining the claims in the revised Abstract, I feel that I am in agreement with the claim "We identify a sequence motif upstream of the stop codon that promotes termination pausing,.." but disagree that the function of this motif was "validated by massively paralleled reporter assays", for the reasons stated above in point 2. Regarding the statement "Unexpectedly, reduced termination pausing increases the likelihood of stop codon slippage, giving rise to proteins with heterogenous C-terminal extensions." , I believe it would be more cautious to say that "reduced pausing is associated with stop codon read-through accompanied by frameshifting" since the MRPA did not provide compelling evidence for causality for the reasons described in point 3 above. Regarding the statement "Mechanistically, we show that sequence-dependent termination pausing arises from post-decoding mRNA scanning by the 3' end of 18S rRNA", I find this statement too strong in view of the shortcomings described above in points 4-5 and think it would be more correct to say that their findings are consistent with (rather than showing) this point, and also think they should add qualifying statements to the manuscript acknowledging the limitations of these experiments. I further contend that there are shortcomings in the experiments leading to the conclusion that the stoichiometry of Rps26... modulates mRNA:rRNA interactions, described above in points 6-9. Finally, in the last sentence, the claims that termination pausing is shaped by ribosome heterogeneity, and cell type-specific translational control is too strong.

    2. Author response:

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

      We thank the Editor and Reviewers for their careful evaluation of our manuscript and for the constructive feedback. We agree with eLife’s overall assessment that, while profiling terminating ribosomes provides important insights into termination dynamics, additional clarification of the underlying mechanisms was needed. In response, we have focused our revision on three major conceptual points:

      (1) We have moderated our interpretation regarding the contribution of putative mRNA:rRNA interactions to sequence-specific termination pausing and clarified the limitations of the current evidence.

      (2) We have refined and clarified our model for the role of Rps26 in regulating translation termination.

      (3) We have expanded and strengthened the discussion of tissue-specific termination pausing, including its potential implications and current uncertainties.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors use high-resolution ribosome profiling (Ezra-seq) and eRF1 pulldown-based ribosome profiling (eRF1-seq) developed in their lab to identify a GA rich sequence motif located upstream of the stop codon responsible for translation termination pausing. They then perform a massively parallel assay with randomly generated sequences to further characterize this motif. Using mouse tissues, they show that termination pausing signatures can be tissue-specific. They use a series of published ribosome structures and 18S rRNA mutants, and eS26 knockdown experiments to propose that the GA rich sequence interacts with the 3′-end of the 18S rRNA.

      Strengths:

      (1) Robust ribosome profiling data and clear analyses clarify the subtle behavior of terminating ribosomes near the stop codon.

      (2) Novel termination or "false termination" sites revealed by eRF1-seq in the 5′-UTR, 3′-UTR, and CDS highlight a previously underappreciated facet of translation dynamics.

      Weakness:

      (1) Modest effects seen in ABCE1 knockdown do not seem to add up to the level of regulation. The authors state "ABCE1 regulates terminating ribosomes independent of the sequence context" on pg 9, and "ABCE1 modulates termination pausing independent of the mRNA sequence context" in the figure caption for Figure S4. Given the modest effect of the knockdown, such phrasing is most likely not supported. Further clarification of "ABCE1 plays a generic role in translation termination" is necessary.

      We acknowledge that the modest effects observed for ABCE1 are likely influenced by incomplete knockdown in HEK293 cells. Importantly, the increased ribosome density occurred at all stop codons rather than in a sequence-dependent manner, supporting the conclusion that ABCE1 functions broadly in termination rather than acting in a sequence-specific context. We have revised the manuscript to clarify this point and to temper our interpretation accordingly.

      (2) The authors propose that the GA rich sequence element upstream of the stop codon on the mRNA could potentially base pair with the 3′-end of the 18S rRNA. In the PDBs the authors reference in their paper and also in 3JAG, 3JAH, 3JAI (structures of terminating ribosomes with the stop codon in the A-site and eRF1), the mRNA exiting the ribosome and the 3′-end of the 18S rRNA are about 25-30 A apart. In addition, a segment of eS26 is wedged in between these two RNA segments. This reviewer noted this arrangement in a random sampling of 5 other PDBs of mammalian and human ribosome 80S structures. How do the authors anticipate the base pairing they have proposed to occur in light of these steric hindrances? RpsS26 is known to be released by Tsr2 in yeast during very specific stresses. Is it their expectation that termination pausing in human/mammalian cells happens during stressful conditions only?

      We agree that structural rearrangements in the absence of Rps26 remain speculative. In the revised manuscript, we have removed overly definitive language and clarified that, while Rps26 dissociation has been reported under stress conditions, its stoichiometry is unlikely to be exclusively stress-dependent. We now present this aspect as a working model supported by indirect evidence rather than a demonstrated structural mechanism.

      (3) The authors say, "It is thus likely that mRNA undergoes post-decoding scanning by 18S rRNA." (pg. 10). It is unclear what the authors mean by "scanning." Do they mean that the mRNA gets scanned in a manner similar to scanning during initiation? There is no evidence presented to support that particular conclusion.

      We appreciate the comment regarding the term “18S rRNA scanning.” We recognize that this wording may have been misleading and have revised the relevant text to more accurately describe post-decoding mRNA–rRNA interactions without implying an active scanning mechanism.

      (4) Role of termination pausing in the testis is highly speculative. The authors state: "It is thus conceivable that the wide range of ribosome density at stop codons in testis facilitates functional division of ribosome occupancy beyond the coding region." It is unclear what type of functional division they are referring to.

      We agree that the functional significance of testis-specific termination dynamics remains unclear. As multiple reviewers raised this concern, we have substantially expanded the discussion of tissue-specific termination pausing, explicitly outlining current limitations and framing this as an important direction for future investigation.

      Reviewer #2 (Public review):

      Summary:

      This paper presents results interpreted to indicate that sequences upstream of stop codons capable of base-pairing with the 3' end of 18S rRNA prolong the dwell time of 80S ribosomes at stop codons in a manner impeded by Rps26 in the 40S subunit exit channel, which leads to the proper completion of termination and ribosome recycling and prevents spurious translation of 3'UTR sequences by one or more unconventional mechanisms.

      Strengths:

      The standard 80S and selective eRF1 80S ribosome profiling data obtained using EZRA-Seq are of high quality, allowing the authors to detect an enrichment for purine-rich sequences upstream of stop codons at sites where termination is relatively slow and ribosomal complexes are paused with eRF1 still engaged in the A site.

      Weaknesses:

      There are many weaknesses in the experimental design, interpretation of results, and description of assay design and assumptions, the data obtained, and the interpretation of results, all of which detract from the scientific quality and significance of this work. In fact, a large proportion of paragraphs in the text and figure panels present some difficulty either in understanding how the experiment or data analysis was conducted or what the authors wish to conclude from the results, or that stem from an overinterpretation of findings or failure to consider other equally likely explanations.

      We appreciate the reviewer’s thoughtful evaluation and constructive suggestions. We recognize that our original description of the MPRA and reporter assay results may have lacked sufficient clarity, particularly regarding the sequence motifs associated with termination pausing. In the revised manuscript, we have carefully rewritten these sections to clarify the experimental design, data interpretation, and relationship between sequence context and termination dynamics. We believe these revisions address the reviewer’s concerns and improve the overall clarity of the manuscript.

      Reviewer #3 (Public review):

      Summary:

      This study from Jia et al carried out a variety of analyses of terminating ribosomes, including the development of eRF1-seq to map termination sites, identification of a GA-rich motif that promotes ribosome pausing, characterization of tissue-specific termination dynamics, and elucidation of the regulatory roles of 18S rRNA and RPS26. Overall, the study is thoughtfully designed, and its biological conclusions are well supported by complementary experiments. The tools and datasets generated provide valuable resources for researchers investigating the mechanisms of RNA translation.

      Strengths:

      (1) The study introduces eRF1-seq, a novel approach for mapping translation termination sites, providing a methodological advance for studying ribosome termination.

      (2) Through integrative bioinformatic analyses and complementary MPRA experiments, the authors demonstrate that GA-rich motifs promote ribosome pausing at termination sites and reveal possible regulatory roles of 18S rRNA in this process.

      (3) The study characterizes tissue-specific ribosome termination dynamics, showing that the testis exhibits stronger ribosome pausing at stop codons compared to other tissues. Follow-up experiments suggest that RPS26 may contribute to this tissue specificity.

      Weaknesses:

      The biological significance of ribosome pausing regulation at translation termination sites or of translational readthrough, for example, across different tissue types, remains unclear. Nevertheless, this question lies beyond the primary scope of the current study.

      We thank the reviewer for the positive assessment of our work. We agree that tissue-specific differences in termination pausing were insufficiently described in the original submission. In response, and in light of similar concerns from other reviewers, we have expanded the relevant sections in the main text and Discussion. We now more clearly articulate both the biological context and the current limitations, identifying tissue-specific regulation of termination as an open question and future research direction.

      Reviewer #4 (Public review):

      Summary:

      This manuscript by Qian and colleagues utilizes ribosome profiling, and reporter assays to dissect translation termination. Unfortunately, the data do not support the conclusions of the paper, controls are missing and several assays are not well validated and do not reproduce previous findings from others.

      Specific comments:

      Translation termination has been studied in several organisms including mammalian cells and yeast. In those cases what is analyzed is not the peak height at the stop codon, but rather the difference in the ribosome density before and after the stop. Thus, analyzing peak height is not validated. I understand that this is relevant only for the ribosome profiling experiments (and Ezra-seq) not the RF1 profiling. But much of the data was acquired that way.

      Moreover, the data do not reproduce previous findings and no effort is made to connect them to previous data. Previous data has shown that stop codon efficacy varies. This is not reproduced (S1C). Similarly, an effect from the +1 residue is not reproduced. The data isn't even stratified by different stop codons as previous work has shown that different surrounding residues have different effects in the context of different stop codons. Thus, none of the sequencing data is validated or trusted and does not reproduce previous findings.

      The GA-rich sequence identified by Ezra-Seq and RF1 seq is not the same and it differs from previous sequences (Wangen &Green).

      The authors claim that the majority of Rf1 peaks is at stop codons, but that is not true. It is only about 30% of the peaks. Also, not all mRNAs have peaks at the stop codons. That is at best problematic. Finally, there are mRNAs that are known to "suffer" from NMD, what do these look like in the Ezra-Seq and RF1-Seq? How about mRNAs that have programmed frameshifts? This raises questions on the validity of the eRF1 data.

      Figure 4: First, instead of M/P ratio, one should analyze M/M+P, to normalize out differences in the loading and effects from collisions, which are guaranteed to occur here, but not considered or analyzed. Second, the data are analyzed as if what matters are codons in the P and E site (and beyond, where there are definitely NOT recognized codons). While there is evidence for some interactions, one would think that an additional analysis based on sequence would be helpful. Also, the supplemental data indicates that very rarely are there reciprocal changes (as should be the case), and as seen for stop codons.

      Regarding the HiBit reporter assay: The two sequecnes clearly have effects on translation without considering stop codon context (Figure 4C), which need to be taken into account. Also, the effect from the sequences varies in the context of the assay in 4C and 4D (2-fold vs .5 fold), further questioning the assay. Moreover, the authors claim that re-initiation cannot account for Hibit levels, but that is clearly incorrect. The western in Figure 4E does not reproduce the data in 4D. While Hibit goes up (as in 4D, the putative GFP-fusion goes down. Finally, while the second reading frame should be more efficient is not explained and further argues for an artifact. Previous work (and work herein) suggests that read-through occurs equally in each reading frame. No controls for these assays are presented: e.g. stimulation by antibiotics, ABCE1 depletion, etc.

      Figure 5 has similar problems. I don't understand how the Figure in 5A is made, but when you overlay the cited structures on Rps26, the molecules are identical. I guess the authors used some fantasy to build non-existing sequences differently into the structure. There is no basis for that. In panel C and the same in Figure 7, the number of analyzed mRNAs varies. This could influence the outcome and the EXACT same set of mRNAs should be analyzed. But the main problem here is that the authors need to analyze readthrough and not peak height as detailed above. Essential controls are missing that show what fraction of the 18S rRNA is mutated. Previous work has shown that 2 nt truncated 18S rRNA is actively degraded. It is hard to believe how 15% of altered ribosomes can abolish 100% of the effect from the C-rich sequences. Important validation is missing: the authors should analyze rRNA sequences in their ribo-seq dataset to demonstrate that they have the mutated rRNAs, and that these enrich and de-enrich as predicted.

      In Figure 5-7 the authors develop a model that the sequence selectivity arises from base pairing between 18S rRNA and the mRNA. If so, then they should really stratify the data by number of WC pairs that can be formed. And only WC pairs, as GU pairs have a totally different geometry that will likely be discriminated against in this context. Also, the mutation is in a part of the helix that has no effect (Figure S3G). Thus, the data within the manuscript are inconsistent.

      Figure 6 does not agree with published data (Li et al., Nature 2022). Previous work did not show testis-depletion of Rps26 in purified ribosomes. This is the critical difference as the authors here did not purify ribosomes. Also, another Rps is an essential control, even if purified ribosomes are used. The validity of this dataset is thus questionable . Depletion from polysomes is hard to believe, as overall there is less signal in the polysomes.

      Figure 7 has similar problems as figure 5. Different pools of mRNAs are analyzed; peak height is not validated. Overexpression of Rps26 is not shown, as only Myc is shown, not Rps26. Beyond that, increased occupancy in ribosomes needs to be shown for the effect to come from ribosomes. Given how sick the cells are it is most likely that all effects are secondary and arise from whatever else is going on in the overexpression or depletion of Rps26. No controls are presented to show specific effects from Rps26.

      The authors need to check Rli1/ABCE levels in their cells. Their data have features that are indicative of low ABCE1 levels. These include a very small effect from ABCE1 depletion. These could be responsible for some of the effects they observe.

      We appreciate the reviewer’s engagement with our study and the opportunity to clarify several points.

      With respect to perceived inconsistencies with prior literature, we emphasize that our findings do not contradict established principles of translation termination. Rather, enabled by the development of eRF1-seq, we provide higher-resolution insight into termination dynamics that extends existing models. We have revised the manuscript to better contextualize our findings within prior studies and to avoid overstating novelty where continuity exists.

      Regarding the analysis of ribosome profiling data, we note that peak height and read density are widely used metrics for inferring ribosome dwell time and pausing. Nevertheless, we recognize that our original presentation may not have sufficiently explained this analytical framework. In the revised manuscript, we have clarified the rationale and interpretation of peak-based analyses, particularly in Figures 5 and 7 involving 18S rRNA mutants and Rps26 perturbation.

      Finally, we appreciate the reviewer’s comments concerning base pairing. We have carefully revised both the Results and Discussion sections to present mRNA–rRNA interactions as a supported but not definitively proven mechanistic model, clearly distinguishing experimental evidence from inference.

      We are grateful for the reviewers’ thoughtful feedback. We believe the revisions have strengthened the manuscript by clarifying interpretations, moderating mechanistic claims, and expanding discussion of tissue-specific regulation, while preserving the central contributions of the study.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Some minor typos are present in the main text and methods section.

      We thank the Reviewer’s attention to detail in reviewing our manuscript. We have now thoroughly revised the main text and methods section.

      (2) S1I is missing or unlabelled.

      We are glad to have this opportunity to fix this mistake. Both S1I and S5D have now been added to the revised figures.

      (3) Could the authors clarify in the main text whether crosslinking was a step in the eRF1-seq protocol? Pg 5: "Without crosslinking, ribosomal proteins were minimally pulled down by the eRF1 antibody, confirming the transient nature of eRF1 binding."

      Yes, crosslinking is needed for eRF1-seq. We tried no-crosslinking but very little was pulled down, as stated in the sentence in Page 5.

      (4) Are termination events in the 5′-UTR or the CDS, as seen in the eRF1-seq data, also influenced by the GA-rich sequence? If the data is disaggregated into those two buckets, can you still pull out the motif?

      Yes, stop codons in 5’UTR and CDS share the same feature. However, the number of 5’UTR stop codons captured by eRF1-seq are too few to generate reliable sequence motif analysis.

      (5) Could the authors please clarify what peaks/fractions they are using as the monosome in Figure 4A? From the manner in which the red boxes are drawn on the sucrose gradient profile traces, it seems that the 40S, 60S, 80S monosome and half of the disome peak are included in the monosome fraction.

      The red box shown in Figure 4A is a bit misleading. For the massive paralleled reporter assay, we selected ribosome fractions based on the sucrose gradient tracing corresponding to monosome and polysomes, respectively. However, the fraction accuracy is not absolute as the fraction tube corresponding to monosome could contain traces of subunits as well as disomes. In practice, 40S and 60S are less concerned than disome, but the primary component is 80S ribosome.

      (6) On page 13, please cite references for Normal mode analysis.

      Normal Mode Analysis (NMA) using the Anisotropic Network Model (ANM) is a computationally efficient method for predicting large-scale, functional, and directional protein motions near equilibrium. We have followed the Reviewer’s suggestion by citing a review paper in the field of structural biology (Bahar, I. et al. 2005).

      Reviewer #2 (Recommendations for the authors):

      (1) The authors interpret the height of RPF peaks at stop codons in their Ribo-Seq data as an indication of pausing by ribosomes during termination, resulting from slow or inefficient decoding of the stop codon and peptide release; although it could equally result from slow recycling of the 60S subunit by ABCE1 following peptide release. Arguing against the latter possibility, they show later in the study that shRNA knockdown of ABCE1 has little effect on the stop codon RPF peaks; however, because the ABCE1 depletion does not elicit collisions near the stop codon in the manner observed in other studies, it appears that the ABCE1 depletion was insufficient to impair recycling substantially. The authors also don't attempt to support their interpretation by showing that depletion of eRF1 increases the stop codon peaks and produces collisions just upstream of the stop codon. They never specify with any precision whether it is stop codon recognition by eRF1, peptide hydrolysis, or recycling of the 60S subunit from the post-termination complex that is delayed, which is very unsatisfying.

      We agree with the Reviewer that the RPF density at stop codons only reflects the dwell time of terminating ribosomes. In fact, it is not possible to dissect molecular details from Ribo-seq data sets, same as interpreting other pausing events. Regarding ABCE1, we did observe the increased termination peak in cells with ABCE1 knockdown (Figure S4C). The lack of collisions is perhaps due to incomplete depletion of ABCE1. Notably, ABCE1 depletion selectively increased ribosome density at the –15 nt position, whereas the forward-shifted –12 nt peak was largely unaffected (Figure S4D). These results suggest that ABCE1 primarily facilitates late-stage termination or ribosome splitting, and its absence delays pre-termination progression. Nevertheless, the main focus of the study is to decipher the sequence context of termination pausing, which seems to be irrelevant to ABCE1. We thank the Reviewer for understanding.

      (2) They found enrichment for a GA-rich motif in the mRNAs with the largest stop codon peaks, which they attribute to its effect in slowing down some aspect of termination or ribosome recycling to increase the dwell time of the terminating ribosomes. They found no motif, however, in mRNAs containing the smallest RPF peaks at stop codon peaks, which presumably terminate more rapidly; even though they conclude later in the study from their massively parallel reporter assays (MPRA) that "C-richness" in the 9 nt 5' of stop codons enables rapid termination. The mRNAs with high pause scores at the stop codon that are enriched for the GA motif also show lower RPFs in 3'UTRs compared to the low pause score mRNAs, which they interpret to mean that long-lived termination complexes produce more efficient peptide termination and ribosome recycling, while short-lived complexes fail to be recycled and continue translation into the 3'UTR. However, because the 3'UTR reads are in all three frames, this could not occur simply by stop codon readthrough but would also require a frameshift upstream or at the stop codon itself to prevent termination and continued translation into the 3'UTR; and it could also arise from unconventional reinitiation by unrecycled post-termination complexes, which has been seen by others on inhibition of 60S recycling. The authors' interpretation is too simplistic.

      We thank the Reviewer’s summary about the sequence features controlling ribosome dwell time at stop codons uncovered by eRF1-seq. We are fully aware of the complex scenarios about 3’UTR translation, however, unconventional reinitiation cannot explain the results of the reporter assay shown in Figure 4D. Unlike frameshifting that generates prolonged products with mixed C-termini, reinitiation is associated with a new start. In Figure 4D, we observed products with C-terminal fused HiBiT, which cannot be explained by reinitiation. We thank the Reviewer for understanding.

      (3) They obtain support for the role of a GA-motif in pausing at stop codons from their selective ribosome profiling of eRF1-bound 80S ribosomes present at stop codons, finding a related GA-motif enriched at stop codons with high occupancies of eRF1-bound RPFs. However, once again, there is no C-rich motif enriched upstream of stop codons with low eRF1-bound RPF occupancies, at odds with later claims for such a motif. They ultimately propose that the GA motif pauses terminating ribosomes by base-pairing with the 3' end of 18S rRNA in the ribosome mRNA exit channel, principally utilizing two UU residues at the penultimate bases in the 18S rRNA that presumably base-pair with either A or G residues in the GA motif.

      The Reviewer might be confused by the results from Ribo-seq and massively paralleled reporter assay (MPRA). Ribo-seq data sets are limited to endogenous sequences that were shaped during evolution. In contrast, MPRA uses completely randomized sequences that offer unbiased analysis of sequence elements. The lack of C-rich motif in eRF1-seq data sets is due to the under-representation of such sequence elements in human genome. Perhaps this sequence bias is beneficial for termination fidelity by minimizing 3’UTR translation. We have further clarified this point in the revised manuscript.

      (4) They claim to have obtained independent confirmation of this last idea from their massively parallel reporter analysis (MPRA), in which sequences upstream of the stop codon of a uORF were randomized to determine those that appear to prevent translation downstream of the uORF and thereby place the mRNA in the monosome fraction versus those that allow downstream translation by any mechanism including leaky scanning of the uORF start codon, stop codon readthrough, or reinitiation (the assay doesn't distinguish between these mechanisms) and place the mRNA in the polysome fraction. In actuality, their results showed that the presence of only GGG triplets at any location in the 9 nt substantially prevents downstream translation, whereas only CCG and CCC proline codons enable downstream translation by one or more mechanisms. In view of their final model, it's very difficult to understand why GGG at any position would be able to base-pair with the U-U residues in the 18S rRNA when the stop codon is in the A site, and also why the many other triplets with two G's, two A's or an A and G base-all consistent with the GA-rich motif identified earlier-would not act similarly. Similarly, it's also puzzling that CCG and CCC can exert their effects at multiple positions upstream of the stop codon, and why the 7 other codons with two C's do not act similarly. Thus, it's unconvincing that a specific C-rich motif (which they refer to repeatedly but never identify) or even C-richness upstream of the stop codon confers elevated downstream translation. It's also important to note that the MPRA does not report on pausing at stop codons explicitly, only on whether ribosomes can be found downstream of the uORF stop codon, and assigning this outcome to the presence or absence of pausing during termination requires an ad hoc assumption that the authors have not identified as such.

      The Reviewer brought up excellent points in this comment regarding the MPRA result. Indeed, MPRA does not report ribosome pausing events as pointed out by the Reviewer. Additionally, MPRA is not designed to distinguish mechanisms underlying translational readthrough. As we mentioned above, both MPRA and Ribo-seq bear different experimental features that partly explain the similar, but not identical sequence motif uncovered by two assays. The prominent GGG motif identified by MPRA is intriguing, reminiscent of our prior study focusing on translation initiation (Jia et al. NSMB 2020). We propose that G-rich sequences upstream of stop codons form G-quadruplexes that block ribosome movement, resulting in monosome enrichment. Supporting this notion, the GGG motif was not identified by eRF1-seq, echoing the importance of using complementary experimental procedures in drawing conclusions.

      (5) They claim to confirm their conclusions from the profiling and MPRA data by measuring translation of the HiBiT sequence inserted downstream of the stop codon of the uORF in two reporters in which the upstream 9 nt contain either a single C-rich sequence or a single G-rich sequence. It's unclear how or why these two particular sequences were chosen. The G-rich sequence does not conform closely to either of the GA-motifs captured in the sequence LOGOs of Figures 1-2, and as noted above, there was no C-rich motif ever identified in these analyses. Thus, it's unclear whether the different effects of these two sequences are representative of sequences that pause or do not pause terminating ribosomes that they identified by the genome-wide analyses. In addition, given that the exact position of the GG or CC sequences relative to the stop codon doesn't seem to matter based on the MPRA data, it is actually possible to find the same number of base pairs with the 3' end of 18S rRNA for both of the two GA-rich and C-rich sequences analyzed in these reporter assays by sampling different registers of pairing between the mRNA and 18S rRNA. What is needed instead is be a systematic analysis using both the polysome:monosome assay, and the HiBiT translation assay of sequences that can pair perfectly with the 18S rRNA or contain increasing numbers of mismatches predicted to destabilize the putative helix that would be formed, and to determine whether the stability of the helices thus formed is highly correlated with the presence of the reporter mRNA in monosomes and with low HiBiT translation.

      We appreciate the Reviewer’s effort to improve our manuscript. The sequences inserted into the reporters were chosen based on several considerations. First, we chose the GA-motif rather than the G-rich sequences because the former represents physiological sequence element uncovered by eRF1-seq. As mentioned above, the G-rich sequences could form G-quadruplex artifacts. Second, the C-rich sequences were uncovered by both eRF1-seq (Figure 2D) and MPRA (Figure 4b). Third, only sequences top ranked were selected for the reporter assay. For the positional effects of inserted sequence elements, it is important to note that the proposed mRNA:rRNA interaction is not static because of the continuous mRNA movement along the channel. Instead of using sequences with perfect pairing, we have conducted experiments by placing the C-rich sequences at different positions of the insert. As shown in Figure S3H, the position relative to the stop codon does not seem to matter. In the revised manuscript, we have rephrased several sentences in the main text to avoid confusion.

      (6) They attempt to support their model by overexpressing a mutant 18S rRNA with mutations of the penultimate U-U residues to G-G, and present evidence that this decreases the stop codon RPF peaks on mRNAs rich in GA sequences upstream of the stop codons, and has the opposite effect on mRNAs that are C-rich; however, they never indicate the criteria used to assign mRNAs to these two bins, and whether it is based on the GA-rich motifs/LOGOs identified by genome-wide analysis or on the few triplets turned up by the MPRA. Clearly, it would be far better to conduct the same analysis of motif enrichment for high and low pause scores that produced the motif in Figure 1C and determine if the motif for high pausing switches from the GA-rich motif for WT 18S rRNA to a C-rich motif for the mutant, and vice versa for the low pause score mRNAs. It should also be noted that the C-rich sequence used in the reporter can form only 2 base pairs with the mutant 18S rRNA when the mRNA's C-C dinucleotide base pairs with the new G-G dinucleotide in rRNA, but it can actually form 4 base pairs with the WT 18S rRNA sequence in a different pairing register, undermining their interpretation of these data. Note also that there was no analysis done to determine what proportion of 40S subunits actually contain the mutant 18S rRNA, which is expected to be only a minor fraction under the best circumstances, and cannot simply be taken for granted, requiring a direct analysis of the sequences of the 3' ends of 18S rRNA in the cells expressing the mutant 18S.

      The Reviewer’s comment on 18S rRNA mutants are insightful. Given the low percentage of ribosomes incorporated with the rRNA mutants, it is not feasible to conduct motif analysis based on ribosome pausing at stop codons. As shown in Figure 5C, stop codon peaks are still evident after 18S mutant transfection albeit less prominent than the wild type. Notably, introducing 18S rRNA mutants into cells is not an easy task, and we have followed closely the protocol published previously (Burman and Mauro. NAR 2012) to obtain meaningful data. We believe (and hope the Reviewer will concur) that the experiment using the 18S rRNA mutants offers critical evidence in support of the mechanism.

      (7) They attempt to implicate Rps26 in the pausing by depleting or overexpressing (OE) the protein and comparing pausing at stop codons between the same two ill-defined GA-rich and C-rich bins of mRNAs mentioned above and by assaying the HiBit reporters. Again, they haven't determined whether the amount of Rps26 in mature 40S subunits is reduced or elevated compared to WT cells, and their interpretation of the OE data actually depends on the occurrence of 40S subunits lacking Rps26 in unstressed WT cells, which seems improbable and requires direct confirmation. Also, they haven't quantified the 80S peaks at the stop codons relative to the CDS reads immediately 5' of the stop codons, which varies with Rps26 OE versus the WT control, and doing so might well contradict their conclusion. Moreover, the C-rich and GA-rich HiBiT reporters behave identically rather than oppositely in response to Rps26 OE, which the authors fail to acknowledge or comment on.

      The Reviewer might be confused by the role of Rps26 partly due to the lack of clarity in our original description of the results. In yeast, Rps26 can dissociate from fully assembled 80S ribosomes under stress (Yang, et al. Sci Adv 2022). Therefore, although quantifying the Rps26 in mature 40S subunits is informative, it does not infer the composition of 80S ribosomes in cells with Rps26 depletion or overexpression. As pointed out by the Reviewer, we also noticed that, in cells with Rps26 depletion or overexpression, mRNAs with C-rich sequences showed no difference of ribosome density at stop codons. This is quite expected because C-rich sequences have minimal interaction with the 3’ end of rRNA. As a result, Rps26 depletion or overexpression is not supposed to affect ribosome dwell time at stop codons with upstream C-rich sequences. In contrast, only stop codons preceded with GA-rich sequences are influenced by Rps26 heterogeneity. In the revised manuscript, we have clarified this confusion in the main text.

      Additional specific comments

      (8) In the Summary statement: "We identify a sequence motif upstream of the stop codon that contributes to termination pausing, which was confirmed by massively paralleled": This is unjustified, as the MPRA showed only that a GGG triplet inserted anywhere in 9 nt 5'of the stop codon reduces ribosomes from traversing a stop codon either by blocking leaky scanning or reinitiation after an upstream uORF, and it is unclear why the position of this triplet does not matter nor why other GA-rich sequences capable of base pairing with the 3' end of 18S rRNA were not identified in the MPRA.

      As mentioned above, eRF1-seq and MPRA assays are complementary with advantages and disadvantages. Nevertheless, the Reviewer’s comments are well-taken and we have rephrased the Abstract of the revised manuscript.

      (9) A supplementary figure explaining EZRA-Seq would be very helpful.

      Since EZRA-seq methodology has been published (Mao, et al. NSMB 2023), we think a citation makes more sense. We thank the Reviewer for understanding.

      (10) The bottom plots/histograms of Figure 1A are very unclear. What is the y-axis of the bottom histogram, and relative to what elongating ribosomes have been analyzed?

      We apologize for the confusion in the histograms of Figure 1A. We stratified all mappable reads into footprints of initiating, elongating, and terminating ribosomes. Like many Ribo-seq results, the majority of footprints are of 29 nt length. If all three ribosome groups are of the same conformation, they are expected to have the same size distribution of the footprint length with the same bar height. It is true for initiating ribosomes (left) but not terminating ribosomes (right). We have now rephrased the figure legend in the revised manuscript.

      (11) Page 5: "A close inspection of stop codon footprints revealed an additional peak at -12 nt, which becomes more prominent when the reads are shorter (Figure 1B)." No explanation is offered for this finding. Do forward-shifted termination complexes have an empty A site owing to dissociation of eRF1? If so, they would be undetectable in eRF1-Seq data.

      Previous toe-printing assays have shown that eRF1 induces a forward movement of terminating ribosomes, shifting the leading edge from +13 nt to +15 nt (Pisarev, et al. Cell 2007). Moreover, single-molecule analyses have identified distinct pre- and post-termination phases catalyzed by eRF1 (Lawson, et al. Science 2023). Together, these observations suggest that the two 5’ end peaks correspond to pre- and post-terminating ribosome states, with the latter likely adopting a rotated conformation. We have revised the relevant paragraph in the main text.

      (12) Page 5: ". It is possible that the two distinct 5' end peaks represent pre- and post-terminating ribosomes, with the latter assuming the rotated conformation. We could not rule out the possibility that these terminating ribosomes have the stop codons at the P-site prior to disassembly." The logic here is difficult to follow.

      We have revised the relevant paragraph in the main text.

      (13) Figure 1C: provide coordinates relative to the stop codon on this motif.

      The motif analysis is position-independent and there is no coordinate on the logo plot.

      (14) Page 6: "This was not due to biased downstream sequences as the +4 nucleotide minimally affected the 3'UTR translation (Figure S1C)." The logic here is unclear.

      We have rephrased this sentence to “This effect could not be explained by downstream sequence bias, as the identity of the +4 nt had minimal impact on 3’UTR translation (Figure S1C).”

      (15) Page 6: "Like Ribo-seq, we also observed a forward shifting of post-terminating ribosomes from eRF1-seq (Figure 2C). " But by definition, they will have eRF1 in the A site, so why are they 26nt vs 29nt?

      Like many Ribo-seq results, the majority of footprints are of 29 nt length. However, ribosome populations with smaller footprint sizes are of physiological meanings, likely due to conformation changes.

      (16) Page 6 "In agreement with the Ribo-seq data sets, eRF1-seq revealed that not all the mRNAs exhibited eRF1 peaks at the annotated stop codons (Figure 2B), echoing the wide range of termination pausing." It should be determined whether eRF1 occupancy is correlated with 80S occupancy at stop codons in the standard Ribo-Seq. And if not, why?

      As shown in Figure 2B, there is a strong correlation between eRF1-seq and Ribo-seq in terms of termination pausing. However, the pausing index will be different between these two data sets due to distinct normalization. We thank the Reviewer for understanding.

      (17) Figure 2D: The plot on the left doesn't specify how far upstream the triplets can be from the stop codon. Is the LOGO significantly more similar to that shown in Fig. 1C than expected by chance alone?

      In Figure 2D, the codon frequency analysis is position independent. Similarly, the sequence logo in Figure 1C and Figure 2D is also position independent.

      (18) Page 7: ". Notably, three different stop codons show similar pausing features and sequence motifs (Figure S1G and S1I)." The figure citations here are incorrect.

      We apologize for the missing Figure S1I, which was also pointed out by Reviewer #1. We have now updated Figure S1 in the revised manuscript.

      (19) Page 7: The term "false termination" is a poor descriptor if termination doesn't occur.

      We have followed the Reviewer’s suggestion by replacing “false termination” with “failed termination”.

      (20) Page 8: "Consistent with previous reports 27, mutating the stop codon UAG abolished the reinitiation event that drives out-of-frame HiBiT translation (Figure 3E)." How is HiBit assayed? No details are given in the legend. This result doesn't confirm any of the actual eIF1 peaks upstream of stop codons, just that REI can occur at some level 5' of stop codons; and the eRF1 peak at the HiBit stop codon would be 3' of the peak at the main stop codon.

      HiBiT assay is a standard reporter like luciferase and Promega offers a detection kit, as described in the methods section. The result shown in Figure 3E is to confirm stop codon-associated reinitiation, which suggests that ribosomes migrated from the stop codon could contain eRF1 before reaching a start codon for reinitiation. We have revised this paragraph to avoid confusion.

      (21) Figure 4A: Unclear what position 0 to 6 in the bottom heat map corresponds to in the inserted 9 nt sequences. Are these codon positions vs. nucleotide positions? The legend lacks explanatory information.

      Figure 4A shows nucleotide positions (x axis) grouped by 3nt to reflect codon information (y axis). For the inserted 9nt random sequences, the last two nucleotides cannot be used because of the fixed nucleotides downstream of the insert. The same analysis has been reported in our prior study (Jia, et al. NSMB 2020).

      (22) Page 8: "For instance, codons enriched in frame 2 belong to NUA and NUG, another indication of in-frame stop codons (Figure S3B, bottom panel). " Need more or better explanation here.

      We have rephrased this sentence in the main text. “Codons enriched in alternative reading frames were also informative; for example, codons enriched in frame 2 predominantly belong to NUA and NUG, consistent with frameshifted presentations of in-frame stop codons (Figure S3B, bottom panel).”

      (23) "This is likely due to the faster turnover of these mRNAs because of 3'UTR translation". Need more or better explanation here.

      MPRA in Figure S3C showed that mRNA variants containing C-rich downstream sequence were depleted from both monosome and polysome fractions. Since 3’UTR translation is well-established to induce mRNA decay, it is possible that these sequences are under-represented due to mRNA turnover. We have added more explanations in this paragraph in the revised manuscript.

      (24) " Figure 4B: The logic and assumptions of this assay are not explained. How do ribosomes traverse the uORF, by leaky scanning or by stop codon read-through that is impeded by a ribosome stalled at the uORF stop codon? Presumably, it can't be read through as the uORF is out of frame and translation would likely terminate quickly.

      The rationale of Figure 4B is very similar to Figure 4A, except for the presence of the stop codon UAG. Under efficient termination, a monosome enrichment is expected, which could be promoted by termination pausing or structural hinderance by G-rich sequences. In contrast, stop codon readthrough or reinitiation would lead to polysome enrichment. We have thoroughly revised this paragraph in the main text.

      (25) Figure 4B results: It's unclear why M/P ratios are so low in Figure 4B vs Figure 4A as all constructs in 4B contain a stop codon and should have the high M/P ratios seen for the constructs in panel (A) with stop codons inserted. It's also unclear why the high M/P ratio should be so limited to GGG triplets vs. other triplets that conform to the GA-rich motifs identified above, and also why this triplet would not function at codon position 6. Similarly, it's unclear why only CCG and CCC and not CCU and CCA have an effect, and why only 3 of 9 codons with 2 or more C's have the effect, all suggesting that specific sequences and not just C-rich sequences are promoting read-through. Yet, no C-rich motif was discernible in the profiling experiments above.

      We appreciate the Reviewer’s careful reading of our manuscript. In profiling experiments shown in Figure 2, we did observe C-rich codons albeit with variations. Possible reasons include sequence differences between human genome and randomized sequence combinations. In addressing the Reviewer's question 23, we have thoroughly revised this paragraph in the main text.

      (26) Page 9: "These results are in line with the sequence specificity in termination pausing revealed by Ribo-seq and eRF1-seq." This is unjustified as the results in 4B are restricted to only GGG triplets rather than numerous triplets that equally conform to the AAGAAGA motif defined above.

      We apologize for the overstatement in this sentence. In addressing the Reviewer's question 23 and 24, we have thoroughly revised this paragraph in the main text.

      (27) Page 9: "This result is congruent with the MPRA assay, suggesting that the C-rich coding sequence preceding the stop codon not only reduces termination pausing, but also promotes downstream translation." This is unjustified as the single C-rich sequence chosen for the analysis in Figure 4C is not representative of the two C-rich triplets identified in Figure 4B, showing strong evidence of read-through.

      In Figure 4C, both C-rich and GA-rich sequences were chosen from shared elements between eRF1-seq and MPRA as they represent physiological sequences associated with termination pausing. The reporter assay is crucial in linking the lack of termination pausing with 3’UTR translation. We thank the Reviewer for understanding.

      (28) The analyses in Figures 4C-D suffer from a lack of the no-stop codon controls to allow the standard quantification of read-through as a percentage of continuous translation in the zero frame in the absence of a stop codon.

      The Reviewer might have missed the no-stop codon control in Figure 4C, which contains reporters with (bottom) and without (top) UAG stop codon. In Figure 4D, it is not feasible to include no-stop codon control for frameshifting reporters as the HiBiT value will be out-of-chart several orders of magnitude.

      (29) Page 10: "Therefore, the C-rich coding sequence triggers ribosome sliding at the stop codon, resulting in 3'UTR translation in all three reading frames." Sliding is an imprecise term. It is presumably a stop codon readthrough accompanied by frameshifting.

      We agree with the Reviewer’s suggestion and have replaced the word of “sliding” with “readthrough”.

      (30) Page 10: The citation to Figure S3H is incorrect, as there is no panel H.

      We are glad to have this opportunity to fix this error. We have now added panel H into the Figure S3 in the revised manuscript.

      (31) Page 10: "When the ribosome occupancy in the CDS was normalized, loss of ABCE1 led to a modest increase of stop codon peaks (Figure S4C)". Is this increase reproducible in replicates and statistically significant, as it seems very slight?

      The increased ribosome peak at stop codons in cells lacking ABCE1 is not significant, partly due to incomplete depletion of ABCE1 as shown in Figure S4A. Since ABCE1 is not the focus of this study, we did not attempt to knock out ABCE1, which could cause cellular toxicity.

      (32) Page 11: "Notably, the elevated ribosome density occurred at all stop codons, an indication of global effects." Where are the data substantiating this claim?

      We apologize for the confusion here. In the revised manuscript, we have deleted this sentence from the main text.

      (33) Page 11: "A closer look revealed that silencing ABCE1 increased the ribosome density at the -15 nt position". This claim is not convincing in the 29 nt read data, where it should be observed.

      We agree with the Reviewer that the increased ribosome density at the -15 nt position is more evident for shorter footprints. We have revised the sentence in the main text.

      (34) Page 11: "Since the 3' end of 18S rRNA contains a highly conserved U-rich sequence (GAUCAUUA), the GA- rich sequence element of mRNA could follow U:A and U:G base pairing near the exit site" (Figure 5A and S5A). By contrast, the C-rich sequence motif on mRNA would escape the 18S rRNA checkpoint, resulting in faster mRNA passthrough." This seems simplistic, as there would also be three G-A or A-G mispairings with 18S rRNA at other positions of the (G/A)AAGAAGA motif. Also unclear what the C-rich motif actually is, making it impossible to determine how many pairings it could make with the 18S rRNA sequence.

      Unlike base pairing on RNA structures, the putative rRNA:mRNA interaction is dynamic because of the continuous movement of mRNA along the ribosome channel. In fact, perfect base pairing might not be instrumental. Therefore, the difference between GA-rich and C-rich sequences is reflected in the accumulated effect. As mentioned above, the C-rich sequences are derived from both eRF1-seq and MPRA.

      (35) Figure S5B: Showing this sequence is misleading. While not described, it is presumably the DNA sequence of the plasmid, not the rRNA sequence, as there is 100% of the mutant sequence. They need to sequence the 3' end of rRNA isolated from ribosomes to confirm the presence of mutant ribosomes at appreciable levels.

      The Reviewer is correct that the sequences shown in Figure S5B are from the plasmids. To avoid such confusion, we have removed the sequences in the updated Figure S5B.

      (36) Page 12: "When mRNAs are stratified based on the sequence motif upstream of stop codons, we found that overexpression of the 18S mutant reduced the differential termination pausing between GA-rich and C-rich sequences (Figure 5C)". It is not explained what GA-rich or C-richness means precisely. Moreover, the same kind of analysis done in Figure 1C should have been conducted here to determine the LOGOs for high and low pausing for WT vs mutant 18S rRNA.

      We understand why the Reviewer repeatedly ask about the GA-rich and C-rich sequences, partly due to the lack of clarity in our original description of the analysis. The GA-rich transcripts were defined as those have the upstream 15-nt sequence with G or A nucleotides more than 65% (9 nt); whereas C-rich transcripts were defined as those with C more than 40% (6 nt). We have now updated the methods section in the revised manuscript.

      (37) Page 12: "Notably, the 3' end sequence of 18S rRNA is highly conserved (Figure S5D)". There is no Figure S5D in the figures.

      We are glad to have this opportunity to fix this error. We have now added panel D and E into Figure S5 in the revised manuscript.

      (38) Page 13: "Further supporting the sequence specificity of termination pausing, testis mRNAs with prominent stop codon peaks are enriched with GA-sequences upstream of the stop codon (Figure S6C). The same group of mRNAs, however, barely exhibit termination pausing in liver." Again, motif analysis of high and low pausing should have been done here.

      The motif analysis in mouse tissue samples is less informative because GA-rich sequences will be over-represented in testis, whereas the same group will be under-represented in liver. We had to select the shared mRNAs for comparative analysis. We thank the Reviewer for understanding.

      (39) Page 13: "While liver exhibited a similar distribution of Rps26 and RACK1 in polysome fractions, testis showed an evident depletion of Rps26 in polysome (Figure 6C). Notably, a substantial amount of Rps26 is present in the ribosome-free fraction of testis." They failed to normalize Rps26 levels in polysomes for bulk polysome levels, as indicated by the A260 tracings to determine if polysomes are depleted of Rps26, or rather, there is less polysomal Rps26 simply because polysomes are less abundant.

      We agree with the Reviewer’s notion regarding different polysome traces between testis and liver. Because the polysome volume is difficult to normalize, we used RACK1, a constitutive component of ribosome, to quantify the amount of polysome.

      (40) Page 14: "Indeed, normal mode analysis (NMA) by anisotropic network models suggests that, in the absence of Rps26, both the -3 to -9 extension of the mRNA and the 3' end of 18S rRNA can twist and approximate to each other with improved mutual parity (Figure 7B)." It is unclear what this means.

      Normal Mode Analysis (NMA) by Anisotropic Network Model (ANM) is a coarse-grained computational method used to study biomolecular dynamics by modeling proteins as a network of nodes connected by springs. Unlike the Gaussian Network Model (GNM), ANM calculates the full 3D directional preference of motion, enabling characterization of conformational changes, domain movements, and flexibility in large macromolecules. We have added a citation (Bahar, I. et al. 2005) in the revised manuscript.

      (41) Page 14: "To investigate whether Rps26 haploinsufficiency affects ribosome dynamics at stop codons, we knocked down Rps26 from HEK293 cells using shRNA (Figure S7A)". Haploinsufficiency properly refers to a heterozygous null/WT genotype, not shRNA knockdown.

      The Reviewer is correct in terms of haploinsufficiency. We have replaced the word of “haploinsufficiency” with “reduced Rps26 levels” in the revised manuscript.

      (42) Page 14: "The reciprocal change echoes the tissue-specific differences in initiation and termination (Figure 6A). " It's unclear why these peaks should be reciprocally related mechanistically, so examining changes in their ratio may not be incisive. Rps26 KD could reduce the efficiency of termination independently of pausing. And does Rps26 KD affect eRF1 occupancies in parallel with 80S occupancies?

      A prior study reported that Rps26 regulates translation initiation by recognizing Kozak sequence elements (Ferretti, et al. NSMB 2017). We therefore speculate that the role of Rps26 in termination might be correlated, although we don’t have direct evidence. We have further clarified this point in the discuss section of the revised manuscript.

      (43) Page 14: "The increased termination pausing, once again, primarily occurs at stop codons preceded by GA-rich sequences (Figure 7C)". No statistical analysis of replicates was done to see if the increase is significant, as it is quite small. They could have stratified mRNAs according to the number of base-pairs they can form with 18S rRNA rather than using this nebulous GA-richness, and see if the conclusion still holds.

      The metagene analysis shown in Figure 7C is standard for comparison of ribosome footprint distribution. We agree that the increase of termination peak at stop codons preceded by GA-rich sequences is not as striking as it should be, this is an underestimate because only a small fraction of ribosomes have sub stoichiometry of Rps26.

      (44) Page 14: "Remarkably, when mRNAs are stratified based on the sequence motif upstream of stop codons, we found that overexpression of Rps26 reduced the ribosome density (>50%) at stop codons preceded by the GA-sequence (Figure 7E)." They failed to normalize reads to the CDS occupancies to control for fewer ribosomes reaching the stop codons, especially considering that depletion of elongating 80S appeared to occur just upstream of stop codons on Rps26 OE. The same problem exists for the C-rich mRNAs. Also, their interpretation of the effects of Rps26 OE depends on there being Rps26-lacking 40S subunits in WT unstressed cells, which seems unlikely and has not been established directly. Finally, they didn't show increased Rps26 content in 40S subunits on Rps26 OE, which is also required.

      This question is the same as #7, which we have fully addressed in this letter (page 7).

      (45) Page 15: "To affirm the mechanistic connection between stop codon pausing and termination fidelity, we conducted HiBiT reporter assays that showed increased 3'UTR translation in cells with Rps26 overexpression (Figure 7F)." But both the C-rich and GA-rich reporters show increased expression on Rps26 OE. Why should that be if the C-rich sequences don't base pair with 18S rRNA in WT cells and are unaffected by Rps26 depletion? These data suggest that some other mechanism underlies the increased expression of the GA-rich reporters seen on Rps26 OE.

      The Reviewer’s concern is valid, and we agree that additional mechanisms might contribute to the increased reporter expression. The simplest explanation is that Rps26 overexpression promotes ribosome biogenesis, which globally increases mRNA translation. Supporting this notion, more polysome could be observed in cells with Rps26 overexpression (Figure S7E).

      (46) Page 15: "Without pausing at stop codons, terminating ribosomes are likely to undergo incomplete dissociation, resulting in continuous translation in 3'UTR." The language here is imprecise. Are they proposing reinitiation by unrecycled 80S ribosomes, or stop codon read-through with or without frameshifting, or both?

      This question is the same as #2, which we have fully addressed in this letter (page 3).

      (47) Page 15: "Importantly, lack of termination pausing leads to stop codon-associated random translation, giving rise to mixed C-terminal extension." Again, what does this mean? Read-through generally accompanied by frameshifting?

      Stop codon-associated random translation differs from ribosome readthrough, reinitiation, or frameshifting. We have extensively clarified this confusion in the revised manuscript.

      (48) Page 16: "For terminating ribosomes, the prolonged dwell time at stop codons offers an extended window for eRF1 loading, peptide cleavage, and ribosome recycling." This sentence is confusing because the eRF1-Seq data suggest that the pause occurs after eRF1 decodes the stop codon, with delayed peptide cleavage and recycling.

      We thank the Reviewer’s effort to improve our manuscript. We have rephrased the entire paragraph in the revised manuscript.

      Reviewer #3 (Recommendations for the authors):

      The manuscript is well-written, and the conclusions are overall well-supported by the data. I have only a few relatively minor questions and comments:

      (1) For termination sites overlapping with coding regions, the lack of 3-nt periodicity downstream of these sites could result from overlapping translation of multiple ORFs, rather than indicating that translation readthrough events can happen in multiple frames. Could the authors clarify this interpretation?

      We appreciate the Reviewer’s positive comments on our manuscript. The Reviewer is correct that overlapping ORFs would result in the lack of 3-nt periodicity. Although it is common for overlapping ORFs near the canonical start codons, ORFs overlapping the canonical stop codons are rare. Nevertheless, we have rephrased the statement in the revised manuscript.

      (2) The observation that multiple eRF1-seq peaks are located within CDS regions suggests that eRF1 may compete with A-site tRNAs during elongation. This is an interesting finding. Do the authors think this competition could lead to premature termination, or is it more likely to represent elongation pausing? Additionally, do the authors observe corresponding ribosome pausing peaks at these sites in conventional Ribo-seq data?

      The Reviewer’s comment on eRF1-seq peaks in CDS is insightful. We agree that pre-mature termination is possible because of competition. However, we do not observe corresponding ribosome pausing peaks in regular Ribo-seq, presumably due to low frequency of which events.

      (3) Regarding the regulation of ribosome pausing across tissue types, how robust are these results? For example, are the tissue-specific effects (such as stronger pausing in the testis) consistent among different mice or across age groups, given that many aspects of translational regulation are known to change with aging?

      We found that tissue-specific distribution of ribosome footprints is highly reproducible, especially liver and testis. Notably, the lack of termination peaks in liver is also reported by other independent studies (Gobert, et al. PNAS 2020), arguing that such effect is not a result of sequencing bias. We haven’t compared mice with different ages, but aging-associated translational regulation is an interesting topic awaits further investigation.

      Reviewer #4 (Recommendations for the authors):

      (1) Translation termination has been studied by ribose in several organisms, including mammalian cells and yeast. In those cases, what is analyzed is not the peak height at the stop codon, but rather the difference in the ribosome density before and after the stop. Thus, analyzing peak height is not validated. I understand that this is relevant only for the ribosome profiling experiments (and Ezra-seq), not the RF1 profiling. But the large majority of the data was acquired that way.

      With due respect, we disagree with the Reviewer’s point regarding how to study ribosome dynamics at stop codons. Comparing footprint density before and after stop codons does not infer dynamics of terminating ribosomes. By establishing eRF1-seq, we are for the first time able to analyze ribosome behaviors at stop codons, which represents a significant advancement of technological development.

      (2) Moreover, the data do not reproduce previous findings, and no attempt is made to connect them to previous data. Previous data have shown that stop codon efficacy varies. This is not reproduced (S1C). Similarly, an effect from the +1 residue is not reproduced. The data isn't stratified by different stop codons, and previous work has shown that different surrounding residues have different effects in the context of different stop codons. Thus, none of the sequencing data is validated or trusted and does not reproduce previous findings.

      We are certainly aware of previous findings regarding stop codon readthrough. We would like to emphasize that our findings do not contradict established principles of translation termination. Rather, enabled by the development of eRF1-seq, we provide new insights into termination dynamics that extend existing models.

      (3) The GA-rich sequence identified by Ezra-Seq and RF1 seq is not the same, and it differs from previous sequences (Wangen &Green).

      We don’t quite understand why the Reviewer is preoccupied with prior studies without accepting new results obtained from newly developed technology. The GA-rich sequences identified by Ezra-Seq and eRF1-seq are similar, albeit not identical. This is simply because eRF1-seq offers much higher resolution to reveal termination pausing than regular Ribo-seq.

      (4) The authors claim that the majority of Rf1 peaks are at stop codons, but that is not true. It is only about 30% of the peaks. Also, not all mRNAs have peaks at the stop codons. That is, at best, problematic. Finally, there are mRNAs that are known to "suffer" from NMD. What do these look like in the Ezra-Seq and RF1-Seq? How about mRNAs that have programmed frameshifts? The eRF1 data is invalid.

      The Reviewer is confused about the eRF1 peak density versus frequency, which has totally different meanings. Additionally, the Reviewer seems to be surprised that not all mRNAs have peaks at the stop codons. The differential ribosome dynamics at stop codons is an exciting feature previously unappreciated, rather than problematic. Regarding programmed frameshifting, we argue that such events are rare in mammalian cells.

      (5) Figure 4 has many flaws; it is hard to know where to start. First, instead of the M/P ratio, one should analyze M/M+P, to normalize out differences in the loading and effects from collisions, which are guaranteed to occur here, but not considered or analyzed. Second, the data are analyzed as if what matters are codons in the P and E site (and beyond, where there are definitely NOT recognized codons). While there is evidence for some interactions, one would think that an additional analysis based on sequence would be helpful. Also, the supplemental data indicate that very rarely are there reciprocal changes (as should be the case), as seen for stop codons. Thus, the assay is at best questionable and likely worse.

      The Reviewer appears to be unfamiliar with massively parallelled assay, which has been widely used to uncover sequence elements crucial in translational regulation. We urge the Reviewer to read our prior study using MPRA to investigate alternative translation initiation (Jia, et al. NSMB 2020). The similar approach has also been used to decipher 5’ UTR sequence elements in mRNA engineering (Sample, et al. Nat Biotech 2019).

      (6) Things do not look up for the HiBit reporter assay. The two sequences clearly have effects on translation without considering stop codon context (Figure 4C), which need to be taken into account. Also, the effect from the sequences varies in the context of the assay in 4C and 4D (2-fold vs. 5-fold), further questioning the assay. Moreover, the authors claim that re-initiation cannot account for Hibit levels, but that is clearly incorrect. The western in Figure 4E does not reproduce the data in 4D. While Hibit goes up (as in 4D, the putative GFP-fusion goes down. Finally, while the second reading frame should be more efficient, it is not explained and further argues for an artifact. Previous work (and work herein) suggests that read-through occurs equally in each reading frame.

      The Reviewer is confused about the HiBiT-based reporter assay shown in Figure 4C-4E. First, we have included important controls, i.e., same reporters without stop codons, to normalize sequence variation. Second, Figure 4C and 4D used totally different reporters and it is not appropriate to directly compare their values. Third, re-initiation events would not generate fusion proteins containing the N-terminal GFP. The Reviewer is encouraged to re-examine the results presented in Figure 4.

      (7) No controls for these assays are presented: e.g., stimulation by antibiotics, ABCE1 depletion, etc.

      We are not sure which assay the Reviewer is referring to. For reporter assays shown in Figure 4, we focused on effects of cis-sequence elements, rather than trans-acting factors. We thank the Reviewer for understanding.

      (8) Figure 5 has similar problems. I don't understand how Figure 5A is made, but when one overlays the cited structures on Rps26, the molecules are identical. I guess the authors chose to build non-existing sequences differently into the structure. There is no basis for that. In panel C, and the same in Figure 7, the number of analyzed mRNAs varies. This could influence the outcome, and the EXACT same set of mRNAs should be analyzed. But the main problem here is that the authors need to analyze readthrough and not peak height, as detailed above. Essential controls are missing that show what fraction of the 18S rRNA is mutated. Previous work has shown that 2 nt-truncated 18S rRNA is actively degraded. It is hard to believe how 15% of altered ribosomes can abolish 100% of the effect from the C-rich sequences. Important validation is missing: the authors should analyze rRNA sequences in their ribo-seq dataset to demonstrate that they have the mutated rRNAs, and that these enrich and de-enrich as predicted.

      The Reviewer’s comment on Figure 5A is baseless. As indicated in the Figure legend, Figure 5A was made from the existing cryoEM structure (PDB: 6ZMW). Regarding 18S rRNA mutants, we simply followed prior studies (Burman and Mauro. NAR 2012) and there is no evidence indicating degradation of such rRNA mutants. Given the low percentage of ribosomes incorporated with the rRNA mutants, the observed effect on termination pausing represent an underestimation, rather than an overstatement.

      (9) In Figures 5-7, the authors develop a model that the sequence selectivity arises from base pairing between 18S rRNA and the mRNA. If so, then they should really stratify the data by the number of WC pairs that can be formed. And only WC pairs, as GU pairs have a totally different geometry that will likely be discriminated against in this context. Also, the mutation is in a part of the helix that has no effect (Figure S3G). Thus, the data within the manuscript are inconsistent.

      As the Reviewer might be aware, GU pairs are commonly found in tRNA and rRNA structures. Since both WC and GU pairs contribute to mRNA:rRNA interaction, there is no point to stratify sequences based on different pairing format. Additionally, we would like to point out that the putative mRNA:rRNA interaction is not static, considering the continuous movement of mRNA along the ribosome channel.

      (10) Figure 6 does not agree with published data (Li et al., Nature 2022). Previous work did not show testis depletion of Rps26 in purified ribosomes. This is the critical difference, as the authors here did not purify ribosomes. Also, another Rps is an essential control, even if purified ribosomes are used. This dataset should not be shared. Depletion from polysomes is hard to believe, as overall, there is less signal in the polysomes.

      The Reviewer finally made a good point regarding Rps26 in testis. In our study, we did not separate different cell types such as spermatocytes and therefore we do not know which cell type dominantly influences termination pausing.

      Regarding varied Rps26 levels in different tissues, we noticed different polysome between testis and liver. Because the polysome volume is difficult to normalize, we used RACK1, a constitutive component of ribosome, to quantify the amount of polysome.

      (11) Figure 7 has similar problems to Figure 5. Different pools of mRNAs are analyzed; peak height is not validated. Overexpression of Rps26 is not shown, as only Myc is shown, not Rps26. Beyond that, increased occupancy in ribosomes needs to be shown for the effect to come from ribosomes. Given how sick the cells are, it is most likely that all effects are secondary and arise from whatever else is going on in the overexpression or depletion of Rps26. No controls are presented to show specific effects from Rps26.

      We are surprised that the Reviewer ignored the supplementary data that shows Rps26 levels. Regarding controls, it is not appropriate to use different ribosomal proteins because every ribosomal protein has its won functionality. We acknowledge that experiments by gene knockdown is not perfect, but the results are still informative especially when different mRNA pools from the same cells are compared.

      (11) The authors need to check Rli1/ABCE levels in their cells. Their data have features that are indicative of low ABCE1 levels. These include a very small effect from ABCE1 depletion. These could be responsible for some of the effects they observe.

      Once again, we are surprised that the Reviewer ignored the supplementary data that already shows ABCE1 levels in cells with or without ABCE1 knockdown (Figure S4A). Constantly addressing the Reviewer’s lack of careful reading of our manuscript is frustrateing. Nevertheless, we have thoroughly revised the entire manuscript by clarifying interpretations, moderating mechanistic claims, and expanding relevant discussion.

    1. Author response:

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

      eLife Assessment

      Plasmodesmata are channels that allow cell-cell communication in plants; based on the functional similarities between facilitated transport within plasmodesmata and into the nucleus, the authors speculate that nuclear pore complex proteins might be involved in plasmodesmata function. If supported, this would transform our understanding of cell-to-cell communication in plants. The authors localize nuclear pore complex proteins to plasmodesmata using proteomics and heterologous overexpression; however, the data are incomplete since key controls for localization, functionality, and expression level of fluorescent protein fusions are absent.

      Thank you for the constructive reviews. We have tried to address the comments as outlined below. Specifically, we added new data to the manuscript with respect to the assessment of the protein levels of three independent stable Arabidopsis lines expressing NUP62-GFP from its own promoter using mass spectrometry quantification. These experiments were carried out to evaluate whether the observed PD localization of NUP62-GFP to peripheral puncta might be an artifact caused by inadvertent overexpression and resulting mistargeting. Quantitative analysis shows no indication for significant overexpression of NUP62-GFP.

      To assess whether the localization of NUPs is distinct from localization of an ER marker, we have now included a comparison of the NUP43-mVenus localization with that of the mCherry-HDEL luminal ER marker, revealing distinct localization patterns. The peripheral puncta thus do not appear to be due to simple ER accumulation.

      To evaluate whether the CPR5-mCitrine fusion is functional, we tested whether the fusion construct was able to complement the loss-of-function cpr5-1 mutant. In two independent complementation lines (cpr5-1/CPR5:CPR5-mCitrine), the roots of 14-d old seedlings were significantly longer compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype. Although we did not detect CPR5-mCitrine fluorescence, the construct appears to be able to restore the wild type phenotype, indicating that the lines express a functional CPR5 protein.

      We have restructured the figures and provided additional information in the figure legends.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Plasmodesmata are channels that allow cell-cell communication in plants; based on the functional similarities between facilitated transport within plasmodesmata and into the nucleus, the authors speculate that nuclear pore complex proteins might be involved in plasmodesmata function. In this manuscript, they localize nuclear pore complex proteins to plasmodesmata using proteomics and heterologous overexpression. They also document a possible plasmodesmata transport defect in a mutant affecting one nuclear pore complex protein.

      Strengths:

      The main strength of this manuscript is the interesting and novel hypothesis. This work could open exciting new directions in our understanding of plasmodesmata function and cell-cell communication in plants. They also localized many NUPs (12/35 Arabidopsis NUPs).

      Weaknesses:

      The main weakness of this manuscript is that the data are incomplete. While the authors appropriately and frequently acknowledge caveats to their data, two controls are essential to interpret the results that fluorescently-tagged NUPs localize to the plasmodesmata: (1) assessment of the expression level of these fluorescently-tagged NUPs to determine whether the plasmodesmata localization might be an overexpression artefact;

      As we outlined in the manuscript, we also considered the possibility that the peripheral localization could be a consequence of overexpression, in particular in the transient expression system. To be able to control the levels, NUP genes were expressed under the control of the b-estradiol-inducible XVE promoter which allows for b-estradiol dose dependent gene expression (Bashandy et al., 2015; Schlücking et al., 2013). We assessed the dependence of localization on expression levels by studying NUP localization under conditions of reduced estradiol concentrations for induction and shortened incubation time. We validated that the fluorescence was substantially reduced relative to the standard estradiol concentration experiments, however we still detected both nuclear and peripheral localization of the NUPs (Figure 4C-F).

      We also considered that in stable transformants the expression of one extra copy of a NUP62-GFP fusion under the control of the native promoter could cause a moderate overexpression and as a consequence lead to artifactual accumulation in the periphery (Figure 3C-E).

      To evaluate the level of NUP62-GFP fusion protein relative to untransformed controls, we quantified the levels of NUP62 in three independent transgenic fluorescent WT/NUP62p:NUP62-GFP Arabidopsis lines and in Arabidopsis WT using mass spectrometry (new Figure 3F). The new data indicate that there is no significant increase in NUP protein amounts in the lines expressing the fusion construct relative to WT.

      We now write in the revised manuscript (line 200-205):

      “NUP62 protein abundance in two-week-old cotyledons of the stable NUP62p:NUP62-GFP transformants was not statistically different to NUP62 protein levels in WT (Figure 3F). Notably, the punctate fluorescence at the cell periphery, encompassing both PD-associated and non-PD-associated localization, were not detectable or absent in roots and young leaves of four-day-old seedlings (Figure 3D). However, it cannot be excluded that the GFP fusion impacts NUP62 localization.” We provide a new Method section for the mass spec analysis of the cotyledons in lines 582-590.

      The use of antibodies in wild type tissue would be a potential way to avoid overexpression when trying to detect the localization of NUPs in planta. To investigate the localization of NUPs at physiological expression levels, we attempted to immunolocalize NUPs using antibodies. However, the anti-NUP antibodies available to us were not optimized for immunolocalization and we were unable to detect any fluorescence in the cells at the NPC nor the periphery.

      (2) assessment of the function of the fluorescently-tagged NUPs, either by molecular complementation of a knockout mutant phenotype or by biochemical methods to test whether the fluorescently-tagged NUP incorporates into nuclear pore complexes. Conducting these experiments for even one fluorescently-tagged NUP would substantially strengthen this manuscript.

      We agree with the reviewer that validation of the functionality of NUP fusion proteins would be valuable. Previously, C-terminally fused Arabidopsis NUPs, such as NUP93a-GFP, GP210-GFP, NUP58-GFP were reported to localize to the nuclear envelope when stably expressed in transgenic Arabidopsis lines (Tamura et al., 2010). As reported for transmembrane NUP GP210 and CPR5 fusion proteins (Gu et al., 2016; Tamura et al., 2010), C-terminally fused GP210 and CPR5 localized to the nuclear envelope but not to the nucleoplasm when expressed heterologously in N.benthamiana (see Figure 3-figure supplement 1). We found several soluble NUPs to also localize to the nucleoplasm (PpNUP98.1, PpNUP62, AtNUP62, AtHOS1) (Figure 1-figure supplement 1, Figure 3, Figure 3-figure supplement 1). Previous studies have reported that several FG NUPs (i.e. NUP98a/b or NUP62) and Y-complex NUPs (i.e. HOS1, NUP96, and NUP107) have been found to also localize in the nucleoplasm rather than specifically to the nuclear envelope when expressed as fusion proteins (Chen et al., 2023; Gallemí et al., 2016; Huang et al., 2024; Lazaro et al., 2012). Of note, for NUP98a, Gallemi and colleagues (2016) discussed the localization to the nucleoplasm as confirmation that, like vertebrate NUP98, Arabidopsis NUP98a is a dynamic NUP rather than just a key structural element of the NPC. HOS1 was reported to interact with ICE1, CO, FVE, and HDA6 in the nucleoplasm (Dong et al., 2006; Jung et al., 2012; Lazaro et al., 2012), indicating that HOS1 might dynamically shuttle between the nuclear pore and nucleoplasm, which could also explain the observed nucleoplasmic localization. In Drosophila, the FG-NUPs NUP98, NUP62, and NUP50 localized in the NPC, and also in the nucleoplasm and interacted with genes (Kalverda et al., 2010). The nucleoplasmic localization could thus have a functional relevance. Yet we cannot rule out, whether soluble NUPs mislocalize in overexpression conditions as we state multiple times in the manuscript.

      For this revision, we generated two new independent transgenic Arabidopsis lines stably expressing CPR5-mCitrine under control of its own promoter in the cpr5-1 mutant background (cpr5-1/CPR5p:CPR5-mCitrine). The roots were significantly longer in the two independent transgenic cpr5-1/CPR5p:CPR5-mCitrine Arabidopsis lines compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype (new Figure 7-figure supplement 1, G–I). However, we could not detect fluorescence in the 10-14 day old seedlings, which could be due to a variety of reasons, such as cleavage of the FP and degradation of the FP without accumulating elsewhere in the cells.

      In the new manuscript we write in lines 275-283:

      “To assess whether the CPR5-mCitrine fusion protein is functional in Arabidopsis, we tested whether CPR5p:CPR5-mCitrine (including all introns) expression in the cpr5-1 mutant background results in a rescue of the severe growth phenotype of the cpr5-1 loss-of-function mutant (Bowling et al., 1997). Indeed, roots were significantly longer in the two independent transgenic cpr5-1/CPR5p:CPR5-mCitrine Arabidopsis lines compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype (Figure 7-figure supplement 1, G–I). However, we could not detect fluorescence in 10-14 day old seedlings, which could be due to a variety of reasons, such as cleavage of the FP and degradation of the FP without accumulating elsewhere in the cells. The lack of fluorescence in the transgenic lines requires further investigation.“

      Reviewer #2 (Public review):

      Summary:

      The authors aim to address whether nuclear pore complex components localize and function at PD in plant cells to mediate cell-to-cell communication.

      Strengths:

      (1) Novelty and Significance:

      The core hypothesis, drawing parallels between PD and NPC transport, is highly original and addresses a critical gap in understanding plant intercellular communication. The idea that phase-separated domains formed by FG-NUPs could act as diffusion barriers at PD offers a plausible and sophisticated explanation for their complex transport properties, including size exclusion and facilitated translocation. This could fundamentally change how we view PD function.

      (2) Comprehensive Evidence:

      The study employs a rigorous and diverse set of experimental approaches, including a comprehensive bioinformatic analysis of both moss and Arabidopsis NUPs in available PD proteomic datasets, extensive imaging analysis of Nup localization in vivo, and functional transport assays using a loss-of-function nup mutant (cpr5). The transport assay is particularly important to provide functional evidence linking CPR5 to PD-mediated transport. The finding that callose levels were not significantly different in cpr5 mutants under these conditions is helpful and supports a distinct, callose-independent mechanism of transport regulation.

      (3) Objectivity:

      The authors are forthright in discussing the limitations and potential artifacts of their own data, clearly distinguishing between observations and definitive conclusions.

      Weaknesses:

      While the claims are generally justified as hypotheses or consistent observations, the authors themselves extensively detail the caveats, which are worth reiterating for clarity:

      (1) Potential Overexpression Artifacts in Localization:

      Although efforts were made to control expression levels, the authors acknowledge that transient overexpression could still lead to NUP accumulation at PD, either as a physiologically relevant accumulation under excess conditions or due to mis-targeting, or even as storage depots. The resolution of confocal microscopy also does not allow for a definitive conclusion on the nature of the location.

      We would like to add that in addition to the experiments using estradiol-controlled transient overexpression for localizing NUP fusions, we also provided localization data obtained from Arabidopsis transformants that stably express one extra copy of a NUP62-GFP fusion under the control of the native promoter. In cotyledons, NUP62-GFP localized to the nucleus and in the periphery, and in many cases to PD (Figure 3C-E). In the course of the revision we tested whether the extra copy of NUP62 could cause overexpression that might lead to artifactual accumulation in the periphery.

      To evaluate the level of NUP62-GFP fusion protein relative to untransformed controls, we quantified the levels of NUP62 in three independent transgenic fluorescent WT/NUP62p:NUP62-GFP Arabidopsis lines and in Arabidopsis WT using mass spectrometry (new Figure 3F). The new data indicate that there is no significant increase in NUP protein amounts in the lines expressing the fusion construct relative to WT.

      We now write in the revised manuscript (lines 200-205):

      “NUP62 protein abundance in two-week-old cotyledons of the stable NUP62p:NUP62-GFP transformants was not statistically different to NUP62 protein levels in WT (Figure 3F). Notably, the punctate fluorescence at the cell periphery, encompassing both PD-associated and non-PD-associated localization, were not detectable or absent in roots and young leaves of four-day-old seedlings (Figure 3D). However, it cannot be excluded that the GFP fusion impacts NUP62 localization.“ We provide a new Method section for the mass spec analysis of the cotyledons in lines 582-590.

      (2) Proteomics Purity:

      The authors note that the presence of NUPs in PD fractions/proteomics cannot definitively rule out contamination, as PD cannot currently be purified to absolute homogeneity and is often contaminated with other organelles, including the nucleus.

      We would like to add that despite their low abundance in plant cells, NUPs were found to be enriched in cell wall, and PD fractions relative to total cell extracts (revised Figure 2-supplement 2). To evaluate whether NUP enrichment might be a consequence of contamination by nuclear fractions, for the revision, we evaluated the enrichment of nucleolar proteins and histones. As shown in the revised Figure 2–figure supplement 2, other nuclear proteins did not show a significant enrichment, supporting the notion that NUPs were specifically enriched in PD fractions, consistent with the localization of NUP-FP fusions. We note however, that these data do not demonstrate unambiguously that NUPs are bona fide PD components.

      (3) CPR5 Mutant Interpretation:

      While cpr5 mutants exhibited reduced macromolecular transport, the authors state that they cannot exclude that the reduced transport is due to secondary effects in the cpr5 mutants, which show rather severe phenotypic defects. This is an important distinction, as CPR5 has known roles in defense responses and hormone signaling that could indirectly influence PD integrity, independent of callose deposition. The lack of effect on small molecule transport is a good control, but the broader pleiotropic effects of cpr5 mutants remain a consideration.

      We agree with the assessment of the reviewer. The mutant is compromised in many ways and thus the effects we observe could be indirect. This is stated also in the manuscript (lines 314-317).

      (4) Conceptual Distinction between NPC and PD:

      The authors correctly point out that while similarities exist, the physical assembly of NUPs at PD must differ from that at the NPC due to the presence of the desmotubule and smaller cytoplasmic sleeve width at PD. Moreover, nucleocytoplasmic transport depends on karyopherin proteins that interact with the NPC central channel to complete the transport. Yet the role of karyopherins in this case is not clear. Therefore, the proposed "PD pore complex" may bear some NPC features, but not be identical.

      Reviewer 2 summarized the key concerns that we highlighted and discussed in the manuscript, which addressed differences in PD and NPC architecture. In particular, we noted that one of the major differences in PD is the presence of the desmotubule (in lines 370-372). We also highlighted that we did not detect all NUPs at PD (in lines 375-376). While a negative result, this observation may also be consistent with differences regarding the assembly of NUPs in or near PD vs the NPC. We fully agree with the reviewer that the proposed “PD pore complex” may be not identical to the NPC, and we also discussed that the NUPs seen at PD could represent sites of accumulation in the ER near PD.

      Reviewer #3 (Public review):

      Summary:

      This manuscript presents a step towards testing the hypothesis that plasmodesmata have homology to nuclear pores. The similarities between the two structures have long been noted as both structures allow the transport of proteins and nucleic acids, and both structures are composed of curved membranes. The manuscript has identified nuclear pore proteins (NUPs) in plasmodesmal protein fractions and uses live imaging in a non-endogenous system and functional assays of a mutant to propose that this might be a bona fide association.

      The conclusions the authors seek to draw are that: NUPs are present in plasmodesmal protein fractions; NUPs localise at plasmodesmata; NUPs might form a pore-gating complex at plasmodesmata, regulating non-specific (2xGFP) and specific (SHR) transport through plasmodesmata

      The authors then use these conclusions to propose the possibility that phase separation mediates transport through plasmodesmata. If there is phase separation at plasmodesmata or a nuclear pore-like complex, it would revolutionise the community. However, this data is insufficient to act as a cornerstone for such a discovery.

      Strengths:

      The strength of the manuscript lies in the boldness and novelty of the idea.

      Weaknesses:

      The weaknesses lie in the lack of informative controls. The authors' own assessments of their data suggest they agree with this - in their abstract alone, they point out that the transport defects they observe might be off-target effects, and suggest there is a requirement in the future to determine whether the NUPs are bona fide PD components.

      Across the proteomic and live imaging experiments, the conclusions could be stronger if they compared the NUP localisation and accumulation with ER proteins - the question of whether NUPs behave like other ER proteins is not addressed. As NUPs reside in the nuclear envelope, continuous with the ER, and the ER traverses plasmodesmata, a comparison between the NUPs and ER proteins would be extremely informative.

      We agree with the comments of the reviewer. To assess whether NUPs show localization patterns that are similar to ER proteins, we transiently co-expressed NUP43-mVenus fusions with the mCherry-HDEL luminal ER marker in N.benthamiana. Comparison of the localization patterns reveals distinct patterns of NUP43-mVenus and mCherry-HDEL (see the new Figure5, new Figure 5-figure supplement 1). NUP43-mVenus appears to be associated with the ER, however restricted to subregions that partially overlay with aniline blue-labeled pit fields (new Figure 5, new Figure 5-figure supplement 1).

      In the new version of the manuscript, we write (lines 209-214):

      “We assessed whether NUP localization is distinct from ER localization in N. benthamiana leaves that heterologously co-expressed NUP43-mVenus and the ER luminal marker mCherry-HDEL. The localization patterns of NUP43-mVenus and of the mCherry-HDEL luminal ER marker were clearly distinct (Figure 5, Figure 5-figure supplement 1). NUP43-mVenus may be associated to the ER, however restricted to subregions of the ER, which partially overlay with aniline blue-labeled pit fields (Figure 5, Figure 5-figure supplement 1).”

      Regarding the proteomic identification of NUPs in plasmodesmal fractions, the authors place significant weight on their own metric for PD enrichment, the PD score. As I understand it, this a metric derived from addition of two factors: a two component enrichment score that is the difference between intensity of peptides of a given protein in the PD fraction and cell wall fraction, added to the difference between intensity of peptides of a given protein in the PD fraction and total cell fraction, and a feature score that is a factor that describes representation of protein domains contained in said given protein in the plasmodesmal fraction relative to the representation of that domain in proteins in the whole proteome. The features chosen for analysis are not indicated, and the feature factor, as I understand it, is a score common to all proteins with a given feature. While each of the factors carries a measure of meaning and information, I do not understand how adding them is mathematically or biologically meaningful.

      The feature score was defined based on PD proteome analysis previously described (Gombos et al., 2023). Features of known PD proteins were extracted and weighted against the entire Arabidopsis proteome. Structural features included Pfam domains PF00722 (GHL), PF06955 (XET_C), PF08372 (PRT_C), PF00335 (Tetraspanin), and PF00168 (C2 domain). Subcellular localization features included plasma membrane (PM), endoplasmic reticulum (ER), extracellular space (EX), and cell wall (CW). Functional features were assigned according to MapMan categories bin 10, 15, 26, and 30. To clarify the approach, we added a more detailed explanation to the feature score in the Methods of the revised manuscript.

      We agree with the reviewer that experimental values and feature factors represent two distinct, independent parameters. The PD score aims to identify proteins that are not only experimentally enriched in the plasmodesmal fraction but also share structural features characteristic of bona fide plasmodesmata-associated proteins, reducing the number of false positive candidates driven by either parameter alone in PD proteome lists. From a mathematical standpoint, we combined the two normalized factors in the PD score by summation, treating them as contributing equally to a protein’s PD association tendency.

      Conclusion:

      The conclusions of the study are not fully supported in the absence of ER controls. Of note, the imaging is ambiguous because the proteins do not show a discrete plasmodesmal association. This is a localisation reminiscent of cortical ER association and needs to be further investigated to determine whether it is a true and specific plasmodesmal association.

      We agree with the reviewer’s comments. In the revised version of the manuscript, we have now included a comparison of the NUP43-mVenus localization with that of the mCherry-HDEL luminal ER marker, which reveals distinct localization patterns (see new Figure5, new Figure 5-figure supplement 1). NUP43-mVenus may be associated with the ER; however, NUP43 is restricted to subregions of the ER, which partially overlay with aniline blue-labeled pit fields (new Figure 5, new Figure 5-figure supplement 1). Whether NUP localization is distinct from cortical ER requires further investigation.

      The conclusions drawn from Figure 1, Figure Supplement 4 are confusing. The text describing this data says that "NUPs were enriched in cell wall and PD fractions compared to total cell extract, while the abundance of other nuclear envelope proteins was unaffected by the PD purification and showed no enrichment in PD fractions". However, the data show that there is no difference in the normalised protein intensity for the NUPs across TC, CW, and PD fractions. The only sample that shows enrichment in PDs is the PDLP/MCTPs.

      To address this point, we rephrased the text (line 146-152). Among all NUPs identified in our PD proteome, 75% were more abundant in PD fractions (Figure 2-figure supplement 2), exceeding the proportions observed in TC (60%) and CW (~50%) fractions. In contrast, other nuclear proteins such as nuclear envelope proteins, nucleolar proteins, or histones showed PD intensities that fell within or overlapped the ranges observed in TC or CW. The native abundance of NUPs was lower compared to that of proteins from other compartments, which may explain why the enrichment significance was not statistically significant (p = 0.24 for PD vs. TC). By comparison, the corresponding p-values for other nuclear compartment proteins were higher, ranging from 0.5 to 0.9.

      Regarding the possibility that there is a pore-gating complex at plasmodesmata. If NUPs are specifically located at plasmodesmata, this is a strong hypothesis. The authors approach this functionally by assaying for protein and dye movement through plasmodesmata in the cpr5 mutants. These experiments suggest that cpr5 mutants have reduced transport through plasmodesmata for both proteins, but not for a smaller dye. They infer that the latter finding suggests that the cpr5 mutant has no alterations in plasmodesmal number, but this is completely unsupported - in their introduction, the authors identify how PD structure can modify transport capacity, so there are many technical and biological phenomena that could explain these data.

      We wrote in the manuscript: “The cpr5 mutants showed no detectable defect in small molecule transport indicative of WT-like PD density and preservation of the capability to mediate small molecule transport as shown by ‘Drop-ANd-See’ trans-leaf diffusion assays.”

      Indeed, we did not study PD density by e.g. quantification of a PD-marker fluorescence. Theoretically, PD density might be changed and permeabilities adjusted by unknown mechanisms to allow for WT-like small molecule transport. Strikingly, we observed transport differences for larger cargo. As we cannot exclude potential changes in PD density, we have rewritten and deleted the conclusion on PD density and now write: “The cpr5 mutants showed no detectable defect in small molecule transport indicative of preservation of the capability to mediate small molecule transport as shown by ‘Drop-ANd-See’ trans-leaf diffusion assays”. (Lines 310-312)

      I note for their DANS assays that the diffusion of dye from ad- to abaxial surface varies in the path followed (indicated by the asymmetry of the surfaces) and is not consistent within a leaf, let alone between leaves. This presents challenges in quantification and data interpretation that have not been addressed, and so the data cannot be confidently concluded to be an indicator of a different phenomenon rather than a less sensitive measure of the same.

      Indeed, in our hands, the spread of the small molecule dye did not proceed radially and was very often asymmetrical. Therefore, we quantified the fluorescent area by identifying pixels with fluorescence above a threshold, instead of determining a diameter of the fluorescent area. We describe the analysis in the figure legend and briefly mention it in the method section.

      “Fluorescent areas on the abaxial side were identified using auto threshold and Fiji YEN-algorithm with user modifications. The same threshold setting was used for the adaxial side. The extent of dye diffusion was quantified by the ratio between the areal spread of fluorescence on the abaxial side and the areal spread of fluorescence on the adaxial side.” (Figure 7)

      Furthermore, to avoid any positional artifacts in the comparison between different plants and genotypes, we only assessed the 4th leaf and 24 hours later the 5th leaf with the same labelling position on the leaf.

      Further, as the authors themselves acknowledge, altered protein movement might also arise from an off-target developmental phenotype. Many proteins have been shown to have no association with plasmodesmata but an indirect effect on their function. This hasn't been investigated and so cannot be ruled out.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      This is a really interesting hypothesis, but the support is incomplete.

      (1) P. 5 "Although the single insertion Arabidopsis lines tested here should have FG-NUP62-GFP levels closer to native conditions than the heterologous overexpression of FG-NUP62-mVenus in N. benthamiana, it cannot be excluded that the levels in tested lines are still higher than the native levels, or that the fluorescence protein fused to the NUP affects localization." I appreciate the authors' cautious interpretation of their results, but they could exclude both of these possibilities. The first is relatively easy: test the expression level of the transgene compared to endogenous NUP expression; although transcript and protein levels are not tightly correlated, this can give some estimate of whether the transgene is overexpressed. The second would be to conduct complementation assays of a knockout mutant. I understand that this would be difficult if nup mutants are lethal, but it is pretty common practice to transform heterozygotes and isolate homozygotes expressing fluorescent protein to conduct complementation assays. Anyhow, there is a defect in the cpr5 mutants that the authors could assess in complementation assays. Alternatively, the authors could use biochemical approaches to determine whether FP-tagged NUPs are incorporated into nuclear pore complexes. These three experiments, even for only one NUP, would provide compelling evidence that the authors are localizing a functional NUP fusion protein at near-native expression levels. This is essential to support their speculation that NUPs play a biological role in PD.

      Thank you for these three important recommendations: the quantification of NUP FP expression, the complementation of a mutant phenotype with NUP FP expression, and the assessment whether NUP FPs are incorporated into the NPC.

      First, to evaluate the abundance of NUP62-GFP fusion protein relative to untransformed controls, we quantified the abundance levels of NUP62 in three independent transgenic fluorescent WT/NUP62p:NUP62-GFP Arabidopsis lines and in Arabidopsis WT using mass spectrometry (new Figure 3F). The new data indicate that there is no significant increase in NUP protein amounts in the lines expressing the fusion construct relative to wild type.

      We now write in the revised manuscript (line 200-205):

      “NUP62 protein abundance in two-week-old cotyledons of the stable NUP62p:NUP62-GFP transformants was not statistically different to NUP62 protein levels in WT (Figure 3F). Notably, the punctate fluorescence at the cell periphery, encompassing both PD-associated and non-PD-associated localization, were not detectable or absent in roots and young leaves of four-day-old seedlings (Figure 3D). However, it cannot be excluded that the GFP fusion impacts NUP62 localization.” We provide a new Method section for the mass spec analysis of the cotyledons in lines 582-590.

      Second, to tested whether a NUP fusion is functional we assessed whether CPR5-mCitrine can complement the cpr5-1 mutant phenotype in complementation lines. We generated two new independent transgenic Arabidopsis lines stably expressing CPR5-mCitrine under control of its own promoter in the cpr5-1 mutant background (cpr5-1/CPR5p:CPR5-mCitrine). The roots were significantly longer in the two independent transgenic cpr5-1/CPR5p:CPR5-mCitrine Arabidopsis lines compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype (new Figure 7-figure supplement 1, G–I). However, we could not detect fluorescence in the 10-14 day old seedlings, which could be due to a variety of reasons, such as cleavage of the FP and degradation of the FP without accumulating elsewhere in the cells.

      In the new manuscript we write in lines 275-283:

      “To assess whether the CPR5-mCitrine fusion protein is functional in Arabidopsis, we tested whether CPR5p:CPR5-mCitrine (including all introns) expression in the cpr5-1 mutant background results in a rescue of the severe growth phenotype of the cpr5-1 loss-of-function mutant (Bowling et al., 1997). Indeed, roots were significantly longer in the two independent transgenic cpr5-1/CPR5p:CPR5-mCitrine Arabidopsis lines compared to the cpr5-1 mutant, and four-week-old plants showed a more WT-like growth phenotype (Figure 7-figure supplement 1, G–I). However, we could not detect fluorescence in 10-14 day old seedlings, which could be due to a variety of reasons, such as cleavage of the FP and degradation of the FP without accumulating elsewhere in the cells. The lack of fluorescence in the transgenic lines requires further investigation.”

      Third, to assess whether NUP FP fusions are also detectable specifically in nuclei, we have provided example images for potential nuclear localization of NUP62-GFP in the stable Arabidopsis line (Figure 3C), and for AtGP210-mVenus, AtNUP98b-mVenus, AtCPR5-mCitrine, and At NUP43-mCitrine in transient expression experiments in N. benthamiana (Figure 3-figure supplement 1).

      (2) The rationale for experiments was sometimes unclear. For example, why study Physcomitrium NUPs, then switch to Arabidopsis? Why use heterologous overexpression lines for SIM, rather than the stable Arabidopsis line for NUP62-GFP?

      Our initial work focused on the PD proteome in Physcomitrium patens. We had identified NUPs in PD-enriched fractions of the moss (Gombos et al., 2023). To evaluate whether this was a specific feature of the moss, or a technical artifact of PD enrichment in moss extracts, we extended the study to Arabidopsis thaliana and subsequently focused on the higher plant. The text in the manuscript reflects this flow.

      The NUP62-GFP stable transgenic Arabidopsis line was generated after the SIM experiments with CPR5-mCitrine. We plan to follow the suggestion of the reviewer to perform SIM experiments with the stable Arabidopsis NUP62p:NUP62-GFP lines.

      (3) The organization of the figures was confusing. Why present transient Physco NUP localization, and also Arabidopsis proteomics in Figure 1? Why split the results on transient localization of Arabidopsis NUPs in benth across Figures 2 & 3?

      We reorganized the Figures and created a separate proteome main figure (now Figure 2 with 2 figure supplements). We classified Arabidopsis NUPs in FG-NUPs and structural NUPs. Thus, we present the data also in two separate Figures: Figure 3 and supplements, dedicated to FG-NUPs, and Figure 4, dedicated to structural NUPs. According to the NPC, FG-NUPs play a direct role in transport facilitation, setting them apart from the structural NUPs.

      (4) Why are several NUPs localized to the interior of the nucleus and not restricted to the nuclear membrane (e.g., Figure 1 Sup 1 top two rows, Figure 2)? How does this unusual nuclear localization alter the authors' interpretation of their results?

      We observed that the transmembrane NUPs tested localized to the nuclear envelope and not to the nucleoplasm (see Figure 3-figure supplement 1 for example AtGP210 and AtCPR5). We found several soluble NUPs to also localize to the nucleoplasm (PpNUP98.1, PpNUP62, AtNUP62, AtHOS1). Previous studies had reported that several FG NUPs (i.e. NUP98a/b or NUP62) and Y-complex NUPs (i.e. HOS1, NUP96, and NUP107) also localized in the nucleoplasm rather than specifically to the nuclear envelope when expressed as fusion proteins (Chen et al., 2023; Gallemí et al., 2016; Huang et al., 2024; Lazaro et al., 2012). Of note, for NUP98a, Gallemi and colleagues (2016) discussed the localization to the nucleoplasm as confirmation that, like vertebrate NUP98, Arabidopsis NUP98a is a dynamic NUP rather than just a key structural element of the NPC. HOS1 was reported to interact with ICE1, CO, FVE, and HDA6 in the nucleoplasm (Dong et al., 2006; Jung et al., 2012; Lazaro et al., 2012), indicating that HOS1 might dynamically shuttle between the nuclear pore and nucleoplasm, which could also explain the observed nucleoplasmic localization. In Drosophila, the FG-NUPs NUP98, NUP62, and NUP50 localized in the NPC, and also in the nucleoplasm and interacted with genes (Kalverda et al., 2010). The nucleoplasmic localization could thus have a functional relevance. Yet we cannot rule out, whether soluble NUPs mislocalize in overexpression conditions as we state multiple times in the manuscript.

      (5) Figure legends are insufficiently detailed. Figure legends should be sufficiently detailed to explain the figure without consulting the main text. For example,

      (a) Figure 1A, 3C don't describe the cell type or even the organism that is being imaged. Are Physco proteins expressed in Physco? Arabidopsis? Benth? Leaves?

      We added the missing information including cell types and organism.

      (b) In Figure 1 Supplement 3, many abbreviations are not defined (HC, MC, etc).

      We now define the abbreviations in the figure legend.

      (c) In Figure 2B, the legend says "At least 15 images from 3 biological replicates were analyzed for each NUP", but there are MANY more than 15 datapoints in Figure 2B. What do the points represent?

      We obtained at least three independent replicates for each data set we show here. We analyzed 15 ROIs derived from three biological replicates of AtNUP50b. In the other cases, a larger number of experiments was performed resulting in more ROIs being analyzed.

      (d) For all microscopy images, are they single images or reconstructions (e.g., maximum projections)?

      We now specify single confocal optical section or maximum projections.

      Reviewer #2 (Recommendations for the authors):

      (1) PD index shall be measured for data in Figures 3D and 3E.

      To address this question, we have performed PD index quantification for the data in Figures 4D and 4E and added the information to the main text (lines 178-184):

      “In leaves transiently expressing NUP43-mCitrine or CPR5-FP fusions, the fluorescence intensity correlated with the estradiol concentration used, with decreased fluorescence intensity for samples where 2µM estradiol was applied versus the intensity in samples exposed to 20µM estradiol (Figure 4 D,E). Notably, the fluorescence ratio between periphery and nucleus did not differ significantly after expression induction by 2 µM compared to 20 µM β-estradiol (Figure 4F) and PD localization was not eliminated (example for localization of NUP43-mCitrine in Figure 4C; PD index(NUP43, 2µM) = 1.42, PD index(CPR5, 2µM) = 1.40).”

      (2) The expression level of the native promoter-driven Nup62-GFP shall be measured and compared with the native level using RT-qPCR. Even if this turns out to be an overexpression line, it would still be useful to support the hypothesis.

      To evaluate the level of NUP62-GFP fusion protein relative to untransformed controls, we quantified the levels of NUP62 in three independent transgenic fluorescent WT/NUP62p:NUP62-GFP Arabidopsis lines and in Arabidopsis WT using mass spectrometry (new Figure 3F). The new data indicate that there is no significant increase in NUP protein amounts in the lines expressing the fusion construct relative to WT.

      We now write in the revised manuscript (line 200-205):

      “NUP62 protein abundance in two-week-old cotyledons of the stable NUP62p:NUP62-GFP transformants was not statistically different to NUP62 protein levels in WT (Figure 3F). Notably, the punctate fluorescence at the cell periphery, encompassing both PD-associated and non-PD-associated localization, were not detectable or absent in roots and young leaves of four-day-old seedlings (Figure 3D). However, it cannot be excluded that the GFP fusion impacts NUP62 localization.“ We provide a new Method section for the mass spec analysis of the cotyledons in lines 582-590.

      (3) Last sentence in the introduction: Nup136 has been considered as the plant homolog of Nup153.

      In the manuscript we wrote:

      “The majority of the FG-NUPs were conserved, with only three FG-NUPs lost in the green lineage (NUP153, POM121, NUP358).“

      As the FG-NUP136 is the plant homolog to NUP153, we now write (lines 90-92):

      “The majority of the FG-NUPs were conserved, with two FG-NUPs apparently lost in the green lineage (POM121, NUP358).“

      Reviewer #3 (Recommendations for the authors):

      (1) Generally, my interpretation of the images in this manuscript is that many of the localisations are not clean and discrete plasmodesmal associations and are rather more consistent with cortical ER association. As the ER is a component of plasmodesmata, the ER is continuous with the nuclear envelope, and the authors also predict and show ER localisation of one of their key NUPs, CPR5 in Figure 4B. This is not necessarily surprising. However, what becomes essential is that the authors need to determine whether NUPs behave any differently from other ER proteins. To that end, I think co-localisations with ER-located proteins would be helpful in interpreting these ambiguous localisations.

      To address this point, we performed additional colocalization experiments using an ER marker. In the new version of the manuscript, we now include a comparison of the NUP43-mVenus localization with that of the mCherry-HDEL luminal ER marker, which reveals distinct localization patterns (see new Figure5, new Figure 5-figure supplement 5-1). NUP43-mVenus may be associated with the ER; however, NUP43 is restricted to subregions of the ER, which partially overlay with aniline blue-labeled pit fields (new Figure 5, new Figure 5-figure supplement 1).

      (2) The super-resolution images of CPR5 show some clear structures peripheral to plasmodesmata. However, again, I would like to see what an ER protein looks like at this location, as the ER feeds into the plasmodesmata. Is this a specific structure or a general feature of the localisation of an ER protein?

      Since mCherry-HDEL (see above) did not show a similar localization or enrichment at PD, we did not perfrom SIM analyses with the marker.

      (3) The authors support their use of the PD score using validated PD proteins as the positive control and contaminants from mitochondria and other organelles as the negative control. No mention is made of where ER proteins are classified. The ER passes through plasmodesmata but might also represent a contaminating pool. As NUPs reside in the nuclear envelope, continuous with the ER, a comparison between the NUPs and ER proteins would be extremely informative.

      To evaluate a potential enrichment of ER proteins in the plasmodesmata fraction, we analyzed ER protein enrichment and added the new data as a graph in Figure 2-figure supplement 2. ER-resident proteins did not show significant enrichment in the cell wall fraction relative to total cell extract, while displaying a slight but consistent enrichment in the plasmodesmata fraction. Notably, NUPs enrichment was higher in both cell wall fraction and plasmodesmata fraction compared to transmembrane ER-resident proteins. While ER membrane co-purification cannot be entirely excluded, the enrichment of NUPs in the plasmodesmata fraction may not be due to desmotubule membrane carryover alone. The analysis was incorporated into the revised manuscript (lines 152-155).

      (4) Regarding the data analysis and use of the Kruskal-Wallis test, the Kruskal-Wallis test tests differences in the distribution of the data, not differences in the mean or median values. In many cases, it can be inferred that the median changes when the data distribution does, but this is not as confident an inference for means. There are other methods available to compare the means of such datasets.

      We used the Kruskal–Wallis test for statistical comparison of more than two nonparametric data sets. However, we did not state in the manuscript that we performed a Dunns´ test for the post hoc pairwise comparison after the Kruskal-Wallis test. In the revised manuscript, we added this information in the Methods, Results and Figure legends. For the bombardment experiment data, we now added mean bootstrapping, as used previously in this context (Johnston and Faulkner, 2021). Mean bootstrap analysis for the bombardment data set was performed with n=5000 resamples and we provide the p values and confidence intervals in the figure legend (Figure 7 B):

      “Mean fluorescent cell counts: n<sub>(WT)</sub> = 2.67, n<sub>(cpr5-T3)</sub> = 1.59, n<sub>(cpr5-1)</sub> = 0.68; median fluorescence cell counts: n<sub>(WT)</sub> = 2, n<sub>(cpr5-1)</sub> = 0, n<sub>(cpr5-T3)</sub> = 1. Based on Bonferroni-corrected Dunn´s test for pairwise comparison after Kruskal-Wallis test: a indicates significant difference to WT with p(<sub>cpr5-1</sub>) < 10<sup>-15</sup>; b indicates significant difference to WT with p<sub>(cpr5-T3)</sub> = 0.0004; c indicates p(cpr5-1 vs. cpr5-T3) = 0.0002. Mean bootstrap analysis according to (Johnston and Faulkner, 2021) with 95% confidence interval (CI) and bootstrap resampling of B = 5000: CI<sub>WT vs. cpr5-1</sub> [1 x 10<sup>-5</sup> , 0.001], p<sub>(cpr5-1)</sub> = 0002 ; CI<sub>WT vs. cpr5-T3</sub> [1 x 10<sup>-5</sup> , 0.001], p<sub>(cpr5-T3)</sub> = 0.0002; CI<sub>cpr5-1 vs. cpr5-T3</sub>, p<sub>(cpr5-1 vs. cpr5-T3)</sub> = 0.0002 [1 x 10<sup>-5</sup> , 0.001].“

      (5) The comments that estradiol induction prevents over-expression, or allows for controlled expression, are not experimentally supported or widely established outside this manuscript. I suggest they tone this claim down.

      As outlined above the reduction in estradiol concentration lead to reduced fluorescence intensity for the NUP-FP fusions as one would expect; here notably with a reduction at both nuclei and periphery (Figure 4C-F). The system has been used previously in the Simon lab, from whom we obtained the constructs. There is substantial literature regarding the use of the b-estradiol-inducible XVE promoter system, specifically for b-estradiol dose-dependent gene expression in N. benthamiana leaves (Bashandy et al., 2015; Bleckmann et al., 2010; Borghi, 2010; Schlücking et al., 2013). We assessed the dependence of localization on expression levels by studying NUP localization with a lower estradiol concentration for induction and shortened incubation time. Interestingly, despite the apparent lower expression, we still find NUPs at PD.

      References

      Bashandy H, Jalkanen S, Teeri TH. 2015. Within leaf variation is the largest source of variation in agroinfiltration of Nicotiana benthamiana. Plant Methods 11:47. DOI: https://doi.org/10.1186/s13007-015-0091-5

      Bleckmann A, Weidtkamp-Peters S, Seidel CAM, Simon R. 2010. Stem Cell Signaling in Arabidopsis Requires CRN to Localize CLV2 to the Plasma Membrane. Plant Physiology 152:166–176. DOI: https://doi.org/10.1104/pp.109.149930

      Borghi L. 2010. Inducible gene expression systems for plants. In: Hennig L, Köhler C (Eds). Plant Developmental Biology: Methods and Protocols. Humana Press. p. 65–75. DOI: https://doi.org/10.1007/978-1-60761-765-5_5

      Bowling SA, Clarke JD, Liu Y, Klessig DF, Dong X. 1997. The cpr5 mutant of Arabidopsis expresses both NPR1-dependent and NPR1-independent resistance. The Plant Cell 9:1573–84.

      Chen G, Xu D, Liu Q, Yue Z, Dai B, Pan S, Chen Y, Feng X, Hu H. 2023. Regulation of FLC nuclear import by coordinated action of the NUP62-subcomplex and importin β SAD2. Journal of Integrative Plant Biology 65:2086–2106. DOI: https://doi.org/10.1111/jipb.13540

      Dong C-H, Agarwal M, Zhang Y, Xie Q, Zhu J-K. 2006. The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proceedings of the National Academy of Sciences 103:8281–8286. DOI: https://doi.org/10.1073/pnas.0602874103

      Gallemí M, Galstyan A, Paulišić S, Then C, Ferrández-Ayela A, Lorenzo-Orts L, Roig-Villanova I, Wang X, Micol JL, Ponce MR, Devlin PF, Martínez-García JF. 2016. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development 143:1623–1631. DOI: https://doi.org/10.1242/dev.130211

      Gombos S, Miras M, Howe V, Xi L, Pottier M, Kazemein Jasemi NS, Schladt M, Ejike JO, Neumann U, Hänsch S, Kuttig F, Zhang Z, Dickmanns M, Xu P, Stefan T, Baumeister W, Frommer WB, Simon R, Schulze WX. 2023. A high-confidence Physcomitrium patens plasmodesmata proteome by iterative scoring and validation reveals diversification of cell wall proteins during evolution. New Phytologist 238:637–653. DOI: https://doi.org/10.1111/nph.18730

      Gu Y, Zebell SG, Liang Z, Wang S, Kang B-H, Dong X. 2016. Nuclear pore permeabilization is a convergent signaling event in effector-triggered immunity. Cell 166:1526-1538.e11. DOI: https://doi.org/10.1016/j.cell.2016.07.042

      Huang P, Zhang X, Cheng Z, Wang X, Miao Y, Huang G, Fu Y-F, Feng X. 2024. The nuclear pore Y-complex functions as a platform for transcriptional regulation of FLOWERING LOCUS C in Arabidopsis. The Plant Cell 36:346–366. DOI: https://doi.org/10.1093/plcell/koad271

      Johnston MG, Faulkner C. 2021. A bootstrap approach is a superior statistical method for the comparison of non-normal data with differing variances. New Phytologist 230:23–26. DOI: https://doi.org/10.1111/nph.17159

      Jung J-H, Seo PJ, Park C-M. 2012. The E3 ubiquitin ligase HOS1 regulates Arabidopsis flowering by mediating CONSTANS degradation under cold stress. Journal of Biological Chemistry 287:43277–43287. DOI: https://doi.org/10.1074/jbc.M112.394338

      Kalverda B, Pickersgill H, Shloma VV, Fornerod M. 2010. Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 140:360–371. DOI: https://doi.org/10.1016/j.cell.2010.01.011

      Lazaro A, Valverde F, Piñeiro M, Jarillo JA. 2012. The Arabidopsis E3 ubiquitin ligase HOS1 negatively regulates CONSTANS abundance in the photoperiodic control of flowering. The Plant Cell 24:982–999. DOI: https://doi.org/10.1105/tpc.110.081885

      Schlücking K, Edel KH, Köster P, Drerup MM, Eckert C, Steinhorst L, Waadt R, Batistič O, Kudla J. 2013. A new β-estradiol-inducible vector set that facilitates easy construction and efficient expression of transgenes reveals CBL3-dependent cytoplasm to tonoplast translocation of CIPK5. Molecular Plant 6:1814–1829. DOI: https://doi.org/10.1093/mp/sst065

      Tamura K, Fukao Y, Iwamoto M, Haraguchi T, Hara-Nishimura I. 2010. Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. The Plant Cell 22:4084–4097. DOI: https://doi.org/10.1105/tpc.110.079947

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      Summary:

      The authors describe the results of a single study designed to investigate the extent to which horizontal orientation energy plays a key role in supporting view-invariant face recognition. The authors collected behavioral data from adult observers who were asked to complete an old/new face matching task by learning broad-spectrum faces (not orientation filtered) during a familiarization phase and subsequently trying to label filtered faces as previously seen or novel at test. This data revealed a clear bias favoring the use of horizontal orientation energy across viewpoint changes in the target images. The authors then compared different ideal observer models (cross-correlations between target and probe stimuli) to examine how this profile might be reflected in the image-level appearance of their filtered images. This revealed that a model looking for the best matching face within a viewpoint differed substantially from human data, exhibiting a vertical orientation bias for extreme profiles. However, a model forced to match targets to probes at different viewing angles exhibited a consistent horizontal bias in much the same manner as human observers.

      Strengths:

      I think the question is an important one: The horizontal orientation bias is a great example of a low-level image property being linked to high-level recognition outcomes, and understanding the nature of that connection is important. I found the old/new task to be a straightforward task that was implemented ably and that has the benefit of being simple for participants to carry out and simple to analyze. I particularly appreciated that the authors chose to describe human data via a lower-dimensional model (their Gaussian fits to individual data) for further analysis. This was a nice way to express the nature of the tuning function, favoring horizontal orientation bias in a way that makes key parameters explicit. Broadly speaking, I also thought that the model comparison they include between the view-selective and view-tolerant models was a great next step. This analysis has the potential to reveal some good insights into how this bias emerges and ask fine-grained questions about the parameters in their model fits to the behavioral data.

      Weaknesses:

      I will start with what I think is the biggest difficulty I had with the paper. Much as I liked the model comparison analysis, I also don't quite know what to make of the view-tolerant model. As I understand the authors' description, the key feature of this model is that it does not get to compare the target and probe at the same yaw angle, but must instead pick a best match from candidates that are at different yaws. While it is interesting to see that this leads to a very different orientation profile, it also isn't obvious to me why such a comparison would be reflective of what the visual system is probably doing. I can see that the view-specific model is more or less assuming something like an exemplar representation of each face: You have the opportunity to compare a new image to a whole library of viewpoints, and presumably it isn't hard to start with some kind of first pass that identifies the best matching view first before trying to identify/match the individual in question. What I don't get about the view-tolerant model is that it seems almost like an anti-exemplar model: You specifically lack the best viewpoint in the library but have to make do with the other options. Again, this is sort of interesting and the very different behavior of the model is neat to discuss, but it doesn't seem easy to align with any theoretical perspective on face recognition. My thinking here is that it might be useful to consider an additional alternate model that doesn't specifically exclude the best-matching viewpoint, but perhaps condenses appearance across views into something like a prototype. I could even see an argument for something like the yaw-averages presented earlier in the manuscript as the basis for such a model, but this might be too much of a stretch. Overall, what I'd like to see is some kind of alternate model that incorporates the existence of the best-match viewpoint somehow, but without the explicit exemplar structure of the view-specific model.

      The design of the view-tolerant model aligned with the requirements of tolerant recognition and revealed the stimulus information enabling to abstract identity away from variations in face appearance. However, it did not involve the notion that such ability may depend on a prototype or summary representation of face identity built up through varied encounters (Burton, Jenkins, & Schweinberger, 2011; Burton et al., 2016; Jenkins et al., 2011; Menon, Kemp, & White, 2018; Mike Burton, 2013).

      We agree with the Reviewer that the average of the different views of a face is a good proxy of its central tendency (i.e., stable identity properties; Figure 1). We thus followed their suggestion and included an additional model observer that compared specific views to full-spectrum view-averaged identities. The examination of the orientation tuning profile of this so-called view-average model observer confirmed the crucial contribution of horizontal identity cues to view-invariant recognition as the horizontal range best predicted the average summary of full-spectrum face appearances across views. This additional model observer is now presented in the Discussion and Supplementary files 2 and 3.

      Besides this larger issue, I would also like to see some more details about the nature of the cross-correlation that is the basis for this model comparison. I mostly think I get what is happening, but I think the authors could expand more on the nature of their noise model to make more explicit what is happening before these cross-correlations are taken. I infer that there is a noise-addition step to get them off the ceiling, but I felt that I had to read between the lines a bit to determine this.

      In the Methods section, we now provide detailed information about the addition of noise to model observer cross-correlations: ‘In a pilot phase, we measured the overall identification performance of each model. Initially, the view-selective model performed at ceiling, yielding a correlation of 1 since there was an exact target-probe match across all trials. To avoid ceiling effects and to keep model performance close to human levels (Supplementary File 2), we thus decreased the signal-to-noise ratio (SNR) of the target and probe images to .125 by combining each with distinct noise patterns (face RMS contrast: .01; noise RMS contrast: .08). Each trial (i.e. target-probe pairing) was iterated ten times with different random noise patterns.’

      We also added a supplemental with the graphic illustration of the d’ distributions of each model and human observers: ‘Sensitivity d’ of the view-tolerant model was much lower than view-selective model and human sensitivity (Supplementary File 2), even without noise. The view-tolerant model therefore processed fully visible stimuli (SNR of 1). This decreased sensitivity in the view-tolerant compared to the view-selective model is expected, as none of the probes exactly matched the target at the pixel level due to viewpoint differences. In contrast to humans who rely on internally stored representations to match identity across views, the model observer lacks such internal representations and entirely relies on (less efficient) pixelwise comparisons.’

      Another thing that I think is worth considering and commenting on is the stimuli themselves and the extent to which this may limit the outcomes of their behavioral task. The use of the 3D laser-scanned faces has some obvious advantages, but also (I think) removes the possibility for pigmentation to contribute to recognition, removes the contribution of varying illumination and expression to appearance variability, and perhaps presents observers with more homogeneous faces than one typically has to worry about. I don't think these negate the current results, but I'd like the authors to expand on their discussion of these factors, particularly pigmentation. Naively, surface color and texture seem like they could offer diagnostic cues to identity that don't rely so critically on horizontal orientations, so removing these may mean that horizontal bias is particularly evident when face shape is the critical cue for recognition.

      Our stimuli were originally designed by Troje and Bulthoff (1996). These are 3D laser scans of white individuals aged between 20 and 40 years, posing with a neutral expression. Different views of the faces were shot under a fixed illumination. Ears and a small portion of the neck were visible while the hair region was removed. All face images had a normalized skin color and we further converted them to grayscales

      While we agree that this stimulus set offers a restricted range of within- and between-identity variations compared to what is experienced in natural settings, we believe that the present findings generalize to more ecological viewing conditions. Indeed, past evidence showed that the recognition of face pictures shot under largely variable pose, age, expression, illumination, hair style is tuned to the horizontal range of the face stimulus (Dakin & Watt, 2009; Dumont, Roux-Sibilon, & Goffaux, 2024). In other words, our finding that view-tolerant identity recognition is mainly driven by horizontal face information would likely replicate with the use of a more ecological stimulus set.

      Moreover, the skin color normalization and grayscale conversion, while limiting the range of face variability, did not eliminate the contribution of surface pigmentation in our study. It is thus unlikely that our findings exclusively reflect the orientation dependence of face shape processing. Pigmentation refers to all surface reflectance properties (Russell et al., 2006) and hue (color) is only one among others. The grayscaled 3D laser scanned faces used here contained natural variations in crucial surface cues such as skin albedo (i.e., how light or dark the surface appears) and texture (i.e., spatial variation in how light is reflected); they have actually been used to disentangle the role of shape and surface cues to identity recognition (e.g., Jiang et al., 2009; Russell et al., 2007; Russell et al., 2006; Troje & Bulthoff, 1996; Vuong et al., 2005). Moreover, a past study of ours demonstrated that the diagnosticity of the horizontal range of face information is not restricted to face shape cues; the specialized processing of face shape and surface both selectively rely on horizontal information (Dumont, Roux-Sibilon, & Goffaux, 2024).

      For these reasons, the present findings are unlikely to be fully determined by shape processing, and we expect them to generalize to more ecological stimulus sets. We discuss these aspects in the revised manuscript.

      Reviewer #2 (Public review):

      This study investigates the visual information that is used for the recognition of faces. This is an important question in vision research and is critical for social interactions more generally. The authors ask whether our ability to recognise faces, across different viewpoints, varies as a function of the orientation information available in the image. Consistent with previous findings from this group and others, they find that horizontally filtered faces were recognised better than vertically filtered faces. Next, they probe the mechanism underlying this pattern of data by designing two model observers. The first was optimised for faces at a specific viewpoint (view-selective). The second was generalised across viewpoints (view-tolerant). In contrast to the human data, the view-specific model shows that the information that is useful for identity judgements varies according to viewpoint. For example, frontal face identities are again optimally discriminated with horizontal orientation information, but profiles are optimally discriminated with more vertical orientation information. These findings show human face recognition is biased toward horizontal orientation information, even though this may be suboptimal for the recognition of profile views of the face.

      One issue in the design of this study was the lowering of the signal-to-noise ratio in the view-selective observer. This decision was taken to avoid ceiling effects. However, it is not clear how this affects the similarity with the human observers.

      In the Methods section, we now provide detailed information about the addition of noise to model observer cross-correlations: ‘In a pilot phase, we measured the overall identification performance of each model. Initially, the view-selective model performed at ceiling, yielding a correlation of 1 since there was an exact target-probe match across all trials. To avoid ceiling effects and to keep model performance close to human levels (Supplementary File 2), we thus decreased the signal-to-noise ratio (SNR) of the target and probe images to .125 by combining each with distinct noise patterns (face RMS contrast: .01; noise RMS contrast: .08). Each trial (i.e. target-probe pairing) was iterated ten times with different random noise patterns.’

      We also added a supplemental with the graphic illustration of the d’ distributions of each model and human observers.

      Another issue is the decision to normalise image energy across orientations and viewpoints. I can see the logic in wanting to control for these effects, but this does reflect natural variation in image properties. So, again, I wonder what the results would look like without this step.

      All stimuli were matched for luminance and contrast. It is crucial to normalize image energy across orientations as natural image energy is disproportionately distributed across orientations (e.g., Hansen et al., 2003). Images of faces cropped from their background as used here contain most of their energy in the horizontal range (Goffaux & Greenwood, 2016; Keil, 2008, 2009). If not normalized after orientation filtering, such uneven distribution of energy would boost recognition performance in the horizontal range across views. Normalization was performed across our experimental conditions merely to avoid energy from explaining the influence of viewpoint on the orientation tuning profile.

      We were not aware of any systematic natural variations of energy across face views. To address this, we measured face average energy (i.e., RMS contrast) in the original stimulus set, i.e., before the application of any image processing or manipulation. Background pixels were excluded from these image analyses. Across yaws, we found energy to range between .11 and .14 on a 0 to 1 grayscale. This is moderate compared to the range of energy variations we measured across identities (from .08 to .18). This suggests that variations in energy across viewpoints are moderate compared to variations related to identity. It is unclear whether these observations are specific to our stimulus set or whether they are generalizable to faces we encounter in everyday life. They, however, indicate that RMS contrast did not substantially vary across views in the present study and suggest that RMS normalization is unlikely to have affected the influence of viewpoint on recognition performance.

      In the revised methods section, we explicitly motivate energy normalization: ‘Images of faces cropped from their background as used here contain most of their energy in the horizontal range (Goffaux, 2019; Goffaux & Greenwood, 2016; Keil, 2009). Across yaws, we found face energy to range between .11 and .14 on a 0 to 1 grayscale, which is moderate compared to the range of face energy variations we measured across identities (from .08 to .18). To prevent energy from explaining our results, in all images, the luminance and RMS contrast of the face pixels were fixed to 0.55 and 0.15, respectively, and background pixels were uniformly set to 0.55. The percentage of clipped pixel values (below 0 or above 1) per image did not exceed 3%.’.

      Despite the bias toward horizontal orientations in human observers, there were some differences in the orientation preference at each viewpoint. For example, frontal faces were biased to horizontal (90 degrees), but other viewpoints had biases that were slightly off horizontal (e.g., right profile: 80 degrees, left profile: 100 degrees). This does seem to show that differences in statistical information at different viewpoints (more horizontal information for frontal and more vertical information for profile) do influence human perception. It would be good to reflect on this nuance in the data.

      Indeed, human performance data indicates that while identity recognition remains tuned to horizontal information, horizontal tuning peak shows some variation across viewpoints. We primarily focused on the first aspect because of its direct relevance to our research objective, but also discussed the second aspect: with yaw rotation, certain non-horizontal morphological features such as the jaw line or nose bridge, etc. may increasingly contribute to identity recognition, whereas at frontal or near frontal views, features are mostly horizontally-oriented (e.g., Keil, 2008, 2009). In the revised Discussion, we directly relate the modest fluctuations of peak location to yaw differences in face feature appearance.

      Recommendations for the authors:

      Reviewing Editor Comments:

      Based on a discussion with the reviewers, we integrated the recommendations and reached a consensus on the eLife assessment. To move from a "solid" to a "compelling/convincing" strength-of-evidence rating, please address the reviewers' comments. Key points are to clarify and test the plausibility of the models (e.g., effects of different noise-addition steps, inclusion/exclusion of specific orientation channels in the view-dependent comparison, and alternative decision criteria), and to address or discuss the limitations of the stimulus set in capturing recognition under more naturalistic scenarios, for example, including texture cues.

      Reviewer #1 (Recommendations for the authors):

      I generally found the paper to be very well-written, so I have only a few minor comments here.

      (1) I didn't really follow why the estimation of the Gaussian functions described in the text was preferred over a simpler ML framework. Do these approaches differ that much? I see references to prior studies in which these were applied, so I can certainly go check these out, but I could see value in adding just a bit of text to briefly make the case that this is important.

      Employing a simpler linear framework, i.e. a linear model predicting d’ from the interaction between orientation and viewpoint, would result in an 8 (orientation) * 7 (viewpoint) design that is difficult to analyze. The interaction term would almost certainly reach significance but its interpretation would be limited. We would either have to rely on numerous local comparisons, which are not particularly informative for our research objectives (e.g., knowing whether d’ differs significantly between two adjacent orientations at a given viewpoint is of little relevance), or to use a polynomial contrast approach (testing the linear, quadratic, … up to the 7th order trends), which would also be difficult to interpret. For such complex, approximately Gaussian-shaped data, the highest-order polynomial trend would likely provide the best fit, but without offering meaningful insight.

      In contrast, a nonlinear approach appears more appropriate. The Gaussian model we used allows us to characterize the parameters of the tuning profile, namely, peak location, peak amplitude, standard deviation (or bandwidth) and base amplitude. These parameters are not merely statistical parameters. Rather, they are directly interpretable in cognitive/functional terms. The peak location corresponds to the orientation at which the Gaussian curve is centred, i.e. the preferred orientation band for identity recognition. The standard deviation represents the width of the curve, reflecting the strength or selectivity of the tuning. The base amplitude is the height of the Gaussian curve base, indicating the minimum level of sensitivity, typically found near vertical orientation. Finally, the peak amplitude refers to the height of the Gaussian curve relative to its baseline, that is, it captures the advantage of horizontal over vertical orientations.

      Moreover, the use of a nonlinear, Gaussian model is motivated by past work that showed that the Gaussian function fits the evolution of recognition performance as a function of orientation (Dakin & Watt, 2009; Goffaux & Greenwood, 2016). Orientation selectivity at primary stages of visual processing has also been modelled using Gaussian (or Difference of Gaussians; Ringach, Hawken, & Shapley, 2003).

      We revised the data analysis section to include a justification for our use of a Gaussian model: “Therefore, fitting the human sensitivity data could be fitted using a simple Gaussian model. seemed most appropriate as it allows characterizing the parameters of the tuning profile, namely, peak location, peak amplitude, standard deviation and base amplitude, which are directly interpretable in cognitive/functional terms. Moreover, the use of a nonlinear, Gaussian model is motivated by past work that showed that the Gaussian function fits the evolution of recognition performance as a function of orientation (Dakin & Watt, 2009; Goffaux & Greenwood, 2016). Simpler frameworks, i.e. a linear model predicting d’ from the interaction between orientation and viewpoint, would result in an 8 (orientation) * 7 (viewpoint) design that is difficult to analyze and interpret.”

      (2) When reporting the luminance and contrast of your stimuli, please make clear what these units and measures are. This was a case where I had to take a second to assure myself that I knew what the values meant.

      We clarified that the luminance and contrast values reported in the manuscript are on a grey scale ranging from 0 to 1.

      (3) In your Procedure section, I think describing the familiarization task right away would help the text flow more clearly. At present, you began talking about the old/new task, and I was immediately wondering how familiarization worked!

      The procedure section now starts with the description of the familiarization task.

      (4) p. 3 - "Culminates" doesn't seem like the right word here.

      We agree and rephrased this way: ‘The tolerance of face identity recognition is stronger for familiar than unfamiliar faces’.

      (5) p. 5 - I think "with the multiple" shouldn't have "the".

      Indeed, we removed the “the”.

      Reviewer #2 (Recommendations for the authors):

      I enjoyed reading the manuscript, but thought the Introduction was a bit long. I wasn't sure about the relevance of the section on temporal contiguity. I think this might have been more relevant if this had been a manipulation in the design. So, I wonder if this might be shortened or removed to focus on the key questions. On the other hand, I found the overview of the view-selective and view-tolerant to be a bit brief. There is plenty of detail here, but I found it difficult to break down what was done when I first read it. It might be good to provide an overview in the Discussion too.

      While past research on the contribution of temporal contiguity to face identity recognition brings interesting insights into the nature of the visual experience leading to view-tolerant performance, we agree with the Reviewer that this aspect is not directly at stake here. We reduced the review of this literature in the Introduction.

      We clarified the description of the model observers as suggested by the reviewer and made sure to provide an overview of the model observers in the Discussion as well.

      References.

      Burton, A. M., Jenkins, R., & Schweinberger, S. R. (2011). Mental representations of familiar faces. Br J Psychol, 102(4), 943-958. https://doi.org/10.1111/j.2044-8295.2011.02039.x

      Burton, A. M., Kramer, R. S., Ritchie, K. L., & Jenkins, R. (2016). Identity From Variation: Representations of Faces Derived From Multiple Instances. Cogn Sci, 40(1), 202-223. https://doi.org/10.1111/cogs.12231

      Collin, C. A., Rainville, S., Watier, N., & Boutet, I. (2014). Configural and featural discriminations use the same spatial frequencies: a model observer versus human observer analysis. Perception, 43(6), 509-526. https://doi.org/10.1068/p7531

      Dakin, S. C., & Watt, R. J. (2009). Biological "bar codes" in human faces. J Vis, 9(4), 2 1-10. https://doi.org/10.1167/9.4.2

      Dumont, H., Roux-Sibilon, A., & Goffaux, V. (2024). Horizontal face information is the main gateway to the shape and surface cues to familiar face identity. PLOS ONE, 19(10), e0311225. https://doi.org/10.1371/journal.pone.0311225

      Goffaux, V., & Greenwood, J. A. (2016). The orientation selectivity of face identification [Article de recherche] [peer-reviewed]. Scientific Reports, 6(34204), 34204. https://doi.org/10.1038/srep34204

      Gold, J., Bennett, P. J., & Sekuler, A. B. (1999). Identification of band-pass filtered letters and faces by human and ideal observers. Vision Research, 39(21), 3537-3560. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10746125

      Hansen, B. C., Essock, E. A., Zheng, Y., & DeFord, J. K. (2003). Perceptual anisotropies in visual processing and their relation to natural image statistics. Network, 14(3), 501-526. http://www.ncbi.nlm.nih.gov/pubmed/12938769

      Jenkins, R., White, D., Van Montfort, X., & Mike Burton, A. (2011). Variability in photos of the same face. Cognition, 121(3), 313-323. https://doi.org/10.1016/j.cognition.2011.08.001

      Jiang, F., Dricot, L., Blanz, V., Goebel, R., & Rossion, B. (2009). Neural correlates of shape and surface reflectance information in individual faces. Neuroscience, 163(4), 1078-1091. https://doi.org/10.1016/j.neuroscience.2009.07.062

      Keil, M. S. (2008). Does face image statistics predict a preferred spatial frequency for human face processing? Proc Biol Sci, 275(1647), 2095-2100. https://doi.org/10.1098/rspb.2008.0486

      Keil, M. S. (2009). "I look in your eyes, honey": internal face features induce spatial frequency preference for human face processing. PLoS Comput Biol, 5(3), e1000329. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19325870

      Menon, N., Kemp, R. I., & White, D. (2018). More than a sum of parts: robust face recognition by integrating variation. R Soc Open Sci, 5(5), 172381. https://doi.org/10.1098/rsos.172381

      Mike Burton, A. (2013). Why has research in face recognition progressed so slowly? The importance of variability. Quarterly journal of experimental psychology, 66(8), 1467-1485. https://doi.org/10.1080/17470218.2013.800125

      Näsänen, R. (1999). Spatial frequency bandwidth used in the recognition of facial images. Vision Research, 39(23), 3824-3833. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10748918

      Oruc, I., Shafai, F., Murthy, S., Lages, P., & Ton, T. (2019). The adult face-diet: A naturalistic observation study. Vision Res, 157, 222-229. https://doi.org/10.1016/j.visres.2018.01.001

      Ringach, D. L., Hawken, M. J., & Shapley, R. (2003). Dynamics of orientation tuning in macaque V1: the role of global and tuned suppression [Research Support, Non-U.S. Gov't

      Research Support, U.S. Gov't, P.H.S.]. Journal of neurophysiology, 90(1), 342-352. https://doi.org/10.1152/jn.01018.2002

      Russell, R., Biederman, I., Nederhouser, M., & Sinha, P. (2007). The utility of surface reflectance for the recognition of upright and inverted faces. Vision Res, 47(2), 157-165. https://doi.org/10.1016/j.visres.2006.11.002

      Russell, R., Sinha, P., Biederman, I., & Nederhouser, M. (2006). Is pigmentation important for face recognition? Evidence from contrast negation. Perception, 35(6), 749-759. https://doi.org/10.1068/p5490

      Troje, N. F., & Bulthoff, H. H. (1996). Face recognition under varying poses: the role of texture and shape. Vision Res, 36(12), 1761-1771. https://doi.org/10.1016/0042-6989(95)00230-8

      Vuong, Q. C., Peissig, J. J., Harrison, M. C., & Tarr, M. J. (2005). The role of surface pigmentation for recognition revealed by contrast reversal in faces and Greebles. Vision Res, 45(10), 1213-1223. https://doi.org/10.1016/j.visres.2004.11.015

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This paper investigates the physical basis of epithelial invagination in the morphogenesis of the ascidian siphon tube. The authors observe changes in actin and myosin distribution during siphon tube morphogenesis using fixed specimens and immunohistochemistry. They discover that there is a biphasic change in the actomyosin localization that correlates with changes in cell shapes. Initially, there is the well-known relocation of actomyosin from the lateral sides to the apical surface of cells that will invaginate, accompanied by a concomitant lengthening of the central cells within the invagination, but not a lot of invagination. Coincident with a second, more rapid, phase of invagination, the authors see a relocalization of actomyosin back to the lateral sides of the cells. This 2nd "bidirectional" relocation of actin appears to be important because optogenetic inhibition of myosin in the lateral domain after the initial invaginations phase resulted in a block of further invagination. Although not noted in the paper, that the second phase of siphon invagination is dependent on actomyosin is interesting and important because it has been shown that during Drosophila mesoderm invagination that a second "folding" phase of invagination is independent of actomyosin contraction (Guo et al. elife 2022), so there appear to be important differences between the Drosophila mesoderm system and the ascidian siphon tube systems.

      Using the experimental data, the authors create a vertex model of the invagination, and simulations reveal a coupled mechanism of apicobasal tension imbalance and lateral contraction that creates the invagination. The resultant model appears to recapitulate many aspects of the observed cell behaviors, although there are some caveats to consider (described below).

      We thank the reviewer for the insightful summary and for bringing the important study by Guo et al. (2022) to our attention. We have now added a dedicated comparison with Drosophila ventral furrow invagination in the Discussion, explicitly highlighting that the second rapid folding phase in Drosophila does not require lateral contractility, whereas in our system lateral contractility is obligatory for the accelerated invagination stage.

      Strengths:

      The studies and presented results are well done and provide important insights into the physical forces of epithelial invagination, which is important because invaginations are how a large fraction of organs in multicellular organisms are formed.

      Thank you for this positive assessment and for recognizing the significance of our work in elucidating the physical mechanisms underlying fundamental morphogenetic processes. We have striven to provide a comprehensive and rigorous analysis, and are grateful for this encouraging feedback.

      Weaknesses:

      (1) This reviewer has concerns about two aspects of the computational model. First, the model in Figure 5D shows a simulation of a flat epithelial sheet creating an invagination. However, the actual invagination is occurring in a small embryo that has significant curvature, such that nine or so cells occupy a 90-degree arc of the 360-degree circle that defines the embryo's cross-section (e.g., see Figure 1A). This curvature could have important effects on cell behavior.

      Thank you for bringing up the issue of tissue curvature. In the initial version of our model, we treated the tissue as flat based on the local geometry of the anterior epidermis. Although the embryo at 13 hpf indeed possesses significant curvature, its overall transverse cross-section is approximately elliptical, and the region undergoing invagination is situated in a relatively low-curvature zone, occupying only a 30° ∼ 40° arc of the entire tissue. More importantly, the embryo undergoes anisotropic elongation and expansion, becoming significantly flattened during the accelerated invagination stage, eventually adopting a very flat geometry by 18 hpf. We have now included Figure 5—figure supplement 1 to clarify these global morphological transitions.

      Nevertheless, the curvature does exist during the early stages, and we agree that clarifying its potential role is essential. Therefore, in the revised manuscript, we have updated our vertex model to incorporate a simplified circular geometry. Furthermore, unlike Drosophila ventral furrow formation (Guo et al., eLife, 2022), the invagination here eventually forms a hollow tubular structure, which led us to introduce a surface bending stiffness term into the mode. Although global tissue growth is not explicitly modeled, we explored the impact of curvature by varying the initial system size. Our results demonstrate that the invagination process, driven by apico-basal tension imbalance and lateral contraction, is highly localized and remains robust across different curvatures.

      (2) The second concern about the model is that Figure 5 D shows the vertex model developing significant "puckering" (bulging) surrounding the invagination. Such "puckering" is not seen in the in vivo invagination (Figure 1A, 2A). This issue is not discussed in the text, so it is unclear how big an issue this is for the developed model, but the model does not recapitulate all aspects of the siphon invagination system.

      Thank you for pointing out this. In our experiments, the similar "puckering" shape is observed during the early stages of morphogenesis (~17 hpf, as seen in Figure 1A) when the tissue size is relatively small. However, this feature rapidly disappears as the tissue grows and the overall geometry becomes flatter. This suggests that "puckering" is more pronounced in highly curved epithelia, a phenomenon that aligns with mechanical expectations. Previous vertex models of Drosophila ventral furrow formation do not exhibit this effect (Brodland et al., 2010; Polyakov et al., 2014), because they modeled cells within a rigid unmovable boundary. However, in our system of siphon morphogenesis, a tubular structure ultimately forms in the epithelium without strong boundary constraints. Thus, the mechanical boundary conditions are basically different.

      Also, the formation of a hollow tubular structure—supported by strong F-actin accumulation at the tissue surface—indicates a bending stiffness of surface tissue (Figure 1), which we have incorporated into the model. This bending term enforces smooth curvature transitions, which can manifest as a "puckering" shape surrounding the invagination. In our previous flat-geometry model, this significant bending stiffness led to a "puckering" effect surrounding the invagination. In our updated curved vertex model, this phenomenon also exists and is found to be related to tissue curvature. By simulating a larger system with low curvature (N = 324 cells in Figure 6D), we find that this puckering is significantly reduced. This confirms that the shape discrepancy is a size-dependent effect of the bending constraints within a fixed system size that did not account for tissue growth. In biological development, continuous growth and flattening of the embryo diminish this effect (Figure 5—figure supplement 1), aligning our model's predictions.

      Furthermore, we note that the cell-cell adhesion between the surface epithelium and the internal bulk cells (a factor not explicitly captured in our current model) likely further suppresses such evagination in vivo, as outward puckering would necessitate the coordinated deformation of the underlying tissues. We aim to investigate the interplay between global growth and local active forces in future work. We have added a detailed description and mechanical explanation of these simulated shapes in the revised manuscript.

      (3) In Figure 2A, Top View, and the schematic in Figure 2C, the developing invagination is surrounded by a ring of aligned cell edges characteristic of a "purse string" type actomyosin cable that would create pressure on the invaginating cells, which has been documented in multiple systems. Notably, the schematic in Figure 2C shows myosin II localizing to aligned "purse string" edges, suggesting the purse string is actively compressing the more central cells. If the purse string consistently appears during siphon invagination, a complete understanding of siphon invagination will require understanding the contributions of the purse string to the invagination process.

      Thank you for this excellent observation. We agree that the ring-like actomyosin structure is a prominent feature during the initial stages of invagination, and its potential role warrants discussion. We carefully re-examined our data. Our analysis confirms that this myosin ring is most pronounced during the early initial invagination stage. This inward compression from the periphery would work in concert with apical constriction to help shape the initial invagination. However, this ring-like myosin pattern significantly diminishes during the accelerated invagination stage, indicating that sustained compression from the purse string is not required for the entire process. We have added a discussion of this point in the revised manuscript. We also agree with that future experiments using laser ablation or optogenetic inhibition specifically targeting this actomyosin ring would be valuable to further dissect its precise contribution during the early invagination stage, and we have noted this as a future direction in the Discussion.

      (4) The introduction and discussion put the work in the context of work on physical forces in invagination, but there is not much discussion of how the modeling fits into the literature.

      We thank the reviewer for this suggestion. We have now incorporated additional references and discussion regarding existing theoretical models and the physical forces involved in tissue invagination. These previous studies provided the foundational framework for our updated curved vertex model. We have also added an explanation of how our model differs from these existing works and discussed potential future directions for further investigation.

      Reviewer #2 (Public review):

      Summary:

      The authors propose that bidirectional translocation of actomyosin drives tissue invagination in Ciona siphon tube formation. They suggest a two-stage model where actomyosin first accumulates apically to drive a slow initial invagination, followed by translocation to lateral domains to accelerate the invagination process through cell shortening. They have shown that actomyosin activity is important for invagination - modulation of myosin activity through expression of myosin mutants altered the timing and speed of invagination; furthermore, optogenetic inhibition of myosin during the transition of the slow and fast stages disrupted invagination. The authors further developed a vertex model to validate the relationship between contractile force distribution and epithelial invagination.

      Thank you for your thoughtful and accurate summary of our work and for your constructive critique.

      Strengths:

      (1) The authors employed various techniques to address the research question, including optogenetics, the use of MRLC mutants, and vertex modelling.

      (2) The authors provide quantitative analyses for a substantial portion of their imaging data, including cell and tissue geometry parameters as well as actin and myosin distributions. The sample sizes used in these analyses appear appropriate.

      (3) The authors combined experimental measurements with computer modeling to test the proposed mechanical models, which represents a strength of the study. It provides a framework to explore the mechanical principles underlying the observed morphogenesis.

      We are grateful for your positive assessment of the multidisciplinary approaches, quantitative analyses, and the integration of modeling with experiments.

      Weaknesses:

      (1) The concept of coordinated and sequential action of apical and lateral actomyosin in support of epithelial folding has been documented through a combination of experimental and modeling approaches in other contexts, such as ascidian endoderm invagination (PMID: 20691592) and gastrulation in Drosophila (PMIDs: 21127270, 22511944, 31273212). While the manuscript addresses an important question, related findings have been reported in these previous studies. This overlap reduces the degree of novelty, and it remains to be clarified how their work advances beyond these prior contributions.

      We thank the reviewer for raising this important point. In the revised Introduction and Discussion, we have explicitly distinguished our findings from prior studies. Specifically: (1) Unlike ascidian endoderm invagination, where actomyosin shifts from apical to basolateral (Sherrard et al., 2010), our system exhibits a bidirectional redistribution between apical and lateral domains, with the basal domain playing a passive role. (2) Unlike Drosophila ventral furrow invagination, where lateral contractility is not essential for the second folding phase (Guo et al., 2022), our optogenetic inhibition demonstrates that lateral contractility is obligatory for the accelerated invagination stage. These comparisons, now clearly stated in the Introduction and Discussion, establish bidirectional actomyosin redistribution as a distinct mechanical paradigm for sequential morphogenesis. We believe these revisions adequately clarify how our work advances beyond prior contributions.

      (2) One of the central statements made by the authors is that the translocation of actomyosin between the apical and lateral domains mediates invagination. The use of the term "translocation" infers that the same actomyosin structures physically move from one location to another location, which is not demonstrated by the data. Given the time scale of the process (several hours), it is also possible that the observed spatiotemporal patterns of actomyosin intensity result from sequential activation/assembly and inactivation/disassembly at specific locations on the cell cortex, rather than from the physical translocation of actomyosin structures over time.

      We thank the reviewer for this important point. We agree that our data do not demonstrate physical translocation of actomyosin structures, and that the observed patterns could arise from sequential assembly/disassembly over time. To avoid overinterpretation, we have replaced “translocation” with “redistribution” throughout the manuscript (including the title) and toned down the language in the Results and Discussion.

      (3) Some aspects of the data on actomyosin localization require further clarification. (1) The authors state that actomyosin translocation is bidirectional, first moving from the lateral domain to the apical domain; however, the reduction of the lateral actomyosin at this step was not rigorously tested. (2) During the slow invagination stage, it is unclear whether myosin consistently localizes to the apical cell-cell borders or instead relocalizes to the medioapical domain, as suggested by the schematic illustration presented in Figure 2C. (3) It is unclear how many cells along the axis orthogonal to the furrow accumulate apical and lateral myosin.

      Thank you for your insightful comments, which will help us significantly improve the clarity and rigor of our actomyosin localization analysis. To address the points raised, we undertake several key revisions: First, we have added new quantitative analyses of active myosin intensity from earlier time points (14-15 hpf) to rigorously support the initial lateral-to-apical redistribution phase (Figure 2B). Second, the schematic in Figure 2C has been corrected to show myosin at the apical cell‑cell borders. We have clarified that redistribution occurs in a domain of approximately 15‑20 cells (the invagination primordium), not only the center cell.

      (4) The overexpression of MRLC mutants appears to be rather patchy in some cases (e.g., in Figure 3A, 17.0 hpf, only cells located at the right side of the furrow appeared to express MRLC T18ES19E). It is unclear how such patchy expression would impact the phenotype.

      Thank you for your observation. We acknowledge that mosaic expression is common in Ciona electroporation. For all quantitative analyses, we only selected embryos in which the central cell, along with more than half of the surrounding cells in the primordium, showed clear expression of the plasmid. This selection criterion has been added to the Materials and Methods section.

      (5) In the optogenetic experiment, it appears that after one hour of light stimulation, the apical side of the tissue underwent relaxation (comparing 17 hpf and 16 hpf in Figure 4B). It is therefore unclear whether the observed defect in invagination is due to apical relaxation or lack of lateral contractility, or both. Therefore, the phenotype is not sufficient to support the authors' statement that "redistribution of myosin contractility from the apical to lateral regions is essential for the development of invagination".

      We have performed the additional immunostaining experiment of myosin II. The new data (Figure 4—figure supplement 2) showed that light stimulation specifically reduced lateral myosin intensity without significantly affecting apical myosin compared to the dark control. Therefore, the observed block of invagination is primarily due to loss of lateral contractility.

      (6) The vertex model is designed to explore how apical and lateral tensions contribute to distinct morphological outcomes. While the authors raise several interesting predictions, these are not further tested, making it unclear to what extent the model provides new insights that can be validated experimentally. In addition, modeling the epithelium as a flat sheet and not accounting for cell curvature is a simplification that may limit the model's accuracy. Finally, the model does not fully recapitulate the deeply invaginated furrow configuration as observed in a real embryo (comparing 18 hpf in Figure 5D and 18 hpf in Figure 1A) and does not fully capture certain mutant phenotypes (comparing 18 hpf in Figure 5F and 18 hpf in Figure 3B right panel).

      Thank you very much for these helpful and constructive comments. We have addressed your concerns through the following model updates and clarifications.

      First, we have reformulated our vertex model from a flat sheet to a curved geometry that incorporates initial tissue curvature. We found that the core mechanical mechanism, mediated by the coupling of apical and lateral active contraction, consistently recapitulates the experimental invagination process. By independently inhibiting apical or lateral contractions in the model, we further clarified their distinct mechanical contributions to tissue bending and cell shortening.

      Regarding the model predictions concerning the apical-to-lateral redistribution of actomyosin in the original version (previously shown in Figure 6E-H), we agree that these lacked direct experimental validation in the current study and may have strayed from the primary focus on the invagination mechanism itself. Therefore, we have removed these predictive components from the revised manuscript. Instead, we have refocused our analysis on the robustness of the localized active process across tissues of varying sizes and curvatures, particularly because the in vivo invagination is accompanied by global tissue growth and geometry changes.

      Finally, we acknowledge that the simulated final shapes do not perfectly match the experimental geometry in every detail. We attribute these discrepancies to the omission of global tissue growth and the simplification of cell-cell adhesions between the surface epithelium and internal bulk cells. While these factors are not the primary drivers of the invagination, they undoubtedly refine the local morphology. We have added discussions of these limitations in the revised manuscript and aim to incorporate precise experimental measurements of tissue growth and inter-layer interactions in future modeling efforts.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript by Qiao et al., the authors seek to uncover force and contractility dynamics that drive tissue morphogenesis, using the Ciona atrial siphon primordium as a model. Specifically, the authors perform a detailed examination of epithelial folding dynamics. Generally, the authors' claims were supported by their data, and the conceptual advances may have broader implications for other epithelial morphogenesis processes in other systems.

      Thank you for your positive summary and for recognizing the broader implications of our work.

      Strengths:

      The strengths of this manuscript include the variety of experimental and theoretical methods, including generally rigorous imaging and quantitative analyses of actomyosin dynamics during this epithelial folding process, and the derivation of a mathematical model based on their empirical data, which they perturb in order to gain novel insights into the process of epithelial morphogenesis.

      Thank you for highlighting the strengths of our multidisciplinary methodology.

      Weaknesses:

      There are concerns related to wording and interpretations of results, as well as some missing descriptions and details regarding experimental methods.

      We have revised the manuscript to address your concerns regarding the wording and the details of the methodology.

      Recommendations for the authors:

      Reviewing Editor Comments:

      Based on the feedback from the reviewers, a focus on the following major points has the potential to improve the overall assessment of the significance of the findings and the strength of the evidence:

      (1) It would be helpful to clearly articulate how these findings advance the field beyond what has already been demonstrated or suggested in other systems.

      We thank the editor for this helpful suggestion. To better articulate how our findings advance the field, we have revised both the Introduction and Discussion to explicitly contrast our system with previously studied invagination models. Specifically, we highlight that our work demonstrates a bidirectional redistribution of actomyosin between apical and lateral domains, which differs from the apical-to-basolateral shift reported in ascidian endoderm invagination. Moreover, we emphasize that lateral contractility is obligatory for the accelerated invagination stage in our system, whereas in Drosophila ventral furrow invagination the second folding phase can proceed without it. These comparisons have been clearly presented in the revised manuscript. We think our findings represent a distinct mechanical paradigm for sequential epithelial morphogenesis.

      (2) It would be helpful to clarify the meaning of "translocation" and more explicitly describe the temporal and spatial patterns of active myosin localization during the two steps of invagination.

      We have replaced the term “translocation” with “redistribution” throughout the manuscript, including the title. We have also added new quantitative analyses of active myosin intensity from earlier time points (14–15 hpf) to rigorously support the initial lateral-to-apical redistribution phase (Figure 2B). High-resolution top-view images have been included to show the ring‑like localization of myosin at the apical cell‑cell junctions during the initial stage (Figure 2A). The schematic in Figure 2C has been corrected to accurately reflect the predominant localization of active myosin at the apical cell‑cell borders.

      (3) It would be helpful to explain how the optogenetic data support the conclusion that "redistribution of myosin contractility from the apical to lateral regions is essential for the development of invagination".

      We have performed additional experiments combining optogenetic inhibition with subsequent immunostaining of active myosin II (anti-pS19 MRLC). We quantitatively compared the distribution of actomyosin in light‑stimulated versus dark‑control embryos. The new data show that after light exposure, lateral myosin intensity is significantly reduced compared to the dark control, whereas apical myosin levels decrease similarly in both groups. This indicates that the optogenetic manipulation effectively attenuates lateral contractility during the accelerated invagination stage without affecting concurrent apical contractility changes. These results directly support the conclusion that lateral contractility acquisition is essential for invagination progression. (Figure 4—figure supplement 2)

      (4) It would be helpful to describe how the modeling work fits within the existing literature on modeling epithelial folding and to address discrepancies between the model and the actual biological observations, such as tissue curvature, limited invagination depth in the model, and the "puckering" surrounding the invagination. In addition, certain descriptions of the modeling results should be clarified, as suggested by Reviewer #3.

      We thank the referees for the detailed and constructive comments on our modeling work. In response to these suggestions, we have significantly updated the theoretical section of the manuscript. Specifically, we have reformulated the vertex model within a curved geometry that represents the entire tissue, and revised the subsequent analyses to better clarify the mechanical principles driving the observed morphogenesis. We have added relevant references and discussed the mechanistic connections and distinctions between our model and previous studies on epithelial invagination. We hope that our point-by-point responses of the modeling work and the corresponding revisions in the manuscript adequately address the reviewers’ concerns.

      (5) It would be helpful to elaborate on the methods for quantitative image analysis and statistical tests.

      We have thoroughly expanded the Materials and Methods section by adding a dedicated subsection “Quantification and statistical analysis”. This subsection provides step‑by‑step descriptions of how apical, lateral, and basal domains were defined (segmented line, width 1 μm), how normalization was performed (basal intensity set to 1), how center cell height, invagination depth, and lateral cell distance were measured (referencing Figure 1B), and what statistical tests were used (two‑tailed Student’s t‑test, with significance levels indicated). (see revised Materials and Methods, “Quantification and statistical analysis” subsection)

      Reviewer #1 (Recommendations for the authors):

      (1) This reviewer has concerns about two aspects of the model. First, the model in Figure 5D shows a simulation of a flat epithelial sheet creating an invagination. However, the actual invagination is occurring in a small embryo that has very significant curvature, such that nine or so cells occupy a 90-degree arc of the 360-degree circle that defines the embryo's section (e.g., see Figure 1A). This curvature could potentially have important effects on cell behavior. Ideally, the developed model would reflect the actual geometry of the observed behavior. A more nuanced analysis would provide important insight into whether the embryo's curvature makes a difference. Importantly, any result comparing the planar versus curved system would be interesting because if the model worked equally well in the high curvature or planar systems, the model is robust, or if invagination requires different strategies for high curvature and for planar systems, this is an important finding that reveals the importance of local geometries. I don't think the consideration of invagination from a planar vs curved epithelium has been previously modeled.

      We fully agree with the reviewer that comparing planar versus curved systems provides valuable insights into the invagination mechanism. As we addressed in our response to Reviewer #1 (Public Review) - Weakness (1), we have now updated our vertex model to incorporate curved geometries and introduced surface bending stiffness to better reflect the embryo's actual shape. Our systematic comparison reveals that the invagination process, driven by apico-basal tension imbalance and lateral contraction, is indeed highly localized and remains robust across different initial curvatures. We have added Figure 5—figure supplement 1 and corresponding discussions in the revised manuscript to highlight these findings on model robustness and the role of local geometry.

      (2) The second concern about the model is that Figure 5D shows the vertex model developing significant "puckering" (evagination) surrounding the invagination. Such "puckering" is not seen in the in vivo invagination (Figures 1A, 2A). This issue is not discussed in the text, so it is unclear how big an issue this is for the developed model. A discussion of this issue in the text would be appropriate. Maybe puckering goes away if a curved epithelium is modeled?

      Thank you for this comment. In our model, the "puckering" effect naturally arises due to the presence of surface bending stiffness and the absence of rigid boundary constraints, which resembles the tissue morphology observed at 17 hpf in our experiments. However, our updated simulations show that this effect significantly diminishes as the tissue curvature decreases. We have addressed this concern in detail in our response to Reviewer #1 (Public Review) - Weakness (2) and have included the relevant analysis and discussions in the revised manuscript.

      (3) Because of the puckering, it is unclear in the model what measurement is being used to define the invagination depth in Figure 5E. Is the depth from the maximal height of the surrounding epithelial cells? Or the location of the apical surface before invagination begins? It would be helpful to have that parameter better defined, and it would also be helpful to add a line to Figure 5D showing how the reference point for invagination depth.

      Thank you for your suggestion. We measured the vertical distance from the baseline connecting the maximal height of apical midpoints of the surrounding cells to the apical surface of the center cell, which is consistent with our experimental measurements. We have now added a schematic line and indicators to Figure 5D.

      (4) In Figure 2A Top View, as well as the schematic in Figure 2C, the developing invagination is surrounded by a ring of aligned cell edges characteristic of a "purse string" type actomyosin cable that would create pressure on the invaginating cells, which have been documented in multiple systems. Notably, the schematic in Figure 2C shows myosin II localizing to aligned "purse string" edges, suggesting the purse string is actively compressing the more central cells. If the purse string consistently appears during siphon invagination, a complete understanding of siphon invagination will require understanding the contributions of the purse string to the invagination process. For this paper, a discussion of the possible involvement of a purse string would be helpful for the readers, but follow-up work could include laser cutting or optogenetic blockage of the purse string contractility.

      Thank you for your suggestion. We agree that the ring-like actomyosin structure is a prominent feature during the initial stages of invagination, and its potential role warrants discussion. We carefully re-examined our data. Our analysis confirms that this myosin ring is most pronounced during the early initial invagination stage (Figure 2A). This inward compression from the periphery would work in concert with apical constriction to help shape the initial invagination. However, this ring-like myosin pattern significantly diminishes in the accelerated invagination stage. We propose that the purse string may play a collaborative role in the early phase. We agree that follow‑up work (e.g., laser cutting or optogenetic manipulation) would be valuable and have noted this as a future direction in the Discussion.

      (5) The introduction and discussion put the work in the context of work on physical forces in invagination, but there is not much discussion of how the modeling fits into the literature. Did the current work advance the state of modeling of such phenomena? What were the strengths and limitations of the modeling in this paper compared to what has been done previously?

      Thank you for this suggestion. While we have incorporated additional literature in the revised manuscript as mentioned in our response to Reviewer #1 (Public Review) - Weakness (4), we would like to further clarify the specific advances and limitations of our modeling framework. Our updated vertex model builds upon established foundational frameworks but advances the state of modeling by: (i) incorporating dynamic apico-lateral tension variations coupled with actomyosin signals, and (ii) achieving localized, activity-mediated morphogenesis without the need for external rigid boundary constraints—a feature that distinguishes it from many classical models. We also recognize the model's current limitations. Specifically, it does not explicitly account for compressive stress and global geometric changes induced by tissue growth. The mechanical interactions between surface epithelial cells and the underlying internal bulk cells are also simplified. These factors represent important directions for our future work. We have added a dedicated paragraph in the Modeling and Discussion sections to contrast our model with existing literature and to explicitly state these strengths and limitations.

      (6) Figure 4D. Minor point, but the labeling on the X-axis is out of register with the bar graphs.

      We have corrected the alignment of the X‑axis labels with the bar graphs in Figure 4D. The figure has been updated accordingly.

      (7) Figure 4B does not have a scale bar.

      We have added a scale bar to Figure 4B (10 μm).

      Reviewer #2 (Recommendations for the authors):

      (1) Live imaging is necessary to demonstrate bidirectional translocation by visualizing the movement of the actomyosin network between the apical and lateral domains. Alternatively, a term other than "translocation" should be used to describe the observation.

      We agree that live imaging of actomyosin movement would be ideal but is technically challenging in this system. Instead, we have replaced the term “translocation” with the more accurate and conservative term “redistribution” throughout the manuscript, including the title, to avoid implying physical movement of the same molecules. This addresses the reviewer’s concern.

      (2) The optogenetic tool could be used to its full potential by manipulating myosin spatially or temporally, for example, by inhibiting myosin at various stages or subcellular locations, which would provide an opportunity to thoroughly test the domain and stage-specific needs for actomyosin. That said, I recognize that such experiments may be challenging in the model system used in this study.

      We thank the reviewer for this suggestion. We have indeed attempted spatially restricted optogenetic activation in the Ciona atrial siphon system, but found it technically very challenging due to tissue geometry and light scattering. We appreciate the reviewer's understanding of these technical limitations.

      (3) Some additional characterization of the optogenetics tool, such as the distribution of active myosin and F-actin post-stimulation, could further strengthen the interpretation of the inhibitory effect on invagination.

      We thank the reviewer for this suggestion. After optogenetic inhibition, we fixed and stained embryos for active myosin II. The results (Figure 4—figure supplement 2) show that light exposure significantly reduces lateral myosin intensity compared to the dark control, while apical myosin decreases similarly in both groups. This confirms that the optogenetic manipulation selectively attenuates lateral contractility without affecting apical changes. We have added this data to the Results section.

      (4) It would be helpful to address how heterogeneity in MRLC mutant overexpression might impact the interpretation of the outcome.

      We acknowledge that mosaic expression is common in Ciona electroporation. For all quantitative analyses, we only selected embryos in which the center cell and more than half of the surrounding cells in the primordium showed clear expression of the plasmid. This selection criterion has been added to the Materials and Methods section.

      (5) For Figure 2, it would be helpful to include the en face view of the cells at different apical-basal depths to better demonstrate the changes in the subcellular localization of myosin at different stages.

      We have added top‑view images in Figure 2A at both the apical and a deeper (lateral) plane. These images clearly show the ring‑like localization of active myosin at the apical cell‑cell junctions during the initial stage. Together with the cross‑sectional views, they adequately demonstrate the subcellular localization changes.

      (6) The Methods section should include more detailed descriptions of image quantification procedures. For example, for Figure 2B, how were the apical and lateral signals defined, and how were background intensities determined? In addition, the methods used for statistical tests should be clearly stated.

      We agree that detailed quantification procedures are essential. We have therefore expanded the Materials and Methods with a new subsection “Quantification and statistical analysis”. This subsection includes precise definitions of apical, lateral, and basal domains (segmented line, width 1 μm), background subtraction (region outside the tissue), normalization (basal intensity set to 1), and descriptions of how cell height, invagination depth, and lateral distance were measured (referencing Figure 1B). Statistical tests (two‑tailed Student’s t‑test) and significance levels are clearly stated.

      (7) The discrepancies between the model and experimental data, as described above, should be acknowledged. Commentary on how the model's assumptions and setup might contribute to these differences would be helpful.

      We thank the reviewer for this suggestion. As detailed in our response to Reviewer #2 (Public Review) - Comment (6), we have included the discrepancies between the model and experimental results in the Modeling and Discussion sections. We have added comments explaining how our key modeling assumptions might contribute to these differences. Specifically, while we have updated the model to a curved geometry, the omission of continuous global tissue growth and expansion could affect the final invagination depth and shape. Meanwhile, the neglect of mechanical interactions between the surface epithelium and the internal bulk cells prevents the model from fully capturing the constraints that refine the local furrow configuration in vivo. By clarifying these limitations, we now provide a more balanced view of the model's scope and its role in identifying the primary mechanical drivers of invagination.

      Reviewer #3 (Recommendations for the authors):

      General comments:

      (1) Methods: More information is needed to describe how imaging and quantification were performed. A couple of examples:

      (a) In Figure 1, how were the apical and basal surface area of the center cell quantified?

      (b) In Figure 1, Supplement 1, how was fluorescence intensity measured? Was there a constant area or volume that was quantified between samples? This is important because a decreasing apical surface can cause the signal to appear "concentrated" and increased.

      We thank the reviewer for this important suggestion. We have added a dedicated subsection “Quantification and statistical analysis” in the Materials and Methods. This subsection includes precise definitions of apical, lateral, and basal domains (segmented line, width 1 μm), background subtraction (region outside the tissue), normalization (basal intensity set to 1), and descriptions of how cell height, invagination depth, and lateral distance were measured (referencing Figure 1B). Statistical tests (two‑tailed Student’s t‑test) and significance levels are also stated.

      (2) The manuscript could use some editing and proofreading for grammar.

      The manuscript has been carefully edited for grammar and clarity. We thank the reviewer for the suggestion.

      Specific points:

      (1) Figure 1A: Could the authors please annotate the location of the center cell throughout the time course? This would make it easier for the reader to understand what is being quantified.

      We have added arrows to indicate the center cell at each time point in Figure 1A. This makes it easier for readers to follow the quantification.

      (2) Figure 1 Supplement 1A, Line 143, "...before 15 hpf, F-actin concentration decreased at the lateral domains..."

      It is not clear that the graph shows a decrease in the lateral domains when taking the error bars into account. It is possible that the F-actin concentration is stable in the lateral domains before 15 hpf. Are there some statistical analyses that can be performed?

      We re-analyzed the F-actin data and agree that the change before 15 hpf is not statistically convincing given the error bars. However, we have added new quantitative analysis of active myosin (p-MLC) at 14–15 hpf (Figure 2B), which shows a clear and significant shift from lateral to apical enrichment during this early phase. This myosin dynamic strongly supports our hypothesis of bidirectional redistribution. The corresponding text has been updated in the Results section.

      (3) Figure 1 Supplement 1A, Line 147-148, "...after 16 hpf, during which apical F-actin levels showed a gradual decline." Based on the graph, it does not appear that apical F-actin levels show a gradual decline after 16 hpf; rather, they may be steady or slightly increase.

      We agree with the reviewer. Our original statement was inaccurate. What we intended to emphasize was that at 16 hpf, the F-actin level at the lateral domain exceeded that at the apical domain. The detailed changes of F-actin after 16 hpf were not a focus of our discussion. We have revised the text accordingly to avoid any misinterpretation. The correction has been made in the Results section.

      (4) Figure 2C Hypothesis and line 169-170, "Initially, actomyosin translocated from the lateral regions to the apical domains..."

      Related to the comment above, it is not clear that one can state that the actomyosin "translocated". The quantification does not necessarily demonstrate a loss of actin at the lateral domain in the initial stage, and even if there was a loss of lateral actomyosin, one would require experiments (perhaps photoconversion experiments) to demonstrate that machinery from the lateral region was transferred to the apical surface, rather than a process of new assembly at the apical surface.

      We fully agree with the reviewer. We have replaced the term “translocation” with “redistribution” throughout the manuscript, including the title, to avoid implying physical movement of the same actomyosin structures. The text in the Results and Discussion has been revised accordingly.

      (5) A similar comment is relevant to the subsequent statement in line 175, "actomyosin translocated from the apical domains to the lateral regions." Without direct experiments to demonstrate movement of the actomyosin machinery, it is possible that there is de novo assembly of actomyosin in the lateral region rather than translocation.

      This wording ("translocation") becomes important primarily because it is in the title and appears to be one of the authors' major conclusions.

      We fully agree with the reviewer that the wording is critical given our main conclusion. We have therefore systematically replaced “translocation” with “redistribution” across the manuscript (title, results, and discussion).

      (6) Figure 4, Lines 215-216, "These results confirm that the redistribution of myosin contractility from the apical to lateral regions is essential for the development of invagination."

      This experiment did not specifically test the redistribution of myosin; rather, the authors demonstrated that myosin contractility globally is necessary for invagination. In these experiments, is it known where the myosin is?

      We have performed additional immunostaining experiments (new Figure 4—figure supplement 2) to directly examine myosin distribution after optogenetic inhibition. The results show that light exposure specifically reduces lateral myosin intensity compared to the dark control, while apical myosin decreases similarly in both groups. This demonstrates that the optogenetic manipulation selectively attenuates lateral contractility. We have revised the conclusion to state that the acquisition of lateral contractility is essential for invagination progression. The new data and revised text are in the Results section.

      (7) Figure 4B, minor point: It would be helpful if the authors included a timestamp for the bottom row images (Dark 1 h).

      Thank you for pointing out this typo. Timestamps have been added to the bottom row images (Dark 1 h) in Figure 4B.

      (8) Figure 5E, F, minor point: It seems that the label on the red curve has a typo; it should be T18ES19E (rather than T18AS19E).

      Thank you for pointing out this typo. We have corrected it in the revised manuscript (now Figure 6A, B).

      (9) Figure 5F and corresponding text: Can the authors please clarify what is meant by "Coupled mode" as marked in the schematic? Is this meant to refer to simultaneous apical constriction and lateral contraction? Or sequential?

      We thank the reviewer for this question. By "coupled mode," we refer to the mechanical synergy between apical and lateral contractions in driving the final invagination. As observed in our experimental data and recapitulated in the model, these two processes occur sequentially rather than simultaneously. We have revised the corresponding text to explicitly clarify this sequential process.

      (10) Figure 6A, B, Lines 274-275: "...the invagination depth increased significantly under higher alphaa (Figure 6A), while the central height remained relatively independent of alphaa (Figure 6B)." This caused me some confusion until I realized that "Figure 6B" might be a typo and should be Figure 6C.

      We sincerely apologize for this confusion. In the revised manuscript, this specific section and the corresponding figures have been updated.

      (11) Line 287, typo: I believe that "Figure 5B" should be Figure 6B.

      We sincerely apologize for this confusion. In the revised manuscript, this specific section and the corresponding figures have been updated.

      (12) Figure 6A, B, comparing invagination depth with varying apical or lateral actomyosin intensity: The authors state that "invagination depth increased significantly under higher alphaa", but describe "mild invagination depth variation" with varied lateral actomyosin intensity. The graphs seem to suggest that there is increased invagination depth when either apical or lateral actomyosin intensity is increased, and that the increase is to a similar extent. Can the authors comment on what they think the differences are, if the apical effect is "significant" but the lateral effect is "mild"?

      We thank the reviewer for this meticulous observation. We agree and feel sorry that our original description was not sufficiently precise. In the revised manuscript, we have re-analyzed the distinct contributions of apical and lateral tensions using the updated curved vertex model, which provides a more accurate mechanical decoupling. We have accordingly replaced the previous wording with a more rigorous description of the simulations and streamlined the corresponding figures to ensure the conclusions are clearly supported.

      (13) Figure 6H, Lines 307-309, "...stronger regional translocation and redistribution contribute to the rapid reduction in height of invaginating cells..."

      It appears from the graph that this is really only apparent at high alpha (total actomyosin); at empirically determined levels (alpha = 1), the effect of varying ratio is less dramatic. Can the authors comment on how significant they consider this effect?

      We thank the reviewer for this insightful comment. We agree that the theoretical predictions regarding translocation strength in the original model lacked sufficient experimental validation. To maintain the scientific rigor of our study, we have removed the sections concerning the translocation ratio and the corresponding Figure 6H from the revised manuscript. Instead, we now refocus our analysis on the core mechanical drivers of invagination that are directly supported by our observations. We also have added discussions acknowledging other factors not fully captured in the current model (e.g., tissue growth), which we aim to investigate in future work.

    1. Author response:

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

      We have addressed all the reviewers’ comments through new experiments, additional analyses, or, in some cases, additional text. Below is a summary of the major changes in the manuscript.

      (1) We have added a considerable amount of new characterization of the biochemical enrichment of the ribosome clusters, including EM of the ribosome clusters, UV absorbance profiles, immunoblots of additional targets, and additional replicates (new Figure 1). In summary, we provide better evidence that (i) the biochemical enrichment is working and (ii) that the loss of FMRP has no effect on this biological enrichment of ribosomal clusters.

      (2) We have now reanalyzed all of the data in Figs. 5-8 using only the data after removing PCR duplicates from the RPFs. Other than the comparison between the nuclease treatments (Fig. 3), only this data is now used. Moreover, we have reanalyzed this data using suggestions from the reviewers, including providing PCA analysis (Fig S5-1), GSEA analysis (Fig 5), and normalizing for group size when comparing significance to total mRNAs, (Fig 6-7). We now also include a new analysis (Fig S7-1) to better explain how the loss of FMRP affects mainly FMRP targets defined by CLIP, but not all mRNAs resistant to run-off.

      (3) We are now more conservative in our nomenclature; we use "pellet" instead of "RNA granule (RG)" and "fraction 5/6" instead of "ribosome clusters (RC)". We have added a section to the discussion about the relationship between the RNA granules measured using imaging of hippocampal neurites and the biochemical purification of ribosome clusters in the pellet, as requested by the reviewers.

      (4) We have made many other minor changes to the text and analysis, which can be found in the specific response to the reviewers.

      (5) One major additional requested change that was not implemented was to repeat our experiments at different time points. We have added a paragraph to the discussion outlining (i) why this was not done and (ii) the caveats of our conclusions without this data being present.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors have investigated the role of FMRP in the formation and function of RNA granules in mouse brain/cultured hippocampal neurons. Most of their results indicate that FMRP does not have a role in the formation or function of RNA granules with specific mRNAs, but may have some role in distal RNA granules in neurons and their response to synaptic stimulation. This is an important work (though the results are mostly negative) in understanding the composition and function of neuronal RNA granules. The last part of the work in cultured neurons is disjointed from the rest of the manuscript, and the results are neither convincing nor provide any mechanistic insight.

      Strengths:

      (1) The study is quite thorough, the methods and analysis used are robust, and the conclusion and interpretation are diligent.

      (2) The comparative study of Rat and Mouse RNA granules is very helpful for future studies.

      (3) The conclusion that the absence of FMRP does not affect the RNA granule composition and many of its properties in the system the authors have chosen to study is well supported by the results.

      (4) The difference in the response to DHPG stimulation concerning RNA granules described here is very interesting and could provide a basis for further studies, though it has some serious technical issues.

      Thank you for these positive comments on the paper.

      Weaknesses:

      (1) The system used for the study (P5 mouse brain or DIV 8-10 cultured neuron) is surprising, as the majority of defects in the absence of FMRP are reported in later stages (P30+ brain and DIV 14+ neurons). It is important to test if the conclusions drawn here hold good at different developmental stages.

      Unfortunately, myelin strongly interferes with the ability to use this protocol to purify ribosome clusters in older brains (See Khandjian et al., 2004). It is possible to redo the ribopuromycylation results at later times in culture, but since we cannot compare this to a comparable time in the brain, we have chosen not to do this experiment. We acknowledge this limitation in the discussion, noting that our results are only a snapshot of development and that different results may be observed at different times.

      (2) The term 'distal granules' is very vague. Since there is no structural or biochemical characterization of these granules, it is difficult to understand how they are different from the proximal granules and why FMRP has an effect only on these granules.

      We agree with the reviewer and have removed all references to distal granules. We clarified that we did not measure RPM puncta close to the neuron because the much stronger RPM signal made defining puncta more difficult, and thus, we cannot determine if there are differences between proximal and distal puncta.

      (3) Since the manuscript does not find any effect of FMRP on neuronal RNA granules, it does not provide any new molecular insight with respect to the function of FMRP

      We would respectfully disagree that the study does not provide molecular insight into the function of FMRP, as disproving that FMRP is important for stalling and determining the position of stalling would remove one of the major hypotheses about the function of FMRP, and showing that a major hypothesis in the literature is unlikely to be correct, is at least to me, providing insight. Moreover, we do show an effect of the loss of FMRP on the RPM puncta that represent neuronal RNA granules containing stalled ribosomes. This also provides insight.

      Reviewer #2 (Public review):

      In the present manuscript, Li et al. use biochemical fractionation of "RNA granules" from P5 wildtype and FMR1 knock-out mouse brains to analyze their protein/RNA content, determine a single particle cryo-EM structure of contained ribosomes, and perform ribo-seq analysis of ribosome-protected RNA fragments (RPFs). The authors conclude from these that neither the composition of the ribosome granules, nor the state of their contained ribosomes, nor the mRNA positions with high ribosome occupancy change significantly. Besides minor changes in mRNA occupancy, the one change the authors identified is a decrease in puromycylated punctae in distal neurites of cultured primary neurons of the same mice, and their enhanced resistance to different pharmacological treatments. These results directly build on their earlier work (Anadolu et al., 2023) using analogous preparations of rat brains; the authors now perform a very similar study using WT and FMR1-KO mouse brains. This is an important topic, aiming to identify the molecular underpinnings of the FMRP protein, which is the basis of a major neurological disease. Unfortunately, several limitations of this study prevent it from being more convincing in its present form.

      In order to improve this study, our main suggestions are as follows:

      (1) The authors equate their biochemically purified "RG" fraction with their imaging-based detection of puromycin-positive punctae. They claim essentially no differences in RGs, but detect differences in the latter (mostly their abundance and sensitivity to DHPG/HHT/Aniso). In the discussion the authors acknowledge the inconsistency between these two modalities: "An inconsistency in our findings is the loss of distal RPM puncta coupled with an increase in the immunoreactivity for S6 in the RG." and "Thus, it may be that the RG is not simply made up of ribosomes from the large liquid-liquid phase RNA granules."

      How can the authors be sure that they are analysing the same entities in both modalities? A more parsimonious explanation of their results would be that, while there might be some overlap, two different entities are analyzed. Much of the main message rests on this equivalence, and I believe the authors should show its validity.

      Thank you for your comments. We have been more conservative in the revised paper, referring to the pellet fraction as the pellet fraction rather than the RNA granule fraction to acknowledge the possibility that these two modalities differ. However, we would respectfully disagree that our main message requires RPM-labeled RNA granules in neurites and the ribosome clusters isolated by sedimentation to be “equivalent”. We do believe they are related and added a section in the discussion on this important point.

      (2) The authors show that increased nuclease digestion (and magnesium concentration) led to a reduction of their RPF sizes down to levels also seen by other researchers. Analyzing these now properly digested RPFs, the authors state that the CDS coverage and periodicity drastically improved, and that spurious enrichments of secretory mRNAs, which made up one of the major fractions in their previous work, are now reduced. In my opinion, this would be more appropriately communicated as a correction to their previous work, not as a main Figure in another manuscript.

      We have removed all discussion of the secretory mRNAs, as our attempts to obtain independent evidence for this finding by examining ribophorin enrichment in the pellet across different Mg<sup>2+</sup> concentrations did not support this interpretation (data not shown in the paper). I understand that the change in nuclease is somewhat out of place narratively, but it is clearly relevant to this work. We would disagree with our previous work requiring a ‘correction’. We believe that the nuclease resistance of the mRNA at the entrance site is important. We reproduce our results from rats with similar nuclease treatment in mice as seen in our previous publication; thus, this work is not wrong. We have a paper in preparation that suggests the secondary structure of the mRNA at this location may be important for stalling and thus feel strongly that this result should remain in the manuscript.

      (3) The fold changes reported in Figure 7 (ranging between log2(-0.2) and log2(+0.25)) are all extremely small and in my opinion should not be used to derive claims such as "The loss of FMRP significantly affected the abundance and occupancy of FMRP-Clipped mRNAs in WT and FMR1-KO RG (Fig 7A, 7B), but not their enrichment between RG and RCs".

      We agree that the changes are small and indeed did not appear in the DEG analysis. However, because we are analyzing a large set of mRNAs in this analysis, the results are highly significant and remain significant when using the new statistical tests suggested by the reviewer below. We now emphasize that these are small changes and remind readers that none of the individual mRNA changes were significant in the DEG analysis.

      (4) Figure 8 / S8-1 - The authors show that ~2/3 of their reads stem from PCR duplicates, but that even after removing those, the majority of peaks remain unaltered. At the same time, Figure S8-1 shows the total number of peaks to be 615 compared with 1392 before duplicate removal. Can the authors comment on this discrepancy? In addition, the dataset with properly removed artefacts should be used for their main display item instead of the current Figure 8.

      We now use only the data after removing PCR duplicates for all the analyses except in Figure 3. The number of peaks observed is determined mainly by the threshold used, as stated in the methods “To be identified as a peak, the zenith of an abundance site for the reads must be 4x higher of the average of the total transcript.” Due the lower number of reads after the PCR duplicates fewer peaks reached this threshold.

      (5) Figure 9 / S9-1, the density of punctae in both WT and FMR1-KO actually increases after treatment of HHT or Anisomycin (Figure S9-1 B-C). Even if a large fraction would now be "resistant to run-off", there should not be an increase. While this effect is deemed not significant, a much smaller effect in Figure 9C is deemed significant. Can the authors explain this? Given how vastly different the sample sizes are (ranging from 23 neurites in Figures S91 to 5,171 neurites in Figure 9), the authors should (randomly) sample to the same size and repeat their statistical analysis again, to improve their credibility.

      The box and whisker plots emphasize the median and not the average. We now also show the averages in Figure S9-1, which indicate a slight decrease for both HHT and anisomycin.

      We apologize for the typo in the figure legend in Figure 9, 171, not 5171. We now use random sampling in Figures 6 and 7, where the sample sizes differ substantially.

      Reviewer #3 (Public review):

      Summary:

      Li et al describe a set of experiments to probe the role of FMRP in ribosome stalling and RNA granule composition. The authors are able to recapitulate findings from a previous study performed in rats (this one is in mice).

      Strengths:

      (1) The work addresses an important and challenging issue, investigating mechanisms that regulate stalled ribosomes that are part of stress granules, and focusing on the role of FMRP. This is a complicated problem, given the heterogeneity of the granules and the challenges related to their purification. This work is a solid attempt at addressing this issue, which is widely understudied.

      (2) The interpretation of the results could be interesting if supported by solid data. The idea that FMRP could control the formation and release of stress granules, rather than the elongation by stalled ribosomes, is of high importance to the field, offering a fresh perspective into translational regulation by FMRP.

      (3) The authors focused on recapitulating previous findings, published elsewhere (Anadolu et al., 2023) by the same group, but using rat tissue, rather than mouse tissue. Overall, they succeeded in doing so, demonstrating, among other findings, that stalled ribosomes are enriched in consensus mRNA motifs that are linked to FMRP. These interesting findings reinforce the role of FMRP in the formation and stabilization of RNA granules. It would be nice to see extensive characterization of the mouse granules as performed in Figure 1 of Anadolu et al., 2023.

      (4) Some of the techniques incorporated aid in creating novel hypotheses, such as the ribopuromycilation assay and the cryo-EM of granule ribosomes.

      Thank you for these positive comments. We have now added a more extensive characterization in Figure 1.

      Weaknesses:

      (1) The RNA granule characterization needs to be more rigorous. Coomassie is not proper for this type of characterization, simply because protein weight says little about its nature. The enrichment of key proteins is not robust and seems not to reach significance in multiple instances, including S6 and UPF1. Furthermore, S6 is the only proxy used for ribosome quantification. Could the authors include at least 3 other ribosomal proteins (2 from the small, 2 from the large subunit)?

      We have increased N to improve the robustness of the enrichment analysis and added several additional RBPs. Along with Coomassie we now include analysis of UV absorbance and include EMs from these fractions showing the presence of 80S ribosomal clusters in the fractions we are using.

      (2) Page 12-13 - The Gene Ontology analysis is performed incorrectly. First, one should not rank genes by their RPKM levels. It is well known that housekeeping genes, such as those related to actin dynamics, molecular transport, and translation, are highly enriched in sequencing datasets. It is usually more informative when significantly different genes are ranked by p-adjust or log2 Fold Change, then compared against a background to verify enrichment of specific processes. However, the authors found no DEGs. I would suggest the removal of this analysis and the incorporation of a gene set enrichment analysis (ranked by p-adjust). I further suggest that the authors incorporate a dimensionality reduction analysis to demonstrate that the lack of significance stems from biology and not experimental artifacts, such as poor reproducibility across biological replicates.

      Thank you for the suggestion. We now use GSEA analysis to examine differences in gene sets between WT and FMR1- mice and find some significant changes (new Fig. 5). The old analysis is still included for comparison to our earlier paper as a supplemental figure. We have now included a PCA analysis (FigS5-1) to show reproducibility across biological replicates.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) RNA sequencing comparison between WT and FMR1 KO mice should be carried out at a later developmental stage, which may provide a better difference between these two groups

      There are a number of studies that have already done this analysis and in specific brain regions 10.1016/j.neuron.2017.07.013; 10.7554/eLife.46919; 10.3389/fnmol.2017.00340; https://doi.org/10.1016/j.neuron.2023.06.009. The main goal of our RNA-seq was to standardize for the RPF studies, not to identify differences in RNA-seq between WT and FMRP. In the response to public review point 1 we explain why we do not look at later developmental timepoints.

      (2) The same is true in characterizing the effect of FMRP on the RNA granules.

      See response to public review point 1, which addresses this point.

      (3) No evidence is provided for the effectiveness of DHPG stimulation in DIV8-10 neurons; this is needed for justification using neurons at this stage.

      We have previously shown that DHPG stimulation in these neurons at this developmental time from cultures made from rat brain is sufficient to decrease the number of RPM puncta and to induce an increase in the synthesis of proteins in an initiation resistant manner (Graber et al, 2013; Graber et al, 2017). This is now more clearly stated in the manuscript. Moreover, here we replicate the result of DHPG in WT mice at reducing the number of RPM puncta.

      (4) In Figure 9 B, it is not clear whether the neurites indicated are axons or dendrites. Since neurons are still in the early stages of dendritogenesis/synaptogenesis, it is important to make that distinction.

      We have previously characterized RNA granules in axons and dendrites in hippocampal cultures from rats at this time (Miller et al, 2009, MCN 40:485-495)) and they are similar. While it is likely that the vast majority of the neurites at this time are dendrites, since we did not use markers, we conservatively just use the term neurites.

      (5) In Figure 1 (and elsewhere), fraction 5/6 is used as a polysome or RNA cluster. The authors have not provided a UV absorption profile and only have s6 as evidence to say this polysome. In the Coomassie gel, this fraction is any different than fractions 7/7 or 9/10; what is the justification for using this fraction?

      The main justification for these fractions is to be consistent with our previous paper (Anadolu et al, 2023) and the Khandian study comparing polysomes to pellet using the same fractionation protocol (El-Fatimy et al, 2016). We now provide a UV absorption profile (Fig. 1C) and EM pictures (Fig. 1D) to show the ribosome clusters in this fraction. We do not believe our results would be fundamentally different from those obtained if we had used other heavy fractions.

      Minor comments

      (1) The font size very small in the figures, please increase it.

      We have worked hard to increase the font size in all the figures.

      (2) In the result section for Figure 3B - it is written 'majority of these mRNA are non-coding mRNA' - this doesn't make sense.

      Corrected

      Reviewer #2 (Recommendations for the authors):

      (1) There are lots of mistakes (e.g. word omissions or duplications, grammatical errors) throughout the text, too many to list here.

      We have carefully edited the text to try to minimize these mistakes.

      (2) In many positions related to their improved nuclease digestion protocol, samples are labelled "M ...", which apparently stands for "high magnesium and high nuclease treatment group". I would suggest switching to something more intuitive, such as "... (improved digestion)".

      We have removed most of the comparisons between these samples. What remains (Figure 3), we just use Low Nuclease when we refer to the sample with low Magnesium and low nuclease.

      (3) Figure 1,3 - It would be tremendously illuminating to see a polysome trace (UV260 absorbance) in addition to Coomassie-stained SDS-PAGE to underscore the interpretation of the different fractions by the authors. As it stands, there is no way of telling whether there are any polysomes present at all. This can also be done by hand using a UV absorption reader if no built-in device is available to the authors.

      We have now done this (Fig. 1C) and also provided EM of this fraction to show the presence of ribosomes in this fraction.

      (4) I don't understand why the authors switched from calling fraction 5/6 the "polysome fraction" in their previous work to calling it "ribosome cluster fraction" in this work. The argument given "[...] due to its structural similarity to ribosomes in RNA Granules (Anadolu et al., 2023), we conservatively call this the ribosome cluster fraction (RC)." does not instill confidence that these two fractions are indeed distinct.

      We agree with the reviewer and regret this decision. We now call the pellet, the pellet and Fraction 5/6, fraction 5/6.

      (5) Figure 1C - There are clear scanning or compression artefacts in the blot images (most prominently in the eEF2 lanes) that should be corrected.

      We have replaced all images in Figure 1 and have increased the N of this experiment considerably.

      (6) Figure 1C - The authors claim that WT mouse RG is enriched in FMRP compared to RC or starter fraction, but there is also a lot more protein loaded in the RG (especially when compared to RC). It is also hard to believe from the Coomassie staining that despite the much stronger presence of low MW bands (which is where ribosomal proteins migrate) in fraction 5/6, the s6 western blot signal is actually comparable between RC and RG. Can the authors please provide more detail on the loading of these fractions and supply quantification of FMRP in all three fractions, normalized by total protein? This might also be the source of their discrepancy, stating that contrary to their expectation, ribosomes (as measured by s6 signal / s6 signal in starter fraction) are actually increased in FMR1-KO brains.

      We have repeated all of these experiments and changed our method of quantification (See methods). We no longer use the starting material in our quantification. Indeed, with the additional data and change in method, we no longer see an increase in S6 in the FMR1- pellet fraction.

      (7) Figure 1 - I believe "D-F)" should only read "D-E)" based on the axis titles, and instead "FG)" should be added before the next sentence. Instead of "Staufen" it should be specified in the Figure that "Stau2" was quantified. "Staufen (59kd)" should read "Stau2 (59 kDa)" and "anti-Staufen (52kb)" should read "anti-Stau2 (52 kDa)" and the same for all other similar instances. It is further hard to believe that e.g., "Staufen2 (59kd)" (see above) is not significantly enriched with N=5, a very low spread, and over 1.5x enrichment. The authors should double-check that the appropriate statistical test was employed.

      Figure 1 has been completely redone, and the two Staufen bands are enriched in this new analysis.

      (8) Figure S4-2 - Most of the detail in the corresponding figure legend should be moved to the Materials and Methods section.

      Details relevant to the methods in this figure legend have been now moved to the Material and Methods section.

      (9) Figure 4A - The displayed/segmented tRNA densities appear unusually distorted. I would recommend displaying segmented densities of the original homogeneous reconstructions, not of separated and later fused partial maps.

      Figure 4 was modified according to the suggestions of this reviewer.’

      (10) Figure 9 C-D, S9-1 B-E - Are not all conditions also including puromycin as in B above? If so, it should be added to both the figure and the figure legend.

      The reviewer is correct and the figure and legend has been changed to reflect this.

      Reviewer #3 (Recommendations for the authors):

      (1) "Loss of FMRP causes Fragile X syndrome. In humans, the loss of FMRP occurs due to the expansion of a CGG repeat in the 5' untranslated region (UTR) of the gene, leading to excessive methylation and transcriptional inhibition."

      Comment: Genes don't have 5'UTR, but exons encoding 5'UTR. I suggest rephrasing this statement.

      This sentence has been rephrased.

      (2) "Several of these functions have been implicated in Fragile X syndrome, including FMRP's regulation of miRNA repression, splicing, translation initiation, and translational elongation".

      Comment: Is this a typo? miRNA instead of mRNA?

      No, this is correct. FMRP has been implicated in the regulation of microRNAs (miRNAs) in a number of studies.

      (3) "elongation rates are also increased in mouse models of FMRP".

      Comment: Mouse models of Fragile X?

      This has been corrected.

      (4) "Parts of this work were included in the Master's thesis of the first author (Li, 2024)."

      This has been removed.

      (5) Comment: Graphs in Figure 1 need proper y-axis labeling. What is the normalization method? What are the values presented in the y-axis?

      Figure 1 has been completely changed and the Y-axes are now clear in this new version.

      (6) "Thus, by looking at the percentage of puromycylation present in the presence of anisomycin, we can estimate the number of ribosomes in this state. "

      Comment: Are the authors really estimating the number of ribosomes in a resistant state? One could argue that they are collecting populational information regarding resistance to anisomycin.

      We have rephrased this sentence to be more conservative about what we are measuring.

      (7) Comment: Page 11 - Why did the authors assume magnesium would affect the conformation state of the ribosomes? What is the rationale behind increasing the [Mg2+]?

      Most preparations using ribosomes use 10 mM MgCl<sub>2</sub>. However, most neuroscientists use physiological buffers that contain 2.5 mM MgCl<sub>2</sub>. In bacteria, this makes a large difference, but evidence from eukaryotes is not clear. Since this is a collaboration between these two schools of thought, we decided to switch to 10 mM MgCl<sub>2</sub>, since in the EM, there were some free 60S ribosomes (Anadolu et al, 2024).

      (8) Page 11- "In other words, high Mg2+ decreased the abundance of mRNAs normally cotranslationally inserted into the ER which are unlikely to be components of transporting RNA granules containing stalled ribosomes and solidified our focus on the M protocol in the analyses below."

      We have removed this from the paper, as additional experiments aimed to solidify this interpretation failed to detect an effect on secretory mRNAs.

      (9) Comment: The whole "abundance", "enrichment", and "occupancy" nomenclature is hard to follow.

      We have rewritten this section.

      (10) Page 13 - "There were only 2 protein coding genes that were significantly different between the abundance of FMR1-KO and WT in protein coding genes - FMR1 and Wdfy1 (Extended Data Table 5-2). There were no significantly different genes between WT and FMR1-KO occupancy and enrichment. Thus, no difference rose to significance, given the large number of mRNAs used in this analysis."

      Comment: It seems like this is repeating the same information three times.

      This has been changed.

      (11) Page 13 - "Similar to previous experiments with rats, the most abundant mRNAs resistant to run off were significantly abundant, occupied and enriched in both WT and FMRP RPFs (Fig 6)"

      The Shah et al dataset we use was based on the most abundant mRNAs resistant to run-off. While we agree it is not surprising that they are also abundant in the pellet we observe, this would not necessarily be true unless the pellet is actually enriched in stalled mRNAs.

      (12) Page 14 - "These mRNAs had been identified by cross-linking FMRP with mRNA, fragmenting the mRNA, immunoprecipitating the mRNA still associated with FMRP and sequencing this mRNA."

      We shortened this description.

      (13) Page 14 - "Interestingly, while still significant, there appeared to be a decrease in the relative abundance of these mRNAs in the FMR1-KO RG (Fig 6B)"

      Comment: It is hard to observe this decrease in the boxplots. Second, the statistical tests for the bioinformatics analyses are not the most appropriate, given the large discrepancy in the number of mRNAs present in the experimental group ("All mRNAs") and the filtered groups.

      We have redone the statistics using multiple random sampling of all the mRNAs such that the total number of mRNAs in the group was the same. This lowered the significance for some groups, but they are mostly still highly significant. This analysis has also been affected by switching to using the data from the PCR-subtracted RPFs. The changes we now observe are more evident in the whisker box plots due to this improvement in the data.

      (14) Page 16 - "To rule out that peaks were due to amplification artifacts in the preparation of RPFs we repeated these analyses after removing PCR duplicates (Fig. S8-1; Extended Data Table S8-3) and found over 95% of the peaks identified without removing PCR duplicates were defined as a peak in at least one of the biological replicates after removing duplicates. More importantly, we found similar results with enrichment of FXS motif and enrichment of negatively charged amino acids in the FMR1-KO only, WT only and both peaks after removing PCR duplicates (Fig. S8-1; Extended Data Table S8-3)."

      Comment: It is unclear why the authors needed to include the analysis without PCR duplicate removal. This is an essential step to guarantee the robustness of ribo-seq findings. I recommend removing the whole analysis from Figure 8 from the manuscript and including only the post-duplicate removal analysis.

      As mentioned above, we completely agree with this statement and now show only this data and moreover have redone all the figures with only this data (except for Fig. 3).

      (15) Figure 9 - I am unsure that the data is convincing enough to demonstrate reinitiation of mRNA granules induced by DHPG. I suggest a colocalization experiment with another protein well known to be localized to RNA granules, such as G3BP1. In addition, repeat the experiment with an additional group where elongation is blocked after the addition of DHPG, which presumably would prevent the reduction in the WT puncta density.

      These are interesting additional experiments, but outside the scope of what we can manage. We have previously shown colocalization of Staufen, FMRP and UPF1 to these puncta (Graber et al, 2013; Graber et al, 2017) and shown that these puromycylated puncta also colocalize with nascent peptides detected using the Sun-Tag technique. While we think doing the experiment in the presence of an elongation inhibitor would be interesting, we disagree that it would prevent the reduction in WT puncta density, since we believe what is happening is the loss of the liquid-liquid phase separation of the ribosome clusters due to dephosphorylation of RBPs like FMRP and UPF1 (Graber et al, 2017), and this would reduce the puncta density whether or not the ribosomes were activated for translation.

      Nevertheless, we have tried to temper the conclusions made from this result, emphasizing what we know (RPM puncta are decreased) as opposed to actual reactivation of stalled polysomes which we are not measuring.

      Discussion - Page 18 - "Nevertheless, if FMRP binding was the critical determinant for presence in neuronal RNA granules, we would have expected to observe more differences." This is not true. If the data is poorly collected, you will not see differences.

      This statement was removed.

      (16) "A proportion of the stalled ribosomes that are not stored in large RNA granules may still be pelleted in the sucrose gradients. This fraction may be greater in the absence of FMRP."

      Comment: The authors are right about this and touch on my original point that the characterization of the biochemical fractionation is not convincing enough. I'd suggest probing against more proteins that are contained in RNA granules.

      We have added several proteins to the biochemical characterization shown in Figure 1. We have added a discussion about the relationship between neuronal RNA granules and the sedimented pellet fraction in the discussion section.

    1. Author response:

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

      We incorporated Reviewer #2’s suggestion to change the name of mll-1 because of overlap with a human gene. We used the updated gene names in our responses below to minimize confusion. Below are the updated gene names for the toxin-antidote system we described.

      tmrl-1 - Toxin-induced Maternal Rod Lethality (formerly mll-1). After we establish that B0250.8 is also a toxin, we refer to this gene as the “N2 tmrl-1 allele”.

      amrl-1 - Antidote of Maternal Rod Lethality (formerly smll-1)

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The article by Zdraljevic et al. reports the discovery of a third toxin-antidote (TA) element in C. elegans, composed of the genes mll-1 (toxin) and smll-1 (antidote). Unlike previously characterized TA systems in C. elegans, this element induces larval arrest rather than embryonic lethality. The study identifies three distinct haplotypes at the TA locus, including a hyper-divergent version in the standard laboratory strain N2, which retains a functional toxin but lacks a functional antidote. The authors propose that small RNA-mediated silencing mechanisms, dependent on MUT-16 and PRG-1, suppress the toxicity of the divergent toxin allele. This work provides insights into the evolutionary dynamics of TA elements and their regulation through RNA interference (RNAi).

      Overall, there are many things to like about this paper and only a few small quibbles, which will not require more than a little rewriting or relatively minor analyses.

      Strengths:

      (1) The discovery of a maternally deposited TA element with delayed toxicity due to delayed mRNA translation of the maternally deposited toxin mRNA is a significant addition to the literature on selfish genetic elements in metazoans.

      (2) Identifying three haplotypes at the TA locus provides a snapshot of potential evolutionary trajectories for these elements, which are often inferred but rarely demonstrated in naturally occurring strains. The genomic analysis of 550 wild isolates contextualizes the findings within natural populations, revealing geographic clustering and evolutionary pressures acting on the TA locus.

      (3) The study employs various techniques, including CRISPR/Cas9 knockouts, FISH, long-read RNA sequencing, and population genomics. The use of inducible systems to confirm toxicity and antidote functionality is particularly robust. This multifaceted approach strengthens the validity of the findings.

      (4) The authors provide compelling evidence that small RNA pathways suppress toxin activity in strains lacking a functional antidote. This highlights an alternative mechanism for neutralizing selfish genetic elements.

      Weaknesses:

      (1) The introduction focuses strongly (for good reason) on bacterial TA systems and then jumps to TA systems in C. elegans. It's unclear why TA systems in other eukaryotes are not discussed.

      We briefly introduced bacterial TA systems because of their ubiquitousness and focused on C. elegans TA systems. We chose certain aspects of previously described Caenorhabditis TA elements that were relevant to the narrative we presented. Furthermore, we have extensively reviewed TA systems previously and have added a citation to that review in the revised manuscript (Burga et al. 2020).

      (2) Similarly, there is a missed opportunity to discuss an analogy between the suppressor mechanism discovered here and the hairpin RNA suppressors of meiotic drive identified by Eric Lai and colleagues. Discussing these will provide a fuller context of the present study's findings and will not affect their novelty.

      Thank you for pointing this out. We added a mention of the Stellate and Dox systems in our discussion.

      (3) While the evidence for RNAi-mediated suppression is strong, the claim that positive selection drove diversification at piRNA binding sites requires further discussion and clarification. The elevated dN and dS are unusual (how unusual relative to other genes in vicinity? What is hyper-divergent statistically speaking?), but there is no a priori reason that there would be selection on piRNA binding sites within the mll-1 transcript to facilitate its recognition by endogenous RNAi machinery; what is the selective pressure for mll-1 to do so? Most TA systems would like to avoid being suppressed by the host. One cannot make the argument that this was motivated by the loss of the antidote because the loss of the antidote would be instantly suicidal, so the cadence of events described requiring hypermutation of the mll-1 transcript does not work.

      We largely agree with the reviewer’s point, which we believe is based on the following sentence in the discussion: “We propose that positive selection for piRNA binding sites in the tmrl-1 transcript drove the diversification of this gene toward the N2 version.” We have removed this argument from the discussion in the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      In the manuscript by Walter-McNeill, Kruglyak, and team, the authors provide solid evidence of another toxin-antidote (TA) system in C. elegans. Generally, TA systems involve selfish and linked genetic elements, one encoding a toxin that kills progeny inheriting it, unless an antidote (the second element) is also present. Currently, only two TA systems have been characterized in this species, pointing to the importance of identifying new instances of such systems to understand their transmission dynamics, prevalence, and functions in shaping worm populations.

      Strengths:

      This novel TA system (mll-1/smll-1) was identified on LGV in wild C. elegans isolates from the Hawaiian islands, by crossing divergent strains and observing allele frequency distortions by high-throughput genome sequencing after 10 generations. These allele frequency distortions were subsequently confirmed in another set of crosses with a separate divergent strain, and crosses of heterozygous males or hermaphrodites resulted in a pattern of L1 lethality in progeny (with a rod arrest phenotype) that suggested the maternal transmission of this TA system from the XZ1516 genetic background. By elegantly combining the use of near-isogenic lines, CRISPR editing to generate knock-outs, and a transgene rescue of the antidote gene, the authors identified the genes encoding the toxin and the antidote, which they refer to as mll-1 and smll-1. Moreover, the specific mll-1 isoform responsible for the production of the toxin was identified and mll-1 transcripts were observed by FISH in early and late embryos, as well as in larvae. Inducible expression of the toxin in various strains resulted in larval arrest and rod phenotypes. The authors then characterized the genetic variation of 550 wild isolates at the toxin/antidote region on LGV and distinguished three clades: (1) one with the conserved TA system, (2) one having lost the toxin and retaining a mostly functional antidote, and (3) one having lost the antidote and retaining a divergent yet coding toxin (this includes the reference strain Bristol N2, in which the homologous toxin gene has acquired mutations and is known as B0250.8). Further, the authors show that this region is under positive selection. These data are compelling and provide very strong evidence of a new TA system in this species.

      Weaknesses:

      The question remained as to how one clade, including N2, could retain the toxin gene but not possess a functional antidote. In the second part of the manuscript, the authors hypothesized that small RNA targeting (RNAi) of the toxin transcript could provide the necessary repression to allow worms to survive without the antidote. Through a meta-analysis of multiple small RNA datasets from the literature, the authors found evidence to support this idea, in which the toxin transcript is targeted by 22G siRNAs whose biogenesis is dependent on the Mutator foci protein, MUT-16. They note that from previous studies, mut-16 null mutants displayed a varied penetrance of larval arrest. In their own hands, mut-16 mutants displayed 15% varied larval arrest and 2% rod phenotypes. In an attempt to link B0250.8 to mut-16/siRNAs, they made a double mutant and examined body length as a proxy for developmental stage. Here, they observed a partial rescue of the mut-16 size defect by B0250.8 mutation. Finally, the authors also highlight data from further meta-analysis, which predicts the recognition of B0250.8 by several piRNAs. Also based on existing data from the literature, the authors link loss of Piwi (PRG-1), which binds piRNAs, to a depletion of 22G-RNAs targeting B0250.8 and an upregulation of B0250.8 expression in gonads, suggesting that piRNAs are the primary small RNAs that target B0250.8 for downregulation. The data in this portion of the manuscript are intriguing, but somewhat preliminary and incomplete, as they are based on little primary experimentation and a collection of different datasets (which have been acquired by slightly different methods in most cases). This portion of the study would require subsequent experimentation to firmly establish this mechanistic link. For example, to be able to claim that "the N2 toxin allele has acquired mutations that enable piRNA binding to initiate MUT-16-dependent 22G small RNA amplification that targets the transcript for degradation" the identified piRNA sites should be mutated and protein and transcript levels analysed in wild-type and in the strain with mutated piRNA sites. At a minimum, the protein levels in wild-type and mut-16, prg-1, and/or wago-1 mutants should be measured by western blot and/or by live imaging (introducing a GFP or some other tag to the endogenous protein via CRISPR editing) to show that the toxin is not accumulated as a protein in wt, but increases in levels in these mutants. mRNA levels in Figure S5A suggest there is still some expression of the B0250.8 transcript in a wild-type situation.

      We thank the reviewer for their thoughtful assessment of our manuscript, and we appreciate that they recognized that the data linking the small RNA machinery to B0250.8 suppression is intriguing. While the reviewer claims our analysis is preliminary and incomplete, we believe we present an appropriate multi-faceted approach for establishing the small RNA-mediated suppression mechanism we describe. 

      First, the reviewer states that we rely on “little primary experimentation”. Our primary experiments show that loss of the N2 tmrl-1 allele partially rescues ∆mut-16 developmental delay and arrest phenotypes. Therefore, we provide direct evidence that the N2 tmrl-1 functionally contributes to the ∆mut-16 phenotype. Furthermore, we overexpressed the N2 tmrl-1 allele to show that this gene is a toxin.

      It is true that we use previously published datasets to establish a small RNA-mediated mechanism that likely explains our observations. The reviewer suggests that our claims are weakened by relying on a “collection of different datasets (which have been acquired by slightly different methods in most cases)”. We believe instead that evidence collected from multiple labs using an array of different techniques strengthens our conclusions. We show that N2 tmrl-1-targeting small RNAs have been identified across multiple datasets (references 26, 32, 33, 34). Taken together, these datasets support a mechanistic framework for the suppression of the N2 tmrl-1 that involves PRG-1-dependent piRNA binding, MUT-16-dependent 22G siRNA, and the secondary Ago WAGO-1 binding. 

      The reviewer suggests several experiments, but we do not view them as essential to support our claims. 

      (a) piRNA site mutatagenesis: we present multiple lines of evidence that the N2 tmrl-1 transcript is post-transcriptionally targeted by small RNAs in a piRNA-mediated manner, not that specific piRNA sites are necessary and sufficient for this silencing. The suggested experiment would be valuable for future work, but is beyond the scope of our study.

      (b) Characterization of TMRL-1 protein levels: We agree that this experiment would provide definitive evidence of complete small RNA-mediated suppression of the N2 tmrl-1 transcript. As we explain above, however, we do show that removing the N2 tmrl-1 allele partially rescues the ∆mut-16 growth defect, demonstrating that when this gene’s regulation is disrupted, it induces toxicity. Importantly, we observed no tmrl-1-induced toxicity when we overexpressed a version of this gene with a stop codon, indicating that it acts as a protein.

      Finally, the reviewer questions our claim that: "the N2 toxin allele has acquired mutations that enable piRNA binding to initiate MUT-16-dependent 22G small RNA amplification that targets the transcript for degradation."

      We agree that this statement is too definitive given our current data. We have revised it to: "Multiple lines of evidence suggest that the N2 tmrl-1 allele is recognized by piRNAs, leading to MUT-16-dependent 22G siRNA production and post-transcriptional silencing of the transcript."

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The paper suggests that antidote pseudogenization occurred because RNAi replaced its function, but does not explore whether this process is ongoing or complete across all N2-like strains.

      We explored this possibility, but we realize that we did not explicitly state so in the manuscript. The B0250.4 (amrl-1) gene is pseudogenized in all strains within the N2 clade. We have modified the following sentence in the results section to explicitly state this observation:

      “While the previously described C. elegans TA elements are characterized by their absence in susceptible strains (2, 3), all members of the N2-like susceptible clade harbor a divergent allele of tmrl-1 with an intact coding sequence, as well as a pseudogenized version of amrl-1.”

      (2) Some figures (e.g., allele frequency distortions) could benefit from additional annotations to guide interpretation. In general, the figures make the reader work harder than they need to.

      We attempted to add clarity to figure captions for clarity.

      Although mll-1 and smll-1 were identified as toxin and antidote genes, their molecular mechanisms remain unclear and are very interesting.

      We agree that identifying the molecular mechanism associated with the toxin and antidote would be of interest, but is beyond the scope of the current paper.

      Reviewer #2 (Recommendations for the authors):

      (1) Because the rod phenotype was important in identifying the TA system, it seems important to include representative images of this phenotype throughout the paper.

      We added a supplemental figure showing the resulting self progeny from a QX1211/XZ1516 heterozygote: Fig S1B

      (2) In Figure 2A, we were confused as to why there were so few reads of mll-1. We may be misunderstanding something, so could the authors explain this to us? We would have expected more reads of mll-1, given the diagram showing that the breakpoints of the NIL were beyond (closer to the right end of) the mll-1 locus, and the phenotype correlates with the presence of the toxin (frequency of .20 L1 arrest).

      The lack of sequencing depth arises because the sequence divergence between QX1211 and XZ1516 is too high to accurately map short sequencing reads derived from QX1211 to the XZ1516 genome. We added the following sentence to the figure caption to add clarity:

      “The XZ1516 and QX1211 genome are so diverged that short reads derived from QX1211 don’t align to the XZ1516 genome in the 200 bp windows with no corresponding read depth, as indicated by a lack of a gray bar.”

      (3) The use of TOF in Figure 4 as a proxy of animal length instead of directly indicating or measuring animal length hinders the comparison of these results with other studies (i.e., most often in the literature, we see images of worms and measurements of their sizes or use of some other morphological marker to demonstrate the proportion of worms in a particular developmental stage). Nonetheless, we think the approach is clever and certainly enables analysis of a large sample population. However, a wild-type control is missing from these experiments to give a sense of the typical distribution one would expect. Without this, one interpretation of the B0250.8 knock out data shown in B is that loss of B0250.8 results in ~10% arrested larval, which seems higher than would be expected for a wild type N2 strain, and should be explained-but again, if the wild type control showed the same pattern, that would be useful to know. The title for Figure 4 should be revised, as this figure suggests, but does not provide definitive evidence that B0250.8 is suppressed by sRNAs/sRNA pathways. See the next point for providing more definitive data to support this model.

      There is a long list of publications that rely on the large particle sorter to infer how growth rate is affected in various mutants and environmental conditions (See Andersen et al. 2015, ref 28 in the manuscript, and the papers that reference this work). As the reviewer pointed out, the use of time of flight, which is simply the amount of time an object obstructs a laser at a constant flow rate, enables accurate measurement of tens of thousands of individual animals for comparison. 

      The reviewer is correct to point out that without a wild type N2 control, it is impossible to tell what a typical distribution looks like. However, the experiment includes all strains necessary to make the comparisons that enable us to draw the conclusion that the N2 tmrl-1 allele contributes to larval arrest in the absence of MUT-16.

      We agree with the reviewers point that this figure does not provide evidence that B0250.8 is suppressed by small RNAs and we have therefore changed the figure title.

      The new figure title: The N2 tmrl-1 allele contributes to larval arrest in the absence of MUT-16

      (4) To be able to claim that "the N2 toxin allele has acquired mutations that enable piRNA binding to initiate MUT-16-dependent 22G small RNA amplification that targets the transcript for degradation" the identified piRNA sites should be mutated and protein and transcript levels analysed in wild-type and in the strain with mutated piRNA sites. At a minimum, the protein levels in wild-type and mut-16, prg-1, and/or wago-1 mutants should be measured by western blot and/or by live imaging (introducing a GFP or some other tag to the endogenous protein via CRISPR editing) to show that the toxin is not accumulated as a protein in wt, but increases in levels in these mutants. mRNA levels in Figure S5A suggest there is still some expression of the B0250.8 transcript in a wild-type situation.

      The reviewer makes several good suggestions for experiments to determine whether the conclusions we make from publicly available high-throughput sequencing datasets apply in our context. However, we disagree that the quoted statement “the N2 toxin allele has acquired mutations that enable piRNA binding to initiate MUT-16-dependent 22G small RNA amplification that targets the transcript for degradation” is not supported by the evidence we present from Reed et al. 2020. The data presented by Reed et al. clearly show that the N2 tmrl-1 transcript is heavily targeted by 22G siRNAs, and that the accumulation of these siRNAs depends on the presence of MUT-16 and PRG-1. The dependence on PRG-1 implicates piRNAs involvement in the mounting of a 22G response.

      (5) Importantly, it is not the mll-1/B0250.8 transcript itself that was not shown to interact with WAGO-1 in the Seroussi et al. eLife paper (Lines 257-259). This study investigated sRNAs associated with every AGO, and computationally inferred the targets of each AGO using those enriched sRNA sequences. Therefore, it is the siRNAs antisense to mll-1/B0250.8 that were detected in association with WAGO-1, making it likely that WAGO-1 is the secondary AGO that targets this transcript. The argument the authors make holds true, but the authors should revise how they describe the evidence supporting that argument to accurately reflect the existing data.

      Thank you for catching this mistake. We have updated the text to accurately reflect the results from the Seroussi et al 2023 publication:

      “Recent work has shown that the N2 tmrl-1 transcript-derived small RNAs co-immunoprecipitated with WAGO-1, providing additional evidence that this transcript is regulated by the endogenous RNAi machinery”

      (6) It seems likely that the authors explored the possibility that another antidote may be present in the third clade. Could they discuss what they did to rule out this explanation in lieu of piRNA/siRNA regulation?

      We did not look for another antidote in the third clade because this clade is defined by the presence of an antidote and the absence of a toxin. Figure 3C shows the result of a cross between a third clade strain (NIC195) and XZ1516. The conclusion we draw from this experiment is that the antidote present in NIC195 provides near complete resistance to the XZ1516 toxin.

      (7) Line 156, legend of Figure S3, and line 273: There was no marker used to indicate that these are the primordial germ cells. Best practices would indicate using a fluorescent marker (e.g., PIE-1 GFP or PGL-1 GFP or PRG-1 GFP, etc.) to definitively identify these as PGCs.

      We agree with the reviewer’s point. As we do not have the perfect experiment, we do not definitively state that tmrl-1 transcripts localize in the primordial germ cells. 

      Minor comments:

      (1) A minor suggestion: incorporating some of the results now shown in the supplementary figures - Figures S1, S3, and S4 - into the main figures may make the manuscript easier to read.

      We constructed the manuscript in a way we thought was straightforward. The figures listed by the reviewer are supplemental to the main conclusions of the manuscript, so we decided to leave them as supplemental figures.

      (2) Line 87, Figure S1A: include numbers in the y-axis.

      The numbers are included on the y-axis and we explain the x-axis tick marks in the figure caption.

      (3) Figures 1B, 2B, 3C, 4B, S1B, S4: statistical analyses missing.

      We have added a summary of the statistical analysis to the captions of Figures 1B, 2B, 3C, and S1B. We added more detail from the analysis of 4A, which is the figure we draw conclusions from. Figure S4 is observational data, and the only conclusion drawn from that figure is that the N2 tmrl-1 gene encodes a toxin. It is toxic in 100% of individuals we looked at and therefore doesn’t warrant statistics. 

      (4) Line 100, "The rod progeny were all homozygous for QX1211 alleles at the locus on the right arm of chromosome V that displayed the allele frequency distortion in the mapping populations". Is this supported by data? While there is strong evidence to suggest it, the way it is currently written makes it seem that the rod progeny have been genotyped (by sequencing or PCR?). Is this the case? If not, the authors should revise the statement accordingly.

      Yes, this is indeed the case and we have updated the text to reflect that we performed PCR of a QX1211-specific indel to verify the genotypes on the right arm of chromosome V.

      (5) Figure 2A: lower panel missing x axis label.

      The top panel is a cartoon representation of a NILs, and the x axis is labeled for the top panel, highlighting the mapped element. 

      (6) Line 140 to 148: The authors should provide data to support these statements.

      Realizing i skipped this one – these are the lines they are referring to -> Long-read RNA sequencing revealed two distinct mll-1 isoforms, a short isoform with three predicted exons and a long isoform with eight predicted exons (Fig. S2A). We constructed plasmids with inducible versions of each mll-1 isoform. When we injected susceptible strains with the short mll-1 isoform array, every F1 individual carrying the array died, with 64% of larvae exhibiting the rod phenotype, indicating that uninduced expression levels of the short mll-1 isoform are sufficient to induce lethality. By contrast, we were able to isolate susceptible strains that maintained the long mll-1 isoform array or a short mll-1 isoform array with a premature stop codon in mll-1. We observed no rod progeny upon induction of these arrays, indicating that the short isoform encodes the functional toxin, and that the toxin acts as a protein.

      (7) Line 193: It would be interesting to see if there is structural conservation between mll-1 and B0250.8 using alpha-fold. Have the authors done this?

      We did attempt to look for structural conservation but we found the confidence in the structural predictions to be very low, which didn’t warrant a comparison.

      (8) Line 206-207: Could the authors explain why the frequency of the rod phenotype is so low when presumably over-expressing B0250.8? Does this indicate that B0250.8 is not as functional a toxin as mll-1, or is it sufficiently repressed by sRNAs and not actually overexpressed? Further, what are "abnormal" phenotypes? This should be clarified for the reader.

      It is likely that the overexpression and misexpression of toxic proteins is causing the abnormal phenotypes. The rod phenotype probably manifests when the gene is expressed at the appropriate developmental stage and tissue to cause the phenotype, whereas abnormal phenotypes manifest when the expression is not in the correct stage or location. A summary of the observed phenotypes is provided in Supplementary Table 7.

      (9) Line 216 and thereafter: indicate that B0250.8 is now referred to as mll-1.

      We incorporated this suggestion.

      (10) Line 228-231: missing to state that this is shown in Figures 4A-B.

      This and the following comment suggests that we did not provide enough clarity in this section. We modified the line to the following:

      Consistent with this report, in an agar plate-based preliminary assay we observed that ~15% of ∆mut-16 progeny arrest at various larval stages, and 2% of progeny are rod, which is suggestive of derepression of tmrl-1 in N2.

      This lets readers know that this initial characterization of the mut-16 knockout strain is different from the data presented in figure 4.

      (11) Line 230: the Figure shows ~25% of arrest for the deletion mutant of mut-16, but the text says ~15%.

      The 15% the reviewer points out was obtained from a preliminary agar plate-based experiment where we attempted to characterize the mut-16 deletion strains. We turned to a more high-throughput approach to screen through more animals for each genotype, which we report in figure 4.

      (12) Line 233: TOF, and not animal length, was compared. The authors should indicate that TOF is used as a proxy for animal length.

      We made the suggested change. The new sentences read:

      To do so, we compared time of flight (TOF) measurements—a proxy for animal length, developmental stage, and growth rate (28)—between a strain with a single knockout of mut-16 and one with a double knockout of mut-16 and the N2 tmrl-1 (a strain with a single knockout of the N2 tmrl-1 served as a negative control). We observed a reduction in TOF and an increase in the fraction of worms in larval stages in the mut-16 knockout strain, and these effects were partially rescued in the double knockout strain (Fig. 4).

      (13) Line 237-239: This claim may be overstated without additional data. Consider adding a "likely" to the statement.

      The line in question: 

      These results indicate that the reduced growth rate observed in the mut-16 knockout strain is partially mediated by derepression of the N2 mll-1 allele.

      We modified it to reflect the reviewer’s concern: 

      These results indicate that the reduced growth rate observed in the mut-16 knockout strain is partially mediated by the presence of the N2 tmrl-1 allele, likely because tmrl-1 is derepressed in mut-16 knockout strains.

      (14) Line 257: Figure S5C should be moved to line 259.

      We made the suggested move. 

      (15) Is the name mll-1 firmly established? We ask because MLL1 is a human mutation commonly associated with leukemia, and it may lead to some confusion in the field. This is a minor point, but we wanted to bring it forth.

      This name was not firmly established. We modified the names to not overlap with known gene names:

      tmrl-1 - Toxin-induced Maternal Rod Lethality

      amrl-1 - Antidote of Maternal Rod Lethality

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Note: This preprint has been reviewed by subject experts for Review Commons. COntent has not been altered except for formatting.

      Reply to the Reviewers

      1. General Statements

      We thank the reviewers for their careful evaluation of our manuscript and for the many constructive suggestions. Overall, the reviewers found the identification of Msc1 as a glucose starvation-responsive NVJ-associated factor to be novel and potentially important, while also raising several important concerns regarding the mechanistic interpretation of our findings and the topology/localization of Msc1. We particularly appreciate the reviewers' comments regarding potential overinterpretation of several conclusions. In the revised manuscript we will substantially revise the wording throughout the text to more carefully distinguish correlation from causation and to avoid unsupported mechanistic conclusions. In addition, we plan to address the reviewers' concerns through a combination of additional experiments, revised data presentation, clarification of methodological details, and expanded discussion of alternative interpretations.

      1. Description of the planned revisions

      In the point-by-point response below, the reviewers' comments are presented in italics, and our responses are provided below each comment.

      Reviewer #1

      Comment:

      *This is a nice, smallish study of Msc1, a fungal protein of unknown function. The authors show it localises to the NVJ when that expands in late-log/stationary phase, at which stage its transcription is increased 80-fold - an induction one whole order of magnitude greater than shown by Nvj1 itself. This indicates that Msc1 may be a previously unappreciated master regulator of the NVJ. There are some interesting phenotypes of deleting Msc1, including some cell death and loss of Nvj1, mostly through destabilisation since the transcriptional effect is marginal. *

      *While no mechanism for Msc1 is discovered, that might be too much to ask for in this first paper. However, there are ways to begin to address this that the authors should look into. *

      *My major issue with the paper is that it makes no link to the previously studied homologues of Msc1 in S pombe (Ish1/Les1 - see Asakawa et all 2022). Admittedly, S. pombe has no Nvj1 homolog, but there is a physical relationship between nucleus and vacuole (Chadwick et al (2020) 10.1088/1478-3975/aba510). Also, the paper on Ish1/Les1 developed a phenotype to test Ish1 (toxicity of over expression) that might be useful for studies of Msc1. *

      *The current MS should link to work on Ish1/ Les1 in S. pombe, relating to several features: *

      *Topology. Given the high similarity between Msc1 and Ish1/Les1, they are (a priori) likely to share considerable form and function. If Msc1 is a soluble protein in the ER lumen, then the previous report that Ish1/Les1 have TMDs is wrong. The report here should make that link and carefully explain how the Pombe paper is wrong. Also explain how is it possible for Msc1 (and Ish1/Les1) to stay restricted to the nuclear envelope? (in many images it is diffuse throughout the NE). The only mechanism I can think of is binding an integral protein that sorts to the inner-NE by known mechanisms (or possibly binding to an outer-NE protein that binds to an inner-NE one, like SUN/KASH). I cannot think of any other example of a soluble proteins restricted to the NE - so this is quite a claim. An alternative view that could be investigated and should definitely be discussed is that Msc1 (and by implication Ish1 and Les1) has a TMD even though it is extracted by carbonate. Something similar has been reported for some single TMD proteins in mitochondria (Kim et al (2015) 10.1002/pro.2817). Investigations would include proteomics showing whether the protein is normally full length (as coded by the open reading frame) or clipped (indicating the signal sequence is removed for a soluble protein). Such data may already be available in published mass spec datasets. *

      We agree that the relationship between Msc1 and the previously characterized S. pombe homologs Ish1/Les1 should be discussed more carefully, particularly with respect to membrane topology. In the revised manuscript, we will cite and discuss the Ish1/Les1 studies and further investigate the topology and localization of Msc1 through several additional experiments. First, as suggested by the reviewer, we will examine whether the N-terminal region of Msc1, which is predicted to function as a signal sequence and as a weak transmembrane domain, undergoes proteolytic processing. To address this, we plan to perform mass spectrometry-based analyses and examine whether the N-terminus is retained in the mature protein. As an alternative approach in case the N-terminal peptide cannot be reliably detected by mass spectrometry, we will generate an Msc1 mutant lacking the predicted N-terminal 22-amino-acid signal sequence and compare its migration on SDS-PAGE with that of the full-length protein. This analysis should provide an additional assessment of whether the predicted signal sequence is removed during Msc1 maturation.

      In addition, following comments from multiple reviewers, we will repeat the alkaline carbonate extraction experiments using additional ER membrane protein controls to more carefully evaluate the membrane association properties of Msc1.

      Furthermore, we plan to perform additional split-GFP localization analyses to test whether Msc1 localizes within the perinuclear ER lumen. Specifically, we will express GFP1-10 either within the ER lumen or within the nucleoplasm and examine in which compartment co-expression of Msc1-GFP11 results in GFP fluorescence.

      Finally, as suggested by the reviewer, we agree that interactions with integral membrane proteins may explain the restricted localization of Msc1 within the nuclear envelope/NVJ region. In our preliminary experiments, we obtained results suggesting a physical interaction between Msc1 and Nvj2. Therefore, we plan to further investigate the interaction of Msc1 with Nvj2, as well as with other known NVJ-associated proteins, to better understand the mechanism underlying its localization and enrichment at the NVJ.

      *Minor Issues *

      *The Abstract switches from response to lack of glucose to terminology about 'stress-response'. This could appear to be an effort to appear more interesting. If the idea is to remain, it needs some support with the introduction of the idea that yeast experiences stress (as opposed to "normal" transcription driven programmatic changes in relation to changing levels of glucose in normal cultures. *

      To avoid overstating our findings, we will revise the Abstract and related text to use more precise terminology and to more clearly describe the observed responses.

      Introduction para 1 seems to be dedicated to the idea that a set of intracellular structures (here MCS) are 'dynamically and coordinately remodeled in response to metabolic and stress conditions'. This conclusion applies widely and may not be noteworthy. The paragraph needs a bit of rethinking.

      While nutrient-dependent changes in the NVJ itself have long been recognized, we believe that dynamic remodeling of multiple MCSs in response to environmental and metabolic conditions has only more recently become appreciated more broadly in the field. We therefore think that discussing the emerging concept that diverse MCSs undergo dynamic reorganization under different physiological conditions provides important context for the present study. Nevertheless, we will revise the Introduction to explain this point more clearly and concisely.

      Figure 2D: I could not find Nsg1 result described in the text.

      We will repeat the experiment independently and quantify the immunoblot results shown in Figure 2D. The resulting quantitative data will be added to Figure 2D, and the Results section will be revised accordingly to describe these findings, including the Nsg1 phenotype.

      P6: "Strikingly, GS-dependent transcriptional activation of NVJ1 was significantly suppressed in msc1∆ cells (Fig. 4B)." This overstates the strength of the result. Instead state that the induction diminishes from 6-fold to 4-fold, and give the p value.

      We will revise the text to provide a more quantitative description of the result, including the corresponding p value.

      *Language: Avoid use of rhetorical wording (e.g. dramatic): just state the results (e.g. 80-fold induction) and let the results be dramatic/striking etc. all by themselves.

      *

      We will also revise the text to avoid rhetorical wording and instead describe the results in a more direct and quantitative manner.

      Reviewer #2 * The study describes the finding of the nuclear envelope protein Msc1 as a new component of the membrane contact site nucleus vacuole junction (NVJ) under the conditions of glucose starvation. Msc1 has previously only been known as a nuclear envelope protein, presumably localizing to the nuclear lumen, and its role in DNA damage repair. The main finding of this study is the glucose starvation-induced upregulation and NVJ-localization of Msc1 (Figure 1). The second main finding is that the loss of Msc1 results in an impaired induction of the expression of Nvj1 (the main component of the NVJ, responsible for the formation of NVJ via direct interaction with Vac8) upon glucose starvation (Fig. 3 A). The effect of Msc1-loss on the Nvj1 expression levels is transcriptional (Fig. 4 B). The glucose starvation-mediated expression induction of some other previously identified NVJ components, Nsg1 and Nsg2 is also impaired in the msc1D mutant, while the expression of Ypf1 is affected to a lesser degree. The data supporting these two main findings are solid (Figure 1; Figure 3 A; Figure 4 A, B).

      The study further shows that the loss of Msc1 results in a loss of NVJ-localization of NVJ components Tsc13, Ypf1 and to a lesser degree Hmg2. The microscopy data looks solid, however the interpretation of this finding is not clear. In my view, the most likely explanation is that the effect of Msc1 loss on the localization of NVJ components to the NVJ is due to the impaired glucose starvation-induced Nvj1 expression in the msc1D mutant.

      MAJOR COMMENTS:

      Here are suggested experiments that would strengthen the study: - It is difficult to imagine how a NE protein could affect expression levels of other NVj proteins - this key finding would be supported by a complementation experiment where MSC1 is expressed from a vector - to test whether this rescues the phenotype (to make sure that the observed phenotype is not due to an off-target effect of msc1D deletion) *

      As suggested by the reviewer, we plan to perform complementation experiments by expressing Msc1 from a plasmid in msc1∆ cells to confirm that the observed phenotypes are specifically caused by loss of MSC1.

      *- If technically feasible under the glucose starvation conditions, this hypothesis could be tested by overexpressing Nvj1 from an inducible or some other promoter. *

      We agree that this is an important point. As suggested by the reviewer, we plan to overexpress Nvj1 using a constitutive promoter and examine whether this suppresses the phenotypes observed in msc1∆ cells.

      *- The effect of msc1D deletion on Tsc13 proteins levels (preferentially using the same Tsc13-GFP strain as used in microscopy - anti Tsc13 or anti-GFP antibodies could be used) *

      We will examine Tsc13 protein levels in msc1∆ cells using the same Tsc13-GFP strain used for microscopy.

      *- The results concerning the localization of Msc1-GFP in elo3D mutant have been interpreted as "accelerated localization", "expansion of the the size of Msc1-NVJ domain" etc. However, the levels of Msc1-GFP in the elo3D mutant are higher compared to WT (Figure 2 D). Considering this, it is very likely that the larger surface area measured in the elo3D mutant is a consequence of this. This could be potentially checked by comparing images set of WT and elo3D that are set to a similar fluorescence intensity. In any case, this possibility should be definitely addressed in the interpretation of the result. *

      We agree that the increased Msc1-GFP signal in elo3∆ cells could contribute to the apparent increase in NVJ area. However, in our previous study (Fujimoto and Tamura, 2026, J. Cell Biol.), we observed accelerated NVJ expansion under glucose starvation and in elo3∆ cells using Ypf1, whose expression levels are largely unchanged under these conditions. We therefore think that the observed phenotype is unlikely to be explained solely by increased Msc1 expression. Nevertheless, because Msc1 protein levels are clearly elevated in elo3∆ cells, we will revise the text to describe these results more carefully and fairly, while citing our previous findings.

      *- There is an impression that the data has been overinterpreted, and the conclusions should be written much more carefully. Examples: o "Here, we show that Msc1 is a GS-responsive NVJ factor that plays an important role in functional NVJ remodeling." - based on data shown, the effect of Msc1 could be indirect. The statement above should be re-written or argumented much better. o "we find that GS-dependent induction of NVJ1 transcription is attenuated in msc1Δ cells, suggesting that proper NVJ remodeling contributes to the execution of stress-responsive transcriptional programs" - this is unclear; which data support this? o "Together, these findings position Msc1 as an upstream regulator linking GS signaling to functional maturation of the NVJ and associated cellular adaptation responses." - same comment as above o "...suggesting that Msc1 functions as a GS-responsive regulator of NVJ functions." o "...these findings suggest that Msc1 acts upstream of Ypf1 in orchestrating GS-induced NVJ functional maturation." o "Collectively, these results indicate that Snf1 acts upstream of Msc1 to drive GS-induced NVJ remodeling, whereas reduced Elo3 activity further accelerates this process and promotes Msc1 accumulation." - not sure if the available data support this. o "These results indicate that although Msc1 ...... it is required for efficient GS-dependent functional maturation of the NVJ domain." o "These observations suggest that loss of Msc1 does not cause a general defect in transcriptional activation but rather impairs the proper execution and dynamic range of GS-dependent transcriptional responses." - this is unclear o "Within this context, the robust induction of NVJ1 appears to be particularly sensitive to Msc1 deficiency." - this sentence would benefit from being re-written. o "Together, these results indicate that Msc1 contributes to transcriptional reprogramming associated with NVJ remodeling during GS." - this sounds overstated. o "the observation that loss of Msc1 attenuates GS-dependent induction of NVJ1 raises the possibility that NVJ remodeling influences stress-responsive gene expression programs." *

      We appreciate the reviewer's concern that several interpretations in the current manuscript may extend beyond what is directly supported by the available data. We will therefore revise these statements throughout the manuscript to provide more balanced interpretations and avoid overstating our conclusions. In addition, several planned experiments, including complementation analyses, Nvj1 overexpression experiments, additional localization analyses, quantitative protein analyses, and identification of NVJ-associated proteins that interact with Msc1, may further clarify the relationship between Msc1, NVJ remodeling, and glucose starvation responses. We will revise the text accordingly based on the results obtained from these additional experiments.

      *OTHER COMMENTS FIGURE BY FIGURE - SOME ARE MAJOR (overlapping to the above comments), SOME ARE MINOR: *

      *Figure 1: *

      *Figure 1 A and B shows that Msc1-GFP expression is upregulated in cells starved for glucose for 24h, but not in nitrogen-starved cells. *

      *o Size of the markers (protein ladder) would be helpful. * We will reprocess the immunoblot images from the original data and revise the figure layout to include molecular weight markers.

      *Figure 2: - Comment: It is not clear if these are the same strains as analyzed by microscopy (GFP-tagged Msc1). This should be specified in the Figure legend 2 D. *

      *- Comment: o Since the levels of Msc1-GFP in the elo3D mutant are higher compared to WT (Figure 2 D), the larger surface area measured in C may be a consequence of this. *

      *o It is not clear if Figure A and D analyze the same strains (western blot and microscopy - do both show GFP-tagged Msc1? - using anti-GFP?). This should be specified in the Figure legend 2 D. Since the increased area measured in Figure 2 C could be due to increased Msc1-GFP levels in this mutant strain, the WB should check the levels of Msc1-GFP in the same strain and under same conditions as analyzed in Figure 2 C.

      o Does Tim23 serve as a loading control in Figure 2 D? *

      We added "Tim23 was used as a loading control." In the legend of Figure 2D.* o Would be good to have protein ladder sized marked in Western blots o Since the increase in Msc1 levels in the elo3D mutant could be significant for the interpretation of the results, it would be helpful to have quantification of the protein levels in WB (normalized to a loading control). *

      We will clarify in the Figure 2 legend that Figure 2A shows GFP-tagged Msc1 expressed cells analyzed by fluorescence microscopy, whereas Figure 2D shows untagged strains analyzed by immunoblotting using an anti-Msc1 antibody. We will also clarify that Tim23 was used as a loading control and add molecular weight markers to the Western blots. We agree that the increased Msc1-GFP levels in elo3∆ cells could influence the apparent increase in NVJ area measured in Figure 2C. As noted above, our previous findings using Ypf1 suggest that accelerated NVJ expansion in elo3∆ cells is unlikely to be explained solely by increased Msc1 expression (Fujimoto and Tamura, J. Cell Biol., 2026). Nevertheless, we acknowledge that elevated Msc1-GFP levels could influence the apparent NVJ area measured in Figure 2C. We will therefore revise the text to more carefully describe these results and discuss them in the context of our previous findings.

      In addition, we will quantify the Western blot signals in Figure 2D normalized to the loading control and include these data in the revised manuscript.

      Figure 3 ** Together these data show that localization of other NVJ-proteins to the NVJ depends on the presence of Msc1. Comment: - From the available data it is possible that Msc1 recruits these components by direct interaction, or by modifying the structure of NVJ, or functions in an indirect manner - this should be discussed in the Discussion. Comment: - The signal of Tsc1-GFP in log-growing cells is very weak, therefore the quantification may be unreliable. I would remove this condition (log-grown cells) form the quantification in C) due to the low signal, since it is not crucial to the interpretation of the data. If the authors prefer to leave it, that is fine. - The title of the Figure 3 is "Msc1 supports stability and recruitment of NVJ-associated proteins" - I am not sure what "stability" is; the data don't address stability or recruitment in a direct manner - I suggest to change the figure title into a statement describing what is shown in the Figure, for example: "The loss of Msc1 results in decreased Nvj1 levels and a decreased localization of NVJ proteins to the NVJ). And have a comment that this data suggests that Msc1 supports recruitment of NVJ-associated proteins, likely in an indirect manner, based on the finding that the loss of Msc1 leads to a lower expression of Nvj1, in the main text (e.g. in the Discussion). - Is it possible that the loss of Msc1 on the loss of NVJ-localized Tsc13 is due to the downregulation of Tsc13 expression? Considering the effect of msc1D deletion on the expression of some NVJ proteins (Figure 3 A), Tsc13 expression levels would be good to be checked, considering the effect of msc1D on Tsc13-GFP localization. It would be optimal to do the WB with the same Tsc13-GFP-expressing strain and under the same growth conditions as was used in the microscopy in the Figure 3 B. - Expression levels of Ypf1 are lower in the msc1D strain, than in the WT (Fig. 3 A) - could this affect lower NVJ-area in his mutant? (Fig. 3 B)

      We agree that the current data do not distinguish whether Msc1 affects localization of NVJ-associated proteins directly, indirectly through changes in NVJ structure, or through other indirect mechanisms. We also agree that the term "stability" used in the current Figure 3 title is not sufficiently supported by the available data, as our experiments do not directly address protein stability. To address this issue, we plan to overexpress Nvj1 in msc1∆ cells and examine the expression and localization of NVJ-associated proteins including Nsg1 and Nsg2. Based on the results obtained from these additional experiments, we will revise the Figure 3 title and discuss these possibilities more carefully in the revised manuscript.

      Regarding the quantification of Tsc13-GFP localization in log-growing cells, although the NVJ signal is relatively small and weak under these conditions, we confirmed the signal carefully during quantification. In addition, we consider this dataset important because it suggests that the effect of Msc1 is relatively limited during logarithmic growth. Therefore, we currently prefer to retain these data in the revised manuscript.

      As suggested by the reviewer, we will revise the Figure 3 title to more directly describe the observed phenotypes.

      We will also examine Tsc13 protein levels in msc1∆ cells using the same Tsc13-GFP strain and growth conditions used for the microscopy analyses. In addition, we will quantitatively analyze expression levels of Ypf1 and other NVJ-associated proteins in msc1∆ cells and discuss how these changes may contribute to the observed localization phenotypes.

      *Figure 4. Figure 4 A shows mRNA levels in glucose starved cells compared to log-.growing cells for MSC1, NVJ1 and YPF1. - Comment: I would move Figure 4 A to Figure 1. Figure 4 B shows mRNA levels of proteins expressed in WT and msc1D mutant strain, in log-growing cells in under glucose starvation. The data show that the loss of Msc1 leads to a decrease in NVJ1 mRNA under the conditions of glucose starvation. Th expression of other NVJ proteins analyzed are not affected. - Comment: Would this Figure 4 A-B better fit together with the data showing Nvj1 levels in the msc1D mutant from a previous figure (3 A)? *

      *Figure 4 C shows PI staining of cells after 5 days of glucose starvation. The loss of Msc1 leads to a double increase in PI-positive cells (in contrast to the nvj1D mutant, which is similar to WT), indicating that the viability of cells after 5 days of glucose starvation is decreased in the absence of Msc1. - Comment: Since there is no phenotype of nvj1D, this is likely not due to the non-functional NVJ, but another function of Msc1 - the question is which. This could be discussed in the Discussion. - Comment: This is informative, however it is not sure why this data is placed together with the mRNA data within the Figure 4. *

      We appreciate these suggestions and agree that the figure organization could be improved. Following the reviewer's recommendations, and taking into account the results of the additional experiments described above, we will reorganize the figure layout to better align related datasets and improve the overall flow of the manuscript. We also agree that the increased PI staining observed in msc1∆ cells is unlikely to be explained solely by loss of NVJ function, since nvj1∆ cells do not show a comparable phenotype. We will therefore discuss this point more carefully in the revised Discussion and consider additional functions of Msc1 that may contribute to cell survival during glucose starvation.

      Figure S1. - Comment - as in Figure 2 - Msc1-GFP has a much stronger signal in elo3D mutant, than in WT, which could influence (or likely influences) the measured area. Perhaps one way to test this is to image WT cells with higher % of laser "a "longer exposition"), to get a stronger signal similar to that seen in the elo3D mutant, and then repeat the quantification.

      • Taken the result as it is presently, I suggest taking the Figure S1 out.

      As discussed above for Figure 2C, increased Msc1-GFP levels in elo3∆ cells could influence the apparent increase in NVJ area. We agree that this analysis is not central to the main conclusions of the current manuscript. Therefore, together with the additional experiments described above, we will re-evaluate the organization of the supplementary figures and revise the figure layout accordingly. Based on the revised dataset, we will determine whether Figure S1 should be removed, relocated, or incorporated into a more appropriate context in the revised manuscript.

      *Figure S3 . Validation of anti-Msc1 antibody - Could be moved as S1. *

      We will move the current Figure S3 to Figure S1 in the revised manuscript.

      Reviewer #3

      *Summary: In this study, the authors identify Msc1 as a factor associated with nucleus-vacuole junctions (NVJs) during glucose starvation. Using Saccharomyces cerevisiae as a model system, and combining immunoblotting and microscopy approaches, they report a functional connection between Msc1 and the NVJ component Nvj1.

      Major comments: - Are the key conclusions convincing? Overall, the main conclusions are largely convincing. However, several interpretations are overstated and should be phrased more cautiously (see specific comments below).

      • Should the authors qualify some of their claims as preliminary or speculative, or remove them altogether? Yes. In several instances, the data support correlation rather than causation, and the authors should clearly indicate when conclusions are speculative.

      • Would additional experiments be essential to support the claims of the paper? Request additional experiments only where necessary for the paper as it is, and do not ask authors to open new lines of experimentation. For some conclusions, either:

      • the interpretation should be weakened, or
      • additional experiments are needed to fully support the claims

      • Are the suggested experiments realistic in terms of time and resources? It would help if you could add an estimated cost and time investment for substantial experiments. If Western blot membranes are available, additional controls could likely be addressed by reprobing, which would require minimal effort and a short timeframe. Suggested microscopy experiments would require strain construction and are therefore expected to take approximately 2-3 weeks.

      • Are the data and the methods presented in such a way that they can be reproduced? Some methodological details are insufficiently described and should be clarified to ensure reproducibility.

      • Are the experiments adequately replicated and statistical analysis adequate? The authors do not specify which tests for normality were performed. It is therefore difficult to assess whether the use of Student's t-test is appropriate. In at least one case (comparison of three groups), a t-test is not appropriate and should be replaced with a suitable multiple-comparison test.

      Minor comments: - Specific experimental issues that are easily addressable. See below

      • Are prior studies referenced appropriately? Yes, mostly/ The authors should provide a reference supporting NVJ expansion during nitrogen starvation.

      • Are the text and figures clear and accurate? Yes

      • Do you have suggestions that would help the authors improve the presentation of their data and conclusions? see below *

      We appreciate the reviewer's overall positive evaluation of our study and the recognition that the main conclusions are largely convincing. We also appreciate the reviewer's careful and constructive suggestions regarding interpretation, experimental support, and presentation of the data. As also pointed out by other reviewers, several interpretations in the current manuscript may extend beyond what is directly supported by the available data. We will therefore revise the manuscript throughout to more clearly distinguish between observations directly supported by the data and more speculative interpretations, and to avoid overstating our conclusions. In addition, we are currently performing several additional experiments, including complementation analyses, Nvj1 overexpression experiments, quantitative protein analyses, and additional localization studies, which may further strengthen some of the interpretations. We will also revise the Methods section to provide more detailed information regarding experimental procedures, statistical analyses, and reproducibility. In addition, we will reanalyze the data using appropriate statistical methods where necessary. In addition, we will revise and reorganize several figures and figure legends, and methodological details, and improve the overall presentation and clarity of the manuscript. We will also add references regarding NVJ expansion during nitrogen starvation as suggested by the reviewer.

      *Figures and data presentation • Figure 1A: The image is difficult to interpret. The authors should improve visibility, for example by: o using grayscale instead of magenta/green for single channels, or o applying an intensity LUT. This is particularly important as the Nvj1 signal is barely visible.

      *

      We will revise Figure 1A to improve visibility of the fluorescence signals, including the Nvj1 signal, by adjusting the image presentation methods as suggested by the reviewer.

        • Figure 1B: The use of Tim23 as a loading control is not appropriate. The authors should justify why a mitochondrial protein was used as a reference.* Although Tim23 is a mitochondrial protein, we previously confirmed that its abundance is not substantially affected by glucose starvation conditions and therefore serves as a suitable loading control in this experimental setting (Fujimoto and Tamura, J. Cell Biol., 2026). In the revised manuscript, we will clarify the rationale for using Tim23 as a loading control. We will also normalize immunoblot signals to Tim23 and explicitly state this in the text.
      • Figure 1C: The experimental design and interpretation are problematic: o Using an ER protein together with mitochondrial markers in the proteinase K protection assay is not appropriate for the stated conclusions. * Because ER and mitochondrial membranes are both present in the membrane fraction used for the proteinase K protection assay, we believe that mitochondrial marker proteins can still serve as controls for proteinase K accessibility. However, we agree that the integrity of the ER membrane itself was not directly assessed in the current experiment. We therefore plan to repeat the experiment using appropriate ER membrane protein controls.

      *o The claim that Msc1 is not an integral membrane protein is not sufficiently supported, particularly if a polyclonal antibody was used. *

      Similar concerns regarding the topology and membrane association of Msc1 were also raised by other reviewers. To address these issues, we are currently performing additional experiments, including detailed analyses of the N-terminal region of Msc1 and further localization studies (see also our response to the first comment from Reviewer #1). We also plan to examine the fission yeast Msc1 homolog Les1, whose localization has been analyzed in greater detail previously (Asakawa et al. Genes Cells. 2022, 27(11):643-656. doi: 10.1111/gtc.12981). In addition, we are currently investigating NVJ-associated proteins that interact with Msc1, which may provide further mechanistic insight into the localization and function of Msc1 at the NVJ.

      *o The authors should provide additional evidence for localization (or use alternative approaches). *

      As also mentioned in our response to Reviewer #1, we plan to perform additional localization analyses using a split-GFP approach. Specifically, we will express GFP1-10 either within the ER lumen or within the nucleoplasm and examine in which compartment co-expression of Msc1-GFP11 results in GFP fluorescence.

        • Figure 1D: o The authors conclude that deletion of NVJ1 and VAC8 reduces Msc1 colocalization. However, an alternative explanation is that NVJs are not formed under these conditions. o This conclusion should therefore be phrased more cautiously. Alternatively, a known NVJ marker should be included to demonstrate NVJ formation. *

      We agree that reduced Msc1 localization in nvj1 and vac8∆ cells could simply reflect impaired NVJ formation itself. To address this possibility, we plan to examine NVJ formation in these mutants using split-GFP-based NVJ probes that we previously developed (Tashiro et al., Front Cell Dev Biol. 2020, doi: 10.3389/fcell.2020.571388). If NVJ formation is indeed disrupted under these conditions, we will revise the interpretation more cautiously.

      *o The argument involving Ypf1 is weak, as the observed effect could be indirect and mediated via another factor. *

      The relationship between Msc1 and Ypf1 will be described more cautiously in the revised manuscript.

        • Figure 2B: The statistical analysis (Student's t-test) is not appropriate for the dataset presented.* The statistical analysis for Figure 2B will be revised using a more appropriate method.
        • Additional point: The authors again use a mitochondrial protein as a loading control in Figure 1D, which requires justification. As mentioned above, Tim23 used as a loading control was selected based on our previous study showing that its abundance remains unchanged during glucose starvation (Fujimoto and Tamura, J. Cell Biol.* 2026). This explanation will be added to the revised manuscript.

      *Conceptual interpretation • The link between transcriptional reprogramming and NVJ remodeling is not convincingly demonstrated. The data suggest a temporal correlation but do not establish causality. • The PI staining experiments show increased cell death in the absence of Msc1. However, a causal relationship to NVJ function is not demonstrated. An alternative explanation (e.g., an additional role of Msc1 in processes such as DNA repair) should be considered or discussed. *

      These points will be appropriately discussed in the revised manuscript, taking into account the results of additional experiments, including those examining the effects of Nvj1 expression in msc1∆ cells.

      • The claim that Msc1 localizes to the perinuclear space is not sufficiently supported: o Appropriate ER/nuclear envelope controls are missing. As noted above, we will perform additional split-GFP-based analyses to further investigate the localization of Msc1.

      we will perform additional experiments to further examine the membrane topology of Msc1, including controls using antibodies against ER proteins and alkaline extraction analysis of Les1, a fission yeast homolog of Msc1 with a characterized membrane topology. In addition, we will test whether Les1 can complement the msc1∆ mutant.

      *o As an alternative, structural predictions (e.g., transmembrane helix prediction) could strengthen this claim. *

      The N-terminal region of Msc1 is predicted to function as a weak transmembrane segment and a signal sequence. We will incorporate these predictions into the revised manuscript and perform additional experiments to examine the topology and potential processing of this region as mentioned above.

      *Literature and references • The authors should provide a reference supporting NVJ expansion during nitrogen starvation.

      *

      The appropriate reference will be cited in the revised manuscript.

      *Methods • The antibody section is incomplete; all antibodies used need to be specified. *

      The antibody information will be completed in the revised Methods section.

        • Cultivation conditions require more detail: o duration of growth o timing and conditions of glucose starvation shift

      * The cultivation conditions will be described in greater detail in the revised Methods section.

      2. Description of the revisions that have already been incorporated in the transferred manuscript

      Reviewer#1

      Previous reports of Msc1 in patches (page 3): the citation of Breker et al (LOQATE) seems wrong because that database shows Msc1 at the ER not at NVJ; Medina-Suarez et al is also not great: it shows NE w some patches - not high penetrance + some cER. So I suggest the authors simply rely on their own BioRxiv paper.* *

      We agree that the LOQATE database only weakly shows punctate localization of Msc1 and will therefore remove this citation. However, we believe that Medina-Suarez et al. still provides relevant support because Msc1 exhibits a localization pattern resembling the NVJ in a subset of cells, and therefore we plan to retain this reference.

      Table S1: needs Msc1-GFP adding to some lines.

      We revised Table S1 accordingly.

      *Avoid unnecessary abbreviations: GS creates a novel word that has no obvious meaning and makes the manuscript hard to read rapidly. It would be better to use "glucose starvation" in all cases, especially the abstract. *

      P7: "These results indicate that loss of Msc1 impairs NVJ function more severely than loss of Nvj1 alone." Here NVJ function might not be the target of Msc1 deletion, since nvj1-deletion does not show increased cell death. Also, in general very little is known about NVJ function as very few phenotypes can be pinned down to loss of the NVJ. Better here to say "cell function" (that may involve some aspect of Msc1's interactions at NVJs) instead.

      We revised the wording accordingly.

      Reviewer#2

      *- It is not certain what the term "stability of multiple NVJ proteins" means. Could another term be used, or this explained? *

      We agree that the term "stability" could imply a specific mechanism that is not directly demonstrated in our study. Therefore, we have revised the text to more accurately reflect our findings by referring to the abundance of NVJ proteins rather than their stability: "Together with these observations, our results suggest that Msc1 plays a central role in maintaining the abundance of multiple NVJ proteins, including Nvj1, Ypf1, Nsg1, and Nsg2, during glucose starvation."

      *o The title of the Figure 2 is: "Snf1 signaling and VLCFA metabolism modulate NVJ partitioning of Msc1" - what is "NVJ partitioning" - for me it would be clearer to write "Snf1 signaling and VLCFA metabolism modulate the localization of Msc1 to NVJ" *

      As suggested by the reviewer, we will revise the Figure 2 title from "Snf1 signaling and VLCFA metabolism modulate NVJ partitioning of Msc1" to "Snf1 signaling and VLCFA metabolism modulate the localization of Msc1 to the NVJ."

      *Figure 1 A and B shows that Msc1-GFP expression is upregulated in cells starved for glucose for 24h, but not in nitrogen-starved cells. - Comments: o Is Tim23 used as a loading control? If yes, it should be stated in the figure legends and/ or main text. *

      We have revised the figure legends to indicate that Tim23 was used as a loading control.*

      *

      • *

      *o Which antibody is used for Western in B? *

      We have revised the figure legend to specify that the immunoblots shown in Fig. B were probed with anti-Msc1, anti-Nvj1, anti-Ypf1, and anti-Tim23 antibodies.

      * - Comment: It would be helpful to explain the abbreviation "PK" in Figure 1C Figure legend. *

      We have revised the Figure 1C legend to define PK as proteinase K.

      * Figure 1 D: Msc1-GFP localization to the NVJ is dependent on Nvj1, Vac8, but not Nsg1 and 2 and Ypf1 - Comment: a typo: "(D) Fluorescence microscopy images of the indicates strains..." should be "indicated". - Comment: "Single focal planes were shown." Would be better in present tense "are shown". *

      We have corrected "indicates" to "indicated" and revised "Single focal planes were shown" to "Single focal planes are shown" in the Figure 1D legend.

      *Figure S2. - The list of genes analyzed and the conditions analyzed are different in the figure and in the legend. Probably the figure is correct. *

      We revised the Figure S2 legend.

      3. Description of analyses that authors prefer not to carry out

      Reviewer#1

      Comment:

      Function/structural form: the manuscript is light on describing what Msc1 is: it shares the same repeat structure that has been described in Ish1/Les1. The S pombe work described the repeats wrongly as motifs, when AlphaFold2 confidently predicts them as structurally characteristic domains with 2 parallel helices separated by a loop. It would be interesting to speculate a bit on how these might function in the NVJ. One major mystery of the NVJ is the extreme uniformity, shown especially well by cryo-ET (MIllen et al (2008) 10.1111/j.1600-0854.2008.00789.x). This suggests some long-range oligomerisation: is it possible that Msc1 provides that? Possible experiments include expressing Pombe Ish1/Les1 either whole or chimeras with Msc1 to see if they function and are extractable. If that is not to be done here it should at least be discussed.

      Regarding the suggested experiments using S. pombe Ish1/Les1 or chimeric constructs, we agree that these would be interesting approaches. However, because we plan to prioritize additional analyses of Msc1 topology, including detailed characterization of the N-terminal region and repeated alkaline carbonate extraction experiments using ER membrane protein controls, we do not currently plan to pursue extensive chimera-based functional analyses within the scope of the present revision.

      With respect to the possibility that Msc1 contributes to long-range oligomerization underlying the structural uniformity of the NVJ, we currently consider this possibility less likely. In density-gradient centrifugation analyses performed under mild detergent conditions, the apparent molecular size of Msc1 was not particularly large, and we therefore did not obtain evidence supporting formation of a stable large oligomeric complex by Msc1.

      Reviewer#2

      - The authors refer to a previous study showing that nvj1D deletion does not affect protein levels of several NVJ proteins, however, it would be nice to have this data shown here - i.e. the localization of Tsc13, Ypf1 (and Hmg2) in the nvj1D mutant, especially since the study cited has not been peer-reviewed yet: "Notably, our previous work showed that loss of Nvj1 or Ypf1 does not affect the protein levels of each other or those of other NVJ-associated factors such as Nsg1 and Nsg2 (Fujimoto and Tamura, 2025)."

      We believe this point may reflect two partially distinct issues: (i) whether loss of Nvj1 affects the protein levels of NVJ-associated factors, and (ii) whether loss of Nvj1 affects their NVJ localization. In our previous study, we showed that loss of Nvj1 does not affect the protein levels of Ypf1, Nsg1, or Nsg2, whereas their NVJ localization does require Nvj1 (Fujimoto and Tamura, 2026; J Cell Biol. 225. doi:10.1083/jcb.202506071, now published). In addition, a previous study demonstrated that Tsc13 localizes to the NVJ in an Nvj1-dependent manner (Kvam et al., 2005). We also showed that loss of Ypf1 prevents efficient accumulation of Hmg2 at the NVJ (Fujimoto and Tamura, J. Cell Biol. 2026). We therefore believe that these localization dependencies have already been sufficiently established in previous studies.

    2. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #2

      Evidence, reproducibility and clarity

      The study describes the finding of the nuclear envelope protein Msc1 as a new component of the membrane contact site nucleus vacuole junction (NVJ) under the conditions of glucose starvation. Msc1 has previously only been known as a nuclear envelope protein, presumably localizing to the nuclear lumen, and its role in DNA damage repair. The main finding of this study is the glucose starvation-induced upregulation and NVJ-localization of Msc1 (Figure 1). The second main finding is that the loss of Msc1 results in an impaired induction of the expression of Nvj1 (the main component of the NVJ, responsible for the formation of NVJ via direct interaction with Vac8) upon glucose starvation (Fig. 3 A). The effect of Msc1-loss on the Nvj1 expression levels is transcriptional (Fig. 4 B). The glucose starvation-mediated expression induction of some other previously identified NVJ components, Nsg1 and Nsg2 is also impaired in the msc1D mutant, while the expression of Ypf1 is affected to a lesser degree. The data supporting these two main findings are solid (Figure 1; Figure 3 A; Figure 4 A, B).

      The study further shows that the loss of Msc1 results in a loss of NVJ-localization of NVJ components Tsc13, Ypf1 and to a lesser degree Hmg2. The microscopy data looks solid, however the interpretation of this finding is not clear. In my view, the most likely explanation is that the effect of Msc1 loss on the localization of NVJ components to the NVJ is due to the impaired glucose starvation-induced Nvj1 expression in the msc1D mutant.

      Major comments:

      Here are suggested experiments that would strengthen the study:

      • It is difficult to imagine how a NE protein could affect expression levels of other NVj proteins - this key finding would be supported by a complementation experiment where MSC1 is expressed from a vector - to test whether this rescues the phenotype (to make sure that the observed phenotype is not due to an off-target effect of msc1D deletion)
      • If technically feasible under the glucose starvation conditions, this hypothesis could be tested by overexpressing Nvj1 from an inducible or some other promoter.
      • The authors refer to a previous study showing that nvj1D deletion does not affect protein levels of several NVJ proteins, however, it would be nice to have this data shown here - i.e. the localization of Tsc13, Ypf1 (and Hmg2) in the nvj1D mutant, especially since the study cited has not been peer-reviewed yet: "Notably, our previous work showed that loss of Nvj1 or Ypf1 does not affect the protein levels of each other or those of other NVJ-associated factors such as Nsg1 and Nsg2 (Fujimoto and Tamura, 2025)."
      • The effect of msc1D deletion on Tsc13 proteins levels (preferentially using the same Tsc13-GFP strain as used in microscopy - anti Tsc13 or anti-GFP antibodies could be used)

      Other Major comments:

      • The results concerning the localization of Msc1-GFP in elo3D mutant have been interpreted as "accelerated localization", "expansion of the the size of Msc1-NVJ domain" etc. However, the levels of Msc1-GFP in the elo3D mutant are higher compared to WT (Figure 2 D). Considering this, it is very likely that the larger surface area measured in the elo3D mutant is a consequence of this. This could be potentially checked by comparing images set of WT and elo3D that are set to a similar fluorescence intensity. In any case, this possibility should be definitely addressed in the interpretation of the result.
      • There is an impression that the data has been overinterpreted, and the conclusions should be written much more carefully. Examples:
        • "Here, we show that Msc1 is a GS-responsive NVJ factor that plays an important role in functional NVJ remodeling." - based on data shown, the effect of Msc1 could be indirect. The statement above should be re-written or argumented much better.
        • "we find that GS-dependent induction of NVJ1 transcription is attenuated in msc1Δ cells, suggesting that proper NVJ remodeling contributes to the execution of stress-responsive transcriptional programs" - this is unclear; which data support this?
        • "Together, these findings position Msc1 as an upstream regulator linking GS signaling to functional maturation of the NVJ and associated cellular adaptation responses." - same comment as above
        • "...suggesting that Msc1 functions as a GS-responsive regulator of NVJ functions."
        • "...these findings suggest that Msc1 acts upstream of Ypf1 in orchestrating GS-induced NVJ functional maturation."
        • "Collectively, these results indicate that Snf1 acts upstream of Msc1 to drive GS-induced NVJ remodeling, whereas reduced Elo3 activity further accelerates this process and promotes Msc1 accumulation." - not sure if the available data support this.
        • "These results indicate that although Msc1 ...... it is required for efficient GS-dependent functional maturation of the NVJ domain."
        • "These observations suggest that loss of Msc1 does not cause a general defect in transcriptional activation but rather impairs the proper execution and dynamic range of GS-dependent transcriptional responses." - this is unclear
        • "Within this context, the robust induction of NVJ1 appears to be particularly sensitive to Msc1 deficiency." - this sentence would benefit from being re-written.
        • "Together, these results indicate that Msc1 contributes to transcriptional reprogramming associated with NVJ remodeling during GS." - this sounds overstated.
        • "the observation that loss of Msc1 attenuates GS-dependent induction of NVJ1 raises the possibility that NVJ remodeling influences stress-responsive gene expression programs."
      • It is not certain what the term "stability of multiple NVJ proteins" means. Could another term be used, or this explained?

      OTHER COMMENTS FIGURE BY FIGURE - SOME ARE MAJOR (overlapping to the above comments), SOME ARE MINOR:

      Figure 1: Figure 1 A and B shows that Msc1-GFP expression is upregulated in cells starved for glucose for 24h, but not in nitrogen-starved cells. - Comments: o Is Tim23 used as a loading control? If yes, it should be stated in the figure legends and/ or main text. o Size of the markers (protein ladder) would be helpful. o Which antibody is used for Western in B? - Comment: It would be helpful to explain the abbreviation "PK" in Figure 1C Figure legend. Figure 1 D: Msc1-GFP localization to the NVJ is dependent on Nvj1, Vac8, but not Nsg1 and 2 and Ypf1 - Comment: a typo: "(D) Fluorescence microscopy images of the indicates strains..." should be "indicated". - Comment: "Single focal planes were shown." Would be better in present tense "are shown".

      Figure 2: - Comment: It is not clear if these are the same strains as analyzed by microscopy (GFP-tagged Msc1). This should be specified in the Figure legend 2 D. - Comment: o Since the levels of Msc1-GFP in the elo3D mutant are higher compared to WT (Figure 2 D), the larger surface area measured in C may be a consequence of this. o It is not clear if Figure A and D analyze the same strains (western blot and microscopy - do both show GFP-tagged Msc1? - using anti-GFP?). This should be specified in the Figure legend 2 D. Since the increased area measured in Figure 2 C could be due to increased Msc1-GFP levels in this mutant strain, the WB should check the levels of Msc1-GFP in the same strain and under same conditions as analyzed in Figure 2 C. o The title of the Figure 2 is: "Snf1 signaling and VLCFA metabolism modulate NVJ partitioning of Msc1" - what is "NVJ partitioning" - for me it would be clearer to write "Snf1 signaling and VLCFA metabolism modulate the localization of Msc1 to NVJ" o Does Tim23 serve as a loading control in Figure 2 D? o Would be good to have protein ladder sized marked in Western blots o Since the increase in Msc1 levels in the elo3D mutant could be significant for the interpretation of the results, it would be helpful to have quantification of the protein levels in WB (normalized to a loading control).

      Figure 3 Together these data show that localization of other NVJ-proteins to the NVJ depends on the presence of Msc1. Comment: - From the available data it is possible that Msc1 recruits these components by direct interaction, or by modifying the structure of NVJ, or functions in an indirect manner - this should be discussed in the Discussion. Comment: - The signal of Tsc1-GFP in log-growing cells is very weak, therefore the quantification may be unreliable. I would remove this condition (log-grown cells) form the quantification in C) due to the low signal, since it is not crucial to the interpretation of the data. If the authors prefer to leave it, that is fine. - The title of the Figure 3 is "Msc1 supports stability and recruitment of NVJ-associated proteins" - I am not sure what "stability" is; the data don't address stability or recruitment in a direct manner - I suggest to change the figure title into a statement describing what is shown in the Figure, for example: "The loss of Msc1 results in decreased Nvj1 levels and a decreased localization of NVJ proteins to the NVJ). And have a comment that this data suggests that Msc1 supports recruitment of NVJ-associated proteins, likely in an indirect manner, based on the finding that the loss of Msc1 leads to a lower expression of Nvj1, in the main text (e.g. in the Discussion). - Is it possible that the loss of Msc1 on the loss of NVJ-localized Tsc13 is due to the downregulation of Tsc13 expression? Considering the effect of msc1D deletion on the expression of some NVJ proteins (Figure 3 A), Tsc13 expression levels would be good to be checked, considering the effect of msc1D on Tsc13-GFP localization. It would be optimal to do the WB with the same Tsc13-GFP-expressing strain and under the same growth conditions as was used in the microscopy in the Figure 3 B. - Expression levels of Ypf1 are lower in the msc1D strain, than in the WT (Fig. 3 A) - could this affect lower NVJ-area in his mutant? (Fig. 3 B)

      Figure 4. Figure 4 A shows mRNA levels in glucose starved cells compared to log-.growing cells for MSC1, NVJ1 and YPF1. - Comment: I would move Figure 4 A to Figure 1. Figure 4 B shows mRNA levels of proteins expressed in WT and msc1D mutant strain, in log-growing cells in under glucose starvation. The data show that the loss of Msc1 leads to a decrease in NVJ1 mRNA under the conditions of glucose starvation. Th expression of other NVJ proteins analyzed are not affected. - Comment: Would this Figure 4 A-B better fit together with the data showing Nvj1 levels in the msc1D mutant from a previous figure (3 A)? Figure 4 C shows PI staining of cells after 5 days of glucose starvation. The loss of Msc1 leads to a double increase in PI-positive cells (in contrast to the nvj1D mutant, which is similar to WT), indicating that the viability of cells after 5 days of glucose starvation is decreased in the absence of Msc1. - Comment: Since there is no phenotype of nvj1D, this is likely not due to the non-functional NVJ, but another function of Msc1 - the question is which. This could be discussed in the Discussion. - Comment: This is informative, however it is not sure why this data is placed together with the mRNA data within the Figure 4.

      Figure S1. - Comment - as in Figure 2 - Msc1-GFP has a much stronger signal in elo3D mutant, than in WT, which could influence (or likely influences) the measured area. Perhaps one way to test this is to image WT cells with higher % of laser "a "longer exposition"), to get a stronger signal similar to that seen in the elo3D mutant, and then repeat the quantification. - Taken the result as it is presently, I suggest taking the Figure S1 out. Figure S2. - The list of genes analyzed and the conditions analyzed are different in the figure and in the legend. Probably the figure is correct. Figure S3 . Validation of anti-Msc1 antibody - Could be moved as S1.

      *Referee cross-commenting

      Rev#1:

      I generally agree with the other reviewers. I found an error (?typo) in one thing Reviewer 3 says about Fig 1C: "The claim that Msc1 is an integral membrane protein is not sufficiently supported, particularly if a polyclonal antibody was used." I think they mean: "The claim that Msc1 is NOT an integral membrane protein is not sufficiently supported, particularly if a polyclonal antibody was used." I see that my own review has lots of typos - I will write separately to the editor about those.

      Rev#2:

      I agree with the Reviewer 3 that the link between transcriptional reprogramming and NVJ remodeling is not convincingly demonstrated.

      I agree with the Reviewer 3 that the localization of Msc1 to the perinuclear space is not sufficiently supported. The authors may re-write the conclusion to include this uncertainty, or add experimental data.

      I am not sure if I agree with the Reviewer 1 in that the loss of Msc1 leads to the downregulation of Nvj1 "mostly through destabilisation since the transcriptional effect is marginal". Available data does not include the quantification of the Nvj1 protein levels in the msc1- mutant compared to WT, therefore, it is presently unclear how large the downregulation at the protein level is.

      I agree with the Reviewer 3 that the Methods section needs a more detailed description, especially of the growth conditions and glucose starvation protocol (at which OD600 were cells diluted to, were cells washed prior to media change, etc.).

      Rev#3:

      I find Reviewer 2's suggestion of a complementation experiment compelling; this assay would require minimal additional effort and would help exclude off-target effects of the msc1Δ phenotype.

      I agree with Reviewer 1 that the use of "GS" is unnecessary and hinders readability; "glucose starvation" should be used throughout.

      I agree with Reviewer 1 that a more thorough comparison with homologous proteins in S. pombe (Ish1/Les1), including topology and functional parallels, would substantially strengthen the manuscript.

      I thank Reviewer 1 for identifying the misleading phrasing regarding integral versus associated membrane proteins. However, I maintain that the assay in Figure 1C still requires stronger support.

      Significance

      General assessment - strenghts and limitations:

      The identification of Msc1 as a new glucose starvation-induced protein that localizes to the NVJ is supported by strong data and represents a novel and a strong point of the paper. Furthermore, the finding that the loss of Msc1 results in the impaired expression of several other NVJ-localized proteins under glucose starvation is convincing, although the solidity of this latter data requires some more experimental controls (detailed above). The weak point is the interpretation of the Msc1 loss on the localization of other NVJ proteins - the present conclusions need to be modified, or supported by the additional experimental data.

      Advance - compare the study to existing knowledge - does it fill the gap?

      The study identifies protein Msc1, which was previously known as a nuclear envelope protein involved in DNA damage repair, as a new component of the membrane contact site nucleus vacuole junction (NVJ), whose expression and the localization to the NVJ is induced by glucose starvation. What kind of advance does it make - conceptual; incremental...? The finding that a nuclear lumen protein, which is required for DNA damage repair, under certain circumstances (glucose starvation) changes localization and potentially has new roles, has a potential of a conceptual advance, however, for that, more experimental data would be needed, specifically to determine the mechanistic role of Msc1 in glucose starvation, and compare it to it role in DNA damage response. The available data supports mainly an incremental advance in our understanding of the structure and regulation of the NVJ.

      Audience - broad; specialized; basic research...? The audience of this paper will be interested in the basic research. Especially interested may be scientists working with yeast.

      Describe your expertise: My expertise is in yeast genetics, in the field of degradation-mediated protein quality control.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, the role of the insulin receptor and the insulin growth factor receptor was investigated in podocytes. Mice, where both receptors were deleted, developed glomerular dysfunction and developed proteinuria and glomerulrosclerosis over several months. Because of concerns about incomplete KO, the authors generated and studied podocyte cell lines where both receptors were deleted. Loss of both receptors was highly deleterious with greater than 50% cell death. To elucidate the mechanism of cell death, the authors performed global proteomics and found that spliceosome proteins were downregulated. They confirmed this directly by using long-read sequencing. These results suggest a novel role for insulin and IGF1R signaling in RNA splicing in podocytes.

      This is primarily a descriptive study and no technical concerns are raised. The mechanism of how insulin and IGF1 signaling regulates splicing is not directly addressed but implicates potentially the phosphorylation downstream of these receptors. In the revised manuscript, it is shown that the mouse KO is incomplete potentially explaining the slow onset of renal insufficiency. Direct measurement of GFR and serial serum creatinines might also enhance our understanding of progression of disease, proteinuria is a strong sign of renal injury. An attempt to rescue the phenotype by overexpression of SF3B4 would also be useful but may be masked by defects in other spliceosome genes. As insulin and IGF are regulators of metabolism, some assessment of metabolic parameters would be an optional add-on.

      Significance:

      With the GLP1 agonists providing renal protection, there is great interest in understanding the role of insulin and other incretins in kidney cell biology. It is already known that Insulin and IGFR signaling play important roles in other cells of the kidney. So, there is great interest in understanding these pathways in podocytes. The major advance is that these two pathways appear to have a role in RNA metabolism.

      Latest comments:

      The new reviewer raised two major points, whether the KO effect on splicing is specific to IGF1 and whether the interpretation could be developmental rather than due to splicing. The reviewer raises some important issues but the evidence to suggest that this is specific is data in the literature that IR/IGF signaling is already known to regulate splicing and that splicing defects were not detected in other models that they have analyzed. I agree with the reviewer (and authors) that the incomplete floxing of the genes is a major complication. The point that there could be a developmental defect with mice being born with fewer podocytes and perhaps the authors should caveat this point. The fact that they mice are born with normal function, that renal function can be maintained with up to 80% loss of podocytes suggest that they are likely born with a good number of podocytes and the dysfunction that occurs at 6 months is due to a process, induced by the loss of IR/IGF signaling that is detrimental to the podocyte.

      Thank you for these insightful comments. We fully acknowledge that the mouse model will not have had full insulin receptor and IGF1R knockdown and that this is likely the reason it took time to develop and not give a prominent early phenotype. We agree with this reviewer and new reviewer 4 that if the model had facilitated near complete IR and IGF1R knockdown then likely a significant neonatal / embryonic phenotype would have been obvious. We considered using an inducible mouse model to allow normal development before cre-excision but our experience is that the CreER and RtTA-tet-on-cre system is less good at excising genes and hence did not pursue this (we show evidence of reduced excision with an inducible system in supplementary Figure 1D using a reporter mouse system [this was included in a previous response to the reviewers only]). This was rationale for making the immortalised podocyte floxed IR and IGF1R cell line to ensure near complete knockdown. This, not surprisingly, was highly detrimental. We then looked mechanistically for pathways (using agnostic proteomics and phospho-proteomics) and found spliceosomal involvement. From our studies we think this was also involved in our mouse model as SF3B4 was found to be significantly down regulated in the podocytes of double receptor knockdown transgenic mice (Figure 3F).

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, submitted to Review Commons (journal agnostic), Coward and colleagues report on the role of insulin/IGF axis in podocyte gene transcription. They knocked out both the insulin and IGFR1 mice. Dual KO mice manifested a severe phenotype, with albuminuria, glomerulosclerosis, renal failure and death at 4-24 weeks.

      Long read RNA sequencing was used to assess splicing events. Podocyte transcripts manifesting intron retention were identified. Dual knock-out podocytes manifested more transcripts with intron retention (18%) compared wild-type controls (18%), with an overlap between experiments of ~30%.

      Transcript productivity was also assessed using FLAIR-mark-intron-retention software. Intron retention w seen in 18% of ciDKO podocyte transcripts compared to 14% of wild-type podocyte transcripts (P=0.004), with an overlap between experiments of ~30% (indicating the variability of results with this method). Interestingly, ciDKO podocytes showed downregulation of proteins involved in spliceosome function and RNA processing, as suggested by LC/MS and confirmed by Western blot.

      Pladienolide (a spliceosome inhibitor) was cytotoxic to HeLa cells and to mouse podocytes but no toxicity was seen in murine glomerular endothelial cells.

      The manuscript is generally clear and well-written. Mouse work was approved in advance. The four figures are generally well-designed, bars/superimposed dot-plots.

      Methods are generally well described.

      Comments on previous version:

      Coward and colleagues have done an excellent job of responding to all the reviewer comments.

      Thank you.

      Reviewer #4 (Public review):

      Summary and background:

      This report entitled "The insulin/IGF axis is critically important (for) controlling gene transcription in the podocyte" from Hurcombe et al is based on a mouse double knockdown of the IR and IGF1R and a parallel cultured mouse podocyte model. Insulin/IGF signaling system in mammals evolved as three gene reduplicated peptides (insulin, IGF-1, and IGF-2) and their two receptors IR and IGF1R that cross-react to variable extents with the peptides, are ubiquitously expressed, and signal through parallel pathways. The major downstream effect of insulin is to regulate glucose uptake and metabolism, while that of the IGF pathways is to regulate growth and cell cycling in part through mTORC1. The GH-IGF-1-IGF1R pathway regulates post-natal growth. IGF-2 signaling is thought to play a major role in regulating intrauterine growth and development, although IGF-2 is also present at high levels in post-natal life. Thus, one would anticipate that reducing IR/IGF1R signaling in any cell would slow growth and cell cycling by reducing growth factor and metabolic mTORC1-mediated and other processes including the splicing of RNA for protein synthesis.

      Thank you for this clear overview. Of note the podocyte is a terminally differentiated cell so the growth / cell cycling elements may be different from more proliferative cell types in relation IR/IGF1R mediated signalling.

      Comments on revised version:

      The second sentence of the Summary reads "This study sought to elucidate the compound role of the insulin/IGF1 axis in podocytes using transgenic mice and cell culture models deficient in both receptors." The study design and rationale for the proteosome analysis described is predicated on the finding that podocyte-specific knockdown of the IR/IGF-1R in mice is associated with development of proteinuria and reduced eGFR by 20months of life. Since the IR/IGF-1R are critically required for normal development and growth of all cells and organs, the obvious explanation for the observation would be that the model system results in defective podocyte development and deployment (caused by reduced IR/IGF-1) that, in turn, causes subsequent development of proteinuria and glomerulosclerosis (that may be much less dependent on a normal level of IR/IGF-1R expression). Thus, the experimental design does not allow a distinction between podocyte development and steady state function which are different biologic processes. The data provided does not examine podocyte status immediately after birth to confirm that podocyte number and size and structure is normal in mice that subsequently develop proteinuria and glomerulosclerosis. The response to the reviewer suggests that since this would require additional mice it has not been undertaken in order to reduce animal usage. This is not a valid argument, particularly when the investigators have not even used state-of-the-art methods to measure podocyte number, size and density in adult mice, key parameters that would be required to interpret their data. Counting podocyte nuclear number in glomerular cross-sections is simply an inadequate method, even if it is used and reported in other journals, and particularly where the examples given to justify its use can hardly be viewed as representing first rate science.

      Thank you for these comments. As discussed above we agree that the mouse model was not optimal as despite using a good cre driver we did not consistently knock down both receptors. It was the reason that we made the IR/IGF1R knockdown cell line. Importantly we found with both receptors >80% knocked down that this was highly detrimental and evidence that spliceosomal dysfunction was prominent. Thank you for the comment about methodology of assessing podocyte number which we and other investigators use.

      If the absence of studies that would answer the above questions, the investigators should add a sentence to the Discussion dealing with study limitations as follows. "The study design does not allow us to determine whether the primary effect of reduced IR/IGF-1R expression on the phenotype is during in utero and post-natal podocyte development and deployment, during periods of rapid growth when IGF-1 levels are highest, in steady state adult podocytes, or under all of the above conditions".

      Thank you. We have added a section describing that we did not investigate the embryonic neonatal early phenotype for more subtle changes in our model. We have also added a sentence saying we would have liked to have used an inducible model but the cre driven excision is less than constitutional driver and we think would have shown either a very mild or no phenotype due to minimal excision.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      The authors address whether theta/beta ratio /TBR) can be used as a clinical biomarker for ADHD.

      Strengths:

      The data were acquired independently from 2 separate datasets, and there are sufficient subjects for adequate statistical power. The authors applied up-to-date EEG data preprocessing, state-of-the-art feature extraction, and statistical analyses, using a multiverse approach. By testing and comparing all meaningful approaches, defined a priori in the previous meta-analysis, the author convincingly demonstrates that TBR cannot be used as a clinical biomarker, and previous positive results can be explained by interactions between different factors (alpha peak frequency, aperiodic component, age).

      Weaknesses:

      There are no apparent issues with data, separate datasets, large sample sizes, and state-of-the-art data analysis.

      We thank Reviewer #1 for their positive evaluation of our manuscript and for the constructive recommendations. The reviewer did not raise additional comments requiring a point-by-point response beyond the recommendations addressed below.

      Reviewer #2 (Public review):

      Summary:

      This manuscript examines whether the theta-beta ratio as derived from EEG data relates to ADHD diagnoses. To do so, it performs a multiverse analysis across a large number of analytical choices, applied to a large EEG dataset, and corroborated in an additional validation set. The results overall show that the TBR is not a reliable indicator of ADHD diagnosis. In discussing the patterns of results across analytical choices, the authors also demonstrate some key points about what appears to be driving the ratio measures, noting that significant results appear to be driven by choices regarding aperiodic-correction and the use of individualized alpha frequencies, suggesting TBR measures can be affected by these features rather than reflecting theta and/or beta activity.

      Strengths:

      This manuscript addresses a clearly posed and important question in the literature, addressing a longstanding discussion on the relationship between TBR and ADHD, and uses a large dataset and an expansive analysis approach to provide a definitive answer. The strengths of the approach allow for a clear answer, providing a notable contribution to the field.

      Weaknesses:

      I find no notable weaknesses in the current manuscript nor any major issues that I think challenge the key findings of this manuscript.

      We thank Reviewer #2 for their positive evaluation of our manuscript and for the constructive recommendations. The reviewer did not raise additional comments requiring a point-by-point response beyond the recommendations addressed below.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript, Strzelczyk, Vetsch, and Langer tackle an incredibly important question in clinical neuroscience: the use of the theta/beta ratio as a biomarker of attention deficit hyperactivity disorder (ADHD). The theta/beta ratio is argued to be so reliable as an ADHD biomarker that, in the United States, the Food and Drug Administration has approved its use as a biomarker for ADHD diagnosis. However, there is mounting evidence that the theta/beta ratio is likely not really measuring the relative power between two oscillations - the theta rhythm and the beta rhythm - but rather reflects differences in a singular, non-oscillatory aperiodic process. In this very convincing study, Strzelczyk and colleagues take a "multiverse" analysis approach to show that aperiodic activity differences between healthy controls and people with ADHD are driving the apparent theta/beta ratio differences. While in a vacuum, where a measure is a measure and if it's related to a diagnosis it's still useful no matter what, this distinction might not seem important, from a neuroscientific perspective this is a critical distinction, because the ratio between two oscillations has fundamentally very different underlying physiological mechanisms than aperiodic differences, and this framing has a major impact on guiding research on the diagnosis and treatment of ADHD.

      Strengths:

      While smaller studies and analyses have already hinted at similar results as shown here, the current study's multiverse analysis approach is comprehensive, convincing, and very well done. The large sample size of 1,499 participants is very impressive, as is the use of an independent validation sample of 381 participants.

      Overall, the technical and statistical aspects are very well done: the multiverse approach, the validation set, the resampling methods, and even the shiny apps. The authors should be applauded for being so thorough and making their data and analyses publicly accessible.

      Weaknesses:

      To be clear, I see no breaking weaknesses in the theoretical foundations, methods, statistical analyses, or interpretations. All of my recommendations below are for the sake of clarity, which I believe is especially important because this is such an important paper that many people should read.

      Comments:

      (1) Some figures are mislabeled. For example, Supplementary Figure 1 says (C) are scalp topographies, but those are (A), while (C) shows power spectra, but it's unclear what (C) is. I assume it's only the aperiodic part of the spectrum (oscillations removed)? But it would be better to plot on a log-log scale if so. In fact, I recommend showing all spectra on a log-log scale.

      The reviewer is correct that the figure legend was mislabeled. Panel (A) shows the scalp topographies, panel (B) shows the 1/f-uncorrected power spectra, and panel (C) shows the reconstructed aperiodic signal with oscillations removed. We have corrected the figure legend accordingly. In addition, the power spectra and the reconstructed aperiodic signal are now plotted on log-log scales to improve readability and interpretability.

      (2) Supplementary Figure 6 is also mislabeled, saying (A) shows age (it does not) and so on.

      We thank the reviewer for noticing this error. We have revised the figure legend so that the panel descriptions now match the displayed plots.

      (3) In Supplementary Figure 7, is (B) the aperiodic-removed spectrum? The authors are very inconsistent with what they're showing in these spectral plots, and not actually explaining what they're showing: raw spectra, semi-logged or not, aperiodic-removed or oscillations-removed, etc.

      Panel (B) in Supplementary Figure 7 shows the aperiodic-adjusted spectrum. We have now corrected the figure labeling and revised the figure legend to explicitly state what is shown in each panel.

      (4) For the HBN data, it is said that, "electrode impedances were kept below 40 kΩ, lower than EGI's standard recommendation of 50 (Net Station Acquisition Technical Manual)." For the validation data: "... electrode impedances were maintained below 5 kΩ." These are big impedance threshold differences. Of course, these recommendations differ by recording system, the use of active electrodes, and so on. But such differences can certainly influence signal-to-noise. The fact that the results are so consistent between them is a strength that perhaps should be explicitly called out.

      We appreciate the reviewer’s suggestion. We now explicitly state in the discussion section that the consistency of the results across datasets with different EEG systems and impedance thresholds strengthens the generalizability of the findings. The revised text reads as follows:

      “Our multiverse results thus converge with this broader literature, providing further evidence that TBR lacks the reliability and discriminative validity required for clinical utility. Beyond methodological convergence across analytical frameworks, the consistency of results across two datasets differing substantially in EEG recording systems and impedance thresholds further strengthens the generalizability of these null findings, suggesting they are unlikely to reflect idiosyncrasies of a specific acquisition protocol.”

      (5) The authors cite a lot of foundational / related work here, such as Finley et al, but they should also cite several other highly relevant ones:

      Saad et al., "Is the Theta/Beta EEG Marker for ADHD Inherently Flawed?", J Atten Disord, 2015

      Donoghue, Dominguez, Voytek, "Electrophysiological frequency band ratio measures conflate periodic and aperiodic neural activity", eNeuro, 2020

      Karalunas et al., "Electroencephalogram aperiodic power spectral slope can be reliably measured and predicts ADHD risk in early development", Develop Psychobiol, 2022

      Donoghue, "A systematic review of aperiodic neural activity in clinical investigations", Eur J

      Neurosci 2025

      We thank the reviewer for pointing us to these additional relevant references. We have added the suggested references to the revised manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) "Multiverse analysis was conducted in RStudio (R version 4.4.1) using the multiverse package (version 0.6.1; Sarma et al., 2021). T" Ok, cool, but it would be useful to explain what it does compared to running the standard stat analysis N times.

      We thank the reviewer for this helpful recommendation. We have now expanded the Methods section to clarify this point. The revised text reads as follows:

      “Multiverse analysis was conducted in RStudio (R version 4.4.1) using the multiverse package (version 0.6.1; Sarma et al., 2021). The multiverse framework differs from simply repeating the same statistical analysis multiple times, because it first requires the researcher to define a structured analysis space consisting of multiple defensible analytic decisions. These decisions are then expanded into all valid combinations, with each combination representing one complete analysis specification, or “universe”, providing a transparent and reproducible record of which analytic decisions were considered and how they were combined. In addition, the package reduces the need to manually write, modify, and track separate analysis scripts for each specification, which helps avoid inconsistencies or coding errors across universes. The results can then be extracted and summarized across the full set of universes to evaluate whether the conclusions are robust across reasonable analytic alternatives or depend on specific combinations of choices.”

      (2) I may have missed it, but how many subjects per group do you end up with after all the cleaning (not what is in Table 1, but like in each dataset you describe how many got removed at each step, so we are left wondering the final numbers).

      We thank the reviewer for pointing this out. The final group sizes after all cleaning and exclusion steps were not described in the original manuscript. We have therefore revised Table 1 so that it now reports only the remaining participants included in the final analyses after all exclusions were applied. The revised table shows the final sample sizes separately for the HC (N = 228), ADHD-Combined (N = 429), and ADHD-Inattentive (n = 465) groups, together with the corresponding demographic and clinical characteristics. We have also revised the accompanying text in the result section 3. 1. 1. The same changes were applied to the validation sample, which is reported in the Supplement.

      (3) Missing reference in my opinion. In the discussion, the sentence "as both oscillatory and aperiodic contributions vary systematically across the lifespan" could do with a reference or two about that

      We have now added references showing that developmental changes in EEG spectra involve both periodic/oscillatory and aperiodic components. The revised text reads as follows:

      “These dynamics may account for the recurring Age ’ IAF interactions observed in our multiverse analyses, as both oscillatory and aperiodic contributions vary systematically across the lifespan (Merkin et al. 2023; Tröndle et al. 2022; Tröndle et al. 2021; McSweeney et al. 2023; Hill et al. 2022; Stanyard et al. 2024).”

      (4) Now the big one: this is a cool visualization, and beta estimates from linear modeling do tell us the strength, BUT I would like to see raw effect sizes. It could be in a table or text, to go with the discussion. What was the theta, alpha, beta power raw or adjusted in each group, what about the aperiodic component - even maybe some violin plots to show canonical vs individual - my point is I am convinced from the frequency analysis since an entire subspace become significant and your interpretation that this is spurious is satisfactory but showing that this subspace as tiny effect sizes driven by interactions would be even more convincing in my opinion.

      To complement the regression coefficients from the multiverse models, we now additionally report descriptive standardized effect sizes across representative analytical subspaces. Specifically, we grouped analytical paths according to frequency band definition (IAF-relative vs canonical) and spectral representation (aperiodic signal, 1/f-uncorrected power, and aperiodic-adjusted power). Within each subspace, we computed Cohen’s d values for theta power, beta power, and TBR between ADHD and healthy control groups across all corresponding analytical paths.

      To visualize the distribution of effects across analytical paths, we added violin plots with overlaid individual paths and mean effect sizes with 95% confidence intervals. Importantly, even in subspaces where interaction effects frequently emerged in the multiverse analysis, the corresponding descriptive group differences remained small, supporting our interpretation that the observed significant effects are driven by subtle interactions and analytical choices rather than large underlying group differences.

      The added text in the Results 3. 1. 4. reads as follows:

      “To complement the regression coefficients from the multiverse models, we additionally examined descriptive standardized effect sizes across representative analytical subspaces. Analytical paths were grouped according to frequency band definition (IAF-relative vs. canonical) and spectral representation (aperiodic signal, 1/f-uncorrected power, and aperiodic-adjusted power). Within each subspace, Cohen's d was computed for theta power, beta power, and TBR for both the HC vs. ADHD-Inattentive and HC vs. ADHD-Combined comparisons. To visualize the distribution of effect sizes across the analytical space, violin plots were constructed with each data point representing the Cohen's d value of a single analytical specification (Figure 8). Across all subspaces and outcome measures, Cohen's d values were small for both comparisons, including subspaces in which interaction effects frequently reached statistical significance in the multiverse analysis. This pattern indicates that even where the multiverse revealed reliable significant effects, the underlying group differences in theta power, beta power, and TBR remained small in magnitude. These findings support the interpretation that the significant interactions observed across analytical specifications are driven by subtle moderation effects and analytical choices rather than large, robust group differences in neural activity.”

      Reviewer #2 (Recommendations for the authors):

      (1) As a minor clarification, the manuscript could specify if the calculation of aperiodic-adjusted power values was done as subtraction with linear or log power values.

      The aperiodic-adjusted power values were computed by subtracting the aperiodic fit from the observed power spectrum in log10 power space. Specifically, both the observed power spectrum and the estimated aperiodic component were log10-transformed, and the aperiodic-adjusted signal was obtained as the difference between these two quantities. The result was then transformed back to linear scale. We have clarified this in the revised manuscript. The revised text reads as follows:

      “The aperiodic component was reconstructed based on its fitted parameters and subtracted from the total power spectrum in log10 power space, resulting in an aperiodic-adjusted, 1/f-corrected power spectrum. The resulting values were then transformed back to linear scale and therefore represent power relative to the estimated aperiodic background.”

      (2) The last section of the abstract is a bit repetitive in stating the main finding of what drives the TBR, and this could be edited/condensed.

      We agree that the final part of the abstract repeated the main interpretation regarding the role of aperiodic activity and IAF. We have therefore condensed this section to avoid redundancy while preserving the central conclusion. The revised text reads as follows:

      Across the multiverse, we found that group differences in TBR were highly contingent on analytical choices, with no evidence for robust main effects of diagnosis, indicating no reliable differences between healthy controls, ADHD-inattentive, and ADHD-combined subtypes. Instead, significant effects emerged primarily as interactions with age and individual alpha frequency (IAF), particularly when TBR was derived from aperiodic-uncorrected power or from the aperiodic signal itself. These interaction patterns replicated across both independent samples and were observed using both categorical and dimensional definitions of ADHD. Together, these findings indicate that previously reported TBR effects are largely driven by variability in aperiodic activity and IAF rather than genuine differences in oscillatory theta-beta dynamics. Our results challenge the interpretation of TBR as a reliable standalone biomarker for ADHD and underscore the importance of multiverse approaches for evaluating candidate neurobiological markers in heterogeneous clinical populations.

      (3) As a minor literature note, the finding that ratio measures often largely reflect aperiodic activity rather than oscillatory theta and/or beta per se activity is consistent with a previous (non-clinical) investigation of band ratio measures in a previous report that should perhaps be cited as relevant prior work:

      Donoghue, T., Dominguez, J., & Voytek, B. (2020). Electrophysiological Frequency Band Ratio Measures Conflate Periodic and Aperiodic Neural Activity. eNeuro, 7(6),ENEURO.0192-20.2020. https://doi.org/10.1523/ENEURO.0192-20.2020

      We appreciate the reviewer’s suggestion. We have added this reference to the Discussion section, where we interpret the observed TBR effects as reflecting variability in the aperiodic background rather than genuine differences in oscillatory theta-beta dynamics. The revised text reads as follows:

      “These results suggest that apparent TBR differences may reflect properties of the aperiodic background signal interacting with individual variability in IAF rather than true oscillatory theta or beta activity. This interpretation is consistent with previous work showing that electrophysiological frequency-band ratio measures can conflate periodic and aperiodic neural activity, such that apparent changes in theta/beta or other band ratios may partly reflect changes in the aperiodic spectral component rather than narrowband oscillatory activity (Donoghue et al., 2020).”

      (4) In Figure 3, it may be useful to highlight the theta and beta ranges in panel B.

      We considered highlighting the theta and beta ranges in Figure 3B, but decided against it. In the multiverse analysis, theta and beta were defined using both canonical frequency bands and IAF-relative bands. The IAF-relative bands differ across participants, therefore marking only the canonical ranges could give the impression that these were the only frequency definitions used in the analyses. We therefore kept the spectra unmarked.

      (5) In Figure 5 (and other figures following this motif), it may be useful to color the significant results as green or red based on direction, to match Figure 4.

      We have updated Figure 5 and the corresponding figures so that significant positive effects are shown in green and significant negative effects are shown in red, matching the color scheme used in Figure 4.

      Reviewer #3 (Recommendations for the authors):

      (1) P10, L30: "Individualized bands were centered on the IAF, defined as theta = IAF-6 Hz to IAF-4 Hz"; why is theta defined using such a narrow, 2 Hz band here, when canonical theta is usually defined as a 4 Hz wide, 4-8 Hz band?

      The individualized theta band was chosen to follow the IAF-based frequency-band framework proposed by the seminal work of Wolfgang Klimesch (1999, 2012), rather than to reproduce the width of the canonical 4-8 Hz theta band. In this framework, frequency bands are defined relative to each participant’s individual alpha frequency. Theta is defined as the range from IAF-6 Hz to IAF-4 Hz, while lower alpha occupies the range closer to the individual alpha peak. The narrower individualized theta band is therefore intended to reduce overlap with lower-alpha activity and to account for inter-individual and developmental differences in alpha peak frequency. The 2020 guidelines from the International Federation of Clinical Neurophysiology (IFCN) reaffirmed Klimesch’s division of the alpha and theta bands (Babiloni, 2020). We have explained the frequency bands selection in more detail in the manuscript. The revised text reads as follows in Methods 2. 5. 7. Extraction of power for statistical analyses:

      The selection of these frequency bands is grounded in the seminal work of Wolfgang Klimesch (1999), who demonstrated that the alpha band can be divided into distinct lower and upper sub-bands. The lower alpha band extends up to 4 Hz below the IAF, covering a broader range of approximately 3.5 to 4 Hz, while the upper alpha band, which lies above the IAF, is narrower, spanning about 1 to 1.5 Hz. Klimesch also characterized the theta band as a frequency range that is approximately 2 Hz below the lower alpha band (Klimesch, 1999; Klimesch, 2012). The 2020 guidelines from the International Federation of Clinical Neurophysiology (IFCN) reaffirmed Klimesch’s division of the alpha and theta bands (Babiloni, 2020).

      (2) Figure 3 and Supplementary Figure 1, 7, 8: "Electrodes highlighted on the topographies..." means just the text labels, right? It might be better to show all electrodes as black dots and highlight the others with white dots or something.

      We have revised the figures to display all electrodes as black dots. In addition, we have clarified in the figure legends that the highlighted electrode labels correspond to the regions of interest used in the analyses.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript titled," Sleep-Wake Transitions Are Impaired in the AppNL-G-F Mouse Model of Early Onset Alzheimer's Disease", is about a study of sleep/wake phenomena in a knockin mouse strain carrying "three mutations in the human App gene associated with elevated risk for early onset AD". Traditional, in-depth characterization of sleep/wake states, EEG parameters, and response to sleep loss are employed to provide evidence, "supporting the use of this strain as a model to investigate interventions that mitigate AD burden during early disease stages". The sleep/wake findings of earlier studies (especially Maezono et al., 2020, as noted by the authors) were extended by several important, genotype-related observations, including age-related hyperactivity onset that is typically associated with increased arousal, a normal response to loss of sleep and to multiple sleep latency testing, and a stronger AD-like phenotype in females. The authors conclude that the AppNL-G-F mice demonstrate many of the human AD prodromal symptoms and suggest that this strain may serve as a model for prodromal AD in humans, confirming the earlier results and conclusions of Maezono et al. Finally, based on state bout frequency and duration analyses, it is suggested that the AppNL-G-F mice may develop disruptions in mechanism(s) involved in state transition.

      Strengths:

      The study appears to have been, technically, rigorously conducted with high quality, in-depth traditional assessment of both state and EEG characteristics, with the concordant addition of activity and temperature. The major strengths of this study derive from observations that the AppNL-G-F mice: (1) are more hyperactive in association with decreased transitions between states; (2) maintain a normal response to sleep deprivation and have normal MSLT results; and (3) display a sex specific, "stronger" insomnia-like effect of the knockin in females.

      Weaknesses:

      The weaknesses stem from the study's impact being limited due to its being largely confirmatory of the Maezono et al. study, with advances of importance to a potentially more focused field. Further, the authors conclude that AppNL-G-F mice have disrupted mechanism(s) responsible for state transition; however, these were not directly examined. The rationale for this conclusion is stated by the authors as based on the observations that bouts of both W and NREM tend to be longer in duration and decreased in frequency in AppNL-G-F mice. Although altered mechanism(s) of state transition (it is not clear what mechanisms are referenced here) cannot be ruled out, other explanations might be considered. For example, increased arousal in association with hyperactivity would be expected to result in increased duration of W bouts during the active phase. This would also predictably result in greater sleep pressure that is typically associated with more consolidated NREM bouts, consistent with the observations of bout duration and frequency.

      Reviewer 1 succinctly summarizes the advances of this study beyond the ground-breaking Maezono et al (2020) study of this “humanized” mouse model exhibiting amyloid deposition. Whereas Maezono et al. conducted sleep/wake studies on male App<sup>NL-G-F</sup> mice at 6 and 12 months of age, we had the unusual opportunity to study both sexes of homozygous App<sup>NL-G-F</sup> mice and WT littermates at 14-18 months of age and to conduct a longitudinal assessment of many of the same individuals at 18-22 months. In addition to baseline sleep/wake and EEG spectral analyses, we (1) measured subcutaneous body temperature and activity to obtain a broader picture of the physiology and behavior of this strain at advanced ages; (2) assessed baseline sleepiness in this strain using the murine version of the clinically-relevant Multiple Sleep Latency Test (MSLT); (3) evaluated the response of App<sup>NL-G-F</sup> mice and WT littermates to a 6-h perturbation of the sleep homeostat; (4) compared the sleep/wake characteristics of male vs. female App<sup>NL-G-F</sup> mice at 18-22 months; and (5) to assess the stability of the phenotypes, analyzed these data over a continuous 14-d recording rather than the conventional 24h recordings typical of most sleep/wake studies including Maezono et al. We found that a long wake/short sleep phenotype was characteristic of homozygous App<sub>NL-G-F</sub> mice at these advanced ages which is also evident in the Maezono et al. (2020) study at 12 months of age (but not at 6 months), although the authors do not comment on this phenotype and instead focus on the reduced REM sleep which is particularly evident in female App<sup>NL-G-F</sup> mice in our study. Remarkably, despite being awake ~20% longer per day, we find that App<sup>NL-G-F</sup> mice are no sleepier than WT mice as determined by the MSLT and that their sleep homeostat is intact when challenged by 6-h sleep deprivation. At both advanced ages, the long wake/short sleep phenotype is due primarily to longer Wake bouts and shorter bouts of both NREM and REM sleep during the dark phase. Moreover, hyperactivity develops in older App<sup>NL-G-F</sup> mice, particularly females, which contributes to this phenotype. We agree with Reviewer 1 that “hyperactivity would be expected to result in increased duration of W bouts during the active phase” and that this could result in more consolidated NREM bouts. Accordingly, we have added the following sentence to the Discussion subsection Impacts of pathology on sleep/wake and activity: “Thus, the hyperactivity evident in Figures 4D, 4D’, and 5D’ could drive the longer wake bouts evident in Figure 7A and result in the longer NREM and REM sleep bouts found in male App<sup>NL-G-F</sup> mice (Figure 12A’ and 12A”).”

      The suggestion of greater sleep pressure is not borne out by our MSLT studies as we did not observe the shorter sleep latencies nor increased sleep during the nap opportunities on the MSLT that we have observed in other mouse strains. Moreover, due to their short sleep phenotype, App<sup>NL-G-F</sup> mice should be entering the sleep deprivation study with a greater sleep debt than WT mice, yet we did not observe a stronger homeostatic response (i.e., enhanced EEG Slow Wave Activity) in this strain during recovery from sleep deprivation. Thus, we have suggested that App<sup>NL-G-F</sup> mice are unable to transition from Wake to sleep as readily as their WT littermates. Our observations summarized above set the stage for subsequent mechanistic studies in aged App<sup>NL-G-F</sup> mice, although realistically, mice of this age and genotype are a rare commodity.

      Reviewer #2 (Public review):

      Summary:

      The authors have used a knock-in mouse model to explore late-in-life amyloid effects on sleep. This is an excellent model as the mutated genes are regulated by the endogenous promoter system. The sleep study techniques and statistical analyses are also first-rate.

      The group finds an age-dependent increase in motor activity in advanced age in the NLGF homozygous knock-in mice (NLGF), with a parallel age-dependent increase in body temperature, both effects predominate in the dark period. Interestingly, the sleep patterns do not quite follow the sleep changes. Wake time is increased in NLGF mice, and there is no progression in increased wake over time. NREMS and REM sleep are both reduced, and there is no progression. Sleep-wake effects, however, show a robust light:dark effect with larger effects in the dark period. These findings support distinct effects of this mutation on activity and temperature and on sleep. This is the first description of the temporal pattern of these effects. NLGF mice show wake stability (longer bout durations in the dark period (their active period) and fewer brief arousals from sleep. Sleep homeostasis across the lights-on period is normal. Wake power spectral density is unaffected in NLGF mice at either age. Only REM power spectra are affected, with NLGF mice showing less theta and more delta. There are interesting sex differences, with females showing no gene difference in wake bout number, while males show a gene effect. Similarly, gene effects on NREM bout number seem larger in males than in females. Although there was no difference in homeostatic response, there was normalization of sleep-wake activity after sleep deprivation.

      Strengths:

      Approach (model extent of sleep phenotyping), analysis.

      Weaknesses:

      The weaknesses are summarized below and are viewed as "addressable".

      (1) The term insomnia. Insomnia is defined as a subjective dissatisfaction with sleep, which cannot be ascertained in a mouse model. The findings across baseline sleep in NLGF mice support increased wake consolidation in the active period. The predominant sleep period (lights on) is largely unaffected, and the active period (lights off) shows increased activity and increased wake with longer bouts. There is a fantastic clue where NLGF effects are consistent with increased hypocretinergic (orexinergic) neuron activity in the dark period, and/or increased drive to hypocretin neurons from PVH.

      Although the DSM-5 definition of Insomnia Disorder indeed emphasizes a subjective “complaint of dissatisfaction with sleep quantity or quality”, I think the Reviewer takes an unnecessarily narrow view of the term “insomnia”. Aside from cases of “psychological” insomnia in which there is a mismatch between subjective and objective measures of sleep, most sleep researchers would likely agree that insomnia is objectively characterized by a greater than normal wake time during the sleep period (i.e., low sleep efficiency) due to difficulty in either initiating or maintaining sleep. This view has led to efforts to identify not only the biological causes of insomnia but also animal models in which this disorder can be studied. A PubMed search on the terms “mouse” and “insomnia” retrieves 844 publications, including an authoritative 2023 review in J Sleep Research entitled "Animal Models of Human Insomnia" co-authored by a clinician-scientist who has done human sleep research throughout his career and is an authority on CBT-I, in particular. Similarly, a PubMed search on the terms “fly” and “insomnia” retrieves 18 publications. So, although our intent in the submitted version of the manuscript was to use “insomnia” as an operational term to succinctly mean “less sleep than usual”, in the revised manuscript, we have eliminated use of the term “partial insomnia” and replaced it with the term “insomnia-like phenotype”. In the Discussion section “Impacts of pathology on sleep/wake and activity”, we have revised the opening sentence to read “Insomnia in humans is typically characterized by subjective reports of reduced sleep quality and can be accompanied by objective measures of sleep fragmentation and reduced sleep amounts.”

      (2) Sleep-wake transitions are impaired: This should not be termed an impairment. It could actually be beneficial to have greater state stability, especially wake stability in the dark or active period. There is reduced sleep in the model that can be normalized by short-term sleep loss. It is fascinating that recovery sleep normalized sleep in the NLGF in the immediate lights-on and light-off period. This is a key finding.

      Due to the Reviewer’s objection regarding “impairment”, we have changed the title of the manuscript to “Long Wake/Short Sleep Bouts and Hyperactivity with Advanced Age in a Mouse Model of Early Onset Alzheimer’s Disease”. In Comments (1) and (2), Reviewer 2 suggests a provocative hypothesis to test. In the section “Impacts of pathology on sleep/wake and activity“, we previously stated “A hyperactive hypocretin/orexin or monoaminergic arousal system or a dysfunctional GABAergic sleep onset system could underlie the longer bouts of Wake in App<sup>NL-G-F</sup>mice.” We have now added this additional sentence: “Indeed, Hcrt neurons in aged mice have been shown to exhibit more frequent neuronal activity driving wake bouts and optogenetic stimulation of Hcrt neurons in aged mice results in prolonged wakefulness (Li et al., 2022).“

      Reviewer #3 (Public review):

      Summary:

      In this study, Tisdale et al. studied the sleep/wake patterns in the biological mouse model of Alzheimer's disease. The results in this study, together with the established literature on the relationship of sleep and Alzheimer's disease progression, guided the authors to propose this mouse model for the mechanistic understanding of sleep states that translates to Alzheimer's disease patients. However, the manuscript currently suffers from a disconnect between the physiological data and the mechanistic interpretations. Specifically, the claim of "impaired transitions" is logically at odds with the observed increase in wake-state stability or possible hyperactivity. Additionally, the description of the methods, the quantification, and the figure presentation could be substantially improved. I detail some of my concerns below.

      Strengths:

      The selection of the knock-in model is a notable strength as it avoids the artifacts associated with APP overexpression and more closely mimics human pathology. The study utilizes continuous 14-day EEG recordings, providing a unique dataset for assessing chronic changes in arousal states. The assessment of sex as a biological variable identifies a more severe "insomniac-like" phenotype in females, which aligns with the higher prevalence and severity of Alzheimer's disease in women.

      Weaknesses:

      The study seems to lack a clear hypothesis-driven approach and relies mostly on explorative investigations. Moreover, lack of quantitative analytical methods as well as shaky logical conclusions, possibly not supported by data in its current form, leaves room for major improvement.

      Since this paper studied sleep states, the "Methods" section is quite unclear on what specific criteria were used to classify sleep states. There is no quantitative description of classifying sleep based on clear, reproducible procedures. There are many reasonably well-characterized sleep scoring systems used in rat electrophysiological literature, which could be useful here. The authors are generally expected to describe movement speed and/or EMG and/or EEG (theta/delta/gamma) criteria used to classify these epochs. The subjective (manual) nature of this procedure provides no verifiable validation of the accuracy and interpretability of the results.

      This was an oversight: the “Classification of Arousal States” section has been modified accordingly.

      One of the bigger claims is that "state transition mechanism(s)" are impaired. However, Figure 7 shows that model mice exhibit significantly more long wake bouts (>260s) and fewer short wake bouts (<60s). Logically, an "impaired switch" (the flip-flop model, Saper et al., 2010) results in state fragmentation. The data here show the opposite: the wake state has become too stable. This suggests the primary defect is not in the transition mechanism itself, but possibly in a pathological increase in arousal drive (hyper-arousal), likely linked to the dark-phase hyperactivity shown in Figures 4 and 5. Also, a point to note is that this finding is not new.

      Reviewers 1 and 2 also make comments conisistent with the alternative interpretation that “the wake state has become too stable.” However, I think we are using different words to say the same thing: that the transition from wake to sleep is impaired whether it is due to hyperarousal or to a defect in the flip/flop switch that results in greater Wake stability. I hope the reviewer would agree that a switch can be impaired in two directions: either it could “flicker” as seems to be the case in narcolepsy or it could get stuck in one position, which is what we suggest here based on the data in Fig. 12A, A’ and A” which show longer bouts of all states (Wake, NREM and REM) in older males. Nonetheless, the hyperarousal hypothesis suggested by the Reviewer is certainly a reasonable alternative. Consequently, we have added the following sentence to the Discussion subsection Impacts of pathology on sleep/wake and activity: “Thus, the hyperactivity evident in Figures 4D, 4D’, and 5D’ could drive the longer wake bouts evident in Figure 7A and result in the longer NREM and REM sleep bouts found in male App<sup>NL-G-F</sup> mice.”

      Figure 3 heatmaps lack color bars and units. Spectral power must be quantitatively defined and methods well-explained in the Methods section. Without these, the reader cannot discern if the "reduced power" in females is a global suppression of signal or a frequency-specific shift. Additionally, the representative example used to claim shorter sleep bouts lacks the statistical weight required for a major physiological conclusion. How does a cooler color (not clear what range and what the interpretation is) mean shorter sleep bout in female mice? The authors should clearly mark the frequency ranges that support their claims. In this figure, there is a question mark following the theta/delta range. The authors should avoid speculation and state their claims based on facts. They should also add the theta and delta ranges in the plot, such that readers can draw their own conclusions.

      The Y-axis in the previous version of this figure was labelled 0-25 Hz. This figure was intended to be a descriptive illustration of how unusual the female App<sup>NL-G-F</sup> mice are relative to WT of either sex rather than a quantitative analysis of spectral power. As suggested by Reviewer 2, we have combined this figure with the previous Fig. 14 as the revised Fig. 3 and we have modified the Y-axis labels to more explicitly indicate EEG frequencies. The question mark was legacy text from an earlier version of the manuscript; sorry for the confusion!

      Figure 8 and the MSLT results show that model mice are "no sleepier than WT mice" and have a functional homeostatic rebound. This presents a logical flaw in the "insomnia" narrative. True insomnia in AD patients typically involves a failure of the homeostatic process or a debilitating accumulation of sleep debt. If these mice do not show increased sleepiness (shorter latency) despite ~19% less sleep, the authors might be describing a "reduced need" for sleep or a "hyper-aroused" state, possibly not a clinical insomnia phenotype.

      Both Reviewer 2 and 3 suggest that we are using “insomnia” incorrectly, which we have used as shorthand to denote less sleep per 24h period. Reviewer 2 states that “Insomnia is defined as a subjective dissatisfaction with sleep” per DSM-5 and Reviewer 3 suggests that the mechanism underlying insomnia in AD patients is “a failure of the homeostatic process or a debilitating accumulation of sleep debt” which is not in DSM-5. Our clinical colleagues tell us that this is not established fact; some argue that the homeostat is intact and that the input(s) to the homeostat are defective. We agree that less sleep in these mice could be due to a reduced need for sleep or to hyperarousal. Consequently, we have changed the title of the manuscript to eliminate “Sleep-Wake Transitions are Impaired…” to the more objective “Long Wake/Short Sleep Bouts and Hyperactivity with Advanced Age in a Mouse Model of Early Onset Alzheimer’s Disease”.

      In Figure 9, LFP power shown and compared in percentages is problematic, as LFP power distribution is known to be skewed (follows power law). This is particularly problematic here because all the frequencies above ~20 Hz seem to be totally flattened or nonexistent, which makes this comparison of power severely limited and biased towards the relative frequency in the highly skewed portion of the LFP power spectrum, i.e., very low frequency ranges like delta, theta, and possibly beta. This ignores low, mid, and high gamma as well as ripple band frequencies. NREM sleep is known to have relatively greater ripple band (100-250 Hz) power bursts in hippocampal regions, and REM sleep is known to have synchronous theta-gamma relationships.

      We completely agree with the reviewer. There are at least 3 ways that spectral power data can be presented: (1) absolute power; (2) relative power (normalized to a baseline); and (3) power density. In this study, we intentionally presented results in terms of spectral power density so that our results could be compared to those in Figure 3A and 3B of Maezono et al. (2020). This was important because Maezono et al. recorded from mice of 6 and 12 months of age whereas we recorded from older mice, which allowed us to determine which parameters are likely changing with age (and, presumably, greater Ab deposition).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) A key finding for the AppNL-G-F mouse model is the emergence of hyperactivity that may be responsible for the altered sleep architecture. Further investigation to help determine the mechanism(s) responsible might include cFos expression to help localize or provide evidence for the distributed neuronal activity increase in this model. Additionally, identification of overly active areas might provide targets for their manipulation to test the authors' hypothesis of the mechanism of the altered sleep architecture. Does chronic hyperactivity caused by other mechanisms (DREADDs, LOF of a K channel) mimic the AppNL-G-F mouse model sleep phenotype? These sorts of findings would impact the study's significance.

      We agree with the Reviewer that identifying the mechanism underlying the long wake/short sleep phenotype of aged App<sup>NL-G-F</sup>mice would increase the study’s significance. However, we want to underscore that the opportunity to study both sexes of homozygous App<sup>NL-G-F</sup> mice and WT littermates at 14-18 months of age and to conduct a longitudinal assessment of many of the same individuals at 18-22 months was very unusual. Our observations of the phenotype described in this manuscript set the stage for subsequent mechanistic studies in aged App<sup>NL-G-F</sup> mice, although realistically, mice of this age and genotype are a rare commodity.

      (2) A more technical area of improvement involves the presentation of the results and the associated critical statistical analyses. Relevant tables and statistics are not always reported (in the results) or properly referenced. In the mixed models, the repeated measures are "time of day", I presume.

      Tables 1-6 present statistical results; these 6 Tables are referred to in the Results section a total of 14 times. The text states “The larger sample size in Experiment 2 (N=31 mice) allowed a mixed-effects model ANOVA to be conducted with Genotype, Sex, and Time as factors”. Although “Time of Day” was specified several places in the Results, thank you for pointing out omission of “of Day” from the “Data Analysis and Statistics” section; we have added this information accordingly.

      (3) The model is presented as age-dependent, but there was little statistical support for this. The subjects spanned a considerable age range, and a direct quantifiable correlation between age and the various measured dependent variables could be helpful in this regard.

      The long wake/short sleep phenotype characteristic of homozygous App<sup>NL-G-F</sup> mice that we describe here is also evident in the Maezono et al. (2020) study at 12 months of age but not at 6 months in either the Maezono et al. (2020) or Calafete et al. (2023) studies, although the authors do not comment on this phenotype and instead focus on the reduced REM sleep. Thus, between these studies, there seems to be an age-dependent progression of the phenotype. We have thus added this sentence to the Discussion subsection Sleep/wake and activity phenotypes of 14-18 month vs. 18-22 month old App<sup>NL-G-F</sup> mice: “This long wake/short sleep insomnia-like phenotype is also evident at 12 months of age (Maezono et al., 2020) but not at 6 months (Calafate et al., 2023; Maezono et al., 2020), suggesting a progression in this symptomatology.”

      (4) Would a more advanced age point be helpful? Would sleep fragmentation be likely to appear with more advanced age?

      The text states “Recordings collected throughout the entire 14-day period when Cohort 2 App KI and App WT mice were 21.0-24.3 months of age”. Mice on a C57BL6/J background are considered old at 18-24 months. Fig. 6B’ shows a strong trend (p=0.0558) toward shorter NREM bouts in App KI mice at 18-22 months during the dark phase at the same time that long wake bouts are evident (Fig. 6A’), strongly indicative of sleep/wake fragmentation but not quite significant with the sample size measured.

      (5) How does the onset of sleep-architecture-related symptoms relate to the cognitive impairment onset in AppNL-G-F mice?

      We have added this sentence to the Conclusions: “In a fear conditioning paradigm, impaired learning ability has been correlated with REM sleep duration in 13 month old but not 7 month old App<sup>NL-G-F</sup> mice (Maezono et al., 2020).

      (6) It is importantly concluded that the AppNL-G-F mouse phenotype is "stronger" in females. What is meant here by "stronger" and can this be quantified?

      We have eliminated use of “stronger” and replaced with “more evident” or “more apparent”.

      (7) Would ovariectomized females still show partial insomnia?

      This is an interesting question, particularly because the hyperactivity evident in Figure 7C is most evident in females. The average age of cessation of estrus cyclicity in C57BL6/J mice occurs between 13-16 months of age (Nelson et al., 1982, Biol Reproduction). The female KI mice in Cohort 2 ranged from 21.0 to 23.3 months of age at the time of recording and thus can be expected to be functionally ovariectomized.

      (8) The statement, "...female AppNL-G-F mice exhibited the most wakefulness and the least amount of sleep each day", sounds like a tautology.

      It was an intentional statement to underscore the long wake/short sleep phenotype.

      Reviewer #2 (Recommendations for the authors):

      (1) Introduction:

      The authors might mention in paragraph 3 that because these studies each used a mutant protein on a powerful, and not the endogenous, promoter, the effects on sleep may be skewed by overexpression in specific brain areas. In addition, they might mention that sleep homeostasis and sleep changes relative to brain temp and activity have not been examined longitudinally.

      We have added the following sentences to the Limitations subsection of the Discussion: “Moreover, because studies of this strain used a mutant protein on a powerful exogenous promoter, the effects on sleep described by us and previous investigators may be skewed by overexpression in specific brain areas” and “Neither the present nor previous studies have assessed the effects of age-related changes in brain temperature on sleep/wake, sleep homeostasis or activity.”

      (2) Results:

      Figure 2: Images in 1B and 1B' look like IHC labeling in well over 1 and 2% of the brain for Iba-1. Are these images correct?

      The use of “%” on the Y-axis was inappropriate and has been corrected. Due to variation in Iba1 immunostaining across WT mice, Iba1 measurements were normalized to WT such that the mean Iba1 area coverage for WT mice within each region of interest was set to 1. The negligible 82E1 signal in WT mice obviated the need for normalization.

      Figure 3: I would move to incorporate into Figure 14 with spectra, as this is descriptive but nicely illustrates Figure 14.

      Done -- thank you for this excellent suggestion!

      Figure 10: The figure supports no significant estrus effects in either WT or NLGF. Could run the analysis, but important finding.

      Agreed but, as indicated in the response to Reviewer 1, the average age of cessation of cyclicity in C57BL6/J mice has been reported to occur between 13-16 months of age (Nelson et al., 1982, Biol Reproduction). The female mice in the older cohort that we recorded were 18-22 months of age.

      (3) Discussion:

      Page 11, last paragraph: It is hard to say whether activity caused more wake or response to wake is different in these mice (anxiety and hyperactivity are both seen in Alzheimer's disease).

      Hypocretin MCH is touched on but could be elaborated upon, given light/dark differences.

      We agree that the directionality is difficult to ascertain. As mentioned above, we have added a discussion on hyperactivity but, having not made any assessment of anxiety in the present study, we have refrained from further speculation.

      Reviewer #3 (Recommendations for the authors):

      (1) Figure 9: Y-axis labels are missing on several plots.

      Due to the density of info on this figure, Y-axis labels were intentionally omitted for those panels for which the Y-axis label of the panel to the left applied. Since the reviewer found this to be confusing, we have added Y-axis labels to all panels at the risk of making the figure even more dense!

      (2) Figure 14: x tick labels are perplexing - why would they be labelled in such arbitrary decimal points?

      As stated in the text, “EEG spectra for each state were analyzed in 0.061 Hz bins”. Consequently, X-axis labels are modulo 0.061 Hz.

      (3) Figure S1 is not aligned; some plots cannot even be read.

      Figure S1 has been reformatted to portrait mode from the previous landscape version (although no alignment issues were evident when viewed in landscape mode).

      (4) For some reason, Tables 1-3 are horizontal, which I couldn't read.

      Our apologies, some of the info in Table 1 was omitted during export. We have retained landscape mode for Table 1 and re-formatted Tables 2 and 3 in portrait mode for ease of accessibility.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      The authors adapt MemPrep, a protocol they originally developed to purify organelle membranes from yeast, for use in human cell lines. To this end, they established immuno-isolation strategies based on tagged versions of the ER sheet protein SEC61β and the ER tubular protein REEP5 in HEK293T cells. Their purification strategy allowed them to generate highly pure ER sheet- and tubule-enriched fractions, which were then subjected to quantitative lipidomic and proteomic analyses.

      Overall, this manuscript is well written and presents a careful interpretation of the data. It introduces MemPrep in mammalian cells as a method that will be useful for studying the membrane lipid and protein composition of organelles, with a particular focus on the ER. As such, the manuscript provides sufficient information and controls to assess the experiments in terms of reproducibility and clarity.

      We thank the reviewer for a positive, thorough assessment and for raising important points that helped us to improve the manuscript.

      Major comments:

      1. Based on the immunofluorescence images in Figure 1, it is not clear that the tagged and slightly overexpressed versions of SEC61β and REEP5 localize specifically to ER sheets and tubules, respectively, or that these proteins are enriched in these distinct ER subdomains. Perhaps reducing the fixation time, for example to a maximum of 2 minutes, or using PFA fixation, could help to better preserve ER sheet and tubular domains.

      To address the localization of the bait proteins in the ER membrane network, we added new co-localization microscopy data and quantifications to the revised manuscript (new Figure 1E,F; new Supplementary Figure S1C,D). Despite its low level of overexpression (new Figure 1C; new Suppl. Fig. S1A), SEC61β localizes to the entire ER membrane network including ER tubules and the nuclear envelope (new Fig. 1E,F).

      Considering the new data, we have carefully rephrased all sections regarding the subcellular localization of bait-SEC61β. In the revised manuscript, we use SEC61β as a general ER marker.

      Intriguingly, quantitative proteomics of the SEC61β MemPrep isolate demonstrates a selective enrichment of ER sheet-associated proteins compared to the REEP5 MemPrep, which selectively enriches proteins associated with ER tubules (Fig. 5). While we do not claim to 'isolate' ER subdomains, we enrich ER subdomains.

      We have performed additional microscopy experiments and adjusted our fixation protocol as suggested by the reviewer (Revision Fig. 1). Shortening the fixation time has no apparent impact on the ER structure, while any PFA fixation seems to largely disrupt the ER.

      Does expression of tagged SEC61β or REEP5 influence the ER sheet:tubule ratio? In addition, does expression of these constructs affect the lipidome or proteome of the cells?

      The reviewer raises an important point, which is experimentally not easy to address. Our imaging modality is not sufficient to make a firm statement about the sheet:tubule ratio in HEK293T cells. We are not aware of any study that firmly quantifies the relative content of sheets and tubules in HEK293T cells. Imaging the ER in HEK293T cells is challenging and most studies on the ER membrane networks use other cell types to study the impact of ER-shaping protein on the ER membrane network.

      In the revised manuscript we state: 'We found no evidence that the expression of the bait constructs disrupts the tubule-to-sheet ratio or other aspects of the ER architecture, but distinguishing ER sheets and ER tubules is challenging in HEK293T cells.'

      Furthermore, we have studied if the expression of the bait constructs affects the cellular proteome (new Suppl. Fig. S1A,B) and lipidome (new Suppl. Fig. S4A-H (previously Suppl. Fig. S3)). The expression of the bait constructs has no substantial impact of the cellular proteome. Most importantly, we find no evidence that proteins characteristic for ER sheets or ER tubules (other than the bait proteins) change their expression level (new Suppl. Fig. S1A,B). In the revised manuscript we state:

      ' We decided to go one step further and compared the proteomes of wildtype HEK293T cells with the two cell lines using TMT multiplexed, untargeted protein mass spectrometry (Suppl. Fig. S1A, B). This experiment revealed that bait proteins have only a minimal, neglectable impact on the cellular proteome (Suppl. Fig. S1A, B). We did not find evidence for a systematic deregulation of proteins known to localize exclusively to ER tubules or other ER subdomains. Furthermore, quantitative proteomics validated the results from immunoblotting (Fig. 1B, C): Expression of bait-SEC61β has barely any impact on the total cellular level of SEC61β (Suppl. Fig. S1A) while the expression of the REEP5-bait results in a 1.8-fold overabundance of REEP5 (Suppl. Fig. S1B).'

      Likewise, the expression of the bait constructs has little to no effect on the cellular lipidome as shown in Suppl. Fig. S4A-J. In the revised manuscript we state:

      'As a control, we also tested the impact of the bait constructs on the HEK293T whole cell lipidome (Suppl. Fig. 4A-J). Overall, the lipid composition of the virally transduced cells was indistinguishable from HEK293T cells with only minor impact on the level of CL and lysolipids (Suppl. Fig. 4A-J).'

      Apart from hypotonic swelling and douncing, could the authors use alternative methods for cell disruption to exclude the possibility that mechanical stress confounds the interpretation of the data?

      Thanks to the reviewer's comment, we became aware of a mistake. Our cell lysis buffer is hypertonic and not hypotonic (15% sucrose w/v, 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)(HEPES) pH 7.4, 300 mM NaCl, 1 mM EDTA freshly supplemented with protease inhibitor cocktail from Roche). We have corrected all relevant sections in the revised manuscript.

      The reviewer is right that different means of mechanical lysis, and/or the incubation of the cells in hypo/hypertonic buffer are likely to have impact on the structure of the ER and to affect the isolation procedure. Changing such critical parameters will likely affect the purity of the preparation. Performing additional MemPrep isolations using different means of cell disruptions goes beyond the scope of this manuscript.

      Upon establishing the MemPrep protocol, we have explored various mechanical cell disruptions: Different cannula, Dounce homogenizers, and a ball-bearing device. We experimented with both hypo- and hypertonic buffers. Given the costs and work associated with lipidomic and proteomic analyses, we have tried to find a suitable conditions for cell disruption without performing a full analysis each time. Therefore, we performed differential centrifugations as exemplary shown in Fig. 2B of the manuscript. Critical factors for our decision whether to further persue a certain condition was 1) the depletion of the mitochondrial TOM22 marker, 2) the enrichment of the ER markers, and 3) the total protein yield in the P100,000 fraction.

      In the revised manuscript we state: 'Compared to the MemPrep procedure in yeast, we tested various means of cell disruption and optimized the differential centrifugation protocol.'

      and

      'Mild cell disruption by Dounce homogenization in a hypertonic buffer is crucial for cracking cells open, but these procedures can disrupt normal ER architecture and might facilitate the undesired mixing of previously well-defined ER subdomains. Despite these limitations, our data underscore the purity of our ER membrane preparations, demonstrate a differential enrichment of ER subdomains (Fig. 5), and establish the lipid composition of the ER membrane (Fig. 6)'.

      What is the total amount of lipids and proteins isolated with REEP5- or SEC61β-based MemPrep? Are there differences in the total lipid:protein ratio between these isolates, and could this reflect differences in the ER sheet:tubule ratio?

      In response to the reviewers' question, we have included a new Supplementary table 1 to the manuscript outlining the yield of total protein and total lipid of MemPrep.

      The mammlian MemPrep protocol is not yet optimized for determining the lipid:protein ratio in the membrane. At this moment, we do not want to make a statement about the protein-to-lipid ratio in the ER or its subdomains. The isolates still contain material originating from the ER lumen.

      The combined analysis of lipid and protein composition demonstrates the capacity of the method. To test that MemPrep can capture changes in ER membrane architecture, it would be useful to compare ER protein and lipid composition across different cellular states, such as stressed versus unstressed cells, or growing versus resting cells.

      We agree with the reviewer that a comparison of the ER under different conditions would be extremely interesting. Currently, we see it beyond the scope of this study.

      Minor comment:

      1. In line 335, the authors state: "To address this possibility, we performed a new round of REEP5 and SEC61β MemPreps for a direct comparison of the isolates (Fig. 5A, B)." It is unclear whether the MemPrep protocol was altered or whether this refers simply to an additional round of purification. Please clarify.

      Thank you. This point was also raised by reviewer 2 and 3. We have clarified our statements. In the revised manuscript we state:

      'Hence, we performed a new round of REEP5 and SEC61β MemPreps in triplicates for a direct comparison of the isolates (Fig. 5A, B) rather than comparing the changes in abundance relative to the respective cell lysates as performed in Figure 3. Knowing that non-ER proteins are less efficiently enriched by the MemPrep procedure than ER proteins (Fig. 3C, D) and that the sensitivity and comprehensiveness of mass spectrometry-based proteomics experiments are reduced with increasing sample complexity (Ting et al, 2011; Beck et al, 2011) , we were hoping to gain a better insight into the distribution of low abundant and challenging to quantify proteins in the two MemPrep isolates'.

      Reviewer #1 (Significance (Required)):

      General assessment:

      The manuscript establishes MemPrep for mammalian cells as an important discovery tool to investigate how cells coordinate membrane lipid composition with membrane protein composition, and vice versa. This is a rapidly growing research field, which attracts a lot of interest.

      MemPrep is based on an immuno-isolation strategy using tagged versions of the ER sheet protein SEC61β and the ER tubular protein REEP5 in HEK293T cells. The purification strategy allowed to generate highly pure ER sheet- and tubule-enriched fractions, which were then subjected to quantitative lipidomic and proteomic analyses.

      The results show that the protein composition differs between the SEC61β- and REEP5-enriched fractions. Yet the lipid composition of ER sheets and tubules is largely indistinguishable. Both fractions are dominated by PC alongside other monounsaturated GPL, and hydroxylated ceramides. These physicochemical properties of the ER lipid bilayer are matched by ER-resident membrane proteins.

      Thorough bioinformatic analysis of a subset of ER membrane proteins further revealed that their transmembrane domains have reduced hydrophobicity and increased polarity compared with those of plasma membrane proteins, matching the ER lipidome.

      Hence the combined analysis of lipid and protein composition demonstrates the capacity of the method. Many variations of this approach will be possible in the future to understand on the molecular level how cells assemble and control their membranes.

      Advance: Other immuno-isolation methods, or "organelle immunoprecipitation" approaches, have been established for lysosomes, the Golgi apparatus, and other organelles.

      MemPrep is an important and complementary addition to the technical toolbox for organelle isolation, with a particular focus on the analysis of membrane lipid and protein content.

      Audience: The manuscript will be of broad interest to researchers in basic biology as well as clinical and translational research.

      Reviewer's field of expertise:

      Molecular membrane biology.

      __Reviewer #2 __

      Jain and colleagues develop a biochemical fractionation procedure in which ER microsomes are enriched through small epitope tags. The manuscript is pitched around the concept that there are ER sheets and tubules and ER proteins differentially localise to them. The authors use REEP5 as a 'tubule' bait and SEC61beta as a 'sheet' bait. These baits are immuoisolated after a sensible membrane fractionation and ER membraned purified. There is a convincing ER proteome as a result, and this is used to compare the TMD properties of the organelles resident membrane proteins. The authors make the interesting observation that the transmembrane domains are more polar in the ER. They then compare the two sheet and tubule preparations and see a different in the proteome, before comparing the lipidome. There is no difference observed between the lipidome of the sheet and tubule preps, however they see a difference in the whole cell lysate and use that to compare the ER lipidome against the whole cell.

      Overall the manuscript has an interesting premise and the data is well presented, the experiments well performed and the interpretations appropriate. I think there are some issues with the mechanistic insight and novelty, and essentially although the premise is with regards to sheets and tubules there is limited progress in that direction in terms of results. I am reluctant to be to critical overall as there are certainly interesting observations that may be insightful for future studies in the field. I have some more specific comments below:

      We thank the reviewer for a thorough, constructive assessment and for highlighting important points that helped us improve the manuscript.

      1) The authors cite nixon-abell, but they do not mention the major point of that manuscript which is that the 'sheets' in the cellular periphery are instead dense tubular networks. I think this is quite an omission for the introduction, as it points to the premise not being as clear as stated.

      In the revised manuscript we refer to the Nixon-Abell study and two additional studies from the Jokitalo lab. Notably, the Nixon-Abell study does not rule out the existence of ER sheets.

      In the revised manuscript we state: ' [...] dense tubular networks in the cell periphery can appear like ER sheets in diffraction-limited microscopy (Nixon-Abell et al, 2016). Furthermore, the edges of ER sheets are populated by curvature-stabilizing proteins also found in ER tubules (Shibata et al, 2010; Shemesh et al, 2014), and ER sheets show different degrees of fenestration dependent on the cell type and the cell cycle phase (Puhka et al, 2007, 2012; Nixon-Abell et al, 2016). Consistent with our microscopic data (Fig. 1E, F) and because ER sheets may be biochemically inseparable from ER tubules, we use SEC61β as a general ER marker.'

      We performed additional co-localization studies of the bait proteins with RTN4 and CLIMP63 (new Fig. 1E,F) suggesting that SEC61B can localize across many ER subdomains including ER tubules and the nuclear envelope.

      We have carefully revised our manuscript accordingly and shifting the focus of our discussion away from a molecular description of discrete ER subdomains.

      2) The first section when the protocol is discussed essentially relies on looking at other papers to understand. As the manuscript is centrally about this protocol, I think a brief but clear description is more appropriate.

      We agree with the reviewer. We added a short section to the results section providing an overview over the MemPrep procedure. We now state:

      'To this end, we adapted the MemPrep procedure originally developed for the isolation of organelle membranes from Saccaromyces cerevisiae (S. cerevisiae) (Reinhard et al, 2023, 2024). Mammalian MemPrep relies on a gentle, detergent-free, mechanical lysis of the cells in a hypertonic buffer followed by differential centrifugation to separate ER-derived microsomes from mitochondria-derived membranes. Next, larger organelle fragments are disrupted by brief pulses of sonication, and the resulting vesicles are subjected to affinity purification using magnetic dynabead-coupled antibodies directed against the cleavable tag of the bait protein. Specifically bound, ER-derived membrane vesicles are washed with harsh, urea-containing buffers and selectively released by proteolytically cleaving the bait tag.'

      3) In figure 1C the two markers are supposed to localise to sheets and tubules differentially. To me they look very similar. This, of course, is a major concern. Have the authors co-expressed them (at the same levels in these lines) and seen that indeed they do differentially localise?

      The reviewer raises an important point regarding the localzation of the bait proteins. While we have not co-expressed the bait proteins in cells, we have performed additional co-localization experiments with RTN4 and CLIMP63 as markers for ER tubules and ER sheets, respectively (new Figure 1E,F; new Suppl. Fig. S1C,D). The implications of these data are discussed in the manuscript.

      In light of these new data, we do not refer to SEC61β as an ER sheet marker any longer, instead we refer to SEC61β as a general ER marker. We carefully revised our discussion of the data throughout the manuscript along the line suggested by the reviewer in point 8.

      4) I found the TMD polarity section very interesting, but it was not clear to me why they needed their proteomics for this? Could this not be done with annotated ER membrane proteins?

      The reviewer is correct. The same type of analysis could have been performed with an even bigger dataset of all ER annotated proteins. One of the co-authors, Joseph Lorent, has performed such analysis at this larger scale (PMID: 40326394). The study by Lorent et al. addressed TMH length and side chain bulkiness (PMID: 40326394) in the ER, Golgi apparatus, and the PM. This work is referenced in the manuscript.

      We focused our analysis on the smaller dataset of 83 single-pass proteins found in our proteomics experiments, because we initially planned to perform a comparative analysis of ER proteins in either of the two isolates.

      In line of the reviewers' suggestion, we validate our new finding on the TMH hydrophobicity in the ER using a larger dataset covering all single pass TMHs of ER proteins (215 instead of 83), Golgi apparatus proteins (260), and plasma membrane proteins (1322) (Suppl. Fig. S3D).

      5) It was not clear to me based on the results section text the difference between the figure 5 proteomics and the previous runs.

      This point was also raised by reviewer 1 and 3. We clarified our statement in the revised manuscript:

      'Hence, we performed a new round of REEP5 and SEC61β MemPreps in triplicates for a direct comparison of the isolates (Fig. 5A, B) rather than comparing the changes in abundance relative to the respective cell lysates as performed in Figure 3. Knowing that non-ER proteins are less efficiently enriched by the MemPrep procedure than ER proteins (Fig. 3C, D) and that the sensitivity and comprehensiveness of mass spectrometry-based proteomics experiments are reduced with increasing sample complexity (Ting et al, 2011; Beck et al, 2011) , we were hoping to gain a better insight into the distribution of low abundant and challenging to quantify proteins in the two MemPrep isolates.'

      6) Again in figure 5- are the authors sure that the difference was not due to the over-expression (albeit mild) of their protein.

      After performing an important control experiment, we are sure that the mild over-expression of the bait proteins has no impact.

      We have compared HEK293T WT cells with the bait protein expressing cell lines by quantitative proteomics (new Suppl. Fig. S1A,B). The bait proteins have no impact of the cellular proteome and do not affect the abundance of proteins known to be enriched in ER sheets or ER tubules. Hence, the enrichment of these proteins in our MemPrep isolates as shown in Fig. 5 suggests that some of the identity of ER sheets and ER tubules is maintained in our preparations even though they are not resolved by our microscopy experiments (Fig. 1). In the revised manuscript, we carefully discuss the implications of these findings.

      7) There were no differences in the ER lipidome between the two baits. This may be because there is no difference between the lipid profile of sheets and tubules, but it is very hard to conclude that.

      The reviewer has a point. Even though our findings suggest that we can differentially enrich for ER subdomains (the proteomics data in Fig. 5 on MemPrep isolates can be regarded as a golded standard for this statement), we do not have any knowledge about their biochemical purity. Hence, we have carefully toned down our statements on the basis of new imaging data (Fig. 1E,F; Suppl. Fig. S1C,D) and new proteomics data (Suppl. Fig. S1A,B).

      Along the reasoning of the reviewer, we also rephrased our statements on the difference/similarity of ER subdomains.

      8) I do not see it as my job as a reviewer to propose reorganisations and rewrites, so I encourage the authors to feel free to ignore this comment. To me the lipidome and TMD polar observations are the key manuscript findings, and there is very limited insight into the tubules and sheets line of inquiry. I wonder if it would be worth changing the focus of the manuscript overall to rather be about the ER, and not the tubules and sheets.

      Again, the reviewer raises an important point that we did not want 'to ignore'. We have carefully revised the manuscript and toned down our interpretations. In the revised manuscript we put more emphasis on the ER lipidome and less so on the composition of specific ER subdomains.

      __Reviewer #2 (Significance (Required)): __

      Overall the manuscript has an interesting premise and the data is well presented, the experiments well performed and the interpretations appropriate. I think there are some issues with the mechanistic insight and novelty, and essentially although the premise is with regards to sheets and tubules there is limited progress in that direction in terms of results. I am reluctant to be to critical overall as there are certainly interesting observations that may be insightful for future studies in the field.

      Reviewer #3

      Summary: Jain et al., provide a clear and thorough manuscript that extends their prior biochemical analysis of the yeast ER-lipidome (MEMPREP) to mammalian cells. They use detergent free lysis and differential speed centrifugation from 293T cells bearing reporters with affinity handles targeted to sheet-like or tubular-like subdomains of the ER and enrich membranes and membrane-embedded proteins from these sites. The lipidomics reveals a distinct ER-lipidome, heavily enriched in PC and PI, contains predominantly mono-unsaturated phospholipids and is surprisingly invariant across sheet-like and tubule-like domains. Additional hydrophobicity analysis suggests that ER-localised TMDs are more polar and shorter than PM-resident TMDs, and the authors speculate about co-evolution of the lipidome and proteome to ensure targeting.

      Major comments:

      I think the data are solid, clear and convincing. The similarity of the lipidomes from sheet and tubule regions of the ER give good indication of the robustness of the technique. Whilst the yield is low, the authors go to good lengths to demonstrate purity of ER capture and de-enrichment of other cellular membranes. There is good discussion of the limitations of the technique and good comparison to recent data from other labs, most notably, a recent preprint and I think the manuscripts support eachother well. There's a fair amount of speculation in the manuscript, e.g., about lipid headgroup charge density being inferred by the charge distribution on the -1 position, but the speculation is clearly acknowledged.

      1. I think that blotting for SEC61B would really help. A clear comparison to endogenous SEC61B would be helpful. I appreciate that the authors lacked an antibody here, but there are several on CiteAb that seem to detect endogenous protein.

      Following the reviewers' advice, we added new data using a commercial antibody directed against SEC61β (new Fig. 1C). We also added proteomics data comparing HEK293T WT cells with the bait expressing cell lines (new Suppl. Fig. S1A,B).

      We also characterized the commercial Proteintech (15087-1-AP) antibody to make sure it recognizes the same epitopes in the tagged and untagged variant of SEC61β.

      It's not brilliantly easy to see the 'sharp decline' in relative frequency of hydrophobic amino acids at 21 aa for ER and Golgi; whilst the individual amino acid information is interesting (and some comment could be made about the favouring of Leucines in ER and Golgi TMDs), would this be clearer if the relative frequencies were binned into hydrophobic/aromatic, polar, positive, negative?

      The reviewer is right. We have removed our statement regarding a 'sharp decline'. In fact, the decline is rather gradual for ER and Golgi TMHs, but more clear for PM TMHs. This is also reflected in the data shown in Suppl. Fig. S3D and discussed in the revised manuscript.

      We state: Confirming our expectations based on the predicted TMH length (Suppl. Fig. S3A), we observed a gradual decline in the relative frequency of hydrophobic and aromatic resides at about 21 amino acids for ER (Fig. 4E) and Golgi-associated TMHs (Fig. 4F). Such decline was more clearly defined for plasma membrane TMHs but only after 24 aa or more (Fig. 4G).'

      We also state: 'We therefore challenged our finding and performed an additional analysis using this larger dataset of all annotated human single-pass TMHs (Fig. S3D) and compared the hydrophobicity profiles of TMHs from the ER (215), the Golgi apparatus (260), and the PM (1322) (Lorent et al, 2025). This analysis further substantiated our finding that the ER and the Golgi apparatus host less hydrophobic TMHs compared to the plasma membrane. Furthermore, we observed that the ER and Golgi profiles display a conical shape with hydrophobic maxima at the center of the membrane's hydrophobic core, while the PM TMH's possess higher hydrophobicity in the cytoplasmic part of the membrane, compared to the exoplasmic part (Fig. S3D).'

      We decided to keep the Fig. 4 with its single amino acid 'resolution' was it was in the original manuscript, because we feel that this representation still has its value. It helps connecting physicochemical parameters of an average TMH in an organelle (Fig. 4A-D; Suppl. Fig. S3A-D) with the preferred amino acid composition and distribution (Fig. 4E-G). Nevertheless, some 'noise' in inherent to the data and we hope that the adaptations to the text avoids any possible confusion of the reader.

      The frequency of leucine residues in TMHs from the PM (24.5%) is comparable to the frequency of TMHs from the ER (24.1%) and from the Golgi apparatus (26.3%). Our attempts to identify an organelle-selective usage of certain amino acids did not yield robust and significant results.

      Related to this point, it's hard to correlate the degree of polar amino acid incorporation in the TMDs of Golgi, ER, PM proteins (which don't appear to vary in 4E, 4F and 4G) with the variance described in 4C. Is there a better way of displaying this data, or are the polarity measurements calculated by some other metric in 4C?

      The reviewer is right. Figure 4A-D and Figure 4E-G are based on different metrics. Figure 4A-D considers different physicochemical parameters of the amino acid sidechains (Fig. 4C: Kyte-Dolittle scale). Figure 4E-G only represents the relative frequencies. We believe that both representations can be useful.

      Notably, the relative incorporation of polar and apolar amino acids is significantly different between TMHs from the ER and the Golgi versus the TMHs from the PM (Suppl. Fig. S3B,C).

      In the revised manuscript we state: 'Our new finding that the TMHs of ER proteins are more polar than the TMHs in the plasma membrane (Fig. 4C) is also reflected by the significantly different number of apolar and polar residues in the TMHs from ER-, Golgi apparatus-, and PM-derived proteins (Suppl. S3B, C)'.

      Indeed, the polarity in Fig. 4A and Fig. 4C is calculated via the Kyte-Dolittle scale, while only the normalized frequency of the amino acid is color-coded in Fig. 4E-G.

      Minor comments:

      1. Panel 2D isn't labelled on the figure

      We represented both MemPreps in a single Panel 2C because we aimed to label in the immunoblots only a single time to avoid redundancies. We are open to change our strategy of panel labeling if our current representation is confusing.

      There is limited co-enrichment of non-ER proteins in the ER-affinity preps, and the authors have done well to deal with misannotated GO terms. It might be worthwhile adding to the discussion that all TMD proteins that localise at steady-state to post-ER compartments must necessarily pass through the ER during biosynthesis. As such, detection of non-ER proteins in ER fractions is not inherently unexpected.

      This is of course correct. In the revised manuscript we state: 'Finding non-ER proteins in an ER proteome is not surprising, because a very large number of proteins are first delivered to the ER, before they are sent to other cellular destinations.'

      I didn't understand the line on L377 about the new round of extraction featureing inherently less complex proteomes.

      This point was also raised by reviewer 1 and 2. We clarified our statement in the revised manuscript:

      'Hence, we performed a new round of REEP5 and SEC61β MemPreps in triplicates for a direct comparison of the isolates (Fig. 5A, B) rather than comparing the changes in abundance relative to the respective cell lysates as performed in Figure 3. Knowing that non-ER proteins are less efficiently enriched by the MemPrep procedure than ER proteins (Fig. 3C, D) and that the sensitivity and comprehensiveness of mass spectrometry-based proteomics experiments are reduced with increasing sample complexity (Ting et al, 2011; Beck et al, 2011) , we were hoping to gain a better insight into the distribution of low abundant and challenging to quantify proteins in the two MemPrep isolates.'

      For line L390-391, in the speculation about progressively more unsaturation as you move ER-Golgi-postGolgi, is there any (published) data from ER-FLIPPR that could inform about the degree of membrane fluidity/packing as you traverse the secretory pathway?

      We agree that mentioning evidence on the biophysical changes along the secretory pathway is helpful in this section. In the revised manuscript we state:

      'These changes of the lipid acyl chains are associated with biophysical changes of the membrane properties along the secretory pathway as observed by molecular probes reporting on lipid packing and membrane tension (Goujon et al, 2019; López-Andarias et al, 2021, 2022; Wong & Budin, 2024).'

      Reviewer #3 (Significance (Required)):

      The strengths of the study are the conceptual novelty and information provided - I think this is the first comprehensive reporting of the ER lipidome. This is a major organelle and I think as the lipid biology field develops, resources like this are really important. Moreover, the MEMPREP protocol is applicable for protein extraction from these domains, which will help with functional characterisation of ER subdomains and is a strong technical advance.

      Weaknesses relate to the single cell type and overexpression (albeit mild) methodologies. I'm not hugely fussed about this as this manuscript describes an important 1st step.

      I'm a cell biologist studying the ER

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Reviewer #1

      Evidence, reproducibility and clarity

      This paper addresses a very interesting problem of non-centrosomal microtubule organization in developing Drosophila oocytes. Using genetics and imaging experiments, the authors reveal an interplay between the activity of kinesin-1, together with its essential cofactor Ensconsin, and microtubule organization at the cell cortex by the spectraplakin Shot, minus-end binding protein Patronin and Ninein, a protein implicated in microtubule minus end anchoring. The authors demonstrate that the loss of Ensconsin affects the cortical accumulation non-centrosomal microtubule organizing center (ncMTOC) proteins, microtubule length and vesicle motility in the oocyte, and show that this phenotype can be rescued by constitutively active kinesin-1 mutant, but not by Ensconsin mutants deficient in microtubule or kinesin binding. The functional connection between Ensconsin, kinesin-1 and ncMTOCs is further supported by a rescue experiment with Shot overexpression. Genetics and imaging experiments further implicate Ninein in the same pathway. These data are a clear strength of the paper; they represent a very interesting and useful addition to the field.

      The weaknesses of the study are two-fold. First, the paper seems to lack a clear molecular model, uniting the observed phenomenology with the molecular functions of the studied proteins. Most importantly, it is not clear how kinesin-based plus-end directed transport contributes to cortical localization of ncMTOCs and regulation of microtubule length.

      Second, not all conclusions and interpretations in the paper are supported by the presented data.

      We thank the reviewer for recognizing the impact of this work. In response to the insightful suggestions, we performed extensive new experiments that establish a well-supported cellular and molecular model (Figure 7). The discussion has been restructured to directly link each conclusion to its corresponding experimental evidence, significantly strengthening the manuscript.

      Below is a list of specific comments, outlining the concerns, in the order of appearance in the paper/figures.

      Figure 1. The statement: "Ens loading on MTs in NCs and their subsequent transport by Dynein toward ring canals promotes the spatial enrichment of the Khc activator Ens in the oocyte" is not supported by data. The authors do not demonstrate that Ens is actually transported from the nurse cells to the oocyte while being attached to microtubules. They do show that the intensity of Ensconsin correlates with the intensity of microtubules, that the distribution of Ensconsin depends on its affinity to microtubules and that an Ensconsin pool locally photoactivated in a nurse cell can redistribute to the oocyte (and throughout the nurse cell) by what seems to be diffusion. The provided images suggest that Ensconsin passively diffuses into the oocyte and accumulates there because of higher microtubule density, which depends on dynein. To prove that Ensconsin is indeed transported by dynein in the microtubule-bound form, one would need to measure the residence time of Ensconsin on microtubules and demonstrate that it is longer than the time needed to transport microtubules by dynein into the oocyte; ideally, one would like to see movement of individual microtubules labelled with photoconverted Ensconsin from a nurse cell into the oocyte. Since microtubules are not enriched in the oocyte of the dynein mutant, analysis of Ensconsin intensity in this mutant is not informative and does not reveal the mechanism of Ensconsin accumulation.

      As noted by Reviewer 3, the directional movement of microtubules traveling at ~140 nm/s from nurse cells toward the oocyte through Ring Canals was previously reported using a tagged Ens-MT binding domain reporter line by Lu et al. (2022). We have therefore added the citation of this crucial work in the novel version of the manuscript (lane 155-157) and removed the photo-conversion panel.

      Critically, however, our study provides mechanistic insight that was missing from this earlier work: this mechanism is also crucial to enrich MAPs in the oocyte. The fact that Dynein mutants fail to enrich Ensconsin is a crucial piece of evidence: it supports a model of Ensconsin-loaded MT transport (Figure 1D-1F).

      Figure 2. According to the abstract, this figure shows that Ensconsin is "maintained at the oocyte cortex by Ninein". However, the figure doesn't seem to prove it - it shows that oocyte enrichment of Ensonsin is partially dependent on Ninein, but this applies to the whole cell and not just to the cell cortex. Furthermore, it is not clear whether Ninein mutation affects microtubule density, which in turn would affect Ensconsin enrichment, and therefore, it is not clear whether the effect of Ninein loss on Ensconsin distribution is direct or indirect.

      Ninein plays a critical role in Ensconsin enrichment and microtubule organization in the oocyte (new Figure 2, Figure 3, Figure S3). Quantification of total Tubulin signal shows no difference between control and Nin mutant oocytes (new Figure S3 panels A, B). We found decreased Ens enrichment in the oocyte, and Ens localization on MTs and to the cell cortex (Figure 2E, 2F, and Figure S3C and S3D).

      Novel quantitative analyses of microtubule orientation at the anterior cortex, where MTs are normally preferentially oriented toward the posterior pole (Parton et al. 2011), demonstrate that Nin mutants exhibit randomized MT orientation compared to wild-type oocytes (new Figure 3C-3E).These findings establish that Ninein (although not essential) favors Ensconsin localization on MTs, Ens enrichment in the oocyte, ncMTOC cortical localization, and more robust MT orientation toward the posterior cortex. It also suggests that Ens levels in the oocyte acts as a rheostat to control Khc activation.

      The observation that the aggregates formed by overexpressed Ninein accumulate other proteins, including Ensconsin, supports, though does not prove their interactions. Furthermore, there is absolutely no proof that Ninein aggregates are "ncMTOCs". Unless the authors demonstrate that these aggregates nucleate or anchor microtubules (for example, by detailed imaging of microtubules and EB1 comets), the text and labels in the figure would need to be altered.

      We have modified the manuscript, we now refer to an accumulation of these components in large puncta, rather than aggregates, consistent with previous observations (Rosen et al., 2000). We acknowledge in the revised version that these puncta recruit Shot, Patronin and Ens without mentioning direct interaction (lane 218).

      Importantly, we conducted a more detailed characterization of these Ninein/Shot/Patronin/Ens-containing puncta in a novel Figure S4. To rigorously assess their nucleation capacity, we analyzed Eb1-GFP-labeled MT comets, a robust readout of MT nucleation (Parton et al., 2011, Nashchekin et al., 2016). While few Eb1-positive comets occasionally emanate from these structures, confirming their identity as putative ncMTOCs, these puncta function as surprisingly weak nucleation centers (new Figure S4 E, Video S1) and, their presence does not alter overall MT architecture (new Figure S4 F). Moreover, these puncta disappear over time, are barely visible at stage 10B, they do not impair oocyte development or fertility (Figure S4 G and Table 1).

      Minor comment: Note that a "ratio" (Figure 2C) is just a ratio, and should not be expressed in arbitrary units.

      We have amended this point in all the figures.

      Figure 3B: immunoprecipitation results cannot be interpreted because the immunoprecipitated proteins (GFP, Ens-GFP, Shot-YFP) are not shown. It is also not clear that this biochemical experiment is useful. If the authors would like to suggest that Ensconsin directly binds to Patronin, the interaction would need to be properly mapped at the protein domain level.

      This is a good point: the GFP and Ens-GFP immunoprecipitated proteins are now much clearly identified on the blots and in the figure legend (new Figure 4G). Shot-YFP IP, was used as a positive control but is difficult to be detected by Western blot due to its large size (>106 Da) using conventional acrylamide gels (Nashchekin et al., 2016).

      We now explicitly state that immunoprecipitations were performed at 4{degree sign}C, where microtubules are fully depolymerized, thereby excluding undirect microtubule-mediated interactions. We agree with this reviewer: we cannot formally rule out interactions through bridging by other protein components. This is stated in the revised manuscript (lane 238-239).

      One of the major phenotypes observed by the authors in Ens mutant is the loss of long microtubules. The authors make strong conclusions about the independence of this phenotype from the parameters of microtubule plus-end growth, but in fact, the quality of their data does not allow to make such a conclusion, because they only measured the number of EB1 comets and their growth rate but not the catastrophe, rescue or pausing frequency."Note that kinesin-1 has been implicated in promoting microtubule damage and rescue (doi: 10.1016/j.devcel.2021).In the absence of such measurements, one cannot conclude whether short microtubules arise through defects in the minus-end, plus-end or microtubule shaft regulation pathways.

      We thank the reviewer for raising this important point. Our data demonstrate that microtubule (MT) nucleation and polymerization rates remain unaffected under Khc RNAi and ens mutant conditions, indicating that MT dynamics alterations must arise through alternative mechanisms.

      As the reviewer suggested, recent studies on Kinesin activity and MT network regulation are indeed highly relevant. Two key studies from the Verhey and Aumeier laboratories examined Kinesin-1 gain-of-function conditions and revealed that constitutively active Kinesin-1 induces MT lattice damage (Budaitis et al., 2022). While damaged MTs can undergo self-repair, Aumeier and colleagues demonstrated that GTP-tubulin incorporation generates "rescue shafts" that promote MT rescue events (Andreu-Carbo et al., 2022). Extrapolating from these findings, loss of Kinesin-1 activity could plausibly reduce rescue shaft formation, thereby decreasing MT rescue frequency and stability. Although this hypothesis is challenging to test directly in our system, it provides a mechanistic framework for the observed reduction in MT number and stability.

      Additionally, the reviewer highlighted the role of Khc in transporting the dynactin complex, an anti-catastrophe factor, to MT plus ends (Nieuwburg et al., 2017), which could further contribute to MT stabilization. This crucial reference is now incorporated into the revised Discussion.

      Importantly, our work also demonstrates the contribution of Ens/Khc to ncMTOC targeting to the cell cortex. Our new quantitative analyses of MT organization (new Figure 5 B) reveal a defective anteroposterior orientation of cortical MTs in mutant conditions, pointing to a critical role for cortical ncMTOCs in organizing the MT network.

      Taken together, we propose that the observed MT reduction and disorganization result from multiple interconnected mechanisms: (1) reduced rescue shaft formation affecting MT stability; (2) impaired transport of anti-catastrophe factors to MT plus ends; and (3) loss of cortical ncMTOCs, which are essential for minus-end MT stabilization and network organization. The Discussion has been revised to reflect this integrated model in a dedicated paragraph ("A possible regulation of MT dynamics in the oocyte at both plus end minus MT ends by Ens and Khc" lane 415-432).

      It is important to note in that a spectraplakin, like Shot, can potentially affect different pathways, particularly when overexpressed.

      We agree that Shot harbors multiple functional domains and acts as a key organizer of both actin and microtubule cytoskeletons. Overexpression of such a cytoskeletal cross-linker could indeed perturb both networks, making interpretation of Ens phenotype rescue challenging due to potential indirect effects.

      To address this concern, we selected an appropriate Shot isoform for our rescue experiments that displayed similar localization to "endogenous" Shot-YFP (a genomic construct harboring shot regulatory sequences) and importantly that was not overexpressed.

      Elevated expression of the Shot.L(A) isoform (see Western Blot Figure S8 A), considered as the wild-type form with two CH1 and CH2 actin-binding motifs (Lee and Kolodziej, 2002), showed abnormal localization such as strong binding to the microtubules in nurse cells and oocyte confirming the risk of gain-of-function artifacts and inappropriate conclusions (Figure S8 B, arrows).

      By contrast, our rescue experiments using the Shot.L(C) isoform (that only harbors the CH2 motif) provide strong evidence against such artifacts for three reasons. First, Shot-L(C) is expressed at slightly lower levels than a Shot-YFP genomic construct (not overexpressed), and at much lower levels than Shot-L(A), despite using the same driver (Figure S8 A). Second, Shot-L(C) localization in the oocyte is similar to that of endogenous Shot-YFP, concentrating at the cell cortex (Figure S8 B, compare lower and top panels). Taken together, these controls rather suggest our rescue with the Shot-L(C) is specific.

      Note that this Shot-L(C) isoform is sufficient to complement the absence of the shot gene in other cell contexts (Lee and Kolodziej, 2002).

      Unjustified conclusions should be removed: the authors do not provide sufficient data to conclude that "ens and Khc oocytes MT organizational defects are caused by decreased ncMTOC cortical anchoring", because the actual cortical microtubule anchoring was not measured.

      This is a valid point. We acknowledge that we did not directly measure microtubule anchoring in this study. In response, we have revised the discussion to more accurately reflect our observations. Throughout the manuscript, we now refer to "cortical microtubule organization" rather than "cortical microtubule anchoring," which better aligns with the data presented.

      Minor comment: Microtubule growth velocity must be expressed in units of length per time, to enable evaluating the quality of the data, and not as a normalized value.

      This is now amended in the revised version (modified Figure S7).

      A significant part of the Discussion is dedicated to the potential role of Ensconsin in cortical microtubule anchoring and potential transport of ncMTOCs by kinesin. It is obviously fine that the authors discuss different theories, but it would be very helpful if the authors would first state what has been directly measured and established by their data, and what are the putative, currently speculative explanations of these data.

      We have carefully considered the reviewer's constructive comments and are confident that this revised version fully addresses their concerns.

      First, we have substantially strengthened the connection between the Results and Discussion sections, ensuring that our interpretations are more directly anchored in the experimental data. This restructuring significantly improves the overall clarity and logical flow of the manuscript.

      Second, we have added a new comprehensive figure presenting a molecular-scale model of Kinesin-1 activation upon release of autoinhibition by Ensconsin (new Figure 7D). Critically, this figure also illustrates our proposed positive feedback loop mechanism: Khc-dependent cytoplasmic advection promotes cortical recruitment of additional ncMTOCs, which generates new cortical microtubules and further accelerates cytoplasmic transport (Figure 7 A-C). This self-amplifying cycle provides a mechanistic framework consistent with emerging evidence that cytoplasmic flows are essential for efficient intracellular transport in both insect and mammalian oocytes.

      Minor comment: The writing and particularly the grammar need to be significantly improved throughout, which should be very easy with current language tools. Examples: "ncMTOCs recruitment" should be "ncMTOC recruitment"; "Vesicles speed" should be "Vesicle speed", "Nin oocytes harbored a WT growth,"- unclear what this means, etc. Many paragraphs are very long and difficult to read. Making shorter paragraphs would make the authors' line of thought more accessible to the reader.

      We have amended and shortened the manuscript according to this reviewer feed-back. We have specifically built more focused paragraphs to facilitates the reading.

      Significance

      This paper represents significant advance in understanding non-centrosomal microtubule organization in general and in developing Drosophila oocytes in particular by connecting the microtubule minus-end regulation pathway to the Kinesin-1 and Ensconsin/MAP7-dependent transport. The genetics and imaging data are of good quality, are appropriately presented and quantified. These are clear strengths of the study which will make it interesting to researchers studying the cytoskeleton, microtubule-associated proteins and motors, and fly development.

      The weaknesses of this study are due to the lack of clarity of the overall molecular model, which would limit the impact of the study on the field. Some interpretations are not sufficiently supported by data, but this can be solved by more precise and careful writing, without extensive additional experimentation.

      We thank the reviewer for raising these important concerns regarding clarity and data interpretation. We have thoroughly revised the manuscript to address these issues on multiple fronts. First, we have substantially rewritten key sections to ensure that our conclusions are clearly articulated and directly supported by the data. Second, we have performed several new experiments that now allow us to propose a robust mechanistic model, presented in new figures. These additions significantly strengthen the manuscript and directly address the reviewer's concerns.

      My expertise is cell biology and biochemistry of the microtubule cytoskeleton, including both microtubule-associated proteins and microtubule motors.

      Reviewer #2

      Evidence, reproducibility and clarity

      In this manuscript, Berisha et al. investigate how microtubule (MT) organization is spatially regulated during Drosophila oogenesis. The authors identify a mechanism in which the Kinesin-1 activator Ensconsin/MAP7 is transported by dynein and anchored at the oocyte cortex via Ninein, enabling localized activation of Kinesin-1. Disruption of this pathway impairs ncMTOC recruitment and MT anchoring at the cortex. The authors combine genetic manipulation with high-resolution microscopy and use three key readouts to assess MT organization during mid-to-late oogenesis: cortical MT formation, localization of posterior determinants, and ooplasmic streaming. Notably, Kinesin-1, in concert with its activator Ens/MAP7, contributes to organizing the microtubule network it travels along. Overall, the study presents interesting findings, though we have several concerns we would like the authors to address. Ensconsin enrichment in the oocyte 1. Enrichment in the oocyte • Ensconsin is a MAP that binds MTs. Given that microtubule density in the oocyte significantly exceeds that in the nurse cells, its enrichment may passively reflect this difference. To assess whether the enrichment is specific, could the authors express a non-Drosophila MAP (e.g., mammalian MAP1B) to determine whether it also preferentially localizes to the oocyte?

      To address this point, we performed a new series of experiments analyzing the enrichment of other Drosophila and non-Drosophila MAPs, including Jupiter-GFP, Eb1-GFP, and bovine Tau-GFP, all widely used markers of the microtubule cytoskeleton in flies (see new Figure S2). Our results reveal that Jupiter-GFP, Eb1-GFP, and bovine Tau-GFP all exhibit significantly weaker enrichment in the oocyte compared to Ens-GFP. Khc-GFP also shows lower enrichment. These findings indicate that MAP enrichment in the oocyte is MAP-dependent, rather than solely reflecting microtubule density or organization. Of note, we cannot exclude that microtubule post-translational modifications contribute to differential MAP binding between nurse cells and the oocyte, but this remains a question for future investigation.

      The ability of ens-wt and ens-LowMT to induce tubulin polymerization according to the light scattering data (Fig. S1J) is minimal and does not reflect dramatic differences in localization. The authors should verify that, in all cases, the polymerization product in their in vitro assays is microtubules rather than other light-scattering aggregates. What is the control in these experiments? If it is just purified tubulin, it should not form polymers at physiological concentrations.

      The critical concentration Cr for microtubule self-assembly in classical BRB80 buffer found by us and others is around 20 µM (see Fig. 2c in Weiss et al., 2010). Here, microtubules were assembled at 40 µM tubulin concentration, i.e., largely above the Cr. As stated in the materials and methods section, we systematically induced cooling at 4{degree sign}C after assembly to assess the presence of aggregates, since those do not fall apart upon cooling. The decrease in optical density upon cooling is a direct control that the initial increase in DO is due to the formation of microtubules. Finally, aggregation and polymerization curves are widely different, the former displaying an exponential shape and the latter a sigmoid assembly phase (see Fig. 3A and 3B in Weiss et al., 2010).

      Photoconversion caveatsMAPs are known to dynamically associate and dissociate from microtubules. Therefore, interpretation of the Ens photoconversion data should be made with caution. The expanding red signal from the nurse cells to the oocyte may reflect a any combination of dynein-mediated MT transport and passive diffusion of unbound Ensconsin. Notably, photoconversion of a soluble protein in the nurse cells would also result in a gradual increase in red signal in the oocyte, independent of active transport. We encourage the authors to more thoroughly discuss these caveats. It may also help to present the green and red channels side by side rather than as merged images, to allow readers to assess signal movement and spatial patterns better.

      This is a valid point that mirrors the comment of Reviewers 1 and 3. The directional movement of microtubules traveling at ~140 nm/s from nurse cells toward the oocyte via the ring canals was previously reported by Lu et al. (2022) with excellent spatial resolution. Notably, this MT transport was measured using a fusion protein containing the Ens MT-binding domain. We now cite this relevant study in our revised manuscript and have removed this redundant panel in Figure 1.

      Reduction of Shot at the anterior cortex• Shot is known to bind strongly to F-actin, and in the Drosophila ovary, its localization typically correlates more closely with F-actin structures than with microtubules, despite being an MT-actin crosslinker. Therefore, the observed reduction of cortical Shot in ens, nin mutants, and Khc-RNAi oocytes is unexpected. It would be important to determine whether cortical F-actin is also disrupted in these conditions, which should be straightforward to assess via phalloidin staining.

      As requested by the reviewer, we performed actin staining experiments, which are now presented in a new Figure S5. These data demonstrate that the cortical actin network remains intact in all mutant backgrounds analyzed, ruling out any indirect effect of actin cytoskeleton disruption on the observed phenotypes.

      MTs are barely visible in Fig. 3A, which is meant to demonstrate Ens-GFP colocalization with tubulin. Higher-quality images are needed.

      The revised version now provides significantly improved images to show the different components examined. Our data show that Ens and Ninein localize at the cell cortex where they co-localize with Shot and Patronin (Figure 2 A-C). In addition, novel images show that Ens extends along microtubules (new Figure 4 A).

      MT gradient in stage 9 oocytesIn ens-/-, nin-/-, and Khc-RNAi oocytes, is there any global defect in the stage 9 microtubule gradient? This information would help clarify the extent to which cortical localization defects reflect broader disruptions in microtubule polarity.

      We now provide quantitative analysis of microtubule (MT) array organization in novel figures (Figure 3D and Figure 5B). Our data reveal that both Khc RNAi and ens mutant oocytes exhibit severe disruption of MT orientation toward the posterior (new Figure 5B). Importantly, this defect is significantly less pronounced in Nin-/- oocytes, which retain residual ncMTOCs at the cortex (new Figure 3D). This differential phenotype supports our model that cortical ncMTOCs are critical for maintaining proper MT orientation toward the posterior side of the oocyte.

      Role of Ninein in cortical anchoringThe requirement for Ninein in cortical anchorage is the least convincing aspect of the manuscript and somewhat disrupts the narrative flow. First, it is unclear whether Ninein exhibits the same oocyte-enriched localization pattern as Ensconsin. Is Ninein detectable in nurse cells? Second, the Ninein antibody signal appears concentrated in a small area of the anterior-lateral oocyte cortex (Fig. 2A), yet Ninein loss leads to reduced Shot signal along a much larger portion of the anterior cortex (Fig. 2F)-a spatial mismatch that weakens the proposed functional relationship. Third, Ninein overexpression results in cortical aggregates that co-localize with Shot, Patronin, and Ensconsin. Are these aggregates functional ncMTOCs? Do microtubules emanate from these foci?

      We now provide a more comprehensive analysis of Ninein localization. Similar to Ensconsin (Ens), endogenous Ninein is enriched in the oocyte during the early stages of oocyte development but is also detected in NCs (see modified Figure 2 A and Lasko et al., 2016). Improved imaging of Ninein further shows that the protein partially co-localizes with Ens, and ncMTOCs at the anterior cortex and with Ens-bound MTs (Figure 2B, 2C).

      Importantly, loss of Ninein (Nin) only partially reduces the enrichment of Ens in the oocyte (Figure 2E). Both Ens and Kinesin heavy chain (Khc) remain partially functional and continue to target non-centrosomal microtubule-organizing centers (ncMTOCs) to the cortex (Figure 3A). In Nin-/- mutants, a subset of long cortical microtubules (MTs) is present, thereby generating cytoplasmic streaming, although less efficiently than under wild-type (WT) conditions (Figure 3F and 3G). As a non-essential gene, we envisage Ninein as a facilitator of MT organization during oocyte development.

      Finally, our new analyses demonstrate that large puncta containing Ninein, Shot, Patronin, and despite their size, appear to be relatively weak nucleation centers (revised Figure S4 E and Video 1). In addition, their presence does not bias overall MT architecture (Figure S4 F) nor impair oocyte development and fertility (Figure S4 G and Table 1).

      Inconsistency of Khc^MutEns rescueThe Khc^MutEns variant partially rescues cortical MT formation and restores a slow but measurable cytoplasmic flow yet it fails to rescue Staufen localization (Fig. 5). This raises questions about the consistency and completeness of the rescue. Could the authors clarify this discrepancy or propose a mechanistic rationale?

      This is a good point. The cytoplasmic flows (the consequence of cargo transport by Khc on MTs) generated by a constitutively active KhcMutEns in an ens mutant condition, are less efficient than those driven by Khc activated by Ens in a control condition (Figure 6C). The rescued flow is probably not efficient enough to completely rescue the Staufen localization at stage 10.

      Additionally, this KhcMutEns variant rescues the viability of embryos from Khc27 mutant germline clones oocytes but not from ens mutants (Table1). One hypothesis is that Ens harbors additional functions beyond Khc activation.

      This incomplete rescue of Ens by an active Khc variant could also be the consequence of the "paradox of co-dependence": Kinesin-1 also transport the antagonizing motor Dynein that promotes cargo transport in opposite directions (Hancock et al., 2016). The phenotype of a gain of function variant is therefore complex to interpret. Consistent with this, both KhcMutEns-GFP and KhcDhinge2 two active Khc only rescues partially centrosome transport in ens mutant Neural Stem Cells (Figure S10).

      Minor points: 1. The pUbi-attB-Khc-GFP vector was used to generate the Khc^MutEns transgenic line, presumably under control of the ubiquitous ubi promoter. Could the authors specify which attP landing site was used? Additionally, are the transgenic flies viable and fertile, given that Kinesin-1 is hyperactive in this construct?

      All transgenic constructs were integrated at defined genomic landing sites to ensure controlled expression levels. Specifically, both GFP-tagged KhcWT and KhcMutEns were inserted at the VK05 (attP9A) site using PhiC31-mediated integration. Full details of the landing sites are provided in the Materials and Methods section. Both transgenic flies are homozygous lethal and the transgenes are maintained over TM6B balancers.

      On page 11 (Discussion, section titled "A dual Ensconsin oocyte enrichment mechanism achieves spatial relief of Khc inhibition"), the statement "many mutations in Kif5A are causal of human diseases" would benefit from a brief clarification. Since not all readers may be familiar with kinesin gene nomenclature, please indicate that KIF5A is one of the three human homologs of Kinesin heavy chain.

      We clarified this point in the revised version (lane 465-466).

      On page 16 (Materials and Methods, "Immunofluorescence in fly ovaries"), the sentence "Ovaries were mounted on a slide with ProlonGold medium with DAPI (Invitrogen)" should be corrected to "ProLong Gold."

      This is corrected.

      Significance

      This study shows that enrichment of MAP7/ensconsin in the oocyte is the mechanism of kinesin-1 activation there and is important for cytoplasmic streaming and localization non-centrosomal microtubule-organizing centers to the oocyte cortex

      We thank the reviewers for the accurate review of our manuscript and their positive feed-back.

      Reviewer #3

      Evidence, reproducibility and clarity

      The manuscript of Berisha et al., investigates the role of Ensconsin (Ens), Kinesin-1 and Ninein in organisation of microtubules (MT) in Drosophila oocyte. At stage 9 oocytes Kinesin-1 transports oskar mRNA, a posterior determinant, along MT that are organised by ncMTOCs. At stage 10b, Kinesin-1 induces cytoplasmic advection to mix the contents of the oocyte. Ensconsin/Map7 is a MT associated protein (MAP) that uses its MT-binding domain (MBD) and kinesin binding domain (KBD) to recruit Kinesin-1 to the microtubules and to stimulate the motility of MT-bound Kinesin-1. Using various new Ens transgenes, the authors demonstrate the requirement of Ens MBD and Ninein in Ens localisation to the oocyte where Ens activates Kinesin-1 using its KBD. The authors also claim that Ens, Kinesin-1 and Ninein are required for the accumulation of ncMTOCs at the oocyte cortex and argue that the detachment of the ncMTOCs from the cortex accounts for the reduced localisation of oskar mRNA at stage 9 and the lack of cytoplasmic streaming at stage 10b. Although the manuscript contains several interesting observations, the authors' conclusions are not sufficiently supported by their data. The structure function analysis of Ensconsin (Ens) is potentially publishable, but the conclusions on ncMTOC anchoring and cytoplasmic streaming not convincing.

      We are grateful that the regulation of Khc activity by MAP7 was well received by all reviewers. While our study focuses on Drosophila oogenesis, we believe this mechanism may have broader implications for understanding kinesin regulation across biological systems.

      For the novel function of the MAP7/Khc complex in organizing its own microtubule networks through ncMTOC recruitment, we have carefully considered the reviewers' constructive recommendations. We now provide additional experimental evidence supporting a model of flux self-amplification in which ncMTOC recruitment plays a key role. It is well established that cytoplasmic flows are essential for posterior localization of cell fate determinants at stage 10B. Slow flows have also been described at earlier oogenesis stages by the groups of Saxton and St Johnston. Building on these early publications and our new experiments, we propose that these flows are essential to promote a positive feedback loop that reinforces ncMTOC recruitment and MT organization (Figure 7).

      1) The main conclusion of the manuscript is that "MT advection failure in Khc and ens in late oogenesis stems from defective cortical ncMTOCs recruitment". This completely overlooks the abundant evidence that Kinesin-1 directly drives cytoplasmic streaming by transporting vesicles and microtubules along microtubules, which then move the cytoplasm by advection (Palacios et al., 2002; Serbus et al, 2005; Lu et al, 2016). Since Kinesin-1 generates the flows, one cannot conclude that the effect of khc and ens mutants on cortical ncMTOC positioning has any direct effect on these flows, which do not occur in these mutants.

      We regret the lack of clarity of the first version of the manuscript and some missing references. We propose a model in which the Kinesin-1- dependent slow flows (described by Serbus/Saxton and Palacios/StJohnston) play a central role in amplifying ncMTOC anchoring and cortical MT network formation (see model in the new Figure 7).

      2) The authors claim that streaming phenotypes of ens and khs mutants are due to a decrease in microtubule length caused by the defective localisation of ncMTOCs. In addition to the problem raised above, However, I am not convinced that they can make accurate measurements of microtubule length from confocal images like those shown in Figure 4. Firstly, they are measuring the length of bundles of microtubules and cannot resolve individual microtubules. This problem is compounded by the fact that the microtubules do not align into parallel bundles in the mutants. This will make the "microtubules" appear shorter in the mutants. In addition, the alignment of the microtubules in wild-type allows one to choose images in which the microtubule lie in the imaging plane, whereas the more disorganized arrangement of the microtubules in the mutants means that most microtubules will cross the imaging plane, which precludes accurate measurements of their length.

      As mentioned by Reviewer 4, we have been transparent with the methodology, and the limitations that were fully described in the material and methods section.

      Cortical microtubules in oocytes are highly dynamic and move rapidly, making it technically impossible to capture their entire length using standard Z-stack acquisitions. We therefore adopted a compromise approach: measuring microtubules within a single focal plane positioned just below the oocyte cortex. This strategy is consistent with established methods in the field, such as those used by Parton et al. (2011) to track microtubule plus-end directionality. To avoid overinterpretation, we explicitly refer to these measurements as "minimum detectable MT length," acknowledging that microtubules may extend beyond the focal plane, particularly at stage 10, where long, tortuous bundles frequently exit the plane of focus. These methodological considerations and potential biases are clearly described in the Materials and Methods section and the text now mentions the possible disorganization of the MT network in the mutant conditions (lane 272-273).

      In this revised version, we now provide complementary analyses of MT network organization.Beyond length measurements (and the mentioned limitations), we also quantified microtubule network orientation at stage 9, assessing whether cortical microtubules are preferentially oriented toward the posterior axis as observed in controls (revised Figure 3D and Figure 5B). While this analysis is also subject to the same technical limitations, it reveals a clear biological difference: microtubules exhibit posterior-biased orientation in control oocytes similar to a previous study (Parton et al., 2011) but adopt a randomized orientation in Nin-/-, ens, and Khc RNAi-depleted oocytes (revised Figure 3D and Figure 5B).

      Taken together, these complementary approaches, despite their technical constraints, provide convergent evidence for the role of the Khc/Ens complex in organizing cortical microtubule networks during oogenesis.

      3) "To investigate whether the presence of these short microtubules in ens and Khc RNAi oocytes is due to defects in microtubule anchoring or is also associated with a decrease in microtubule polymerization at their plus ends, we quantified the velocity and number of EB1comets, which label growing microtubule plus ends (Figure S3)." I do not understand how the anchoring or not of microtubule minus ends to the cortex determines how far their plus ends grow, and these measurements fall short of showing that plus end growth is unaffected. It has already been shown that the Kinesin-1-dependent transport of Dynactin to growing microtubule plus ends increases the length of microtubules in the oocyte because Dynactin acts as an anti-catastrophe factor at the plus ends. Thus, khc mutants should have shorter microtubules independently of any effects on ncMTOC anchoring. The measurements of EB1 comet speed and frequency in FigS2 will not detect this change and are not relevant for their claims about microtubule length. Furthermore, the authors measured EB1 comets at stage 9 (where they did not observe short MT) rather than at stage 10b. The authors' argument would be better supported if they performed the measurements at stage 10b.

      We thank the reviewer for raising this important point. The short microtubule (MT) length observed at stage 10B could indeed result from limited plus-end growth. Unfortunately, we were unable to test this hypothesis directly: strong endogenous yolk autofluorescence at this stage prevented reliable detection of Eb1-GFP comets, precluding velocity measurements.

      At least during stage 9, our data demonstrate that MT nucleation and polymerization rates are not reduced in both KhcRNAi and ens mutant conditions, indicating that the observed MT alterations must arise through alternative mechanisms.

      In the discussion, we propose the following interconnected explanations, supported by recent literature and the reviewers' suggestions:

      1- Reduced MT rescue events. Two seminal studies from the Verhey and Aumeier laboratories have shown that constitutively active Kinesin-1 induces MT lattice damage (Budaitis et al., 2022), which can be repaired through GTP-tubulin incorporation into "rescue shafts" that promote MT rescue (Andreu-Carbo et al., 2022). Extrapolating from these findings, loss of Kinesin-1 activity could plausibly reduce rescue shaft formation, thereby decreasing MT stability. While challenging to test directly in our system, this mechanism provides a plausible framework for the observed phenotype.

      2- Impaired transport of stabilizing factors. As that reviewer astutely points out, Khc transports the dynactin complex, an anti-catastrophe factor, to MT plus ends (Nieuwburg et al., 2017). Loss of this transport could further compromise MT plus end stability. We now discuss this important mechanism in the revised manuscript.

      3- Loss of cortical ncMTOCs. Critically, our new quantitative analyses (revised Figure 3 and Figure 5) also reveal defective anteroposterior orientation of cortical MTs in mutant conditions. These experiments suggest that Ens/Khc-mediated localization of ncMTOCs to the cortex is essential for proper MT network organization, and possibly minus-end stabilization as suggested in several studies (Feng et al., 2019, Goodwin and Vale, 2011, Nashchekin et al., 2016).

      Altogether, we now propose an integrated model in which MT reduction and disorganization may result from multiple complementary mechanisms operating downstream of Kinesin-1/Ensconsin loss. While some aspects remain difficult to test directly in our in vivo system, the convergence of our data with recent mechanistic studies provides an interesting conceptual framework. The Discussion has been revised to reflect this comprehensive view in a dedicated paragraph ("A possible regulation of MT dynamics in the oocyte at both plus end minus MT ends by Ens and Khc" lane 415-432).

      4) The Shot overexpression experiments presented in Fig.3 E-F, Fig.4D and TableS1 are very confusing. Originally , the authors used Shot-GFP overexpression at stage 9 to show that there is a decrease of ncMTOCs at the cortex in ens mutants (Fig.3 E-F) and speculated that this caused the defects in MT length and cytoplasmic advection at stage 10B. However the authors later state on page 8 that : "Shot overexpression (Shot OE) was sufficient to rescue the presence of long cortical MTs and ooplasmic advection in most ens oocytes (9/14), resembling the patterns observed in controls (Figures 4B right panel and 4D). Moreover, while ens females were fully sterile, overexpression of Shot was sufficient to restore that loss of fertility (Table S1)". Is this the same UAS Shot-GFP and VP16 Gal4 used in both experiments? If so, this contradictions puts the authors conclusions in question.

      This is an important point that requires clarification regarding our experimental design.

      The Shot-YFP construct is a genomic insertion on chromosome 3. The ens mutation is also located on chromosome 3 and we were unable to recombine this transgene with the ens mutant for live quantification of cortical Shot. To circumvent this technical limitation, we used a UAS-Shot.L(C)-GFP transgenic construct driven by a maternal driver, expressed in both wild-type (control) and ens mutant oocytes. We validated that the expression level and subcellular localization of UAS-Shot.L(C)-GFP were comparable to those of the genomic Shot-YFP (new Figure S8 A and B).

      From these experiments, we drew two key conclusions. First, cortical Shot.L(C)-GFP is less abundant in ens mutant oocytes compared to wild-type (the quantification has been removed from this version). Second, despite this reduced cortical accumulation, Shot.L(C)-GFP expression partially rescues ooplasmic flows and microtubule streaming in stage 10B ens mutant oocytes, and restores fertility to ens mutant females.

      5) The authors based they conclusions about the involvement of Ens, Kinesin-1 and Ninein in ncMTOC anchoring on the decrease in cortical fluorescence intensity of Shot-YFP and Patronin-YFP in the corresponding mutant backgrounds. However, there is a large variation in average Shot-YFP intensity between control oocytes in different experiments. In Fig. 2F-G the average level of Shot-YFP in the control sis 130 AU while in Fig.3 G-H it is only 55 AU. This makes me worry about reliability of such measurements and the conclusions drawn from them.

      To clarify this point, we have harmonized the method used to quantify the Shot-YFP signals in Figure 4E with the methodology used in Figure 3B, based on the original images. The levels are not strictly identical (Control Figure 2 B: 132.7+/-36.2 versus Control Figure 4 E: 164.0+/- 37.7). These differences are usual when experiments are performed at several-month intervals and by different users.

      6) The decrease in the intensity of Shot-YFP and Patronin-YFP cortical fluorescence in ens mutant oocytes could be because of problems with ncMTOC anchoring or with ncMTOCs formation. The authors should find a way to distinguish between these two possibilities. The authors could express Ens-Mut (described in Sung et al 2008), which localises at the oocyte posterior and test whether it recruits Shot/Patronin ncMTOCs to the posterior.

      We tried to obtain the fly stocks described in the 2008 paper by contacting former members of Pernille Rørth's laboratory. Unfortunately, we learned that the lab no longer exists and that all reagents, including the requested stocks, were either discarded or lost over time. To our knowledge, these materials are no longer available from any source. We regret that this limitation prevented us from performing the straightforward experiments suggested by the reviewer using these specific tools.

      7) According to the Materials and Methods, the Shot-GFP used in Fig.3 E-F and Fig.4 was the BDSC line 29042. This is Shot L(C), a full-length version of Shot missing the CH1 actin-binding domain that is crucial for Shot anchoring to the cortex. If the authors indeed used this version of Shot-GFP, the interpretation of the above experiments is very difficult.

      The Shot.L(C) isoform lacks the CH1 domain but retains the CH2 actin-binding motif. Truncated proteins with this domain and fused to GST retains a weak ability to bind actin in vitro. Importantly, the function of this isoform is context-dependent: it cannot rescue shot loss-of-function in neuron morphogenesis but fully restores Shot-dependent tracheal cell remodeling (Lee and Kolodziej, 2002).

      In our experiments, when the Shot.L(C) isoform was expressed under the control of a maternal driver, its localization to the oocyte cortex was comparable to that of the genomic Shot-YFP construct (new Figure S8). This demonstrates unambiguously that the CH1 domain is dispensable for Shot cortical localization in oocytes, and that CH2-mediated actin binding is sufficient for this localization. Of note, a recent study showed that actin network are not equivalent highlighting the need for specific Shot isoforms harboring specialized actin-binding domain (Nashchekin et al., 2024).

      We note that the expression level of Shot.L(C)-GFP in the oocyte appeared slightly lower than that of Shot-YFP (expressed under endogenous Shot regulatory sequences), as assessed by Western blot (Figure S8 A).

      Critically, Shot.L(C)-GFP expression was substantially lower than that of Shot.L(A)-GFP (that harbored both the CH1 and CH2 domain). Shot.L(A)-GFP was overexpressed (Figure 8 A) and ectopically localized on MTs in both nurse cells and the ooplasm (Figure S8 B middle panel and arrow). These observations are in agreement that the Shot.L(C)-GFP rescue experiment was performed at near-physiological expression levels, strengthening the validity of our conclusions.

      8) Page 6 "converted in NCs, in a region adjacent to the ring canals, Dendra-Ens-labeled MTs were found in the oocyte compartment indicating they are able to travel from NC toward the oocyte through ring canals". I have difficulty seeing the translocation of MT through the ring canals. Perhaps it would be more obvious with a movie/picture showing only one channel. Considering that f Dendra-Ens appears in the oocyte much faster than MT transport through ring canals (140nm/s, Lu et al 2022), the authors are most probably observing the translocation of free Ens rather than Ens bound to MT. The authors should also mention that Ens movement from the NC to the oocyte has been shown before with Ens MBD in Lu et al 2022 with better resolution.

      We fully agree on the caveat mentioned by this reviewer: we may observe the translocation of free Dendra-Ensconsin. The experiment, was removed and replaced by referring to the work of the Gelfand lab. The movement of MTs that travel at ~140 nm/s between nurse cells toward the oocyte through the Ring Canals was reported before by Lu et al. (2022) with a very good resolution. Notably, this directional directed movement of MTs was measured using a fusion protein encompassing Ens MT-binding domain. We decided to remove this inclusive experiment and rather refer to this relevant study.

      9) Page 6: The co-localization of Ninein with Ens and Shot at the oocyte cortex (Figure 2A). I have difficulty seeing this co-localisation. Perhaps it would be more obvious in merged images of only two channels and with higher resolution images

      10) "a pool of the Ens-GFP co-localized with Ch-Patronin at cortical ncMTOCs at the anterior cortex (Figure 3A)". I also have difficulty seeing this.

      We have performed new high-resolution acquisitions that provide clearer and more convincing evidence for the localization cortical distribution of these proteins (revised Figure 2A-2C and Figure 4A). These improved images demonstrate that Ens, Ninein, Shot, and Patronin partially colocalize at cortical ncMTOCs, as initially proposed. Importantly, the new data also reveal a spatial distinction: while Ens localizes along microtubules extending from these cortical sites, Ninein appears confined to small cytoplasmic puncta adjacent but also present on cortical microtubules.

      11) "Ninein co-localizes with Ens at the oocyte cortex and partially along cortical microtubules, contributing to the maintenance of high Ens protein levels in the oocyte and its proper cortical targeting". I could not find any data showing the involvement of Ninein in the cortical targeting of Ens.

      We found decreased Ens localization to MTs and to the cell cortex region (new Figure S3 A-B).

      12) "our MT network analyses reveal the presence of numerous short MTs cytoplasmic clustered in an anterior pattern." "This low cortical recruitment of ncMTOCs is consistent with poor MT anchoring and their cytoplasmic accumulation." I could not find any data showing that short cortical MT observed at stage 10b in ens mutant and Khc RNAi were cytoplasmic and poorly anchored.

      The sentence was removed from the revised manuscript.

      13) "The egg chamber consists of interconnected cells where Dynein and Khc activities are spatially separated. Dynein facilitates transport from NCs to the oocyte, while Khc mediates both transport and advection within the oocyte." Dynein is involved in various activities in the oocyte. It anchors the oocyte nucleus and transports bcd and grk mRNA to mention a few.

      The text was amended to reflect Dynein involvement in transport activities in the oocyte, with the appropriate references (lane 105-107).

      14) The cartoons in Fig.2H and 3I exaggerate the effect of Ninein and Ens on cortical ncMTOCs. According to the corresponding graphs, there is a 20 and 50% decrease in each case.

      New cartoons (now revised Figure 3E and 4F), are amended to reflect the ncMTOC values but also MT orientation (Figure 3E).

      Significance

      Given the important concerns raised, the significance of the findings is difficult to assess at this stage.

      We sincerely thank the reviewer for their thorough evaluation of our manuscript. We have carefully addressed their concerns through substantial new experiments and analyses. We hope that the revised manuscript, in its current form, now provides the clarifications and additional evidence requested, and that our responses demonstrate the significance of our findings.

      Reviewer #4 (Evidence, reproducibility and clarity (Required)):

      Summary: This manuscript presents an investigation into the molecular mechanisms governing spatial activation of Kinesin-1 motor protein during Drosophila oogenesis, revealing a regulatory network that controls microtubule organization and cytoplasmic transport. The authors demonstrate that Ensconsin, a MAP7 family protein and Kinesin-1 activator, is spatially enriched in the oocyte through a dual mechanism involving Dynein-mediated transport from nurse cells and cortical maintenance by Ninein. This spatial enrichment of Ens is crucial for locally relieving Kinesin-1 auto-inhibition. The Ens/Khc complex promotes cortical recruitment of non-centrosomal microtubule organizing centers (ncMTOCs), which are essential for anchoring microtubules at the cortex, enabling the formation of long, parallel microtubule streams or "twisters" that drive cytoplasmic advection during late oogenesis. This work establishes a paradigm where motor protein activation is spatially controlled through targeted localization of regulatory cofactors, with the activated motor then participating in building its own transport infrastructure through ncMTOC recruitment and microtubule network organization.

      There's a lot to like about this paper! The data are generally lovely and nicely presented. The authors also use a combination of experimental approaches, combining genetics, live and fixed imaging, and protein biochemistry.

      We thank the reviewer for this enthusiastic and supportive review, which helped us further strengthen the manuscript.

      Concerns: Page 6: "to assay if elevation of Ninein levels was able to mis-regulate Ens localization, we overexpressed a tagged Ninein-RFP protein in the oocyte. At stage 9 the overexpressed Ninein accumulated at the anterior cortex of the oocyte and also generated large cortical aggregates able to recruit high levels of Ens (Figures 2D and 2H)... The examination of Ninein/Ens cortical aggregates obtained after Ninein overexpression showed that these aggregates were also able to recruit high levels of Patronin and Shot (Figures 2E and 2H)." Firstly, I'm not crazy about the use of "overexpressed" here, since there isn't normally any Ninein-RFP in the oocyte. In these experiments it has been therefore expressed, not overexpressed. Secondly, I don't understand what the reader is supposed to make of these data. Expression of a protein carrying a large fluorescent tag leads to large aggregates (they don't look cortical to me) that include multiple proteins - in fact, all the proteins examined. I don't understand this to be evidence of anything in particular, except that Ninein-RFP causes the accumulation of big multi-protein aggregates. While I can understand what the authors were trying to do here, I think that these data are inconclusive and should be de-emphasized.

      We have revised the manuscript by replacing overexpressed with expressed (lanes 211 and 212). In addition, we now provide new localization data in both cortical (new Figure S4 A, top) and medial focal planes (new Figure S4 A, bottom), demonstrating that Ninein puncta (the word used in Rosen et al, 2019), rather than aggregates are located cortically. We also show that live IRP-labelled MTs do not colocalize with Ninein-RFP puncta. In light of the new experiments and the comments from the other reviewers, the corresponding text has been revised and de-emphasized accordingly.

      Page 7: "Co-immunoprecipitations experiments revealed that Patronin was associated with Shot-YFP, as shown previously (Nashchekin et al., 2016), but also with EnsWT-GFP, indicating that Ens, Shot and Patronin are present in the same complex (Figure 3B)." I do not agree that association between Ens-GFP and Patronin indicates that Ens is in the same complex as Shot and Patronin. It is also very possible that there are two (or more) distinct protein complexes. This conclusion could therefore be softened. Instead of "indicating" I suggest "suggesting the possibility."

      We have toned down this conclusion and indicated "suggesting the possibility" (lane 238-239).

      Page 7: "During stage 9, the average subcortical MT length, taken at one focal plane in live oocytes (see methods)..." I appreciate that the authors have been careful to describe how they measured MT length, as this is a major point for interpretation. I think the reader would benefit from an explanation of why they decided to measure in only one focal plane and how that decision could impact the results.

      We appreciate this helpful suggestion. Cortical microtubules are indeed highly dynamic and extend in multiple directions, including along the Z-axis. Moreover, their diameter is extremely small (approximately 25 nm), making it technically challenging to accurately measure their full length with high resolution using our Zeiss Airyscan confocal microscope (over several, microns): the acquisition of Z-stacks is relatively slow and therefore not well suited to capturing the rapid dynamics of these microtubules. Consequently, our length measurements represent a compromise and most likely underestimate the actual lengths of microtubules growing outside the focal plane. We note that other groups have encountered similar technical limitations (Parton et al., 2011).

      Page 7: "... the MTs exhibited an orthogonal orientation relative to the anterior cortex (Figures 4A left panels, 4C and 4E)." This phenotype might not be obvious to readers. Can it be quantified?

      We have now analyzed the orientation of microtubules (MTs) along the dorso-ventral axis. Our analysis shows that ens, Khc RNAi oocytes (new Figure 5B), and, to a lesser extent, Nin mutant oocytes (new Figure 3D), display a more random MT orientation compared to wild-type (WT) oocytes. In WT oocytes, MTs are predominantly oriented toward the posterior pole, consistent with previous findings (Parton et al., 2011).

      Page 8: "Altogether, the analyses of Ens and Khc defective oocytes suggested that MT organization defects during late oogenesis (stage 10B) were caused by an initial failure of ncMTOCs to reach the cell cortex. Therefore, we hypothesized that overexpression of the ncMTOC component Shot could restore certain aspects of microtubule cortical organization in ens-deficient oocytes. Indeed, Shot overexpression (Shot OE) was sufficient to rescue the presence of long cortical MTs and ooplasmic advection in most ens oocytes (9/14)..." The data are clear, but the explanation is not. Can the authors please explain why adding in more of an ncMTOC component (Shot) rescues a defect of ncMTOC cortical localization?

      We propose that cytoplasmic ncMTOCs can bind the cell cortex via the Shot subunit that is so far the only component that harbors actin-binding motifs. Therefore, we propose that elevating cytoplasmic Shot increase the possibility of Shot to encounter the cortex by diffusion when flows are absent. This is now explained lane 282-285.

      I'm grateful to the authors for their inclusion of helpful diagrams, as in Figures 1G and 2H. I think the manuscript might benefit from one more of these at the end, illustrating the ultimate model.

      We have carefully considered and followed the reviewer's suggestions. In response, we have included a new figure illustrating our proposed model: the recruitment of ncMTOCs to the cell cortex through low Khc-mediated flows at stage 9 enhances cortical microtubule density, which in turn promotes self-amplifying flows (new Figure 7, panels A to C). Note that this Figure also depicts activation of Khc by loss of auto-inhibition (Figure 7, panel D).

      I'm sorry to say that the language could use quite a bit of polishing. There are missing and extraneous commas. There is also regular confusion between the use of plural and singular nouns. Some early instances include:

      1. Page 3: thought instead of "thoughted."
      2. Page 5: "A previous studies have revealed"
      3. Page 5: "A significantly loss"
      4. Page 6: "troughs ring canals" should be "through ring canals"
      5. Page 7: lives stage 9 oocytes
      6. Page 7: As ens and Khc RNAi oocytes exhibits
      7. Page 7: we examined in details
      8. Page 7: This average MT length was similar in Khc RNAi and ens mutant oocyte..

      We apologize for errors. We made the appropriate corrections of the manuscript.

      Reviewer #4 (Significance (Required)):

      This work makes a nice conceptual advance by showing that motor activation controls its own transport infrastructure, a paradigm that could extend to other systems requiring spatially regulated transport.

      We thank the reviewers for their evaluation of the manuscript and helpful comments.

    1. Author response:

      Response to the eLife Assessment

      We thank the Editors and the Reviewers for their helpful suggestions, which will help us strengthen and test the key conclusions of this study of condensate dynamics at atomic resolution. In response to the Editors, we will make clearer in the Results and Discussion how the present work advances beyond our initial study of MUT-16 condensates, the scaffold of Mutator foci (Gaurav K et al., Biophys. J. 2025; 124:3987–4004). That study used a multiscale approach — residue-level (CALVADOS2) and near-atomic (Martini3) coarse-grained simulations together with in vitro experiments — to establish that the foci-forming region (FFR) phase separates whereas the adjacent MUT-8-binding region (M8BR) does not, and used atomistic simulations of that non-phase-separating region to dissect client–scaffold recognition. In this way the multi-scale simulations helped to provide a molecular basis for previous in vivo observations by Uebel et al. (PLOS Genet. 2018; 14(7):e1007542). That study did not, however, resolve with atomic resolution the interactions within the phase-separated FFR condensate itself. The present study addresses precisely this gap: from 10 µs of atomistic molecular dynamics of the FFR condensate, we characterise the sub-µs contact dynamics and the protein–ion and protein–water interactions that govern the condensed phase at atomistic resolution — observables inaccessible to the coarse-grained models used previously, but key to understanding the properties of Mutator foci and ultimately how they underpin biological function in small RNA biology.

      Reviewer 1:

      (1) I have several questions regarding the system preparation that require clarification. The authors state that "65 copies of the coarse-grained MUT-16 FFR were embedded in a slab-shaped simulation," but it is not clear how this initial configuration was generated. Were the molecules randomly distributed in the simulation box, or were they initially arranged in a preformed condensate? Alternatively, were they randomly inserted and allowed to self-assemble into a condensate during NpT simulations? In Figure 1, the atomistic snapshot appears to show a well-defined condensate at the center of the simulation box. It would be important to clarify how this configuration was obtained: Was it generated from coarse-grained simulations starting from random initial conditions? Or was a preassembled condensate used as input? Related to this, how do the authors ensure that the simulations are equilibrated? While 20 μs appears to be a reasonably long simulation time for coarse-grained simulations, it would be useful to demonstrate equilibration explicitly. For example, the authors could plot the center-of-mass positions (in the long axis of the simulation box) of individual proteins over time to show that all molecules reach a steady state and remain within the condensate without systematic drift.

      We thank the reviewer for these important clarifying questions regarding system preparation and equilibration.

      The initial structure for the atomistic simulation was generated by randomly inserting 65 copies of the coarse-grained MUT-16 FFR into a slab-shaped simulation box using the gmx insert-molecules tool. The molecules were therefore not pre-arranged in a condensate; instead, they were allowed to spontaneously self-assemble from this random configuration during NpT simulations using the Martini3-IDP force field over 20 μs. The well-defined condensate visible in Figure 1 is thus the product of this unbiased self-assembly process.

      To make this workflow transparent to the reader, we will revise Figure 1 to include a two-panel illustration of the Martini3 simulation: a snapshot at t = 0 ns showing the randomly distributed chains, and a snapshot at t = 20 μs showing the assembled condensate, connected by an arrow indicating the subsequent backmapping step to the atomistic representation. We believe this will clearly communicate the sequential nature of the pipeline (random insertion → coarse-grained self-assembly → atomistic backmapping).

      We appreciate the concrete suggestion for demonstrating equilibration. We will add a supplementary figure showing the center-of-mass positions of individual protein chains along the long axis of the simulation box as a function of simulation time. This will allow readers to verify that molecules converge into the condensate phase and reach a steady state without systematic drift, providing explicit evidence that 20 μs coarse-grained simulation time is sufficient for equilibration under these conditions.

      (2) The authors experimentally observe UCST behavior for these condensates. Do the coarse-grained or atomistic simulations reproduce this behavior?

      While atomistic simulations may be too computationally demanding to systematically explore temperature dependence, coarse-grained simulations could be used to test whether condensates are stable at lower temperatures and dissolve at higher temperatures. Such an analysis would provide valuable support for the experimental observations.

      We thank the reviewer for this valuable suggestion. In previous coarse-grained simulations we have used a coarse-grained force field that does not capture UCST vs LCST behavior (Gaurav K et al. Biophys. J. 2025; 124:3987–4004). It will be very interesting to revisit these coarse-grained simulations with a coarse-grained simulation force field that can capture UCST and LCST behavior such as the Mpipi-T (Chakravarti & Joseph, Protein Sci 2025;34(10):e70284) and HPS-T models (Dignon GL et al. ACS Cent. Sci. 2019; 5(5):821–830). We plan to perform additional coarse-grained simulations at multiple temperatures using the HPS-T force field. The HPS-T model has been shown to capture UCST versus LCST behavior (Changiarath A et al. bioRxiv 2024) in accordance with previous in vitro experiments. These simulations will allow us to test whether the MUT-16 FFR condensates remain stable at lower temperatures and dissolve at higher temperatures, providing direct computational support for the experimentally observed UCST behavior. We will include this analysis in the revised manuscript.

      (3) Regarding the analysis of ions, several points could be clarified and extended:

      a) It would be helpful to report the total number of ions and quantify how many are located inside vs. outside the condensate. While qualitative trends can be inferred from density profiles, quantitative analysis would strengthen the conclusions.

      b) It would also be interesting to analyze the number of contact ion pairs (e.g., Na⁺-Cl⁻ pairs), as described in J. Chem. Phys. 156, 044505 (2022). It is known that some ion models tend to overestimate ion pairing and underestimate solubility (e.g., J. Chem. Phys. 153, 010903 (2020)).

      c) In this context, the use of scaled-charge models has been shown to improve the description of ionic solutions and biomolecular systems (e.g., J. Phys. Chem. Lett. 2019, 10, 23, 7531-7536). I would suggest that, at least for one trajectory, the authors perform a test simulation using scaled charges (e.g., scaling by ~0.8) to evaluate whether ion distributions and protein-ion interactions are significantly affected.

      We thank the reviewer for these insightful suggestions regarding the ion analysis. We agree that a more quantitative treatment of ion behavior would strengthen the manuscript. To address all three points collectively, we will expand the existing Figure S7 with additional panels. These will include quantitative counts of Na<sup>+</sup> and Cl<sup>-</sup> ions partitioning inside versus outside the condensate complementing the existing density profiles, the Na<sup>+</sup>–Cl<sup>-</sup> radial distribution functions to estimate contact ion pair populations following J. Chem. Phys. 156, 044505 (2022).

      Following the Reviewer suggestion we will run a simulation with scaled charges (~0.8 scaling factor, J. Phys. Chem. Lett. 2019, 10(23):7531–7536) to evaluate the sensitivity of our results to the choice of ion model. We will compare ion distributions obtained with standard versus scaled charges . We will discuss the contact ion pair results in the context of known force field limitations regarding ion pairing (J. Chem. Phys. 153, 010903 (2020)) and assess whether the scaled-charge treatment leads to any qualitatively different conclusions.

      (4) Finally, while the selected water model is known to be accurate, it would be useful to assess its performance for concentrated salt solutions. For example, the authors could estimate the density of a 6 m salt solution and compare it with experimental data or validated models (e.g., J. Chem. Phys. 151, 134504 (2019)). This would help clarify to what extent the conclusions depend on the chosen force field.

      We thank the reviewer for this important suggestion. We agree that while the chosen water model is well established for biomolecular simulations, its performance under concentrated salt conditions is a legitimate concern that is worth explicitly validating in the context of this work. We will perform a short bulk simulation of a 6 m NaCl solution and compute the solution density, comparing it to experimental data (J. Chem. Phys. 151, 134504 (2019)). This straightforward validation will allow us to quantify how well our water and ion force field combination reproduces the thermodynamic properties of concentrated salt solutions, and to transparently discuss any deviations and their potential implications for the ion partitioning and protein–ion interaction results presented in the manuscript. The results will be added to the supplementary information alongside the expanded ion analysis in Figure S7.

      (5) In the Introduction, it would be helpful to elaborate further on the possible driving forces of LLPS in this region. Are there prior hypotheses or evidence pointing to specific interactions (e.g., cation-π, π-π, electrostatic interactions)? While this work addresses these questions, a brief discussion of previous experimental or theoretical insights would provide useful context.

      We thank the reviewer for this helpful suggestion. We will expand the Introduction to briefly discuss the known molecular driving forces of LLPS in IDR-containing proteins. Specifically, we will discuss the role of π–π interactions between aromatic residues (Vernon et al. eLife 2018; 7:e31486), cation–π interactions between aromatic and positively charged residues such as tyrosine–arginine pairs, which have been experimentally demonstrated to drive condensate formation in proteins such as FUS (Qamar et al. Cell 2018; 173:720–734), and the broader sequence-encoded molecular grammar governing these interactions in prion-like RNA-binding proteins (Wang et al. Cell 2018; 174:688–699, Rekhi et al. Nat Chem 2024 16:1113–1124 ). We will discuss previous findings on how ions shape interactions in condensates (MacAinsh et al. eLife 2024; 13:RP100282). We will also note the contribution of electrostatic interactions arising from charge patterning within the IDR, and contextualize how these general principles apply to the specific sequence composition of MUT-16 FFR, motivating the simulation-based investigation presented in this work.

      (6) On page 18, the authors state: "MUT-16 FFR satisfies the length (172 residues), aromatic content (20.35%), and Arg enrichment (85.71%) criteria. Its charge content (10.47%) and charge balance (38.89% positive charge fraction) are slightly below the nominal thresholds." It would be very helpful to include a schematic representation of the protein sequence highlighting these features (aromatic residues, charge distribution, etc.) in the corresponding figure, to provide a more intuitive understanding.

      We thank the reviewer for this helpful suggestion. We will include a figure showing a schematic representation of the MUT-16 FFR sequence, with aromatic residues, charged residues (positive and negative), and arginine content highlighted.

      (7) A question regarding ion hydration: What is the coordination environment of the ions that bridge proteins? Are they still hydrated by water molecules, or does the reduced water content inside the condensate significantly affect their solvation. Typically, Na<sup>+</sup> and Cl<sup>-</sup> ions have coordination numbers around 5-6 in aqueous solution. Do protein interactions and reduced solvent conditions within the condensate alter this coordination? A brief analysis or discussion would be valuable.

      We will calculate the coordination numbers of Na⁺ and Cl⁻ ions that mediate residue–residue bridging interactions inside the condensate and compare them against ions in the bulk dilute phase. This will directly reveal the degree to which bridging ions retain or lose their hydration shell when engaging with protein residues, and whether the condensate environment meaningfully perturbs ion solvation. The results will be presented as an additional figure in the Supplementary Information.

      Reviewer 2:

      (1) The large amount of detail in the results section sometimes makes it difficult to identify the central take-home messages. I encourage the authors to more clearly highlight the principal findings and the physical insights that may generalize to other condensate-forming systems. The authors may also consider streamlining parts of the Results section to improve focus and readability.

      We thank the reviewer for this constructive feedback. We will revise the Results section by adding brief concluding remarks at the end of each subsection that explicitly state the key physical insight emerging from that analysis. We will consider which secondary findings can be moved to the Supplementary Information. We will also strengthen the Conclusion section to more clearly distil the principal findings of the study as a whole and highlight the broader insights that may generalize to other condensate-forming systems, ensuring the central take-home messages are clearly communicated to the reader.

      Reviewer 3:

      (1) In its current form, several technical issues need to be addressed before the main conclusions can be considered robust. Most importantly, the simulated sequence is 172 residues long, while the atomistic slab has box dimensions of only 12 nm in two directions. This length scale is comparable to the expected end-to-end distances of a disordered 172-residue chain. It is therefore not clear whether individual protein chains interact with their own periodic images, which could substantially affect overall chain dynamics and subsequently bias contact lifetimes, residue-residue interaction statistics, and the inferred condensate dynamics. The authors should check, for each chain, histograms of end-to-end distances. For chains for which more than ~2-3% of the end-to-end distances exceed ~11 nm, the authors should explicitly check for self-image interactions (for example, using "gmx mindist -pi") and report whether such interactions occur and for what fraction of the trajectory. Without this control, at least in the Supporting Information, I do not think the simulation-derived contact dynamics are sufficiently trustworthy.

      We thank the reviewer for raising this important point. Indeed the box size in x and y dimensions is only marginal, which may influence the dynamics in our simulations and could affect our conclusions. In response, we will perform a control simulation with a larger box, increasing the x and y dimensions to ~16 nm. We will compare the contact dynamics of the resulting trajectory with our original results. This control simulation is initiated from an independently assembled coarse-grained condensate (see our response to Question 6) and therefore also addresses the replica-independence concern raised there.

      (2) A second major concern is the treatment of ions. The manuscript makes important conclusions about Na<sup>+</sup> association and Na<sup>+</sup>-mediated bridging, but the atomistic ion model is not explicitly stated. This is a reproducibility problem and also affects interpretation - for example, standard Amber ions are known to bind too strongly to the oppositely charged residues. In their results, one acidic residue appears to interact on average with roughly two Na⁺ ions, which is not obviously expected from charge balance alone. The authors should state the exact Na<sup>+</sup>/Cl<sup>-</sup> parameters used, justify their compatibility with TIP4P-D and the protein force field, and explicitly interpret why such a strong Na<sup>+</sup> association with acidic residues is observed.

      We thank the reviewer for raising this important point. We will explicitly state in the Methods section how the Na<sup>+</sup> and Cl<sup>-</sup> ions, including the force field parameters of the ions, were modelled in our setup, and discuss its compatibility with TIP4P-D and the protein force field. In the presented simulations we have used the Joung and Cheatham parameters (Joung et al, J. Phys. Chem. B 2008, 112 (30), 9020–9041) with σ = 0.243934 nm and ε = 0.365846 (kJ mol<sup>-1</sup>) for Na<sup>+</sup> and σ = 0.447766 nm and ε = 0.148913 (kJ mol<sup>-1</sup>) for Cl<sup>-</sup>. While similar setups have been used, these ion parameters have not been optimized for TIP4P-D (originally developed for TIP3P water) and thus a lack of compatibility of the parameters could affect our conclusions.

      In response to the Reviewer and also in response to Reviewer 1 (Question 3), we will perform a sensitivity check by running an additional molecular dynamics simulation with scaled ion parameters as suggested by Reviewer 1 ( J. Phys. Chem. Lett. 2019, 10, 23, 7531-7536). In this way we will assess to what extent the degree of Na<sup>+</sup> association with acidic residues is sensitive to the choice of ion parameters and discuss the implications for our conclusions regarding Na⁺-mediated bridging interactions.

      (3) More generally, because the manuscript is centered on contact lifetimes, the choice of the atomistic force field needs stronger justification. Salt bridges, cation-pi contacts, pi-pi stacking, ion coordination, and water-mediated interactions are all force-field-sensitive. Since there is no direct experimental observable used here to validate the simulations, the authors should discuss the expected limitations of the chosen force field (while I do acknowledge that testing different force fields would be computationally too demanding).

      We thank the reviewer for this fair comment. We will add a short discussion justifying the choice of both TIP4P-D and Amber99sb-star-ILDN-q force field, discussing their performance for disordered proteins. We will explicitly acknowledge that absolute contact lifetime values should be interpreted with caution given the inherent force field sensitivities of salt bridges, cation-π, and π-π interactions, while relative trends and qualitative insights are expected to be more robust. We believe this transparent discussion will strengthen the manuscript and place our findings in the appropriate context for the reader.

      (4) I also find the sequence-comparison section somewhat confusing. The authors compare one specific IDR, MUT-16 FFR, with the average properties of human IDRs and then frame it as more representative than FUS LCD. It is not clear how informative this is because IDR behavior depends strongly on sequence-specific patterning, molecular connectivity, and the particular interaction network of each protein. Averages over human IDRs may provide a broad context, but they do not necessarily define what is physically or biologically representative for phase separation. In addition, FUS LCD is not intended to be a representative human IDR; it is an unusually low-complexity, phase-separating domain. Therefore, the "more representative than FUS" framing should be toned down. At most, this analysis shows that MUT-16 FFR is compositionally less extreme than FUS LCD.

      We thank the reviewer for this valid criticism. We agree that the framing of MUT-16 FFR as "more representative than FUS LCD" is an overstatement, and we will revise the text accordingly. The comparison against human IDR averages was intended to provide broad compositional context rather than make claims about functional or dynamical representativeness, and we will make this distinction explicit. We will reframe the statement to simply note that MUT-16 FFR is compositionally less extreme than FUS LCD, without implying broader representativeness, which as the reviewer correctly points out cannot be inferred from sequence composition alone given the strong dependence of IDR behavior on sequence-specific patterning and interaction networks.

      (5) The ion- and water-bridging analyses are also potentially overinterpreted. A distance-based simultaneous contact with two residues does not by itself establish functional mediation or regulation of condensate dynamics. The authors should either add appropriate controls, such as local-density-normalized baselines or randomized-contact expectations, or soften the language to describe these as geometrically defined co-contact events rather than mechanistic bridging interactions.

      We thank the reviewer for this valid point. We agree that distance-based co-contact events do not by themselves establish mechanistic bridging or functional regulation, and we will revise the manuscript language throughout to describe these observations as geometrically defined co-contact events rather than mechanistic bridging interactions. We will also explore appropriate controls such as local-density normalized baselines or randomized-contact expectations. In this respect we will also consider our results in light of a recent paper that showed that salt-bridges are overestimated in atomistic molecular dynamics simulations (Ivanović et al, JACS Au 2026, 6(3), 1900–1913). We will ensure the interpretation is appropriately cautious and does not overstate the mechanistic implications of these findings.

      (6) Finally, the independence of the atomistic replicas is unclear. The manuscript should state whether all ten all-atom simulations were initiated from the same coarse-grained condensate configuration or from distinct CG frames. If the starting structures came from one CG trajectory, the authors should report how far apart those frames were in simulation time and provide evidence that the initial atomistic configurations are structurally independent. If only velocities differ, the simulations should not be described as fully independent structural replicas.

      We thank the reviewer for this important clarification request. We confirm that all ten atomistic replicas were initiated from the same coarse-grained condensate configuration following backmapping, but were equilibrated independently using different random velocity seeds. Only the last 800 ns of each trajectory was used for analysis, discarding the initial 200 ns as equilibration. We will add these details explicitly to the Methods section and make clearer that these simulations are not fully independent structural replicas. We will report the overlap of residue–residue contact maps between replicas to provide an indication of how the contact statistics have decorrelated, given the shared starting structure.

      In response to this question and also question 1, we are initiating an all-atom simulation from an independently formed CG condensate (16 nm x 16 nm x 60 nm). This will provide a valuable check as to the conclusions from our ten initial simulation trajectories.

      References

      Blazquez S, Conde MM, Abascal JLF, Vega C. J. Chem. Phys. 2022;156(4):044505.

      Chakravarti A, Joseph JA. Protein Sci. 2025;34(10):e70284.

      Changiarath A, Flores-Solis D, Michels JJ, Herrera Rodriguez R, Hanson SM, Schmid F, Zweckstetter M, Padeken J, Stelzl LS. bioRxiv. 2024. doi:10.1101/2024.03.16.585180.

      Dignon GL, Zheng W, Kim YC, Mittal J. ACS Cent. Sci. 2019;5(5):821–830.

      Gaurav K, Busetto V, Páez-Moscoso DJ, Changiarath A, Hanson SM, Falk S, Ketting RF, Stelzl LS. Biophys. J. 2025;124:3987–4004.

      Ivanović MT, Holla A, Nüesch MF, von Roten V, Schuler B, Best RB. JACS Au. 2026;6(3):1900–1913.

      Joung IS, Cheatham TE III. J. Phys. Chem. B. 2008;112(30):9020–9041.

      Kirby BJ, Jungwirth P. J. Phys. Chem. Lett. 2019;10(23):7531–7536.

      MacAinsh M, Dey S, Zhou HX. eLife. 2024;13:RP100282.

      Panagiotopoulos AZ. J. Chem. Phys. 2020;153(1):010903.

      Qamar S, et al. Cell. 2018;173:720–734.

      Rekhi S, Garcia CG, Barai M, Rizuan A, Schuster BS, Kiick KL, Mittal J. Nat. Chem. 2024;16:1113–1124.

      Uebel CJ, Anderson DC, Mandarino LM, Manage KI, Aynaszyan S, et al. PLOS Genet. 2018;14(7):e1007542.

      Vernon RM, Chong PA, Tsang B, Kim TH, Bah A, Farber P, Lin H, Forman-Kay JD. eLife. 2018;7:e31486.

      Wang J, et al. Cell. 2018;174:688–699.

      Zeron IM, Abascal JLF, Vega C. J. Chem. Phys. 2019;151:134504.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      This manuscript used deep learning to highlight the role of inhibition in shaping selectivity in primary and higher visual cortex. The findings hint at hitherto unknown axes of structured inhibition operating in cortical networks with a potentially key role in object recognition.

      The multi-species approach of testing the model in macaque and mouse is excellent, as it improves the chances that the observed findings are a general property of mammalian visual cortex. However, it would be useful to delineate any notable differences between these species, which are to be expected given their lifestyle.

      The overall performance of the model appears to be excellent in V1, with over 80% performance, but it falls substantially in V4. It would be important to consider the implications of this finding; for example, in the context of studying temporal lobe structures that are central to recognizing objects. Would one expect that model performance decreases further here, and what measures could be taken to avoid this? Or is this type of model better restricted to V1 or even LGN?

      While the manuscript delineates novel axes of inhibitory interactions, it remains unclear what exactly these axes are and how they arise. What are the steps that need to be taken to make progress along these lines?

      Reviewer #2 (Public review):

      The classic view of sensory coding states that (excitatory) neurons are active to some preferred stimuli and otherwise silent. In contrast, inhibitory neurons are considered broadly tuned. Due to the gigantic potential image space, it is hard to comprehensively map the tuning of individual neurons. In this tour de force study, Franke et al. combine electrophysiological recordings in macaque (V1, V4) and mouse (V1, LM, LI) visual cortex with large-scale screens based on digital twin models, as well as beautiful systems identification (most/least activating stimuli). Based on these digital twins, they discover dual-feature selectivity (which they validate both in macaques and mice). Dual-feature selectivity involves a bidirectional modulation of firing rates around an elevated baseline. Neurons are excited by specific preferred features and systematically suppressed by distinct, non-preferred features. This tuning was identified by excellently combining advances in AI & high-throughput ephys.

      The study is comprehensive and convincing. Overall, this work showcases how in silico experiments can generate concrete hypotheses about neuronal coding that are difficult to discover experimentally, but that can be experimentally validated! I think this work is of substantial interest to the neuroscience community. I'm sure it will motivate many future experimental and computational studies. In particular, it will be of great interest to understand when and how the brain leverages dual-feature selectivity. The discussion of the article is already an interesting starting point for these considerations.

      Strengths:

      (1) Using computational models to predict neuronal responses allowed them to go through millions of images, which may not be possible in vivo.

      (2) The cross-species and cross-area consistency of the results is another major strength. Pointing out that the results may be a fundamental strategy of mammalian cortical processing.

      (3) They show that the feature causing peak excitation in one neuron often drives suppression in another. This may be an efficient coding scheme where the population covers the visual manifold. I'd like to understand better why the authors believe that this shows that there are low-dimensional subspaces based on preferred and non-preferred stimulus features (vs. many more, but some axes are stronger).

      We thank the reviewers for their constructive and helpful feedback on our manuscript. We are delighted that they found the study to be “comprehensive and convincing” and a “tour de force” in its combination of electrophysiological recordings with large-scale digital twin screening. We appreciate that the reviewers highlighted the strengths of our multi-species approach and the “cross-species and cross-area consistency” of the results, noting that the work showcases how in silico experiments can generate concrete, experimentally validatable hypotheses. Overall, we agree with the assessment of the reviewers. We have performed the following changes to the text to clarify and strengthen the manuscript, without introducing new analyses or altering the conclusions. 

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Page 3: The authors state that RFs were mapped using sparse noise, with the goal to ensure that the RFs align with the visual stimulus, but no data appear to be shown regarding this alignment. It would be important to provide a full analysis of the sparse noise-mapped RFs for both V1 and V4. Also, is it correct that the V4 data analyzed here came from a single animal? This could potentially be problematic and would need to be addressed, for example, by performing analyses also in V1 for participant animals separately. Please elaborate.

      We have added a sentence to the Results section clarifying the sparse noise RF mapping procedure, noting that probe insertions were targeted orthogonal to the cortical surface so that neurons sampled along the probe depth share overlapping receptive fields, allowing a single stimulus configuration to adequately drive the entire recorded population. We have also corrected the text to clarify that V4 data were collected from 2 animals (not 3 as previously stated in an earlier draft), consistent with the Methods section.

      (2) Page 4: Only half the neurons in V4 are "high confidence" in terms of test image performance, which seems a little low and probably significantly lower than the corresponding value for V1 of 84%. It is unclear how to interpret this confidence, but it seems to suggest that half of the V4 neurons are not well captured by the model. If true, this fraction appears large enough to cast doubt on the validity of the V4 results. Please elaborate.

      We have expanded the text to explicitly discuss the lower proportion of high-confidence in-silico neurons in V4 relative to V1. We attribute this to the greater complexity of V4 tuning compared to V1, as well as missing contextual information such as image surrounds and sequential image context—factors that likely limit model performance in higher visual areas. We note that our restriction of analyses to high-confidence neurons provides resilience against these limitations, and that the goal was not to maximize predictive performance per se but to identify response patterns—dual-feature selectivity—that are robust across neurons, areas, and species.

      (3) Page 5: It seems that identical L2 norms are valid for discounting contrast variations, particularly if the neural responses are linear, since the L2 norm is computed on the entire RF. It might be judicious to attenuate the claim that contrast variation has no effect.

      We have softened the claim that contrast variation has no effect. The revised text now states that L2 normalization controls for root-mean-squared contrast but does not fully equate effective contrast in nonlinear cells, whose responses depend on the spatial structure of the stimulus beyond its total energy. We note that residual contrast dependent effects, particularly in the suppressive regime, cannot be entirely excluded.

      (4) Page 6: The authors acknowledge that, at least for simple cells, a phase shift in the grating and concomitant ON-OFF overlap is an inhibitory axis, which is correct. It does not really become clear what other axes were found, and whether any of these represent a novel discovery about V1.

      We have clarified the description of inhibitory axes in V1, noting that while phase-shifted stimuli represent a well-established suppressive axis for simple cells reflecting linear On-Off subfield structure, and complex cells exhibit no coherent suppressive pattern due to phase pooling, neither model class accounts for the multidimensional suppressive structure we observe. We have made explicit that our unbiased approach reveals suppressive structure spanning simultaneous changes across orientation, spatial frequency, phase, and texture, exceeding what any single known suppressive mechanism predicts.

      (5) Page 7: Dreamsim is based on human similarity judgements, whereas the data is from macaques. Is there any evidence suggesting that macaque similarity judgements might be similar to those of humans?

      We have added a paragraph to the Discussion acknowledging that DreamSim was trained on human perceptual similarity judgments while our neuronal data are from macaques. We note that this cross-species application is supported by the deep homology between primate ventral visual streams, and that natural-image similarity judgments have been found to be highly consistent across macaques and humans. Importantly, we clarify that we deploy DreamSim not as a model of macaque perception but as an image feature embedding to test whether stimuli that cluster in perceptual space evoke similar neuronal responses—a use that is robust to the precise calibration of the metric. We also note that we are developing custom macaque-specific embeddings for future work.

      (6) Page 7: How many images were in the test set?

      We have added the number of test images to the relevant text (n=75 for V1, n=150 for V4) and to the Figure 1 caption.

      (7) Page 8: As mentioned above, performing the analysis on V1 data of individual subjects and demonstrating similar digital twins might be an additional way to confirm the models' accuracy.

      We have added text noting that for V4, 1digital twin models were fit independently per neuron without sharing information across animals, and that extreme image sets identified by the model elicited correspondingly extreme responses in neurons from the other animal, confirming that identified selectivity patterns are not idiosyncratic to individual subjects.

      (8) Page 11: The mouse data is presented very briefly only, and the authors seem to imply that there is a high degree of coding similarity between this rodent species and macaques and, by extension, humans. Were there any notable differences between the mouse and macaque data?

      We have added text explicitly noting that while macaque and mouse visual cortex differ substantially in their functional organization and the complexity of neuronal selectivity, the broader principle—that non-sparse neurons are jointly defined by distinct excitatory and suppressive feature sets—generalizes across mammalian visual systems. We clarify that this does not imply that mouse and macaque visual cortex share similar functional organization or equivalent complexity of neuronal selectivity; rather, within the representational regime of each area, neurons are organized such that excitatory and suppressive feature sets are jointly structured and distinct.

      (9) Page 13: One main finding of the study is that inhibition appears to operate along additional dimensions that had not been previously recognized, but what is the nature of these dimensions, how do they arise and relate to known inhibitory effects in V1 such as centre-surround effects? The fact that suppression is tuned in response to natural images or other complex objects is not a new finding, and there is plenty of published work along these lines; the authors may want to cite Tamura et al 10.1152/jn.01267.2003. I am not sure introducing the term "dual feature selectivity" is really a major conceptual advance.

      We have added a citation to Tamura et al. (2004) in the Discussion, alongside other prior work documenting suppression by non-optimal stimuli. We have also expanded the Discussion to more carefully position our findings relative to existing work on feature-selective suppression, noting that while prior work has established that inhibition can be structured and feature-selective, our results suggest a broader organizing principle: within each visual area, there exists a set of feature combinations from which individual neurons draw both their excitatory and suppressive preferences.

      (10) Page 14: The authors enumerate a number of technical limitations, which is to be commended. It would be useful for them to comment on the particular advantages of the digital twin model, compared to a more traditional analysis of the responses to the thousands of natural images that were experimentally obtained. It seems likely that the main finding, i.e. tuned inhibition, is also evident directly in this population (?). While the digital twin is to some degree validated by the test images, its responses to the much larger set of images studied are not validated, and one must trust that the ResNet50 indeed captures V4 selectivity. It would be useful to discuss some of these points, and highlight a potential way that digital twins (maybe as a shared model between laboratories) can learn from a large number of animals and datasets, and maybe even be used to generate novel visual stimuli suitable to test emergent hypotheses.

      We have added a paragraph to the Discussion explicitly contrasting the advantages of digital twin models with direct analysis of experimentally recorded responses, noting that digital twins enable screening of more than one million images per neuron in silico, gradient-based synthesis of stimuli precisely optimized to drive or suppress individual neurons, and cross-model verification of identified selectivity patterns—a test that has no analog when working with fixed experimental image sets.

      Reviewer #2 (Recommendations for the authors):

      Minor comments:

      (1) Call out Figure 1/b in the main text. 

      We have added a callout to Figure 1b in the main text

      (2) Can you make a supplementary figure illustrating more examples with skewness around the middle (e.g. 1.5, 2, 2.5)? Namely, you state that 2 is a good threshold for deciding if it is non-sparse, but you only present clear-cut cases in Figure 2 (with <0.75 and >3.5). I am wondering if 2 is a good threshold?

      We have revised the text to clarify that the skewness threshold of 2.0 is adopted purely for analytical convenience to focus subsequent analyses on neurons with sufficiently graded response distributions, and that the key findings are not dependent on the exact threshold chosen. We explicitly note that the underlying distribution of sparsity is continuous, consistent with recent findings (Gondur et al., 2025).

      (3) The reference "A tale of two tails: Preferred and anti-preferred natural stimuli in visual cortex." Has no authors. I know it's anonymous, but maybe put that for now? I also congratulate including a paper that is anonymously under review at ICLR 2026. I don't find Unk, 2025 in the list of references. Perhaps related?

      We have updated the reference “A tale of two tails” to include the authors (Gondur et al., 2025) and ensured it appears consistently in the reference list. We have also resolved the missing “Unk, 2025” citation, which now correctly refers to this same work.

      (4) Why do you use a different model for the analysis in Figure 8?

      We have added text to the Methods and Results clarifying why a distinct architecture was used for the V4 evaluator model in Figure 8. Specifically, the V4 generator model uses a fixed, pretrained ResNet50 backbone whose weights are deterministic; any re-trained model sharing this backbone would not constitute a genuinely independent evaluation. By contrast, for V1, the ConvNeXt core is fine-tuned from different random initializations, producing architecturally equivalent but computationally independent models. A truly independent V4 evaluator therefore required a fundamentally different architecture.

    1. Author response:

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

      In preparation for release of the analysis code used in the paper, we made many analyses more parallel to one another in their exact preprocessing. This resulted in very slight changes to many panels, but these changes are nearly invisible and conclusions did not change. In one case, though, we realized that the way we were presenting data was potentially misleading (the timing plot in Figure 3A). The original plot was of the distribution of pixel values from the spatially smoothed map instead of distributions over individual neurons. We have now swapped it out for better interpretability and changed the accompanying text accordingly.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Here, the authors address the organization of reach-related activity in layer 2/3 across a broad swath of anterodorsal neocortex that included large subregions of M1, M2, and S1. In mice performing a novel variant water-reaching task, the authors measured activity using two-photon fluorescence imaging of a GECI expressed in excitatory projection neurons. The authors found a substantial diversity of response patterns using a number of metrics they developed for characterizing the PETHs of neurons across reach conditions (target locations). By mapping single-neuron properties across the cortex, the authors found substantial spatial variation, only some of which aligned with traditional boundaries between cortical regions. Using Gaussian mixture models, the authors found evidence of distinct response types in each region, with several types prominent in multiple cortical regions. Aggregating across regions, four primary subpopulations were apparent, each distinct in its average response properties. Strikingly, each subpopulation was observed in multiple regions, but subpopulation members from different regions exhibited largely similar response properties.

      Strengths:

      The work addresses a fundamental question in the field that has not previously been addressed at cellular resolution across such a broad cortical extent. I see this as truly foundational work that will support future investigation of how the rodent brain drives and controls reaching.

      The quantification is thoughtful and rigorous. It is great that the authors provide an explanation for and intuition behind their response metrics, rather than burying everything in the Methods.

      The Discussion and general contextualization of the results are thorough, thoughtful, and strong. It is great that the authors avoid the common over-interpretation of classical observations regarding cortical organization that are endemic in the field.

      All things considered, this is the best paper regarding spatial structure in the motor system I have ever read. The breadth of cellular resolution activity measurement, the rigor of the quantification, and the clear and open-minded interrogation of the data collectively have produced a very special piece of work.

      Thank you! We really, really appreciate this!

      Weaknesses:

      The behavioral task is very impressive and an important contribution to the field in its own right. However, given that it appears substantially different from the one used in the previous paper, the characterization of the behavior provided in the Results is too brief. More illustration of the behavior would be helpful. For example, it is rather deep into the paper when the authors reveal that the mice can whisk to help localize the target location. That should be expressed at the outset when the behavior is first described. Other suggestions for elaborating the behavior description are included below.

      Thank you. Although the task will be treated in greater detail in the next paper (where we more closely relate neural activity to the kinematics), we have added more exposition of the task here. In particular, we now include a figure with a characterization of the trial-to-trial variability across reaches to the same target versus across reaches to different targets (Figure 2-figure supplement 1B). This supports the idea that the mice aimed their reaches. We have also expanded that text.

      Regarding whisking, we have now revised that text to make clear that we do not know how the mice localize the spout. The original work by Galinanes and Huber argued that they find the spout by sniffing the water; they may do the same here, or may find it via whisking. It is also possible that the whisking they do is simply because the spout moves in and they are excited, or startled, or do it by reflex. We simply have no evidence one way or another. We have therefore revised the text to make it clearer that whisking-related activation could have occurred for a variety of reasons.

      Statistical support for key claims is lacking. For example, "The five areas of interest varied in the fraction of neurons that were modulated: M2 had 14%, M1 had 23%, S1-fl had 30%, S1-hl had 25%, and S1-tr had 27%" - I cannot locate the statistical tests showing that these values are actually different. Another example is Figure 7, where a key observation is that distributions of PETH features are distinct across regions. It is clear that at least some distributions are not overlapping, but a clearer statistical basis for this key claim should be provided.

      Good idea. For the proportions, we have now added first a Chi-square test for homogeneity to show that there is variation in the proportions, then shown the results of pairwise two-proportion Z tests (Bonferroni-corrected for multiple comparisons) as a binary matrix in Figure 3-figure supplement 1B. For the area distributions in the t-SNE space (Figure 7), we have added a 2-dimensional Kolmogorov-Smirnov test, again corrected for multiple comparisons, with p-values quoted in the text.

      I understand that the authors are planning a follow-up study that addresses the relation between activity patterns and kinematics. One question about interpreting the results here though, is how much the activity variation across target locations may relate to the kinematic differences across these different conditions, as opposed to true higher-order movement features like reach direction.

      We agree this is a very important question. However, having done many of the analyses to examine the question for the next paper in the series, we do not know of a shortcut to the right answer. This question requires thorough treatment, and so we leave it to be covered in subsequent work. Instead, after our speculation about how responses suggest function, we are now explicit that these hypotheses needs testing:

      “In each of these cases, determining the relationships of the observed activity patterns to function will require specific attempts to link the activity to kinematics, target location, sensory feedback, and more; these relationships will be addressed in future work.”

      Reviewer #2 (Public review):

      Summary:

      The functional parcellation of cortical areas is a critical question in neuroscience. This is particularly true in frontal areas in mice. While sensory areas are relatively well characterized by their tuning to sensory stimuli, the situation is much less clear for motor areas. This has become even more ambiguous since recent studies using large-scale neuronal recordings consistently report mixed sensory and motor-related activity throughout the brain, and motor mapping studies have shown that movements evoked by cortical stimulation are by no means limited to motor areas alone. Here, the authors use a correlation approach combining large-scale functional imaging at cellular resolution with movement-tracking in mice executing a reaching task. Across multiple recording sessions in the same animals, the authors have imaged a large portion of the sensorimotor cortex at cellular resolution in mice performing a reaching task, recording the activity of nearly 40,000 neurons. By aligning the calcium signal of each neuron to three task events-the Go cue triggering the reach, the onset of paw lift, and the contact between the paw and the target-for different target positions, the authors identified different response patterns distributed differently across cortical areas. They defined a set of features that describe the neurons' response pattern, representing the temporal dynamics and tuning properties for the different target positions. These features were used to construct cortical maps, and the authors show that, interestingly, gradient maps obtained from the first derivative of the feature maps reveal sharp discontinuities at the boundaries between anatomically defined cortical areas. Using dimensionality reduction of the neuronal response features, the authors found that, despite clear differences in their average response properties, individual neurons from the same cortical areas do not form distinct clusters in the reduced-dimensional space. In fact, most areas contain heterogeneous neuronal populations, and most neuronal populations are present in multiple areas, albeit in different proportions. Interestingly, the authors identified four neuronal subpopulations based on the distance between the components of the Gaussian mixture model used to model the distribution of neurons within each area. One of these subpopulations is almost exclusively represented in the anterior M2 cortex, while another is broadly distributed across the different areas.

      Strengths:

      This article is based on an impressive dataset of nearly 40,000 neurons covering a large portion of the sensorimotor cortex and on innovative analytical approaches. This study is likely the first to clearly demonstrate boundaries between cortical areas defined based on the responses of individual neurons. This innovative approach to functional mapping of cortical areas potentially opens up new perspectives for higher-resolution mapping of frontal cortical areas, using a broader repertoire of sensory and motor evoked responses.

      Thank you!

      Weaknesses:

      The second part of the article, which presents multimodal responses in the cortical areas, seems to be a perhaps overly complicated way of showing what has already been demonstrated in numerous recent publications, but these new analyses expand upon these previous observations by revealing an interesting functional organization of the sensorimotor cortex, highlighting interesting similarities and differences between certain areas.

      We understand the concern: a number of recent papers have also noted different neuron response characteristics distributed throughout the motor system. We compare and contrast in greater detail following the more specific comments on this below, but we briefly summarize here. The way previous work handled the data – for example, starting with PCA – mixes what neurons are tuned for and when they are tuned for it with what we refer to as the “response format”: properties like tuning sharpness, response duration, etc. We focused primarily on this response format, and designed our features to be mostly independent of tuning preferences or peak response timing. We therefore pick up on different properties of neurons’ responses than those prior works. In addition, no previous work we know of examined these properties across large swathes of cortex at single-cell resolution in the context of forelimb control. Together, these aspects of our work allowed us to produce high-resolution mapping of response properties in a way we have not seen in any prior work.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In addition to addressing the weaknesses stated above, I suggest the authors also consider the following.

      The one big question left unresolved here is whether we should be thinking about these four subpopulations as distinct types with a biological basis and importance, or just reflections of activity pattern heterogeneity. The authors say that "we did not observe tight clusters in feature space separated by gaps," but their discussion here is light and a bit unclear, and their engagement with the issue of types versus heterogeneity, in my view, could be improved. We do not need "gaps" where the density goes to zero in parameter space, but we do need reproducible troughs between peaks. The authors should clarify if there are substantial and reproducible troughs in the parameter space between their four subpopulations.

      This is a great idea, and we have added three analyses and additional text to address it. We break this concern down into two more specific questions, based on the next comment by this reviewer.

      (1) Are the clusters well separated / do they have troughs between them? (Note that even with troughs, clustering might not be stable if the clustering algorithm is poorly matched to the shapes of the clusters.)

      (2) Is the clustering stable? (It can be stable even without troughs, if, for example, the distribution has a long tail and a GMM needs one Gaussian for the body of the distribution and a second for the tail.)

      First, to directly address the presence or absence of troughs between clusters, we have added Figure 9-figure supplement 2A and 2B. For each pair of subpopulations, we trained a logistic regression classifier to separate the 5D feature vectors of the neurons in one subpopulation from the feature vectors of the neurons in the other subpopulation, then projected the feature vectors onto this axis. Note that because the subpopulations are defined by GMMs, which have nonlinear boundaries, the (linear) logistic classifier does not typically produce perfect classification. Nevertheless, this analysis provides a window onto how well separated each cluster is from each other cluster in feature space. In 5 of the 6 pairwise comparisons, it is obvious that the distributions are different and have at least some dip in the distribution density at the boundary. The one pair of clusters without a trough between them were the forelimb somatomotor and hindlimb somatomotor subpopulations. This was surprising to us, given that their likelihood maps are so strongly distinct, but this presumably reflects trying to capture a nonlinear classifier boundary with a linear one (see below). Overall, this analysis argues that the clusters do have fuzzy edges that blend into one another, but reflect concentration of mass near the centers of the clusters we identified.

      Second, to address the same question with a different nonlinear method, we have added a version of the t-SNE plot from Figure 7 that is instead colored and contoured by subpopulation identity instead of area (Figure 9-figure supplement 2B). Agreement with the GMMs is not a given here either, because t-SNE is a fundamentally different and independent nonlinear transform from that performed by the GMM classification. Nevertheless, the subpopulations were again nicely separated – though not with troughs, possibly thanks to the inherent difficulty of interpreting point density with t-SNE. Interestingly, here the hindlimb somatomotor subpopulation was the best separated from the other subpopulations, supporting the idea that the lack of separation we observed above with the logistic projections was indeed due to a nonlinear boundary. This analysis again argues that neurons are more likely to have features that lie near the center of a cluster, but that the edges of the clusters run into one another. Additionally, this analysis makes clear that treating the hindlimb somatomotor subpopulation as a second cluster can be supported by other analyses, even if not by the logistic regression projection.

      Third, to address the question of cluster stability, we have performed random splits of our data, GMM clustered the two halves independently, applied the GMM from one half to the other, and asked how similar the clusterings are using the Adjusted Rand Index. This produced a value of 0.856, which for this sensitive measure argues that the clustering is rather stable (at least for the three clusters that can be found with all data together, which does not include the smaller-in-size Anterior subpopulation). Note that we did not perform this analysis on the more complicated version where we fit a GMM to each area separately then cluster those; in our main analysis, the hierarchical clustering agreed with what we found by eye, but determining the number of clusters for hierarchical clustering is in general very unstable and so we did not have an objective way to determine the “true” number of clusters.

      In addition to these new analyses, we note that three analyses we had already included bore strongly on this issue. Regarding separability of the clusters, the fact that our likelihood maps (Figure 9C-F) were quite distinct for different subpopulations argues that we picked up on ‘real’ differences. Second, Figure 9B found that when clustering non-overlapping data – different cells from different areas – we obtained clusters that were nearly identical in their feature distributions. Third, Figure 10E used the clusterings from different areas’ data to create likelihood maps, and found that they were extremely similar. These analyses together argue strongly that we are finding ‘types’ in a meaningful sense; given that we know the areas do have different distributions of properties, if there weren’t types then clustering would yield different clusters for different areas. Given the importance of the question, however, we are grateful that the reviewer encouraged us to find additional ways to make this point!

      The original t-SNE plot is beautiful and quasi-fractalic, but it does not show clear signs of four cell types. The single-neuron activity profiles are clearly heterogeneous in very interesting ways, but heterogeneous does not imply a strong or reproducible multimodality that would indicate meaningful cell types. Clustering algorithms will always spit out an answer. If you just have elements uniformly distributed across a parameter space, plus some noise, when you ask for X clusters, you will get X clusters that have different centroids. When you ask an algorithm to cluster without defining the number of clusters, noise can lead the algorithm to produce a particular number of clusters that again will have distinct centroids. The salient question, though, is whether in the present case there is a parameter space in which the clusters are substantially and or reproducibly distinct. Distinct here would mean that peaks in the density across some parameter space are separated by troughs - again, we don't need true gaps. The more substantial the differences between clusters are (again, not the differences between centroids but the prominence of the density troughs between them), the more biologically meaningful the clustering is likely to be. Reproducibility here could be addressed with resampling methods (e.g., how often do two separate halves of the cells produce the same clusters?).

      Please see the reply above, which includes our addressing of this concern.

      The Introduction is generally good, but it could further develop existing ideas about how function is distributed across cell types and regions. We would like to be able to imagine different answers to the question of how activity patterns are organized that might have divergent implications for how the circuit works. I understand we have very little to go on in terms of data, but I think it would be helpful for readers to be given more of a sense of what *could* be important.

      Good idea. We have added such a paragraph to the Introduction:

      “To frame possible outcomes, consider that single neuron responses can vary along many dimensions. Cells could differ according to which movements or time periods they are recruited for (tuning), what movement parameters their activities reflect (encoding), or how their responses are structured across different movements (e.g., nonlinear encoding structure). Further, differences in these response properties across cells could be distributed over the cortical sheet in a variety of ways. Cells could form distinct “categories” or clusters that are spatially well-aligned to the boundaries of anatomically defined regions. Or, categories of neurons might span area boundaries in spatial footprints that do not relate obviously to area boundaries, and that either abut or overlap. At a fine-grained scale, cells with similar responses could be physically located near one another as in primate and feline visual cortex, or similarly-responsive neurons might be salt-and-pepper intermingled as seen in rodent visual cortex or in primate motor cortices during reaching behaviors.”

      It should be clarified in the Results how the cue relates to the target location. Most would assume a different cue for each location, but this does not appear to be the case. The authors should clarify whether there was some amount of searching for the precise target location after the reach, or else how the block structure or other sensory information allowed mice to learn where exactly the target would be. In the absence of target-specific cues, some sense of how the mice achieved target-specific reach trajectories should be offered.

      Related to this, in Figure 1, it would be good to see some individual trajectories, as they all overlap near the target in the current plot. Clearly, the reaches were targeted, but it is unclear how targeted. Some of the adjustments at the end may reflect searching or palpation to resolve the precise spout location. It is very much ok if the mice were not reaching with micron precision each time to each of 15 different targets, but it would be good to provide the reader a better sense of what the mice were doing.

      These are important points. First, to clarify, the Cue is just a Go cue, and was the same for all targets. It is now described in the Results as “non-target-specific”. For additional explanation about supplemental analyses to assess “aiming”, see replies to Reviewer #1 Public Review comments above. Finally, regarding how the mice locate the target: we just don’t know. As discussed above, Galiñanes and Huber found evidence for the mice using stereo sniffing, but whisking, listening to the motors, or some other strategy are also conceivable. We simply don’t have data to weigh in on this. We now make this limitation clear where we describe the task.

      In Figure 1A, CFA does not look well aligned with Tennant et al. (2011). CFA should only extend to +1 AP. The overlap of CFA and RFO seems strange. RFO also does not totally align with the injection coordinates used in An et al, biorxiv 2022.

      Thank you for your attention to these points. Our designation of the name CFA to the red dashed outline in Figure 1A was consistent with an earlier version of our previous work (Grier et al 2026) wherein we referred to the anatomical outline “MOp-ul” from Munoz-Casteneda et al 2021 as CFA. We have since revised that nomenclature to now refer to the outline as M1-fl, or the forelimb representation of primary motor cortex.

      Our placement of RFO was obtained by aligning the Allen CCF from Figure 1K of An et al 2022 to our version of the Allen CCF and outlining the hotspot of RFO with a circle. We have slightly adjusted the location of RFO posterior and medial to more closely align with the injection coordinates reported in the methods of An et al. 2022 of “1.5-1.88 mm anterior from Bregma, 2.25-2.63 mm lateral from the midline.” Because (as far as we understand) the injection coordinates and the map are not perfectly in register, we show a compromise between the two.

      We stress that the Figure 1A map is meant to be descriptive in its illustration of the variety of organizational zones that have been identified across mouse sensorimotor cortex.

      Discrepancies in the alignment procedure, animal strain, and mapping modality all introduce heterogeneity across mapping attempts that we do not aim to reconcile or resolve here.

      Related to this, aspects of the results do seem consistent with the distinction between RFA and CFA, but this is not acknowledged or discussed. For example, the barriers in Figure 6H that lie along the M1/M2 border - these seem consistent with the gap between RFA and CFA. The same could be said for the dim trough along the M1/M2 boundary that appears to separate RFA and CFA in Figure 3B. A slightly more rostral and lateral location of CFA compared to Tennant's definition or the regions backlabeled from cervical spinal injections (see Wang, Maunze et al. J Nsci, 2018) could be expected if flattening the brain under the coverslip for imaging effectively stretches the ML axis, and Bregma (notoriously hard to define reliably at this spatial scale) was defined a bit more caudally here than in other studies. Related to this, it would be better for the field if people described their method for defining Bregma in the Methods. I suggest the authors do this here.

      We appreciate the suggestion and have acknowledged the suggested correspondence in the discussion. Given the difference in our approach from those that originally characterized RFA (through ICMS and deep layer projection tracing) we have avoided making overly strong conclusions about this correspondence in our data. See the quoted text below.

      “The spatial distribution of modulated cells in Figure 3 suggests a distinction between the caudal forelimb area (CFA, involving M1 and S1-fl) and the rostral forelimb area (RFA) in M2, while the feature gradient boundaries suggest a distinction between M1 and M2 more generally. The absence of a clearly delineated RFA was surprising, given its distinct projection patterns (Carmona et al. 2024; Hira et al. 2013b; Wang et al 2018) and functional differences from CFA (Kristl et al. 2025; Morandell and Huber 2017; Saiki-Ishikawa et al. 2025), but our results might suggest that the activity in layer 2/3 of RFA does not differ markedly from other nearby subregions of M2.”

      Regarding bregma, we did not use it for atlas alignment here. Alignment was accomplished through a combination of paw vibration mapping and the location of the central sinus. Bregma’s location was only relevant for our injection of tdTomato labeling, and that labeling was used here only to stabilize the image plane. We include an estimate of it on the map solely in an attempt to be helpful, but we cannot claim we have the most reliable method for defining it.

      The authors focus on activity aligned to cue timing. This is sensible, but it could be meaningful to know how this choice affects the definition of organization. If response clustering is largely different across time, it would seem important. I understand that addressing this question may be beyond the scope of this paper. I just wanted to raise the issue with the authors for their future consideration.

      We agree that this is important to address directly. There are two aspects to this comment: (1) does it matter if activity from approximately the same time period is aligned to the paw lift or contact instead of the cue? (2) What changes if we use data from a different period of time?

      Regarding the first question (alignment), if we switch to aligning our data based on lift or contact, we have more statistically modulated neurons (see Figure 3C), but everything else is qualitatively similar with one exception: the GMM optimization doesn’t separate out the Anterior subpopulation from the Forelimb Motor subpopulation. The Anterior subpopulation only has a relatively small number of members, and they mostly exhibit the strongest peaks in their PETHs when Cue-aligned, so this makes sense. We now show the modulation maps for all of the locking events (Figure 3-figure supplement 1).

      The issue of the time window is a little more complicated. There are many choices we made in this work, of course, not least of which are the task we used and the features we chose based on hand-inspection of thousands of PETHs. As we noted in the Discussion, different tasks or different features would likely distinguish more subpopulations from one another. We think of the time window as a feature choice, albeit an implicit one. We chose not to include later time points because this begins to strongly include reward signals, which are known to be large (Levy et al 2020) and can dominate other aspects of the responses. The largest differences we noted when trying time windows that extended later are that mouth-related areas are separated out in the subpopulation analyses, perhaps because of later licking/consummatory responses, but we have not explored fully enough to speak confidently on this point without much more work and another 10 figures. To keep the scope of the paper manageable, we now call out this choice explicitly (see text below). We thank the reviewer for raising these important points.

      “Crafting additional PETH features, or using end-to-end neural network approaches to discover other features, might enable the discovery of additional structure (Minderer et al. 2019; Wang et al. 2023b). For example, our PETH features were chosen to be invariant to the onset time of activity, but these onset times were markedly later in lateral M1 than in adjacent M2 or S1-fl. Including onset times, using a wider window of time that includes more of the reward/licking period, aligning data to other behavioral events, or adding other PETH features would presumably result in finer subdivisions of sensorimotor cortex.”

      The map in Figure 4 is very cool, and the spatial structure is quite striking. In terms of the actual values of the onset times in each region, I am a little concerned with a dependence on the level of reach-related activity modulation, especially relative to the level of background activity (potentially related to posture). Less reach-related activity and more background activity, which we might expect for trunk and hindlimb regions, could seemingly skew the onset times earlier. We could be getting the right answer, or an answer that makes intuitive sense, for the wrong reason. Can this potential confound be excluded with some sort of control analysis?

      The previous text wasn’t clear. We have now clarified what we meant, very much in line with the reviewer’s thoughts. In addition, note that our change to what is displayed in the histogram (now neurons, previously pixel values) makes clearer that there is a multi-peaked distribution of onset times and it is mostly the prevalence of each peak in each area that varies. The text now reads:

      “These distributions over neurons revealed clear differences in the overall profile of activation: early onsets were more prevalent in S1 trunk and hindlimb regions, perhaps due to activity related to the animal stabilizing itself even if the neurons became more active later; then M2, and finally S1-fl and M1. Nevertheless, each area contained neurons activated at any given time in the trial.”

      The "Peak time variation" metric could potentially vary with activity level, with lower, noisier activity levels making cells appear less persistent. Perhaps a control analysis, based on SNR or some reasonable assumptions of the linkage between calcium signals and spiking, could be performed to measure the extent to which this could be creating differences between regions.

      Good idea. We have now performed this analysis, and the reviewer was correct: the correlation between peak time variation and a simple metric of SNR (assessed as range of PETH / max s.e.m.) was substantial: ⍴=-0.53. We now report this correlation and describe in the Results that this metric is driven by both true peak time variation and trial-by-trial variation. Thank you for this!

      “Peak time variation. To quantify whether a neuron’s firing peaked at the same time for every target or varied by target, we found the peak firing rate of the response to each target, then computed the standard deviation of these peak times across targets. This value is therefore higher if the peak time varied and nearly zero if the timing was consistent. Notably, this measure correlated substantially with overall signal-to-noise ratio of a neuron’s PETH (Spearman’s ⍴=-0.53; Methods), and thus partly measures trial-to-trial variability, not just true peak timing variability. This metric was quite low in M1, indicating highly consistent timing of the activity peak (and reliable responses), and was highest in the posteromedial part of M2 (presumably corresponding to the hindlimb representation) and the posterior tip of S1-hl (Figure 5B).”

      One could argue that the likelihood calculations illustrated in Figure 8 are biased higher for neurons within each region since they were used for defining the likelihood for that region. I think these likelihood calculations should be done for separate neurons other than the ones used to compute the mixture model for each region.

      We agree with the point about bias: the by-area GMM in Figure 8 is biased toward cells within the area, though the effect is probably quite mild given the large numbers of neurons and modest number of parameters. However, this model was intended to make the point that even if you give an area an unfair advantage, you still can’t cleanly isolate it. This was intended to help motivate the following analysis of subpopulations, and we have now made this logic clearer. Doing it this way has the advantage that the GMM components are identical between Figures 8 and 9, while if we held out the test neurons it would not be possible to make them the same without some complicated version of bagging on the GMM components. The reviewer is right that we should make this bias explicit, though, and we have now done so:

      “This mapping approach is explicitly biased toward finding feature differences between areas, allowing for a direct test of the hypothesis that response profile distributions are area-specific.”

      To me, the last Results section (Spatial overlaps between subpopulations indicate intermingled members) does two things: it shows you get the same results when you map each cell to a subpopulation independently of its area, and it shows that defining the subpopulations with cells from each area gives you essentially the same results, arguing against spatial variation of properties within subpopulations. I worry that these two points are getting merged together or not made clearly enough here, especially the first one. In general, the logic of this section does not seem well conveyed.

      Thank you for the feedback. In particular, your first point is made by Figure 9-figure supplement 4 when we fit an area-agnostic GMM to all modulated cells in the five main areas. However, your second point is one of the two main goals of the last Results section, along with the demonstration of the spatial distributions of cells after hard-clustering them by subpopulations. We have tried to clarify these main points further through substantial edits of the results section for Figure 10.

      One set of ideas that is highly relevant and should be raised concerns an ethological organization of the motor cortex. Since the observations of Graziano, there has been a steady stream of results describing ethological organization in rodents as well. This literature is briefly reviewed in Kristl et al., Nature Communications, 2025. For example, because of the potential for a differential involvement of grasping movements across different target locations, some of the variation in neuronal tuning described in the present manuscript may stem from a region preferentially involved in grasping.

      We agree that the Graziano literature, and the substantial literature in rodent that was inspired by Graziano’s work, is highly relevant to understanding the organization of motor areas. Kristl 2025 handles these issues very thoughtfully. The challenge here is that there are many possible different reconciliations of the stimulation results with ours, and some seriously unresolved challenges in doing so. To name a few:

      Our subpopulations and high-gradient boundaries both give quite different pictures than microstimulation does in rodent motor and sensory cortices. In particular, microstim produces more subregions that evoke different movements than we identify, and the borders don’t generally line up. This implies that the mapping between the two approaches is probably complicated.

      There is a completely alternative possibility to explaining the Graziano-like results: microstimulation is thought to preferentially hit axons, and some of these projections reach the medullary motor regions. Given that the medullary motor regions have known topography in the movements they evoke (Yang et al 2023) – but may or may not be driving the movements during flexible behavior – the two approaches may not be reconcilable. Or, it may require a much deeper understanding of medulla as driving the primary movement and cortex acting as a residual controller. This is an exciting set of ideas, but as yet very underdeveloped in our understanding.

      We don’t know if the subpopulation structure exists at all in L5, or in the PT cells, and if it does whether it differs. This is crucial given the frequent targeting of deep layers by ICMS stimulation protocols.

      As we caution in the Discussion, it is possible that our subpopulation findings are at least partly specific to the task we used.

      Although it is beyond the scope of this paper and will be addressed thoroughly in separate work, we have spent significant time with encoding models for joint angles and high-level target encoding in these same data. Given those results, we are fairly confident that the reviewer’s reasonable guess, of tuning variation due to intersections between body parts, does not seem to be the main driver of the subpopulation structure we find.

      After careful thought and discussion amongst the authors, we did not think that including this discussion in the paper was likely to improve interpretability of the present results for most readers. We very much agree with the point, though, and when we can narrow down the possible explanations in the future (likely in our next paper on this topic, which will address encoding) we plan to address it. We thank the reviewer for encouraging us to think through this.

      Minor:

      (1) Page 3: "densely shared" - perhaps "broadly shared"? Dense implies most/all the neurons get the same signals, which may not be true.

      Changed to “widely”.

      (2) Page 4: "data-driven approaches" - could be more specific - isn't everything we do data-driven?

      Changed to “bottom-up”.

      (3) Page 4: "spanned areas" - perhaps "spanned multiple cortical areas", since everything spans an area.

      Changed to “spanned multiple areas” (we mention cortex just a few words earlier).

      (4) Page 5: "intervals were generally fast" - awkward, "short" perhaps.

      Agreed, changed.

      (5) Page 5: "which asks whether the activity for a neuron changes over time consistently in relation to any target" - Rephrase to disambiguate between consistent temporal variation in firing for all targets and variation across targets in the firing patterns. In other words, are we talking about cells that are just modulated during reaching, or cells whose firing patterns differ across targets?

      Changed ending to “to any given target”. The ZETA measure really does simply ask whether there is a change in firing rate over time that is consistent across trials, for each target independently. A neuron that exhibits an identical bump for all targets would register as modulated. We chose this measure in part because of the number of temporally-modulated but untuned cells. This wasn’t very clear as we had written the text, so we now note this explicitly in the Methods. Thank you for pointing out that this wasn’t clear.

      “For all analyses, only neurons modulated by the relevant locking event were included. Note that this measure looks for modulation over time to any target; it is indifferent to whether the neuron exhibits tuning across targets.”

      (6) Figure 1: It seems like some of the abbreviations used in 1A have not been defined yet in the paper.

      Yes. It’s a long list, and we wanted to put the citations for the description of each area together with the definition of the acronym. Moreover, we wanted all this info together with the description of how we aligned these area descriptions from others’ work with one another on the Allen atlas. This was impractical in the caption, and would be a long digression for what is intended as a simple point in the Results, which is why we refer to the Methods here.

      (7) Page 8: "Given that these areas have known spatial organization within them and structure was apparent by eye in the spatial scatterplot of modulated neurons (Fig. 3A)," - it is not clear what spatial structure we are supposed to see in 3A.

      Good point. We have changed the parenthetical to: “(for example, the less modulated band along the M1/M2 border in Fig. 3A)”

      (8) Page 8-10: The region-wide onset analysis breaks up the flow from PETHs to the metrics used to quantify them. I suggest moving this section (Onset of neural activity varied with somatotopy and subregion) to later in the manuscript.

      We appreciate the reviewer’s input on organization. We went back and forth many times in how to organize the many results in this paper. The reviewer is right that this analysis breaks the flow, but the reason we included it where we did was threefold. First, it uses an easily-understood metric to introduce the reader to how we made maps from single-neuron features. Second, it easily introduces the power of making such maps. Finally, it makes clear that if we are not careful with how we handle time in the feature design, timing will dominate.

      All these things said, this has helped inspire us to add a result in which we re-examine timing broken down by subpopulation (Figure 9-figure supplement 2C). It shows that subpopulations timing distributions appear more distinct than distributions for areas, but there is still substantial heterogeneity in timing that is explained by location in cortex and not subpopulation membership alone.

      (9) Page 12, Target tuning linearity: This metric should be clarified in the Results. It is not clear how the 2D of targets is turned into 1D. Also, the plot in the figure has correlation on the y-axis, and it is not clear how each target location gets its own correlation value. The phrase "optimized anchor target" is unclear.

      Agreed this needed to be clearer. The text in the Results now reads: “To quantify how linearly a neuron’s activity related to target location in physical space, we correlated the 15D vector of mean activity of the neuron for each target with the 15D vector of the targets’ ordinal distances from the neuron’s preferred target (Methods).” In agreement with your suggestion, we have dropped use of the phrase “anchor target” in favor of “preferred target”, which should be clearer. We have also revised the Methods text accordingly to clarify.

      To directly answer your question, we turn the targets from 3D positions into 1D by computing the ordinal distance of each target from a preferred target. (Note that the preferred target is actually the one that maximizes the resulting correlation; this is detailed in the Methods). There therefore aren’t 15 correlations; we’re correlating two 15D vectors, where each has one element per target and the “ordinal distance” vector has a zero for the preferred target. Hopefully the new description makes this clearer.

      The figure schematic was unclear, thank you for catching that. We have updated the Y axis to read “mean activity” and the X axis now reads “dist. to pref. target.”

      (10) Page 12, paragraph beginning "We also compared our metric maps simply using the top 20 PCs." - This paragraph is unclear, since both sentences refer to using the metrics. I would guess the authors mean that the metric maps were compared with and without PCA and basis rotation, but this is not clearly stated.

      Thank you, this was unclear as written. We have changed it to:

      “We also compared our metric maps with maps generated from the top 20 PCs of the PETHs (Methods), rotated using VARIMAX to identify a sparser basis (Musall et al. 2019).”

      (11) Page 18: "These results make clear that the working hypothesis - of areas with well-separated feature distributions - is incorrect." This is the clearest statement of the impact of the results. The authors could consider including this in the Abstract or Introduction.

      Thank you for pointing this out. We agree, and have added a similar phrase to the Abstract.

      (12) Figure 9: It would be great to also just see the average PETHs for each of the four clusters to get a better sense of how their time series differ.

      Good idea. The feature computations are a many-to-one mapping, so it’s not possible to literally generate a PETH from the mean of the cluster, but we have added PETHs from well-modulated neurons that are near the means of their subpopulations (Figure 9-figure supplement 1).

      (13) Figure 9B: Colorbar has no label.

      Fixed, thanks.

      (14) Figure 9C: Need a colorbar - need to see the difference in density for locations.

      The color map is the same Figure 8B, which is now noted in the caption for Figure 9C. The scaling of likelihoods is almost totally uninformative; they’re not well-behaved like probability distributions, so you’ll note that even on Figure 8B the labels are simply “max likelihood” and “min likelihood”. The important pieces of information here are that these are log likelihoods (noted in the Figure 8 caption), and the visualization of the color map itself (from the color bar). Given these considerations, we have elected to keep the maps themselves a little larger by not trying to squeeze in a minimally-informative colorbar to all of the plots, but thank you for noting that the reference to 8B was needed.

      (15) Page 22: "additional spatial structure could be present" - The nature of the additional spatial structure here is a bit opaque. The authors could clarify what additional structure may be present.

      Good idea. This paragraph now reads:

      “The overlaps in the subpopulation likelihood maps above imply that members of different subpopulations are spatially intermingled, but it is less clear whether each subpopulation has homogeneous response profiles across space. In particular, the use of likelihoods mixes two properties: the fraction of neurons in a given neighborhood that are members of each subpopulation, and the heterogeneity of response profiles amongst members of that subpopulation. These properties could vary systematically with respect to one another, and the spatial structure shown by the likelihood map does not disentangle them.”

      (16) Figure 10E, legend: "GMM component" - I think this should be "GMM subpopulation" to avoid confusion with the previous use of "component" above, referring to the components of the GMM models for each region.

      Thank you – good catch. Changed to “Likelihood map”.

      (17) Page 24: "Note that this consistency also validates the use of clustering to combine components and identify the subpopulations in the first place." - I don't totally get this, and how this result validates the method of combining components, as opposed to just clustering all the cells from all regions at once. Perhaps the implied opposing strategy is not clear here.

      We have changed this sentence to:

      “Note that this consistency mirrors the low Bhattcharyya distances between corresponding GMM components in Figure 9B, and further validates the use of clustering to combine components from different areas.”

      Regarding the reviewer’s larger point, we have three thoughts. First, we do also show the result of fitting the GMM to all cells together (Figure 9-figure supplement 4).The result is similar, but the Anterior subpopulation is lost because its membership is low and so the ICL criterion can’t justify a fourth cluster. Second, because we imaged more neurons in some areas than others, fitting the GMMs to each area separately put their representations on a more equal footing. Finally, doing the analysis this way allowed us to most directly compare our two hypotheses, as illustrated in Figures 8A and 9A.

      (18) Page 25: "in the zones where different subpopulations overlapped" - I would omit this, since "intermingled" seems to mean exactly this.

      We included this phrase to prevent quickly-skimming readers from incorrectly concluding that the subpopulations overlapped entirely and were therefore intermingled everywhere. The reviewer is right that it’s unnecessary for a careful reader, but we aimed to prevent misinterpretation by readers that might skip to the Discussion for a results summary.

      (19) Page 25: "content of the activity, but also its format" - the difference between content and format is not entirely clear. Metaphor not quite metaphoring here. Agreed. We have added examples to clarify.

      “This makes clear that there are potentially important differences not just in the content of the activity (e.g., encoding target vs. movement commands (Grier et al. 2026)), but also its format (e.g., linear encoding vs. nonlinear, persistent vs. brief responses).”

      (20) Page 30, bottom: In the description of the behavior, more details should be provided, especially since the paradigm is new. For example, it says the block size was reduced - what was the ultimate block size?

      Targets were cued randomly in the behavior performed during neural recordings. Blocked trials were used during training and were phased out incrementally as performance improved. This and various other details have been added. Please let us know if there are other specific details you would like to see in the final version.

      (21) Page 39, citation of An, Mulcahey et al.: There is a biorxiv version with a different author list that could be cited.

      This was an error with our citation manager, and has been corrected. Thanks for catching it.

      Reviewer #2 (Recommendations for the authors):

      Overall, this is a remarkable study with well-designed in-depth analyses, and I only have some minor suggestions that could help improve the clarity of the paper.

      Thank you!

      General:

      It is not immediately clear to me why the GMM approach used in this study is more interesting than a clustering approach based on single-neuron response patterns (See Esmaeli et al., Neuron 2021 or Oryshchuk et al., Cell Report 2024). But my impression is that it led to the same observation that most clusters are widely distributed across cortical areas, with different proportions, but a few clusters are quite specific to a few areas. A noticeable difference perhaps is the number of clusters - or response profile - that seems particularly low (only 4) in the current study. Could the authors clarify and comment on that, maybe?

      The reviewer brings up an interesting point: at heart, these works ask related questions, albeit about different effectors, tasks, recording modalities, and types of information encoded. Those differences probably mean that results cannot be directly compared, but we can certainly discuss the methodological tradeoffs. The two papers mentioned take a more traditional first step, using PCA on the vectorized PETHs to reduce dimensionality, then layer on a spectral approach to improve clusterability. These are good methods; we use something similar as our alternate method, applying VARIMAX to the PCs instead of spectral methods to preserve linearity of transforms. For the kinds of responses both they and we have, PCA will tend to most strongly pick up two aspects of the responses: tuning and timing. This is because vectorized PETHs will have large values in the rows corresponding to the target/condition and time points where the high activity is, and the alignment of these profiles with those of the other neurons will capture a large fraction of the variance. For data like either theirs or ours, this would tend to cluster apart left-tuned cells from right-tuned, and (more importantly here for revealing spatial structure) early-response cells from later response cells. That intuition is consistent with what those papers report, and examining our VARIMAX’ed PC plots closely (which have sharpened in the latest version thanks to improved normalization), we can see that they break apart sub-regions largely based on timing. In our feature approach, we intentionally chose our features to be largely invariant to both tuning preferences and timing. Instead, we chose our features to pick up on what we call the single cell “response format”: response duration; peak time variation (but not absolute timing); and tuning sharpness, persistence, and linearity. These different methods pick up on different aspects of responses.

      To double-check that the PCA-then-spectral approach reveals similar structure to our use of VARIMAX on the PCs, we tried applying the suggested method to our data. We applied spectral clustering to the N x 20 PETH PC feature matrix, then fit an area-agnostic GMM to the spectral features. We plot the likelihood map for the components of a GMM with 10 modes. The GMM components did not display clear spatial structure beyond that observed in the VARIMAX’ed PCs (Figure 5-figure supplement 1) and were less interpretable than those identified by area-agnostic clustering of our response features (Author response image 1). As noted, the number of subpopulations identified by the clustering of our hand-engineered features is lower than what would be obtained from clustering the PCs of the PETHs. This is likely the result of the substantial heterogeneity in activity onset and preferred target that is preserved by PCA. Because our central approach is largely agnostic to these two sources of variation, the number of identified clusters reflects the dominant patterns of variation beyond these two sources.

      Author response image 1.

      GMM fit to spectrally transformed PETH PCs, agnostic to anatomical areas. One GMM was fit to the spectrally-embedded PC feature vectors of cells from all 5 main areas. Each component of a 10 component model is shown.

      Also, I think it would greatly help the reader to return to PETHs at some point, if possible, to show the response profiles of each identified neuronal subgroup (page 20). To what extent are they similar or different across the cortical areas (for the same neuronal subgroup)?

      This is a good idea. We have added a figure to address this question and the related question by R1 (Figure 9-figure supplement 1). In short, given the wide variety of PETHs we observed, there is of course still substantial variation within subpopulation, and some mild but systematic differences in the distribution of what we observe across areas. We now discuss the conclusions from this plot in the Results:

      “As a qualitative depiction of the response profiles identified with each subpopulation, we plotted the two highest-likelihood cells for each area/subpopulation combination (Figure 9-figure supplement 1). These examples reveal stereotypy in the subpopulation responses across areas, but also show variation across areas, especially for the two somatomotor subpopulations.”

      Specific:

      (1) Figure 2B and M&M: the 3D spatial organization of the target locations is not immediately clear. What is the spacing between target locations? What is the 'final azimuthal spacing'?

      Added, thanks. The pairwise horizontal distances between targets were between 1.72 and 6 mm apart and the vertical spacing within a column was 1 mm. “Final azimuthal spacing” just referred to the targets being closer together during training and our gradually spacing them apart to their final locations. We have also added some relevant details about the training.

      (2) Figure 2C: It would help to have a scale bar (mm).

      Added, thanks.

      (3) Figure 2C: It would be easier to appreciate the variability of the trajectories across trials to plot an overlay of trajectories to one target only (could be a Supplementary Figure).

      The reviewer has a good point: the variability and accuracy of aiming was hard to ascertain from the plot. We experimented with a few options for making this clearer most effectively. We have now added Figure 2-figure supplement 1 that shows in the third subpanel of panel A the finger centroid trajectories for one of the 15 targets highlighted for the mouse shown in Figure 2C, mouse 3. The centroid trajectories for all other mice are shown as well to illustrate similarities and differences across animals as well as the overall variability. As noted elsewhere we have also included an analysis of the variability of the centroid trajectories, showing that reaches to a given target were more similar than reaches to different targets. We think this provides a fuller picture of the behavior and intend to provide still more detail in future work. Thank you for suggesting additional detail here!

      (4) Figure 4: It would be nice to also show the amplitude-normalized grand-average PETHs for the different areas.

      This is an interesting suggestion. After careful consideration, we think that this analysis is not as effective for depicting overall timing and modulation profiles as the current ones, given the strong amount of target selectivity and response time heterogeneity (now better visible in the revised Figure 4A). When computing the grand mean of all cells within each area, the dominant features distinguishing areas are onset time and response duration. The differences across areas in these two features are better supported by the analyses of Figures 4 and 5 due to the large amount of heterogeneity in responses within each area. We thank the reviewer for encouraging this exploration; more complicated spin-offs will likely inform additional timing analysis in the next paper on these data.

      (5) Figure 7C: figure legend - although it is quite self-explanatory, please explicitly indicate which pattern corresponds to the 'Three contour levels (98%, 95%, 90%)'.

      We have now added this as a legend on the figure panel itself (here and on similar plots). Thanks for pointing this out.

      (6) Figure 8: Is there also an interesting asymmetry between sensory are motor areas, with neurons in sensory areas being more likely associated with motor areas (B and C), whereas neurons in motor regions are less likely to arise from the distribution of sensory areas (dark blue color in frontal regions in D, E, and F)?

      This is an interesting observation, but we understand it to be an artifact of colormap scaling. As mentioned above, likelihoods are not well-behaved like probability distributions are: for example, they are not bounded at 1, and their sums over a dataset can have any positive value. The only things that can be interpreted are their relative values. This makes their scaling functionally arbitrary – you’ll notice we used “min likelihood” and “max likelihood” instead of numbers, which would be nearly meaningless – and therefore presents a problem for scaling the colormaps. We don’t know of a principled way around this problem. To deal with it, we simply put the ends of our colormap at the extreme pixel values. It so happens that both the M1 and M2 maps had a handful of neurons in a less-sampled spot at the bottom of M2 that were very low-likelihood, which results in what you noticed. We debated removing those neurons for this purpose, but we had no basis on which to do that kind of manipulation, so we left it as the most honest representation of the data we could produce.

      To clarify this, we now mention in the caption “The ends of the colormap were set to the maximum and minimum likelihood values for each map.”

      (7) Figure 9B: there are two-time 'S1-hl: 1' indicated at the two bottom rows of the distance matrix. I suppose one of them should be 'S1-tr: 1' instead?

      Fixed, thanks for catching it.

      (8) Page 20: 'This hinted at a second hypothesis: that some of the 'modes' (groups of neurons) discovered separately in each area might correspond.' ???

      We had meant “mode” as in “multimodal”, but it was very unclear. We have rewritten the sentence:

      “This hinted at a second hypothesis: that a peak in the multimodal distribution from one area might correspond to a peak in the multimodal distribution of a different area.”

      (9) Figure 9S2: Please indicate for which area each map is computed.

      The caption was not clear enough about what we were doing here: we fit the GMM on all neurons together, ignoring which area they came from. We have now clarified it in the caption:

      “One GMM was fit to the feature vectors of cells from all 5 main areas. Each map plots the likelihood for all cells to each of the three components of this area-agnostic GMM.”

      (10) M&M, Subjects and surgical procedures: 'ambient temperature of 71.5 {degree sign}F', please use international units.

      Done.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      It was nice to see that the authors could distinguish differences between the OFC signals that they observed and those in the visual regions based on changes through the session. However, the linkage between these brain activations and a functional role in generating behavior was left unexplored. Without further exploration, it is hard to tell exactly what role the signals might be playing, if any, in the behavior of interest.

      To link the behavioral with the fMRI data, we now correlated fMRI decoding accuracy with behavioral performance. We studied behavioral performance in two ways: the difference in high versus low noise environment learning rates, and mean accuracy (i.e., absolute prediction error). We correlated both measures with the decodability of the environment in the central OFC. Each correlation was calculated either in the full experiment, or only the second half. However, none of these correlations were significant (all p > .1). Given the difficulty of interpreting this result, and our lack of statistical power for doing individual difference analyses, we decided not to report these analyses in the final paper.

      Reviewer 2 (public review):

      (1) The authors make the distinction between meta-learned "global" learning rates and within environment learning rate adaptation in response to "local" fluctuations/observations. Though the experimental paradigm is novel, there are certainly links to prior work - for instance, though change point structures don't entail revisiting unique environments, they do require meta-learning from environmental statistics that is distinct from transient local adaptation to prediction errors. This tendency to increase one's learning rate after large prediction errors is appropriate in change point environments, though, as is true in this study, the amount of increase should be dependent on. This represents a similar kind of slower-timescale learning or reuse of more "global" parameters, and can be seen to different extents in prior work. It might benefit readers if the authors were to link the current work to previous research more explicitly to draw clearer connections between the approaches and findings.

      We thank the reviewer for their very helpful literature suggestions and now contextualize and discuss our findings in light of relevant literature.

      (2) Throughout much of the paper, the authors refer to the distinctions between environments primarily as differences in "initial learning rates" or "environment-specific learning rates." This is particularly prominent when discussing fMRI results. Though the optimal initial learning rate did differ across environments, this was the result of differences in underlying task statistics. It will be important to clarify this throughout the text, because of the confounds between task statistics and initial learning rate (and to some extent, the position on the screen), it is not possible to separate the impact of these specific variables. This is also relevant to understanding the justification for using methods like RSA to test whether brain regions represent task states similarly. If the main hypothesis is that neural activity reflects the (initial) learning rate itself, then a univariate analysis approach would seem more natural.

      We agree that task statistics are not the same as differences in learning rates. However, we do not consider this as a confound: The point of the differences in task statistics is exactly to generate differences in learning rates. With our paradigm, we deliberately tried to dissociate variations in learning rate that were induced by learned environmental differences versus local task statistics. We tried to make this dissociation more clear, especially when discussing the fMRI results.

      (3) For the neuroimaging results in particular, the specificity of some of the results (e.g. ventral striatum showing an effect of prediction error only in the low noise condition in the second half of task experience, only on the first trial) is a bit surprising. Additional justification of or context for these results would be useful to help readers gauge how expected or surprising these findings are.

      We agree some of these findings were unexpected. We now also highlight that while we expected the ventral striatum to be involved in prediction error processing, we had no strong a priori expectations regarding these further modulations by time and environment. We also tried to contextualize these interactions more.

      (4) There are some methodological details that are unclear (e.g., how were the positions of the crabs selected relative to the location they emerged from? Looking at Figure 1C, it looks like the crabs spread out unevenly, and that the single position they emerge from is not necessarily at the center of the crab locations.) Additional detail and clarity would help address some unanswered questions (more details below).

      We clarified the experimental procedure at several places, and now added a video that helps illustrate the trial timeline better.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) With regards to the primary weakness mentioned above, it would be nice to have some link between the brain signals of interest and upcoming behavior. For example, can you read something out of OFC that enables you to better predict what the participant will do next? Or even better, do so beyond any behavioral variability that is explained by the computational model?

      To link the behavioral with the fMRI data, we now correlated fMRI decoding accuracy with behavioral performance. We studied behavioral performance in two ways: the difference in high versus low noise environment learning rates, and mean accuracy (i.e., absolute prediction error). We correlated both measures with the decodability of the environment in the central OFC. Each correlation was calculated either in the full experiment, or only the second half. However, none of these correlations were significant (all p > .1; see plots in Author response image 1). Given the difficulty of interpreting this result, and our lack of statistical power for doing individual difference analyses, we decided not to report this analysis in the paper.

      Author response image 1.

      (2) A number of the learning analyses are based on splitting the session into halves. As a first pass, this seems like a reasonable thing to do, but I certainly wonder what the dynamics of the meta-learning actually look like, and it seems like the data collected would be sufficient to gain some insight into those dynamics through some sort of sliding window analysis.

      We thank the reviewer for this interesting suggestion, which was also raised by Reviewer 2. We now calculated the learning rate in a sliding window of 20 trials (i.e., trial x to x + 19), and provide revised figures for each experiment separately (Fig. 2E and Fig. 4E, respectively).

      (3) The model selection procedures described make sense, but it would still be useful if the authors justified them by showing that they work in synthetic data (ie, generate a confusion matrix). I may be confused about what delta-SE is, but I'm confused about why two models with very different fits have the same value (211) for that metric.

      We report model recovery on synthetic data, which yielded model recovery rates of 100%, and added these to our Methods section. To clarify the Reviewer’s second point, ∆SE is the standard error of the difference between a model’s LOOIC and the top ranked model’s LOOIC. There is no one-to-one mapping between the ∆SE and a model’s LOOIC.

      (4) Was the central OFC anatomical ROI overlapping with the cluster surviving in the whole brain analysis? I didn't see this mentioned in the text, and it certainly would be important for interpreting the two results together.

      The central OFC indeed overlapped with the cluster surviving whole brain analysis, which we report on page 17-18.

      (5) The authors found regions that reflected learning rate at the "island presentation" phase of the task - it could be distinguishing this analysis and its meaning from other work that has focused on representations of learning rate at the time of feedback.

      We agree that this is an important distinction worth emphasizing. Therefore, we added the following lines to our discussion paragraph: 

      “Importantly, previous studies examined neural correlates of learning rates during outcome evaluation, where learning rates may be adjusted online as a function of locally experienced prediction errors (e.g., (Behrens et al., 2007; Browning et al., 2015; Nassar et al., 2012). In contrast, our RSA analysis targeted neural activity at island presentation, before any outcome information was available. At this moment, learning rates cannot be updated based on current feedback and instead reflected the retrieval of a previously learned, environment-specific learning-rate settings. This difference reflects our hypothesis that the OFC represents the latent states in a cognitive map of the task (Knudsen & Wallis, 2022; Moneta et al., 2024; Schuck et al., 2018; Wilson et al., 2014), which are expected to activate as soon as the agents can infer which task state it is in. Several studies have identified such “partially observable” task states in the medial OFC (Bradfield et al., 2015; Schuck et al., 2016; Tan et al., 2025; Wimmer & Büchel, 2019), in line with the region identified here (but see e.g., (Ongur & Price, 2000), for important anatomical distinctions between medial and lateral OFC and (Tan et al., 2025) for an example of related functions in lateral OFC). Our finding extends this notion by suggesting a link between OFC and meta learning, wherein meta-learned information becomes encapsulated in task states (Hattori et al., 2023; Moneta et al., 2024).”

      (6) "Specifically, it showed a more negative response to larger (location) prediction errors, which is consistent with its documented role in showing a more positive response to more positive reward prediction errors (Calderon et al., 2021) - keeping in mind that being closer to the centre of where the crabs appeared (i.e., smaller location prediction errors) is less negatively or more positively surprising (i.e. smaller negative or larger positive reward prediction errors)."

      I found this sentence very hard to parse. Do PE responses in the high noise environment get "compressed" in their representation over time (ie, it takes a larger error to get the same BOLD response)? If so, this relates to claims made in Diederen 2016... but see also Mah 2024 Cell Reports, who fails to see learning rate encoded in DA system in striatum of rodents that appear to adjust their learning rates.

      Thank you for pointing to this. We agree that this sentence was hard to parse, and so we now split it in three revised sentences. We also agree with the Reviewer’s interpretation, and would like to thank the Reviewer for their useful literature suggestions which we now added to our discussion. 

      (7) Figure 7 should use a different color scheme because many of the activations just appear black, and I can't tell whether they are positive or negative. It was also notable in Figure 7A that regions are not visible, including ACC, which is typically thought to encode prediction errors in such paradigms. It would probably be useful for the authors to include a table of all clusters exceeding multiple comparisons correction and to on differences to other work examining absolute prediction errors. ACC does appear on the second trial, which made me wonder whether there were changes in the prediction error coding from first to subsequent trials. 

      Thank you for pointing this out. We now revised our color scheme which we agree makes it much clearer now. Although the ACC is frequently implicated in prediction error–related signals (e.g., Behrens et al., 2007), models suggest that ACC responses more strongly reflect unsigned prediction errors, surprise, or the need for control and model updating (Alexander & Brown, 2019; Hayden et al., 2011; Silvetti et al., 2018). In our task, ACC activity only emerged on the second trial, when participants had formed an initial estimate and prediction errors could meaningfully signal the need to update internal models or control settings. We now added a to the Discussion highlighting this distinction and relating our findings to this prior work emphasizing prediction errors and control-related signals in ACC.

      (8) The authors suggest that fast learning would presumably occur in a neural activation space, whereas slow learning would occur through weight adjustments. This makes sense, but activity-based dynamics have been suggested to do rapid adjustments by encoding a "latent state" though (Razmi 2022 j neurosci) -- and such a latent state has been shown in OFC (Schuck etc)... but here OFC is more implicated in the slow learning. I am curious about whether authors could on this a bit in the discussion. 

      Thank you for bringing up this interesting question. We can only speculate but a crucial factor is on which level of resolution tasks states operate. On the one hand “detailed” trial-level states are needed that map a specific sensory input onto a specific latent state and its value. Such states would change quickly, possibly through activation dynamics, and are in line with how they have been operationalized in Razmi or Schuck etc. On the other hand, successful task performance also needs “higher level” states that describe entire task phases or full tasks, as in the present experiment. Due to the different speeds of learning, it appears plausible that these would be learned with synaptic changes. We expand on this in the discussion as follows: 

      “Our finding extends this notion by suggesting a link between OFC and meta learning, wherein meta-learned information becomes encapsulated in task states (Hattori et al., 2023; Moneta et al., 2024). Consistently, OFC has been shown to represent task states (Moneta et al., 2024; Stalnaker et al., 2015; Wilson et al., 2014). While earlier evidence shows that the OFC represents concrete aspects of task states, such as task-relevant stimulus features (Schuck et al., 2016), we hypothesized that the OFC also represents more abstract aspects, such as learned, environment-specific learning rates. Indeed, we showed that the central OFC gradually came to represent these environment-specific learning rates (or the environment-specific statistics that drive them). While previous work speculated that these different levels could have different neural underpinnings (Sharpe et al., 2019), our findings indicate OFC might signal states on multiple levels. This does not imply identical learning dynamics; fast-changing trial-specific states might be learned through activity dynamics, while higher-level contextual states could involve synaptic plasticity.”

      (1.9) Also, as a more minor point in the same section, the sentence about blocking synaptic plasticity in OFC sounded interesting, but should have a reference.

      Thank you for noticing, we now added the reference (Hattori et al., 2023).

      Reviewer #2 (Recommendations for the authors):

      (1) Additional links to prior literature: In terms of prior work in which there is something akin to more "global" adaptation, some examples of potentially relevant prior work include:

      McGuire, Nassar, Gold, & Kable (2014) Neuron 

      D'Acremont & Bossaerts (2016) Cerebral Cortex 

      Lee, Gold, & Kable (2020) Decision 

      Bakst & McGuire (2021) JEP: General 

      Bakst & McGuire (2023) Cognition

      We would like to thank the reviewer for pointing us to these different literature suggestions which we agree help us contextualize and discuss some of our findings better. We now refer to McGuire et al. (2014) when discussing the fMRI results, and d'Acremont & Bossaerts (2016) when discussing potential alternative strategies in the high noise environment (the Reviewer’s last point). Finally, we integrated the clearly relevant works of Bakst & McGuire (2021; 2023) and Lee et al. (2020) in our discussion of meta-learning different adaptive strategies. 

      (2) Individual differences: Though not always the focus of work on predictive inference, one common finding has been that there are pronounced individual differences in behavior (see, e.g., coefficients in Figure 2 in Nassar et al. 2019 eLife, or Figure 2 McGuire et al. 2014 Neuron, or Bakst & McGuire 2023 Cognition). There appears to be substantial variability between individuals in your data as well (i.e., Figure 2B, 4B, and the modeling figures). It would be interesting to see some direct exploration of this variability: baseline learning rate appears to differ between participants to a large extent, does their rate of adaptation (across trials within a block) also differ? Does their metalearning occur at different rates (in fact, do some participants not show evidence of appropriate meta-learning at all)? 

      Relatedly, your computational modeling approach fits the six candidate models hierarchically, and therefore the reported results show the overall best fit for the group. It might be worthwhile to determine whether individuals have different best-fitting models. This could be another way to characterize the variability between individuals. 

      In concert with this, it could be a useful complement to determine whether either the strength of the OFC neural similarity results or their time course reflects aspects of behavior. Put another way, is it the case that not only does OFC activity and behavior both come to reflect task structure, but that these changes happen to a similar extent and over a similar time course across individuals?

      We agree it would be highly interesting to investigate meaningful individual differences in both fast and slow adaptations in learning rate. However, our sample was not set up and is underpowered to conduct such analyses. In response to a similar by Reviewer 1, we did run correlational analyses between differences in learning rate, performance accuracy, and the responsiveness of the OFC. However, none of these analyses yielded a significant effect. We decided to not include these results in the paper, for reasons of statistical power, but we report them in Author response image 1.

      (3) fMRI:

      (3a) The primary finding in OFC is restricted to the central OFC. The manuscript would benefit from additional explanation regarding this specific subregion. 

      Thank you for bringing up this important distinction. In the discussion we now clarify as follows: 

      “This difference reflects our hypothesis that the OFC represents the latent states in a cognitive map of the task (Wilson et al., 2014; Schuck et al. 2018; Knudsen & Wallis, 2022; Moneta et al, 2023), which are expected to activate as soon as the agents can infer which task state it is in. Several studies have identified such “partially observable” task states in the medial OFC (Schuck et al., 2016; Bradfield et al., 2015; Wimmer et al., 2019; Tan et al., 2025), in line with the region identified here (but see e.g., Öngur & Price, 2000, for important anatomical distinctions between medial and lateral OFC and Tan et al., 2025, for an example of related functions in lateral OFC).”

      (3b) Though the main clusters visible in Figure 6 are the occipital and OFC clusters, there appear to be others. Did other clusters indeed rise to statistical significance in the whole-brain analysis? If so, is there a reason they aren't included or discussed? 

      All clusters visible in Figure 6C survived FDR correction. However, we refrained from interpreting these other clusters, because we had no prior hypotheses about them like we did for the OFC.

      (3c) Why do you posit that the ventral striatum becomes less sensitive to RPE on the second trial over time? And why is the ventral striatum only sensitive to RPE in the low noise environment generally?

      We reasoned the ventral striatum should be more responsive to more positive reward prediction errors. While we further assumed this response could be modulated by both time and environment, we would like to emphasize that we had no specific hypotheses about the direction of this modulation. We now also make this clearer in the manuscript. This being said, we believe both the pattern that its responsiveness to the second trial decreases over time, and the pattern that it was most sensitive to the low noise environment, can be considered fitting with its broader involvement in coding behaviorally relevant reward prediction errors. Namely: 

      First, we believe that as the participants learn more about the global reward structure of the task, they should obtain a better understanding of the fact that, per round, all crabs always center around a fixed mean. Therefore, the first RPE is most behaviorally relevant, and every later RPE has an exponentially decreasing relevance. As participants obtain more experience with this aspect of the task over time, the VS should show a lower responsiveness to the second RPE over time.

      Second, as participants learn more about the local differences between the three different environments, they should learn that especially in the low noise environment, RPEs are most behaviorally informative. That is, in this environment it makes most sense to have a high learning rate and thus let the RPEs substantially inform the placement of the cage on the next trial. Accordingly, participants showed that the ventral striatum was most responsive to RPEs in these environments.

      (4) Methods

      (4a) This section could generally benefit from some proofreading. 

      We now proofread the method section. 

      (4b) The main results text states that 49 participants performed Experiment 1, while the methods section reports 50 participants. Which is correct? 

      (4c) Following this, on page 8, statistical results are reported with a df = 49 (which would be appropriate only if n=50). 

      The correct sample size was actually 50, we adjusted the text and degrees of freedom where incorrect accordingly (note: only text is in track changes, but degrees of freedom were also changed accordingly). 

      (4d) Additionally, I am a bit surprised by the Experiment 1 findings that learning rates on the second trial were significantly different between low and high noise conditions, in that the effect size found using all trials was stronger than both the first half of trials (no significant effect) and the second half (significant but weaker than all trials). Are these all the same type of statistical test? Double-checking the statistics might be worthwhile. 

      It is not the effect size that is larger across the full experiment, but the t-statistic. This is possible because a t-statistic depends on both effect size and noise estimate, and the latter is smaller with more data. 

      (4e) The methods and results both state that the five crabs always emerged from one position in the sand. How were the locations of the crabs selected relative to this position? Looking at Figure 1C, it looks like the crabs spread out unevenly, and that the single position they emerge from is not necessarily at the center of the crab locations. 

      The crabs did indeed spread out evenly. However, we can see how the graphic in Figure 1C can be confusing, as two crabs are shown to be caught, which breaks the symmetry of the dispersion (because some crabs can run away after the even spreading phase, see Methods). We emphasized the even spreading more clearly in the new version of the paper. We think the flow of events will be much clearer with our newly added animation (Video 1).

      (4f) The methods section states that the crabs "spread out to cover the same proportion of the screen width as the cage (18.75%)" (page 23). The corresponding visual in Figure 1C appears to show something different. 

      This looks different because the graphic illustrates the last 500 msec, where crabs can run away (see also response to 4e, and the novel animation that was added).

      (4g) Information on the timing of the trials would be useful to include in Figure 1C or similar. 

      The reader can find this information in the Methods section. We chose not to include it in the caption to avoid information overload.

      (4h) The methods section specifies that there was a 3-7s ITI after the first and second trials of each block. How was the ITI selected for each trial? Were there ITIs between the other trials? If so, what were they? 

      The ITIs were selected from a truncated exponential distribution. This selection was not random, but rather a distribution was carefully constructed for each environment (and event of interest: boat presentation, first trial of each block, second trial of each block) separately to ensure that enough longer ITIs were selected for each environment (and event of interest). Of course, the order in which the ITIs were used across blocks, was random. The same approach was used to determine the duration of the presentation of the boat at the start of each block. There were no ITIs after later trials.

      (4i) Please provide a link to the data and analysis materials on OSF in the text. 

      We now provide a link to the data and analysis materials in our methods section.

      (4j) In the methods section, there are some references to information provided "below" (page 26: "The two approaches resulted in different posterior densities (see below) for estimate uncertainties, but in similar posterior densities (see below) for learning rates..."). Where in the paper is this referencing? 

      We indeed did not detail this further as we considered it not further relevant to our main study, and now removed the references to “below”.

      (4k) The methods section specifies using uniform priors between the lower and upper bounds of the relevant parameters. This seems likely to be 0 and 1, but should be listed explicitly. 

      Thank you for noticing. We now added this to our manuscript.

      (4l) For parameter recovery, correlations are provided to indicate effective recovery. These correlations are indeed high and suggest excellent recovery, but correlations wouldn't reveal if there was systematic over- or underestimation occurring. It might be useful to provide some visualizations of the parameters and their estimates to speak to this potential issue. 

      We now visualize the parameter recovery results in Author response image 2, which show that, indeed, there was a slight underestimation of the decay rates, but not the learning rates. Importantly, our main analyses and results all pertain to the learning rates, and we never made hypotheses or conclusions about the decay rates.

      Author response image 2.

      (4m) The methods section ends with a reference to a reward localizer (page 32). This localizer doesn't appear to be mentioned/used elsewhere. 

      Indeed. We implemented the localizer because we wanted to independently identify reward processing areas. However, this localizer did not succeed in localizing a reward area (no significant results), possibly due to the fact that (1) it was performed by the end of the experiment when participants may have been fatigued, and (2) there was no learning component in this localizer task. For these reasons, we did not use it after all.

      (5) Analysis: 

      (5a) Did you consider fitting a Bai model that only allowed for environment-specific initial learning rates (with a non-environment-specific decay rate)? Given that the data (e.g., Figure 2, Figure 4) seems to support differences in initial learning rate but not necessarily a difference in the rate of change, it might be worthwhile to see whether a model like that fits best. 

      We now fitted this extra model, which we called the semi-environment-specific Bai model. See Author response tables 1 and 2 for result in experiments 1 and 2, respectively) for the results. This new model has the best (in Experiment 2) and second-to-best (in Experiment 1) LOOIC. In a way, this is not surprising, because the model formulation is entirely based on the data. We think that we can draw the same substantive conclusions with or without this extra model, so for simplicity we did not include this new model in the paper itself.

      Author response table 1.

      Note. Models are ranked in descending order according to how well they fit the data. LOOIC refers to a model’s approximated expected log pointwise predictive density. Higher values indicate higher out-of-sample predictive fit. SE refers to the standard error of a model’s LOOIC. ∆LOOIC refers to the difference between a model’s LOOIC and the top ranked model’s LOOIC. ∆SE refers to the standard error of the difference between a model’s LOOIC and the top ranked model’s LOOIC.

      Author response table 2.

      Note. Models are ranked in descending order according to how well they fit the data. LOOIC refers to a model’s approximated expected log pointwise predictive density. Higher values indicate higher out-of-sample predictive fit. SE refers to the standard error of a model’s LOOIC. ∆LOOIC refers to the difference between a model’s LOOIC and the top ranked model’s LOOIC. ∆SE refers to the standard error of the difference between a model’s LOOIC and the top ranked model’s LOOIC.

      (5b) If part of the goal is to investigate whether there is a distinct local change in LR between conditions (dependent on prediction errors), then there might be more direct ways of doing so as a complement to the modeling approach. One potential way could be to visualize the LR or change in LR as a function of PE. 

      We agree that it’s beneficial to use a direct (model-free) approach to represent learning rate as a function of condition; that is also part of our approach. For example, see Figures 2, 4, which shows learning rate as a function of condition, but in a model-free manner. We think learning rate as a function of prediction error is less informative, because the idea is that prediction error can (in Kalman-filter terminology) be indicative of either noise variance or process variance, and participants are able to distinguish between them. This is also why we constructed the conditions in such a way that on the very first trial, prediction errors were on average the same across conditions. The fact that participants did respond appropriately to prediction errors on the very first trial (i.e., larger updates or learning rates in the low noise condition), suggested they are able to assign the prediction error to process variance (in the low noise condition) versus noise variance (in the high noise condition).

      (5c) In addition to looking at the evolution of LR across trials within a block separated by task epoch (i.e., Figure 2C-D & Figure 4C-F), the structure of the task would lend itself very nicely to visualizing the evolution of the second trial LR on its own across instances. This could provide additional insight into the meta-learning process.

      We thank the reviewer for this interesting suggestion, which was also raised by Reviewer 1. We now calculated the learning rate in a sliding window of 20 trials (i.e., trial x to x + 19), and provide revised figures for each experiment separately (Fig. 2 and 4, respectively).

      (6) The environment-specific Bai model appeared to become less good at capturing participant behavior with increased environmental noise. Why do you think this is?

      We thank the reviewer for raising this point. In this environment, individual outcomes are considerably less indicative of the latent mean, which may reduce the usefulness of the trial-by-trial, prediction-error–driven learning-rate adjustments that we see in the other environments. Under such extreme conditions of variability, people may rely less on delta-rule updating and more on alternative strategies (D'Acremont & Bossaerts, 2016; Reynders et al., 2026), such as exploratory adjustments or heuristics that are not explicitly captured by the Bai model but also outside the scope of the present paper.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Demeshkina and Ferré-D'Amaré showed that extrachromosomal circular DNA (eccDNA) and chromatin-associated proteins are present in stress granules, based on proteomic and sequencing analyses. Using HCR-FISH combined with imaging, the authors showed the colocalization of eccDNA with stress granule proteins. Furthermore, they found that CRISPR machinery targeting the eccDNA component of stress granules disrupts stress granule assembly, and that this effect is largely independent of Cas9 endonuclease activity. Notably, expression of cytoplasmic chromatin factors restores stress granule formation in the presence of CRISPR machinery in yeasts. This also rescues the growth defect caused by hypoxic stress, which correlates with impaired stress granule formation. Together, this manuscript provides insight into the presence of eccDNA in cytoplasmic membraneless organelles, specifically stress granules, and suggests a functional role for eccDNA within these structures under stress conditions.

      Strengths:

      The authors used a panel of ribonucleases to demonstrate that stress granule cores isolated from yeast and HEK293 cells are resistant to plasmid-safe DNase, an enzyme that does not degrade circular double-stranded DNA. To further support the presence of extrachromosomal circular DNA (eccDNA) in stress granules, they performed Circle-Seq on stress granule cores. The gel electrophoresis and sequencing experiments complement each other well, providing consistent evidence for eccDNA within these granules. Overall, this study provides insight into potential cytoplasmic roles for eccDNA, an area that remains largely unexplored.

      Weaknesses:

      (1) Figure 1F suggests that stress granule cores are susceptible to DNase I but not to plasmid-safe DNase (psDNase). However, its smearing pattern in the psDNase condition appears similar to that in the DNase I treatment shown in Figure 1E, although psDNase produces more discrete bands. The authors should comment on these differences between Figures 1E and 1F, or consider revising Figure 1F to improve consistency with Figures 1E and 1D.

      We suggest that the appropriate comparisons are between the DNase I and psDNase treatments within each figure panel, and not between panels (e.g., Figures 1E vs. 1F). The electrophoretic gels in the different panels were run for different lengths of time, and therefore the comparison between gels would be spurious. In Figure 1E, electrophoresis after DNase I treatment results in a characteristic smear, while after psDNase treatment yields discrete bands (lanes 2–3 vs. 4–5). Electrophoretic conditions for this figure were optimized to minimize diffusion and allow quantitative evaluation. The electrophoresis shown in Figure 1F, which compares yeast and mammalian stress granule core nucleic acids, was run for a longer period — as evidenced by the greater migration distance from the loading wells — yet still clearly shows the same qualitative difference between DNase I (smear, lane 3) and psDNase (discrete bands, lanes 1–2) treatments for the yeast samples. The apparent discrepancy noted by the referee therefore simply reflects the difference in electrophoretic conditions between the gels shown in the two separate figure panels.

      (2) The authors should clearly define "colocalization". Does it refer to complete spatial overlap between two signals (i.e., VCP and T30), or partial overlap (i.e., AHNAK DNA and G3BP)? Figure 3 and the associated text are descriptive. Quantitative analysis would strengthen the conclusions. For example, the authors could analyze the fraction of molecules localized to stress granules or provide Pearson's correlation coefficient or similar measurements.

      In our considered opinion, categorizing colocalization as either "partial" or "complete" implies a level of molecular precision that is physically unattainable at the resolution limits of any current light microscopy modality, and would therefore be misleading. Our approach employs super-resolution confocal laser scanning microscopy (Airyscan) with hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) or with immunofluorescence. The detection method used offers higher spatial resolution and signal-to-noise ratio than single-point detector/physical pinhole confocal (or widefield epifluorescence) microscopy used in most prior stress granule studies. Despite these enhancements, the system retains inherent diffraction-imposed limits: a lateral (XY) resolution of ~130 nm and an axial (Z) resolution of ~350–400 nm, defining the minimum separable distance between two fluorescent signals. Structures smaller than these thresholds remain unresolved within a single point spread function (PSF) maximum – a volume sufficiently large to simultaneously accommodate multiple stress granule cores or tens of thousands of individual proteins (such as G3BP) and dozens of nucleic acid molecules several thousand nucleotides in length. Consequently, any detected fluorescence signal may represent the superimposition of a large and indeterminate number of individual molecules or particles. True molecular interaction analysis remains for future studies using technologies with angstrom resolution (e.g., cryo-electron tomography, cryo-EM, X-ray crystallography, smFRET, EPR, NMR, etc.). Metrics such as Pearson's correlation coefficient report solely on the degree of signal overlap at the PSF scale (hundreds of nanometers) and would not provide any insight beyond what is already conveyed by our data.

      (3) The authors used a CRISPR-based approach to target the Ty1 LTR retrotransposon, an abundant stress granule eccDNA, and they observed a loss of stress granule formation. However, this phenotype may be specific to Ty1 eccDNA rather than representative of all eccDNA species present in granules. In particular, the title "Cytoplasmic circular DNA is a key constituent of stress granules" implies a broader role. To support this claim, the authors should consider approaches that more globally deplete eccDNA rather than targeting a single eccDNA.

      We respectfully disagree with the referee that further depletion of eccDNA would alter our conclusions. A central finding of our study is that stress granules can be abrogated cytoplasmically by co-expressing a Cas9 endonuclease, active or inactivated by point mutations (D10A /H840A), and a gRNA (which is itself a fusion of the crRNA and trcrRNA, natively separate RNAs in the source bacterium). We show in Figure 4 that when the gRNA targets the Ty1 sequences, endonucleolytically active holoenzyme co-expression in the cytoplasm results in loss of the corresponding eccDNAs, as assayed by sequencing of the relevant cytoplasmic fractions. Critically, when a catalytically inactive Cas9 protein (dCas9) is co-expressed with the gRNA instead of the wild-type endonuclease, depletion of the eccDNAs containing Ty1 sequences no longer takes place (Figures 4D and 4E), but stress granule formation is still abrogated (Figure 4C).

      In our manuscript, we indicated (as "data not shown”) that co-expression with Cas9 of a gRNA "targeting" a sequence that is absent from the S. cerevisiae genome still results in abrogation of stress granule formation. These data are shown in Author response image 1. The gRNA is targeted to the sequence 5’-agaatcgatgcattt, which is absent in the genome of the yeast strain used.

      Author response image 1.

      It follows from our experiments that stress granule abrogation (1) is not a result of the catalytically active Cas9 endonuclease; (2) is not a result of the presence of a gRNA-directed but catalytically inactive Cas9 holoenzyme, but (3) is the result of the presence of a CRISPR holoenzyme (as defined above) in the cytoplasm.

      To reiterate, abrogation of stress granules occurs when a Cas9-gRNA complex is present in the cytoplasm, regardless of whether the nuclease activity exists, or the gRNA targets a sequence that is present in the genome. Importantly, the holoenzyme is required for this phenomenon: presence of the endonuclease or the gRNA alone does not abrogate stress granule formation (Figures S5).

      It is because of this unexpected observation that we next hypothesized that activities of the Cas9-gRNA complex other than sequence-specific gRNA-targeted endonucleolytic activity is driving the suppression of stress granule formation. The best documented such activity is DNA sequence sampling (1-dimensional diffusion). We think that 1-dimensional diffusion of the Cas9-gRNA holoenzyme is displacing from the cytoplasmic eccDNA interactors whose association with the DNA is required to drive stress granule assembly. The fact that the stress-granule suppressive effect of cytoplasmic Cas9-gRNA expression can itself be suppressed by two completely unrelated proteins whose only shared feature is action on chromatin (CHD1 and GCN5) strongly supports this hypothesis (Figures 4G, 4H and S6; also response to point 4, below), in addition to confirming that cytoplasmic eccDNA is packaged by histones in a conformation that CHD1 and GCN5 can both recognize.

      (4) The authors should provide additional experimental evidence to support the claim that eccDNA is packaged in a chromatin-like state. The rescue of stress granule formation by ectopic expression of modified chromatin-associated proteins (CHD1NES and GCN5NES) following CRISPR treatment does not necessarily demonstrate that eccDNA is packaged like chromatin under basal conditions.

      We would like to reiterate the temporal order in our experimental design (detailed in full in Methods and summarized in Results). Cas9<sub>NES</sub>-gRNA and CHD1<sub>NES</sub> (or GCN5<sub>NES</sub>) were expressed simultaneously (not sequentially) in the cytoplasm. This was intentional, so as to give each player ample opportunity to engage its preferred substrate under non-stress conditions, prior to the brief oxidative stress. The referee appears to believe that cytoplasmic eccDNA was pre-exposed to Cas9<sub>NES</sub>-gRNA, and then the bound endonuclease challenged with chromatin-modifying enzymes.

      Our experimental design accounts for the contrasting substrate specificities of CRISPR and chromatin-modifying enzymes. Cas9-gRNA (holoenzyme) binds to nucleosome-free DNA with sub-nanomolar dissociation constant (Kd 0.1–1 nM) but its association with chromatinized DNA is impeded 5- to 100-fold (Isaac et al., 2016; Yarrington et al., 2018; Strohkendl et al., 2021). In contrast, whereas CHD1 binding to DNA is strictly nucleosome-dependent — its chromodomains actively block engagement with protein-free DNA (Hauk et al., 2010), and its productive binding (Kd 10–200 nM) relies on obligate multivalent contacts with the histone octamer, H4 tail, and wrapped DNA (Farnung et al., 2017; Sundaramoorthy et al., 2018).

      Our observation that stress granule formation was unperturbed following oxidative stress is most parsimoniously interpreted as CHD1<sub>NES</sub> outcompeting the CRISPR machinery for cytoplasmic binding to eccDNA by virtue of the latter existing in a histone-bound state that is recognized as chromatin by CHD1 –simultaneously favoring CHD1<sub>NES</sub> engagement and impeding Cas9 access. Thus, our experiment in effect employs stress granule formation as a readout for differential binding to chromatin or chromatin-like eccDNA.

      Farnung, L., Vos, S.M., Wigge, C., and Cramer, P. (2017). Nucleosome-Chd1 structure and implications for chromatin remodelling. Nature, 550(7677), 539–542.

      Hauk, G., McKnight, J.N., Nodelman, I.M., and Bharat, T.A.M. (2010). The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol Cell, 39(5), 711–723.

      Isaac, R.S., Jiang, F., Doudna, J.A., Lim, W.A., Narlikar, G.J., and Bhatt, D.L. (2016). Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. Nature Struct Mol Biol, 23(12), 1097–1103.

      Strohkendl, I., Saifuddin, F.A., Gibson, B.A., Bhatt, D.L., Russell, R., and Bharat, T.A.M. (2021). Inhibition of CRISPR-Cas9 by bacteriophage-encoded proteins. Mol Cell, 81(8), 1665–1679.

      Sundaramoorthy, R., Hughes, A.L., Singh, V., Wiechens, N., Ryan, D.P., El-Mkami, H., Petoukhov, M., Svergun, D.I., Treutlein, B., Sproll, P., and Owen-Hughes, T. (2018). Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. eLife, 7, e35720.

      Yarrington, R.M., Verma, S., Schwartz, S., Trautman, J.K., and Carroll, D. (2018). Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo.PNAS, 115(38), 9450–9455.

      Reviewer #2 (Public review):

      Summary:

      The authors report the presence of extrachromosomal circular DNAs (eccDNAs) within the core of stress granules purified from both yeast and mammalian cells.

      Strengths:

      This study is important for understanding the molecular mechanisms underlying stress granules containing eccDNAs and is likely to have a major impact on future research. A major strength of the study is the extensive experimental validation performed in yeast cells. In particular, cytoplasmic CRISPR-mediated targeting of eccDNAs suppresses stress granule formation and impairs recovery from hypoxic stress in yeast cells.

      Weaknesses:

      The conclusions would be further strengthened by validating the functional findings in an additional model system, such as mammalian cells.

      Comments:

      (1) Section: "Stress granule cores contain eccDNA"

      (a) The presence of eccDNAs would be more convincingly demonstrated using an orthogonal validation approach, such as DNA FISH targeting MYC and Centromere 8 (CEN8) on metaphase spreads from HEK293T cells (as performed in PMID: 34819668).

      The relationship between eccDNA dynamics and stress granule assembly across distinct cell cycle phases remains an important and poorly explored question. To our knowledge, no published data currently describe how stress response mechanisms are regulated during mitotic division, particularly in metaphase. Our identification of eccDNA as a component of stress granule cores can provide a first tractable framework to investigate this relationship. However, a systematic and in-depth characterization of this phenomenon warrants a dedicated future investigation.

      (b) The study would also benefit from assessing the presence of eccDNAs in the extracellular medium. For example, DNA could be extracted from conditioned media and analyzed by PCR using primers spanning eccDNA breakpoint junctions (as performed in PMID: 40074906; PMID: 36123406).

      We agree with the referee that eccDNA biology represents a fascinating and rapidly evolving area of research, particularly given the emerging role of eccDNA in oncogenesis. In this context, our identification of eccDNA as a core structural component of stress granules opens a novel avenue for exploring the connection between stress-dependent translational regulation and disease-associated eccDNA dynamics. While we acknowledge the importance of this direction, a rigorous investigation of this relationship requires extensive multifaceted experimentation that falls beyond the scope of the current study.

      (2) Section: "eccDNA-CRISPR abrogates stress granules"

      These findings should be further validated under additional stress conditions, such as drug-induced stress (like methotrexate) or nutrient deprivation in the cell medium. In addition, the same set of experiments should be performed in HEK293T cells to support the broader relevance of the observations.

      We agree with the referee that the composition and dynamics of stress granules arising from different stressors is an important endeavor. However, given the range of stressors documented to result in stress granule formation, those studies fall well beyond the scope of this manuscript. We will note however that the presence of eccDNA in stress granules of yeast and human cells is strong evidence for conservation of function(s). We think that exploration of the role of eccDNA in stress granule formation across the kingdoms of life (stress granules were first observed in heat-shocked tomato plants), cell cycle stages, stressors, etc. will be important research programs for the future.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Figures 3D and 3I: The use of magenta and red makes it difficult to distinguish between the two labeled signals. Consider using more contrasting colors to improve visual clarity.

      We appreciate the comment regarding color choices in the figures. In our view, magenta and red are sufficiently distinguishable as nucleic acid labels, particularly when combined with the green signal representing G3BP in these panels.

      (2) Figures 3F and 3G: Do the authors have an explanation for why AHNAK or MAPT DNA (white) does not colocalize with the anti-DNA immunofluorescence signal?

      Immunofluorescence (IF) is standard for detecting protein antigens but has limitations when the target is a non-protein molecule such as DNA, owing to its compacted chromatinized state. Anti-DNA antibodies can miss a significant fraction of their targets because the DNA backbone remains largely inaccessible, a limitation that DNA-FISH overcomes by directly hybridizing probes to denatured DNA sequences with high specificity. The fixation step required for both IF and FISH imaging can introduce additional steric barriers that disproportionately restrict antibody access compared to small nucleic acid probes. Even under optimized conditions, the IF signal with anti-DNA antibodies is inherently reflective of a subset of the total cellular DNA content.

      (3) Adding a subtitle on page 12 ("The abundant histones in purified stress granule...") would improve the overall structure and readability of the manuscript.

      We think that an additional subtitle would not substantially improve the readability of what is, admittedly, a very dense manuscript that employs a diversity of experimental approaches.

      (4) It would strengthen the analysis if statistical significance were included for the different time points in Figure 5C.

      We appreciate the reviewer’s suggestion. Figure 5C shows the largest difference at 40–45 hours after stress recovery, which is statistically significant between Cas9NES-gRNA (or dCas9NES-gRNA) and Cas9NES or gRNA only (two-tailed Student’s t-test, *, p ≤ 0.05). All primary experimental data are publicly available (FigShare) so further analyses can be performed by interested future parties.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      RESPONSE TO REVIEWERS

      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      Summary:

      This is an interesting and ambitious study by Tabilo-Agurto and co-workers. It combines deep learning structure prediction (AlphaFold2), targeted molecular dynamics simulations, and in vivo functional assays to probe structural, functional, and evolutionary aspects of the metamorphic protein RfaH. More broadly, the work addresses an important question: whether intermediate structural states may exist along evolutionary trajectories of metamorphic proteins. A particular strength of the study is the integration of computational and experimental approaches. The manuscript is generally well written and clearly organized.

      Major comments:

      A key aspect of the study is the classification of predicted structures into three classes based on the conformation of the C-terminal domain (CTD): the autoinhibited alpha-helical fold, a beta-barrel fold, and a mixed alpha/beta fold. These classes are further described as corresponding to metamorphic (alpha fold), mixed alpha/beta, and monomorphic (beta fold) proteins.

      While I can see how this organizational scheme is helpful in some respects, it may also overstate what can be concluded from the data. As the authors are well aware, AlphaFold2 tends to predict a single conformation even for genuine metamorphic proteins, and therefore does not, on its own, distinguish between monomorphic and fold-switching proteins. I note in particular that the functional data indicates that the "monomorphic" variants studied in the in vivo assays behave similarly to the RfaH E48A mutant. However, E48A is known to remain metamorphic, populating both alpha and beta folds with roughly equal probability. This suggests that the sequences in this class may retain some degree of fold-switching capability, even if the underlying regulatory mechanism differs from that of wild-type RfaH. In other words, the presented data does not fully support these sequences as monomorphic. I am not suggesting that the authors must revise their classification scheme. However, it may strengthen the manuscript if the authors explicitly acknowledge this alternative interpretation and moderate the corresponding claims.

      We appreciate the comment from the reviewer, which can be seen from two different perspectives.

      On the one hand, it might be reasonable to think that the ‘monomorphic’ RfaH orthologs have lower transcription elongation activity than E. coli RfaH. Other highly divergent orthologs of E. coli RfaH (Salmonella enterica serovar Typhimurium, Klebsiella pneumoniae, Yersinia enterocolitica and Vibrio cholerae) have similar in vitro recruitment and pausing at the C45 nucleotide from the ops element, as well as restoring the RfaH-dependent hemolytic activity of E. coli in a strain that lacks chromosomal RfaH to levels similar to the wild-type strain (doi: 10.1128/jb.186.9.2829-2840.2004). However, V. cholerae RfaH (43% sequence identity to E. coli RfaH) exhibits diminished antitermination effects in in vitro transcription assays, better resembling the antitermination levels in the absence of RfaH (doi: 10.1128/jb.186.9.2829-2840.2004), despite this protein also being predicted in the alpha-folded state when using AF2 (10.1016/j.csbj.2022.10.024). A particular observation from the RfaH complementation work is that increasing the concentration of V. cholerae in in vitro transcription assays lessens the transcription elongation effects observed when using concentrations similar to E. coli RfaH. These transcription elongation defects can be extrapolated to potentially similar issues with transcription in vivo and, therefore, luciferase translation in our in vivo translation assays for our ‘monomorphic’ proteins.

      On the other hand, it is possible that these so-called ‘monomorphic proteins’ still populate the alpha-folded state, but that their predominant fold in solution is the one corresponding to the active beta-fold. This can be biophysically tested using circular dichroism to distinguish their alpha or beta propensity, as proposed in a remarkable work from Porter et al (10.1038/s41467-022-31532-9).

      In both cases, quantification of the protein titers obtained after attempts of protein purification of the ‘monomorphic’ RfaH orthologs would be required. In this way, we can ascertain whether the differences in activity are due to differences in expression levels and determine if sufficient amounts of stable and well-folded protein can be obtained for these RfaH orthologs, followed by measuring their circular dichroism spectra to ascertain their secondary structure propensity.

      Our current attempts are to recombinantly express these proteins for determining their protein titers and solubility in the supernatant, which will enable us to indirectly ascertain their expression levels, and test those solubly expressed proteins biophysically using circular dichroism experiments. If the circular dichroism experiments prove to be unsuccessful due to problems with the solubility of the purified proteins, we strongly believe that the aforementioned discussion should be included in the manuscript to take into account the limitations of the methods utilized in our work.

      Therefore, we will add the following paragraph in the discussion, while we work on ascertaining the feasibility of the circular dichroism assays:

      “It is worth noting that, in the absence of RBS (Figure 5C-F), the putative monomorphic RfaH orthologs have similar or lower in vivo activity than the E. coli RfaH E48A mutant; a similar mutant (E48S) exhibits a 1:1 equilibrium between the autoinhibited and active states (Burmann et al, 2012). This observation can be partly explained by two factors. First, sequence divergence and expression levels may limit functional compatibility with the host machinery. Highly divergent V. cholerae RfaH ortholog, which shares only 43% sequence identity with E. coli RfaH but is predicted to fold into the autoinhibited state (Artsimovitch & Ramírez-Sarmiento, 2022), maintains both ops-dependent recruitment and hemolysin secretion in the ∆rfaH E. coli strain, yet exhibits transcription elongation defects in vitro, requiring a 5-fold higher concentration than E. coli RfaH to match increased elongation rates of E. coli RNAP (Carter et al, 2004). Low in vivo protein titers or structural mismatches between the monomorphic orthologs and E. coli RNAP may prevent higher luciferase expression relative to the E48A mutant. This limitation is supported by the fact that IPTG-induced overexpression rescues activity when an RBS is present (Figure 5B). Second, these proteins may be predominantly folded in the active state while still transiently populating the autoinhibited state. Confirming this conformational equilibrium would require overexpression and purification of these proteins followed by biophysical assays, such as circular dichroism (Porter et al, 2022).”

      Reviewer #1 (Significance (Required)):

      An intriguing, but speculative, aspect of the study is the finding that some sequences are predicted to adopt a CTD with mixed alpha/beta secondary structure, and that such structures also appear in targeted molecular dynamics simulations. If this idea holds up, it could represent an intermediate along the evolutionary pathway between the alpha-helical and beta-barrel folds of RfaH. Although the evidence is only computational, it is a compelling idea and it would benefit from further investigation.

      It is indeed very compelling, and this is something that we should immediately address in a revised version of our manuscript. We somehow missed an article published in 2025, regarding the study of the structural interconversion of the isolated CTD using NMR, finding at least three intermediate states along the fold-switching pathway of RfaH (doi: 10.1073/pnas.2506441122). One of such intermediate states observed, which is also one of the highest populated ones (~23%), corresponds to an ensemble of largely unfolded structures that include the formation of transient alpha-helix a5 (corresponding to helix a2 in our article) and beta-hairpin (b1/b2) secondary structure elements, which fold to form a compact ensemble of structures in which the beta-hairpin lies on top of the alpha-helix. This is fully consistent with our predictions of a mixed alpha/beta state in full-length.

      We will add this external experimental validation of the mixed alpha/beta secondary structure of the CTD of RfaH in the discussion of our final manuscript:

      “Interestingly, a recent nuclear magnetic resonance spectroscopy study of the E. coli RfaH CTD, aimed to uncover transient states potentially en route of the αCTD interconversion (Cai et al, 2025), described an intermediate state (populated in ~23% of the captured ensembles) in which a β-hairpin formed by β-strands β1-β2 lies on top of a transient α-helix α5 that corresponds to helix α2 in our article. This finding is fully consistent with the mixed α/β CTD structures found both in our TMD simulations and our AF2 predictions of divergent RfaH orthologs.”

      In summary, the work is a valuable contribution to the field of protein fold switching. The combination of computational tools with experimental validation makes it interesting and the results should be of broad interest. The manuscript should be well positioned for publication in a high-impact journal.

      We are very thankful for the reviewer’s comments on our manuscript.

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      Summary:

      In their paper "Exploration of the structural and functional diversity in the metamorphic RfaH subfamily," Tabilo-Agurto et al. use AlphaFold2 to predict the structures of ~3,900 RfaH homologs, sort the predicted C-terminal domains into α-helical (autoinhibited), β-barrel (NusG-like), and mixed α/β topologies, and find that about 14% of homologs come out predominantly in the β-barrel state. They then take nine representative homologs and run them through a heterologous *E. coli* DH5α Δ*rfaH* reporter assay. The putative monomorphic candidates behave a lot like the constitutively active E48A variant - active across every ops context and even without an RBS - while the mixed α/β candidates barely show activity. Targeted MD simulations of *E. coli* RfaH, run through AF2Rank, also pulls out the mixed α/β state as its own distinct cluster, hinting that it sits somewhere along the fold-switching transition path.

      This is a genuinely interesting piece of work that pulls together structure prediction, in vivo activity, and genomic context to make a concrete case for extant monomorphic βRfaH proteins - a long-hypothesized but until now unseen intermediate in the proposed stepwise evolution of RfaH from NusG. The experimental design is thoughtful, especially the five-construct ops/RBS matrix, and comparing the monomorphic candidates against the E48A benchmark is a nice touch as a positive control. Overall, I think the paper deserves to be published, but a few things would need shoring up before acceptance.

      Major comments:

      1. The paper would be a lot stronger with at least one biophysical measurement (a CD spectrum, say) on a purified monomorphic candidate. I get that this might be outside the planned scope, but even a single CD trace showing β-rich content for an isolated full-length protein would move the claim from "putative" to "demonstrated."

      We agree with the comment from the reviewer, and as such we are currently attempting to recombinantly express these proteins for determining first their solubility after purification (which will largely determine our ability to characterize them by circular dichroism) and then follow up with circular dichroism experiments if the solubility and protein concentration of these ‘monomorphic’ homologs is sufficient to pursue these experiments. In case this is unfeasible, we will include the solubility analysis in our revised version of the article, as well as a discussion on this topic – and also on the topic of why the activity of the ‘monomorphic’ proteins resembles the E48A mutant of E. coli RfaH that co-exists between two folds – as indicated in our response to the major comment from reviewer #1.

      1. Only nine homologs were tested - three per category. The conclusions about monomorphic behavior generalizing across the whole βRfaH clade are basically resting on three proteins. Bringing in even one or two phylogenetically distant βRfaH candidates would help guard against the possibility that what they're seeing is just a genus-specific quirk. If new experiments aren't on the table, the limitation should at least be called out explicitly in the Discussion.

      We agree with the reviewer that drawing conclusions from a single clade of RfaH could raise concerns about bias, although we must note that the tested putative monomorphic candidates were selected before a phylogenetic tree was constructed. What we propose is to perform a phylogenetic analysis for the InterPro sequences and look at their genomic neighborhood as well, replicating what was done in the manuscript for the Genomic Cluster group. We hope this would provide more compelling evidence that the predictions, phylogeny and gene organization of these extant monomorphic RfaH is distinct from those metamorphic.

      1. The classification thresholds (α > 32.5% / β 30.0% / α

      Thanks to the reviewer for raising this concern. We will perform a sensitivity analysis by slightly nudging the cutoffs by ±5% as recommended by the reviewer and indeed we see minimal changes in the number of structures in each class. We have added a small paragraph indicating this sensitivity test:

      “To determine that these values were adequate for our analysis, we performed a sensitivity test by changing the thresholds by ±5% over the data for all structures predicted from all databases, showing that the predictions of RfaH orthologs with monomorphic CTD and mixed secondary structure in their CTD is robust, and only metamorphic RfaH orthologs were reduced with an increase in uncategorized structures (Supplementary Figure S13)”

      1. The Discussion notes that uncontrolled, ops-independent RfaH recruitment could be lethal, since RfaH outcompetes the much more abundant NusG. But if monomorphic RfaH proteins really are extant and stably maintained in these genomes, there has to be something keeping them from interfering with NusG's essential functions - maybe very low expression, restricted induction, or compensating differences in NusG affinity. The paper would benefit from tackling this directly, even speculatively.

      We agree with the reviewer in this point, and after careful consideration we believe that we did not emphasize this point appropriately in the manuscript. In fact, we included Figure 7 to state our perspective on how RfaH may have evolved but we did not emphasize how this perspective stems from a previous work that we thoroughly discussed in the introduction (doi: 10.1038/emboj.2008.268) and that explicitly states that low solubility of the dissociated NTD and CTD could be a factor imposing this restricted action in cis operons. We have included this in our revised version of the manuscript as follows:

      “Our findings are in line with the previous hypothesis regarding the emergence of RfaH within the universally conserved family of NusG transcription factors (Belogurov et al, 2009). Under that model, a gene duplication event produced an intermediate variant (NusG2 in Figure 7) that lost its Rho-binding capability and acquired a deletion in the NTD that reduced the protein's overall size and remodeled its hydrophobic profile. Crucially, this intermediate retained an exposed, hydrophobic RNAP-binding region, a feature shared by monomorphic RfaH and the ancestor of all RfaH orthologs (NusGSP in Figure 7). This increased hydrophobicity would have reduced solubility, restricting its regulatory activity to the site of synthesis, i.e. in cis. Indeed, when structural alignment is used to identify conserved NTD residues that bind to RNAP, orthologs contain more than 70% hydrophobic residues (Supplementary Figure S11) at those positions. This percentage is much closer to that of RfaH (80%) than NusG (57.14%). The protein only regains solubility and the ability to operate in trans when its CTD refolds into a helical conformation. Ultimately, our results strengthen this evolutionary model by demonstrating that several extant RfaH orthologs appear to resemble this insoluble, cis-acting ancestral state.”

      Minor comments:

      Table 1 should show percentages alongside the raw counts. 7/7 LPS-in-operon for monomorphic candidates is striking, but with n=10, the small denominator really deserves to be flagged.

      We agree with the reviewer in that the higher raw count of metamorphics may undersell the message the article conveys. We added the percentages next to raw counts in Table 1, regarding “Total” and “Next to operon” categories. We also modified the legend as follows:

      “A summary of genomic contexts of RfaH orthologs classified according to the AF2 predictions. The numbers indicate how many rfaH genes are next to an operon and whether the operon contains lipopolysaccharide biosynthesis genes, and the percentages next to them display the relation to the previous category, i.e, “Next to operon”/”Total” and “LPS in operon”/”Next to operon”.”

      In Figure 3, the sequence logo on top is informative - consider adding the number of sequences per dataset to the axis labels so readers can interpret the boxplot widths.

      We believe that this would be rather confusing for the readers, because it is counting all 5 structures predicted by AlphaFold2 for each sequence in each dataset that fit each classification, and thus the same sequence can lead to structures that are monomorphic, metamorphic of have mixed secondary structure in their CTD. Thus, the number of sequences per box plot will be higher than the number of sequences per dataset. For example, one sequence from InterPro can be present in more than one box plot, because different AlphaFold2 models can lead to the prediction of different states from the same sequence. We believe it is less confusing if it is presented as it is.

      There's some redundancy between the Results (pp. 14-17) and the Discussion that could probably be trimmed, particularly the recap of the ops/RBS construct logic.

      Thanks for the recommendation. We reduced this redundancy in the new version of the manuscript, mainly on page 16:

      “The orthologs classified as monomorphic, and thus expected to be constitutively active, exhibited activity across all tested ops contexts, including in the absence of RBS (Figure 5B-F). Notably, their activity levels were comparable to the ops-independent E. coli RfaH E48A mutant, in which the key salt bridge at the NTD:CTD interface is disrupted. All monomorphic orthologs were found to lack a few key residues that make contacts to ops DNA in RfaH, as well as the conserved residues in loop 2 that mediate contacts with Rho in NusG (Supplementary Figure 11). This mosaic architecture enables these orthologs to promote the expression of the long lux operon even when the RBS is absent. Our study provides the first indirect evidence of putative, constitutively active RfaH proteins, which are predicted to have monomorphic NusG-like fold, in other bacteria.”

      Reviewer #2 (Significance (Required)):

      If the central claim holds up, this is a meaningful contribution to the metamorphic-protein and bacterial-transcription literatures: it identifies what appear to be extant evolutionary "way-stations" in the NusG→RfaH transition, and it does so using a tractable computational pipeline that could be applied to other suspected fold-switch families. The work is timely given the ongoing discussion about how AF2 and its descendants handle conformational heterogeneity. With the strengthening suggested above - particularly any direct biophysical confirmation of a monomorphic candidate - I would expect this to be a well-cited paper in its niche.

      We are very thankful for the reviewer’s comments on our manuscript.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      Summary:

      The manuscript by Tabilo-Agurto et al. uses in silico and experimental methods to elucidate the diversity of the metamorphic RfaH protein family. Of particular note is the sophisticated usage of AlphaFold2 to reconstruct the evolutionary tree of RfaH as well as the in vivo luminescence assays to substantiate the different structural states of the RfaH-CTD. Overall this is a well-written manuscript providing deeper insight into the structural and functional diversity of RfaH proteins, potentially relevant for other metamorphic proteins as well.

      Minor comments:

      1. 3rd paragraph of the introduction: The sentence starting with "To date, ...and nuclear magnetic resonance of these ancestors.." seems incomplete as this reviewer believes the author´s wanted to say "..and structural characterization by nuclear magnetic resonance spectroscopy of these ancestors..."

      Thanks for the attention to these details, we will amend this paragraph appropriately.

      1. 4th paragraph of the introduction: "..., that binds Rho or the ribosome (Mooney et al. 2009b). Whereas this citation is correct for NusG-Rho interactions it does not indicate ribosome binding. The direct interaction of NusG with the ribosome was shown in Burmann et al. Science 2010 and this reference should be added here.

      Thanks for the recommendation, we will include both citations in this section of the manuscript.

      1. More a curiosity question, did the author also test for a subset of the RfaH variants the AlphaFold3 predictions and obtain similar or different results?

      Thanks for the comment. The reason we did not use AlphaFold3 predictions to check on the variability of the results is that there is much more known about the use of AlphaFold2 – and its limitations – regarding their use in the study of metamorphic proteins, whereas a deep understanding of the advantages and limitations of AlphaFold3 for studying metamorphic proteins is still under development.

      Referees cross-commenting:

      Overall there is an agreement among all reviewers that the present MS is an interesting and timely study. The point raised by reviewer 2 to add simple biophysical characterization, if feasible, would be clearly an excellent addition and likely make the MS stronger. In general all three reviewers mainly point to minor changes and additions to improve the MS in a rather short timeframe.

      We indeed agree with this comment, which is why we will commit to attempt the recombinant expression and protein purification of the RfaH orthologs and to perform circular dichroism assays if the solubility of the obtained proteins allows for such experiments to be done.

      Reviewer #3 (Significance (Required)):

      The present MS is an interesting large-scale usage of the AlphaFold2 algorithm to reconstruct the evolutionary tree of the specialized transcription elongation factor RfaH. Revealing a different degree of this evolution in a diverse set of bacterial strains indicating its evolutionary distance from the cognate NusG transcription elongation factor. Of particular note is the experimental verification of the obtained in silico finding by in vivo luminescence approaches.

      We are very thankful for the reviewer’s comments on our manuscript.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Manuscript number: RC-2026-03474

      Corresponding author(s): Priyanka, Verma

      [Please use this template only if the submitted manuscript should be considered by the affiliate journal as a full revision in response to the points raised by the reviewers.

      • *

      If you wish to submit a preliminary revision with a revision plan, please use our "Revision Plan" template. It is important to use the appropriate template to clearly inform the editors of your intentions.]

      1. General Statements [optional]

      Point-by-point rebuttal is presented below. Reviewer’s comments are in BLACK; author’s response is in BLUE and figure numbers corresponding to the manuscript are in RED.

      2. Point-by-point description of the revisions

      • *

      Reviewer #1 (Evidence, reproducibility and clarity (Required):

      ALC1 suppression has been shown to potentiate PARP inhibitor lethality in HR-deficient cells. Rather than revisiting the underlying mechanism, which has been characterized and remains an active area of investigation, this study aims to define the clinical contexts in which combined ALC1 and PARP inhibition may be beneficial. The clinical efficacy of PARP inhibitors, and their FDA approval, is largely restricted to HR-deficient tumors. This study dissects the combined effects of ALC1 and PARP suppression across a panel of HRD ovarian cancer cell lines, multiple classes of PARP inhibitor, and cells harboring distinct PARPi resistance mechanisms. In doing so, the authors delineate both the potential utility and the limitations of combined ALC1 and PARP inhibitor treatment in HRD ovarian cancers. The most impactful finding of the study, however, is likely the demonstration that ALC1 suppression sensitizes HR-proficient, CCNE1-amplified high-grade serous ovarian cancers to PARP inhibitors. These tumors are associated with particularly poor outcomes owing to the current absence of effective targeted therapies, making this observation of considerable clinical relevance.

      We thank the reviewer for appreciating the significance of our work in “HR-proficient, CCNE1-amplified high-grade serous ovarian cancers to PARP inhibitors” which is a critical unmet need.

      Of note, the study relies on genetic rather than pharmacological depletion of ALC1, a choice likely reflecting the current lack of a commercially available ALC1 inhibitor. While genetic suppression may not fully recapitulate the effects of combined drug treatment, it offers the advantage of not being tied to any specific compound, allowing the authors to establish more general principles. I have only a few comments.

      We are grateful to the reviewer for providing the unique perspective on our genetic study that “it offers the advantage of not being tied to any specific compound, allowing the authors to establish more general principles.”

      We have included this in our discussion to strengthen the study.

      The effect of ALC1 KO on PARPi sensitivity is less pronounced in OVSAHO cells (BRCA2-mutated) than in BRCA1-mutated cells. In these cells, it looks like there is an additive effect rather than synergy. 1- The authors should calculate, if possible, whether there is synergy or additive effect of ALC1-KO lethality (BLISS).

      We thank the reviewer for recognizing our limitations to perform BLISS score analysis, as our experiments were conducted at a single level of total protein depletion. Ideally, synergy assessments require a range of depletion levels to generate a full response matrix. Regardless, to address the reviewer’s concern regarding the impact of ALC1 on olaparib response in BRCA1- and BRCA2-mutant cells, we performed a BLISS score calculation under the conservative assumption that total ALC1 depletion alone has no effect on cell viability. We then employed the following formula for BLISS score calculation:

      Bliss Score =Eobs- (EA+EB-EAX EB)

      Where Eobs is viability of ALC1-depleted cells at a given drug concentration. This is observed impact upon combined loss of ALC1 and olaparib treatment.

      EA is impact on viability upon ALC1 depletion only. This was considered to be zero.

      EB is impact on viability on ALC1 WT in the presence of drug. This assesses the impact of drug alone.

      BLISS score was calculated at all non-saturating drugs concentration and then averaged to obtain a final BLISS value. We used the following cut off:

      > 10: Synergistic (the interaction is considered significant);

      -10 to 10: Additive (no significant interaction);

      __

      Olaparib

      Rucaparib

      Niraparib

      Veliparib

      Cisplatin

      UWB1.289

      22.34

      25.21

      13.24

      14.95334

      0.26

      JHOS-4

      37.27

      47.14

      26.3

      27.94

      -0.37

      OVSAHO

      19.34

      27.6

      23.2

      19.15

      7.04

      Kuramochi

      11.38

      11.98

      -3.56

      6.79

      -0.39

      We observe that ALC1 loss synergistically enhances olaparib and rucaparib response in both BRCA1- and 2-mutant cells. However, as correctly noted by the reviewer, we notice that the BLISS score is higher in BRCA1-mutant cells compared to BRCA-2 mutant, OVSAHO.

      In the revised manuscript, we have also included data for another BRCA-2-mutant cell line: KURAMOCHI (Fig.1d; Supp. Fig1b). We chose this cell line because, despite having a BRCA2-mutation, it is highly resistant to PARP inhibitors and cisplatin, owing to KRAS amplification. Notably, we observe that ALC1 loss can synergistically enhance the response of Kuramochi to olaparib and rucaparib.

      We have included a statement in the manuscript that the impact of ALC1 loss was more profound in BRCA1- versus BRCA2-settings. However, if acceptable to the reviewer, we would prefer not to include the BLISS values in the manuscript, as these calculations were not performed using the standard approach of titrating multiple levels of protein depletion.

      2- Another BRCA2-mutated cell line should be included.

      As discussed above, we have now included data from another BRCA2-mutant cell line, Kuramochi. Consistent with data in other BRCA-mutant cell lines, loss of ALC1 enhances olaparib and rucaparib sensitivity in these cells (Fig. 1d; Supp. Fig.1b).

      Minor comments: • Figure key is missing for S2C (I assume it's grey DMSO, blue olaparib)

      We apologize for this oversight. Figure key has now been included.

      • Page 8: "BRCA1-mutant ovarian cancer cells eventually develop chemoresistance when exposed to PARPi for a prolonged period. Mechanistically, this is due to rewiring of ATR signaling, which enables RAD51 loading at DNA breaks and reversed forks independent of BRCA1 protein(25)." This sentence suggest this is the only existing resistance mechanism, which should be correct. Modify to "mechanistically, this CAN be due to", or "this is OFTEN due to".

      We thank for the reviewer for suggesting this important correction. This has now been fixed.

      Reviewer #1 (Significance (Required)):

      ALC1 inhibitors have been developed and clinical trials are starting. The significance of this manuscript lies in establishing the clinical potential for combined ALC1-PARP inhibition in high grade serous ovarian cancer. Especially, the authors demonstrate that combined ALC1 suppression with PARP inhibition efficiently kills HR-proficient CCNE1-amplified ovarian cancers, which represent 20% of ovarian cancers and are resistant to current therapies.

      __Reviewer #2 (Evidence, reproducibility and clarity (Required)): __ The manuscript by Lindsey et al. explores the role of ALCN1 (Amplified in Liver Cancer 1) loss in enhancing the sensitivity of PARPi in ovariar carcinomas, including BRCA1/2 mutated tumors (both sensitive and resistant to platinum) as well as cyclin E amplified settings. The data are interesting but the in some cases there is an overinterpretation of the results. I have listed below my major concerns.

      We appreciate that the reviewer finds our data interesting. We also appreciate the reviewer insightful comments and have addressed them below.

      Figure 1. Could the authors demonstrate that OVASAHO cells are BRC2 muted? Indeed, I have always though they were BRCA wt type (10.1016/j.ygyno.2015.08.017).

      OVSAHO cells have a homozygous deletion in the BRCA2 gene (PMID:23839242), which could be the reason why a mutation was not detected in the study referred to by the reviewer (PMID: 26321251). We have now included the Domcke et al; 2013 reference in manuscript. The loss of BRCA2 expression in OVSAHO is also evident in our blots (Fig. 1a), as well as in data from protein atlas analysis.

      While the data on cisplatin suggest that indeed ALC1 loss do not impact its sensitivity, I disagree with the statant that "the correlation between dispensability of ALC1 in platinum response suggests that this chromatin remodeler likely does not contribute to MMEJ (page 6)" or " is dispensable for HR (page 7). Indeed, it is has to be stressed that cisplatin induced DNA damage (interstrand crosslinks) are substrates also for nucleotide excision repair, that has a key role in repairing these lesions.

      We agree with the reviewer that transcription-coupled NER is the key pathway for the resolution of cisplatin-induced damage. We therefore have revised this statement in the manuscript as “Our data showing the dispensability of ALC1 in cisplatin response, both in BRCA1 and 2-mutant settings, is consistent with previous reports demonstrating the dispensability of this remodeler for MMEJ or transcription-coupled nucleotide excision repair.” We have cited previous work where ALC1 has been shown to be dispensable for MMEJ or TC-NER. Similarly, we have modified the text on page 7 as “Furthermore, ALC1 loss did not impact sensitivity to cisplatin in HRP cyclin E1-high cells. This observation is consistent with previous studies showing its dispensability for HR repair.”

      Figure 2. Please explain better why niraparib is not active in cyclinE1-high cells.

      Our comprehensive studies examining the impact of ALC1 depletion on PARPi response uncover the generalized theme that targeting is most effective in enhancing sensitivity of olaparib and rucaparib, which have moderate PARP1/2 trapping ability, as compared to niraparib and talazoparib, which are strong trappers. One possible explanation could be that moderate PARP1/2 trappers are more amenable for combination strategies because their effects do not reach full saturation, preserving a dynamic range that allows for additive or synergistic enhancement. This was included in the discussion section of the manuscript.

      It is not clear to me if the authors consider a cyclin E "gain" an overexpressing tumor (i.e. OVCAR8). The authors need to show the response to PARPi in one (possibly two) cell lines with very low expression of cyclin E and knock-down of ALC1.

      We have present data in multiple BRCA1-WT cell lines with very low expression of cyclin E compared to OVCAR8. These include: FT282 cell line (Fig. 4), two FT282 clones of BRCA1-/+ FT cells (Fig. 5), and full length BRCA1 addback UWB1.289 (Fig. 3c). Additionally, we have added immunoblotting data showing that in OVCAR8, the level of cyclin E1 protein and activity as assessed by pCdk2 is comparable to OVCAR3 and OVCAR4, two CCNE1-amplified lines (Fig. S2d). In contrast, FT 282 and UWB1.289 BRCA1 add back cells have low levels of cyclin E and thus low pCdk2.

      The deletion of ALC1 do interfere with tumor take and tumor growth? No clear is the in vivo experiments.

      Tumor uptake: We injected OVCAR8 cells in mice three days post-transduction of sgALC1. Depletion of ALC1 is only achieved at 14 days post transduction. This explains why tumor uptake is not impacted. We do not observe a significant impact of ALC1 loss on tumors derived from OVCAR8 cells. This is consistent with the dispensability of ALC1 in the proliferation of HR-proficient cells (PMID: 33333017; PMID: 33462394). We have added text in the manuscript to clarify this point.

      Injecting OVCAR8 cells in the peritoneum is not associated with the formation of ascites?

      We thank the reviewer to bring up this important point. The objective of this study is to examine how ALC1 loss can enhance PARPi responses and therefore we chose an earlier time point (~50 days) to assess the impact on tumor growth. Ascites formation upon intraperitoneal injection of OVCAR8 cells has primarily been reported at late stages of disease development. For example, Anirban Mitra et al. (2015) (PMID: 26050922) reported consistent ascites formation, but only at extended timepoints (up to ~90 days post-injection). Similarly, Yong-Tae Shen et al. (2019) (PMID: 31117198) injected 5-10 x106 cells and observed ascites emergence beginning around day 49, with progressive accumulation toward the endpoint, indicating that fluid buildup coincides with advanced peritoneal dissemination. In contrast, studies using comparable inoculation doses (e.g., 1×10⁶ cells) and shorter observation periods (~6 weeks) such as Luis Hernandez et al. (2016) (PMID: 27235858) did not report detectable ascites. Taken together, these findings suggest that, while OVCAR8 cells can generate ascites, this phenotype typically manifests at later stages of disease progression and is not expected within shorter experimental windows. Therefore, the absence of ascites in our model is consistent with the study design and timeframe, rather than indicative of a failure of tumor establishment.

      We have added relevant discussion in the results section to clarify this point.

      How was tumor weight calculated?

      Tumor burden was quantified by direct collection and measurement of peritoneal tumor nodules. For the sacrificed mice, all visible tumor nodules within the peritoneal cavity were carefully excised, counted, and pooled per animal. The total tumor weight was then determined by weighing the combined mass of all collected nodules using an analytical balance. Thus, “tumor weight” represents the cumulative mass of macroscopic peritoneal implants per mouse. No estimations or indirect calculations were used. This has now been elaborated on in the methods section.

      It seems that tumors grow as solid mass, but how were nodulesAll mice at endpoint exhibited disseminated peritoneal disease, characterized by multiple tumor nodules and invasion into the peritoneal wall. Tumor nodules were quantified by direct visual inspection during necropsy. Small nodules ( Why survival curves were not shown?

      Survival analysis was not included because the study was designed with a predefined experimental endpoint to enable controlled comparison of tumor burden across groups. Animals were therefore euthanized at the same timepoint rather than followed longitudinally to survival. As a result, Kaplan–Meier analysis was not applicable to this experimental design. We agree that survival is an important outcome and would be valuable in future studies specifically powered and designed for that purpose.

      The dose of 50mgr/kg every third day is a very low olaparib dose. Generally the in vivo dosing is 100mgr/kg , 5 days a week for 4 weeks (doi: 10.1158/1535-7163.MCT-21-0420; 10.1158/2767-9764.CRC-22-0423).

      We agree that higher doses of olaparib (e.g., 100 mg/kg, 5 days/week) are commonly used and have demonstrated single-agent efficacy in vivo. In this study, however, our objective was to specifically evaluate the combinatorial effect of olaparib with genetic knock-out of ALC1. To enable this, we intentionally employed a reduced dosing regimen (50 mg/kg every third day) to minimize single-agent activity. This approach allowed us to establish a condition in which olaparib in sgAAVS1 control tumors had limited impact on tumor burden, thereby providing a dynamic range in which to detect potential sensitization effects mediated by sgALC1. Using a fully efficacious dose would likely mask such interactions by producing a near-maximal response in the control group. Thus, the selected dosing strategy reflects a deliberate experimental design to assess potentiation effects rather than to model maximal therapeutic efficacy of olaparib as a monotherapy.

      Figure 4. I could not find the data of the minimal impact of ALC1 in UWB1.289 cells. What the author refer to? They refer to the fact that ALC1 deletion di not cause any cell growth alteration or to something else? But were there the data?

      The minimal impact being referred to was PARPi responses in BRCA1-proficient UWB1.289. We have now fixed the statement to read: “The minimal impact of ALC1 in BRCA1-proficient UWB1.289 cells on PARPi responses suggested that targeting this remodeler may have minimal impact on normal healthy cells.” and included the relevant figure number (Fig.3c) for clarity.

      The modest increment in pRPA in hTER-FT282 is statistically significant and not very different from what observed in UWB.289, suggesting that ACL1 deletion could indeed impact normal cells. These data should be interpreted more conservatively.

      The increase in pRPA levels upon ALC1 loss in hTERT FT282 BRCA1 het cells and UWB1.289 cells is 1.2 and 1.4 respectively. This is consistent with the literature that BRCA1-/+ het cells have compromised replication stress response. Unresolved replication stress gets processed into double-strand breaks (DSBs). Consistent with the proficiency of hTERT FT282 BRCA1-/+ het cells in DSBs repair, ALC1 deficiency does not increase yh2ax in these cells. Hence, despite an increase in pRPAS33 signal in hTERT FT282 BRCA1 het cells, these cells can resolve downstream breaks. In contrast, a profound, 1.7-fold increase in yh2ax signal was observed upon ALC1 loss in BRCA-mutant UWB1.289 cells, reinforcing that ALC1 loss has a more profound response in BRCA-mutant cancer cells.

      To align with the reviewer’s suggestion, we have removed the word “modest’ and have retained the fold differences in the median values.

      Figure 6. Questionable is the OS as endpoint in this heterogeneous patient population (treated in front line and recurrent) and in my opionion OS, much more than PFS, is influences by the many different treatment these patients underwent and that could influence the OS. Why not considering PFS after/or on PARPi treatment? The authors should clarify the patient population, Indeed, 48 patients were treated with PARPI and were platinum sensitive and possibly HRD. What patients are the HPR patients? How many were they? It is not clear the HRP and high replication stress cohort were treated with PARPi? How many of these were Cyclin E amplified or with high levels? Figure 6F should also include, beside UVB+BRCA1, other tumor cells with no Cyclin E overexpression and non BRCA mutation or HRD. The discussion of limitations should be addressed to strengthen the manuscript.

      We thank the reviewer and agree that PFS is often preferred for evaluating treatment-specific effects. However, in this cohort, PFS was not a reliable endpoint for several reasons. Tumor samples were obtained at diagnosis, whereas PARPi was administered later, in either the frontline maintenance or recurrent setting, introducing temporal and prognostic heterogeneity that limits the interpretability of PFS. These factors confound attribution of PFS specifically to PARPi response. We therefore selected OS from the time of PARPi exposure as a more consistently defined endpoint across this heterogeneous cohort, while acknowledging its limitations.

      Reviewer #2 (Significance (Required)):

      The manuscript by Lindsey et al. explores the role of ALCN1 (Amplified in Liver Cancer 1) loss in enhancing the sensitivity of PARPi in ovarian carcinomas, including BRCA1/2 mutated tumors (both sensitive and resistant to platinum) as well as cyclin E amplified settings. The data are interesting but the in some cases there is an overinterpretation of the results.

      __Reviewer #3 (Evidence, reproducibility and clarity (Required)): __ The manuscript by Aubuchon, Wong et al. presents strong insights into the value of ALC1 as novel target for sensitization strategies against PARPi. The authors show that a PARPi resistance is reversible when ALC1 is knocked down and convincingly highlight the genetic circumstances for these approaches. Also, the authors point out that especially the weak PARP-trappers olaparib and rucaparib could benefit from concomitant ALC1 inhibiton and high levels of replication stress by elevated p-T21 RPA2 could serve as biomarker in clinical settings. Furthermore, the authors show that benign fallopian tube cells are not affected by ALC1-kd, which is an important finding for in vivo approaches.

      We thank the reviewer for acknowledging that our work provides “strong insights” and makes “important finding for in vivo approaches”.

      As the manuscript covers a broad experimental field, I would only suggest a few additional experiments to further strengthen the overall story:

      1. How does an ALC1 knock-down affect the expression of PARP1 and if so, how does this contribute to the effects seen by ALC1-kd? The authors could add Western Blot experiments for cell lines belonging to the respective groups that are distinguished in the manuscript: BRCA wt, BRCA mutated and Cyclin E1-high cancer cells and also a benign fallopian tube cell line.

      This was an interesting point brought up by the reviewer. To address this, we examined and compared total PARP1 protein levels in BRCA1 add-back UWB1.289, BRCA1-mutant UWB1.289, cyclin E1-high OVCAR8, and FT282, between ALC1 WT and depleted cells. However, we do not observe any consistent alteration in PARP1 level upon ALC1 depletion (Fig. Supp. Fig. 6a, b).

      In some of the Western Blot data, it also looks like BRCA1 expression is affected by ALC1 kd. The authors could provide some quantified protein expression or qPCR data if there is a correlation between both expressions.

      To address the reviewer’s question, we quantified changes in BRCA1 levels upon ALC1 loss across all cell lines used in this study. As expected, BRCA1 levels were higher in UWB del 11q and Cyclin E1-overexpressing cell lines. In contrast, cell lines harboring heterozygous BRCA1 mutations or BRCA1 promoter methylation were among those with the lowest BRCA1 expression. This trend provides us confidence in reliably quantifying our immunoblotting data. Although minor fluctuations in BRCA1 protein levels were observed following ALC1 depletion, no consistent trend towards either an increase or decrease was evident (Fig. Supp. Fig. 6c). Likewise, when cell lines were grouped according to their sensitivity to PARP inhibition upon ALC1 loss, no clear pattern emerged (Fig. Supp. Fig. 6d). Together, these data suggest that ALC1 depletion does not substantially affect BRCA1 protein levels, consistent with our previous RNA-seq and functional studies indicating that this chromatin remodeler is dispensable for transcriptional regulation or homologous recombination (PMID: 33462394).

      To further strengthen the hypothesis that the effects of strong PARP-trappers are not improved by ALC1 kd, the authors should add data regarding the viability of the cells presented in Figure 3b upon treatment with niraparib and talazoparib in sgALC1 cells (versus vector control). Also, the authors should add cell viability data using talazoparib for the sgALC1 OVCAR cell lines (versus vector control) in Figure 2 and Supplement Figure 3.

      Sensitivity to niraparib and talazoparib upon ALC1 depletion have now been added in Figure 3b, and for OVCAR lines in Supplement Figure 3. As correctly pointed by the reviewer, we consistently observe that impact of ALC1 loss is more profound on olaparib and rucaparib compared to niraparib and talazoparib.

      Some minor points I noticed while reading the manuscript:

      We apologize for the oversight and thank the review for pointing this out.

      • in Figure 3b, both graphs have the same title. I think the right one should be "SYr14" instead of "SYr12" again

      Fixed. - In the heading of Figure 2 an "in" is missing

      Fixed.

      • There are some citations, that seem to be made with another citation style (superscript numbers) than numbers in brackets across the manuscript.

      Fixed.

      Reviewer #3 (Significance (Required)):

      The most important aspect resulting from this manuscript is that ALC1 inhbitors could improve the response to some PARPi without damaging healthy cells. Thereby, the authors also mention the limitation of the use of ALC1 as a target and offer a potential biomarker for combinatory approaches. This study offers a very detailed insight into the potential role of ALC1 as a target for sensitization approaches under the different genetic conditions that can occur in HGSOC. These novel insights contribute to further broaden the therapeutic options by PARPi in clinical settings if the results can be approved by in vivo trials.

      • *
    1. The individual term digital humanist may be problematic because it may seem both too general in not relating to a specific discipline or competence (thus deemphasizing the discipline-specific or professional) and too specific in emphasizing the “digital” part of the scholarly identity (if you are scholar) or giving too much prominence to the humanities part of your professional identity (if you are a digital humanities programmer or a system architect)

      I agree with the authors critique of the term digital humanist, most specifically the point about the term being too specific in emphasizing the "digital" part, as I don't believe we exist in a digital vacuum where there could be something that is purely digital. I think that the world we exist in has a lot of digital technology at play, but it is almost redundant to emphasize something coming from a digital perspective.

      I found an additional article (URL below) that also discusses this paradox in the term digital humanist. https://www.sciencedirect.com/science/article/pii/S2666659624000015?via%3Dihub

    2. In a conceptual and disciplinary map of the digital humanities, the encounters described above and the examples cited earlier would be distributed over a rather diverse territory. One important, distinguishing parameter is how different perspectives and initiatives relate to information technology and the digital. For example, as we have seen, traditional humanities computing tends to have a rather instrumental relationship to information technology, which serves primarily as a tool, whereas a cultural or media studies-based approach is more likely to focus on digital culture and the cultural construction of information technology as a study object.

      Interdisciplinarity solves some of these problems, I think. Rather than viewing the "digital" and the "humanities" and separate entities that we are trying to reconcile, perhaps there is value in addressing them as partners in addressing a unique problem according to its inherent complexities. The interesting question becomes, then, not which discipline owns the problem, but what kinds of relationships are required to understand it.

      This perspective aligns closely with the work of Julie Thompson Klein. In her foundational text, Interdisciplinarity: History, Theory, and Practice, Klein (1990) argues that “Interdisciplinarity is a means of solving problems and answering questions that cannot be satisfactorily addressed using single methods or approaches” (p. 196). Currently, this is the perspective that I maintain. Interestingly, this article and work on interdisciplinarity seem to have emerged around the same time. Perhaps this represents a societal as well as an academic turning point. As social, technological, and cultural problems became increasingly complex, traditional disciplinary boundaries may have become less capable of addressing them independently, creating a need for collaborative and interdisciplinary approaches to knowledge preservation and production.

      References

      Klein, J. T. (1990). Interdisciplinarity: History, theory, and practice. Wayne State University Press.

    1. Sample definitions are in Section 3.3. Panel A of Table 3 is a politician-level panel with one observation per politician per reference election. We use four reference elections (2008/2012/2016/2020) and include every politician who is a career politician at the reference election, defined as either currently holding elected office (mayor or councillor incumbents) or having won at least one prior election, regardless of whether they ran at the reference election themselves. Including sat-out career politicians (e.g. term-limited mayors taking a forced break before running again) avoids conditioning on having chosen to run in a given cycle, which would mechanically exclude precisely the politicians the filing event may push out of the cycle. First-time / never-won candidates are excluded: an improbidade allegation against such a politician cannot be tied to a documented office tenure. The mayor subsample additionally excludes politicians who are term-limited at the next election (consecutive two-term mayoral incumbents ending at the reference cycle), since they are mechanically barred from running for mayor again at lead and their Running=0 is not behavioural. Panel B is the case-level Disposition-OLS sample: cases filed in the one-to-four year window before the politician’s next election, restricted to politicians who held office at filing time (mayor or councillor at the pre-filing election) or have any prior electoral win. The lower bound at one year excludes filings landing in the election year itself, when no pre-election disposition is feasible. The upper bound matches Panel A’s window and keeps the case-filing event term-aligned. For Panel A, filed before electioni equals one if politician i had at least one improbidade case filed against them in the one-to-four year window before the corresponding next election. For Panel B, defined at the case level, convicted before electionij and acquitted before electionij equal one if case j naming politician i was decided as a conviction (resp. acquittal) before the politician’s next election, and zero otherwise. The two indicators are mutually exclusive within a case; their common zero category is the case still being pending as of the next election (cases decided after the election cannot affect voters by definition and are equivalent to pending cases for this analysis).

      I think all of these can be dropped. This is just repetition from Section 3.3. Sample construction, Instead, this paragraph should be straight to the point, saying something like: To estimate the association between filing and electoral outcomes, we estimate:"

      Then introduce the equations, and explain the variables, with emphasis on the variable of interest.

      I also think it is better if we explain the equation for Panel A first, and then for Panel B. We could potentially split into two paragraphs. All variables should be explained, and all outcomes.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Reviewer #1 (Public review):

      Summary:

      Eroglu and Hobert demonstrate that injecting CRISPR guides and repair constructs to target three genes at a time, tagging each with a different fluorescent protein, and selecting which gene to tag with which fluorophore based on genes' expression levels, can improve efficiency of gene tagging.

      Strengths:

      This manuscript demonstrates that three genes can be targeted efficiently with three different fluorophores. It also presents some practical considerations, like using the fluorophore least complicated by agar/worm autofluorescence for genes with low expression levels, and cost calculations if the same methods were used on all genes.

      Weaknesses:

      Eroglu has demonstrated in a previous publication that single-stranded DNA injection can increase efficiency of CRISPR in C. elegans, while inserting two fluorescent proteins and a co-CRISPR marker into three loci, and Paix et al 2015 demonstrated simultaneous insertion of two fluorescent tags. The current work is valuable and incremental advance. In general, I applaud the authors' willingness to strategize about how whole proteome tagging might be accomplished. I predict that the advance here will be one of many small advances that will get the field to that goal. The title oversells the advance presented, in my view, since seems like one among many key advances, and the first sentence of the Discussion seems a more apt summary of the key advance here.

      Some injections targeted genes on the same chromosome together, which will create unnecessary issues when doing crossing that will be useful for some future experiments. This made me wonder if injecting 3 together really is helpful vs targeting each gene separately, since only 5 worms need to be injected. It cuts time down by 2/3, but perhaps avoiding targeting the same chromosome with two tags would be useful.

      The limited utility of current blue fluorescent proteins makes me wonder if it's worth using at this stage, before there are better blue fluorescent proteins, or better yet, far red, to avoid issues with live imaging under phototoxic UV or near-UV illumination.

      These comments are a repeat of the original comments, and we refer the reader to our response to the original comments.

      Reviewer #2 (Public review):

      Original Review:

      The manuscript by Eroglu and Hobert presents a set of strains each harboring up to three fluorescently tagged endogenous proteins. While there is technically nothing wrong with the method and the images are beautiful, we struggled to appreciate the advance of this work - who is this paper for?

      As a technical method, the advance is minimal since the first author had already demonstrated that three mutations (fluorophore insertion and co-CRISPR marker) could be introduced simultaneously.

      As a pilot for creating genome-scale resources, it is not clear whether three different fluorophores in one animal, while elegantly designed and implemented, will be desired by the broader community.

      Finally, the interpretation of the patterns observed in the created lines leaves much to be desired. A Table with all the observations must be included and can replace the tedious (and often wrong) descriptions of the observations with the different lines. It would be too much to point out every mistaken expectation of protein expression. Two examples include:

      The expectation that ACDH-10 is enriched in the intestine and epidermal tissues (hypodermis) is naïve - there are multiple paralogs of this protein (look at WormPaths or WormFlux) that may share functions in different tissues. There is also no reason to assume that fatty acid metabolism does not occur in other tissues (including the germline). Finally, there are no published studies about this enzyme, so we really don't know for sure what it's doing.

      The expectation that HXK-1 is ubiquitously expressed is similarly naïve. There are three paralogous enzymes that are all associated with the same reaction, and we have shown that these three function redundantly in vivo, perhaps in different tissues (PMID: 40011787). Moreover, single cell RNA-seq data (PMID: 38816550) also shows enrichment of hxk-1 in gonadal sheath cells.

      The table should have at least the following information: gene/protein name - Wormbase ID - TPM levels of single cell data assigned to tissues for L2, L4 and adult (all published) - tissues in which expression is observed in the lines presented by the authors.

      Other points:

      (1) We would encourage the authors to provide systematic validation of the reported insertions. The manuscript reports that 24 of 30 tags were isolated and visible but does not clearly state whether each isolated line was confirmed by sequence‑level validation to be correctly in‑frame and free of unintended mutations at the target locus.

      (2) The manuscript presents aggregated success counts (e.g., 8/10 mTagBFP2 tags, 9/10 mStayGold, 7/10 mScarlet3) and useful narrative descriptions of injection outcomes. We suggest also to include per‑locus success rates.

      (3) For pools that required re‑injection after initial failures, we would like to see a description of the specific changes that were made to the injection mixes or procedures (e.g., new repair template prep, different Cas9 reagent lot, guide redesign). This will be useful troubleshooting information for others.

      (4) The authors states that the fluorophore sequences are codon-optimized for C. elegans. We suggest they provide the exact donor/tag sequences used specifically state whether the fluorophore sequences contain any synthetic/artificial introns or other sequence modifications (e.g., silent PAM‑disrupting mutations) were included in the donor templates.

      (5) Page 3: Include a reference for "The C. elegans genome encodes around 20,000 genes"

      We hope these comments are useful.

      Comments on Revised Version:

      Overall, we found the responses to be quite recalcitrant.

      We have one remaining composite concern about the comparison between observed expression patterns with the new strains versus published data.

      First, the authors only report patterns for one stage while it should be not too much effort to image the different life stages. However, since this is a revision, we are not formally requesting they do this.

      Second, in the now provided Table (thank you) 'observed expression' (last column) is lacking for 9 of the 30 proteins, and for 6 of these the procedure was not successful. Why not report patterns for the other three? It is confusing also because on page 5, the authors say that "overall, 24 of 30 tags ...all of which were visible with fluorescence stereomicroscopy" - are we missing something? Also, they then said that they "obtained 6/9 of the originally failed tags"; why are the corresponding patterns not included in table 1, and are 9 proteins still labeled as "no" in the "success?" Column?

      We appreciate the chance to clarify this matter: There are only 6 “no” in the “success” column. In two cases, HAT-1 and CBP-1, expression was dim at F1 but still sufficient to pick positive worms and quantify success rate at the locus. We noted these as “dim” on the table to indicate that if expression was lower, we likely would not have been able to isolate them at F1. In one case, COX-6B, expression was too dim at F1 to be isolated but was sufficient at F2 to be visualized and isolated from parents that were positive for the other two tags. We now clarified this distinction in the table and accompanying text: “Fluorescent signals of HAT-1::mScarlet3 and CBP-1::mScarlet3 in F1 progeny were dim but still sufficiently visible for quantification of knock-in efficiency, indicating that they are at the lower end of detectability for mScarlet3.”

      We imaged worms that had multiple tags as proof of principle and are happy to provide strains to those who would like to image/study them. At this point we are not convinced that imaging more worms would add to the conceptual framework.

      Third, we strongly feel that the response to our comments about expression patterns is not adequate. On page 5 the authors say that "all proteins were expected to be ubiquitously expressed" and that "scRNA-seq indicated that transcript abundance was ubiquitous and without strong tissue-specific enrichment with few exceptions". However, in their rebuttal, the authors now argue for tissue-specific expression for proteins with paralogs, turning around their own argument! Moreover, their Table indicates that many genes show tissue-enriched expression by RNA-seq while many of their tagged proteins exhibit ubiquitous expression.

      We respectfully disagree that there is contradiction. In our response, the discussion on paralogs was added as a clarification in response to the referee’s original comments (e.g., regarding ACDH-10): “There is also no reason to assume that fatty acid metabolism does not occur in other tissues (including the germline).” We wanted to make it clear that we were not concluding fatty acid metabolism (or other processes) does not occur in other tissues.

      We wish to stress that we never argued that paralogs could not fulfil the same essential function across tissues. The proteins were selected because their biological functions (e.g., glycolysis, fatty acid β-oxidation, translation) are broadly required, and that scRNA seq generally predicted broad expression with few exceptions as detailed in the text. Paralogs with similar activities (e.g., hxk-1, -2, -3) may overlap broadly in expression, or individual paralogs may carry out the process in different tissues provided one carries out the reaction in each tissue. For acdh-10 and hxk-1 specifically, both appear broadly expressed across tissues by scRNA-seq, with no consistent enrichment or depletion across datasets. So, our central point is that: for a specific gene involved in an essential process, transcript data alone are not sufficient to accurately predict tissue specific enrichment. Not that the processes do not occur in tissues where one paralog is absent. The possibility that a paralog may compensate for lack of expression is in no way contradictory with our conclusion.

      The table does not generally show tissue-enriched expression: it simply lists three tissues with the highest quantitative value in the respective dataset. For instance, taking the first gene from the list (Y82E9BR.3) and looking at the Ghaddar dataset, the top 3 tissues (log2(TPM)) are: pharyngeal muscle (13.4), gonadal sheath (12.9), marginal cells (12.9). The next 3 tissues are: body wall muscle (12.9), pharyngeal epithelium (12.8), and intestine (12.3). Even when there were apparent enrichments among the top 3 tissues, there were significant disagreements between datasets, and beyond top 3 even greater disagreements (the datasets agreed on the top tissue only 4 times over the 30 genes). These indicate that much of the variation is attributable to experimental noise rather than true predicted enrichment. The referee points to HXK-1 being correctly gonadal sheath enriched in one scRNA dataset; however, the other two datasets actually show different sites as being highest, and the same dataset misses effects in other cases. This is precisely why protein level data is needed.

      We further clarified this issue in the text: “We thus selected 30 genes across a variety of bulk transcript expression ranges which are generally predicted to be broadly expressed based on molecular function or, where molecular function was unknown (e.g., ZK632.9), single cell RNA sequencing (scRNA-seq) data (Table 1, Fig. 2A, B) (Gao et al., 2024; Ghaddar et al., 2023; Taylor et al., 2021).”

      Overall, this indicates that both the overall accomplishment of generating tagged protein strains and analyzing their expression is oversold.

      We have tried to make clear that our contribution is not a handful of new tagged strains added to the many that already exist. Rather, as stated in the abstract and elsewhere, we propose a strategy and provide proof-of-concept for scaling up tagging efforts. We believe the importance of this cannot be oversold.

      Reviewer #3 (Public review):

      Summary:

      The authors argue that establishing the expression pattern and sub-cellular localisation of an animal's proteome will highlight hypotheses for further study. This claim is probably accepted by many in the community. This manuscript seeks to confirm the feasibility of establishing such a resource, by using current transgenic methods to knock in DNA encoding different colored fluorescent tags into C. elegans genes.

      Strengths:

      The authors make the points above. For example, they provide evidence that the C. elegans germline harbors two populations of mitochondria that differ qualitatively in the proteins they express. They also confirm that labelling the whole proteome is an achievable goal with relatively limited resources and time.

      Weaknesses:

      The work is somewhat incremental in that it uses existing transgenic technology. Cell biology in C. elegans is challenging because of the small size of many of its cells, notably neurons. This can make establishing the sub-cellular localisation of a fluorescently tagged protein, or co-localizing it with another protein, tricky. The authors point out in their introduction that advances in light microscopy such as diSPIM, STED and ISM (a close relative of SIM), have increased the resolution of light microscopy. They also point out that recent advances in expansion microscopy can similarly help overcome the resolution limit. However, they do not use these technologies to characterize their transgenic strains.

      Reviewer #4 (Public review):

      Summary:

      Tagging the entire proteome of a metazoan would be a landmark achievement, providing a powerful complement and extension to existing "omic" catalogs in model systems. Here, Eroglu and Hobert argue that efficiently tagging multiple loci in a single "batch" would make the community-based achievement of this goal realistic. They provide rigorous evidence that such an approach is indeed feasible, exploring issues related to efficiency, design and screening strategies, disruption of gene function, and the potential for endogenously tagged alleles to reveal unexpected aspects of protein expression and localization. While the work has some minor gaps that are important to rigorously assess the feasibility of the proposed effort, the detailed and valuable insights that emerge should provide impetus to the community to coordinate efforts to make this ambitious goal a reality.

      Strengths:

      The work has numerous strengths. The authors provide compelling evidence that:

      Three distinct loci can be efficiently targeted with three distinct fluorescent tags in a single injection.

      Thoughtful targeting design can reduce the likelihood of disruption of function by the tag.

      Systematic design principles based on expression level and predicted localization/function can be used to optimize tagging strategies.

      The resulting tags can provide unexpected insight into patterns of protein production and subcellular localization.

      Not all of these advances are novel in themselves, but taken together, they represent an important technical and conceptual advance. The most important strength comes from the exceptionally high value of the goal itself, in that the work is that it has the potential to spur a community-wide effort toward achieving the ambitious goal of proteome-wide tagging.

      We appreciate the referee’s enthusiasm and hope that this will engage members of the community in a collective effort.

      Weaknesses:

      The work's shortcomings are minor.

      One concern has to do with the feasibility of the proposed screening strategies. The experimental design cleverly coinjects tags for three loci in different gene expression 'zones'; this expression level determines which tag will be used. As the authors allude to, there is an important distinction between genes with the same overall FKPM value between those that are expressed broadly and those focally expressed in a specific tissue. The proposed strategy claims that there are a sufficient number of highly expressed genes "to be used as visible markers" for recovering successfully edited animals. It would be useful for the authors to discuss the issue of broad vs focused expression among this set of genes a bit more thoroughly, with an eye toward the issue of how likely it is that these genes could indeed consistently be used as visible markers, particularly for those at the low end of this limit.

      To give two examples, this principle aided us with screening F54C8.1 and HAT-1. We added additional discussion on this to the first paragraph of the discussion: “For instance, we could clearly visualize F54C8.1::mScarlet3 in adult sperm by fluorescence stereomicroscopy despite a bulk FPKM of 16. Similarly, nuclear localized proteins will likely be easier to detect even at low expression levels, given the concentration of signal in small subcellular compartments. Indeed, this helped us detect HAT-1::mScarlet3 (56 bulk FPKM), which may have been too dim if distributed more broadly within cells.”

      What fraction of the proteome (on a per-gene basis) is secreted proteins? How difficult will it be to screen these for successful tags? Are there specific tags that would be more optimal for secreted proteins? (The authors mention the use of an SL2 or T2A cassette to label the cells in which these proteins are expressed but note that there are technical challenges associated with doing this at scale.)

      We added some of these points to the discussion: “Moreover, around 17% of the C. elegans genome (3,484 genes) may encode for secreted proteins (Suh and Hutter, 2012). Endogenous tagging of a substantial fraction of these proteins could reveal spatial patterns of secretion, distinguishing components that remain near their cell of origin from those that disperse to distal sites (Keeley et al., 2020). Tagging secreted proteins can also reveal sites of secretion – such as apical or basolateral membranes, or neurites – as has been observed for specific insulins (Sural et al., 2025) and for neuropeptides that localize selectively to synaptic regions (Toker et al., 2025).”

      Various tags have been used for secreted proteins including Venus, TagRFP, and mNeonGreen. The pH of secretory vesicles is ~5.0-5.5, so chosen FPs should have a pKa below this range to avoid denaturation. All 3 fluorophores used here (mStayGold, mScarlet3 and mTagBFP2) have pKa’s below this range and would likely be fluorescent within secretory vesicles.

      For secreted and/or weakly expressed genes, it would be useful for the authors to estimate for what fraction of these would successful insertions need to be screened by PCR, and what resources (time and money) this would likely entail. 

      We think that the bulk of ECM proteins would likely be visualizable without PCR due to their broad and stable expression, and as mentioned a good portion of these have been already tagged. However, it is likely that most of the secreted small peptides will have to be screened by PCR. We use homemade Taq, which makes material cost of the reagents minimal. A pair of genotyping primers costs ~$8 (~$27,872 for all secreted genes).

      Hands on time for lysis of 48-96 worms is approximately 20-30 minutes, with time to set up PCR around 5-10 minutes per target, and time to load a gel of 10 mins. In a given pool, 2/3 could be a putative secreted protein; thus, the same lysed population would enable screening for two targets at once. Collectively, around 40-60 mins of hands-on time would be required for two genes (around 20-30 mins per gene). Given 18 targets are injected per day, if 12 are screened by PCR, the screening could be done in 6 hours per day without affecting throughput. Most of the time spent on PCR would be replacing fluorescence screening time and would not overlap with the rate limiting injection step, performed by a separate specialist.

      For how many genes would a single tag not capture all predicted isoforms?

      Around 25% of C. elegans genes are thought to undergo alternative splicing (PMID: 21177968), with on average, ~2 isoforms per transcript. Among our selected genes, we only had one case where a single tag would not capture all isoforms (flad-1). We examined an additional 30 random genes and found no more examples by chance. So, in our view, this will be rare though we recognize in some cases a practical decision will need to be made, which could involve consideration of expression levels of each terminal exon.

      Finally, some readers might object to the authors' assertion in the abstract that this work is "a first step in this direction" (presumably referring to designing a strategy for whole-proteome tagging). There is no concern that the authors are disregarding the extensive work of other groups, as they explicitly mention the contributions of other groups to the foundation that enables the present work. However, the spirit of the abstract could be misinterpreted by a well-intentioned reader.

      We appreciate the referee’s perspective and have reworded this phrase in the abstract to: “As proof-of-principle for scalable pooled tagging, we undertook a pilot study in the nematode C. elegans, in which we set out to tag 30 different genetic loci with three different fluorophores, with 3 tags being introduced at a time.”

    1. Author response:

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

      eLife Assessment

      This study uses the yeast two-hybrid assay to identify proteins that may interact with yeast Set1 and other subunits of COMPASS/Set1C, the histone H3K4 methyltransferase, providing also some evidence for Set1 sumoylation and a role of SET1C methylating other factors in vitro. The results are valuable, and they should contribute to understanding the functions of the conserved SET1C complex, as they suggest potential functional connections with RNA biogenesis, chromatin remodeling, and non-histone methylation, whose implications would yet need to be explored. Nevertheless, apart from the fact that only a small subset of the Y2H interactions is further examined, the validating experiments are only partial or inconclusive, the strength of evidence being at this point incomplete.

      We present a systematic SET1C interaction map that provides a structured resource for generating and testing new hypotheses on SET1C function. We emphasise that these interactions represent a hypothesis generating resource rather than a set of validated protein–protein interactions. To reflect this, the manuscript has been carefully revised to distinguish clearly between observation and interpretation, and to avoid overstatement of the data. Accordingly, we have revised the title and the abstract. Selected examples are explored further to illustrate how candidates from the dataset can be followed up, but the primary contribution of this work is to provide a structured framework and resource that can guide future mechanistic studies of SET1C function.

      We thank the reviewers for their thoughtful comments. We have followed their recommendations by modifying the structure of the manuscript, removing distracting results and relocating some figures to the supplementary materials to improve the readability of the manuscript. At the same time, the reviewers acknowledge that the dataset is extensive and that aspects of the validation work are valuable.

      The changes made to the manuscript's structure in accordance with the reviewers' recommendations are as follows:

      (1) Figure 1 is accompanied by a table (Table S2) with the raw data describing all the interactions from the ten 2H screens. This table also lists common interactors found in the independent screens. I'm afraid Table S2 was omitted from the initial submission of the manuscript

      (2) Figure 2 has been modified to include an AlphaFold modeling of a seven-subunit Set1C complex (Set1– Bre2–Sdc1<sub>2</sub>–Swd1–Swd3–Spp1) together with Kap104. Figure 2D has been moved to a new Figure S2

      (3) The initial figure S2, which was problematic, has been removed, along with the accompanying text.

      (4) Figure 3 of the original paper has been moved to the supplementary material and is now shown as a new Figure S3.

      (5) Figure 5 in the original paper becomes Figure 3 in the revised version

      (6) Figure S3 (Co-IP between Set1 and Prp22), which serves as validation data, has been moved to the main figures and is now presented as Figure 4.

      (7) Figure 6 in the original paper becomes Figure 5 in the revised version

      (8) Figure 4 from the original paper has been repositioned as the first figure (new Figure 6) of the biochemical characterization of the interaction between Snf2 and Set1C.

      (9) Figure 7 has been removed from the manuscript. We have kept the original Figure 7E as a new Figure S6.

      (10) Figures 8, 9, 10 become Figures 7, 8, 9.

      Public Reviews:

      Reviewer #1 (Public review):

      We thank Reviewer 1 for the careful and thoughtful evaluation of our manuscript. We fully agree that yeast two hybrid screening provides candidate interactions that require cautious interpretation, and we recognise that our original version did not always make this sufficiently explicit.

      In the revised manuscript, we have made substantial changes to address this central concern. All Y2H interactions are now consistently presented as candidate or potential interactions, and speculative statements have been either removed or explicitly framed as hypotheses. Our intention is that the reader can clearly separate the dataset itself from any proposed biological implications.

      Second, we have refocused the manuscript to better reflect its primary contribution. We now present the Y2H screens as a comprehensive resource that defines a set of candidate interactions for SET1C, rather than as a set of validated functional relationships. In line with this, we have reduced the emphasis on speculative models and removed sections where the connection to experimental evidence was not sufficiently strong. This includes the removal of Fig. S2 and Fig. 7 and the associated text, as well as the relocation of several figures to the supplementary material. Where appropriate, we have added statements highlighting the limitations of the approaches used and the need for future work to establish physiological relevance.

      More generally, we agree with the reviewer that the value of Y2H data lies in generating testable hypotheses rather than establishing conclusions. We have therefore revised the manuscript throughout to ensure that the interpretation remains proportionate to the strength of the evidence.

      We hope that these changes address the reviewer’s concerns and result in a clearer and more appropriately balanced presentation of the data.

      The manuscript by Luciano et al is a collection of experiments about the yeast histone 3 lysine 4 methyltransferase, Set1, starting with 10 yeast two-hybrid screens (Y2H). Y2H screens were briefly popular 20+ years ago, but the persistently unfavourable false-to-true positive ratios limited their utility, and the conclusion emerged that Y2H is an unreliable approach for gathering protein-protein interaction data. Y2H outcomes are candidate interaction lists at best, strongly contaminated by false positives. Here, the authors employed a company (Hybridomics) to perform the Y2H screens.

      The primary data is not presented, and the outcomes are summarized using the Hybridomics in-house quality scoring system in Figure 1A. It is not possible to evaluate these data, and the manuscript presents cartoon summaries that the reader must accept as valuable.

      Hybrigenics brings extensive experience from conducting numerous screens, enabling the team to recognize recurring false positives that commonly arise in screening assays. In their detailed analysis, Hybrigenics reports the number of clones recovered and the extent of overlap among interaction regions, both of which contribute to the confidence scores they assign. Table S2, provided in the revised version, more accurately reflects the raw data obtained by Hybrigenics. Nevertheless, we agree that false positives contaminate the list of potential interactors. Some interactions may also be indirect through a common interactor and do not reflect a physiological interaction.

      (1) Based on the extensive knowledge about Set1C/COMPASS acquired from genetics and biochemistry by many labs (including the Geli lab), the results presented here from the 10 Y2H screens are notably patchy. Of the 7 subunits of this complex, only one (Spp1) was identified using Set1 as bait. Conversely, as baits, Swd2, Spp1, Shg1, captured Set1, and the Bre2-Sdc1 interaction was reciprocally identified. These interactions were scored at the highest confidence level, which lends some confidence to the screens. However, the missing interactions, even at the third confidence level, indicate that any Y2H conclusions using these data must be qualified with caution. The authors do not appear to be cautious in their lengthy evaluations of these candidate interactions, which are illustrated with cartoons in Figures 2 and 3, with some support from the literature but almost without additional evidence. Snf2 is a particularly interesting candidate, which the authors support with pull-down experiments after mixing the two proteins in vitro (Figure 4). After Y2H, this is the least convincing evidence for a protein-protein interaction, and no further, more reliable evidence is supplied.

      We thank the reviewer for raising this important point regarding the strength of the evidence supporting the Set1– Snf2 interaction. We agree that the current data do not establish a definitive physiological interaction. In the discussion, we explicitly note the limitations of the current data.

      For Figure 2, as recommended by referee 2, we performed AlphaFold modeling of a seven-subunit Set1C complex (Set1–Bre2–Sdc1<sub>2</sub>–Swd1–Swd3–Spp1) together with Kap104. Consistent with the Y2H data, the model recapitulates binding of the Kap104 SID to the PY-NLS region of Set1 (residues 40–90).

      We have moved Figure 3 in the supplementary materials.

      (2) Figure 5 continues the cartoon summary of extrapolations from the Y2H screens, again without supporting evidence, except that the authors state.

      Figure 5 is now Figure 3. We have added the statement in the text: “It is not feasible to validate all of these interactions within the limits of this manuscript, and their validity should therefore be interpreted with caution. Nonetheless, these findings provide a useful basis for future research”.

      "We have refined the interaction region between Set1, Prp8 and Prp22, showing that Prp8 and Prp22 interact strongly with Set1-F4 (n-SET). Prp22 interacts in addition with Set1-F1 (Figure S2)." However, Figure S2 does not show this evidence and is incoherent.

      When we say that we have refined the interaction region between Set1, Prp8, and Prp22, we mean that we have restricted the interaction regions according to Y2H criteria. Indeed, we have not shown the spots illustrating the results. This statement has been deleted as well as Fig. S2

      The figure legends for Figure S2B and C do not correspond to the figure.

      (B) Expression of the F1-F5 fragments in yeast cells. Fusion proteins were detected with an anti-GAL4 monoclonal antibody. TOTO yeast cells (Hybrigenics) were transformed with the different pB66-Set1-F1 to F5 plasmids and subsequently with either P6, pP6-Snf2 762-968, pP6-Prp8 37-250, or pP6-Prp22 379-763 that were identified in the Y2H screens. Transformed cells were incubated 3 days at 30{degree sign}C on SD-LEU-TRP and then restreaked on SD-LEU-TRP-HIS with 3AT. Cell growth was monitored after 2 days at 30{degree sign}C.

      (C) Solid and dotted arrows indicate that transformed TOTO cells transformed with pB66-Set1-F1 to F5 and the indicated prey (Snf2, Prp8, and Prp22) are growing in the presence of 20 mM and 5 mM of AT, respectively.

      Figure S2D is two almost featureless dark grey panels accompanied by the figure legend D) Control experiment showing that TOTO cells transformed with p6 and pB66-Set1-F4 are not gowing (sic) in the presence of 5 mM or 20 mM AT.

      We agree that the legend for Figure S2 was unclear and does not accurately describe the panels shown in the figure. Fig; S2 has been deleted in the revised version. The results shown in the original Fig. S2 add limited information and may detract from the clarity of the main points.

      In the revised version, we have moved the CoIP analysis demonstrating the interaction between Set1 and Prp22 (previously shown in Figure S3) into the main figures (now Figure 4) to further support and validate the two-hybrid screening results presented there.

      Line 343. Interestingly, the two-hybrid screens reveal that Set1 1-754 interacted with Gag capsid-like proteins of Ty1 (Figure S5), raising the possibility that Set1 binding to Ty1 mRNA is linked to the interaction of Set1 1-754 with Gag.

      This is another example of the primary mistake repeatedly made by the authors -Y2H interactions are candidate results and not conclusive evidence.

      This statement is supported by our previous findings showing that Set1 binds Ty1 mRNA independently of its dRRM domain and represses Ty1 mobility at a post-transcriptional stage (Luciano et al., Cell Discovery, 2017; PMID: 29071121). One possible explanation for Set1 association with Ty1 mRNA is its interaction with the Gag capsidlike protein. In this context, the observed interaction between Set1(1–754) and Gag capsid-like proteins is consistent with this model.

      To further illustrate this point, the authors highlight the candidate interaction between Nis1 and 3 Set1C subunits.

      While we agree that the Nis1-Set1C interaction has not been demonstrated beyond doubt, we feel that our Y2H and in vitro binding experiments provide reasonable evidence that the interactions may be relevant. It is important to consider that any interaction assay can provide negative (and false positive) results, this includes Y2H, in vitro binding and mass-spec analysis of purified complexes from cells. We feel that it is not appropriate to only trust protein interactions that are strong and stable enough to be demonstrated via purified complexes. It is clear that some protein interactions do occur in transient and weak manner and therefore are not compatible with biochemical purification approach. This indeed is the strength of alternative methods like Y2H and in vitro binding assays, that interactions can be identified and tested even if the physiological context of the interaction may be more complex.

      (3) After multiple speculations based on the Y2H candidates, the authors changed to focus on sumoylation of Set1, which has previously reported to be sumoylated. Evidence identifying two sumoylation sites in Set1, in the N-SET and SET domains, is valuable and adds important progress to the role of sumoylation in the regulation of H3K4 methyltransferase, relevant for all eukaryotes. This illuminating part of the manuscript is only tenuously connected to the preceding Y2H screens and concomitant speculations.

      We thank Referee 1 for their comment. While it is true that there is only a modest connection between Set1 interactors involved in direct or indirect sumoylation and the characterization of Set1 SUMOylation sites, we believe that this does not constitute a weakness of the manuscript.

      (4) The manuscript then describes a red herring exercise involving Set1 methylation of Nrm1. In an already speculative and difficult manuscript, it is exasperating to read a paragraph about a failed idea. Apart from panel E, Figure 7 is a distraction, and I believe it should not be shared.

      (5) However, despite the failure with Nrm1, Line 443 - The H3K4-like domain in Nrm1 raised our attention to other yeast proteins that carry such sequences.

      This line of thinking is even less connected to the Y2H screens than the sumoylation work.

      However, the authors present a reasonable evaluation of the yeast proteome screened for six amino acids similar to the known H3K4 motif ARTKQT (Figure 7e).

      (6) However, this evaluation goes nowhere and has no connection with the next section of the manuscript, which is entirely speculation about the regulation of metabolism and stress responses based on the Y2H results and selected evidence from the literature.

      In response to comments 4 and 5, we have removed Fig. 7 and the paragraph titled “The transcriptional corepressor Nrm1 interacts with SET1C.” Part of this paragraph and the section describing the screen of the yeast proteome for six–amino acid sequences resembling the H3K4 motif (ARTKQT) has been kept as Fig. S6.

      In the abstract, we have removed the sentence: We demonstrate that the transcriptional corepressor Nrm1 is methylated by SET1C in vitro suggesting that H3K4-like domains may represent a class of non-histone substrates for SET1C.

      At the end of the introduction, we have deleted “the transcriptional corepressor Nrm1” in the sentence: In addition, we demonstrate that the transcriptional corepressor Nrm1 and the Snf2 AT-hook are both methylated by SET1C in vitro

      (7) The manuscript then describes more failed experiments regarding lysine methylation of Snf2 by Set1C, which unexpectedly reports arginine methylation rather than lysine. The manuscript does not currently meet the standard expected for this type of paper - the composition is somewhat incoherent and there are no previous reports of arginine methylation by SET domain proteins.

      We have integrated extensive in vitro reconstruction experiments with complementary in vivo studies, all conducted according to the rigorous standards expected by leading journals. These approaches have allowed us to reach the conclusions presented in this manuscript. While some of these findings are unexpected, they are supported by the data. We have carefully discussed the results and their limitations to provide a comprehensive interpretation.

      The manuscript presents a very experienced grasp of the literature and a sophisticated appreciation of the forefront issues, but a surprising failure to eliminate uninformative failures and peripheral distractions. The over interpretation of Y2H results is a dominating failure. There are some valuable parts within this manuscript, and hopefully, the authors can reformat to eliminate the defects and appropriately qualify the candidate data.

      We thank Referee 1 for these insightful comments. In the revised version, we have followed the advice to remove non-informative failures and peripheral distractions. Additionally, we exercise greater caution to avoid over-interpreting the Y2H results.

      Reviewer #2 (Public review):

      Summary:

      This paper starts with a large-scale yeast two-hybrid (Y2H) screen using Set1 (full-length and smaller parts) and other Set1C/COMPASS subunits as bait. There are hundreds of possible interactions identified, but only a small number are given any follow-up. While it's useful to document all the possible interactions, the unfocused and preliminary nature of the results makes the paper feel scattered and incomplete.

      Strengths:

      The Y2H screen was very comprehensive, producing lots of interesting possible leads for further experiments.

      Weaknesses:

      The results are useful but incomplete because only a small subset of the Y2H interactions is further examined. Even in the case of those that were further tested, the validating experiments are only partial or inconclusive.

      Referee 2’s comments align in some respects with those of Referee 1. In the revised version, we have followed the detailed Referee 2 suggestions to reduce the scattered nature of the manuscript. In addition, we include an AlphaFold model of the interaction between the Set1 N-term 1-754 with the SID domain of Kap104 that involves the proposed Set1 PY-NLS sequence.

      Reviewer #3 (Public review):

      The SET1C/COMPASS complex is the histone H3K4 methyltransferase in Saccharomyces cerevisiae, where it plays pivotal roles in transcriptional regulation, DNA repair, and chromatin dynamics. While its canonical function in histone methylation is well-established, its full interactome remains poorly defined. Moreover, whether SET1C methylates non-histone substrates has been an open question. In this study, Luciano et al. employ systematic yeast two-hybrid (Y2H) screening to uncover novel interactors and functions of SET1C. Their findings reveal potential functional connections to RNA biogenesis, chromatin remodeling, and non-histone methylation.

      The authors performed multiple Y2H screens using Set1 (full-length, N-terminal, and C-terminal fragments) and each of its seven subunits as baits. They identified high-confidence interactors that link SET1C to diverse cellular processes, including chromatin regulation (e.g., the SWI/SNF complex via Snf2), DNA replication (e.g., Mcm2, Orc6), RNA biogenesis (e.g., spliceosome components Prp8 and Prp22; polyadenylation factors Pta1 and Ref2), tRNA processing (e.g., Trm1, Trm732), and nuclear import/export (e.g., importins Kap104 and Kap123). Some of these interactions were further validated by immunoprecipitation or in vitro assays.

      Given the interaction of Set1 with Slx5 and Wss1 - proteins involved in SUMO-dependent processes - the authors investigated and convincingly demonstrated that Set1 is sumoylated. This modification may influence the function and regulation of the SET1C complex.

      Finally, the authors provide evidence that SET1C methylates proteins beyond histone H3K4, notably Nrm1, a transcriptional corepressor, and Snf2, the catalytic subunit of the SWI/SNF chromatin remodeling complex. Although Nrm1 contains a domain resembling the H3K4-methylated sequence (H3K4-like domain), this region does not appear to be required for its methylation. The search for other proteins containing similar domains as potential methylation candidates (p.12, first paragraph) seems less justified, given the lack of evidence supporting the requirement for the H3K4-like domain in methylation.

      This study offers valuable insights into the interactome of SET1C, suggesting potential links between the complex and a wide range of cellular processes. However, the functional implications of the Y2H interactions remain to be explored further. Additionally, the study provides intriguing information on the possible regulation of Set1 by sumoylation. The discovery of Nrm1 and Snf2 as methylation substrates could significantly expand the known targets and functions of SET1C.

      The results are supported by high-quality data.

      We thank referee 3 for their positive comments

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Restructure the manuscript into at least two papers.

      We thank the reviewer for this suggestion. In the revised manuscript, we have addressed this concern by substantially restructuring and streamlining the presentation. We consider the dataset, validation experiments, and functional observations to be closely integrated, and we believe that presenting them together provides the most coherent and impactful account of the work.

      Minor points

      There are several basic flaws in the manuscript that I feel indicate the co-authors have not proofread the manuscript sufficiently - 4 examples from early in the manuscript are listed below.

      (1) The reference for Hybridomics is (73) - obviously from an earlier version that used a different referencing system that has not been corrected.

      Thank you. This has been corrected.

      (2) Line 194 - 197. These screens have proven their power and effectiveness. In particular, they identified ...... the CTD of Rpb1 as an interactor of the N-terminal region of Set1 (Bae et al, 2020) (Figure S1). Rbp1 interaction is not identified in the screens presented here, and Figure S1 is a cartoon and not primary evidence.

      The interaction between the CTD of Rpb1 (Rpo21) and Set1 is reported in Table S2. The detailed characterization presented in Bae et al. (2020) was subsequently carried out as a direct follow-up to this screen.

      (3) Line 205-211. The highly confident interactors of the seven SET1C subunits are shown in Figure 1C-E. We found that Spp1, Shg1 and Swd2 interact alone with Set1 (Figure 1C). The minimum Set1 region for which an interaction is found for each of these 3 subunits is shown in Figure 1C. The high confidence interactors of the seven SET1C subunits are shown in Figure 1C-E. We found that Spp1, Shg1 and Swd2 display Y2H interactions with Set1 (Figure 1C). The high confidence interactors of Spp1, Shg1 and Swd2 are indicated in Figure 1D (see also Table S2).

      It is possible that Table S2 was omitted from the original submission, as it was requested during the production stage.

      (4) Line 335. We have classified all Set1 and subunit interactors according to these SET1C roles (Figure S5). However, this refers to Figure S4 - many further references to Figure S5 are also to Figure S4.

      Thank you. This has been corrected.

      Reviewer #2 (Recommendations for the authors):

      General recommendations:

      (1) Figures 1, 2, 3, and 5 and their associated main text are essentially just lists of interactors, put in graphic form and grouped to allow speculation about possible biological functions for the interactions. But almost none of the ideas are tested, so these sections take much more space than warranted. Having so much preliminary Y2H data actually distracts attention from the follow-up experiments that are shown. I would move most or all of this to the supplement, consolidating the Y2H results into fewer figures (or even just the Table).

      As mentioned earlier, the manuscript has been reorganized and Table S2 is provided.

      (2) The Snf2 interaction gets the most follow-up, so separating Figure 4 from Figures 8-10 broke the flow of that story. I would group these figures together since all are related to the Snf2 AT hook story.

      This was done accordingly.

      (3) I understand that it's impossible to validate all the possible interactions, particularly if resources are limited. However, at least for the interactions that get further attention, it could be very useful to try some AlphaFold multimer predictions. A high confidence AlphaFold score would provide a second orthogonal piece of evidence to support the Y2H results.

      We generated an AlphaFold model (Figure 2C) that recapitulates the key predictions for the Set1-Kap104 Y2H interaction.

      Comments on specific sections:

      (1) Y2H results. The text says Figure 1 shows all the high-confidence interactors. But the Set1 NTD interaction with the Rpb1 CTD is not shown here (it's in the supplement).

      In Table S2, an interaction is observed between full-length Set1 and the Rpb1-CTD (14 repeats), where Rpb1 is referred to as Rpo21.

      Figure 2 shows additional high-confidence interactors that do not appear in Figure 1, while others (like the Shg1Mog1 interaction) are shown in both Figures 1 and 2. It's confusing to scatter the data like this, which is why I recommend consolidating into a single figure or table.

      In Figure 2, the high-confidence interactors of Set1 (1–754) are highlighted in red and green (Snf2, Gbp2, and Kap104), and all are also present in Figure 1. Dbp1, identified as a high-confidence interactor of Spp1, likewise appears in Figure 1. Table S2 summarizes all of these interactions.

      (2) Line 219. How does a "high confidence" Set1-Kap104 Y2H interaction suggest the interaction is direct? Couldn't an indirect interaction also be tight and reproducible? This is an example where it would be worth seeing if AlphaFold also predicts an interaction and, if so, whether it involves the proposed NLS sequences.

      Y2H screening indicated that Kap104 binds to the N-terminal region (aa 1–754) of Set1 via its Set1 interaction domain (SID). To validate this, we used AlphaFold to model the seven-subunit Set1C complex (Set1-Bre2-Sdc1(x2) Swd1-Swd3-Spp1) with Kap104. The resulting model showed borderline confidence for the overall fold (pTM = 0.53) and low confidence in subunit positioning (ipTM = 0.5). Visualization in PyMOL confirmed Kap104 SID binding to Set1(1–754), consistent with Y2H results. The structure highlights Kap104 SID interaction with Set1’s PY-NLS at residues 40–90; the second PY-NLS is neither visible nor engaged in this model.

      (3) In the discussion of nuclear import interactors, what does it mean to say the Shg1-Mog1 interaction is "along the same line" as Set1-Kap104?

      We meant that the interaction between Shg1 and Mog1 represents another example of an interaction between a Set1C subunit and a protein involved in nuclear import. Along the same line has been deleted in the revised version.

      (4) To follow up on the Swd1-Nrm1 Y2H interaction, the paper shows that Nrm1 is methylated by Set1 in vitro (Figure 7), but it's not clear whether this has any biological significance. Without any in vivo follow-up, this figure is probably more appropriate for the Supplement.

      As noted above, Figure 7 has been removed, only panel E of Figure 7 is retained in the revised version.

      (5) Figures 6 and S8 show that Set1 is SUMOylated. Although it's not clear what this does to Set1 function or which E3 is responsible, the modification data looks convincing. The legend to Figures 6A and B says the Elutes samples are purified on nickel columns. Why are the Myc-Set1 and GB-Set1 proteins without the his-SUMO modification also binding to the nickel column? That's not happening in panels C and D. In the blots on the right for his-SUMO, is there any way to show that one of those bands is Set1? Maybe IP for MYC and then probe for the His tag?

      We thank the reviewer for this observation. His-SUMO purification using Nickel beads was used to purify HisSUMOylated proteins. Purified proteins were analyzed by Western blot using anti-MYC or anti-GAL4 antibodies to detect SET1-His-SUMO, as well as anti-His antibodies to confirm the presence of purified His-SUMOylated proteins. As mentioned by the reviewer, we detected unmodified MYC-Set1 and GAL4-Set1 in both the (-) and (+) His-SUMO eluates. This phenomenon is most likely due to the stickiness of unmodified Set1 to the beads. This is a commonly observed phenomenon in this type of biochemical assay, particularly when analyzing large proteins such as Set1 (124 kDa). This stickiness behavior has been observed in similar SUMOylation assays, e.g., for Hpr1 (88 kDa) (Bretes H, 2014. PMID: 24500206), Nup1 (114 kDa), and Nup2 (78 kDa) (Folz H, 2019. PMID: 30837289). This stickiness was not observed when using Set1 fragments (panels C and D), most likely because the fragments lost the stickiness to the beads, a characteristic belonging only to the full-length Set1. We mention this point in the legend of the new figure 5.

      (6) The Snf2 interaction gets the most follow-up. The GST pulldown validation of Set1 interaction with Snf2 AThook looks pretty good. However, the RGG repeats are necessary for the Set1 interaction with recombinant Snf2 proteins, but not for the co-IP of in vivo material. Again, AlphaFold could lend further support here.

      Thank you for this helpful suggestion. We agree that structural modelling could, in principle, provide an additional and orthogonal line of support for the Set1-Snf2 interaction. We did explore this using AlphaFold. However, both Set1 and Snf2 contain extensive intrinsically disordered regions, including the regions implicated in the interaction, and none of the models we obtained provided interpretable structural insight into the interaction interface. In particular, the predicted complexes showed low confidence in relative domain positioning, which limits their usefulness for supporting or refining the interaction model. One possible explanation is that additional components are required to stabilise a meaningful interaction in silico. While we modelled Set1 within a seven-subunit Set1C complex, Snf2 was necessarily included in isolation from its native context. Given that Snf2 functions as part of multiple, heterogeneous chromatin remodelling complexes, the absence of its physiological binding partners may prevent AlphaFold from resolving a relevant interaction interface. In light of these limitations, we have not included the AlphaFold models in the manuscript, as we felt they would not provide reliable or informative support. Instead, we have focused on the experimental evidence presented. We have clarified this point in the revised discussion to acknowledge both the potential and the current limitations of structural prediction approaches in this context.

      (7) The Snf2 methylation by Set1 is less convincing, and its biological significance is still unclear. I think it's pretty unlikely that Set1 could methylate arginine. The mass spectrometry is used for in vivo validation (mass spec), but mutating the lysines (Figure S11, S12) or Set1 deletion (Figure S14) doesn't seem to affect the signal. Could there be quantitative differences? Is there any way to quantitate the mass spec data to estimate the modified/unmodified ratio?

      We thank the reviewer for highlighting the unexpected nature of the methylation results. We agree that the observation of arginine methylation in this context is surprising, particularly given that SET domain proteins are classically associated with lysine methylation. This is why we performed multiple in vitro and in vivo experiments, and careful interpretation data that were clear led us to conclude that Set1C methylates the arginines within the ARTSTRGR motif of the AT-hook. We agree that the biological significance of this modification remains unclear. We obtained data showing that deletion of the SID domain of Snf2 impairs yeast growth on lactate, whereas this mutant grows normally on glucose and galactose, in contrast to the Snf2Δ mutant, which exhibits poor growth on both glucose and galactose. In comparison, deletion of the RG motif of Snf2 does not affect growth on lactate. These results provide insight into the interaction between Set1 and Snf2 but do not shed light on the potential importance of methylation of the RG motif. We therefore chose not to include them. In the discussion, we acknowledge the limitations of the current evidence. Our intention is to retain these findings as potentially interesting observations while ensuring that their interpretation remains appropriately cautious.

      Minor comments:

      (1) Lines 153 and 163: Stress response is listed twice, but with different references. Maybe these need to be further defined or else combined?

      We have deleted stress response line 163 and moved the references “Deshpande et al, 2022 and Nadal-Ribelles et al, 2015” line 153.

      (2) Line 193: better to say the proteins were fused to the C- or N-terminus (rather than upstream/downstream). It would be worth mentioning if there was a reason why Swd2 was fused to the N-terminus, unlike all the others.

      This has been done accordingly. In our hands, C-terminal fusions of Swd2 are not functional.

      (3) Is the scoring scheme (highest, high, good) that produces the colors in Figure 1 shown in the table? It doesn't say what the tan color (two of the Bre2 interactors) means.

      It is a mistake, Tea1 should be blue and Swi1 should not appear here. This has been fixed.

      (4) Line 206. It's not clear what it means to say that three of the subunits "interact alone with Set1". It can't mean they only interact with Set1, since other interactors are shown in Figure 1B. If it meant to say the interactions don't require other COMPASS subunits? I don't see how you can tell that from the Y2H assay. Please clarify.

      It means that these 3 subunits interact directly with Set1 without the need of another subunit, unlike of the other subunits.

      (5) Line 252. While discussing the Set1 - Snf2 interaction, the paper cites Hirschhorn et al. That paper talks about Swi-Snf, but doesn't mention Set1 anywhere. Maybe the authors meant to cite a different paper?

      We agree, this reference is not appropriated. It has been deleted.

      (6) Figure S2 panels A and C are redundant and could easily be combined.

      Figure S2 has been deleted.

      (7) Figure S4: Should the green category also include transcription? Ssl1 is a TFIIH subunit, which could be involved in either transcription initiation or NER. Sen1 and Nrd1 are transcription termination factors, although Sen1 may also function in R-loop resolution.

      We agree but it is already complicated as it is.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors identify and investigate a specific population of PVNOT neurons (oxytocin neurons of the paraventricular hypothalamus) that seem to be involved in both behavioral and autonomic thermoregulation. These cells are activated by social thermoregulatory behaviors, but can influence thermoregulation in both social and nonsocial contexts, specifically during transitions and when mice are at low core body temperature (Tb).

      Strengths:

      The manuscript has many strengths.

      This is a novel study, with a clear question that is addressed using an array of well-designed experiments employing integrative methods. Most of the figures are well-developed, and the analysis is generally rigorous and well-detailed. The authors are clearly very experienced in this field, and indeed, their scholarly introduction and discussion sections are to their credit.

      We are grateful for the reviewer’s careful reading and positive assessment, including their remarks on the clarity of the question, experimental design, and analysis.

      The link between thermoregulation and the oxytocin system is well established, as is the link between social behavior and the same broad system. However, the link between these three things is novel, if it can be well substantiated. I am not persuaded that was achieved here, but I do think this manuscript has many novel and useful offerings.

      We thank the reviewer for this thoughtful comment and for recognizing the novelty of the study. We wish to clarify the central goal of the manuscript: while social thermoregulation provided the initial influence for studying PVNOT neurons, our principal finding is that PVNOT activity during rest-to-arousal transitions is independent of social context. As stated in the manuscript, "To our surprise, these peaks were observed in both social and non-social contexts." Thus, our study demonstrates a broader role for PVNOT neurons in state-dependent thermoregulatory transitions—one that includes, but is not limited to, social contexts. We have revised the text to make this emphasis clearer throughout.

      We also added a short piece to the Discussion on this point. This is the fourth and final paragraph of the Discussion section called “State-dependent PVNOT activity during thermo-behavioral transitions.”

      The authors use a cooling floor, and only go down to 10 degrees Celsius. This is fine, but I would like to see the effects using ambient temperature also. This is not a crucial issue, as it is not necessary for the authors' interpretations, but it could improve measurement sensitivity.

      Both Reviewer 1 and Reviewer 2 raise important and related points: manipulating floor temperature provides a thermal stimulus that is distinct from manipulating whole-chamber ambient air temperature, and these modalities could engage partially different sensory pathways and circuits. (Note this response is copy-pasted to other relevant comments).

      We intentionally used floor cooling/heating because it provides a reliable, well-controlled stimulus that elicits thermoregulatory behaviors while keeping the experimental environment stable (e.g., avoiding changes in airflow/humidity that can accompany ambient cooling). To prevent conflation of these modalities, we revised the manuscript to consistently describe the manipulation as “floor temperature” (and not “ambient temperature”), and we added to the Discussion acknowledging that conductive floor temperature changes may differentially recruit peripheral thermoreceptors compared to ambient air temperature.

      While extending these experiments to whole-chamber ambient temperature changes could be informative in future work, it is not required for the central interpretations here, which focus on PVNOT activity dynamics during thermoregulatory behavior under controlled thermal conditions.

      Through an elegant behavioral experiment in Figure 1, the authors identify c-Fos patterns in the PVN that are activated by active social huddling, and they show that at the RNA level these cells overlap with oxytocin, indicating that they are oxytocin-producing cells. But this is not well discussed or indeed quantified.

      We thank the reviewer for catching this; Reviewer 2 made a similar comment. A typo in the figure legend led to this confusion. Figure 1I is in fact a quantification of the percent Oxytocin:Fos colocalized cells (not Fos:DAPI, as was written) in dorsal and ventral subregions of the PVN during active huddling and quiescent huddling. We have corrected the legend and clarified the quantification in the revised manuscript.

      The authors engage in a deep analysis of fiber photometry experiments, first by observing PVNOT neuron overall activity during a variety of different behaviors in the context of three different temperatures. Activity was associated with nesting, quiescence, and both types of huddling (when social opportunities exist). Social situations did not strongly affect this, nor did temperature conditions. These analyses indicate that the PVNOT neurons are involved in mediating specific behavioral outputs.

      With more detailed analysis, the authors investigated how PVNOT neuronal activity relates to behavioral state transition. They found that the probability of peak PVNOT neural activity strongly predicts the offset of quiescence or quiescent huddling, and therefore can be argued to signal an increase in physical activity, and as such, increased metabolism. However, the opposite pattern was observed for huddling and nesting (onset being associated with PVNOT activity), again arguing for increased thermogenesis as a function.

      What is particularly compelling is that these peaks of activity tend to occur during low Tb, again arguing for the function in increasing body warmth.

      The authors then employ an impressive setup where they image brown adipose tissue (BAT) in tandem with DeepLabCut (DLC) based animal tracking. Crucially, BAT activity and surface temperature correlated with the calcium peak of PVNOT neurons.

      Lastly, optogenetic activation of PVNOT neurons increased Tb when it was in the lower range, but not when in the higher range. It also affected BAT and rump temperature, again at low Tb. However, there is no real effect on behavior, except a trend in activity.

      The authors do some interesting tracing work at the end, though this is not functionally explored. That is not a criticism, as it does seem like this would be a whole follow-up study.

      Weaknesses:

      While novel and valuable, the manuscript feels incomplete in its current form.

      The main evidence lacking is a loss of function of the experiment. Ideally, the authors would chronically and/or acutely inhibit PVNOT neurons to establish their necessity. I know this seems obvious, but I think it is important.

      We agree with the reviewer that loss-of-function experiments are a valuable component of circuit mapping and we appreciate this suggestion. For transparency, we did attempt a chronic chemogenetic inhibition experiment using DREADDs in PVNOT neurons. However, the results were inconclusive, primarily owing to the confounding effects of pharmacological injections: both drug and vehicle-treated animals exhibited stress-induced hyperthermia following injection, and because inhibition could not be delivered while animals were asleep/resting the experimental conditions did not recapitulate the low-Tb quiescent state during which PVNOT peaks naturally occur. Given these confounds, we do not believe these data meet the standard required for inclusion in this manuscript.

      We did consider acute optogenetic inhibition. However, a clear prediction about inhibition was not as apparent in our model. Our photometry data identified a, testable hypothesis for activation: PVNOT peaks precede the exit from quiescence, therefore activation during quiescence should increase the transition, which it did (Figures 5 and 6).

      That said, new analyses of our data, driven by these reviews, have now uncovered what might be inhibition of PVNOT neurons during the approximate 60 seconds prior to entry to resting states (i.e., quiescence and quiescent huddling); see the new Fig. S3I-L. This raises the possibility that an appropriately timed photoinhibition of PVNOT neurons could facilitate the establishment of resting states. We believe that, in light of our chemogenetic and optogenetic activation experiments, for an inhibition experiment to be done appropriately would require a real-time, closed loop setup that is currently not available in our laboratory.

      We have added a caveat to the Discussion acknowledging the lack of LOF data as a limitation and have identified this as an important direction for future investigation.

      The relative lack of behavioral analysis following optogenetic activation of PVNOT neurons is puzzling. The authors must surely want to study what this intervention does to behavioral state transitions. I feel that the current level of analysis limits the overall conclusions of this study to a large extent.

      We appreciate this concern and wish to clarify two points.

      First, our decision to perform optogenetic activation in isolated (solo-housed) animals was driven by our initial finding that PVNOT activity profiles are mostly social-context independent during the transition from rest to arousal (Figures 2 and 3). By studying isolated animals, we could test the fundamental relationship between PVNOT activation and the rest-to-active transition without confounding social feedback. Additionally, we encountered technical challenges when using the SGBS thermographic model in paired contexts: the high thermal intensity at the point of contact between huddling mice created a thermal merging artifact that prevented accurate segmentation of individual body regions (BAT vs. rump).

      Second, we did examine the post-stimulation behaviors of solo-housed animals (Fig. S5B). While PVNOT activation significantly increased the probability of exiting quiescence, it did not trigger a singular, stereotyped behavioral output. Instead, it facilitated a generalized transition to an active state, within which animals engaged in various context-appropriate actions (nesting, grooming, locomotion). We note in the discussion that “Analysis of manually- annotated behaviors suggested that PVNOT stimulation did not activate a specific motor pattern output but instead resulted in combined increases in the time spent in nesting (linear mixed model estimate coefficient of ChR2+ stimulation: +38.0 sec), locomotion (+54.0 sec), and grooming (+14.5 sec), but not in eating/drinking (-0.4 sec) (Fig. S4B).”

      That photostimulation had relatively larger effects on nesting and locomotion is consistent with our model.

      Last, in the Discussion we acknowledge that future experiments should seek to disentangle the effects of PVNOT light simulation in the non-social vs social context (last paragraph of the Discussion section called “State-dependent PVNOT activity during thermo-behavioral transitions”).

      A broader criticism is that the social dimension of this manuscript seems overplayed. Naturally, oxytocin signaling can be implicated in social behavior based on a large literature. However, the focus on social thermogenesis seems like a crude integration of social behavior and thermogenesis. Given that the authors see their effects in both social and nonsocial cases of thermoregulation, I am not sure the attempts at integrating social functions and thermogenic functions of PVNOT neurons are warranted. That is, unless the authors have further experiments or analysis that can convincingly justify this link.

      We thank the reviewer for this comment. We understand the concern and wish to reframe our position. We argue that the equivalence of PVNOT signals across social and non-social contexts is itself a central finding. While the oxytocin system is widely regarded as a mediator of social bonding, and therefore a candidate mechanism underlying huddling, our data demonstrate that PVNOT neurons provide a signal for state-dependent thermoregulatory transitions that is unbiased by social context. Rather than overplaying the social dimension, we believe our study contextualizes the social function within a broader homeostatic role: PVNOT neurons facilitate transitions from rest to thermogenesis and arousal regardless of whether the resting state involves social huddling or solitary quiescence.

      While the thermoregulatory transitions are present in both contexts, we note that social context appears to modestly enhance some PVNOT downstream effects. Specifically, peak probability and frequency were slightly higher in the paired compared to solo context (Fig. 3F-I, Fig. S2D), and peaks were associated with a somewhat stronger increase in physical activity when a cagemate was present (Fig. 3B-E). Additionally, quiescent huddling (paired) bouts were associated with stronger body temperature regulation compared to solo quiescence (Fig. S3Q-V). This nuance supports that the social dimension is not overplayed but rather situated within a broader homeostatic function.

      We have revised the manuscript to ensure that this framing is consistent and clear. We emphasize that our goal was to uncover neural mechanisms underlying physiological transitions across behavioral and arousal states, using our social thermoregulation assay as a starting point (based on our previous publication). Counter to our initial hypothesis, the PVNOT signals generalized beyond the social setting.

      In addition, the analysis of virgin females and lactating mothers seems out of place in Figure 4.

      This point was echoed by Reviewers 1 and 3, and one we have taken several actions to address this. (Note this response is copy-pasted to the other reviewers).

      We agree with the reviewers that the rationale for the lactation data should be made more explicit. The primary purpose of this experiment was to validate the identity of oxytocinergic neurons of the PVN.

      Our efforts to use IHC to validate the identity of AAV-transfected cells were inconclusive, and we have now added new data to illustrate this point. We have added Fig. S4 that includes quantitative data on expression specificity. We observed significant variability in co-staining (OT+/GCaMP+) across brain slices, likely reflecting the dynamic nature of oxytocin peptide synthesis and storage, particularly with respect to processes lining the third ventricle. This finding is in accordance with other studies that are now cited in the text.

      We now emphasize that, because IHC provided variable co-localization, we employed the lactation model as an independent physiological validation of the identity of the recorded neurons.

      It is well established that PVNOT neurons undergo dramatic changes in firing dynamics and synchrony during lactation to support milk ejection (Yaguchi et al., 2023; Yukinaga et al., 2022). Conversely, AVP and CRF cell populations in the PVN do not appear to display synchronized pulsatile bursting during lactation (see response to Reviewer-2 comment-2 in ‘Recommendation for authors’ and our updated Discussion). Observing these characteristic changes in our recorded population provides high-confidence functional evidence that we are targeting oxytocin neurons. We have revised the text to clarify that Figure 4 serves primarily as a functional verification of genetic targeting.

      We also acknowledge in the Discussion the possibility that our Cre-line may capture a small percentage of nonoxytocinergic neurons, while noting that the dramatic shift in calcium dynamics during lactation (Figure 4I–L) strongly suggests the recorded population is dominated by oxytocin neurons.

      The c-Fos/oxytocin overlap needs to be quantified.

      We thank the reviewer for catching this; Reviewer 2 made a similar comment. A typo in the figure legend led to this confusion. Figure 1I is in fact a quantification of the percent Oxytocin:Fos colocalized cells (not Fos:DAPI, as was written) in dorsal and ventral subregions of the PVN during active huddling and quiescent huddling. We have corrected the legend and clarified the quantification in the revised manuscript. (Note this response is copy-pasted to other relevant comments).

      The methods section could be improved by explaining how the authors exclude animals that exhibit both types of huddling, if they occur within a 90-minute time window. This seems like it could cause significant confounds.

      We have clarified in the Methods that animals were not excluded if they exhibited both active and quiescent huddling during the recording session. Importantly, a prerequisite for inclusion in the FOS study was that animals had to be continually engaged in the target behavior for a minimum of 15 consecutive minutes from behavior onset, an established approach for behavior-driven immediate early gene mapping. The 90-minute window was then counted from that same onset for FOS IHC. Because active huddling frequently transitions directly into quiescent huddling (and vice versa), excluding such animals would have eliminated the majority of recordings. The heterogeneity of behavioral states within the FOS integration windows is precisely why we turned to fiber photometry, a technique with the temporal resolution necessary to dissociate neural signals associated with each behavioral state.

      The computer vision model is not well-explained. The authors need to be far more explicit here about how it was validated.

      We thank the reviewer for this comment and agree that the original manuscript did not sufficiently detail the validation framework. We have revised both the Methods and Results to explicitly detail how SGBS was evaluated.

      First, we now clearly describe model validation on a held-out dataset (20% of manually annotated images not used for training), reporting standard segmentation metrics (per-class IoU and Dice/F1) and directly comparing SGBS to an unmodified Mask R-CNN trained under identical conditions (same backbone initialization, dataset split, and training schedule). As shown in Fig. 5D, the skeleton-guided model converged more rapidly and achieved a lower final loss than the baseline network, demonstrating improved segmentation performance in occlusion-rich thermographic recordings.

      Second, we more explicitly describe an independent physiological validation step. SGBS-derived surface temperature trajectories were temporally aligned with simultaneously recorded implanted thermologger measurements, which were not used during model training. As shown in Fig. 5E, SGBS-derived signals strongly corresponded with core body temperature dynamics and reproduced expected thermophysiological relationships (e.g., BAT warming preceding core temperature rise). This establishes external validity beyond pixel-level segmentation metrics.

      The authors should cite and consider this preprint: https://www.biorxiv.org/content/10.1101/2024.09.17.613378v1

      We have cited this preprint (Raam et al., 2024) in the revised manuscript and integrated relevant findings into the Discussion, in the section called “Limitations and caveats”.

      Reviewer #2 (Public review):

      Summary:

      This is a very interesting study from Vandendoren and colleagues examining the role of PVN oxytocin neurons during thermoregulatory behaviors, in particular during thermoregulatory huddling. The findings are important and compelling, and have implications for the thermoregulation field as well as the social/naturalistic behavior field.

      Strengths:

      The study is very creative and tackles a challenging task to examine how natural and social behavior influences neural circuits for a homeostatic system such as thermoregulation. The authors use a combination of state-of-the-art tools (photometry, optogenetics, automated behavior tracking, thermal imaging, and core body temperature measurement), often in combination with each other, to produce a rigorous and high-dimensional dataset. Carrying out tightly temperature-controlled experiments and examining natural behavior, neural activity, and body physiology simultaneously is quite a feat. I applaud the authors for taking this on in a rigorous and detailed manner. This paper will be valuable for both the thermoregulation field as well as for researchers interested in naturalistic social behaviors. The conclusions are supported by the data.

      We appreciate the reviewer’s careful read and positive assessment of our integrated behavioral, neural, and physiological measurements and their relevance to both thermoregulation and social behavior.

      Weaknesses:

      I have a number of questions and suggestions for clarification that would help improve the interpretation of the findings.

      (1) Figure 1D-F: It would be helpful to include representative images of cFos expression in the PVN, LS, and DMH during both quiescent and solo huddling conditions, to better illustrate the reported differences.

      We have now addressed this in the revised manuscript. We had originally shown active huddle FOS expression in Fig. 1D-F and quiescent huddle in Fig. S1A-C. We have now added solo groom FOS expression to Fig. S1D-F.

      (2) Figure 1C: The data suggest a general suppression of neural activity during sleep-associated quiescent huddling, which somewhat complicates the interpretation of what specifically the active huddling cells are responding to. A more informative control might have been a comparison between huddling and a more generic form of social engagement (e.g., dyadic sniffing) to assess whether huddling-responsive neurons are broadly tuned to social stimuli. While it may not be feasible to add this experimentally at this time, a brief discussion of this limitation in the main text would be valuable.

      We thank the reviewer for this thoughtful suggestion. We agree that comparing huddling-responsive neurons with a more generic social engagement is an important consideration.

      We first note that the FOS study required animals to be continuously engaged in the target behavior for a minimum of 15 consecutive minutes, ensuring that FOS expression reflects sustained behavioral engagement rather than brief social contact. Furthermore, we believe the FOS association with active huddling in Figure 1C is likely driven by preceding bouts of quiescent huddling. Because these experiments were conducted during the light phase, active huddling bouts were almost always preceded by bouts of quiescent huddling.

      Given that FOS protein often integrates neural activity over ~60-90 minutes, the FOS signal during active huddling may reflect cumulative PVNOT activity during the quiescent to active transition, rather than active huddling by itself. This interpretation aligns with our fiber photometry data, which show that PVNOT peaks are concentrated at the offset of quiescent states and the onset of active states. Moreover, a broad-scale analysis of calcium data driven by these reviews, now shows there is a local minimum of PVNOT neurons during the transition into quiescent states and a local maximum of calcium activity during the offset of resting states and the onset of nesting and active huddling (Fig. S3I-L).

      To directly address whether PVNOT neurons are broadly tuned to social engagement or specifically associated with thermoregulatory state transitions, we examined neural activity during "Contact Initiated" (ConI) and "Contact Received" (ConR) events—brief social interactions (e.g., dyadic sniffing) that occur outside the context of huddling. These interactions, which typically last less than one second, did not trigger the large-amplitude calcium peaks observed during rest-to-arousal transitions. Specifically, there was no significant association between ConI or ConR events and PVNOT peak frequency or amplitude (Fig. S2H; Table S1; p = 0.505, p = 0.575, respectively). This reinforces our conclusion that PVNOT peaks are not a generic response to social stimuli but are specifically aligned with the coordinated autonomic and behavioral transitions required to exit a low-temperature quiescent state. We have added a clarifying paragraph to the Discussion.

      (3) Figure 2H-J vs. Figure 1: The fiber photometry data suggest increased PVN activity during quiescent huddling vs active huddling, which appears to contrast with the cFos results from Figure 1. It would be helpful for the authors to comment on possible reasons for this discrepancy-e.g., methodological differences, temporal resolution, or cell-type specificity.

      We agree that this apparent contrast deserves explicit discussion. The difference arises from the dramatically different temporal resolutions of the two techniques. Fiber photometry captures real-time neural dynamics at subsecond resolution, revealing that PVNOT neurons exhibit high-amplitude bursts primarily during the offset of quiescence (and to a lesser extent the onset of post-quiescence behaviors) (Figs. 3 and 5). Because these peaks occur while the animal is categorized as "quiescent," they appear as quiescence-associated activity in the photometry ethogram.

      Conversely, FOS integrates neural activity over ~30–90 minutes. In retrospect, and in light of our photometry data, an animal categorized as "Active Huddling" in the FOS study is one that has likely experienced PVNOT bursts and subsequently transitioned to an active state. The higher FOS signal in active animals therefore likely represents the cumulative activity of the transition itself and sustained activity in the active state.

      We have added a clarifying statement to the Discussion section, in the section called “State-dependent PVNOT activity during thermo-behavioral transitions”.

      (4) Figure 2O: A comparable linear regression for active huddling would be informative to assess whether the observed relationships extend across behavioral states.

      We agree. We have added linear regression analyses for active huddling and nesting to Fig. S2K-N including rsquared values, to complement the resting analyses in Figure 2O and 2L.

      This analysis shows that active huddling peak counts are also positively correlated with active huddle duration (but not nesting duration). The text has been updated accordingly.

      (5) Temperature manipulation: The use of floor temperature changes presents a distinct physiological and sensory experience from, for example, manipulation of ambient temperature. A discussion of how this choice may affect neural circuit engagement or interpretation of thermoregulatory responses would be beneficial.

      Both Reviewer 1 and Reviewer 2 raise important and related points: manipulating floor temperature provides a thermal stimulus that is distinct from manipulating whole-chamber ambient air temperature, and these modalities could engage partially different sensory pathways and circuits. (Note this response is copy-pasted to other relevant comments).

      We intentionally used floor cooling/heating because it provides a reliable, well-controlled stimulus that elicits thermoregulatory behaviors while keeping the experimental environment stable (e.g., avoiding changes in airflow/humidity that can accompany ambient cooling). To prevent conflation of these modalities, we revised the manuscript to consistently describe the manipulation as “floor temperature” (and not “ambient temperature”), and we added Discussion acknowledging that conductive floor temperature changes may differentially recruit peripheral thermoreceptors compared to ambient air temperature.

      While extending these experiments to whole-chamber ambient temperature changes could be informative in future work, it is not required for the central interpretations here, which focus on PVNOT activity dynamics during thermoregulatory behavior under controlled thermal conditions.

      (6) Correlations with behavior: Across the manuscript, it would be informative to see correlations between huddle duration and neural activity (e.g., cFos expression, calcium signal magnitude). Similarly, do longer huddles produce greater thermogenic effects?

      This is a great suggestion. The first point about huddle duration and neural activity echoes the Reviewer’s comment (4) above. For this point, we now show that the duration of active huddling is positively correlated with PVNOT peak count (Fig. S2K), which is similar to what we had shown for quiescence and quiescent huddling (Fig. 2K-P).

      Next, the point about huddle duration and thermogenic effects is also helpful. We have now added new analysis and panels to address this (Fig. S3M-R). We find that the duration of quiescent huddle bouts is negatively correlated with Tb (Fig. S3V). The other behaviors examined did not show correlations between duration and Tb. This finding supports our previous demonstration that quiescent huddling is an energy saving state in mice (Landen et al., 2024).

      Finally, we note that longitudinal correlations between bout length and peak counts are already reported in Fig. S3A-H.

      (7) Lactating vs. virgin mothers: The inclusion of maternal data is intriguing but feels somewhat disconnected from the central huddling-thermoregulation narrative. If these experiments are to remain, additional explanation of their rationale and how they fit into the broader story would help clarify their relevance.

      This point was echoed by Reviewers 1 and 3, and one we have taken several actions to address this.

      We agree with the reviewers that the rationale for the lactation data should be made more explicit. The primary purpose of this experiment was to validate the identity of oxytocinergic neurons of the PVN.

      Our efforts to use IHC to validate the identity of AAV-transfected cells were inconclusive, and we have now added new data to illustrate this point. We have added Fig. S4 that includes quantitative data on expression specificity. We observed significant variability in co-staining (OT+/GCaMP+) across brain slices, likely reflecting the dynamic nature of oxytocin peptide synthesis and storage, particularly with respect to processes lining the third ventricle. This finding is in accordance with other studies that are now cited in the text.

      We now emphasize that, because IHC provided variable co-localization, we employed the lactation model as an independent physiological validation of the identity of the recorded neurons.

      It is well established that PVNOT neurons undergo dramatic changes in firing dynamics and synchrony during lactation to support milk ejection (Yaguchi et al., 2023; Yukinaga et al., 2022). Conversely, AVP and CRF cell populations in the PVN do not appear to display synchronized pulsatile bursting during lactation (see response to Reviewer-2 comment-2 in ‘Recommendation for authors’ and our updated Discussion). Observing these characteristic changes in our recorded population provides high-confidence functional evidence that we are targeting oxytocin neurons. We have revised the text to clarify that Figure 4 serves primarily as a functional verification of genetic targeting.

      We also acknowledge in the Discussion the possibility that our Cre-line may capture a small percentage of non-oxytocinergic neurons, while noting that the dramatic shift in calcium dynamics during lactation (Figure 4I–L) strongly suggests the recorded population is dominated by oxytocin neurons.

      (8) Optogenetic manipulation: Have the authors tested the effect of PVN OT neuron stimulation or inhibition during huddling? Even a negative result would be of interest to the field. If these data exist (main or supplementary), I apologize for missing them. If not, the authors might consider including them or commenting briefly on any attempts or challenges in carrying out these experiments.

      We thank the reviewer for this question. We have not performed optogenetic manipulation during huddling. Our decision to perform optogenetic activation in solo-housed animals was driven by our fiber photometry finding that PVNOT activity profiles during the rest-to-arousal transition are social-context independent (Figures 2 and 3). Had the GCaMP data suggested that PVNOT peaks were specific to social huddling, optogenetic manipulation during huddling would have been the natural next experiment. However, because peaks aligned with thermoregulation broadly, rather than social behavior specifically, we designed our functional experiments to test the circuit's role in driving the autonomic and behavioral arousal transition.

      We also note that our experience with chemogenetic manipulation suggests that pharmacological approaches to study the rest-arousal transitions during huddling are not currently feasible. As described to our response to Reviewer 1, our DREADD inhibition experiments were confounded by stress-induced hyperthermia following injection, and because drug delivery could not occur while animals were asleep and resting, the experimental conditions failed to recapitulate the low-Tb quiescent state during which PVNOT peaks naturally occur. We share this experience because we believe it will be informative for others in the field considering similar approaches.

      Additionally, as described above (Reviewer 1, #5), the SGBS thermographic model encounters artifacts in paired contexts due to thermal merging between huddling mice. We have added a note in the Discussion addressing this, in the section called “Limitations and caveats”.

      Reviewer #3 (Public review):

      Summary:

      The authors aimed to elucidate the relationship between physiological state (i.e., behavioral status and thermogenic sympathetic activity) and the activity of hypothalamic paraventricular oxytocin (PVNOT) neurons in female mice. They studied this by combining automated classification of mouse behavior via video-based analysis with calcium imaging of PVNOT neuron activity. Sympathetic thermogenesis was inferred from surface temperature changes captured by infrared thermography, and the authors provided their custom analysis scripts in the manuscript. Notably, they found that a strong, pulsatile activation of PVNOT neurons was "occasionally" observed immediately before the animals transitioned from a resting to an active state. This pulsatile activity was observed in both pair-housed and individually housed animals. While PVNOT neurons are often associated with social behaviors, this finding suggests that the oxytocinergic system is also engaged during naturalistic behaviors, even in the absence of social interactions. If experiments were more convincingly performed and presented, the results would point to a broader physiological role of central oxytocin, including in the regulation of fundamental brain states and homeostatic processes, and offer a new perspective on the functional significance of central oxytocin signaling.

      Strengths:

      The oxytocinergic neural system is believed to subserve a wide range of physiological functions, and elucidating these roles requires monitoring PVNOT neuronal activity under various behavioral contexts, as well as manipulating this activity to establish causal links. In the present study, the authors show a technically sound experimental framework that integrates behavioral tracking in both individually and group-housed mice with the observation and manipulation of PVNOT neuron activity. This experimental setup represents a valuable methodological resource for researchers investigating the physiological functions of oxytocin.

      We thank the reviewer for the thoughtful review and for recognizing the value of our integrated framework for monitoring and manipulating PVNOT neuronal activity across behavioral contexts.

      Weaknesses:

      While this study successfully established a new experimental setup for simultaneous analyses of behavior and PVNOT neuronal activity, there are several concerns regarding the interpretation of the results and the robustness of the conclusions, which should be more thoroughly addressed.

      (1) The study relies on the assumption that calcium imaging and optogenetic manipulation were restricted only to PVNOT neurons. However, the specificity of AAV-mediated gene expression was not verified quantitatively. A fair number of cell bodies in the PVN expressed GCaMP8s, but not OT, indicating potential off-target expression (see Figure S2A, B). The lack of quantitative validation weakens confidence in the causal interpretation of the results.

      This point was echoed by Reviewers 1 and 3, and one we have taken several actions to address this.

      We agree with the reviewers that the rationale for the lactation data should be made more explicit. The primary purpose of this experiment was to validate the identity of oxytocinergic neurons of the PVN.

      Our efforts to use IHC to validate the identity of AAV-transfected cells were inconclusive, and we have now added new data to illustrate this point. We have added Fig. S4 that includes quantitative data on expression specificity. We observed significant variability in co-staining (OT+/GCaMP+) across brain slices, likely reflecting the dynamic nature of oxytocin peptide synthesis and storage, particularly with respect to processes lining the third ventricle. This finding is in accordance with other studies that are now cited in the text.

      We now emphasize that, because IHC provided variable co-localization, we employed the lactation model as an independent physiological validation of the identity of the recorded neurons.

      It is well established that PVNOT neurons undergo dramatic changes in firing dynamics and synchrony during lactation to support milk ejection (Yaguchi et al., 2023; Yukinaga et al., 2022). Conversely, AVP and CRF cell populations in the PVN do not appear to display synchronized pulsatile bursting during lactation (see response to Reviewer-2 comment-2 in ‘Recommendation for authors’ and our updated Discussion). Observing these characteristic changes in our recorded population provides high-confidence functional evidence that we are targeting oxytocin neurons. We have revised the text to clarify that Figure 4 serves primarily as a functional verification of genetic targeting.

      We also acknowledge in the Discussion the possibility that our Cre-line may capture a small percentage of nonoxytocinergic neurons, while noting that the dramatic shift in calcium dynamics during lactation (Figure 4I–L) strongly suggests the recorded population is dominated by oxytocin neurons.

      (Note, we have updated Figure S2A,B to more accurately reflect the extent of co-localization in this image).

      (2) The study focuses on the transition from rest to active states following pulsatile activity of PVNOT neurons. However, the physiological significance of this pulsatile activity remains unclear. According to the authors, pulsatile activity occurred with an approximately 20% probability within 100 seconds prior to the end of the resting state. This implies that, in the remaining 80% of rest-to-active transitions, pulsatile PVNOT activity did not occur, suggesting that it is not essential for initiating the transition. A comparative analysis of behavioral and thermogenic changes between transitions with and without pulsatile PVNOT activity would help to further clarify the functional relevance of this phenomenon and strengthen the authors' interpretation of the findings.

      These are excellent points, and here we address them separately.

      (1) probability of transitions.

      We agree that our wording could be misread and we have revised the text for clarity. The “~20%” value is not the fraction of rest-to-active transitions that exhibit pulsatile PVNOT activity within a 100-s window. Instead, Fig. 3F,H report an instantaneous (per-second) probability of observing a calcium peak as a function of time-to-bout offset (logistic regression). In other words, the probability of a peak increases sharply as the animal approaches rest offset (e.g., from ~2–3%/s near onset to ~14%/s for quiescence and ~25%/s for quiescent huddling near offset), indicating a strong state-dependent increase in peak likelihood rather than an all-or-none trigger.

      We further clarify in the Discussion that we do not claim PVNOT peaks are essential for initiating every transition; rather, PVNOT activity biases or enhances the probability of transition toward thermogenesis and behavioral arousal (added to section called “State-dependent PVNOT activity during thermo-behavioral transitions”).

      (2) the effect of peaks on transitions

      This is a very helpful suggestion and we agree that directly comparing transitions with vs. without pre-offset pulsatile PVNOT activity could strengthen interpretation of the functional relevance of these events. We have therefore added a new transition-aligned analysis of thermogenic dynamics at rest-to-active transitions (new Fig. 3P&S; and corresponding text in the Results and Statistics sections).

      Briefly, we extracted peri-transition body temperature (Tb) traces (−300 to +300 s) aligned to the offset of quiescence and quiescent-huddling bouts and classified each transition as Peak+ if it contained one or more calcium peaks in the 100 s preceding bout offset, and Peak− otherwise. To account for inter-individual differences in “balance point,” Tb was z-scored within mouse. We then quantified the post-offset thermogenic rise for each transition as the change in scaled temperature from a pre-offset baseline (−60 to 0 s) to the post-offset interval (0 to 300 s) and tested Peak+ vs Peak− differences using linear mixed-effects models. This revealed that Peak+ transitions exhibited significantly larger post-offset increases in scaled Tb than Peak− transitions for both quiescence offsets and quiescent-huddling offsets.

      Together, these results indicate that while pulsatile PVNOT activity is not present prior to every rest-to-active transition, when it occurs it is associated with a stronger thermogenic rise, consistent with a probabilistic modulatory role in promoting the transition rather than being strictly required to initiate it.

      We are grateful for this suggestion as this new data is very informative in the context of our model.

      (3) The study identifies a correlation between pulsatile activity of PVNOT neurons and rest-to-active transitions, and tests for a causal relationship using optogenetic stimulation. However, since PVNOT neurons are known to co-release other neurotransmitters such as glutamate, it remains unclear whether the observed effects are mediated specifically through oxytocin receptor signaling. To address this question, functional intervention experiments using oxytocin receptor antagonists or receptor knockout mice are necessary.

      We agree with the reviewer that PVNOT neurons co-release glutamate and that isolating the specific contribution of oxytocin signaling versus co-transmitted signals is an important question. However, our study was designed to identify the functional role of the PVNOT cell type during thermoregulatory state transitions, not to dissect the molecular mechanism of signaling at downstream targets. By demonstrating that the endogenous activity of this specific population aligns with the rest-arousal window and that their activation is sufficient to drive the phenotype, we provide an anatomical and functional framework for future mechanistic investigations.

      We also note that we provide anatomical evidence supporting a possible peptidergic mechanism: PVNOT neuron projections to the rostral medullary raphe (rMR), a key thermogenic control site, alongside oxytocin receptor mRNA expression in this region (Fig. S5). This anatomical link suggests a plausible pathway for oxytocinergic modulation of thermogenesis, but of course does not rule in/out glutamatergic signaling. We acknowledge this limitation in the Discussion and frame pharmacological and receptor knockout studies as important next steps.

      We address these points in the Discussion, in the section called “Limitations and caveats.”

      (4) The authors attempted to detect BAT thermogenesis and skin vasomotion using infrared thermography. This technique measures only skin hair temperatures (since the skin was not shaved), but does not measure "BAT temperature" or "vasomotor tone". As seen in Figure 5E, the temperatures of the body surface areas ("BAT", "Rump", and "Dorsal surface") mostly changed in parallel, indicating that these temperatures are strongly affected by body core temperature. Therefore, the thermographic measurements in this study did not provide convincing information on BAT thermogenesis or skin vasomotion. To avoid misleading reports, the authors need to use other techniques to directly measure temperatures, such as telemetry.

      We agree that infrared thermography measures surface radiance rather than internal tissue temperature. We have revised the manuscript to use more precise language (e.g., "surface temperature over the interscapular BAT region" rather than "BAT temperature"). However, surface measurements are not merely passive reflections of core temperature. Here we add background and explanation about our thermography data:

      Background on our approach

      Infrared thermography provides a non-invasive readout of heat emission over the interscapular region and has been validated as reporting UCP1-dependent BAT thermogenesis in mice under adrenergic stimulation (Crane et al., 2014). That said, there are known confounds (insulation/adiposity, blood flow, protocol variability) and standardized protocols are needed (Law et al., 2018). Direct telemetry or implanted thermocouples offer superior precision for measuring BAT temperature, so long as the probe is sutured to BAT itself or to Sulzer’s vein–a technical challenge because probes tend to drift over time (e.g., (Dodson et al., 2024)).

      Our BAT findings in context:

      Using SGBS, we demonstrate that the interscapular BAT region is significantly warmer than the adjacent rump surface (Fig. 5C). If surface temperature were purely a reflection of uniform core temperature, this consistent regional hotspot would not be observed.

      Our cross-correlation analysis from the photometry (Fig. 5E) shows the rise in BAT surface temperature precedes changes in other body regions by approximately 90 seconds, suggesting that BAT acts as a primary heat source during rest-to-arousal transitions rather than passively following core temperature. This finding is consistent with another study, using telemetric probes placed in BAT, finding that episodic onset of BAT temperature started to increase 3 minutes before body temperature (Ootsuka et al., 2009).

      Based on this Reviewer’s comment here and the subsequent one (5), we have now added a new analysis of the temporal patterning of arousal and thermogenesis in the optogenetic cohort of animals; see below for details.

      Vasomotor tone

      We agree that infrared thermography does not directly measure vasomotor tone. We have revised the text to remove language implying that our measurements directly quantify vasomotor tone, vasodilation or vasoconstriction.

      We note that the established approach for non-invasive assessment of vasomotion uses glabrous skin of the tail and ears (Garami et al., 2011; Meyer et al., 2017; Škop et al., 2020). Rump surface temperature measured over hairy, non-glabrous skin correlates more closely with core body temperature than with cutaneous vasomotor tone (Meyer et al., 2017; Škop et al., 2020) and is used in the literature as a reference point for calculating BAT thermogenesis.

      In our data, rump surface temperature decreased following PVNOT calcium peaks while BAT and dorsal surface temperatures increased (Fig. 5L-M). This pattern is consistent with sympathetically-driven thermogenesis in which peripheral heat loss is reduced while BAT drives core temperature upwards. We now acknowledge that our rump measurements do not isolate vasomotor contributions. We have revised the manuscript accordingly, replacing references to rump vasoconstriction with language describing the observed thermal pattern while avoiding attribution to a specific thermoeffector mechanism.

      Finally, we note that telemetry would strengthen deep-body temperature interpretation, but telemetry does not itself quantify vasomotor tone; the same distal heat-loss readouts described above would be required regardless of core Tb methodology.

      In sum, infrared thermography enables non-invasive, simultaneous tracking of multiple thermal features in freely moving, undisturbed animals—a requirement for studying the naturalistic state transitions central to this study. We have added a section to the Discussion acknowledging the limitations of surface infrared thermography.

      (5) Photostimulation of PVNOT neurons increased Tb after 400 sec (6.6 min) (Figure 5). This latency is too long to conclude that the neuronal stimulation elicited BAT thermogenesis. A more reasonable explanation is that the increase in Tb was caused by the induction of physical activity (Figure S4C), which slowly generates heat and contributes to the elevation of Tb. However, this view contradicts the authors' claim. To address this concern, the authors should directly measure BAT thermogenesis and compare it with the rate of Tb elevation. If BAT thermogenesis occurs, the rate at which the BAT temperature increases must exceed the rate at which Tb rises.

      We thank the reviewer for this thoughtful critique. With this response we first provide additional context about the timeline of temperature increases, and second add a new analysis addressing the relative contributions of activity and BAT-surface to Tb changes.

      (1) Additional context on the temporal progression

      First, the observed timescale does not, per se, rule out a contribution of BAT thermogenesis. While the kinetics of BAT activation and associated Tb increases can operate on a fast timescale in anesthetized animals, in vivo activation of BAT thermogenesis pathways can take several minutes to yield a statistically detectable difference. For example, activation of DMH→rMR glutamatergic signaling, a canonical thermogenic command pathway, takes several minutes to produce a significant increase in both Tb and BAT using telemetric temperature probes (Kataoka et al., 2014).

      This timescale could also be consistent with peptidergic neuromodulation by PVNOT neurons, which are more likely to be modulators (and not drivers) of the canonical thermogenic pathway. Oxytocin is known to act via volume transmission and metabotropic receptor signaling, which operate on slower timescales than ionotropic neurotransmission (Ludwig and Leng, 2006). Downstream recruitment of sympathetic outflow and BAT thermogenesis is likewise a multistep autonomic process, not an immediate synaptic event.

      Next, the thermal dynamics reported in Figure 5 and Figure S4 are not consistent with activity-induced heat production alone. Specifically:

      - Thermal increases were spatially localized to interscapular/dorsal regions corresponding to BAT depots before generalized surface warming.

      - Importantly, photostimulation-induced warming was observed even during behavioral states characterized by low baseline activity, suggesting that thermogenic activation was not simply a byproduct of movement.

      While we did not directly measure BAT sympathetic nerve activity, our surface thermography approach was designed specifically to resolve regional temperature dynamics over the interscapular BAT area. The spatial specificity and temporal profile of the warming are consistent with BAT thermogenesis rather than uniform musclegenerated heat.

      We acknowledge that direct measurement of BAT sympathetic activity or oxygen consumption would provide additional mechanistic resolution. However, given (i) the known role of PVN oxytocin neurons in autonomic regulation, (ii) the spatially localized dorsal temperature increase, and (iii) the temporal dissociation between stimulation onset and gradual systemic Tb rise, we conclude that BAT thermogenesis remains the most parsimonious explanation.

      We have revised the Discussion to more explicitly acknowledge these temporal dynamics by clarifying that photostimulation likely follows the timescales of peptidergic neuromodulation.

      (2) New analysis

      We have added a new analysis to address the relationship between Tb and BAT-surface temperature and locomotion the optogenetic cohort. In short, we show that across all mice changes in BAT typically precede changes in Tb, and that the effect of optogenetic stimulation on core Tb can’t be explained by physical activity (nor can it be explained by BAT-surface temperature).

      First, cross-correlation of derivatives suggested BAT surface temperature changes typically precede changes in dTb/dt across mice, whereas physical activity changes did not consistently precede dTb/dt. This result, now shown in Fig. S5G, is consistent with our cross-correlation analysis of the fiber-photometry cohort.

      Next, we used a lagged regression analysis to test whether photostimulation-evoked increases in core temperature are fully mediated by physical activity. Specifically, we modeled the derivative of core Tb (dTb/dt) using an impulseresponse representation of photostimulation, while controlling for distributed lags (0–120 s) of physical activity and BAT surface temperature derivative, with random effects for mouse and trial. Photostimulation remained a significant predictor of dTb/dt while controlling for activity and BAT-surface (likelihood ratio test, χ<sup>2</sup>=7.66, p=0.0056), indicating that the relationship between stimulation and Tb is not fully explained by activity.

      Recommendations for the authors:

      Editors note:

      We suggest including key statistical support for the claims in the main text (e.g., results or figure legends).

      We have added statistical support for key claims in the main text results. We have also added references to Table S1 where appropriate (e.g., where there is a long list of statistical results); we hope this aids the readability of the report.

      Reviewer #1 (Recommendations for the authors):

      See above - the authors should decide what to prioritize, but I only mention significant concerns above. The manuscript could be improved to 'Convincing' or even 'Compelling' with sufficient effort.

      Thanks for the careful reading of the manuscript. We’ve addressed many of these points, and feel the manuscript has been strengthened as a result.

      There were also some text errors here and there.

      Several text errors were identified and fixed. Thank you.

      Reviewer #2 (Recommendations for the authors):

      (1) Figure 1I: The quantification shown here is a bit unclear from the figure and legend - are the authors reporting the percentage of cFos+ cells within the OXT+ population, or within the general DAPI+ population? If the latter, including a co-localization analysis to estimate the proportion of OXT+ cells activated would strengthen the interpretation.

      We thank the reviewer for catching this; Reviewer 1 made a similar comment. A typo in the figure legend led to this confusion. Figure 1I is in fact a quantification of the percent Oxytocin:Fos colocalized cells (not Fos:DAPI, as was written) in dorsal and ventral subregions of the PVN during active huddling and quiescent huddling. We have corrected the legend and clarified the quantification in the revised manuscript. (Note this response is copy-pasted to other relevant comments).

      (2) PVN cell types: It would be useful to briefly discuss the potential involvement of other PVN populations (e.g., CRF, AVP neurons) in huddling, given their known roles in social behavior, stress, and thermoregulation.

      Thank you for the insightful comment. We address these points in two parts.

      (1) PVN cell types and huddling

      Regarding the specific connection between these cell types and huddling: to our knowledge, no study has directly tested the effect of PVN CRF or PVN AVP neuron manipulation on huddling behavior. The most relevant data come from Bendesky et al. (Bendesky et al., 2017), who found that intracerebroventricular administration of AVP in Peromyscus inhibited nest building but had no effect on huddling, licking, or pup retrieval (though this pharmacological approach does not isolate PVN AVP neurons specifically). Their chemogenetic manipulation of PVN AVP neurons in Mus musculus confirmed the nest-building effect but did not assess huddling. For CRF, the available evidence suggests an opposing role to OT in social care contexts: chemogenetic activation of PVN CRF neurons impairs maternal behavior in postpartum mice (Melón et al., 2018), and intracerebroventricular CRF administration suppresses maternal care and can induce pup-killing in virgin rats (Pedersen et al., 1991).

      That said, PVN AVP neurons do promote wakefulness via lateral hypothalamic orexin neurons (Islam et al., 2022) and a recent preprint has implicated PVN AVP neurons in temperature-dependent maternal thermoregulatory behaviors, including co-nesting and shepherding, via projections to the central amygdala (Adahman et al., 2025). Notably, while that study focused on AVP neurons, their c-Fos data also revealed significant temperature-dependent modulation of PVNOT neurons (Fig. 3B), with suppressed activity at thermoneutrality relative to cooler conditions, a pattern suggesting that OT neurons are active under conditions where thermoregulatory effort is required. This data is consistent with our findings on PVNOT neuron involvement in rest-to-arousal transitions driven by thermoregulatory need.

      Additionally, Inada et al. (Inada et al., 2025) used an elegant series of viral-genetic experiments to demonstrate that PVN AVP neurons facilitate paternal caregiving behaviors via AVP to oxytocin receptor crosstalk in the preoptic area. Critically, their fiber photometry and circuit mapping data showed that chemogenetic activation of PVN AVP neurons did not recruit PVN OT neurons (Fig. 4), indicating that these populations operate independently in this context. We believe this finding is consistent with our interpretation that the thermoregulatory signals we observe reflect a cell-type specific property of PVNOT neurons. Future work examining how PVNOT, AVP, and CRF population interact during thermoregulatory state transitions would be valuable.

      (2) PVN cell types and stress and thermoregulation

      PVN CRF and AVP neurons have established roles in stress responses and social behavior, and future studies examining their involvement in huddling would be valuable. However, their direct roles in thermoregulation are limited. PVN CRF neurons are primarily stress-axis regulators whose thermoregulatory influence is mediated indirectly through downstream targets such as the DMH (reviewed in (Morrison and Nakamura, 2019)). AVP's thermoregulatory role is principally as an endogenous antipyretic acting via preoptic area neurons (Tabarean, 2021), rather than through PVN magnocellular AVP neurons.

      Importantly, the synchronized pulsatile bursting pattern that is characteristic of OT neurons during lactation (which serves as a key validation benchmark for our PVNOT calcium peaks), appears to be specific to OT neurons and does not generalize to other PVN populations. One study (Popescu et al., 2019) directly demonstrated that lactation-induced IPSC burst upregulation occurs selectively in OT magnocellular neurons, with no change in VP neurons within the same nucleus. VP neurons do exhibit phasic bursting, but these patterns are asynchronous, of longer duration, and serve antidiuretic rather than neuroendocrine-pulsatile functions (De Mota et al., 2004; Poulain et al., 1977; Wakerley et al., 1978). To our knowledge, no studies have reported synchronized burst activity in PVN CRF neurons during lactation or at rest. We have added a brief discussion of these points to the manuscript.

      (3) Figure 2B: Several behavioral abbreviations (e.g., LMA) are not intuitive and are missing from the legend. Spelling them out or including schematic illustrations would improve clarity.

      We have expanded the figure legends to define all behavioral abbreviations: LMA (Locomotor Activity), EaDr (Eating or Drinking), Groom (Grooming), Nest (Nesting or Nest Building), Quies (Quiescence), Sta (Stationary), ConI (Contact Initiated), ConR (Contact Received), AHud (Active Huddle), QHud (Quiescent Huddle).

      Reviewer #3 (Recommendations for the authors):

      (1) Figures 1D-F and S1A-C: The current magnification is insufficient to clearly resolve the distribution of FOS signals. FOS fluorescence is generally expected to be localized within cell nuclei. However, particularly in Figure 1F, the signals exhibit punctate or fibrous staining in addition to nuclear localization.

      This raises concerns about the quality of the tissue staining and the reliability of subsequent analyses. Including higher-magnification images would strengthen the credibility of the data presented.

      Thanks for the careful observation. We used a well-validated FOS protocol (see Methods; c-Fos (9F6) Rabbit mAb, Cell Signaling, 14609, 1:1000 dilution in block solution).

      To address this issue, in Figure 1 we have included better images of the regions of interest (DMH, LS, and PVN). We also show an inset with DAPI and the FOS IHC. These inset images show that the FOS signal does co-localize with nuclei.

      The reviewer notes that there is a fibrous staining in the PVN. We too noted this type of staining, due to clusters of bright dots in the PVN but not in other regions. This pattern was reproducible across several histological experiments. Fortunately, these bright dots were easily removed in our image processing routine using a selective median filter (pixel radius < 2.0 and and pixel intensity > 50).

      (2) Figures 2A, 4C, and 6A: As mentioned in the Public Review, the specificity of AAV-mediated gene expression is critical for the strength of the conclusions. Quantitative data demonstrating the expression specificity should be included.

      This point was echoed by Reviewers 1 and 3, and one we have taken several actions to address this. (Note this response is copy-pasted to the other reviewers).

      We agree with the reviewers that the rationale for the lactation data should be made more explicit. The primary purpose of this experiment was to validate the identity of oxytocinergic neurons of the PVN.

      Our efforts to use IHC to validate the identity of AAV-transfected cells were inconclusive, and we have now added new data to illustrate this point. We have added Fig. S4 that includes quantitative data on expression specificity. We observed significant variability in co-staining (OT+/GCaMP+) across brain slices, likely reflecting the dynamic nature of oxytocin peptide synthesis and storage, particularly with respect to processes lining the third ventricle. This finding is in accordance with other studies that are now cited in the text.

      We now emphasize that, because IHC provided variable co-localization, we employed the lactation model as an independent physiological validation of the identity of the recorded neurons.

      It is well established that PVNOT neurons undergo dramatic changes in firing dynamics and synchrony during lactation to support milk ejection (Yaguchi et al., 2023; Yukinaga et al., 2022). Conversely, AVP and CRF cell populations in the PVN do not appear to display synchronized pulsatile bursting during lactation (see response to Reviewer-2 comment-2 in ‘Recommendation for authors’ and our updated Discussion). Observing these characteristic changes in our recorded population provides high-confidence functional evidence that we are targeting oxytocin neurons. We have revised the text to clarify that Figure 4 serves primarily as a functional verification of genetic targeting.

      We also acknowledge in the Discussion the possibility that our Cre-line may capture a small percentage of non-oxytocinergic neurons, while noting that the dramatic shift in calcium dynamics during lactation (Figure 4I–L) strongly suggests the recorded population is dominated by oxytocin neurons.

      (3) Figure 2D: The authors should show an expanded view of a representative "PVNOT peak" from the spikes presented.

      We have added a representative peak to Fig. 2D.

      (4) Figure 2E-J: All the abbreviations of the behavioral states must be defined in the figure or legend.

      We added these abbreviations to the legend, and a text box reading “See legend for abbreviations” to the schematic.

      (5) Figure 2F, G, I, and J: The units on the y-axis should be indicated to facilitate interpretation.

      We have added these units. Thanks.

      (6) Figure 3A: Three large PVNOT peaks occurred between 01:30 and 02:00. However, these peaks did not cause an obvious transition in behavioral states or an increase in Tb within several minutes. Therefore, statements such as "PVNOT neurons predict transitions towards thermogenesis and behavioral arousal" in the text and subheading (pages 7 and 9) are questionable.

      We thank the reviewer for this careful observation. The three peaks between 01:30 and 02:00 that do not immediately lead to a behavioral transition illustrate a key aspect of our findings: the relationship between PVNOT activity and state transitions is probabilistic and state-dependent, not deterministic. Our logistic regression analysis (Fig. 3F, H, J, L) demonstrates that peaks increase the probability of a transition (up to ~20% per second) rather than acting as an obligatory "on switch." While individual variability exists in any single trace, the group-level analysis reveals a statistically significant increase in physical activity following PVNOT peaks (Fig. 3B–E).

      We therefore use ‘predict’ in a probabilistic sense: PVNOT peaks increase the conditional probability of impending state transitions in a manner that depends on behavioral context, rather than acting as an obligate trigger in every instance. We have taken care to not claim that PVNOT neurons are a necessary causal factor for transitions towards thermogenesis and arousal.

      We have updated the figure legend to clarify that Figure 3A shows an individual example trace, and revised the subheading on page 7 to more accurately reflect the probabilistic nature of this relationship: "PVNOT neurons predict increased likelihood of transitions towards thermogenesis and behavioral arousal in social and non-social contexts".

      We qualified the word “predicts” with “probabilistically” in the third paragraph of this section.

      Finally, this comment is related to the Reviewer’s comment-2 in the Public Reviews. To address that comment, we added a new analysis (now Fig. 3P&S) which shows that the presence of a peak in a bout of rest increases the thermogenic trajectory compared to bouts without a peak.

      (7) Figure 3F and H: If PVNOT peaks contribute to the initiation of transitions into the active state, the probability of peak occurrence should reach its maximum prior to the quiescence offset. However, the figures do not present the probability trajectory after the offset, which limits the ability to evaluate the authors' interpretation. Reanalysis extending to 150 seconds post-offset would be needed to clarify this issue.

      Thank you for this suggestion. We agree that examining PVNOT dynamics around the period following quiescence (and quiescent huddling) offset can further inform how PVNOT activity relates to rest-to-active transitions, and this has led to new insights within the manuscript.

      For background, in the original analysis (Fig. 3F,H), we used logistic regression to quantify how peak probability differs between bout onset versus near bout offset. We focused these analyses on the the timeframe of the bouts themselves (plus a small margin) because, in freely behaving animals, the pre-onset and post-offset period is heterogeneously composed of multiple potential subsequent behaviors (e.g., brief re-entry into quiescence, nesting, active huddling, locomotion, etc), which would confound a single post-offset probability trajectory (unless offsets are stratified by the identity of the subsequent behavioral state–beyond the scope of this paper).

      To address this concern, we now expand our peri-event baseline calcium analysis to include three minutes before and three minutes after both bout onset and bout offset for all four behaviors (new Fig. S3I–L). These extended traces show that for the two resting states (quiescence and quiescent huddling), baseline PVNOT calcium reaches a minimum near bout onset and a maximum near bout offset, whereas for the two active states (nesting and active huddling) baseline calcium shows the opposite pattern (maximum near onset, minimum near offset). Thus, the expanded post-offset analyses provide a more complete view of PVNOT calcium dynamics across the requested post-offset epoch and further support the conclusion that PVNOT activity is aligned with (and elevated around) behavioral transitions in a state-dependent manner. We have updated the Results text accordingly and now explicitly reference these new extended peri-event baseline analyses.

      (8) Figures 4H and I: Figure 4H shows that the waveform in the PPD2-7 group has a narrower FWHM than the Virgin group, which is the opposite of the group data in Figure 4I. Presenting scaled waveforms in parallel would allow for a clearer comparison across groups.

      Thank you for pointing out the inconsistency between the representative waveform in Fig. 4H and the group summary in Fig. 4I. You were correct: the PPD2–7 and Virgin waveforms in Fig. 4H had been mislabeled. We have corrected the labeling. (We verified that the underlying data are correct).

      As suggested, to enable visual comparison of waveform width across groups independent of amplitude differences, we derived peak-normalized average waveforms using a normalization procedure for every peak prior to averaging. Specifically, for each peak we (1) baseline-subtracted the trace by subtracting the mean fluorescence in a pre-peak baseline window, and then (2) divided the baseline-subtracted waveform by its own maximum value to scale the event amplitude to 1. We then computed the mean ± SEM of these peak-normalized waveforms across events within each group.

      We believe these changes resolve the discrepancy and improve the clarity of the figure, consistent with your suggestion.

      (9) Figure 5: In studies of thermoregulatory processes, tail blood flow or temperature is commonly used as an indicator of vasomotor responses. Is it feasible to track tail temperature using the SGBS system? If not, it may be helpful to acknowledge this as a technical limitation.

      We agree that tail temperature is a commonly used indicator of vasomotor responses. While SGBS could in principle be trained to segment the tail, the current model was optimized for dorsal body regions viewed from an overhead perspective. Reliable tail tracking presents substantial technical challenges in our configuration of homecage recordings. The tail’s thin geometry and rapid, multidirectional movement frequently result in partial or complete occlusion (e.g., beneath bedding or the animal’s body). In addition, during vasoconstriction the tail temperature approaches ambient floor temperature, reducing thermal contrast and making segmentation unreliable with the current thermal resolution limited by our camera. We have acknowledged this as a technical limitation in the Discussion, in the section called “Thermal tracking and validation of PVNOT recording specificity”.

      (10) Figure S5: Please describe the reason and histological background for the intravenous injection of FluoroGold.

      Intravenous injection of FluoroGold (FG) was used to histologically differentiate between magnocellular and parvicellular oxytocin neurons in the PVN. Because the posterior pituitary is located outside the blood-brain barrier,

      i.v. FG is selectively taken up by terminals of magnocellular neurons and retrogradely transported to their cell bodies. This allows us to infer the neuroanatomical identity (magno- vs. parvicellular) of the PVNOT neurons of interest. We have updated the Methods with a detailed description of the FG injection protocol as follows:

      “To distinguish between peripheral-projecting magnocellular and central-projecting parvicellular neurons, mice received 15 uL intravenous injection of 4% Fluoro-Gold (Fluorochrome) diluted in 100 uL of sterile saline. Prior to injection, mice were given an analgesic dose of carprofen (20 mg/kg, s.c.). Mice were briefly restrained using a modified 50 mL conical tube, in which holes were drilled to allow for proper air flow and respiration. Mouse tails were interposed between two heating pads to enhance visibility of the tail vein. Tails were wiped down with 70% ethanol and FG was administered via either right or left lateral tail vein using a 0.5 mL 28G syringe. Mice were sacrificed 24- 48 hours post-FG administration.”

      The following are minor points.

      (11) Figure 2E-G, Figure 3F,G, Figure S2G,I, Figure S3A: "quiesence" > "quiescence". This typo may appear elsewhere in the manuscript as well.

      Thanks. These edits have been made.

      (12) Page 7, line 14: Peaks were NOT significantly increased at 29{degree sign}C in Figure 2N.

      Thanks for the very careful read. By way of explanation: this difference had been significant in an earlier draft; however, when we added more replicates, the difference went away. We have corrected this sentence.

      (13) There are mislabeled figure numbers in the main text. The authors should carefully check this throughout the manuscript.

      We found mislabeled figure numbers and have corrected them.

      (14) Page 13, lines 1- 2: To make the description clearer, it might be better to rephrase the part that says, "some blue light stimulations occurred." As it stands, it could give the impression that the stimulations happened spontaneously. Using a phrase like "were delivered" would more clearly indicate that these were intentional, experimenter-controlled events.

      Agreed. Thanks. The edit has been made.

      Additional comments:

      The oxytocin system is thought to support a wide range of physiological and behavioral functions, and the circuits involving oxytocin neurons are likely to be regulated in complex and dynamic ways. As oxytocin research continues to expand, the growing body of evidence not only deepens our understanding but also highlights the system's complexity. In this context, the development of an approach that enables the observation of oxytocinergic neuron activity in parallel with naturalistic behavior represents a promising methodological contribution. It is likely that similar experimental frameworks will become increasingly common in future studies. While reading this manuscript, as a reader rather than a reviewer, I was wondering how OXT neurons detect or define the "rest balance-point," and how they might contribute to shifting the brain toward an "awake balance-point" (Figure 7). Given that eLife allows authors to include an "Ideas and Speculation" subsection within the Discussion, it would be appreciated - though not essential - if the authors could briefly share their perspective on this point. I believe such mechanistic insight would make the manuscript more intellectually stimulating.

      This is a great suggestion. We have added a new “Ideas and Speculation” section of the Discussion.

      References

      Adahman Z, Ooyama R, Gashi DB, Medik ZZ, Hollosi HK, Sahoo B, Akowuah ND, Riceberg JS, Carcea I. 2025. Hypothalamic Vasopressin Neurons Enable Maternal Thermoregulatory Behaviors. DOI: https://doi.org/10.1101/2025.01.23.634569

      Bendesky A, Kwon Y-M, Lassance J-M, Lewarch CL, Yao S, Peterson BK, He MX, Dulac C, Hoekstra HE. 2017. The genetic basis of parental care evolution in monogamous mice. Nature 544:434–439. DOI: https://doi.org/10.1038/nature22074

      Crane JD, Mottillo EP, Farncombe TH, Morrison KM, Steinberg GR. 2014. A standardized infrared imaging technique that specifically detects UCP1-mediated thermogenesis in vivo. Molecular Metabolism 3:490– 494. DOI: https://doi.org/10.1016/j.molmet.2014.04.007

      De Mota N, Reaux-Le Goazigo A, El Messari S, Chartrel N, Roesch D, Dujardin C, Kordon C, Vaudry H, Moos F, Llorens-Cortes C. 2004. Apelin, a potent diuretic neuropeptide counteracting vasopressin actions through inhibition of vasopressin neuron activity and vasopressin release. Proceedings of the National Academy of Sciences 101:10464–10469. DOI: https://doi.org/10.1073/pnas.0403518101

      Dodson AD, Herbertson AJ, Honeycutt MK, Vered R, Slattery JD, Goldberg M, Tsui E, Wolden-Hanson T, Graham JL, Wietecha TA, O’Brien KD, Havel PJ, Sikkema CL, Peskind ER, Mundinger TO, Taborsky GJ, Blevins JE. 2024. Sympathetic Innervation of Interscapular Brown Adipose Tissue Is Not a Predominant Mediator of Oxytocin-Induced Brown Adipose Tissue Thermogenesis in Female High Fat Diet-Fed Rats. Current Issues in Molecular Biology 46:11394–11424. DOI: https://doi.org/10.3390/cimb46100679

      Garami A, Pakai E, Oliveira DL, Steiner AA, Wanner SP, Almeida MC, Lesnikov VA, Gavva NR, Romanovsky AA. 2011. Thermoregulatory Phenotype of the Trpv1 Knockout Mouse: Thermoeffector Dysbalance with Hyperkinesis. The Journal of Neuroscience 31:1721–1733. DOI: https://doi.org/10.1523/JNEUROSCI.4671-10.2011

      Inada K, Hagihara M, Yaguchi K, Irie S, Inoue YU, Inoue T, Miyamichi K. 2025. Vasopressin-to-oxytocin receptor crosstalk in the preoptic area underlying parental behaviors in male mice. Nature Communications 16:10844. DOI: https://doi.org/10.1038/s41467-025-66908-0

      Islam MT, Rumpf F, Tsuno Y, Kodani S, Sakurai T, Matsui A, Maejima T, Mieda M. 2022. Vasopressin neurons in the paraventricular hypothalamus promote wakefulness via lateral hypothalamic orexin neurons. Current Biology 32:3871-3885.e4. DOI: https://doi.org/10.1016/j.cub.2022.07.020

      Kataoka N, Hioki H, Kaneko T, Nakamura K. 2014. Psychological Stress Activates a Dorsomedial HypothalamusMedullary Raphe Circuit Driving Brown Adipose Tissue Thermogenesis and Hyperthermia. Cell Metabolism 20:346–358. DOI: https://doi.org/10.1016/j.cmet.2014.05.018

      Landen JG, Vandendoren M, Killmer S, Bedford NL, Nelson AC. 2024. Huddling substates in mice facilitate dynamic changes in body temperature and are modulated by Shank3b and Trpm8 mutation. Communications Biology 7:1186. DOI: https://doi.org/10.1038/s42003-024-06781-7

      Law J, Chalmers J, Morris DE, Robinson L, Budge H, Symonds ME. 2018. The use of infrared thermography in the measurement and characterization of brown adipose tissue activation. Temperature 5:147–161. DOI: https://doi.org/10.1080/23328940.2017.1397085

      Ludwig M, Leng G. 2006. Dendritic peptide release and peptide-dependent behaviours. Nature Reviews Neuroscience 7:126–136. DOI: https://doi.org/10.1038/nrn1845

      Melón LC, Hooper A, Yang X, Moss SJ, Maguire J. 2018. Inability to suppress the stress-induced activation of the HPA axis during the peripartum period engenders deficits in postpartum behaviors in mice. Psychoneuroendocrinology 90:182–193. DOI: https://doi.org/10.1016/j.psyneuen.2017.12.003

      Meyer CW, Ootsuka Y, Romanovsky AA. 2017. Body Temperature Measurements for Metabolic Phenotyping in Mice. Frontiers in Physiology 8:520. DOI: https://doi.org/10.3389/fphys.2017.00520

      Morrison SF, Nakamura K. 2019. Central Mechanisms for Thermoregulation. Annual Review of Physiology 81:285– 308. DOI: https://doi.org/10.1146/annurev-physiol-020518-114546

      Ootsuka Y, de Menezes RC, Zaretsky DV, Alimoradian A, Hunt J, Stefanidis A, Oldfield BJ, Blessing WW. 2009. Brown adipose tissue thermogenesis heats brain and body as part of the brain-coordinated ultradian basic rest-activity cycle. Neuroscience 164:849–861. DOI: https://doi.org/10.1016/j.neuroscience.2009.08.013

      Pedersen CA, Caldwell JD, McGuire M, Evans DL. 1991. Corticotronpin-releasing hormone inhibits maternal behavior and induces pup-killing. Life Sciences 48:1537–1546. DOI: https://doi.org/10.1016/00243205(91)90278-J

      Popescu IR, Buraei Z, Haam J, Weng F, Tasker JG. 2019. Lactation induces increased IPSC bursting in oxytocinergic neurons. Physiological Reports 7:e14047. DOI: https://doi.org/10.14814/phy2.14047

      Poulain DA, Wakerley JB, Dyball REJ. 1977. Electrophysiological differentiation of oxytocin-and vasopressinsecreting neurones. Proceedings of the Royal Society of London. Series B. Biological Sciences 196:367– 384. DOI: https://doi.org/10.1098/rspb.1977.0046

      Škop V, Guo J, Liu N, Xiao C, Hall KD, Gavrilova O, Reitman ML. 2020. Mouse Thermoregulation: Introducing the Concept of the Thermoneutral Point. Cell Reports 31:107501. DOI: https://doi.org/10.1016/j.celrep.2020.03.065

      Tabarean IV. 2021. Activation of Preoptic Arginine Vasopressin Neurons Induces Hyperthermia in Male Mice. Endocrinology 162:bqaa217. DOI: https://doi.org/10.1210/endocr/bqaa217

      Wakerley JB, Poulain DA, Brown D. 1978. Comparison of firing patterns in oxytocin- and vasopressin-releasing neurones during progressive dehydration. Brain Research 148:425–440. DOI: https://doi.org/10.1016/00068993(78)90730-8

      Yaguchi K, Hagihara M, Konno A, Hirai H, Yukinaga H, Miyamichi K. 2023. Dynamic modulation of pulsatile activities of oxytocin neurons in lactating wild-type mice. PLOS ONE 18:e0285589. DOI: https://doi.org/10.1371/journal.pone.0285589

      Yukinaga H, Hagihara M, Tsujimoto K, Chiang H-L, Kato S, Kobayashi K, Miyamichi K. 2022. Recording and manipulation of the maternal oxytocin neural activities in mice. Current Biology 32:3821-3829.e6. DOI: https://doi.org/10.1016/j.cub.2022.06.083

    1. Author response:

      The following is the authors’ response to the previous reviews

      We thank the reviewers for their additional feedback. Below, we provide detailed responses to each reviewer’s major concerns. In addition, we identified an error in the previously submitted Fig. 6C and have corrected the X-axis labels accordingly.

      Public Reviews:

      Reviewer #1 (Public review):

      Motion-related signal in ACC: the new Fig. 2E looks good, but it is hard to visualize how it is just a reordering of the old Fig. 5C.

      We thank the reviewer for this feedback. Fig. 2E and the original Fig. 5C do bear resemblance. The primary difference is the temporal window and organization of the data. In the original Fig 5C, the time window was only ± 5 sec whereas Fig. 2E is ± 30 sec. The main objective we aim to highlight is that ACC shows both activation and inhibition in response to shuttle on an extremely prolonged order, up to 30 sec. Data is sorted to separate inhibition and activation to illustrate the sustained activity persists for both populations.

      All categories in the new Fig. 4D appear to respond to shuttle initiation, with less than 1s latency. For example, type 2a/2b consists of 40% of the population and their response to movement onset is apparent. Thus, it is not clear whether most neurons respond to shuttle crossing as described in the manuscript.

      We thank the reviewer for drawing attention to this discrepancy. It was not our intention to strike comparison between shuttle initiation versus shutting crossing responses across neurons, and we do not dispute that ACC responds to both events. While shuttle initiations and crossings provide a consistent temporal alignment point, they do not define the temporal focus of much of our analyses. Given that most shuttle responses terminate within ~2 sec, the extended windows analyzed (i.e. ± 5 sec; Fig. 4) largely reflect post-action ACC activity. Overall, although ACC neurons show mixed responses to initiations or crossings, the most consistent feature is prolonged modulation that persists beyond shuttle termination. We have revised the text to reflect this focus.

      Given this and the reviewer’s feedback, we further examined whether ACC activity is more strongly aligned with shuttle initiation, crossing, or termination. To determine which shuttle event (initiation, crossing, or termination) captured the most acute changes in ACC neuronal firing, we conducted an event-locked modulation analysis (Fig. S4). Our results showed that shuttle crossing was associated with the largest fraction of significantly modulated ACC neurons (Fig. S4). These findings suggest that shuttle crossing represents the most prominent event for ACC engagement during shuttle behaviors.

      Could the authors use relatively simple analysis, such as comparing spike rate before and after crossing, or before and after initiation, to quantify the response properties of each neuron? This could also help validate the classification analysis performed in Fig. 4.

      As mentioned above, we have added a new supplemental figure to directly address this question (Fig. S4).

      Reviewer #2 (Public review):

      I think the authors did a very admirable job revising the manuscript. It is much improved. However, I believe a formal analysis of action-state versus action-content neurons on A-->B versus B-->A crossing is still warranted. I appreciate the fact that this analysis may not be as reliable with smaller ensemble sizes, but with careful pseudo-ensemble and resampling approaches, such an analysis would go a long way towards increasing the strength of evidence.

      At present, we are not sure what the reviewer means as “formal analysis”. Below is our best effort in addressing this concern.

      Firstly, in our first revised manuscript, we implemented a generalized linear model-based classification of action-content and action-state neurons using direction specific regressors. Specifically, this analysis classified neurons as action-content or action-state based on coefficient contrasts (Δβ), with appropriate statistical testing and multiple comparison correction (see Methods; Fig. 7 C–E). Neurons were classified as action-content neurons if the corrected p-value for Δβ was significant and the absolute effect size exceeded a predefined threshold (|Δ β |> 0.5). Neurons were classified as action-state neurons if Δβ was not significant but both β1 and β2 were individually significant after correction. We believe our generalized linear model-based classification offers a sophisticated and formal classification of these two neurons classes.

      Subsequently, we performed an SVM decoder to distinguish A→B from B→A shuttles. Decoding accuracy depended on action-content neurons, as their removal drastically decreased decoding accuracy, whereas removal of non-action-content neurons had no effect, further strengthening the conclusion that these populations encode distinct information.

      In the updated revision, we performed an additional SVM decoding analysis while controlling for unequal neuronal population sizes between action-state and action-content neurons (Fig. S8). Specifically, we constructed pseudo-ensembles by randomly resampling neurons within each category and training SVM decoders on size-matched ensembles. Decoder performance was evaluated across repeated resamples to generate distributions of accuracy. We found that only decoders using action-content neuronal activity predicted shuttle content with high accuracy (>95%), whereas decoders trained using non-action-content neurons performed at chance levels (Fig. S8).

      Reviewer #3 (Public review):

      The only remaining comment that was not addressed pertains to anatomy and recording details. Some electrodes appear to be clearly in M2 (Fig 2A), and the tetrodes were driven each day. I would strongly suggest that this be included as a further limitation, particularly given the statement on line 178.

      We thank the reviewer for this feedback. In the previous revision, we added a supplemental figure showing tetrode locations for each mouse (Fig. S2) and described recording details in the Methods (Lines #481–488). We agree that this should also be noted as a limitation, and we have now added this to the Discussion (Lines #384–388).

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Reviewer #1

      Evidence, reproducibility and clarity:

      In this paper, Tomasek and colleagues describe a series of experiments illuminating the effects of OM-89, a bacterial lysate taken orally for prevention of recurrent UTI, on intracellular dynamics of UPEC, using cell culture and organoid models. Suggestions for improvement and for clarification of the authors' conclusions and relevance to human UTI (and OM-89 use) are offered below.

      Major points:

      1. The data indicate that OM-89 exposure in the organoids enhances lysosomal degradation pathways and (in mBOs) autophagic flux, and the authors conclude this is a mechanism by which UPEC regrowth after antibiotic treatment (modeling rUTI) is inhibited by OM-89. They also show enhanced cellular uptake of fluorescently labeled antibiotics (ampicillin) in organoids - this leads them to conclude (and state in the paper's title) that increased intracellular antibiotic concentration effects increased killing of UPEC and decreased regrowth. These are two separate proposed mechanisms, and especially with regard to the antibiotics, they have not shown that increased intracellular antibiotic concentration actually kills intracellular UPEC in their model - only that regrowth as measured microscopically is less. In total, a mechanistic connection between the observed lysosomal effect and the intracellular antibiotic uptake, and which one is more important for UPEC control in this model, is incomplete. The precise wording of the paper's title should be reconsidered accordingly.

      We agree with the point raised by the reviewer that we did not show a mechanistic connection between the observed lysosomal effect and the intracellular antibiotic uptake. Further experiments dissecting the exact involved mechanistic pathways driving both - either in conjunction or separately - would improve our understanding on how OM-89 leads to its positive effects. In future studies we will focus on dissecting the underlying pathways and determining whether a mechanistic connection exists to explain the observed positive effects of OM-89 between lysosomal degradation and enhanced intracellular antibiotic accumulation.

      Accordingly, we changed the title to "Targeted lysosomal activation in bladder epithelium enhances clearance of intracellular uropathogenic ____Escherichia coli". This revised title avoids implying a direct causal link between increased intracellular antibiotic accumulation and bacterial clearance, while still reflecting the central biological process identified in our study.

      Additionally, we incorporated changes in the introduction, as highlighted in our reply to point number one raised by reviewer number two.

      OM-89 is taken orally for rUTI prevention, and some "components" reach the urinary tract (line 81). But it isn't explained how applying OM-89 directly to organoids models how its components may reach the bladder epithelium (from the basolateral side, if the OM-89 is applied outside the organoids) in the whole animal or human. At the least, this limitation should be stated in the Discussion.

      We thank the reviewer for pointing out this limitation. Although advanced in vitro models help to better mimic the in vivo situation, they still do not fully recapitulate all aspects of drug exposure and delivery observed in vivo. We included the following statement of limitation now in the discussion in line 449-459: "One limitation of our study is that OM-89 was applied directly to epithelial cultures and organoids, whereas in clinical use it is administered orally. Although pharmacokinetic studies have demonstrated systemic distribution and urinary accumulation of OM-89-derived components following oral administration (van Dijk, 1982), our experimental setup does not recapitulate the exact route, kinetics or concentration profiles encountered ____in vivo. Rather, our models were designed to determine whether bladder epithelial cells are capable of responding directly to OM-89-mediated signals and to identify the intracellular pathways involved. Given the documented systemic exposure following oral administration, direct effects on the urothelium are biologically plausible. However, future studies will be required to determine how the epithelial responses identified here integrate with the complex systemic and immune-mediated effects of OM-89 under physiological administration conditions."

      In the lysosome studies starting on line 319, the cultured cells are all infected (and either treated with OM-89 or not). What observations regarding number and size of vesicles, etc (all the measures in Fig 6) are evident when cells are treated with OM-89 only? These data should be presented (at least as a supplemental figure) to enable optimal interpretation of the OM-89+UPEC data in Fig 6. As the authors themselves indicate, OM-89 may be having a generalized effect on endocytic and/or autophagic flux by bladder epithelial cells, independent of infection.

      We thank the reviewer for this suggestion and agree that evaluating OM-89 treatment in the absence of infection provides important context for interpreting the infection-associated phenotypes shown in Figure 6. Our original intention was to focus the main manuscript on the effects of OM-89 during UPEC infection, and we therefore did not include the corresponding uninfected conditions.

      As part of the planned revision, we will include additional supplementary data examining the effects of OM-89 alone in both murine and human bladder epithelial cells. Specifically, we will present analyses of Lamp1-positive lysosomal vesicles, lysosomal acidification (LysoSensor), and Cathepsin L activity under uninfected conditions. These experiments will allow readers to assess the extent to which OM-89 activates epithelial lysosomal pathways independently of infection and will provide important context for interpreting the infection-associated responses presented in the main figures.

      We agree with the reviewer that OM-89 may exert broader effects on epithelial lysosomal pathways beyond the setting of infection, and inclusion of these data will strengthen the interpretation of OM-89 as a direct modulator of epithelial antimicrobial function.

      With the organoids, beyond the microscopic quantification of UPEC, can CFUs be measured?

      We understand the wish of the reviewer to see CFU measurements performed on organoids. However, this imposes strong technical limitations, mainly due to the tedious and technically challenging microinjections, e.g. the exact same amount of organoids would need to be infected by microinjections in both conditions (OM-89 and control) and injections would need to be performed extremely precise with no bacteria spreading into the surrounding extracellular matrix (frequently, organoids would get penetrated with the microneedle all the way, leading to bacteria being not injected into the lumen but rather into the wall of the organoid or even be released on the other side of the organoid) as otherwise also bacteria escaping into the extracellular matrix would be collected upon recovering the organoids from the extracellular matrix domes, strongly affecting the CFU measurements.

      However, using differentiated monolayers of mouse bladder epithelial cells and performing a classic gentamicin protection assay would add an additional layer of information on the purely intracellular bacterial population, whilst overcoming the previously mentioned technical challenges. Therefore, we aim to perform CFU measurements on monolayers with and without OM-89 treatment to support our microscopic quantification and specifically be able to make a statement on reduced intracellular bacterial burden with OM-89 treatment. The CFUs will therefore provide an orthogonal measure of intracellular bacterial burden and complement the microscopy-based quantification during the infection and antibiotic-treatment phases.

      Adding to this point of the reviewer, we wanted to clarify that with the higher-throughput microscopic quantification used in our approach (Thunder widefield microscope at 25x magnification), we cannot distinguish between strictly intracellular or tissue-associated bacteria, hence we used the wording "intra-organoid" in our methods section. We now added this information also into the results section for clarification (line 116): "Hence, the microscopy data represent the total "intra-organoid" bacterial burden at each experimental stage, without distinguishing the exact localization of the bacteria - which can be luminal, intracellular or tissue-associated.". To further reflect this, we stepped back from referring to antibiotic-mediated "killing", but changed the wording to antibiotic-mediated "clearance" or referred to reduced bacterial burden throughout the manuscript.

      __Minor points:____ __

      1. In Fig 1A, the "co-application" horizontal line is under the 7-10 hour window, but the text suggests that the application of antibiotics and OM-89 in this experiment is between 4-7 hours.

      We thank the reviewer for pointing this out. Indeed, in the co-application regime, OM-89 is added at the same timepoint as the antibiotic - meaning straight after monitoring the growth phase at 4h post-infection (pi). We now adapted the horizontal line for the "co-application" treatment in Figure 1A accordingly to represent the time-point of OM-89 addition better. Additionally, we added a line for the antibiotic-treatment in order to further facilitate readability.

      How are antibiotics and OM-89 "removed" at the 7-hour mark? This was not detailed in the Methods.

      Although we had specified this in the methods section at line 603 "For every media exchange (e.g. antibiotic treatment or withdrawal), each well was washed with 9 ml of the respective media before leaving 1 ml in the well.", we realized the positioning was not optimal as we had mentioned this part under the point "Bacterial injection" in "Injection experiments". We therefore now separated this part, together with the lid preparation, from the "Bacterial injection" part and created the new subsection "Lid preparation for media changes" (line 613 onwards).

      What time point was used for the transcriptomic profiling of organoids? This is not clear from the relevant Methods or Results sections.

      As stated in the methods section, RNA for transcriptomic profiling from mBOs was extracted at 4h post-infection (pi) (line 842).

      In showing that OM-89 "attenuated" the magnitude of inflammatory responses (Fig 2C and S3B), it would be helpful to add a panel showing the comparison of OM89+UPEC to PBS alone - this would be expected to convey activity (red) in the infection-related pathways, but to a lower magnitude than seen in UPEC vs PBS.

      We thank the reviewer for this suggestion, as well as comment number 5 below. We comment more on both suggestions below.

      Similarly, in the results outlined starting on line 196, it would be helpful to add a panel showing OM89+UPEC vs OM89 alone.

      We performed the requested, combined GOBP analyses and they confirm that infection-associated pathways remain strongly activated in OM89-treated infected organoids relative to baseline (PBS) controls and relative to OM89-treated uninfected organoids. These results confirm the reviewer's hypotheses and further confirm the results presented in Figure 2C. In fact, induction of genes involved in detrimental effects of UPEC infections are induced at a lower extent when organoids are exposed to OM-89 only.

      However, because the direct comparison between OM89+UPEC and PBS+UPEC already highlights the effect of OM-89 while controlling for the infection status, we believe our original analysis presented in Figure 2C remains the most informative representation of attenuation. Therefore, we will include the new comparison in the supplementary section of the manuscript.

      In line 236, what is meant by lysosomal "activation"? A more specific term should be chosen here.

      We thank the reviewer for this question and aim to increase readability of this section. With lysosomal activation in the first sentence of the mentioned paragraph, we referred to the observed effect of upregulated lysosomal pathways and altered lysosomal vesicles in the previous paragraph. However, to make the connection to the previous paragraph better, and given the comment number two of reviewer number two, we changed the whole first paragraph of this section. Therefore, the first sentence of this paragraph (line 235 onwards) reads now: "To test whether the observed effects on lysosomal pathways could mechanistically, at least in parts, explain OM-89-mediated protection, we first used Genebridge analysis (Li et al, 2019) to examine how the lysosomal gene signature identified in our RNA-seq data relates to host defense programs in the human bladder."

      In the Abstract (line 25), the phrase "Using bladder organoids..." is a dangling modifier.

      We thank the reviewer for pointing this out and changed the sentence accordingly to "In bladder organoids and differentiated epithelial monolayers, OM-89 promotes lysosomal acidification and increases lysosomal protease activity, driving intracellular UPEC toward degradative compartments."

      Typographical and copyediting:

      We thank the reviewer for pointing out the typographical errors below and we corrected them all.

      1. Line 74 should read "For instance..."

      2. Line 76 should read "when combined with antibiotic therapy..."

      As this sentence is to emphasize the already observed protective effects of OM-89, and the two studies mentioned were either performed without or in combination with antibiotics, we changed the sentence to "For instance, rodent infection studies have demonstrated protective effects of OM-89 alone (Bosch et al, 1988; Lee et al, 2006) and in combination with antibiotic therapy (Canton et al, 2025; Bessler et al, 2010), although this observed in vivo protection could not be linked to any major quantitative changes in bladder immune cell infiltration (Canton et al, 2025), leaving the underlying molecular mechanism not fully resolved." for better readability.

      Line 122 should read "...regrowth following antibiotic treatment" or "regrowth post-antibiotic treatment"

      Line 138 should use "regimen" not "regime"

      Line 196 delete comma after "Although"

      Line 244 fully hyphenate "OM-89-mediated"

      Line 374 should read "...significantly enhance antibiotic-mediated killing"

      • *

      __Significance:____ __

      The paper is very well written and though a lot of data are included, the presentation is excellent and helps the reader to follow the story. The paper makes a strong contribution to the UTI pathogenesis field, and the use of mouse and human bladder organoids is innovative in studying intracellular UPEC. My scientific expertise as a reviewer is in UPEC pathogenesis, directly relevant to the content of this paper.


      Reviewer #2


      Evidence, reproducibility and clarity:

      This study examined the effect of OM-89 on UPEC infection, antibiotic clearance, and resurgence in mouse and human organoid models. The goal of the study was to understand the molecular mechanisms by which OM-89 is effective at preventing rUTI in patients.

      Major comments:

      The manuscript is well-written and the figures are well presented. Adequate background information is provided to give the study context and sufficient experimental details are provided to allow replication by other groups. Experiments contain appropriate controls and sufficient replicates to allow appropriate statistical analyses. The authors are careful to acknowledge the differences they observed between the mouse and human system and provide satisfactory potential explanations for these differences. The conclusions they draw are well supported by their data and none of their claims from their data are overstatements. Below are some, which I believe if addressed could improve the paper.

      1. I think the authors overstate the novelty of the concept that the urothelium is an active targetable determinant of infection and treatment outcomes. This is not an entirely new concept since previous studies have examined antimicrobial peptides and other factors from the urothelium.

      We thank the reviewer for this important point and agree that the urothelium has long been recognized as an active participant in host defense through mechanisms such as antimicrobial peptide production, pathogen sensing and regulation of inflammatory responses. We have therefore revised the manuscript to avoid implying that urothelial involvement in infection outcome is itself a novel concept. Instead, we now emphasize the specific advance of our study: the identification of lysosome-centered epithelial activation as a therapeutically targetable mechanism that enhances intracellular bacterial clearance and potentiates antibiotic efficacy.

      In the abstract we changed: "Our findings position the bladder epithelium from a passive barrier to an active, targetable determinant of treatment outcome and suggest host-directed modulation of epithelial antimicrobial pathways as a promising strategy to enhance intracellular bacterial clearance." to "Our findings demonstrate that bladder epithelial antimicrobial pathways can be pharmacologically reinforced to influence treatment outcomes by enhancing intracellular bacterial clearance." in line 30.

      In the introduction we changed: "Together with increased intracellular accumulation of antibiotics across different classes, this leads to improved intracellular killing and reduced bacterial regrowth across diverse UPEC strains." to "Together with increased intracellular accumulation of antibiotics across different classes, this leads to improved intracellular clearance and reduced bacterial regrowth across diverse UPEC strains." in line 91 and "Together, these findings reveal a previously unrecognized epithelial lysosome-centered mechanism by which OM-89 enhances intracellular antibiotic performance and repositions the bladder epithelium from a passive reservoir of infection reactivation to an actively transformable antimicrobial compartment influencing treatment outcomes." to "Together, these findings reveal a previously unrecognized epithelial-centered mechanism by which OM-89 enhances intracellular antibiotic performance and establishes lysosomal activation as a therapeutically targetable component of epithelial host defense against intracellular UPEC." in line 96.

      In the discussion we changed: "Together, these findings provide a mechanistic framework for the long-observed clinical efficacy of OM-89. Our findings reveal that the urothelium itself can be therapeutically targeted to reduce pathogen regrowth by transforming the epithelial barrier from a passive refuge for UPEC into an active defense site." to "Together, these findings provide a mechanistic framework for the long-observed clinical efficacy of OM-89 and identify epithelial lysosomal pathways as a therapeutically targetable component of host defense that can be used to improve intracellular bacterial clearance." in line 398 and "In the face of rising antimicrobial resistance (2024), strengthening epithelial antimicrobial function offers a complementary route to shift the bladder mucosa from a passive niche of bacterial survival and infection reactivation toward an active site of accelerated pathogen clearance." to "In the face of rising antimicrobial resistance (2024), our findings provide a mechanistic rationale for the clinical use of OM-89 and support epithelial lysosomal pathways as a promising target for host-directed therapeutic strategies that enhance intracellular bacterial clearance and improve the efficacy of existing antibiotics." in line 469.

      Depending on the target audience, the Module-Module association analysis could need more introduction. I am not a computational biologist and it was not obviously apparent how Figure 4A is generated and what it actually showing. How specifically does this analysis demonstrate a functional link between lysosomal activity and immune defense pathways? Without further explanation, it is my opinion that this figure panel is an unnecessary distraction that is not required for any of the conclusions that the group can already draw from the rest of their data.

      We thank the reviewer for this constructive critique. We agree that the rationale and interpretation of this analysis were not sufficiently explained in the original manuscript. We have therefore expanded the description of the MMAS approach and clarified how these data support the translational relevance of the lysosomal pathways identified in our experimental models. We also agree that for a broader biological audience, the computational framework and the strategic necessity of Figure 4A required a clearer introduction and stronger justification.

      To address the reviewer's concerns, we have thoroughly revised the text (lines 235-250) to clarify the methodology and emphasize the essential translational value this analysis adds to our study:

      • How the figure is generated and what it shows: We have added explicit language clarifying that we used a computational Module-Module Association Score (MMAS) to evaluate the transcriptional correlation between the lysosomal gene network and functional biological pathways. Rather than relying on a single experimental dataset, this analysis compiles data across eight independent human bladder transcriptomic datasets encompassing over 1,400 clinical samples.
      • Demonstrating the link to immune pathways: We have explicitly named the specific host defense modules highlighted in Figure 4A, namely "Response to molecule of bacterial origin", "cell activation involved in immune response", and "innate immune response" to guide the reader directly to the strong positive correlations shown in the panel.
      • Justifying its inclusion (mouse-to-human translational bridge): While the rest of our data characterizes the cellular mechanics of OM-89 in murine organoids and cell culture, Figure 4A demonstrates that the link between lysosomal activity and bacterial defense is a conserved feature of bladder tissue biology across species. This cross-species alignment (our mouse-data at this stage of the manuscript compared to human-derived data) provides critical clinical justification for targeting epithelial lysosomal pathways as a therapeutic strategy in human patients. The new paragraph reads as follows: "To test whether the observed effects on lysosomal pathways could mechanistically, at least in parts, explain OM-89-mediated protection, we first used Genebridge analysis (Li et al., 2019) to examine how the lysosomal gene signature identified in our RNA-seq data relates to host defense programs in the human bladder. To evaluate the translational relevance of our experimental findings, we used a computational Module-Module Association Score (MMAS) analysis across eight independent human bladder transcriptomic datasets comprising over 1,400 clinical samples. This network-based approach evaluates the transcriptional correlation between the lysosomal gene network and functional biological pathways across diverse human cohorts. Module-Module association analysis performed on these human bladder datasets indicated that the lysosome module has strong positive associations with specific host defense modules, including "response to molecule of bacterial origin", "cell activation involved in immune response", and "innate immune response" (Figure 4A), highlighting a conserved functional link between lysosomal activity and immune defense pathways in the bladder epithelium. Altogether, these positive correlations suggest that lysosomal activation represents a conserved pathway integrated within mucosal immunity across species, rather than an isolated cellular response unique to our experimental models."

      __Significance:____ __

      General assessment: Solid experimental design with appropriate controls. Appropriate statistical rigor. Conclusions justified by the data. Limitations acknowledged. Differences in results between mice and humans acknowledged.

      Advance: Moderate technical advance building on prior organoid models. Significant mechanistic advance because OM-89 has been widely used for a long time without detailed understanding of why it works. Moderate conceptual advance that urothelial cells are a targetable determinant of treatment outcomes.

      Audience: I am a basic science researcher in the field of female urogenital tract microbiome and infections. Other researchers studying UTI will certainly be interested in this study. It also may be of interest to people studying other bladder conditions that involve the urothelium (bladder cancer).

    1. Author response:

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

      As the reviewers noted, the evidence we provide is the strongest on the mechanistic link between hepatic cardiolipin deficiency and electron leak from the electron transport chain. This narrative is supported by our assessment of site-specific electron leak as well as reconstitution of exogenous cardiolipin in the small unilamellar vesicles deficient with CL. On the other hand, as pointed out by the Reviewer 2, the mechanistic link between cardiolipin to MASLD/MASH is less robust. At this moment, we have not experimentally demonstrated that the MASLD/MASH induced by CLS deletion can be rescued by replacement of mitochondrial CL in vivo. Taken together, our current narrative makes an incomplete loop between CL deficiency, electron leak, and MASLD/MASH. Nevertheless, as indicated by all the reviewers, this manuscript highlights a previously undescribed role that CL potentially plays in MASH pathology, particularly with the data that human MASH coincides with reduction in liver mitochondrial CL. We focused this revision primarily on additional descriptive experiments in CLS-LKO mice that were requested by the reviewers. Even though it is not a component of the current manuscript, we have recently successfully developed mice with hepatocyte-specific CLS overexpressing mice and began performing experiments to test causality of CL deficiency to MASLD/MASH which we hope to complete in a few years. We are hopeful that the MASLD/MASH research community will still find evidence on CL contained in this manuscript plausible, and that it provides critical information to our understanding of mechanisms for MASH pathogenesis.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript by Brothwell and colleagues describes a central role for hepatic cardiolipin deficiency in MASH. The authors identify cardiolipin as a mediator of two long-standing problems in the field: how dysregulated lipid metabolism relates to altered mitochondrial metabolism during MASLD, and what the innate changes are in the steatotic liver that cause the increased respiration. The authors identified reduced liver cardiolipin in humans with MASH and in a variety of mouse models with MASH. When they knocked out hepatic cardiolipin synthesis, mice developed steatosis and inflammation. These mice also recapitulated the elevated hepatic oxidative metabolism and oxidative stress found in obese humans with MASLD. Some of the in vivo functional data related to glucose homeostasis and substrate metabolism could be stronger, and interpretation of the in vitro flux data needs some clarification, but in both cases, the data are not essential to the main conclusions of the manuscript. Overall, the study offers compelling evidence that cardiolipin is reduced in MASLD and that impaired cardiolipin synthesis is sufficient to recapitulate many features of MASLD.

      We thank the reviewer 1 for the positive feedback emphasizing novel and important findings in our manuscript.

      Strengths:

      The main strengths of the study are:

      (1) The identification of reduced cardiolipin levels in the liver of humans with MASLD and in a variety of mouse models of MASLD.

      (2) The finding that loss of cardiolipin synthesis recapitulates steatosis and inflammation in MASH.

      (3) The finding that loss of cardiolipin increases mitochondrial respiration, ROS production, and fat oxidation (in a separate hepatocyte cell line), again recapitulates several previous studies in obese humans with MASLD.

      (4) Evidence, though less definitive, that cardiolipin deficiency promotes electron leak by disrupting respiratory supercomplexes and preventing CoQ reduction.

      Weaknesses:

      (1) Figure 3A-D tries to make the point that liver CLS KO causes defects in substrate handling in vivo, based on glucose and pyruvate tolerance tests. The KO mice have a blunted response to a glucose tolerance test, but the pyruvate tolerance test showed very little (almost no) effect on glucose levels in either WT or LKO mice. The small blunting of the response in the LKO is impossible to interpret (if it's real), since the ability to clear glucose is also increased, and no tracers were used. It might be useful to monitor pyruvate and lactate levels during the experiment. However, this reviewer doesn't think the data is essential to prove the authors' main points.

      Thank you for pointing this out. We have now revised our manuscript to correctly reflect our findings on GTT and PTT. In our initial submission, we failed to clearly articulate that CLS deletion appeared to increase systemic glucose handling, which is the opposite of what one might expect in liver with steatosis. We agree that additional experiments would be helpful to better understand the systemic substrate handling in the CLS-LKO mice. As the reviewer indicates, we decided to focus this particular manuscript on intracellular and mitochondrial metabolism because of cardiolipin’s known localization to mitochondria, and the central role that this organelle plays in the pathogenesis of MASLD.

      (2) After presenting convincing evidence that respiration is elevated in isolated mitochondria from CLS KO liver, the authors follow up the findings by investigating whether 13C-palmitate and 13C-glucose oxidation are altered by CLS knockdown in murine Hepa1-6 cells (Figure 4).

      A few comments are worth mentioning about Figure 4:

      (a) It is not clear why the authors chose to use a hepatoma cell line rather than primary hepatocytes from LKO mice. The latter would be more convincing, since there could be important differences in metabolism between hepatoma cells and hepatocytes (e.g., preference for fatty acids vs glucose). Nevertheless, I think the approach is sufficient to test the general effect of loss of CLS on substrate metabolism.

      We appreciate the sentiment and agree that primary hepatocytes would have been a better model. We simply have not had prior expertise to culture primary hepatocytes and do not have the system working. We completely agree that it’s important to discuss the limitation of hepa1-6 cells as a hepatoma cells and now discuss this in our manuscript.

      (b) The authors use the M+2 enrichments of TCA cycle intermediates to infer rates of oxidation of [U-13C] palmitate or [U-13C] glucose. It is important to note that this kind of data reports fractional carbon sources (i.e., substrate preference) rather than rates of oxidation. For example, data from the 13C-palmitate experiment indicates that the CLS KD cells increase the fractional contribution from 13C palmitate (compared to glucose, for example) to the TCA cycle, but the actual rate of palmitate oxidation is not implicit in the data. However, it is reasonable to suggest that, in combination with the increased rates of O2 consumption observed in isolated mitochondria, this data supports increased fat oxidation.

      We agree with the reviewer that the nuances are important: that M+2 enrichments from [U-13C] palmitate or [U-13C] glucose reflects the fractional contributions of labeled substrates to the TCA cycle rather than oxidation. We have now revised the text to clarify that the data represent carbon incorporation patterns.

      (c) I have some concern that the [U-13C] glucose experiment is more complicated to interpret than the description implies. I'm not sure what happens in this cell line, but in the liver, most labeling from pyruvate (i.e., originating from glucose in this case) enters the TCA cycle via pyruvate carboxylase, with smaller amounts entering via PDH (depending on the nutritional state). Since one could expect pyruvate carboxylase to contribute M+3 labeled TCA cycle intermediates initially, and M+2 on the first turn of the cycle, it's hard to conclude what the data indicates about glucose oxidation. The authors could generalize the conclusion by framing the TCA cycle enrichment data as the contribution of glucose carbons and noting in Figure 4A that pyruvate carbons can enter the TCA cycle via PDH or pyruvate carboxylase, without attempting to assign their relative contributions. There are better ways to do it, but it's a small nuance here since the authors aren't making a critical point about the pathways.

      This expert comment is much appreciated. We have revised the text to more broadly describe glucose carbon entry into TCA cycle through PDH and PC. We also revised the schematic to reflect this notion.

      Reviewer #2 (Public review):

      In this study, the authors show that alterations in the lipid composition of the inner mitochondrial membrane, particularly changes in cardiolipin (CL) content, lead to defects in electron transport, supercomplex formation, and oxidative stress. Using liver-specific CLS knockout mice, which are characterized by dysfunctional capacity for cardiolipin synthesis, the authors highlight an underappreciated role for CL in MASH pathology. Overall, this is an interesting study highlighting the importance of functional/physiological electron transport (and in this context, electron leakage) in MASH pathophysiology. Despite that, this manuscript has several weaknesses that require attention.

      We thank the reviewer 2 for the constructive criticisms and identifying areas of weakness were additional data or explanations can improve the manuscript.

      (1) For all LKO studies, it is stated that the decrease in hepatic CL is causal for the observed phenotype. However, it is evident that many other lipids are impacted by CLS KO, including a marked increase in hepatic PG. In this respect, the authors show no evidence that the observed metabolic phenotype is indeed due to the reduction in CL and not to other accompanying changes.

      Thanks for this comment. We agree that because deletion of CLS promotes changes in mitochondrial lipids other than CL, we cannot conclusively attribute phenotypes we observed to CL and not to other lipids such as PG. In our experience, rescuing mitochondrial phospholipids by exogenous supplementation is problematic as they most certainly are not exclusively destined to the tissue of interest, nor to the organelle of interest, and often metabolized to produce other lipids, etc, making it difficult to interpret the data. We now have mice that conditionally overexpress CLS, which could be used to address this question, but the study is in its early phase and are outside the scope of the current study.

      The one experiment we performed is the ex vivo CL supplementation by SUV fusion to mitochondria, which has an ability to rescue electron leak. While they do not demonstrate the role of CL in all phenotypes found in the CLS-LKO mice, we think that bioenergetic phenotype associated with CLS deletion is therefore likely due to the reduction in CL. We now provide these additional discussions in lines.

      (2) In the results, the authors highlight that 'MASLD has been shown to alter the total cellular lipidome in liver.' Given that this study focused on CL, it would be useful to include specific studies that pointed to changes in hepatic CL content in MASLD/MASH/fibrosis.

      We now provide citations for these studies (PMID: 30042157, PMID: 34257827).

      (3) The initial human mitochondrial lipidomics studies show a reduction in mitochondrial CL and PG content. What was the content/expression of CL synthase and PGP synthase in these samples? If this cannot be assessed, is there any association of CLS or PGPS expression and MASLD/fibrosis (etc) in publicly available databases (e.g, GEP liver) that may explain the reduction in mitochondrial PG and CL content?

      Thanks for this suggestion. Quantification of mitochondrial lipidome require a good amount of tissue, and we do not have sufficient biomaterials left to quantify gene expression. Upon our survey of publicly available database (including GepLiver), we did not find that human MASLD was associated with an increase in CLS or other enzymes of CL biosynthesis compared to healthy controls.

      (4) The validation of MASH in patients (Figure 1B) is not convincing (ie., no quantification/scoring provided). NAS /fibrosis scoring (according to Kleiner) would help to define if all patients have indeed MASH, and what subset has fibrosis. Could the reduction in CL/PG content be (also) associated with fibrosis? In addition, Masson's Trichrome should be added to Figure 1B.

      The diagnosis was based on obvious bridging fibrosis and/or regenerative nodules on H&E staining (see additional zoomed-out images in Figure 1 – figure supplement 1). Due to the severity of these cases, formal NAS scoring was not applied. We do not have the Trichrome staining available but all MASH samples had fibrosis. Thus, it is possible that reduced CL/PG is related to fibrosis. We now added more descriptions on this point.

      (5) In human lipidomics, the authors suggest that reductions are observed in tetralinoleoyl CL (Figure 1C). However, Figure 1C only shows the combined FA acyl chain length + unsaturation, therefore not allowing for FA-specific ID (unless such data are available from the LC/MS analysis).

      Thanks for pointing this out. Per lipidomic nomenclature guideline we assign combined FA acyl chain length + unsaturation when MS2 is not performed. We have validated that our 72:8 peak corresponds to TLCL, but we do not perform MS2 on every lipid species for every sample. We now clarify this point in our manuscripts.

      (6) Figures 1 J/K/I. It is obvious that the background in all murine immunoblotting analysis has been altered. The authors should provide unaltered images for these immunoblots.

      We apologizes with the confusion. In Figure 1J/K/L/M, each panel actually represents two western blots (not one, similar to Figure 3H). The above represents a western blot with OXPHOS antibody cocktail (CV, CIII, CIV, CII, and CI), while the bottom represents the second western blot with citrate synthase (CS). Thus, we had not manipulated parts of the western blot to look different. To clarify, we now place an outline in each of the western blot to clearly demarcate individual blots to avoid confusion (new Figure 1J-M).

      (7) For Figure 1, it is unclear what is meant by 'we performed all mitochondrial lipidomic analyses by quantifying lipids per mg of mitochondrial proteins'. Was the murine lipidomics carried out on fractionated mitochondria or whole liver? If whole liver, then how were the data corrected, particularly given that PG is not a mitochondria-specific lipid?

      The data are all from lipidomic analyses performed in isolated mitochondria.

      (8) While total CL content seems indeed decreased across the different mouse models, this is mostly due to 1-2 CL species showing a pronounced reduction, with the remainder being unaltered. This should at least be acknowledged in the results. This is similarly the case in the LKO livers.

      Thanks for pointing this out. We now provide additional clarification in the text.

      (9) Figure 2. A secondary biochemical analysis of changes in lipid content should be provided, e.g., total triglyceride content, particularly given that the histology analysis does not show any major changes in hepatic lipid droplets/steatosis. In addition, the Masson's Trichrome staining shows almost no collagen deposition.

      We now provide a quantification of triglycerides in Figure 2J.

      (10) Figure 3. 'CLS deletion modestly reduced glucose handling' should be reworded. The LKO mice show improved glucose tolerance (despite the MASH phenotype), which is not evident from the above wording.

      We modified our text accordingly.

      (11) Looking at the mechanism behind the increase in hepatic steatosis, the authors state that lipid accumulation can occur due to increased lipogenesis, or dysfunctional VLDL secretion or beta oxidation, and subsequently assessed the relevant proteins/pathways. What about fatty acid uptake, which is also one of the four major pathways impacted in MASLD? This should be included in this assessment in Figure 3.

      Thank you for this comment. We now provide data for genes involved in fatty acid uptake, which was not reduced with CLS deletion (Figure 3E).

      (12) For Figure 5A, it is simply stated 'CLS deletion promotes liver fibrosis in standard chow-fed condition', and it is unclear what is highlighted within the selected EM images and what the arrows refer to. The authors should clarify this within the text.

      We have modified the text accordingly.

      Reviewer #3 (Public review):

      Summary:

      Mitochondrial oxphos causes lipid accumulation, leading to MASH, although the mechanism has been poorly understood. In this study, Funai and colleagues identify that reductions in cardiolipin in the mitochondria cause disruptions in the electron transport chain. Knockout of cardiolipin synthase was sufficient to drive MASH phenotypes, increase respiratory capacity, and cause electron leak at complexes II and III. It is well established that loss of cardiolipin increases ROS. Studies to date have been performed on whole tissue lysates, but to rule out which changes in mitochondrial lipids are driven by changes in mitochondrial number versus lipid synthesis/turnover, the authors uniquely purified mitochondria from human and mouse livers in MASH and NASH models for this study. This study provides critical information to the field that will inevitably help us better understand the mechanisms underlying MASH and NASH onset. The evidence provided is both convincing and compelling. With further suggested revision experiments, this study has the potential to change our understanding of MASH and NASH pathogenesis.

      We would like to thank the reviewer 3 for the highly-encouraging feedback.

      Strengths:

      The authors use a unique approach of lipidomics on purified mitochondria. They also analyze many distinct MASH models and provide a unique resource for the field of comprehensive lipidomics analysis of the different ways in which MASH can be induced. The use of human tissue elevates the impact/significance of the findings.

      Weaknesses:

      The data on the super complexes was the least compelling, and frankly, I do not think the authors needed those data to make a compelling argument! The authors should shift their focus more to the compelling electron leak data they have collected. If possible, it would also strengthen the work to include cardiolipin rescues on more of the experiments. Finally, expanding their explanations of the model systems would be very helpful for the readership.

      Thank you for this comment. We have now revised our argument to highlight the electron leak data and less emphasis on the supercomplexes.

      Reviewer #4 (Public review):

      Summary:

      Here, the authors wish to shed light on factors that contribute to the development of liver disease in what used to be called 'the metabolic syndrome'. This is a human-health problem of considerable significance, and the insights they provide, namely the implication of a defect in mitochondrial cardiolipin (CL) content to the progression from metabolic dysfunction associated steatotic liver disease to steatohepatitis, are plausible.

      We would like to thank the reviewer 4 in an encouraging feedback.

      Strengths:

      The experimental evidence proffered is derived from the observation of lower levels of (CL) in mitochondria from the liver of patients undergoing liver transplant or resection due to endstage steatohepatitis compared with mitochondria derived from livers of patients with other conditions. This correlation is buttressed by observations made in mice with liver-selective compromise in CL synthesis and which suggest a pathological environment associated with mitochondrial dysfunction and enhanced oxidative stress, features deemed to play a role in the progression from steatotic liver disease to steatohepatitis.

      The paper is well written, and the findings are well explained and superficially convincing.

      Weaknesses:

      It is unclear how much can be learned from compromising a key enzyme that produces a key mitochondrial lipid in a busy metabolic organ like the liver - isn't the discovery of a mitochondrial defect in such a context rather trivial? And how reliably can these findings be related to the human observations? Most importantly, the chain of causality implied by the title is unproven: the key question of whether or not (somehow) preventing the drop in cardiolipin content affects the course of steatohepatitis remains unanswered.

      We agree with the reviewer that the current manuscript does not directly provide evidence that reduction in CL causes MASLD in humans, which as the reviewer describes, must be tested by rescuing CL content in the context of MASLD. We have now obtained mice with conditional overexpressor and have begun the experiments, but findings from these mice are beyond the scope of the current study. We have modified our title to “Cardiolipin deficiency disrupts electron transport chain AND drives steatohepatitis” to reduce the implication for causality.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The manuscript states that loss of mitochondrial respiration is expected in MASLD. Forexample, line 187 "MASLD is known to be associated with reduced mitochondrial oxidative capacity". A more accurate statement is that "MASH" is known to be associated with reduced mitochondrial oxidative capacity and increased ROS production in humans. As you correctly cite later for an ex vivo human mitochondrial respiration study, early MALSD, especially with obesity, is associated with elevated mitochondrial respiration (40). Since those measurements are maximal respiration rates, which might not reflect actual in vivo flux, you might also make readers aware that your data is consistent with in vivo human studies that found increased hepatic oxidative flux (TCA cycle flux) in obese subjects with moderate steatosis (PMID: 22152305), which appears to wane with severe steatosis and/or inflammation (PMID: 31012869, PMID: 40272888).

      Thank you for these suggestions. We have made the suggested changes to the text.

      Reviewer #3 (Recommendations for the authors):

      (1) Throughout the manuscript, the authors refer to the inner mitochondrial membrane, although they never perform assays to distinguish the inner vs outer mitochondrial membrane. It would be better to just refer to the cardiolipin being measured as "mitochondrial."

      Thank you. We made these changes.

      (2) In figures showing changes in cardiolipins, not all of them change; only a handful of them are reduced in NASH. Could the authors add commentary in the manuscript about what is known about these different cardiolipin species, and speculate as to why certain CLs are changing while others are not?

      Thank you. Reviewer #2 had similar comments and we provided additional discussions.

      (3) In the human tissues, what do the other mitochondrial inner membrane lipids (PC, PE, PI, PS, LPC, LPE) look like in the healthy vs NASH patients (Figure 1A-D)?

      Thank you for this request. We did not include these data in the manuscript as we have a separate ongoing study (the second author is the lead author on this paper) where we are following up on hepatic mitochondrial PS and PE, which we found to be decreased in human MASH samples compared to healthy livers. This turned out to be a convoluted story so we decided not to include it in the paper.

      (4) The descriptions of the different MASLD/MASH models are a little sparse. Especially needing more detail is the model for carbon tetrachloride injection, causing NASH. The authors should explain how each of these models typically induces MASLD/MASH.

      We now provide these details.

      (5) In figures 2E and F, total body mass is unchanged in CLS-LKO mice, but liver mass is decreased; yet on the chow diet, there appears to be lipid accumulation in the liver as well; I am wondering what the authors' reasoning is for this decreased liver mass.

      It is difficult to say conclusively, but we suspect it is due to cell death evidenced by fibrosis. It’s important to note that while there is lipid accumulation in the liver, steatosis is relatively mild and the increase in liver triglyceride is quite marginal (Figure 2J).

      (6) The lipidomics analysis and comparison of livers in these different models is a wonderful dataset that needs far more depth in terms of unpacking and describing the findings. For example, all the models of MASH show similar changes in most of the lipid species analyzed. NASH appears to be quite different than MASH. This, among other trends, is certainly worth highlighting as it will be of interest to the field.

      Thanks for this comment. We agree that while CL phenotype were common to mouse and human MASH samples, there were other changes that we observed in other lipids that may be biologically significant. As described above, we have an ongoing study pursuing mitochondrial PS in the liver.

      (7) Figure 2B - It is interesting that the CLS KO only impacts certain CLs. The 72:8 CL, which is regulated by CLS, is also a CL that appears to change in the human patient samples. The information on the specific CL that is changing seems critical to the mechanism of the role of the CL in the disease. Throughout the manuscript, it is important to specify which specific CL is being referred to, instead of broadly characterizing the changes to cardiolipins, especially since most of the cardiolipins shown do not change; only a handful of them do.

      Thank you for this suggestion. We have included additional discussions on 72:8 CL in the manuscript.

      (8) One potential non-specific mechanism whereby CLS knockout can cause MASH would be if the mice change their overall food consumption. It is an important control to test if the total food intake is different in WT vs KO mice to formally rule out this possibility.

      The food intake was not different between the group (Figure 2E).

      (9) To determine the extent to which de novo cardiolipin synthesis underlies the change in MASH/fatty liver observed in the HFD, GAN, and CCl4 models in Figure 1, the authors should also put the CLS KO mice on these diets and perform liver histology, analysis of inflammation markers, and analyze immune cell infiltration. Alternatively, the authors could try to rescue the CLS KO model by supplementing cardiolipin in the diet or by injection.

      Thank you. We have an ongoing experiment to examine the effect of hepatocyte-specific CLS overexpression on protection from GAN-induced MASLD.

      (10) Figure 3F shows a decrease in UQCRC2 by RNA but no change at the protein level in Figure 3H. The authors should comment a bit more on this disparity, and the data in Figure 3F don't mean much for the main point of the study if the levels of the proteins are unchanged.

      The reviewer is correct. We initially performed RNAseq in trying to broadly capture how CLS knockout influences liver health, which implicated that transcriptional program for mitochondrial proteins were downregulated. Nevertheless, gold standard measurements of mitochondrial content (mitochondrial protein or mtDNA) did not show change in the abundance with CLS deletion.

      (11) The increase in respiration and spare respiratory capacity upon CLS KO shown in Figure 3J is extremely interesting! The explanation of the experiment and its meaning should be significantly expanded upon.

      Thank you. We included additional discussion on this point.

      (12) Figure 4 - It is interesting that the fraction of the TCA cycle metabolites labeled is increasing with the palmitate tracer and decreasing with the glucose tracer. This implies a "fuel switch," such that more of the TCA cycle carbons originate from fatty acids than glucose upon loss of CLS. The authors should make note of this point. Also, to understand if the total molar quantity of labeling in the TCA cycle from palmitate and glucose is changing, the authors should also report the relative abundance (instead of just the fraction labeled) of the labeled metabolites and unlabeled metabolites.

      Thanks for this suggestion, we have now added this discussion.

      (13) In Figure 5C-F, the authors show that CLS deletion can activate the caspase pathway, but do not see any change in cytochrome c localization. Can the authors clarify if CLS deletion is sufficient to induce apoptosis?

      CLS deletion certainly causes cell death that induces tissue fibrosis. Activation of the caspase pathway suggests that the cell death may be due to apoptosis but we did not see changes in cytochrome c localization. Our lab is currently performing additional experience to test the possibility that CLS deletion may induce ferroptosis.

      (14) Figure 6A-C- The authors discuss the I + III2 + IV supercomplex substantially and consistently decreasing in the CLS-KO mice, however, the quantifications do not look statistically significant. Can the authors confirm if these changes are or are not significant and adjust the text accordingly?

      The reviewer is correct. Abundances of I+III2+IV supercomplexes are decreased in CLS-LKO mice compared to control mice when quantifying with supercomplex antibody cocktail or with UQCRSF1 (complex III subunit) antibody, but not with complex I antibodies. The discrepancy for these results are not entirely clear but it’s likely a combination of antibody sensitivity and a tricky nature to dissolve high molecular weight protein complexes.

      (15) The most compelling data to indicate electron leakage increasing upon CLS knockout is in Figures 7A-E. I would suggest the authors decrease their emphasis on the rearrangement of the supercomplexes and focus their discussion on the very compelling results of Figure 7.

      Thanks for this suggestion. We have modified our text.

      (16) Figure 7D shows that a major site of electron leak is from site II, and these results also fit with the profound succinate-induced respiration observed in earlier experiments. It would be nice if the authors could test the ability of cardiolipin to rescue these phenotypes, similar to the assay in Figure 5I. Assessing this rescue on the CoQ redox state would also strengthen the claims.

      Thank you for this comment. We are encouraged with your suggestions. We have thought about this quite extensively during the preparation of the manuscript but we refrained from making conclusive statements regarding complex II because the magnitude of the increase in electron leak is equally elevated at complex II and III. It’s true that CLS deletion increases succinate-induced respiration, but this might also be because succinate elicits the highest increase in respiration even in wildtype mice (see values in Figure 3K and L compared to other substrates). It would be intriguing to examine the influence of CLS deletion on complex II/III electron leak as well as succinate-induced respiration in tissues where succinate is not a preferred substrate. We have attempted cardiolipin rescue in SUV but unfortunately, we could not get this assay to work for site-specific electron leak measurements.

      (17) In Figure 7G-H, it would be nice to see a ratio of oxidized to reduced CoQ, in the CLS deletion mice and in human NASH livers, if samples are available.

      Thanks for this suggestion. Data shown (Figure 7- figure supplement 1P-S).

      (18) CoQH2 can also deliver electrons to complex II (via its reversal). Complex II shows a remarkable contribution to the electron leak phenotype (Figure 7D). Also, as the complex II monomer showed much larger changes in the native gels of Figure 6 than the complexes involving complex III. A more likely model is that oxidized CoQ accumulates in the CLS knockout model because of increased CoQH2 leak via complex II.

      Perhaps. We also thought about this but we are not sure if this fits with the observation that CLS deletion increases succinate-induced respiration, which suggests increased succinate to fumarate conversion, a notion that I am not sure can be congruent with increase CoQH2 reversal to complex II. Overall, I think we lack the tools or evidence to conclusively implicate whether CLS deletion primarily acts on complex II or III. Nevertheless, we appreciate the reviewer’s enthusiasm on these topics as we perform additional experiments on the mechanism of interactions between CL and the ETC.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      Cruz-Gonz´alez and colleagues draw on DNA methylation and paired genetic data from 621 participants (n=308 controls; n=313 participants with Alzheimer’s Disease). The authors generate a panel of epigenetic biomarkers of aging with a primary focus on the Horvath multi-tissue clock. The authors find weaker correlations between predicted epigenetic age and chronological age in subgroups with higher African ancestry than within a subgroup identified as White. The authors then examine genetic variation as a potential source for between-group differences in epigenetic clock performance. The authors draw on a large collection of publicly available methylation quantitative trait loci datasets and find evidence for substantial overlap between clock CpGs located within the Horvath clock and methQTLs. Going further, the authors show that methQTLs that overlap with Horvath clock CpGs show greater allelic variation in African ancestral groups pointing to a potential explanation for poorer clock performance within this group.

      Thank you for this summary.

      Strengths:

      This is an interesting dataset and an important research question. The authors cite issues of portability regarding polygenic risk scores as a motivation to examine between-group differences in the performance of a panel of epigenetic clocks. The authors benefit from a diverse cohort of individuals with paired genetic data and focus on a clinical phenotype, Alzheimer’s disease, of clear relevance for studies evaluating age-related biomarkers.

      Thank you.

      Weaknesses:

      While the authors tackle an important question using a diverse cohort the current manuscript is lacking some detail that may diminish the potential impact of this paper. For example:

      (1) Information on chronological ages across groups should be reported to ensure there are no systematic differences in ages or age ranges between groups (see point below).

      Thank you for pointing out this omission. The distributions are now presented in Supplementary Figure 1. While there is some variation in median age, the age ranges are similar across cohorts (median 73.1 to 79.3). The small differences do not explain the differences in accuracy between the cohorts, e.g., the median age of the African Americans (76.4) is lower than the median age for the White cohort (77.7).

      (2) The authors compare correlations between chronological age and epigenetic age in sub-groups within to correlations reported by Horvath (2013). Attempting to draw comparisons between these two datasets is problematic. The current study has a much smaller N (particularly for sub-group analyses) and has a more restricted age range (60-90yrs versus 0-100 yrs). Thus, is an alternative explanation simply that any weaker correlations observed in this study are driven by sample size and a restricted age range? Reporting the chronological ages (and ranges) across subgroups in the current study would help in this regard. Similarly, given the lack of association between AD status and epigenetic age (and very small effect in the white group), it may be of interest to examine the correlation between chronological age and epigenetic age in each group including the AD participants: would the between-group differences in correlations between chronological age and epigenetic be altered by increasing the sample size?

      Our conclusions about the reduced accuracy of the clock in admixed individuals are based on the comparison within the MAGENTA cohorts, not a comparison of MAGENTA to previously published studies. We find significantly reduced accuracy in the admixed cohorts compared to the White MAGENTA cohort. Further supporting this conclusion beyond he MAGENTA cohort, we analyzed three independent whole blood methylation datasets. Two focused on African American individuals—the Grady Trauma Project (n = 422) and the GENOA study (n = 1,394)—and one focused on White Swedish individuals (n = 729). As observed in MAGENTA, the Horvath clock had significantly lower accuracy for the African American cohorts (Figure 3 than for the White Swedish cohort.

      When comparing results across studies, the reviewer is correct that lower correlations are generally seen for older cohorts. Indeed, other studies applying the Horvath clock have seen similar correlations in older cohorts to those observed in MAGENTA (Marioni et al., 2015, Horvath 2013, and Shireby et al., 2020). We now also include the chronological age distributions of the cohorts in this study, along with their mean and standard deviations (Supplementary Figure 1). This shows that the distribution of chronological ages for White individuals is similar to the cohorts where the clocks did not perform as well. Finally, as suggested, we correlated chronological and epigenetic age with the inclusion of AD cases in each cohort for the Horvath clock. The significantly lower performance of the clock on Puerto Ricans and African Americans, relative to White individuals, remains even after including all individuals in each cohort. Thus, combining cases and controls did not qualitatively change the performance relationships for the African Americans and Puerto Ricans relative to the Whites (Supplementary Figure 3).

      (3) The correlation between chronological age and epigenetic age, while helpful is not the most informative estimate of accuracy. Median absolute error (and an analysis of MAE across subgroups) would be a helpful addition.

      We used correlation because it is commonly used to evaluate the performance of epigenetic age clocks, but we agree that other error quantification metrics provide a complementary perspective. We now include MAE and MSE comparisons across sub-groups in the revision (Supplementary Table 1). We find that across all accuracy metrics, the African American and Puerto Rican cohorts perform worse than the White and Peruvian cohorts. Interestingly, the Cubans show relatively high error despite a high correlation between predicted and chronological age. However, there are only 21 non-demented Cuban controls. In addition, we evaluated the same metrics in three replicate datasets (two African American cohorts and one for White Swedish individuals) and found the same patterns of lower accuracy across metrics in African ancestry individuals, albeit with some variation in accuracy between cohorts (Supplementary Table 2). Notably, as discussed above, this is not driven by differences in chronological age distributions: when we subset to older individuals (≥ 55 years old) in order to facilitate comparisons to MAGENTA study individuals, the median age for the White Swedish individuals (70 years old) is higher than that of the GENOA (62.7 years old) and Grady (58 years old) individuals. Despite the difference in median ages, the clock performs better on White Swedish individuals across all accuracy metrics than the African ancestry cohorts with younger individuals.

      (4) More information should be provided about how DNAm data were generated. Were samples from each ancestral group randomized across plates/slides to ensure ancestry and batch are not associated? How were batch effects considered? Given the relatively small sample sizes, it would be important to consider the impact of technical variation on measures of epigenetic age used in the current study. The use of principal Component-based versions of these clocks (Higgins Chen et al., 2023; Nature Aging https://doi.org/10.1038/s43587-022-00248-2) may help address concerns such concerns.

      Thank you for pointing out the need for additional context on data generation. We have added details to the Methods. All omics data from the MAGENTA study were generated using standard protocols that ensure minimal technical artifacts and batch effects. Samples were randomized across plates and chips to ensure that ancestry, age, and sex were not confounded with each batch. We also performed a principal components analysis of the normalized methylation data used as inputs for all MAGENTA analyses. We found that the samples did not stratify by sample plate, cohort, ethnicity, or ascertainment center along the principal components (Supplementary Figure 2).

      We also thank the reviewer for their suggestion to apply the principal component clock to account for potential technical variation. As outlined in the new section “Principal component versions of the methylation clocks also have lower age prediction accuracy for genetically admixed individuals,” using the principal component version of the Horvath clock did not result in consistent improvement in age prediction accuracy or generalization across MAGENTA cohorts (Supplementary Figures 4 and 5). The lower accuracy for age prediction in individuals with substantial African ancestry was present for the PC clock in the replication cohorts, just as in the MAGENTA cohorts (Supplementary Figure 6).

      (5) Marioni et al., (2015) found a very weak cross-sectional association between DNAm Age and cognitive function (r∼0.07) in a cohort of >900 participants. Given these effect sizes, I would not interpret the absence of an effect in the current study to reflect issues of portability of epigenetic biomarkers.

      We agree that previous links between DNAm Age and AD or cognitive function have been relatively small in magnitude. For example, the PhenoAge paper (Levine et al., 2018) and a study using the Horvath clock (Levine et al., 2015) found age acceleration of less than a year in AD patients relative to non-demented individuals. Similar results have also been observed in studies with smaller sample sizes (e.g., 700 for Levine et al. 2015 and 604 for Levine et al. 2018). Given these small effect sizes, we agree that accounting for statistical power is essential for interpretation of our results. We performed power calculations based on an effect of the size observed in previous studies (0.5 year acceleration). We have 86% power in the full MAGENTA data set to detect an effect of this size. Stratifying by cohorts, we have 75% power for the African Americans, 72% for the Puerto Ricans, 72% for the Whites, 65% for the Peruvians, and 47% for the Cubans. Thus, we believe we have high enough power that the consistent lack of association outside of the White cohort in MAGENTA is likely meaningful. Based on these calculations, there is only a 1% chance that we would not observe an effect in any of the other cohorts if the effect was present across cohorts. Nonetheless, we have added caveats about power and the small sample size to our suggestion that the reduced accuracy of the clocks contributes to the lack of AD association outside of Whites.

      (6) The methQTL analyses presented are suggestive of potential genetic influence on DNAm at some Horvath CpGs. Do authors see differences in DNAm across ancestral groups at these potentially affected CpGs? This seems to be a missing piece together (e.g., estimating the likely impact of methQTL on clock CpG DNAm).

      We agree. Thank you for this suggestion. We have added Figure 6 in the main text to address this gap. In short, we analyzed additional whole blood methylation data from inidividuals with African ancestry and found that a substantial proportion of the CpGs in methylation clocks are differentially methylated in African ancestry individuals relative to European ancestry individuals. In the case of the Horvath clock, we find that 84/353 (23.8%) of the clock CpGs are differentially methylated between ancestries. In parallel, we found that 56 of these differentially methylated clock CpGs are also affected by meQTL, many of which are at different frequencies between populations. We also investigated whether the meQTL-affected clock CpGs are associated with increased clock error in the MAGENTA individuals. We found 56 clock CpGs whose methylation levels associated with increased clock error, and 42 of these have at least one meQTL. Thus, while meQTL are not the only factor to affect the portability of methylation clocks across global populations, we suggest that they are a significant contributor, especially in the case of the Horvath clock.

      Reviewer #2 (Public review):

      Summary:

      This paper seeks to characterize the portability of methylation clocks across groups. Methylation clocks are trained to predict biological aging from DNA methylation but have largely been developed in datasets of individuals with primarily European ancestries. Given that genetic variation can influence DNA methylation, the authors hypothesize that methylation clocks might have reduced accuracy in non-European ancestries.

      Strengths:

      The authors evaluate five methylation clocks in 621 individuals from the MAGENTA study. This includes approximately 280 individuals sampled in Puerto Rico, Cuba, and Peru, as well as approximately 200 self-identified African American individuals sampled in the US. To understand how methylation clock accuracy varies with proportion of non-European ancestry, the authors inferred local ancestry for the Puerto Rican, Cuban, Peruvian, and African American cohorts. Overall, this paper presents solid evidence that methylation clocks have reduced accuracy in individuals with non-European ancestries, relative to individuals with primarily European ancestries. This should be of great interest to those researchers who seek to use methylation clocks as predictors of age-related, late-onset diseases and other health outcomes.

      Thank you for this summary.

      Weaknesses:

      One clear strength of this paper is the ability to do more sophisticated analyses using the local ancestry calls for the MAGENTA study. It would be valuable to capitalize on this strength and assess portability across the genetic ancestry spectrum, as was recently advocated by Ding et al. in Nature (2023). For example, the authors could regress non-European local ancestry fraction on measures of prediction accuracy. This could paint a clearer picture of the relationship between genetic ancestry and clock accuracy, compared to looking at overall correlations within each cohort.

      Thank you for this suggestion. To model portability across genetic ancestry as a spectrum, we regressed the Horvath clock error on the proportions of African ancestry in the genomes of the MAGENTA individuals, adjusting for chronological age. The proportion of African ancestry is significantly associated with increased Horvath clock error (p = 0.039), with the clock making less accurate age predictions by 1.46 years for individuals with full African ancestry compared to no African ancestry. We have added this new analysis to the Results.

      The authors present two possible reasons that methylation clocks might have reduced accuracy in individuals with non-European ancestries: genetic variants disrupting methylation sites (i.e., ”disruptive variants”) and genetic variants influencing methylation sites (i.e., meQTLs). The authors conclude disruptive variants do not contribute to poor methylation clock portability, but the evidence in support of this conclusion is incomplete. The site frequency spectrum of disruptive variants in Figure 4 is estimated from all gnomAD individuals, and gnomAD is comprised of primarily European individuals. Thus, the observation that disruptive variants are generally rare in gnomAD does not rule them out as a source of poor clock portability in admixed individuals with non-European ancestries.

      In the revision, we now additionally report ancestry-specific allele frequencies to demonstrate the rarity of CpGclock disrupting variants (Supplementary Figure 9). The global allele frequencies were so low that even if they all occurred in individuals of non-European ancestries, they would still be extremely rare.

      It is also unclear to what extent meQTLs impact methylation clock portability. The authors find that the frequency of meQTLs is higher in African ancestry populations, but this could reflect the fact that some of the analyzed meQTLs were ascertained in African Americans. The number of meQTL-affected methylation sites also varies widely between clocks, ranging from 6 to 271; thus, meQTLs likely impact the portability of different clocks in different ways. Overall, the paper would benefit from a more quantitative assessment of the extent to which meQTLs influence clock portability.

      We agree that the meQTL likely influence the clocks in different ways and that the ascertainment of the meQTLs in different populations makes direct comparisons challenging. To more directly link meQTL to clock performance, we identified 56 Horvath clock CpG sites whose methylation levels significantly associate with increased clock error in the MAGENTA study individuals. Of these, 42 (75%) are affected by an meQTL, including nine that are affected by an African ancestry-differentiated meQTL. As such, meQTL, and specifically meQTL that were likely not present in the training data of the Horvath clock, associated with both the methylation of CpG sites and clock error. However, as the reviewer suggests, determining causality among these factors is challenging. Given our incomplete knowledge of meQTL in different ancestries, we have added caveats to our conclusions about the effect of meQTL on clock portability.

      The paper implies that methylation clocks have an inferior ability to predict AD risk in admixed populations relative to white individuals, but the difference between white AD patients and controls is not significant when correcting for multiple testing. This nuance should be made more explicit.

      We agree that the signal is not strong in the white cohort; however, it is similar in magnitude to previous studies. As outlined in response to Reviewer 1’s Point 5, we have now added power calculations that indicate reasonable power (≥72%) to detect small effect sizes (0.5 year increase) in the white, Puerto Rican and African American cohorts. We now interpret the AD association tests in the context of these power calculations and multiple testing correction.

      Finally, this paper overlooks the possibility that environmental exposures co-vary with genetic ancestry and play a role in decreasing the accuracy of methylation clocks in genetically admixed individuals. Quantifying the impact of environmental factors is almost certainly outside of the scope of this paper. However, it is worth acknowledging the role of environmental factors to provide the field with a more comprehensive overview of factors influencing methylation clock portability. It is also essential to avoid the assumption that correlations with genetic ancestry necessarily arise from genetic causes.

      We entirely agree and have now clarified the scope of our analyses and importance of environmental factors in the revision. We intersected clock CpGs with enviromental-factor-associated CpGs from multiple epigenome-wide association studies (EWAS) and found overlaps that suggest an environemtnal contribution to differences in clock CpG methylation. However, given the lack of environmental data on the MAGENTA study individuals, as well as the lack of datasets for replication, we cannnot directly compare the environmental and genetic contributions to clock accuracy. Nevertheless, the new analyses in the revision highlight the contribution of both genetic and environmental factors to lack of portability for certain methylation clocks.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 64: An association between methylation patterns and genetic ancestry does not presuppose that meQTLs vary in frequency between genetic ancestries; environmental factors could also play a role. It would be nice to comment on this further in the Introduction.

      We agree that environmental factors likely play a role in the decrease in methylation clock performance in admixed populations. We have added text highlighting this in the revised Discussion. Regarding meQTL, we agree that associations between methylation patterns and genetic ancestry do not necessarily imply that meQTL will vary in frequency between genetic ancestries. However, our new analyses in the revision find African-ancestry differentiated meQTL that associate with Horvath clock CpG methylation levels and overall clock error (Figure 6E-F and Supplementary Figure 13).

      (2) Line 116 implies Puerto Ricans have “substantial amounts of African ancestry” but the median ancestry is 15% (which is not much more than the Peruvian and Cuban cohorts).

      Thank you for pointing this out. We have clarified this statement in the text. While the median proportion of African ancestry in Puerto Ricans is 15% (vs. 6% and 2% for the Peruvian and Cuban individuals in MAGENTA), there are many individuals with substantially higher African ancestry. The upper quartile is >25% and several Puerto Ricans have >50% African ancestry.

      (3) In Figure 2B, Puerto Ricans have worse accuracy than Peruvians but a higher proportion of inferred CEU ancestry, which is interesting and defies intuition - is there any hypothesis for why this might be the case?

      In light of our new meQTL analyses, we hypothesize that the African ancestry differentiated meQTL that affect Horvath clock CpGs drive the increase in clock error for these individuals, despite having more European ancestry across their genome. Given that the Peruvians (and Cubans, for that matter) hold very little African ancestry, and also very few of the African-differentiated meQTL, this could explain some of the large difference in clock errors for the cohorts.

      (4) Figure 2C would be improved with confidence intervals.

      We thank the reviewer for this suggestion and have added confidence intervals for Figure 2C.

      (5) It’s interesting that the correlation with Cubans is positive in Figure 3B (for one clock, significantly so). Is there any rationale for this?

      We noticed this as well, but have not been able to come to a definitive conclusion. It is possible that environmental factors contribute. However, the Cuban cohort is the smallest in MAGENTA (22 cases and 21 controls) and the none of the differences are statistically significant, so more investigation in a large cohort is required.

      (6) Line 231: Which population(s) is allele frequency estimated in?

      This is the global frequency reported in gnomAD, which is calculated across all populations in gnomAD v3.0. As noted above, we now also report allele frequencies by gnomAD population (Supplementary Figure 9).

      (7) Were the meQTLs pruned? How many independent variants are there per methylation site? It would be nice to see a distribution for the sites in the Horvath clock.

      We now report the distribution of meQTL across clock CpG sites. The mean number of variants is 108; the median is 36; and the maximum is 1,699. We have now included a plot of the distribution for all 271 (out of 353) Horvath clock CpG sites (Supplementary Figure 14). We did not perform any pruning in these initial results for several reasons. First, we sought to demonstrate the great potential for meQTL to influence these CpGs and to compare the distributions of these common meQTL across populations (based on gnomAD data). Second, identifying the causal variant or variants is challenging. Given that many of these meQTLs likely reflect redundant signals, for the new analyses of African-differentiated meQTL, we restrict to a single variant per clock CpG site. We focus on the variant with the greatest absolute beta, as reported by the original meQTL study from which the variant originates.

      (8) Figure 5C might benefit from a geom density rather than overlapping bar plots; the trends are hard to see.

      We appreciate the reviwer’s suggestion and have now reworked the figure and based it on just the density curves so that readers may better appreciate the differences in allele frequencies.

      (9) Several figures would be more legible with larger font sizes.

      We appreciate this recommendations and have made the font sizes for all plots larger and more legible.

      Reviewer #3 (Public review):

      This manuscript examines the accuracy of DNA methylation-based epigenetic clocks across multiple cohorts of varying genetic ancestry. The authors find that clocks were generally less accurate at predicting age in cohorts with large proportions of non-European (especially African) ancestry, compared to cohorts with high European ancestry proportions. They suggest that some of this effect might be explained by meQTLs that occur near CpG sites included in clocks, because these variants may be at higher frequencies (or at least different frequencies) in cohorts with high proportions of non-European ancestry relative to the training set. They also provide discussions of potential paths forward to alleviate bias and improve portability for future clock algorithms.

      The topic is timely due to the increasing popularity of DNA methylation-based clocks and the acknowledgment that many algorithms (e.g., polygenic risk scores) lack portability when applied to cohorts that substantially differ in ancestry or other characteristics from the training set. This has been discussed to some degree for DNA methylationbased clocks, but could of course use more discussion and empirical attention which the authors nicely provide using an impressive and diverse collection of data.

      Thank you for this summary.

      The manuscript is clear and well-written, however, some key background was missing (e.g., what we know already about the ancestry composition of clock training sets) and most importantly several analyses would benefit from being taken one step further. For example, the main argument of the paper is that ancestry impacts clock predictions, but this is determined by subsetting the data by recruitment cohort rather than analyzing ancestry as a continuous variable. Extending some of the analyses could really help the authors nail down their hypothesized sources of lack of portability, which is critical for making recommendations to the community and understanding the best paths forward.

      Thank you for this suggestion. As noted in our response to Reviewer 2’s Point 1, we have analyzed ancestry as a continuous variable and found that the proportion of African ancestry in the genomes of the MAGENTA individuals significantly associates with increased difference in chronological and predicted age, even after controlling for chronological age (1.46 years more error for 100% vs. 0% African ancestry; p = 0.039). As outlined below, we have also added details on the training of previous clocks and the important additional previous work highlighted by the Reviewer.

      Reviewer #3 (Recommendations for the authors):

      Major comments

      There is previous literature addressing who is in the training set for methylation clocks. To my knowledge, this work has been primarily led by Nancy Krieger. It would be a valuable addition to discuss her work (and any similar work by other investigations) in the introduction. In other words, what do we currently know about the degree of bias in the training sets for methylation-based clocks? The assumption of the introduction is that the training sets are overwhelmingly European ancestry (which I assume is true) but I think some quantitative information about this would be helpful for understanding the source and magnitude of the problem.

      We thank the reviewer for bringing the work of Dr. Nancy Krieger to our attention. It directly supports the rationale for this study: the sociodemographic characteristics of the individuals used to train these clocks are poorly reported, limited to outdated population descriptors (for example, the use of “Caucasians” to describe some of the individuals used to train the Horvath and the Hannum clocks) or race and ethnicity labels. Moreover, where labels are available for training individuals, they tend to underrepresent the individuals of diverse backgrounds, as in the Horvath clock. We have incorporated Dr. Krieger’s work into the Introduction, including details of how this supports the rationale and purpose of our study.

      Related to the above comment, there has been pretty extensive previous work on the effects of race and ethnicity on epigenetic clock estimates (e.g., https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1030-0), and that seems like it could be more explicitly weaved into the introduction and discussion.

      We thank the reviewer for highlighting this relevant article. We have added discussion of it into the Introduction. Several factors make direct comparison with our results challenging. First, the grouping of individuals based on race and ethnicity without consideration of genetic ancestry complicates comparisons. Race and ethnicity commonly do not match genetic ancestry components (see Gouveia et al., 2025 https://www.cell.com/ajhg/fulltext/S00029297(25)00173-9). Second, the study reports differences in epigenetic age accelerations (intrinsic and extrinsic) in individuals from various race and ethnic groups. It does not directly evaluate the accuracy of the epigenetic age predictions in these groups. Thus, it is challenging to interpret whether the differences in acceleration are driven by biological factors or biases in the performance of the clocks themselves.

      The main analysis that felt like it was missing was asking whether the age deviations are larger for individuals with greater proportions of African ancestry. The authors have the ability to analyze ancestry as a continuous variable, but instead performed analyses in various a priori subsets of the data; the subsets do have average differences in ancestry, but also there is heterogeneity within groups. Given that the authors calculated admixture proportions already, it seems like a missed opportunity not to use these estimates. This would also sidestep the issue of the problematic labels applied to the subsets, which mix ancestry, nationality, and race terms (note that I thought the legacy reasons why these labels are used were well-explained, but they are nevertheless problematic for biological explanations that center on ancestry/genetic information as the driver of bias).

      We appreciate the reviewer’s suggestion to investigate clock accuracy in the context of African ancestry proportions. As noted in the response to Reviewer 2’s Point 1, we modeled the clock error as a function of the fraction of African ancestry of each individual, adjusting for an individual’s chronological age. The proportion of African ancestry is significantly associated with increased Horvath clock error (p = 0.039), with the clock estimated to give less accurate age predictions by 1.46 years for individuals with 100% African ancestry compared to no African ancestry. We now report this in the Results.

      Another missed analysis opportunity occurs in lines 259-261, where the authors state “Thus, the clock with the largest decrease in performance in admixed cohorts (in terms of predicting chronological age and identifying age acceleration in AD) has the most and largest fraction of meQTLs influencing its CpGs.” This is another place where the authors make generalizations about a given cohort based on average ancestry rather than testing the claim empirically on an individual basis (e.g., by examining the number of meQTL variants a given individual is heterozygous for or has the non-European allele for).

      We thank the reviewer for this comment. This feedback motivated us to evaluate the relationship between differences in meQTL frequencies and methylation clock error. We found differences in meQTL frequency in the MAGENTA individuals, specifically many of the clock CpG affecting meQTL are most common in the African American cohort, consistent with our theory (Figure 6E,F). Nonetheless, there are 84 Horvath clock CpGs (24%) that are differentially methylated in AFR individuals, and 56 of these are affected by an meQTL, including 11 that are affected by an African ancestry-differentiated meQTL (Figure 6G). Finally, we find that 42 Horvath clock CpG sites in MAGENTA individuals with methylation levels that are significantly associated with increased clock error, and that are also affected by an meQTL (Figure 6B). However, at the individual level we do not find a clear relationship between the number of meQTL or ancestry-differentiated meQTL and methylation clock error. In light of these data, we have reframed our conclusions to state that meQTL likely contribute to clock error, while also being clear that they are not the sole cause.

      Can the authors explain or offer an investigation into why predicted age is often better in Cubans than Whites? They gave much attention to the opposite effect (of similar magnitude) in African Americans and Puerto Ricans but didn’t really discuss the surprisingly accurate prediction in Cubans.

      We did not focus on the results in the Cuban cohorts for several reasons. As discussed in response to Reviewer 2’s comment, the Cuban cohort had the smallest sample size (22 cases and 21 controls). Thus, while the correlation between methylation age and chronological age is similar to Whites, and in a few cases higher, the differences were not statistically significant. Second, looking at other error metrics, like mean absolute error, the clocks are comparatively less accurate in Cubans than on the White cohort (Supplementary Table 2). Finally, the clocks consistently find that Cubans with AD have lower predicted age than controls, though this is only significant for the ZhangEN clock. However, given these inconsisencies and the very small sample size, we caution against over-interpretation of these results. We clarify this in the manuscript and suggest that more work is needed on larger Cuban cohorts before any clear conclusions can be made.

      I was not a conceptual fan of the ensemble clock. The clocks are trained on very different things (e.g., chronological age versus clinical biomarkers) and are designed to capture different aspects of biology. Without more validation and motivation, I don’t think it makes sense to average values that are not designed to measure the same thing.

      We agree that combining the first and second-generation clocks for the task of age prediction is not sensible. However, for AD risk stratification, combining values from multiple clocks that capture different aspects of biology and aging could be beneficial. As mentioned in the main text, we took inspiration from approaches in polygenic risk scores, as well as the broader machine learning field, where ensembling often makes for better predictors. Nonetheless, consistent with the Reviewer’s intuition, we do not see improvement here.

      Minor comments

      (1) Typo in line 91.

      Thank you for bringing this to our attention. Fixed.

      (2) Lines 111-115, sample sizes would be helpful.

      We have added the sample sizes of the non-demented controls that were used to calculate these correlations in each cohort.

      (3) Line 137-138, the correlation stats would be helpful here. This is a common issue throughout the paper, more in-text statistics would help readers to evaluate the authors’ claims. For example, lines 249-251 as well. The authors refer the reader to Figure 5C, which itself has no statistics, this has two plots so it’s unclear which the authors are putting forward as the primary evidence.

      We have added more statistical details in the text and figures to address this comment. In this instance, we have removed the referenced figure.

      (4) Lines 258 and 261, I believe the authors report the same result in both these lines.

      Thank you for pointing out this lack of clarity. These lines report different, but related, results about the frequency of clock-affecting meQTL in different ancestral contexts. The first reports the frequency of clock CpGaffecting meQTL in individuals of African ancestry across all of gnomAD. The second result gives the frequency of those meQTL in different local ancestry backgrounds in admixed individuals. This is distinction is relevant since admixed individuals’ genomes are mosaics of multiple genetic ancestries. As such, a genetic variant might be present in haplotype whose ancestry is not in line with expectations based on global ancestry (e.g., an African American individual inherits a genetic variant within a European ancestry block). This local ancestry difference could modify the effect of the variant or obscure causal variants. Given the potential for confusion and similar results considering global and local ancestry context in this case, we have focused on the first result in the Main Text.

      (5) Somewhere, it would be helpful to provide the distribution/range of ages broken by cohort. Similarly, I didn’t see the breakdown of AD versus control cases within each cohort. Both of these features will impact power within a given cohort for certain analyses.

      We have added the distribution of ages by cohort in Supplementary Figure 1. Table 1 provides a breakdown of cases versus controls for each of the cohorts in the MAGENTA study.

      (6) Figure 3 is pretty hard to read. It would also be helpful if the authors put the white cohort in Figure 3A as a ’baseline’ comparison, as they use this as the baseline comparison in the text.

      We have made these changes to the figure and used larger text overall.

      (7) The various acronyms in the labels in Figure 5 are not explained. For Figure 5C - this is over-plotted and therefore hard to see.

      We have added the full population descriptors from gnomAD to the boxplots showing allele frequencies (Figure 6E). In addition, what used to be Figure 5C has been simplified and moved to Supplementary Figure 12.

      (8) The authors correct for cell type heterogeneity, which is known to vary across populations and can impact clock estimates. However, as far as I can tell, the cell type proportion estimates are coming from the DNA methylation data. The deconvolution algorithms for cell type proportions also have the same problem as the clocks of being trained on a very specific subset of human genetic and environmental diversity. Do the authors have any empirically derived estimates of cell type heterogeneity to sanity-check these deconvolution estimates? At the very least, it would be helpful to acknowledge this limitation.

      We thank the reviewer for commenting on this. There are no empirically derived estimates of cell type counts for the samples in the MAGENTA study. This is an inherent limitation of our study, and we have included text to make note of this.

      (9) There are very different sample sizes for each group, did the authors consider that their null results for the AD analyses in different cohorts are just a lack of power? This could be evaluated with power analyses or by comparing against sample sizes from similar studies in the literature.

      We agree that this is an important analysis and have added it to the manuscript. Given these small effect sizes, accounting for statistical power is essential for interpretation of our results. We performed power calculations based on an effect of the size observed in previous studies (0.5 year acceleration). Considering the full study, we have 86% power to detect an effect of this size. Stratifying by cohorts, we have 75% power for the African Americans, 72% for the Puerto Ricans, 72% for the Whites, 65% for the Peruvians, and 47% for the Cubans. Thus, we have high enough power that the consistent lack of association observed outside of the White cohort in MAGENTA is likely meaningful. Based on these calculations, there is only a 1% chance that we would not observe an effect in any of the other cohorts if the effect was present across cohorts. Nonetheless, we have added caveats about power and the small sample size to our suggestion that the reduced accuracy of the clocks contributes to the lack of association outside of Whites.

      (10) There has been a fair amount of discussion recently that single CpG-based clocks are much more variable than clocks that combine information across CpG sites, either using PC-based or window-based approaches. For example, the PC clock R package from the Levine Lab (https://github.com/MorganLevineLab/PC-Clocks) is very easily implemented and generally gives much less variable age estimations than site-level clocks. It would be nice to consider integrating or discussing these later-generation clocks as ways to improve clock performance in diverse human groups.

      We thank the reviewer for their suggestion to apply the principal component clock to account for potential technical variation. As outlined in the new section “Principal component versions of the methylation clocks also have lower age prediction accuracy for genetically admixed individuals,” using the principal component version of the Horvath clock did not result in consistent improvement in age prediction accuracy or generalization across MAGENTA cohorts (Supplementary Figures 4 and 5). The lower accuracy for age prediction in individuals with substantial African ancestry were present for the PC clock in the replication cohorts, just as in the MAGENTA cohorts (Supplementary Figure 6)

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Strengths:

      Great care was taken in selecting and cleaning the data, and in making sure that intramural vs. extramural projects were compared appropriately. The data has statistical validation. The trends are clear and convincing.

      We thank the reviewer for highlighting the strengths of the manuscript.

      Weaknesses:

      The Discussion is too short and descriptive, and needs more perspective - why are the findings important and what do they mean? Without recommending policy, at least these should discuss possible implications for policy.

      The Discussion has been substantially expanded. We added several new paragraphs discussing: the 2024 Senate HELP Committee proposal for NIH reform; implications for portfolio management (positioning extramural for basic research, intramural for clinical translation); generalizability to other agencies (DoD, NSF FFRDCs, DoE national labs); and the extramural program's role in workforce training as a societal benefit distinct from research outputs.

      The biggest problem I have with this submission is Figure 3, which shows a big decrease in clinical-related parameters between 2014 and 2019 in both intramural and extramural research (panels C, D and E). There is no obvious explanation for this and I did not see any discussion of this trend, but it cries out for investigation. This might, for example, reflect global changes in funding policies which might also influence the observed closing gaps between intramural and extramural research.

      We added an explicit explanation in the Results: because the dataset is truncated at 2020, clinical citations naturally approach zero near the window's end, consistent with the ~7-year lag for clinical citations to accrue documented in prior work (Hutchins et al., 2019). The APT metric declines less steeply because it uses the forward citation network for predictions.

      Reviewer #2 (Public review):

      Strengths:

      The authors leveraged publicly available data (including RePORTER and the iCite repository) and used robust validated metrics (RCR, APT, clinical citations). They carefully considered a large number of confounders, including those related to the PI, and performed several well-described regression analyses.

      We thank the reviewer for highlighting these strengths of the manuscript

      Figure 3A shows intramural projects producing about 2.75 papers per year in 2009, whereas extramural projects are producing just over 1 paper per year. Extramural projects appear to catch up over the next five years. While the authors attempt to explain the difference in their figure legend, another explanation is that the intramural projects started well before 2009 but, as the authors state, intramural data only became available in 2009.

      We added a methodological note acknowledging that some intramural projects may have had start dates prior to 2009 that are not captured in the data, and that the ramp-up of new intramural projects is slower because they are more tied to new PI hiring. We also note the exclusion of projects matched in 2008 as possible continuations. However, the slow ramp-up of Intramural costs in Supplemental Figure 3 is consistent with hiring-associated lagged investment suggesting that our filtering of continuing projects was very successful. Nevertheless, because we cannot completely rule out some continuing projects made it through despite our efforts, we have made the caveats mentioned above in the “Comparison of research topics” section of the Results and the Data section of the Methods.

      As the authors note, funding information is often complex and difficult to characterize for an analysis like this. How did the authors handle: i) publications linked to multiple extramural grants; ii) publications linked to intramural and extramural grants; iii) publications linked NIH grants and non-NIH grants?

      I would think it necessary to somehow apportion credit, as otherwise it would appear that extramural projects are more productive than they truly are.

      We have now explicitly stated that papers with both intramural and extramural funding links were excluded, while papers with multiple links within the same funding type were retained. A new Supplemental Figure 6 was added showing the distribution of papers by number of funding sources for both extramural and intramural grants, demonstrating that the vast majority acknowledged only one project. These changes are in the Methods, Data section and Supplemental Figure 6

      Apportioning credit among a many-to-many graph like the ones used here is indeed a high value problem to solve, but one with many researcher-degrees-of-freedom about analytical design decisions that impact the results. We are working on a rigorous methodology for this, but the amount of time required to do this well is its own research project, and out of scope for manuscript revisions.

      Also, it is not clear if the authors took account of the indirect costs paid by the NIH to universities that have received extramural grants.

      We added explicit language clarifying that all cost comparisons use inflation-adjusted total costs (direct + indirect) for extramural grants. We also added a new sensitivity analysis (Supplemental Figure 4) inflating extramural indirect costs by 30% to approximate unrecovered university expenditures, with the finding that the fundamental pattern holds even under this adjustment. These are found in the “Comparison of funding” and “Comparison of cost effectiveness” sections of the Results, as well as Supplemental Figure 4.

      Reviewer #3 (Public review):

      Strengths:

      The authors clearly presented their methods for processing the NIH project data and classifying projects into either intramural or extramural categories. The limitations of the study are also well-addressed.

      We thank the reviewer for highlighting these strengths of the manuscript

      Weaknesses:

      The article would benefit from a more thorough discussion of the literature, a clearer presentation of the results (especially in the figure captions), and the inclusion of evidence to support some of the claims.

      The Introduction was updated with more specific framing of prior literature (e.g., explicit mention of risk management, funding disparities, and diminishing marginal returns as the focus of prior work). New references were added throughout, including Sampat (2012) on mission-oriented NIH research, Ioannidis et al. (2019) on grant competition inefficiencies, Drummond et al. (2005) on health economic evaluation methods, and the Cassidy (2024) Senate report, throughout the introduction and discussion.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      The article would benefit from a more detailed analysis/discussion about the recovery of indirect costs for extramural research.

      I note that the authors are from the University of Wisconsin, which is part of the IRIS network (https://iris.isr.umich.edu/iris-members-map/). They could work with IRIS (also called UMETRICS) to get a better sense as to the true costs of extramural research for each project (e.g., all labor costs, all equipment costs). The IRIS data are extraordinarily robust. Here's an example of an IRIS / UMETRICS paper: https://www.science.org/doi/10.1126/sciadv.abb7348.

      They could, for example, re-do the analyses assuming that the recorded indirect cost covers only 70% of the true indirect costs. Thus, if they get $700,000 indirect costs from RePORTER, they should assume that the true indirect costs were $1,000,000. Similarly, they can add the costs of the time the PI spent writing the grant proposal, using the Bergstrom paper as a guide.

      Another option would be to conduct sensitivity analyses taking into account ~30% incomplete indirect cost recovery (see https://docs.house.gov/meetings/AP/AP07/20171024/106525/HHRG-115-AP07-Wstate-DroegemeierK-20171024.pdf) and lost efficiency due to excess time writing grant proposals (see https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000065).

      We conducted a sensitivity analysis as requested inflating extramural indirect costs by 30%, citing the Droegemeier (2017) Congressional testimony as the basis for this estimate. The cost of grant-writing time is now acknowledged in the Discussion as an unreimbursed hidden cost of the extramural system, citing Ioannidis et al. (2019). This narrowed the gap between extramural research and intramural research, but did not close it completely. In addition, our updated regression (Supplemental Figure 4) showed similar trends as our main Figure 4, but with the Intramural advantage heightened and the Extramural advantage diminished. Both remained significant. We have also added to the discussion that there are additional costs and benefits that may not be fully captured in an analysis such as ours.

      The authors appear to have used an agency-perspective for their cost-effectiveness analyses. Generally, it is preferable to use a wider societal perspective. While that may be difficult, the article would benefit from some discussion from the perspective of the government and universities.

      We added a new paragraph explicitly acknowledging the agency-centered perspective and its limitations, noting that it does not capture the full economic cost borne by universities (startup costs, philanthropy, endowments, state contributions, graduate student training, faculty retention, infrastructure). The extramural program's contribution to the US workforce pipeline is specifically highlighted as a societal benefit not captured by the cost-effectiveness metrics.

      Reviewer #3 (Recommendations for the authors):

      Line 84-87: "The overrepresentation of viral research is likely because of the outsize investment toward the intramural Vaccine Research Center, and the cancer/genetics overrepresentation due in part because National Cancer Institute intramural investigators conduct research at that institute as well as at the NIH Clinical Center for their human genetics work." What evidence is there to support this claim?

      A citation to the NCI Center for Cancer Research website was added to support the claim about NCI intramural investigators working at the Clinical Center and Center for Cancer Research, where vaccine research is extensively discussed.

      Lines 107-109. "Given that NIH funding for intramural research has remained relatively constant as a percent of total funding over the years, this indicates larger single awards for intramural research while extramural investigators may increasingly require multiple concurrent grants to sustain their labs." Authors may consider adding a panel to Figure 2 showing the percentage of total funding of intramural vs. extramural funding.

      Rather than adding a panel to Figure 2, we added a new Supplemental Figure 3 showing the cost breakdown and intramural percentage of total funding by year.

      Discussion section: Are any of the findings of this study relevant to other funding agencies in the US (such as the National Science Foundation, the Department of Energy, and the Department of Defense)?

      A new paragraph to the Discussion was added discussing implications for the Department of Defense (including the Congressionally Directed Medical Research Programs), NSF FFRDCs, and the Department of Energy's national labs and FFRDCs, arguing that the incentive-alignment logic likely generalizes across agencies.

      Methods section: Please add an explanation of the technique used for propensity score matching.

      A detailed step-by-step description of the PSM procedure was added, covering propensity score estimation, within-year matching, matched cohort construction, outcome regression on matched data, and visualization of results.

      Figure 1: Please clarify if the relative ratio of intramural projects is calculated from the numbers of grants (as suggested in lines 95-96 and 98-100) or the numbers of publications (as suggested in lines 82-83 and 97-98).

      Also, this figure would be more intuitive if, for each topic, it showed the relevant intramural number (as it currently does) and also the relevant extramural number.

      The caption and Methods were updated to clarify that clustering and ratio calculation are based on projects/grants, not publications. A formula was added to the Methods to make the ratio calculation explicit. The figure itself was not modified to add extramural bars, though the ratio calculation already implicitly encodes both.

      Figure 2: Please change "(red)" to "(blue)" in the caption, and remove the A as there is only one panel in this figure

      Figure 4: Please change "(red)" to "(blue)" in the caption.

      These changes have been made.

      Lines 19-21: I suggest rewriting this sentence as follows:

      "We find that extramural awards are more cost-effective for producing outputs commonly used for academic evaluation, such as publications and citations per dollar, while intramural awards are more cost-effective for generating research that influences future clinical work, more closely in line with agency's health goals."

      The sentence was rewritten substantially in line with the reviewer's suggestion, now reading more clearly with "per dollar" removed as a parenthetical and the structure of the comparison clarified.

      Lines 31-34: Please rewrite this sentence along the following lines to provide more context on previous research into the grant funding system:

      Certain aspects of the grant funding system have been the focus of research, such as AAAA (Azoulay et al., 2009), BBBB (Goldstein and Kearney, 2020), CCC (Hoppe et al., 2019), DDDD (Lauer et al., 2017), EEEE (Wahls, 2018a) and FFFF (Wahls, 2018b), but the relative merits of intramural and extramural funding have received little attention to date.

      The sentence was rewritten to name specific contributions of each cited paper (e.g., risk management, funding disparities, diminishing marginal returns), replacing the generic list of citations.

      Lines 41-44: Please explain "merit score" and please add a reference to an article or website that explains the review process at the NIH.

      "Merit score" was revised to "percentile ranking of overall impact merit score" and a citation to the NIH CSR website ("What happens to your application during and after review?," 2025) was added.

      Lines 53-54: Please change Intramural to intramural (two instances, and also in line 284), and Extramural to extramural.

      "Intramural" and "Extramural" were corrected to lowercase throughout.

      Line 65-67: This sentence ("Potential advantages of the intramural approach are that researchers in the NIH's own laboratories allow the NIH to hire researchers whose research agendas more closely align with its mission.") reads awkwardly. Please clarify.

      The sentence was rewritten to read more clearly: "An advantage of the intramural approach are that NIH has the direct ability to hire scientists whose research closely aligns with agency goals, and researchers do not need to devote time and effort on preparing and submitting grant applications."

      Line 95-97: Authors should consider including an equation to help explain the following sentence: "The relative ratio of intramural projects for each topic was calculated by taking a ratio of the proportions of total grants a topic represented in the intramural vs. extramural portfolios. A relative ratio >1 signifies a higher share of intramural project publications on that topic relative to their share across all topics."

      A formula was added to the Methods defining the topic-level ratio calculation explicitly.

      Line 143: The phrase "may reflect the extra attention intramural investigators are afforded" reads awkwardly - please reword.

      Reworded to "may reflect the extra time intramural investigators save because they do not have teaching and grant writing responsibilities."

      Lines 303-304: This sentence ("First, as the renewal of project contracts may alter the topic and arrangement of the projects, we dropped 70,297 projects with renewal records in our data.") reads awkwardly. Please clarify.

      Reworded to "Since the scientific focus of a study may drift over time, we dropped 70,297 projects with renewal records in our data."

      Line 378-379: Please specify the model of ChatGPT used.

      Done.

    1. Author response:

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

      In the revised version, our primary focus has been to more clearly demonstrate the unique contribution of the brain-cognitive gap (BCG) beyond what is captured by cognitive performance alone, and to show that the BCG is not trivially driven by the observed cognitive scores. Additional analyses now demonstrate that the BCG provides complementary and nuanced information regarding factors associated with cognitive resilience, above and beyond the cognitive measures themselves.

      In response to the comment regarding the inclusion of a baseline predictive model, we would like to clarify that the central aim of our study is to compare predictive utility across different cognitive states (resting state, movie watching, and n-back), rather than to establish a single universally optimal prediction model. Several previous studies have already systematically compared deep learning approaches with more traditional machine learning methods for functional connectome-based prediction. In contrast, the goal of the present study is to examine how brain state modulates the ability of AI-based functional connectome models to capture individual differences in working memory and episodic memory.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors attempted to identify whether a new deep-learning model could be applied to both resting and task state fMRI data to predict cognition and dopaminergic signaling. They found that resting state and moving watching conditions best predict episodic memory, but only movie watching predicts both episodic and working memory. A negative 'brain gap' (where the model trained on brain connectivity predicts worse performance than what is actually observed) was associated with less physical activity, poorer cardiovascular function, and lower D1R availability.

      Strengths:

      The paper should be of broad interest to the journal's readership, with implications for cognitive neuroscience, psychiatry, and psychology fields. The paper is very well-written and clear. The authors use two independent datasets to validate their findings, including two of the largest databases of dopamine receptor availability to link brain functional connectivity/activity with neurochemical signaling.

      Weaknesses:

      The deep learning findings represent a relatively small extension/enhancement of knowledge in a very crowded field.

      It's unclear from these results how much utility the brain gaps provide above and beyond observed performance. It would be helpful to take a median split of the dataset on observed performance and plot aside the current Figure 3 results to see how the cardiovascular and physical activity measures differ based on actual performance. Could the authors perform additional analyses describing how much additional variance is explained in these measures by including brain gaps?

      We thank the reviewer for raising this important point. In response to their request, we first examined the relationship between the BCG and the cognitive measure itself. We did not find any significant relationship in either the DyNAMiC sample (r =0.01, p =0.939) or the COBRA sample ((r =0.01, p=0.894) (see Author response image 1).

      Author response image 1.

      We then conducted additional analyses, splitting the sample into high and low EM performers, and compared their levels of physical activity and Framingham cardiovascular disease (CVD) risk scores. We found no significant difference in physical activity (DyNAMiC: p =0.56, 95% CI: –14.99 - 8.13; COBRA: p =0.29, 95% CI: –3.54 - 1.05) or Framingham CVD risk score (DyNAMiC: p =0.11, 95% CI: –1.08 - 10.72; COBRA: p =0.41, 95% CI: –1.86 - 4.58) between high and low EM perfprmers. Given the significant difference in physical activity and Framingham CVD risk score between positive and negative BCG groups, our results support that BCG provides unique information, beyond the observed cognitive measure (episodic memory score), regarding factors that contribute to cognitive resilience. These results have been added to Section 2.4, and Figure 3 has been updated.

      Some of the imaging findings require deeper analysis. For Figure 1f - Which default mode regions have high salience? DMN is a huge network with subregions having differing functions.

      Grad-CAM provides a coarse, gradient-based attribution that reflects how the learned feature maps contribute to the model output. It is not designed to produce specific input-level interpretations, such as symmetric edge-wise importance values. Therefore, the primary interpretation remains at the network level rather than at the level of individual FC edges.

      Along the same lines, were the striatal D1R findings regionally specific at all? It would be informative to test whether the three nuclei (Accumbens, Caudate, Putamen) and/or voxelwise models would show something above and beyond what is achieved from averaging D1R across the striatum. What about cortical D1R, which is highly abundant, strongly associated with cognitive (especially WM) performance, and has much unique variance beyond striatal D1R? https://www.science.org/doi/full/10.1126/sciadv.1501672. The PET findings are one of the unique strengths of this paper and are underexplored. It's also unclear if the measure of brain entropy should simply be averaged across all regions.

      In this study, we focused on D1DR/ D2DR averaged across the caudate and putamen, which has been reported in our previous work to be more strongly associated with cognitive functions (Johansson et al., 2023, Nyberg et al., 2016), compared to the nucleus Accumbens, which tends to show lower D1DR/D2DR levels and limited association with these cognitive domains. Following the Reviewer’s suggestion, we examined regional variations and found that while both caudate and putamen D1DR showed significant associations with BCG, there were no significant associations for D1DR in the nucleus accumbens or DLPFC with BCG. For D2DR, we observed a significant association between caudate/putamen D2DR and BCG.

      D1DR:

      Partial correlation between:

      Caudate_Bilateral vs. NegGap, (r =0.37, p =0.02

      Putamen_Bilateral vs. NegGap, r =0.34, p =0.03

      Accumbens_Bilateral vs. NegGap, r =0.07, p =0.69

      Mean (LRCaud, LRput, LRacc) vs NegGap, r =0.35, p =0.03

      DLPFC_Bilateral vs NegGap, r =0.21, p =0.21

      Striatum_Bilateral (Mean (LRCaud, LRput)) vs. NegGap, r =0.40, p =0.01

      Caudate_Bilateral vs. PosGap, r=–0.37, p=0.02

      Putamen_Bilateral vs. PosGap, r=–0.53, p=0.02

      Accumbens_Bilateral vs. PosGap, r=–0.25, p=0.31

      Mean (LRCaud, LRput, LRacc) vs PosGap, r=–0.41, p=0.08

      DLPFC_Bilateral vs. PosGap, r=–0.30, p=0.21

      Striatum_Bilateral (Mean (LRCaud, LRput)) vs. PosGap, r=–0.49, p=0.03

      Author response image 2.

      D2DR:

      Correlation between:

      Caudate_Bilateral vs. NegGap, r=0.36, p=0.0003

      Putamen_Bilateral vs. NegGap, r=0.22, p=0.03

      Accumbens_Bilateral vs. NegGap, r= –0.01, p=0.91

      Mean (LRCaud, LRput, LRacc) vs PosGap, r= –0.24, p=0.01

      Striatum_Bilateral vs. NegGap, r=0.39, p=0.0001

      Caudate_Bilateral vs. PosGap, r= –0.34, p=0.004

      Putamen_Bilateral vs. PosGap, r= –0.37, p=0.002

      Accumbens_Bilateral vs. PosGap, r= –0.21, p=0.09

      Mean (LRCaud, LRput, LRacc) vs PosGap, r= –0.38, p=0.001

      Striatum_Bilateral vs. PosGap, r= –0.49, p=0.0001

      We have added the following sentence to the Results section to highlight these regional differences in D1DR/D2DR in relation to BCG.

      “Both D1DR and D2DR availability in the striatum were associated with BCG, such that lower dopamine receptor availability was linked to a greater behavioral-cognitive gap. However, these associations varied by region. For D1DR, significant correlations with BCG were observed in the caudate (positive gap: r = –0.37, p =0.02; negative gap: r= 0.37, p =0.02) and putamen (positive gap: r = –0.53, p=0.02; negative gap:r=0.34, p=0.03), but not in the nucleus accumbens (positive gap: r= –0.25, p= 0.31; negative gap: r =0.07, p=0.69) or the DLPFC (positive gap: r = –0.30, p=0.21; negative gap: r =0.21, p=0.21). For D2DR, both caudate (positive gap: r = –0.34, p=0.004; negative gap: r =0.36, p=0.0003) and putamen (positive gap: r = –0.37, p=0.002; negative gap: r =0.22, p=0.03) showed significant associations with BCG.”

      Author response image 3.

      It is not clear from the text that the authors met the preconditions for mediation analysis (that is, demonstrating significant correlations between D1R and entropy, in addition to the correlation with brain gap. The authors should report this as well.

      This is a fair question. We recalculated entropy in the striatum, given that D1DR is more strongly expressed in this region and, therefore, reduced striatal D1DR may have a more pronounced impact on local entropy (as the reviewer suggested, it may not be appropriate to compute entropy across all brain regions). Our analyses showed that lower D1DR/D2DR levels were associated with higher entropy, which in turn was related to higher BCG.

      DyNAMiC; negative gap:

      Partial correlation between:

      Entropy and D1DR, r = –0.33, p=0.04.

      Entropy and NegGap, r = –0.36, p=0.03.

      DyNAMiC; positive gap:

      Partial correlation between:

      Entropy and D1DR, r = –0.56, p=0.01.

      Entropy and PosGap, r r =0.47, p=0.04.

      COBRA; negative gap:

      Correlation between:

      Entropy and D2DR, r = –0.22, p=0.03.

      Entropy and NegGap, r = –0.27, p=0.007.

      COBRA; positive gap:

      Correlation between:

      Entropy and D2DR, r = –0.26, p=0.03.

      Entropy and PosGap, r = 0.25, p=0.03.

      We have added these results under the result section 2.6. We have further updated Figure 4 in the revised manuscript, reporting these correlation results.

      Was age controlled for in the mediation analysis? I would not consider this result valid unless that is the case.

      We utilized the mediation package in R, and to control for a covariate age in the mediation analysis, we added age as a covariate in both the mediator model and the outcome model. The following information has been added in the method section in the revised version of the manuscript.

      “To assess the statistical significance of this mediation effect, we employed the bootstrapping method as outlined by Preacher and Hayes (145) and age has been controlled for in all statistical analysis.”

      The discussion section is long, but the authors would do better to replace some less helpful sections (e.g., the paragraph on methodological tweaks to parcellations and model alignment) with a couple of other important points, including:

      (1) Discuss the 'sweet-spot' of movie watching for behavior prediction in the context of studies showing that task states 'quench' neural variability: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007983. This may not be mutually exclusive of the discussion on dopamine and signal-to-noise ratio, but it would be helpful for the authors to discuss their potential overlap vs. unique contributions to the observed findings.

      Thank you for the comment. We have now eliminated the section about methodological tweaks and extended the discussion on the sweet-spot of the task for behavioral prediction by referencing the paper that the reviewer suggested. Here comes the paragraph discussing this topic:

      “Additionally, previous research showed that movie-watching alters the propagation of activity across cortical pathways (105), particularly within and between regions involved in audiovisual processing and attention. These alterations lead to a less segregated and more integrated network organization (106). Similarly, the n-back task has been associated with increased integration of task-positive cortico-cortical connectivity (104, 107) and striato-cortical connectivity (102). Our findings also suggest that certain task contexts strike an optimal balance between reducing neural variability and maintaining sufficient richness to capture individual differences. Prior work shows that task states quench neural variability, leading to a more reliable and predictable neural signal (108). In this context, movie watching may represent such a sweet spot constraining neural dynamics through shared audiovisual stimulation, while simultaneously engaging a broad range of cognitive processes that preserve individual differences.”

      (2) The argument that dopamine signaling increases signal-to-noise ratio is based on some preclinical data as well as correlational data using fMRI with pharmacological challenges. It is less clear how PET-derived estimates of D1R and D2R availability equate to 'dopamine signaling' as it is thought of in this context. Presumably, based on these data, higher D1R or D2R availability would be related to greater levels of tonic dopaminergic signaling. However, in the case of the COBRA dataset with D2R estimates, those are based on raclopride -- which competes with endogenous dopamine for the D2 receptor. Therefore, someone with higher levels of endogenous dopamine signaling should theoretically have lower raclopride binding and lower D2R estimates. I'm not arguing that the authors' logic is flawed or that D1R and D2R are not good measures of dopamine signaling, but I'd ask the authors to dig into the literature and describe more direct potential links for how greater receptor availability might be associated with greater dopamine signaling (and hence lower entropy). Adding this to the discussion would be very valuable for PET research.

      Thank you for raising this important point. We agree that D1R and D2R availability should not be taken as direct proxies of dopamine signaling. However, prior work has suggested meaningful associations between pre- and post-synaptic markers. For instance, a well-powered study demonstrated a significant correlation between D2R availability and dopamine synthesis capacity measured by FMT (Berry et al., 2018). This finding supports the idea that postsynaptic receptor markers may, under certain conditions, serve as an indirect proxy for dopaminergic signaling. Moreover, the number of dopamine-producing neurons innervating the striatum during development has been proposed to shape the structural maturation and arborization of dendrites (McAllister, 2000; Whitford et al., 2002), potentially providing a structural and functional basis for observed associations between pre- and post-synaptic measures.

      At the same time, smaller-scale studies have yielded mixed findings, reporting either non-significant associations (Heinz et al., 2005; Kienast et al., 2008) or negative correlations (Ito et al., 2011). Importantly, the latter studies employed [18F]FDOPA to index dopamine synthesis, which has been argued to provide a less reliable estimate of synthesis capacity compared to FMT, as used in Berry et al. (2018). These inconsistencies underscore that the relationship between pre- and post-synaptic markers is not straightforward and requires further examination in larger, well-powered samples. The following paragraph has been added to the discussion.

      “An important caveat is that D1DR and D2DR availability do not provide a direct measure of dopamine signaling. Instead, they reflect receptor availability, which interacts with endogenous dopamine in a complex manner. PET measures of D1R and D2R availability reflect the density of unoccupied dopamine receptors and the degree to which endogenous dopamine competes with radioligand binding. D2R binding potential is sensitive to competition from synaptic dopamine, such that higher ambient dopamine generally reduces tracer binding; D1R binding, however, is less affected by endogenous dopamine under physiological conditions, reflecting more directly receptor expression levels. Previous studies demonstrated a significant association between D2R availability and dopamine synthesis capacity measured by FMT (117, 118), suggesting that postsynaptic receptor markers may, under certain conditions, serve as a proxy for dopaminergic signaling. Developmental factors, such as the number of dopamine-producing neurons innervating the striatum, may further influence the structural and functional relationship between pre- and post-synaptic markers. By contrast, smaller studies have reported non-significant (119, 120) or negative (121) associations, although these studies relied on [18F]FDOPA, which is considered a less precise index of dopamine synthesis than FMT. Taken together, these reports indicate that the relationship between pre- and post-synaptic markers is complex and not necessarily linear. Accordingly, our observation that lower receptor availability is associated with greater neural variability should not be interpreted as direct evidence of weaker dopaminergic signaling, but rather as reflecting the interplay between receptor density and endogenous dopamine occupancy, particularly in the case of D2DR.”

      Reviewer #2 (Public review):

      Summary:

      The authors developed a deep learning model based on a DenseNet CNN architecture to predict two cognitive functions: working memory and episodic memory, from functional connectivity matrices. These matrices were recorded under three conditions: during rest, a working memory task, and a movie, and were treated as images for the CNN algorithm. They tested their model's performance across different conditions and a separate dataset with a different age distribution (using the same MRI scanner, scanning configurations, and cognitive tests). They also calculated the "brain cognition gap" based on the model trained on resting functional connectivity to predict working memory. Extending from the commonly used index "brain age," the brain cognition gap was defined as the difference between the working memory score predicted by their model (predicted working memory) and the working memory score based on the working memory test itself (observed working memory). This brain cognition gap was found to be associated with physical activity, education, and cardiovascular risk. The authors also conducted additional mediation tests to examine whether regional functional variability mediated the relationship between PET-derived measures of dopamine and the brain cognition gap.

      Strengths:

      The major strength of this manuscript is the extensive effort the authors have put into creating a new 'biomarker' that links deep learning with fMRI, PET, physical activity, education, and cardiovascular risk across two studies. This effort is impressive.

      Weaknesses:

      There are several weaknesses in the current methods and results, making many of the claims unconvincing. These weaknesses include:

      (1) The lack of baseline models to benchmark the predictive performance of their DenseNet models.

      (2) The inappropriate calculation of the brain cognition gap due to the lack of control for regression-toward-the-mean and the influence of the working memory itself (a common practice in brain age studies).

      (3) The lack of benchmarking of the brain cognition gap against the 'corrected' brain age gap and the direct prediction of physical activity, education, and cardiovascular risk.

      (4) Minimal justification for their PET mediation analysis.

      We appreciate the reviewer’s constructive comments on the strengths and weaknesses of our study. In this revised version, we’ve addressed the concerns regarding the calculation of the brain-cognitive gap, clarified the unique variance that the brain-cognitive gap contributes beyond cognition itself, and provided additional justification for the PET mediation analysis. For the lack of a baseline model, it is important to highlight that our aim has never been to compare the predictive power of different deep learning or machine learning approaches. Therefore, the text in the introduction and discussion has been amended to avoid miscommunication on this topic.

      Regarding the impact of the work on the field and the utility of the methods and data to the community, I see its potential. However, addressing all the weaknesses listed above is crucial and likely to change the conclusions of the results.

      It is important to note that many statements in the manuscript are overstated, making the contribution of the manuscript seem exaggerated.

      We have run additional analysis based on the reviewer’s suggestions. The effect sizes and statistical values were adjusted due to the corrections; the overall conclusions remain largely consistent. The relationships between the brain-cognition gap and key factors such as physical activity, and cardiovascular risk persisted. We have updated the manuscript accordingly and revised the relevant sections to reflect these refinements and the resulting interpretations.

      For instance, the abstract claims "there is a lack of objective biomarkers to accurately predict cognitive function," and the discussion states, "across various studies, the correlation between predicted and actual fluid intelligence typically hovers around 0.25 (98-100)." However, a meta-analysis by Vieira and colleagues (2022 https://doi.org/10.1016/j.intell.2022.101654) found over 37 studies up to 2020 predicting cognitive abilities from fMRI with machine learning, with 24 studies published in 2019-20 alone. Since 2020, with the rise of machine learning and AI, even more studies have likely been published on this topic, all claiming to show objective biomarkers to accurately predict cognitive function. Vieira and colleagues also found an average performance of these objective biomarkers in predicting general cognition at r = .42, similar to what was found in this manuscript. Based on this alone, it is unclear how novel or superior their method is without a proper systematic benchmark.

      We appreciate the opportunity to clarify our study’s contribution relative to prior work. We have revised the introduction and discussion to highlight the contribution of other methods when it comes to biomarkers. As for the comment related to the work by Vieira and colleagues, Vieira et al. (2022) indeed present a comprehensive meta-analysis of studies predicting general and fluid intelligence using neuroimaging and machine learning. However, there are two critical differences between ours verus previous work:

      Target Cognitive Domains:

      Our study does not focus on general or fluid intelligence, but rather on comprehensive EM (3 tests) and WM (3 tests), two distinct cognitive domains that are critically important for aging research. These distinct abilities, in this context (measured by three independent tests to boost the reliability) are less frequently studied as predictive targets in the existing fMRI-ML literature, particularly using deep learning methods.

      Critically, our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back), with the aim of identifying the states that best capture individual differences across domains. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.

      Our primary objective is to test how brain state influences the ability of functional connectivity to predict domain-specific cognitive performance, using a deep learning framework. As now stated explicitly in the revised manuscript, this objective is operationalized through three clearly defined aims:

      (1) To compare the predictive utility of functional connectomes derived from different brain states (resting state, movie watching, and n-back task) for EM and WM;

      (2) To introduce and evaluate a brain-cognition gap as a marker of individual differences beyond chronological age; and

      (3) To examine the contribution of dopaminergic integrity to variability in connectome uniqueness and brain-cognition gaps.

      We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework for some of the prediction models, we did not conduct a comprehensive benchmark across all available machine learning methods nor was this the aim of the present study. Accordingly, we have adjusted the text to avoid implying methodological/biomarker superiority beyond the scope of our analyses.

      Modeling Approach:

      While Vieira et al. show that the majority (76%) of prior studies used linear modeling approaches, including CPM and penalized regressions, these models are often vulnerable to overfitting, especially when applied to high-dimensional fMRI data. Our use of a DenseNet-based CNN architecture is motivated by the need to leverage inductive biases suited to functional connectivity data, and we evaluate this approach across multiple cognitive tasks and independent datasets.

      Vieira and colleagues report that studies predicting general intelligence from fMRI (particularly from the HCP dataset) average around r =0.42, while those predicting fluid intelligence average around r =0.15. Our original claim about the correlation hovering around 0.25 is therefore not incorrect – and aligns with the Vieira meta-analysis. We have, however, nuanced this statement in the manuscript, now stating that correlations are higher for general intelligence than fluid intelligence.

      Altogether, we considered the reviewer’s comments and therefore conducted a careful revision of the manuscript text to moderate and clarify statements that may have come across as overstated. We have refined the language throughout the Introduction and Discussion sections to better align with the strength of the evidence and the scope of our contributions. A few examples are:

      “Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back), with the aim of identifying the states that best capture individual differences across domains. The relative performance of deep learning and other non-linear approaches depends on multiple factors, including sample size, model architecture, feature representation, and domain-specific characteristics of the prediction target. In this context, deep learning was employed as a flexible framework capable of modeling high-dimensional functional connectivity patterns across cognitive states, rather than as a claim of inherent methodological superiority. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.”

      Also in page 14.

      “Our study introduces a deep neural network architecture that features dense connections and incorporates an attentional mechanism. While our findings demonstrate that a deep learning framework can provide reasonable predictive accuracy, it is important to note that other machine learning approaches (e.g., tree-based models) may offer comparable predictive power, as suggested by prior benchmarking work (29, 30).”

      Similarly, the authors claim superior performance of deep learning and mischaracterize machine learning algorithms: "In particular, deep neural networks (DNN) methods have been successfully applied to behavioral and disease prediction (24-26), and have been found to outperform other machine learning approaches (27-29)," and "Deep learning approaches overcome the limitation of predictive techniques that solely rely on linear associations between connectivity and behavioral phenotypes (17)." However, the superiority of deep learning is debatable. Studies show comparable performance between machine learning (such as kernel regression) and deep learning (such as fully-connected neural networks, BrainNetCNN, Graph CNN (GCNN), and temporal CNN), e.g., He and colleagues (2019) and Vieira and colleagues (2024) https://doi.org/10.1016/j.neuroimage.2019.116276 and Vieira and colleagues' https://doi.org/10.1101/2024.03.07.583858.

      We agree that the performance gap between traditional machine learning models and deep learning (which is a subcategory of machine learning) in neuroimaging is debatable and task-dependent. Indeed, both He et al. (2019) and Vieira et al. (2024) offer evidence that kernel regression can achieve performance on par with deep learning models, applied to appropriate datasets.

      We have therefore nuanced the statements in the revised version of the manuscript as follows:

      Introduction:

      “In particular, deep neural networks (DNN) methods have been successfully applied to behavioral and disease prediction (24-26), and were initially expected to outperform other machine learning approaches (27-29). However, this superiority remains debatable, as recent studies have reported comparable performance between DNNs and traditional methods (He et al.,2019; Vieira et al.,2024). Accordingly, the present study does not aim to benchmark deep learning against traditional machine learning approaches, but instead uses a consistent predictive framework to examine how brain state influences the utility of FC for cognitive prediction.”

      “Deep learning approaches offer a flexible modeling framework capable of capturing complex non-linear associations in high-dimensional data with potentially less sensitivity to training on a smaller subsample (Vieira et al., 2024)”.

      Discussion:

      We agree that traditional methods, such as kernel-based models, tree ensembles, and non-linear SVRs, can also effectively capture such relationships. The relative performance of our model and other non-linear approaches depends on several factors, including data size, model architecture, and domain-specific considerations. We have included additional explanations in the discussion to address this.

      Moreover, many non-deep learning predictive techniques are non-linear, e.g., XGBoost, CatBoost, random forest, kernel ridge, and support vector regression with non-linear kernels (such as RBF and polynomial). Thus, stating that machine learning can only model linear relationships is incorrect. Moreover, for the small amount of data the authors had, some might argue that a linear algorithm might be more appropriate to balance the bias-variance trade-off in prediction. Again, without a proper systematic benchmark, it is unclear how well their DenseNet algorithm performs compared to other algorithms.

      Thank you for bring this up. We have now removed statements implying that machine learning can only model linear relationship.

      Regarding the Brain Age literature, the authors also misinterpreted recent findings: "However, a recent study suggests that brain age predictions contribute minimally compared to chronological age for explaining cognitive decline (65), implying that cognitive predictions are more reliable." In this study, Tetereva and colleagues (2024) (https://doi.org/10.7554/eLife.87297.4) showed that non-deep-learning machine learning can make good predictions from MRI on both chronological age (with r up to .88) and fluid cognition (with r up to .627). Using the combination of functional connectivity matrices across rest and tasks to predict fluid cognition, they found performance at r = .565, comparable to what was found in the current manuscript with deep learning. Nonetheless, while brain age predicted chronological age well (and brain cognition predicted fluid cognition well), it was problematic to predict fluid cognition from brain age. They showed that, because brain age, by design, shared so much common variance with chronological age, brain age and chronological age captured the same variance of fluid cognition. When chronological age was controlled for in the prediction of fluid cognition, brain age no longer had high predictive ability. In the case of the current manuscript, the brain cognition gap is not appropriately controlled for cognition (to be more precise, a working memory score). I expect the performance in predicting physical activity, education, and cardiovascular risk will drop dramatically once cognition is controlled for. There are at least two ways to control cognition according to Tetereva and colleagues' study (see more in the recommendations).

      We thank the reviewer for breaking down the findings in the study by Tetereva and colleagues (2024). It was not our intention to suggest that Tetereva et al. showed brain age has little predictive value in general. Our understanding of the findings reported in that study is on par with the reviewers’ clarifications. We have now revised the introductions to avoid any misunderstanding:

      “A recent study demonstrated that while brain age can predict chronological age with high accuracy from MRI, its utility for predicting cognition is limited. Specifically, Tetereva and colleagues (2024) showed that brain age strongly tracks chronological age and that brain cognition (using functional connectivity) can predict fluid cognition. Yet, when used to predict cognition, brain age largely overlapped with chronological age, such that controlling for chronological age eliminated the predictive contribution of brain age. This finding suggests that brain-age models may provide little unique explanatory power for cognitive decline beyond what is already captured by chronological age. Building on this observation and extending the concept of a brain-age gap to a brain-cognition gap (BCG, defined as the discrepancy between predicted and observed cognitive performance), we propose that a BCG may serve as an informative marker of individual differences.”

      In addition, in response to the first comment from Reviewer 1, we have extended our results in the manuscript. We first showed that BCG is not significantly associated with cognition itself (see Author response image 1). Moreover, we conducted additional analyses, splitting the sample into high and low EM performers, and compared their levels of physical activity and Framingham cardiovascular risk scores. We found that no significant difference in physical activity (DyNAMiC: p =0.56, 95% CI: -14.99 – 8.13; COBRA: p =0.29, 95% CI: -3.54 – 1.05) or Framingham CVD risk score (DyNAMiC: p =0.11, 95% CI: -1.08 – 10.72; COBRA: p =0.41, 95% CI: -1.86 – 4.58) between high and low EM performers. Given the significant difference in physical activity and Framingham CVD risk score between positive and negative BCG groups, our results support that BCP provides unique information, beyond cognitive measures, regarding factors that contribute to cognitive resilience. This text has been added into the result section, and Figure 3 has been updated in the manuscript.

      The authors mentioned, "The third aim of the current study is to uncover the contribution of dopamine (DA) integrity to brain-cognition gaps." However, I fail to see how mediation analysis would test this. The authors also mentioned, "Insufficient DA modulation can affect neurocognitive functions detrimentally (69, 74, 76-78)." They should test if DA levels are related to working memory scores in their study, and if so, whether the relationship is mediated by the "corrected" brain-cognition gaps. Note see more on the recommendation for the calculation of the "corrected" brain-cognition gaps.

      Our mediation was not designed to test whether DA predicts episodic memory performance directly, nor whether BCG mediates such a relationship. Instead, we specifically investigated whether the effect of DA on BCG operates through functional variability, the theoretical framework emphasizing the role of DA on neuronal grain and signal-to-noise ratio (see our recent work in Korkki et al., 2025). We agree that future work could extend our approach by directly examining whether BCG mediates the link between DA and cognitive outcomes. However, in the present study, our primary focus was on testing the mechanistic pathway of DA → entropy → BCG.

      In line with this aim, we found that lower DA receptor availability was associated with larger BCGs (Figure 4). We then asked whether this relationship is mediated by functional signal variability, such that lower DA is linked to reduced signal-to-noise ratio (i.e., greater entropy), which in turn contributes to less reliable prediction of cognition and, consequently, larger BCGs. Our mediation analysis supports this pathway (please see also our reply to Reviewer 1, Comment 6).

      Reviewer #3 (Public review):

      Summary:

      This paper by Esmaeili and co-authors presents a connectome prediction study to predict episodic memory and relate prediction errors to other phonotypic variables.

      Strengths:

      (1) A primary and external validation dataset.

      (2) Novel use of prediction errors (i.e., brain-cognitive gap).

      (3) A wide range of data was investigated.

      Weaknesses:

      (1) Lack of comparisons to other methods for prediction.

      (2) Several different points are being investigated that don't allow any particular one to shine through.

      (3) Some choices of analysis are not well-motivated.

      (4) How do the n-back connectomes perform for prediction if the authors do not regress task activations from the n-back task?

      We thank the reviewer for raising these important points. For the lack of comparisons to other methods, it is important to highlight that our aim has never been to compare the predictive power of different deep learning or machine learning approaches. Rather, our primary objective was to test how brain state influences the ability of functional connectivity to predict domain-specific cognitive performance, using a deep learning framework.Therefore, the text in the introduction and discussion has been amended to avoid miscommunication on this topic.

      We chose to regress out task-evoked activations based on prior work demonstrating that failing to do so can produce spurious but systematic inflation of task functional connectivity estimates (Cole et al., 2019). In that study, as well as subsequent reports (e.g., Gao et al., 2020; Gonzalez-Castillo & Bandettini, 2018), connectomes derived without activation regression tended to capture task-evoked coactivations rather than background task functional interactions, which can artificially boost predictive performance but limit interpretability (whether it is co-activation or intrinsic connectivity during an entire goal-oriented task) and generalizability. For this reason, our analyses focused on the more conservative approach of regressing out task activations. Accordingly, we compared predictive performance only under this preprocessing strategy.

      We have added the following sentence to clarify this in the method: “To avoid spurious inflation of task functional connectivity by task-evoked activations, we regressed out task activation patterns from the n-back data prior to estimating functional connectivity, following recommendations by Cole et al. (2019) and related work.”

      (5) I am a little concerned about overfitting with the convolutional neural net. For example, the drop-off in prediction performance in the external sample is stark. How does the deep learning approach used here compare to something simpler, like a connectome-based predictive model or ridge regression?

      (6) It may be nice to try the other models in the validation dataset. This would also provide a sense of the overfitting that may be going on with overfitting.

      We thank the reviewer for raising this point. The prediction performance indeed dropped for episodic memory when models trained on the DyNAMiC sample were applied to the COBRA sample, whereas performance for working memory remained nearly identical across datasets. Moreover, our prediction power is on par with previous studies reporting reliable prediction of intelligence using deep learning approach (Vieira et al., 2021; Fan et al.,2020). While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework, we did not conduct a comprehensive benchmark across all available machine learning methods nor was this the aim of the present study.

      We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. Finally, We have added the following paragraph to the discussion:

      “Our study used a deep neural network architecture that features dense connections and incorporates an attentional mechanism. While our findings demonstrate that a deep learning framework can provide reasonable predictive accuracy, it is important to note that other machine learning approaches (e.g., tree-based models) may offer comparable predictive power, as suggested by prior benchmarking work (29, 30). Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back) to identify the states that best capture individual differences across domains. The relative performance of deep learning and other non-linear approaches depends on multiple factors, including sample size, model architecture, feature representation, and domain-specific characteristics of the prediction target. In this context, deep learning was employed as a flexible framework capable of modeling high-dimensional functional connectivity patterns across cognitive states, rather than as a claim of inherent methodological superiority. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.”

      (7) While predictive models increase the power over association studies, they still require large samples to prevent overfitting. Do the authors have a sense of the power their main and external validation sample sizes provide?

      We thank the reviewer for this important point. Our main sample size, together with the external validation in COBRA, is moderate for deep learning applications. To reduce the risk of overfitting, we employed several strategies, including external validation, early stopping, dropout, and regularization. As noted, performance for episodic memory decreased in the external sample, which we acknowledge, but key associations such as the link between BCG and resilient factors remained significant. Importantly, prediction of working memory was maintained across datasets, reducing the likelihood that the observed findings are driven by overfitting. We have added a statement in the Discussion to reflect on the limitations of sample size and the implications for generalizability.

      We added the following sentence to the discussion:

      “We acknowledge that our main and validation samples are moderate in size for deep learning, which constrains statistical power and generalizability. Although external validation, early stopping, dropout, and regularization help mitigate overfitting, larger samples will be needed in future work to fully establish the robustness of these predictive models.”

      (8) I am not sure that the Mann-Whitney is the correct test for comparing the distributions of prediction performances. The distributions are dependent on each other as they are each predicting the same outcomes. Using the typical degrees of freedom formula would overestimate the degrees of freedom.

      We appreciate the reviewer’s comment and agree that applying statistical tests directly to bootstrapped samples can lead to inflated or misleading p-values, as the degrees of freedom are determined by the number of bootstrap iterations rather than the actual number of independent observations.

      In our analysis, the Mann-Whitney U test was applied to 1000 bootstrapped correlation coefficients (r) for each model. While this number is relatively low and was chosen to limit overestimation of significance, we recognize that these bootstrapped samples are not independent, and thus the use of a Mann-Whitney U test can still be problematic. To address this concern, we have revised our statistical analysis. Rather than applying the Mann-Whitney U test to the bootstrapped r distributions, we now compute the difference in correlation coefficients (Δ r = r<sub>actual</sub> − r<sub>rest</sub>) for each bootstrap iteration. We then calculate a 95% confidence interval for Δr. If this interval does not include zero, we consider the difference statistically significant. This approach avoids artificially inflating the sample size and adheres more closely to proper statistical inference.

      We have updated the Methods (the following text) and Results sections accordingly and clearly stated the limitations regarding the degrees of freedom for all tests.

      “For the bootstrap-based comparison of model performance (bootstrap resampling with 1000 iterations), no test statistic with an associated degree of freedom is reported. Instead, statistical inference is based on the bootstrap distribution of the difference in correlation coefficients (Δr) and its 95% confidence interval. As bootstrap confidence-interval–based inference does not rely on an analytic sampling distribution, degrees of freedom are not defined for this procedure.” This has now been explicitly stated in the Methods section to avoid ambiguity.

      In the result section, we have reported with corresponding CI.

      (9) The brain cognition gap is interesting. It is very similar conceptually to the brain age gap. When associating the brain age gap with other phenotypes, typically age is regressed from the brain age gap and the other phenotype. In other words, age is typically associated with a brain age gap as individuals at the tail ages often show the largest gaps. Is the brain cognition gap correlated with episodic memory and do the group differences hold if episodic memory is controlled for?

      We thank the reviewer’s comment regarding the relationship between the brain cognition gap and episodic memory.

      Since this question was raised by all reviewers, we have conducted additional analyses. We did find that BCG is independent from the cognitive measure and provided additional information, beyond cognition alone, about factors contributing to resilience. Please visit our response to the first comment of Reviewer 1.

      (10) I have the same question for the dopamine results. Particularly, in the correlations that are divided by brain cognition gap sign. I could see these types of patterns arise due to a correlation with a third variable.

      For dopamine results, we explored whether age or cognition alone might confound the dopamine–brain cognition gap relationships. However, neither was significantly correlated with the brain cognition gap groups. The associations remained significant after controlling for age, suggesting that the observed patterns are not likely due to these potential third-variable confounder. This is also inline with our observation of significant associations between DA and GAP in an age-homogeneous COBRA sample. That said, we found that entropy, indeed, mediates the direct link between DA and BAG, suggesting that individuals with lower DA exhibit greater regional variability, and in turn larger BCG.

      These results have now been embedded into the manuscript. We also highlighted that age has been controlled for in reported correlation and mediation analyses.

      Recommendations for the authors:

      Reviewing Editor Comment:

      We particularly recommend that the authors: (a) compare the performance of their deep learning model with other baseline models, and (b) adjust for cognitive performance within the brain-cognition gap. These steps would strengthen the evidence base.

      We thank the editor for their comments. As for the first comments, our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back), with the aim of identifying the states that best capture individual differences across domains. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach. We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework, we did not conduct a comprehensive benchmark across all available machine learning methods, nor was this the aim of the present study. Accordingly, we have adjusted the text to avoid implying methodological superiority beyond the scope of our analyses. Finally, we have added the following paragraph to the discussion:

      “Our study used a deep neural network architecture that features dense connections and incorporates an attentional mechanism. While our findings demonstrate that a deep learning framework can provide reasonable predictive accuracy, it is important to note that other machine learning approaches (e.g., tree-based models) may offer comparable predictive power, as suggested by prior benchmarking work (29, 30).

      Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back) to identify the states that best capture individual differences across domains. The relative performance of deep learning and other non-linear approaches depends on multiple factors, including sample size, model architecture, feature representation, and domain-specific characteristics of the prediction target. In this context, deep learning was employed as a flexible framework capable of modeling high-dimensional functional connectivity patterns across cognitive states, rather than as a claim of inherent methodological superiority. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.”

      As for the second comment, we followed the instructions by Reviewer 1. In response to their request, we first examined the relationship between the Brain-Cognitive Gap (BCG) and the cognitive measure itself. Surprisingly, we did not find any significant relationship in either the DyNAMiC sample (r =0.01, p =0.939) or the COBRA sample (r =0.01, p =0.89) (see Author response image 1).

      We then conducted additional analyses, splitting the sample into high and low EM performers, and compared their levels of physical activity and Framingham cardiovascular disease (CVD) risk scores. We found no significant difference in physical activity (DyNAMiC: p =0.56, 95% CI: –14.99 - 8.13; COBRA: p =0.29, 95% CI: –3.54 - 1.05) or Framingham CVD risk score (DyNAMiC: p =0.11, 95% CI: –1.08 - 10.72; COBRA: p =0.41, 95% CI: –1.86 - 4.58) between high and low EM perfprmers. Given the significant difference in physical activity and Framingham CVD risk score between positive and negative BCG groups, our results support that BCG provides unique information, beyond the observed cognitive measure (episodic memory score), regarding factors that contribute to cognitive resilience. These results have been added to Section 2.4, and Figure 3 has been updated.

      Reviewer #1 (Recommendations for the authors):

      (1) The top and bottom triangles of the saliency maps, particularly in Figure 2, do not look symmetrical (this is most notable in the hotspot representing the between-network correlation of DMN and FPN). What is going on here? Was the image compressed or altered in some way, or is this a visual artifact of the interpolation method?

      We appreciate the reviewer’s insightful comment. Minor differences in the saliency maps between the upper and lower triangles of the FC matrix can arise due to several factors. For instance, Grad-CAM generates saliency maps at the resolution of the convolutional feature maps, which are then upsampled to match the input matrix dimensions. We initially used the default bilinear interpolation, which may have introduced slight asymmetries or blurring, resulting in interpolation artifacts. In response, we have reprocessed the saliency maps using spline interpolation in MATLAB. The updated saliency figures have been included in the revised version of the manuscript.

      (2) Pages 11-12. Please make it explicit in the text that the brain gap-education association was not significant in the COBRA dataset.

      Thanks for pointing this out. We added the following sentence to the discussion.

      “Note that the association with education was significant only in the DyNAMiC sample and did not reach significance in the COBRA dataset.“

      (3) Please overlay individual data points onto the boxplots in Figure 3 so that we can appropriately evaluate the data distributions.

      Figure 3 has now been updated.

      (4) Section 2.6: Was entropy calculated on movie-watching data, resting data, or all fMRI data? Please specify.

      We thank the reviewer for pointing this out. We have updated the text (Section 2.6) to clarify that entropy was calculated from the resting-state data. We intended to examine the mediating role of regional variability in the relationship between dopamine and the BCG of the winning model for episodic memory. Because resting state and movie-watching were the winning conditions for EM prediction, but movie-watching was not available in COBRA, we focused on entropy during rest, which exists in both datasets.

      (5) Was entropy during the resting state correlated with entropy during the task state, across individuals?

      We agree this is an interesting question. However, investigating the correlation of entropy between rest and task states goes beyond the scope of the present study. Our aim here was to test whether regional variability mediates the effect of dopamine on the BCG. Specifically, we examined whether individuals with lower striatal D1DR show higher local variability, which in turn relates to less accurate prediction and a larger gap. We assessed both the relationship between D1DR and entropy and the association between entropy and the gap, and these results have now been added to the manuscript (see also our response to Reviewer 1’s public comment).

      Reviewer #2 (Recommendation for authors):

      (1) The lack of baseline models to benchmark the predictive performance of their DenseNet models makes their results hard to interpret. This problem is quite common across ML literature. For instance, many DL-based algorithms were developed for tabular data without proper benchmarking against other ML algorithms. When they were properly tested, most weren't better than many tree-based ML algorithms (e.g., https://proceedings.neurips.cc/paper_files/paper/2022/file/0378c7692da36807bdec87ab043cdadc-Paper-Datasets_and_Benchmarks.pdf). I can see that a similar problem might happen here.

      For this particular manuscript, the authors made strong statements without doing a proper benchmark, e.g., from the discussion, "Indeed, the predictive power in the current study is stronger than for CPM-based predictions reported before." And "Unlike the BrainNet convolutional neural network, which focuses on staged transformations, our densely connected model promotes extensive feature reuse, possibly leading to more robust feature extraction." I hope to see the performance of the proposed algorithm against 1) other DL algorithms (e.g., fully-connected neural networks, BrainNetCNN, Graph CNN (GCNN), temporal CNN, GRU, and LSTM, see https://doi.org/10.1016/j.neuroimage.2019.116276 and https://doi.org/10.1002/hbm.26415), 2) ML algorithms (e.g., SVR with linear, RBF and polynomial kernels, Elastic Net, XGBoost, random forest, CPM), 3) data reduction algorithms (e.g., PCA regression, Partial Least Square). The results of this benchmark will substantiate the claims made by the authors.

      Our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach. We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework, we did not conduct a comprehensive benchmark across all available machine learning methods, nor was this the aim of the present study. Accordingly, we have adjusted the text to avoid implying methodological superiority beyond the scope of our analyses. Finally, we have added the following paragraph to the discussion:

      “Our study used a deep neural network architecture that features dense connections and incorporates an attentional mechanism. While our findings demonstrate that a deep learning framework can provide reasonable predictive accuracy, it is important to note that other machine learning approaches (e.g., tree-based models) may offer comparable predictive power, as suggested by prior benchmarking work (29, 30). Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back) to identify the states that best capture individual differences across domains. The relative performance of deep learning and other non-linear approaches depends on multiple factors, including sample size, model architecture, feature representation, and domain-specific characteristics of the prediction target. In this context, deep learning was employed as a flexible framework capable of modeling high-dimensional functional connectivity patterns across cognitive states, rather than as a claim of inherent methodological superiority. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach.”

      (2) From Figure 6b, it looks like the functional connectivity matrices were converted to different images, and each of the four images (in grey, blue, yellow, and red) was treated as a separate channel. What are these grey, blue, yellow, and red images?

      In our study, the inputs to the deep learning models were subject-specific FC matrices of size 273×273. To augment the data, we created different versions of each FC matrix by reordering specific brain networks within the matrix. To visualize that the inputs were augmented, we used different color codings (grey, blue, yellow, and red) in Figure 6b. These colors were intended solely to represent different augmented versions of the same subject’s FC matrix. They were not treated as separate channels in the model. To avoid any confusion or misinterpretation, we have revised this part of the figure and now use only grey coloring to represent the augmented FC matrices.

      (3) The differences in performance between within vs. outside studies might simply be due to the fact that the models trained from DyNAMiC captured the brain variation due to age, which is also related to cognitive abilities. I was wondering if age is controlled for, would performance be more similar across the studies? The authors should provide the performance of models that are controlled for age.

      We initially conducted partial correlation between FC features and cognitive measures while controlling for age. This is further supported by the fact that the model trained on the age-heterogeneous DyNAMiC sample provided a fairly reasonable prediction in the age-homogeneous COBRA dataset, particularly for working memory (see figure 2d). Moreover, in our post hoc analyses, we additionally controlled for age when examining associations, for example, between GAP and dopamine measures.

      (4) Related to point (3), from the discussion, "Validation outcomes thus affirm that the models, particularly those constructed from rest data, are robust to the particulars of the dataset." The performance dropped around half, so I am not sure if this conclusion is warranted.

      We thank the reviewer for raising this point. The prediction performance indeed dropped for episodic memory when models trained on the DyNAMiC sample were applied to the COBRA sample, whereas performance for working memory remained nearly identical across datasets. Although both EM and WM are sensitive to age, the divergence in cross-dataset performance suggests that factors beyond age alone may contribute to these differences. To address this, we have revised the discussion as follows:

      “Differences between the DyNAMiC and COBRA datasets make cross-dataset prediction a harder problem, as the age ranges of samples significantly vary, and prior studies highlight the importance of individual characteristics like age in predicting behavior from FC (33). In line with this, model performance decreased when predicting EM in the COBRA sample whereas prediction of WM remained largely unchanged. Thus, validation outcomes suggest that the models, particularly those predicting WM, show robustness across datasets, whereas the reduced EM performance highlights potential data-specific influences that limit generalizability.”

      (5) Please report the degree of freedom in all of the statistical analyses. Was the Mann-Whitney U test done on the bootstrapped r? If so, the degree of freedom was arbitrarily set by the number of bootstrapping, and hence the p-value can be higher or lower depending on the number of bootstrapping. This could lead to misleading conclusions.

      We appreciate the reviewer’s comment and agree that applying statistical tests directly to bootstrapped samples can lead to inflated or misleading p-values, as the degrees of freedom are determined by the number of bootstrap iterations rather than the actual number of independent observations.

      In our analysis, the Mann-Whitney U test was applied to 1000 bootstrapped correlation coefficients (r) for each model. While this number is relatively low and was chosen to limit overestimation of significance, we recognize that these bootstrapped samples are not independent, and thus the use of a Mann-Whitney U test can still be problematic. To address this concern, we have revised our statistical analysis. Rather than applying the Mann-Whitney U test to the bootstrapped r distributions, we now compute the difference in correlation coefficients (Δr = r<sub>actual</sub> − r<sub>rest</sub>) for each bootstrap iteration. We then calculate a 95% confidence interval for Δr. If this interval does not include zero, we consider the difference statistically significant. This approach avoids artificially inflating the sample size and adheres more closely to proper statistical inference.

      We have updated the Methods (the following text) and Results sections accordingly and clearly stated the limitations regarding the degrees of freedom for all tests.

      “For the bootstrap-based comparison of model performance (bootstrap resampling with 1000 iterations), no test statistic with an associated degree of freedom is reported. Instead, statistical inference is based on the bootstrap distribution of the difference in correlation coefficients (Δr) and its 95% confidence interval. As bootstrap confidence-interval–based inference does not rely on an analytic sampling distribution, degrees of freedom are not defined for this procedure.” This has now been explicitly stated in the Methods section to avoid ambiguity.

      In the result section, we have reported with corresponding CI.

      (6) For predictive performance, the correlation was reported in the table, while R<sup>2</sup> is reported in the text. This is confusing. Also, could you clarify if the R<sup>2</sup> is calculated using the sum square definition, not Pearson r squared? If Pearson r squared was used, then R<sup>2</sup> of a negative Pearson r would be positive, which is misleading (see 10.1001/jamapsychiatry.2019.3671). Also, other performance indices apart from Pearson r and R² should be reported (e.g., MSE and MAE, again see 10.1001/jamapsychiatry.2019.3671). This will allow a better understanding of the models' performance.

      We thank the reviewer for this helpful comment. We acknowledge the inconsistency in reporting predictive performance metrics and have revised the manuscript for clarity. In the text, we have reported the r value, whereas in the table, we have reported r<sup>2</sup> using the sum-of-squared definition. Specifically, we now consistently report Pearson correlation (r), mean squared error (MSE), and mean absolute error (MAE) across both the text and Tables 1 and 2.

      Regarding r<sup>2</sup>, we confirm that it was calculated using the sum-of-squares definition (i.e.,

      rather than as the square of the Pearson correlation coefficient. This ensures that negative correlations do not result in misleading positive R<sup>2</sup> values, as pointed out by the reviewer and discussed in Poldrack et al. (2020). All performance metrics (r, r<sup>2</sup>, MSE, and MAE) are now reported in Tables 1 and 2 to allow a more comprehensive and interpretable comparison of model performance.

      We have included a description of the method under section 4.9. Statistical significance analysis.

      (7) Could you clarify how data are standardized across training, validation, and tests (including Z-standardization for the cognitive tests)? This is to prevent data leakage.

      Thanks for the comments. We did standardization the cognitive test from both training and test, separately.

      We have added the following paragraph to the method section:

      “A composite score of performances across the three tests was calculated and used as the measure of the cognitive domain in question (i.e., episodic memory, working memory). For each of the three tests, scores were summarized across the total number of trials. The three resulting sum scores were z-standardized and averaged to form one composite score for each domain. The standardization has been carried out independently for the training (DyNAMiC) and test (COBRA) samples.”

      (8) There is really no ground truth to confirm that Grad-CAM provides actual feature importance used by the models. Perhaps the authors should compare that with Haufe transformation, which is commonly used in the predictive model for cognition (e.g., https://doi.org/10.1016/j.neuroimage.2021.118648 and https://doi.org/10.1016/j.neuroimage.2023.120115).

      We appreciate the reviewer’s comment and the suggested references. The Haufe transformation is primarily applied in traditional machine learning models, particularly in cognitive neuroscience, to interpret linear predictive models by mapping classifier weights back to the input space. However, its direct applicability to deep learning models, especially convolutional neural networks, remains an open research area with no widely established methodologies. Furthermore, the Haufe transformation does not provide feature importance in the same manner as Grad-CAM. Grad-CAM highlights spatial regions within an image that contribute to a model’s decision, making it particularly useful for interpreting convolutional networks in vision tasks. In contrast, the Haufe method offers a weight transformation that is more suited for understanding linear models and may not be as intuitive for feature attribution in complex hierarchical representations such as those learned by deep neural networks.

      While we acknowledge that Grad-CAM, like other interpretability methods, does not provide absolute ground truth validation for feature importance, it remains one of the most widely used and validated techniques for deep learning interpretability, particularly in medical imaging applications. Given its integration with frameworks such as Keras and TensorFlow and its ability to provide spatial attributions aligned with domain knowledge, we believe it is a suitable choice for our study. Future work may explore additional interpretability techniques, including adaptations of the Haufe transformation if applicable to deep learning architectures.

      We have added more details on Grad-CAM implementations in the Method.

      (9) Related to Grad-CAM, "These edges, indicated by a salience intensity of {greater than or equal to}.5, exert a significant influence on the model (Figure 1f)." What does 'significant' in this context mean? And how did the authors come up with the .5 threshold? Is it based on permutation or bootstrapping tests?

      We appreciate the reviewer’s comment and the opportunity to clarify our approach. In this context, the term "significant" refers to the regions' relative contribution to the model’s decision, as shown by the Grad-CAM saliency map. However, to avoid implying statistical testing, we will revise the term to "highly contributing."

      Regarding the 0.5 threshold, this value was selected empirically based on the normalized Grad-CAM activation values, where saliency scores range between 0 and 1. A threshold of 0.5 was used as a heuristic to highlight regions with relatively strong activation. However, this was not determined through statistical methods such as permutation or bootstrapping tests. We recognize the importance of rigorous threshold selection and will clarify this in the text. Future work could incorporate statistical methods to define thresholds more objectively.

      We have included the following text in the Method section:

      ”Grad-CAM saliency maps were interpreted qualitatively, with a heuristic threshold (≥ 0.5) applied to highlight regions with relatively higher contribution to the model’s predictions. These values do not reflect statistical significance and should therefore be interpreted descriptively.”

      (10) Still related to the saliency map, I believe the upper and lower triangles of the functional connectivity matrix are the same. If so, why are there some differences in saliency? While the difference is not prominent, this might affect the accuracy of Grad-CAM.

      Minor differences in the saliency maps between the upper and lower triangles of the FC matrix can arise due to several factors. For instance, Grad-CAM generates saliency maps at the resolution of the convolutional feature maps, which are then upsampled to match the input matrix dimensions. We initially used the default bilinear interpolation, which may have introduced slight asymmetries or blurring, resulting in interpolation artifacts. In response, we have reprocessed the saliency maps using spline interpolation in MATLAB. The updated saliency figures have been included in the revised version of the manuscript.

      (11) Why did the authors only report the cross-study for EM on rest, and for WM on n-back? This is a bit unexpected since COBRA has both rest and n-back. If there is no good justification, please report both.

      We focused on reporting cross-study results for EM using rest because rest was the winning condition for predicting EM in the DyNAMiC sample. Importantly, n-back did not significantly predict EM in DyNAMiC, and rest did not significantly predict WM. For this reason, we highlighted only the conditions that showed meaningful predictive power in the original analyses.

      (12) Are codes, trained models, and data available? To ensure transparency and reproducibility, I hope to see the code from preprocessing to modeling and statistical analyses.

      The analysis code is openly available on our GitHub page https://github.com/MorEsm/AI-based-Prediction-of-Cognitive-Function. Due to ethical considerations and GDPR restrictions in the European Union, we are not permitted to publicly share the raw data. However, we can provide detailed information about preprocessing steps and analysis pipelines to facilitate reproducibility.

      (13 &14) The authors did not appropriately control for regression-toward-the-mean and the influence of the working memory itself when calculating the brain cognition gap. This is commonly done to brain age (see https://doi.org/10.7554/eLife.87297.4https://doi.org/10.1002/hbm.25533https://doi.org/10.1016/j.nicl.2020.102229https://doi.org/10.3389/fnagi.2018.00317). Otherwise, the brain cognition gap still depends on the cognition/working memory score itself. Based on Tetereva et al., "If, for instance, Brain Age was based on prediction models with poor performance and made a prediction that everyone was 50 years old, individual differences in Brain Age Gap would then depend solely on chronological age (i.e., 50 minus chronological age)." Because of this, Tetereva and colleagues found that the 'uncorrected' brain age gap that predicted chronological age the worst became the best index to predict fluid cognitive abilities. This shows the pitfall of the 'uncorrected' brain age gap. You can apply the same logic to the brain cognition gap.

      (14) Additionally, another way to show the unique contribution of brain cognition, over and above cognition per se, is to add both brain cognition and cognition together to predict physical activity, education, and cardiovascular risk.

      We thank the Reviewer for raising this important point. In response to their request and also the request from Rev. 1, we first examined the relationship between the Brain-Cognitive Gap (BCG) and the cognitive measure itself. Surprisingly, we did not find any significant relationship in either the DyNAMiC sample (r =0.01, p =0.939) or the COBRA sample (r =0.01, p =0.894) (see Author response image 1).

      We then conducted additional analyses, splitting the sample into high and low EM performers, and compared their levels of physical activity and Framingham cardiovascular risk scores. We found that no significant difference in physical activity (DyNAMiC: p =0.56, CI: -14.99 – 8.13; COBRA: p =0.29, CI: -3.54 – 1.05) or Framingham CVD risk score (DyNAMiC: p =0.11, CI: -1.08 – 10.72; COBRA: p =0.41, CI: -1.86 – 4.58) between high and low EM perfprmers. Given the significant difference in physical activity and Framingham CVD risk score between positive and negative BCG groups, our results support that BCP provides unique information, beyond cognitive measure, regarding factors that contribute to cognitive resilience. These results have been added to Section 2.4, and Figure 3 has been updated.

      (15) Related to the brain age gap, the brain cognition gap is actually just another way to quantify how generalizable models are to another sample, similar to MAE or MSE. If the models built from DyNAMiC don't fit well with samples from COBRA, you will get a higher (i.e., wider) brain cognition gap, which means a poor fit. The authors should discuss this interpretation - should your biomarker's performance be due to a fit of the model?

      We appreciate this insightful comment. We agree that BCG can be interpreted not only as a marker of individual differences and resilience factors but also as a measure of model fit, analogous to error metrics, such as MAE or MSE. A higher gap may, in part, reflect poorer generalizability of models across samples. We have now revised the Discussion to explicitly acknowledge this alternative interpretation and to emphasize that BCG should be viewed both as a candidate biomarker and as a reflection of model performance.

      We added the following paragraph in the discussion:

      “An important caveat is that BCG can also be conceptualized as an error metric, similar to mean absolute error or mean square error, reflecting the extent to which models trained in one sample generalize to another. From this perspective, a larger gap may not only indicate individual differences related to resilience factors and dopaminergic function, but also reduced model fit or generalizability across datasets. Thus, BCG likely reflects a combination of meaningful biological variability and methodological variance.”

      (16) It is unclear why the authors binarized the brain cognition gap when predicting physical activity, education, and cardiovascular risk, and not doing so with the striatal D1DR. It is rarely a good idea to binarize a continuous variable (see 10.1136/bmj.332.7549.1080). In this case, people who had a bigger negative brain cognition gap were treated equally to people who had a smaller negative brain cognition gap. I also do not think it is necessary to separately analyze positive and negative gaps. Perhaps the authors should correlate the corrected brain cognition gap with physical activity, education, and cardiovascular risk and provide scatter plots and effect sizes.

      Following the reveiwer suggestion, we directly correlated BCG with physical activity and cardiovascular risk. Our results confirmed our initial analysis that individuals with a negative gap exhibited lower physical activity and higher Framingham CVD risk across both COBRA and DyNAMiC datasets. We have reported these results on page 10.

      Author response image 5.

      (17) Given that the motivation is to move away from brain age, the authors should benchmark the corrected brain cognition gap against the corrected brain age gap, as well as against the performance when directly predicting physical activity, education, and cardiovascular risk from the functional connectivity metrics.

      Author response image 6.

      We agree that benchmarking BCG against BAG in predicting lifestyle and vascular risk factors would be valuable. We have calculated adjusted BAG and related it to lifestyle and vascular risk factors. Interestingly, we did not find any significant association, suggesting that BCG might be more sensitive to cognitive resilience. However, this investigation was beyond the scope of the present study. Our aim was not to compare BCG with BAG, but rather to examine whether BCG provides information beyond cognition itself. We also note that introducing BAG would open a separate line of investigation, namely, which cognitive state (rest, movie-watching, n-back) best estimates biological age. While this is an interesting question in its own right, addressing it here would considerably broaden the scope and complexity of an already dense manuscript. To prevent misunderstanding, we have clarified this point in the Discussion and added a caveat noting that future work should explicitly benchmark these approaches. That said, if the Reviewer and/or the Editor incline to add these additional findings into the manuscript, we are open to doing so in a revision.

      We have added the following sentence to the Discussion.

      “While our focus was to investigate whether the brain–cognition gap provides information about factors contributing to cognitive resilience, we acknowledge that benchmarking BCG against the brain-age gap in predicting lifestyle and vascular risk factors would be valuable. However, addressing this question lies beyond the scope of the present study, and future work should systematically compare these approaches.”

      (18) Why was only the working memory score used to create brain cognition, and not episodic memory as well? Including both could provide a more comprehensive measure.

      We initially attempted to predict both episodic memory (EM) and working memory (WM). However, EM prediction was only reliable within and across samples for the resting state, whereas WM prediction generalized most strongly from the movie-watching condition. Because COBRA does not include a movie-watching paradigm, we could not evaluate WM prediction across datasets. For this reason, we focused on EM when examining the brain–cognition gap.

      (19) The PET mediation analysis seemed to come out of the blue. Is there existing literature showing the relationship between striatal D1DR and cognition? If so, did the authors find a similar relationship in the current data? I also suggest rewriting this section to strengthen the justification for the PET mediation analysis.

      We have previously conducted studies in which DA found to be associated with memory (Johansson et al., 2023, Nyberg et al., 2016).

      The third aim of our study was to examine whether DA integrity is implicated in brain–cognition gaps (BCG), which we propose as a marker of cognitive resilience. In line with this aim, we found that lower DA receptor availability was associated with larger BCGs (Figure 4). We then asked whether this relationship is mediated by functional signal variability, such that lower DA is linked to reduced signal-to-noise ratio (i.e., greater entropy in functional connectivity), which in turn contributes to less reliable prediction of cognition and, consequently, larger BCGs. Our mediation analysis supports this pathway (see also our reply to Reviewer 1, Comment 6).

      Thus, our mediation was not designed to test whether DA predicts episodic memory performance directly, nor whether BCG mediates such a relationship. Instead, we specifically investigated whether the effect of DA on BCG operates through functional variability. We agree that future work could extend our approach by directly examining whether BCG mediates the link between DA and cognitive outcomes. However, in the present study, our primary focus was on testing the mechanistic pathway of DA → entropy → BCG.

      Minor recommendations:

      (1) Task-based connections are not truly task-based, as they are around 70-80% related to the resting state, capturing non-task-specific functional connectivity. Task-based connections should refer to techniques that derive task-related connectivity, such as psychophysiological interaction and beta-series correlation. Perhaps use terms like "functional connectivity during tasks."

      Thank you. This has been corrected throughout the manuscript.

      (2) Are there really two studies? The same MRI was used with the same configurations, and participants were from the same city. The only difference is the age range. It may be more appropriate to refer to this as "across age groups" rather than "cross-datasets."

      Thank you for this comment. While the two samples share some similarities, there are also several marked differences beyond age range. For example, Movie-watching was administered in DyNAMiC but not collected in COBRA. The resting-state fMRI sequence was 12 minutes in DyNAMiC but only 6 minutes in COBRA. Moreover, DyNAMiC included dopamine D1-receptor PET, whereas COBRA assessed dopamine D2-receptor availability. Even the questionnaires used to measure physical activity differed between the two studies. Given these methodological and measurement differences, we believe that referring to them as “cross-datasets” rather than “across age groups” more accurately captures the distinction.

      (3) What kind of movie is "Cockpit"? Can you explain? Different movies may elicit different patterns of connectivity.

      We apologize for not providing information about the movie, which has been presented in our recent work (Johansson et al., 2023).

      The participants’ reactions to the content of the movie were not monitored, but the clips were selected to be as neutral in their content as possible. The content of the movie: Following his termination as a pilot and the end of his marriage, Valle embarks on a quest to secure new employment. Faced with desperation in the job market, he resorts to disguising himself as a woman with the intention of obtaining a position at a company specially seeking a female pilot.

      This information is added to the method section.

      “During the fMRI session, participants viewed a 12-minute segment from the Swedish comedy film Cockpit (2012). We did not monitor participants’ responses to the movie, and the chosen clips were selected to be relatively neutral in emotional content. The storyline follows Valle, a recently fired pilot whose marriage has ended, as he struggles to find new employment. In a desperate attempt to secure a job at an airline specifically recruiting a female pilot, he presents himself as a woman.”

      (4) There is a typo in the equation numbering (i.e., two equations are designated as #1).

      We have now corrected the typo.

      (5) From the discussion: "Importantly, this prediction generalizes across conditions." This is not surprising given the similarity between conditions, with around 70-80% variance.

      We agree with the reviewer that the high similarity of FC across states likely increases the chance of cross-condition generalizability. However, this generalization is not guaranteed for all models. For example, the model trained on FC during movie-watching successfully predicted episodic memory during rest, but it did not generalize to episodic memory during the n-back condition, although movie-watching and n-back FC patterns are themselves highly correlated. Thus, the observed generalization is meaningful in demonstrating that not all models transfer equally well across states.

      That said, we have added the following sentence to the Discussion:

      “Importantly, this prediction generalizes across conditions and datasets, suggesting that features derived from resting state FC serve as a relatively stable marker of individual differences in EM, though with reduced strength in COBRA. While such generalization is partly facilitated by the similarity of functional connectivity across states, it is not a trivial outcome. For instance, the model trained on movie-watching data generalized to EM prediction during rest but failed to do so for the n-back condition, even though movie-watching and n-back connectivity patterns are themselves highly correlated. This indicates that successful generalization depends not only on shared variance across states but also on the cognitive processes most relevant to the target behavior.”

      (6) It might be helpful to include some figures for the cognitive tasks used. The description is a bit hard to follow without visual aids.

      Thanks for the comment. We have had a figure describing this in the initial paper about DyNAMiC (Nordin et al., 2022). We have added the Supplementary Figure (Fig S3) in the manuscript.

      Fig S3. Overview of the cognitive tests included in the DyNAMiC study. Adopted from Nordin et al. with permission.

      (7) It may not be appropriate to use the term "cross-validation" here, as one dataset was used for testing and the other for training, but not vice versa (so no "cross" per se).

      We thank the reviewer for pointing this out. We agree that the term “cross-validation” is not precise in this context, since we trained the model in one dataset and tested it in another without performing the reverse. We have revised the manuscript to use the term “external validation” instead of “cross-validation” to more accurately describe our cross-dataset approach.

      (8) I don't have access to the supplementary materials or code/data, so all of the comments here are based on the main text.

      We have added the supplementary materials and inserted the GitHub link to the code.<br />

      Reviewer #3 (Recommendations for the authors):

      I suggest benchmarking against other simpler algorithms and controlling for memory in the brain cognition gap analyses.

      The authors might also want to simplify some aspects of the paper. There is a lot going on, which leaves less space to go into enough details for some analyses to warrant claims in the discussion. For example, the authors only compare the deep net to CPM and kernel ridge based on the literature. Direct comparisons would be needed.

      Thanks for the comment. We have made an attempt to address the concerns outlined in the public recommendation. Our study explicitly compares predictive power across different cognitive states (rest, movie watching, n-back), with the aim of identifying the states that best capture individual differences across domains. Thus, our goal was not to propose a universally superior prediction model, but rather to test how brain state influences predictive utility for WM and EM using a deep learning approach. We have revised the manuscript text to make this focus clearer and to avoid any misinterpretation of our aims. Specifically, we removed statements in the Discussion that could be read as suggesting that our deep learning approach outperforms prior machine learning methods. While we compared our model with the connectome predictive modeling (CPM) approach and observed better performance with our deep learning framework, we did not conduct a comprehensive benchmark across all available machine learning methods, nor was this the aim of the present study. Accordingly, we have adjusted the text to avoid implying methodological superiority beyond the scope of our analyses. Furthermore, we have controlled for memory as suggested by the reviewer and outlined in response to reviewer 1.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study used whole genome data to investigate Beefalo ancestry for the first time, filling the gap in the field of Beefalo ancestry. The authors used preserved semen samples to generate genomic data on 47 registered Beefalo and 3 bison hybrids, further questioning the ABA's stated goal of ⅜ bison ancestry. In addition, the authors also show that ancestry profiles of Beefalo and bison hybrid genomes are consistent with repeated backcrossing to either parental species, demonstrating the value of genomic information in examining gene flow between species in the genus Bison. This is an interesting study that still has some major weaknesses that exist, but overall, the work demonstrates the utility of genomic information in validating specific breeding claims for a more complete understanding of gene flow and genetic variation among bovine species.

      We thank the reviewer for their thoughtful assessment of our work.

      Strengths:

      Numerous genetic analysis methods such as PCA, ADMIXTURE, F4 ratios, and local ancestry inference techniques revealed that no single Beefalo set meets the ancestry requirements set by the American Beefalo Association (ABA) and some beefalo had detectable indicine cattle ancestry.

      Weaknesses:

      While this study contributes to our knowledge of Beefalo ancestry, there are some key issues that need to be addressed in terms of analysing the specific results as well as writing the article.

      We have followed the reviewer’s suggestions for improving our study in detail (specified below), and appreciate their close reading of the manuscript.

      Reviewer #2 (Public review):

      Summary:

      Shapiro et al. set out to verify the American Beefalo Association's claim that Beefalo cattle possess 37.5% bison ancestry. They employ a comprehensive range of well-established population genomics methods to estimate ancestry in these hybrid populations, including PCA, ADMIXTURE, D and F statistics, and local ancestry inference. Their findings conclusively demonstrate that most Beefalo lack the claimed bison ancestry, with only 8 out of 47 samples showing any detectable bison ancestry, ranging from 2 - 18%.

      We thank the reviewer for their thoughtful assessment of our work.

      Strengths:

      The primary strength of this analysis lies in the comprehensive dataset available to the authors, which includes important foundational Beefalo individuals and various reference populations. The rigorous and multi-faceted methodological approach employs several well-established techniques in population genomics for detecting and measuring admixture. Each method used has a firm basis in the field, providing consistent and robust results. The authors' approach of using PCA to initially assess the data within a global context, followed by more specific analyses using ADMIXTURE and D-statistics, provides a clear and logical progression of evidence. The presentation of these results in figures is particularly effective, clearly illustrating the key findings of the study. Additionally, the examination of both autosomal and sex chromosome ancestry offers a more complete understanding of Beefalo genetic composition and the mechanics of bison-cattle hybridisation.

      Weaknesses:

      One limitation of this analysis is the relatively low coverage (~2x) of many Beefalo samples. However, the authors have taken steps to mitigate biases that may arise from this. Another weakness is the limited sampling of contemporary Beefalo populations, as the study focuses primarily on historical samples. This may limit our understanding of how Beefalo genetics may have changed over time.

      The reviewer is correct that the low coverage obtained for many Beefalo is one potential limitation, although we believe that the downsampling experiment we performed (Fig. S4) shows that this level of coverage is appropriate for summarizing species-level ancestry across Bos, as the reviewer notes.

      Sampling contemporary Beefalo individuals would be valuable, though as the focus of our study was to understand the origins of bison ancestry in Beefalo, we prioritized sampling individuals which played an important role in establishing the breed. We also note that contemporary Beefalo breeding involves crossing between Beefalo individuals or backcrossing to cattle, with no additional bison ancestry input since the formation of the Beefalo. As such, sampling individuals that existed close to the breed’s founding should provide the most insight into bison ancestry in Beefalo.

      Appraisal:

      The authors have clearly achieved their primary aim using a rigorous and comprehensive methodology. Their extensive dataset and multi-faceted analytical approach provide strong support for their conclusions. The study not only addresses its main research question but also reveals unexpected insights into Beefalo genetics, particularly the presence of zebu ancestry.

      Discussion:

      This study is valuable for several reasons beyond its primary findings. First, it definitively addresses and refutes the claim of 37.5% bison ancestry in Beefalo, providing crucial information for those studying these interspecies hybrids and the viability of their offspring. Second, it reveals the unexpected presence of zebu ancestry in many Beefalo, raising intriguing questions about the breed's development and the potential role of zebu cattle in achieving desired traits. This finding suggests that the distinctive appearance of Beefalo may be due in part to zebu admixture rather than bison ancestry. Third, the study highlights the significant barriers to admixture between bison and cattle, both in controlled breeding programs and potentially in wild populations. This has important implications for conservation genetics and our understanding of gene flow between these species. Lastly, the study demonstrates the power of genomic analysis in verifying breed claims and understanding the complex history of domestic animal breeds. These findings open new avenues for research in bovine genomics, breed development, and the dynamics of interspecies hybridisation.

      Reviewer #3 (Public review):

      Summary:

      I really like this topic and study. But I think much can be more focused and tightened up. All the components are here - just some more refining to really make the storyline clear, the journey of discovery, and the impact of such knowledge.

      We thank the reviewer for their thoughtful assessment of our work.

      Strengths:

      The authors dive directly into the question of genomic ancestry as compared to the breed club's reported ancestry with heavy, quantitative data and critical analytical methods. The questioning line is direct and does not meander. The reader learns about the challenges of breeding associations, and values of understood ancestry, and presents a clear need of re-evaluating the breed standards and expectations of beefalo (if ancestry is indeed the primary goal instead of a phenotype-driven breed mission).

      Weaknesses:

      Much of the quantitative results are only referred to in the main text with qualitative language. Please incorporate more written quantitative results to highlight evidence that underlines the study narrative because it is quite an interesting study!

      The reviewer highlights an important point, and we agree that the qualitative language used to describe the results was generally lacking. We have now described the results quantitatively throughout the manuscript where possible.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) This study is not the first to question claims surrounding bison ancestry in the breed and is the sample size too small to be representative of the entire genetic structure of Beefalo?

      The reviewer correctly points out that this study is not the first to address uncertainty in the amount of bison ancestry present across beefalo. All earlier studies, to our knowledge, have been highlighted in the introduction and discussion (Lenoir and Lichtenberger, 1978 and Stormont et al, 1986). However, these studies examined a narrow range of Beefalo sources and used older methods (karyotyping and blood typing), such that comprehensive statements about the proportion of bison ancestry in Beefalo could not be made.

      We also agree that an appropriate sampling scheme is crucial for making definitive statements about Beefalo ancestry across the breed. As Beefalo breeding typically involves breeding select “full-blood” individuals with cattle, the ancestry across contemporary Beefalo is likely complex, with the cattle component coming from a wide range of breeds. Therefore, our sampling emphasized “full-blood” representatives, especially those that were involved in the founding of the breed and from which later Beefalo descend. This involved an exhaustive survey of the Beefalo individuals contained within the USDA’s National Animal Germplasm Program. Although we did not extensively evaluate current Beefalo diversity, we believe this approach is most suited for characterizing bison ancestry within Beefalo, as bison ancestry is maintained primarily through the continued use of genetic material from these “full-blood” individuals rather than repeated hybridization between bison and cattle.

      (2) Although genomic information is important for breeding research, this requires quality of data. The coverage of the data used in this study was mainly ~2X, and although multiple methods of analysis gave similar results, the ability to identify rare variants (e.g. insertions or deletions of long segments of the genome) may be limited at low coverage, affecting the confidence of the results.

      This is an important consideration, and we agree with the reviewer that the sequencing depth obtained for most individuals in our study precludes accurate genotype calling. Therefore, we did not attempt to perform traditional genotype calling. Rather, we used a pseudohaploid calling approach in which a random base was selected to represent the genotype at each position for each individual, using a pre-ascertained set of variants discovered in gaur, a closely related outgroup to bison and cattle. This pseudohaploid approach is common in other situations where coverage is low, for example in analyzing ancient DNA.

      Furthermore, our ancestry analyses focused on biallelic SNPs which were discovered in gaur and we did not attempt to call structural variants, given the limitations in coverage. As this outgroup ascertainment approach seeks to target SNPs which were polymorphic in the ancestor of both bison and cattle, which should yield unbiased results in population genetic analyses, we were less interested in discovering rare variation within the species and populations we examined here.

      Finally, we performed downsampling experiments comparing low coverage read data to genotypes called from high coverage data, and obtained consistent results between low and high coverage analyses using read-level data and called genotypes (Fig. S7).

      (3) Missing from the conclusions is the very important presentation of the results of genomic calling, the basics of what these data look like, coverage histograms, number of SNPs, categorization, annotations, and so on. These are necessary prerequisites for subsequent population analysis.

      The reference to “5.29M” on page 14 has been replaced with the exact number of SNPs used in analyses (5,291,534). The average sequencing depth for each sample is also included in Table S1.

      (4) The manuscript mentions "most" in a number of places, but can the authors give an accurate number based on the current data? "Most" is not a rigorous description. Based on the simulations of genomic data, how many Beefalo cattle were not detected as hybridized? This may be related to both sample size and where the authors sampled.

      We thank the reviewer for this important suggestion. We have now replaced vague summaries of results with precise numbers. However, we are unsure what “simulations” means in this context, as all results were obtained by analyzing empirical data from Beefalo, bison, cattle, and other bovines, rather than simulations.

      (5) The information in the third and fourth paragraphs of the Introduction is not sufficiently coherent and could be further consolidated into a more logical presentation.

      We have now condensed these paragraphs and edited them for clarity.

      (6) "For some analyses we also incorporated published genomes from outgroups". The description here is unclear as to what criteria were used to select these data, and it is possible that the choice of outgroups could lead to different conclusions from the analyses. In addition, ancient DNA data from cattle may be useful for this study and the authors are encouraged to consider it.

      Outgroup choice can certainly have a large impact on population genetic analyses. For the species examined in our study, we considered other Bos species, including yak, gaur, and banteng, as suitable outgroups, along with water buffalo, which is the closest outgroup outside of Bos. We have added comparisons of D-statistics using yak as an outgroup as a supplementary figure (Fig. S4), in addition to those using water buffalo as the outgroup which were presented in Figure 2.

      As we were examining species-level ancestry, and given the high level of divergence between bison and cattle, relative to that between published ancient and modern cattle genomes, we believed that it was most appropriate to use high quality modern cattle data, rather than poorer quality ancient cattle genomes, for analyses. Additionally, as any hybridization which took place between bison and cattle in the formation of Beefalo would have occurred within the past ~50 years, modern cattle are likely to be the most appropriate proxy for the cattle ancestry in Beefalo, especially given the lack of published historical North American cattle genomes.

      (7) The coordinates of the PCA plot need to be further supported by providing values.

      We have now updated axis labels for the PCA in Fig. 1A to include the proportion of variance explained for the first two components.

      (8) In Figure 1, Beefalo has one individual, NAGP9109, which belongs exclusively to the indicine group. For this individual, wouldn't it be nicer to label it separately in the PCA and ADMIXTURE plots, like Joe's Pride (JP), to make the presentation of the results clearer?

      This individual was one which was determined to be mislabeled as Beefalo within the NAGP and is actually a Brahman cattle. Therefore, we have relabeled it as zebu, rather than Beefalo, throughout the figures.

      (9) As the sex chromosome data do not fully support the authors' claims, some caution may be needed in describing the results.

      We interpret the sex chromosomal results as being fully consistent with patterns seen in the autosomes. However, they do shed some light on the dynamics of bison-cattle hybridization, and suggest male-mediated gene flow in which bison ancestry in Beefalo was introduced primarily through bison bulls.

      (10) Would it be appropriate to analyse the results at K = 3 only? The admixture analysis of all bison, cattle, bison hybrids, and buffalo individuals at different K values should further refine the results.

      We now also show ADMIXTURE results at K=2 and K=4 (Fig. S2) and present the cross-validation results from ADMIXTURE (Fig. S3).

      (11) The conclusions of this article about bison ancestry in Beefalo individuals are completely inconsistent with the American Beefalo Association, and should a description of possible reasons for this discrepancy be added to the discussion?

      Our analyses make it clear that there was much less hybridization between bison and cattle leading to the formation of the Beefalo that was previously believed. As the genetic data does not provide insight into exactly why this might be the case, we can only speculate on the precise reasons bison-cattle hybridization did not take place, which we have avoided here.

      Reviewer #2 (Recommendations for the authors):

      The manuscript is well written, the figures are easily understandable, and the claims made are justified by the results obtained.

      It is need to clarify cattle breeding terminology, particularly concerning breeds like the Brahman. While often described as zebu-taurine hybrids, Brahman cattle typically show over 90% zebu ancestry when analysed using ADMIXTURE against panels including European Bos taurus, African Bos taurus, and Bos indicus animals. This context would help explain why "NAGP9109" clusters with the Zebu group.

      We thank the reviewer for this useful context, and agree that most Brahman cattle have a high proportion of zebu ancestry. In fact, the zebu group we included primarily consists of Brahman individuals, which we have now clarified in the text, which now reads:

      “The reported pedigree in the NAGP for this animal lists its composition as 1/2 Brahman, 1/4 Charolais, 1/8 bison, 1/16th Hereford, and 1/16th Shorthorn, but the American Brahman Breeders Association records this animal (#309519) as purebred Brahman, which is a zebu breed (5 of the other 6 zebu individuals analyzed here are Brahman cattle).”

      I suggest three other improvements:

      (1) Standardise terminology: The manuscript alternates between "zebu" and "indicine" when referring to these cattle. While both terms are correctly defined in the introduction as "indicine (zebu; Bos indicus)" using one term consistently throughout would improve readability. I prefer "zebu" but leave this choice to the authors.

      We agree that this mixed terminology was confusing and have replaced all instances of “indicine” with “zebu.”

      (2) Add PCA metrics, including the percentage of variance explained by each principal component would demonstrate the genetic distinctiveness between bison and cattle, and between Taurus and zebu cattle. This would also support the selection of K=3 for the ADMIXTURE analysis.

      The axis labels for the PCA have been updated to include the proportion of variance explained for each component. We now also show ADMIXTURE results at K=2 and K=4 (Fig. S2) and present the cross-validation results from ADMIXTURE (Fig. S3).

      (3) Improve quantitative precision: The authors could improve precision by replacing qualitative statements with exact counts. For example "39 of 47 Beefalo showed no detectable bison ancestry." The same suggestion applies when describing how many Beefalo had zebu ancestry.

      We thank the reviewer for this useful suggestion, and agree that the manuscript used imprecise language in describing the results of certain analyses. We have now added quantitative detail throughout the Results section.

      Reviewer #3 (Recommendations for the authors):

      (1) Introduction

      The introduction sets a tone that is heavily focused on the genetic revelation that the economics of beefalo are somewhat of a facade. Beefalo are indeed not part-buffalo (bison). It is unclear to me if the introduction also could benefit from motivating this with more of a theoretical framework based on evolution, inheritance, or trait transmission. If this is really meant to be an economics-focused article, then lean more heavily into that. As it stands, it straddles a bit of economics, a bit of legacies that appear false (beefalo are not part bison at all!), and a bit of admixture genetics theory.

      We intended the focus of this study to be on documenting the species-level ancestry of Beefalo, and concentrated the information presented in the Introduction on this topic. Given that less hybridization between bison and cattle appears to have taken place to form the Beefalo breed than was previously described, we believe that broader theoretical statements about admixture are less relevant here, beyond highlighting examples of successful and failed interspecies hybridization in Bos. We also avoided speculating on the history of the establishment of the breed beyond what could be understood from the genetic data.

      Can the authors give a bit more details about beefalo breeding? Did the breeders select for any quantitative traits and is there a targeted phenotype for beefalo they used as a standard?

      Limited information exists about the precise origins of Beefalo, which were never publicly shared—possibly in part for reasons this manuscript addresses. The only criteria defining Beefalo is the proportion of bison ancestry, and so no quantitative traits or specific phenotypes are related to breed standard.

      Can the authors provide a few examples of what is known about the incompatibilities and reproductive challenges? What is known from past research or from the Beefalo Association documenting the breeding history?

      We provided a general summary of hybridization and incompatibility across Bos, but unfortunately cannot provide details about incompatibilities in Beefalo specifically. Though there is a long history of challenges interbreeding bison and cattle (referenced in the third paragraph of the Introduction), to our knowledge no examination has been carried out of Beefalo specifically and little is known about Beefalo pedigrees (again, perhaps for reasons related to information presented in this study).

      (2) Results Section Sequencing Beefalo genomes

      Please report the number of polymorphic sites to accompany the genomic read depth averages. It seems the authors could include a larger summary of the genomic data that was used for downstream analyses (like the PCA in the next section). Also, does this dataset include the sex chromosomes? How many variants that are retained for analyses are autosomal, sex-linked, or haploid? Please provide more characteristics of the data that was generated after QC and filtering.

      We have now replaced “5.29M” on page 14 with the exact number of SNPs (5,291,534) and added a description of genotype calling to the Results section. We have also included the number of SNPs used for sex chromosomal analyses.

      (3) Results section Estimating bison ancestry in beefalo

      What is a "foundational" individual? Is this a beefalo pedigree founder, a common sire, or an individual with remarkably high bison content? I see in the introduction Joe's Pride was the "most expensive cattle" but there are surely other aspects of "foundational" that the reader should understand as the results are presented.

      We agree that this terminology was imprecise, and have now clarified that we use foundational to mean an early individual that was important in the founding of the Beefalo breed, such as those that were first bred by Bud Basolo.

      For the sentence "The reported pedigree in the NAGP for this animal [NAGP9109] lists its composition as 1⁄2 Brahman, 1⁄4 Charolais, 1⁄8 bison, 1/16th Hereford, and 1/16th Shorthorn, but the American Brahman Breeders Association records this animal (#309519) as purebred Brahman.", this is difficult for a reader with limited cattle breed knowledge to infer significance of this. What is the origination of Brahman breed cattle? Does Brahman ancestry come from another mixed origin that could explain this discrepancy? Does the PCA have references to resolve the origin of Brahman? I realize this may sound extraneous but if membership to a breed that is recently formed from several other lineages or breeds, could you be seeing the deeper parts that compose Brahman cattle? How could one validate that the contributors erroneously labeled this individual as a beefalo?

      We have now noted that the Brahman breed has primarily zebu ancestry. The placement of this individual in the PCA supports the American Brahman Breeders Association metadata, and suggests that the NAGP labeling is incorrect:

      “The reported pedigree in the NAGP for this animal lists its composition as 1/2 Brahman, 1/4 Charolais, 1/8 bison, 1/16th Hereford, and 1/16th Shorthorn, but the American Brahman Breeders Association records this animal (#309519) as purebred Brahman, which is a zebu breed (5 of the other 6 zebu individuals analyzed here are Brahman cattle). We believe NAGP9109 was erroneously labeled as Beefalo by the contributors.”

      Figure 1A: Please add % explained by each PC.

      We have now updated axis labels for the PCA to include the proportion of variance explained for each component.

      Figures 1B and 1C are identical except for the Y axis. Please combine them into a graph with 2 Y-axes (one for PC1 and one for ADMIXTURE). Also, please include the bison in this panel as well.

      We have now updated these panels to include bison, although have kept the labeling so that they may be referenced separately in the text.

      I see that the authors did both unsupervised and supervised. Can the main text have the supervised graphical result instead of the unsurprised? That is more relevant for ancestry proportions via an assignment probability to ancestry groups. Or, if possible, could the authors consider STRUCTURE to also obtain the probability of assignment to a prior defied parental up to 2-generations back? This is by far the best way to leverage the ancestry information of the cattle and bison parental references in addition to the known F1/bison hybrids. Swap the Supplementary Figure 1 with Figure 1D!

      The supervised and unsupervised ADMIXTURE results are highly consistent, as could be expected given the high levels of divergence between species. We prefer to show the unsupervised results in the main text, as this makes the fewest assumptions about the ancestry of the examined individuals, and so also shows that the panels used to represent each species (taurine cattle, zebu cattle, and bison) do not contain individuals which were themselves highly admixed, which could have influenced the supervised ADMIXTURE analyses.

      For the unsupervised ADMIXTURE analyses, what were the cross-validation values per K value tested? How did the authors decide that K=3 was the best one to show?

      We now also show ADMIXTURE results at K=2 and K=4 (Fig. S2) and present the cross-validation results from ADMIXTURE (Fig. S3).

      Regarding "D-statistics ..... are consistent with 0 for most individual Beefalos....", I have two comments. First, by "consistent with", do you mean "are not significantly different from 0", indicating that (explain what this means in your words). Next, "most individual beefalos" means how many? Please provide numbers and values to highlight points or specific findings.

      The interpretation of the D-statistics has been clarified and Z-scores and numbers of individuals to quantitatively describe these results have been added. The text now reads:

      D-statistics of the form D (taurus, Beefalo; bison, water buffalo), which test whether Beefalo share more alleles with bison than taurine cattle, again show 39 Beefalo have no excess affinity with bison compared to taurine cattle (-13.04 < Z < 3.14), although the same eight Beefalo identified in PCA and ADMIXTURE as having bison ancestry also have an excess of bison alleles (6.16 < Z < 34.86), confirming their bison ancestry (Fig. 2A).”

      "In Beefalo with bison ancestry, that ancestry tends to be present in large contiguous blocks, often tens of megabases in size, indicative of recent admixture (Figure 3A, B)". Please display the quantitative results (mean, max, range, standard deviation, etc.) in the main text and point the reader to the table that contains the values for each individual. The rest of this paragraph also uses the words "most' or "always" - please provide numbers. Is most 30/46 beefalo? Is it always exactly all 47 beefalo? Readers want to see numbers!

      The reviewer is correct that this section lacked specificity. We have now provided the exact number of individuals identified with bison and zebu ancestry.

      The section starting "Several lines of evidence attest to the efficacy of using these source panels..." could realistically come first in the Results section and before beefalo results are presented. This would build confidence for the reader that this panel of samples passes a QC and will indeed be able to resolve ancestry-based questions.

      This section specifically refers to the local ancestry analyses, which we have now clarified in the text.

      Figure 3A-C: Please include on each of these figure panels the documented (breeder association) ancestry percentage and the percentage of bison ancestry you obtained from your genomic analyses. Moving it from the legend to the figure is more immediately powerful for the reader. If the authors dated the admixture events as well, please include the meta-data of the association pedigree reporting when bison entered the target individual's genome versus the genome-estimated number of generations since admixture.

      Figure 3 has now been updated to include the reported bison ancestry. No attempt was made to date the admixture event or compare with reported pedigrees, as documented Beefalo pedigrees are typically very sparse (and may be unreliable, as our results suggest).

      Figure 3 legend: Move the following text from the figure legend to the Results section: "Three bison hybrids are inferred to have ~75% bison ancestry, while eight Beefalo have detectable bison ancestry, ranging from 2-18%. Indicine ancestry is detected in most Beefalo at variable levels, ranging from 2-38%, with most Beefalo having between 2-18%.".

      This sentence has been removed from the legend and is now worked into the main text. The corresponding paragraph in the results now reads:

      “Local ancestry inference across individual Beefalo and bison-cattle hybrid genomes provides similar estimates of overall Beefalo ancestry, inferring an absence of bison ancestry across the 37 Beefalo that lacked evidence for such ancestry in previous analyses (Fig. 3). Three bison hybrids are inferred to have ~75% bison ancestry, while eight Beefalo have detectable bison ancestry, ranging from 2-18%. Zebu ancestry is detected in 38 Beefalo at variable levels, ranging from 2-38%, with all but two of Beefalo having between 2-18%.”

      (4) Results section Beefalo sex chromosome ancestry

      Check that the authors do not reference Figure 4B before Figure 4A.

      Thank you to the reviewer for noticing this, it has now been corrected.

      Figure 4A: Could this panel be considered to merge with the autosomal admixture plot? It helps with comparison. Not a firm request - but it is nice to see what is consistent versus what is discordant.

      To avoid cluttering the figure with two highly similar plots, we preferred to separate the autosomal and sex chromosomal results.

      Figure 4C: Could this panel be merged with the autosomal ancestry bar graph to help the reader with visual comparisons?

      We thank the reviewer for this suggestion, but do not understand exactly which figures they are suggesting to be merged.

      (5) Materials and Methods: Modeling Beefalo ancestry:

      The language used in this sentence "This approach allows for directly understanding the ancestry of Beefalo individuals relative to these three groups while mitigating the effects of the low sequencing depth obtained for many Beefalo." conflicts with a sentence later in this paragraph which called PCA a model-free analysis. Please correct.

      Unfortunately, we are unsure what the reviewer refers to here and believe that this sentence does not conflict with the characterization of PCA as a model-free analytical approach.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      The pupil traces in Figure3 (main results) are heavily pre-processed (per-participant demeaned), loosing any feature besides the effect of interest. As I argued in my first review, I worry that this format gives unrealistic expectations about the effect (the perception of dark/bright colors do not generate a net dilation/constriction of the pupil; perception-related modulations of pupil size are always relative and generally small compared to the numerous other effects registered in pupil size; these include a pupil dilation that is more prominent in the controls and that gets analyzed later on in the manuscript; I do not think that eliminating one of the effects of interests from a main results figure helps the reader understand the results). In the revised manuscript, the authors addressed this concern by adding a Supplementary Figure 4, where a more complete representation of the results is shown (traces from individual trials are baseline corrected and averaged, resulting in more informative timecourses). I would strongly recommend that Supplementary Figure 4 is brought to the main text (Figure 3 could be presented in Supplementary).

      We agree that it is important to counter unrealistic interpretations of the effect. However, figures in the main article are the ones that are depicting the effects. Instead, it seems that additional clarification on these effects is needed. First and foremost, Figure 3 in the main manuscript visualizes the core effect: pupil size reveals that synesthesia is a sensory process and the phenomenology of the synesthetic experience can be measured physiologically. Secondly, this allows to advance synesthesia (and phenomenology) research as a new and powerful method.

      No doubt, our effect is relative in nature (as almost any pupillometry, fmri, eeg effect etc.). Including variation that is unrelated to the effect would increase rather than decrease confusion, as individual differences (i.e., how the pupil of an individual responds irrespective of the synesthetic experience) are unmeaningful to the question we set out to answer. Individual variations in pupil response shape irrespective of synesthetic color brightness are removed in Figure 3 but still present in Supplementary Figure 4. Thus, Figure 3 is better suited to illustrate our core effect than Supplementary Figure 4, as individual average responses (illustrated on the right) cannot be meaningfully related to the core effect anymore, only the difference can be.

      At the same time, the reviewer is correct that this may, not so much among researchers as among a general audience, create the expectation that the pupil will always net dilate when experiencing a dark synesthetic percept. This is clearly not the case, but only over its counterfactual (i.e., not seeing that dark synesthetic percept). We now counter such an unrealistic expectation:

      “Note that the effects here are visualized as counterfactuals. So while the pupil dilated for dark relative to bright experienced colors in synesthetes, this does not mean that the pupil net dilates and constricts to dark and bright experienced colors relative to baseline, but only relative to the counterfactual (see Supplementary Figure 4 for net pupil size changes).”

      We updated the caption of Supplementary Figure 4 as follows:

      "Supplementary Figure 4: Pupil size change to graphemes, split by 0.5 reported color lightness (dark gray = low lightness; light gray = high lightness) without demeaning (i.e., removing the average pupil response shape in the 4s stimulus interval per individual irrespective of brightness perception). (…)"

      Responses to physical brightness modulations were only measured in the synesthethes group, not in controls. The authors point out that pupillary light responses have been thoroughly characterized in previous studies, and conclude that synesthethes' responses were in line with the expectations both in terms of amplitude and latency. However, as we are not dealing with standardized measurements, subtle differences in pupil reactivity across the two populations remain a possibility. I recommend that this possibility is mentioned in the discussion.

      We agree with the reviewer, if there were any differences in the PLR between the two groups, they must be minor given that the responses follow those reported in the literature so closely. Yet, subtle differences cannot be ruled out fully unless tested and it doesn’t hurt mentioning this in the discussion, which we now do as follows:

      Finally, pupil light responses in Block 2 were only assessed in synesthetes. While these closely match such of control populations [50,51], subtle between-group differences cannot be excluded and could ideally be assessed in future and replication work.

      Reviewer #2 (Public review):

      Synesthesia is a neurological condition where stimulation of one sensory channel leads to involuntary, automatic, and consistent experience of another, unrelated percept. For example, Sir Francis Galton (1880, Nature) famously described the robust tendency of some individual (synesthetes) to associate numerals with a distinct color. Ever since, synesthesia keeps attracting a broad interest in the cognitive neurosciences in light of its implications for the study of domains such as perception, consciousness, and brain connectivity, among others.

      Strauch, Leenaars, and Rouw measured pupil size in a group of 16 grapheme-color synesthetes and two matched control groups. The participants were presented with gray digits - that is, visual stimuli having identical physical properties in terms of brightness. Each participant subsequently rated the corresponding evoked color and brightness: unlike controls, synesthetes did so in a very consistent and reliable fashion. Accordingly, this was also shown in their pupils: despite the same objective luminance, digits associated with brighter percepts caused their pupils to constrict and digits associated with darker percepts caused their pupils to dilate more than controls. These results highlight how crossmodal correspondences are deeply rooted in synesthetes, and puts forward pupillometry as a particularly appealing biomarker for some phenomenological experience (at least those grounded in "brightness").

      Further strengths of the technique are its temporal resolution and its responsiveness to several constructs. Across several tasks, the authors show for example that responses to synesthetic light are somewhat slower than responses to real light (i.e., they are likely mediated), but at the same time faster than responses to mental imagery. The role of mental imagery can also be reasonably dismissed when considering the second feature of pupil size: its responsiveness to mental effort and cognitive load. The pupils tend to dilate with demanding, challenging tasks, and this was the case when control participants were asked to report the color of a digit for which they did not consistently experience a synesthetic association. The same task was, instead, seemingly effortless for synesthetes, again speaking in favor of the automaticity of number-color correspondences in their case.

      Overall, the findings by Strauch, Leenaars, and Rouw are highly significant for the field and likely to be impactful. The strength of their evidence, when accounting for the relatively small sample size and the inherent variability of both phenomenology (color perception and subjective reporting) and physiology (pupil size), is adequate and sufficiently convincing.

      Comments on revisions:

      I thank the authors for addressing all my comments in a satisfactory way. I think that the paper has improved, especially in terms of transparency of the reporting and clarity of the results.

      We thank R1, R2, and R3 for their very useful input to improve our manuscript.

    1. Not many of us, however, have been trained to read ac-tively, to engage a writer and his or her writing, to ask why we like one piece of writing and not another. Similarly, most of us do not ask our-selves why one piece of writing is more convincing than another.

      I agree schooling is often the reason many of us read mainly for ideas rather than reading actively. However, it is important for our reading and growth as writers to question the text, consider the author's purpose, and think about why one piece may be more effective than another.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Reviewer #1

      Evidence, reproducibility, and clarity

      Summary: Edvalson and colleagues use transcriptomics, cell biology and genetics to study variation between segregation distorter (meiotic drive) strains and find several important results. These include apparent suppression of small RNAs mapping to responder (the drive target) in one of the lines, a general pattern of differential expression consistent with the drive mechanism being upstream of sperm individualization (where defects have been seen previously), and genetic confirmation that perturbing Rsp expression can influence the strength of drive.

      Major comments: I found the total RNA sequencing experiment a bit oddly presented. This is partly because it was in the middle of the results (might fit better first), partly because few specific genes were discussed (this might be appropriate given then question, but maybe the question should be more clearly stated), and the complexity of the approach (WCGNA + PANGEA) and how it all fits together. I suggest working to clarify the main points of this section (which are a bit different than the main focus of the Rsp work).

      We thank the reviewer for these important points. We liked the suggestion to swap the order of our results. We attempted the change, but we found that we weren't able to make the flow of the results much better. Instead, we primed the transition from smRNA to totRNA in the last paragraph of the smRNA results (lines 190-196). This paragraph now reads:

      The dearth of Rsp smRNAs in SD-Mad heterozygotes could be due to a disruption in transcription of the locus or subsequent processing steps. Many factors can influence piRNA production. For example, the piRNA pathway can amplify piRNAs independently of transcription, such as the ping pong cycle, (Czech and Hannon 2016). Notably, Rsp piRNAs do not have a strong ping pong signature in testes (Wei et al. 2021; Chen et al. 2021a). To distinguish between a disruption in transcription or some downstream process, we examined total RNA.

      The main reason we elected to describe patterns rather than specific genes is that the 2nd chromosomes we tested (R-16, SD-Mad, SD-5) have all diverged from each other and any single differentially expressed gene could be due to differences in genetic background. Therefore, we elected to point out more broad systematic changes in pathways and correlated gene networks rather than specific genes. We have made it more obvious throughout the total RNA section in the text what our question is regarding the transcriptome and the reasoning for using WGCNA and gene set analysis.

      We also appreciate the reviewers point that the complex approach we used to extract changes in pathways and networks is difficult to follow. We have modified our wording to better describe the flow of analyses.

      We also note that we have extended our analysis for the comparison of SD-Mad and SD-MadRev, which only differ by the Sd-RanGAP locus. Here we do discuss individual genes that are differentially expressed. See below for details about this new analysis.

      Minor comments:

      Abstract - Probably worth mentioning Sd-RanGAP here, even if you are using it as a straw man. I agree that the specific mechanism is not known, but some of the genetics are established.

      This is a good point. While our study doesn't address RanGAP, it is important to point out that, although its role in drive is unclear, Sd-RanGAP is a necessary component of the system. We added the following language to the abstract:

      SD is a multigene complex, frequently associated with chromosomal inversions, where the main driver locus, a truncated duplication of the gene RanGAP kills wild-type sperm containing a satellite DNA called Responder (Rsp).

      Line 80 and elsewhere - it would be helpful to be specific here - you are looking at both small and total RNA

      We've modified our wording throughout the manuscript to specify when we are referring to total RNA and small RNA.

      Fig 1B - is there a reason not to show the values of the replicates here? It would be more transparent.

      We thank the reviewer for this comment. We replaced Fig 1B with a chart that is computed from the DESeq2 normalized counts for each comparison and added replicates to all related graphs.

      Line 139 - does the experimental design control for 1.688 genomic copy number? Where is it located?

      We indeed control for the 1.688 copy number here. Most 1.688 repeats are found on the X chromosome and all flies in our experiments have identical X chromosomes. We changed the text to specify that copy number for 1.688 are the same between conditions.

      144-146 - this could be written clearer, and I think it should only refer to 1C, not 1B. Part of the issue is that there are several repeats not discussed, and it isn't clear what is happening with them. I suggest expanding this description so it is more clear.

      Thank you for this feedback. We have expanded the description to make this section clearer.

      Line 161 - what do you mean (specifically) by "repetitive loci"?

      Repetitive loci in this case refers to transposons, satellite DNAs (except simple satellites), and piRNA clusters. We have added text explaining what is included the grouping of "repetitive loci". We have added the following sentence to the text:

      Our results demonstrate that SD-Mad and SD-5 haplotypes, despite sharing the same main drive locus, have different effects on smRNAs derived from repetitive loci such as complex satellites (including Rsp), transposable elements, and piRNA clusters.

      193-203 - This is an important finding that is somewhat lost in trying to keep track of WCGNA and PANGEA and the different Modules. I suggest clarifying to drive home the point that differential expression appears to start prior to individualization, which suggests and earlier mechanism of drive.

      We thank the reviewer for this feedback. We have added wording to out discussion that points out this finding in lines 501-505 which reads:

      We suspect that the timing of the proximal cause of SD-mediated drive may align with early spermatogenetic processes; perhaps where cell cycle-related genes are active and appear to be broadly differentially expressed (Figure 2B, Module H). This earlier timing is consistent with temperature shift experiments that place the critical period for SD at or before meiosis (Mange 1968).

      Fig 3B & 3C, Fig 4 - same as 1B, is there a reason not to show the actual data points?

      A similar issue was brought up earlier, in response we modified all our figures to show replicate points where applicable.

      Line ~245 - was the same experiment done with SD-5? (as you do below for Rsp overexpression)

      We originally did not include SD5 in this experiment, but we have since measured drive strength of SD5 in a kipfKO background. We found a small but statistically significant difference in drive strength. We added the new SD5 results to the figure and moved the kipfKD data to the supplement along with some added data on a Rsp deletion line generated from Iso1 that bolsters our confidence in the SDMad results.

      Significance

      This is a strong paper that moves the field forward, even if it leaves questions still to be answered (why the difference between drivers? what is the mechanism? how is rsp interacting with drive?

      Several findings move the field forward: the Rsp small RNA results, the differential expression hinting at a molecular mechanism that is upstream of sperm individualization.

      The audience is moderately broad. Genetic conflict is gaining in general interest, but aspects of this will be mostly interesting to the hardcore drive crowd.

      Reviewer #2

      Evidence, reproducibility and clarity

      I have only one request: I found it unclear whether the authors were referring to small RNAs or their precursor (long RNA). By reading the text carefully, I could deduce that Fig1A/Table S2 represent the small RNA sequencing, while FigS3A represents total RNA seq (detecting precursor). However, the labeling in the Fig1A and Table S2 only says 'piRNA cluster' or 'Rsp' (without clarifying 'piRNA from piRNA cluster' or 'piRNA from Rsp'), and it took quite some time for me to understand which Fig/data is smallRNA vs. longRNA.

      This is helpful feedback. We have added more clarity to which type of RNA is being represented in our figures throughout.

      Significance

      This manuscript by Edvalson et al. describes their study on SD (segregation distorter) meiotic drive system, examining the role of piRNA derived from Rsp satellite. Although the exact mechanism of drive is still unknown, this study represents a significant step forward in understanding SD-mediated drive.

      By using two SD alleles (SD-5 and SD-Mad), they show that Rsp-derived piRNA is depleted in SD-Mad. The authors used total RNA sequencing/small RNA sequencing mutants and carefully designed controls (such as deletion of Sd-RanGAP) to reach the model that Rsp-derived piRNA is involved in SD-Mad-mediated drive. The result that kipferl depletion (that lead to sat DNA expression) rescues SD-Mad's drive phenotype is very interesting. This supports that the decreased Rsp piRNA indeed corresponds to SD-Mad-mediated drive. They further back up this idea by overexpressing Rsp.

      Interestingly, SD-5 was not impacted by changes in Rsp expression. Based on this result, the authors state that there are mechanistic variations in the same (SD) drive system. This statement is certainly justified by the data, but I cannot help wondering there might be a unifying mechanism that explains both SD-5 and SD-Mad. I am not suggesting to edit the manuscript or add the discussion: but do they have any speculations on this? For example, SD-5 is simply epistatic to Rsp piRNA production? For example, SD-RanGAP > SD-Mad (some gene on SD-Mad inversion) > Rsp piRNA production > SD-5 > sperm killing?

      We thank the reviewer for this insight. We indeed think that the proximal cause of sperm dysfunction could be the same, but there are components of SD5 that act downstream of Rsp piRNAs. The small difference in drive strength in the SD5 KipfKO experiments might support this hypothesis, although it is also possible instead that drive is influenced by changes in some other piRNAs (from the piRNA clusters or satellites).

      We modified our wording in the first paragraph of the discussion to point out this possibility. Lines 367-370 now reads

      These results suggest that, while SD chromosomes share a target and main drive locus (Sd-RanGAP), the modifiers accumulated on each haplotype may influence the drive mechanisms, either by creating new pathways to drive or acting as tuning knobs on drive strength.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      Summary

      In the presented manuscript Edvalson and Wei et al use Drosophila genetics and NGS experiments to investigate the mechanism of meiotic drive through the Segregation Distorter (SD) system. They reveal that two driving haplotypes seem to function via different mechanisms, with drive through SD-Mad but not SD-5 involving small RNAs produced from the Responder (Rsp) satellite, the target of SD drive. SD-Mad testes displaying drive are characterized by lower levels of Rsp sRNAs compared to non-drive controls as well as SD-5, and the ectopic overexpression of Rsp sRNAs through two distinct mechanisms decrease drive in SD-Mad genetic background, specifically. With this work, the authors are adding an important piece of information to the highly complex SD system, indicating that sperm killing is likely achieved by different mechanisms in different SD haplotypes, despite sharing a common driver.

      Major comments

      Fig1C: It might be interesting to show the fold change between SD-Mad and SD-MadRev in addition to what is displayed. Moreover, can the authors comment on what might be causing the increased smRNA counts for 38C2? Is this because R16 has particularly low 38C2 values?

      We appreciate the reviewer's comment concerning the fold change between SD-Mad and SD-MadRev. We have made a figure showing the difference between and put it in Figure S1.

      We suspect that the expression difference in 38C2 between the R16 heterozygotes and SD heterozygotes may be due to genetic divergence, since these are different 2nd chromosomes. We have added language pointing this out to the manuscript in line 182. The paper now reads:

      *There is no evidence that either 38C2 or Flamenco are involved in SD-mediated drive. *

      Fig1/S1: Could the authors also display the Rsp smRNA counts for all Gla crosses similar to panel 1B? What is the interpretation for the increase in Rsp smRNAs in SD-5/Gla relative to R16/Gla but the lack of such an increase in the SD-5/iso1 vs R16/iso1 comparison? Do SD-Mad and SD-5 induce the same strength of drive against each of the two wildtype chromosomes? Experiments: smRNAseq for SD-MadRev/Gla.

      We have added a plot to Fig S1 to show the abundance of Rsp small RNAs in the Gla background, similar to Figure 1.

      It is difficult to interpret the apparent overabundance of Rsp small RNAs in the SD-5/Gla background. Because differences in Rsp smRNA abundance for SD-5 are inconsistent between the Iso1 and Gla background, our interpretation is that SD-5 is not manipulating Rsp levels. The apparent overabundance of Rsp in the Gla background could be due to an epistatic interaction between Rsp and other components of that particular background. Consistent with this interpretation, the SD-Mad induced reduction of Rsp smRNAs in the Gla background is less dramatic than in the Iso1 suggesting that something about that background is increasing Rsp expression slightly when paired with an SD chromosome.

      Fig1: The authors note changes in smRNA levels for other satellites as well as piRNA clusters but do not give any interpretation to this observation. Are they meaningful? Should they be attributed to genetic background?

      Our interpretation of the observation that some satellites or piRNA clusters are differentially expressed is that these differences are likely due to epistatic effects from the different 2nd chromosomes used in the study or are incidental to mechanism of SD.

      FigS2: Same question also for the deregulated TEs: do they share sequence features with Rsp or are they overrepresented in the clusters that change? Are these explained by differences in insertions between genotypes? Do their total RNAseq values change in any way? What do the percentages in line 162 correspond to? Number of TEs that are deregulated? At which cutoff? It might be informative to compare the data to a cross between driver and R16, or even better the SD-MadRev control. Experiments: totRNAseq for SD-MadRev crosses and optionally crosses to R16.

      The Rsp repeat unit does not share significant homology to portions of the genome outside of the pericentromere of 2R with the exception of ~6-12 copies in the intron of Ago3.

      As far as TEs are concerned, we surprisingly don't see a strong correlation between piRNA cluster content, dysregulation, and TE transcript abundance. For example, in the SD/Gla backgrounds the total RNA for R1, R2, IGS, and Tc1-Mariner family TEs is down regulated. However, the only major piRNA cluster that is upregulated in both SD/Gla backgrounds (80F) is not enriched for TE fragments matching any of those 4 families. One thing we can note is that the definition of the major piRNA clusters are given in relation to the Iso1 genome which may differ from that of our experimental backgrounds. Without long read resolved genomes for our specific experimental lines generated at the same time as the RNA samples it is difficult to determine how expression at the major piRNA clusters and the corresponding TEs are related. We have described this lack of a correlation in lines 210-217 in the text along with our interpretation for why this could be. The paper now reads:

      On the other hand, we did find some differences in repetitive elements related to rDNA (R1, R2, and IGS) and Tc1-Mariner family TEs (all backgrounds; Figure S6). Interestingly, there was no correlation between the expression of TEs and the expression of piRNA clusters that contain fragments of these TEs in the total RNA, nor was there any correlation between the small RNAs from piRNA clusters and the total RNAs for those TEs. PiRNA clusters are usually defined in one isolate of Iso1: rapid turnover of TEs and piRNA sources could explain why we do not see a correlation between piRNA cluster expression and TE expression in our backgrounds.

      We investigated differences in TE and piRNA cluster expression in our SD-Mad/Iso1 vs SD-MadRev/Iso1 comparison, but a lack of power due to inter-sample variation prevents us from confidently making any assessments on any TEs or piRNA clusters in that comparison. We did however generate additional gene level transcriptomic data using 3' Digital Gene Expression to bolster our confidence in the totRNA data and found some interesting genes that were in the top most differentially expressed. We have noted those genes in lines 276-287 which read:

      To identify genes that might interact to cause drive, we compared the gene expression of SD-Mad/Iso1 to SD-MadRev/Iso1. These genotypes only differ by the presence of the main drive locus, Sd-RanGAP. We performed both totRNA and 3' Digital Gene Expression (DGE) RNA sequencing and examined the overlap in differential expression between the totRNA and DGE sequencing. There are 69 differentially expressed genes where the DGE comparison is significant (PDGE {less than or equal to} 0.01), and the sign of the Log2FC of the totRNA matches that of the DGE. Among this set of differentially expressed genes, 57 show at least a 50% difference in gene expression (absolute Log2FC value of at least 0.58 in DGE). These genes are not enriched in any Reactome gene sets. The top 20 most differentially expressed genes consists of 9 lncRNAs (3 anti- sense RNAs) and 11 protein coding genes: 8 of which are uncharacterized. The 3 characterized genes are Artemis (Arts), Gr61a, and Tono (Figure S98, Supplemental File 1).

      We discuss two of these genes in further detail in the discussion in lines 476-486 which read:

      First, Tono, a BTB zinc finger-containing transcription factor is upregulated (Log2FCDGE = 1.7) in all SD-Mad comparisons. Tono plays a role in regulating transcription in muscle cells in response to mechanical pressure (Zhang et al. 2024) but also shows enrichment in male germ cells (Li et al. 2022). The putative DNA-binding capacity and ability to form nuclear condensates (Zhang et al. 2024) makes this an interesting candidate gene for interacting with the Rsp satellite. Second, the importin-4 ortholog, Artemis (Arts), which facilitates Ran-mediated import of H3 and H4 is overexpressed in SD-Mad (Log2FCDGE = 2.5). Interestingly, Arts expression is antagonistic to male fertility (VanKuren and Long 2018). Also of note, Apollo, a duplicate of Arts which supports male fertility (VanKuren and Long 2018) is downregulated (Log2FCDGE = -0.6) though it is not in the top-most differentially expressed genes.

      Figure S3: Am I reading the PCA plots right in that there are very few gene expression changes when the drivers are in iso1 background but much more in the Gla background? Comment on possible explanations for that. Please indicate the number of significantly changed genes in each comparison. Again, are these changes correlated between the two drivers or can they be attributed to genetic background of Gla vs R16? Would it be interesting to see how SD-Mad/Gla and SD-5/Gla gene expression profiles compare? Experiment: totRNAseq for SD-MadRev crosses.

      There did tend to be more differences in the Gla background compared to Iso1. This difference can best be explained by inter-sample variation in the SD-Mad/Iso1 background which we see in the PCA plot in Fig S4A. Another reason for the difference could be that the Gla and Iso1 chromosomes are very different from each other which prevents us from making any 1-to-1 comparisons between the SD/Iso1 and SD/Gla backgrounds. We generally avoid comparing between genetic backgrounds for this reason unless they share differences as these are more likely related to drive.

      In Figure S5A it seems that totalRNA levels of Rsp are strongly increased in SD-Mad/Gla but not in SD-Mad/iso1. The iso comparison (less piRNAs but same transcript) could indicate that it is actually transcription of the Rsp that is affected here. This is even pointed out in line 205 without discussion of the fact that the Gla comparison (less piRNAs but more transcript) would rather indicate that transcription is intact, but processing into piRNAs is defective. Could this be clarified using FISH as in Figure S8? If true, SD-Mad/Gla should have much more FISH signal than SD-Mad/iso1. Either way, this discrepancy should be further discussed. Experiments: comprehensive smFISH panel for all crosses (including SD-MadRev).

      The reviewer makes an excellent point. Why would Rsp long RNAs be overexpressed in the SD-Mad/Gla background? Earlier we noted that in the Gla background specifically the genotypes that contain an SD chromosome seem to have a higher level of Rsp small RNAs than we might expect given our Iso1 results. We conclude that this is likely due to an epistatic interaction between the 2nd chromosomes used in the study and the rest of the chromosomes. This interpretation could extend to the long noncoding precursors as well.

      Further, although the difference between SD-Mad/Gla is significant and SD-5/Gla is not, they do move in the same direction. This is also true in the Iso1 backgrounds but in the opposite direction. Given an interpretation that Rsp expression is higher than expected in the SD/Gla background due to epistatic effects, it becomes clearer that changes in long RNA abundance are related to changes in small RNA abundance though not perfectly indicative. However, due to lower count levels for Rsp in the totRNA, we do not have the power to confidently draw that conclusion.

      In general, the totRNA profiles of repeats don't seem to correlate well between the genotypes (iso vs Gla crosses, neither for SD-5 nor for SD-Mad). Is this because values are in general small and/or replicates don't correlate? Should these data even be considered? Also panels 2A and S5C are very different from each other. The additional comparison with the SD-MadRev allele crossed into both Iso1 and Gla should give additional insight. Experiment: totRNAseq for SD-MadRev crosses.

      The reviewer brings up a good point. While some repetitive elements had relatively small counts in the totRNA (like Rsp) most had adequately high counts. But these differences are to some degree expected. Although the other chromosomes are controlled for, the second chromosomes are different by design including the two SD haplotypes. In this context, similarities between the two haplotypes may be helpful in determining some unifying aspects of the SD mechanism but differences could be incidental to the genotype and not necessarily related to SD.

      It may be generally informative to set the sRNA and RNA comparisons into perspective, for example by including the comparison of SD-Mad crosses versus SD-MadRev crosses to exclude unrelated genetic background components as much as possible.

      The reviewer is correct here. Differences in the transcriptomes of SD-Mad and our revertant are much more likely due to the drive phenotype. Due to variation between SD-Mad total RNAseq replicates, we have substantially less power when comparing SD-Mad/Iso1 to SD-MadRev/Iso1. We therefore generated new data to address this point: we did digital gene expression for three biological replicates of SD-Mad/Iso-1 and SD-MadRev/Iso1. We described the results of this new analysis above.

      FigS6: I assume this is given, but as it is not specified: is the directionality of differential expression taken into account here? Or could it be significantly up in one and down in the other? Please specify / adjust color scale to allow this distinction.

      This is a good point. We have modified the figure to not only indicate significance but also direction and magnitude.

      FigS8: Please add a scale bar for all images. 1.688 is labeled as 359 in the legend, please unify or/and explain nomenclature. Consider adding a nuclear outline based on DAPI. It looks like 1.688 is actually more different between control and SD-Mad/Iso than Rsp. Could the authors comment on this? In the text the authors mention that these experiments were done for both SD-Mad and SD-5 heterozygotes, but only the SD-Mad data are shown.

      The most abundant component of 1.688 repeats is the 359bp repeat, which is used as a proxy for 1.688 and our 359-bp probe cross hybridizes with other abundant variants of 1.688 on chromosome 3. We agree, there does seem to be some differences in the 1.688 RNA FISH, however we do not yet have evidence that 1.688 is related to the drive phenotype. We have expanded that figure (now supplemental figure 7) with multiple images for each genotype to demonstrate the lack of change in Rsp and 1.688 localization. We have added an explanation of the nomenclature.

      The reference to SD-5 in the text was made in error. We do not have RNA FISH images of SD-5/Iso1 heterozygotes. We've modified the text to reflect this.

      FigS9B: What does the y-axis label mean? Fold change relative to what? Is this not displaying counts?

      This is a good catch by the reviewer. The y-axis is mislabeled and should read "TPM". We have made this change.

      To set the KipfKD/KO data in context, please give also the k value for SD-MadRev and compare the smRNA values in this context to the data displayed in F1B. Experiment: drive analysis for SD-MadRev.

      Our basis for concluding that Rsp smRNA overexpression may reduce drive strength is in demonstrating that kipfKO is sufficient to rescue wild type sperm in driving backgrounds. We did not introduce KipKD (or KO) to the SD-MadRev background because this chromosome does not drive.

      The note that the 3XP3-dsRed cassette needs to be flipped out for Rsp overexpression to influence drive is interesting. It would be great if the authors could show a more detailed scheme of the structure of this insertion including the directionality of the promoter relative to the Rsp fragment and the rest of cluster 38C (including dm6 coordinates perhaps). Small RNA sequencing compared to totRNA sequencing should reveal if the transcription or the processing into piRNAs of the inserted piece is affected, and if more of the 38C piRNAs are affected. Genic transcription has been previously observed to limit Rhino-dependent piRNA production from piRNA clusters (Andersen et al 2017). It might be of interest to the general piRNA community to see how cluster output is influenced through the integration of an internal genic promoter.

      We agree that this is an interesting result. We have added more detail to Fig 4A to indicate directionality and genomic location of the insert in terms of dm6.

      Figure panel 4A should be adjusted to include annotations of the black boxes and to give genomic locations. It is unclear what the blue brackets mean, and where exactly the insertion took place. Are the attP sites relevant for the experiments? It might be nice to see a piRNA profile over the locus, to put the levels of additional Rsp piRNAs into perspective.

      We have removed the black boxes from the schematic as they were only there as an aesthetic choice. We have indicated where exactly the insertion was made. The attP sites are there for future experimental flexibility.

      Minor comments

      Figure 3B: fold change of satellite RNA is shown. It might be obvious that the fold change relates to KipfKO / WT but this should be stated explicitly. What is the genetic background here?

      Thank you for the comment. We added information on the genetic background in the figure.

      Figure legends should be extended for clarity throughout the manuscript in main and supplementary figures. All color codes and abbreviations as well as samples / genotypes and assay used should be clearly explained. Few examples include: F1B: smRNA or totalRNA? F3B: fold change relative to what? F4B: what are these data relative to? F4C: smRNA or totalRNA? S2: Is this smRNAseq? Further description of the color code in the volcano panels would be desirable. FS3: typo in A-B should be A-D. Fold changes relative to what. Etc.

      Thank you for these helpful suggestions. We have edited the figure legends as suggested to improve the clarity. We appreciate the feedback.

      The abbreviation for Kipferl is kipf, not kip.

      Thank you for pointing this out, we have made the corrections.

      I don't understand the sentence on lines 310-312.

      We agree that sentence was confusing. We replaced it with:

      "Identifying potential proteins that interact with Rsp may therefore provide important clues about why satellites like Rsp are targets of drive."

      **Referee cross-commenting**

      I agree with the other reviewer's assessments

      Reviewer #3 (Significance (Required)):

      General assessment

      This study of a highly complex and poorly understood drive system adds a very interesting piece to the puzzle of understanding the interplay between a RanGAP duplication and a large satellite array. It's strengths lay in the use of genetics tricks to modify drive (SD-MadRev allele, KipfKO, Rsp cluster insertion). The main weakness of the study is the relatively low correlation of several observations between drive crosses to the Iso1 and Gla lines and lack of explanations thereof. Neither gene nor repeat expression seem to give a convincing overlap in any direction.

      Furthermore, it is interesting that SD-Mad and SD-5 have such different dependencies on Rsp sRNA. While outside the scope of this work, it would be very interesting to see how other drive haplotypes behave: is SD-5 the exception or is it SD-Mad (as the authors have also wondered in the discussion). Such additional comparisons may clarify also the discrepancies in RNAseq.

      Advance

      While it has been previously shown by the same group that Rsp satellites give rise to smRNAs through the piRNA pathway, it is to my knowledge unclear how and if these smRNAs influence drive. This study thus presents a conceptual advance in that it demonstrates that the role of Rsp smRNAs is not shared among driving haplotypes.

      Audience

      This study is relevant for a highly specialized audience interested in meiotic drive. It contributes to the understanding of the SD system and may serve as a basis for future research in this area. In addition, results reported in Figure 4 may be of peripheral interest for the Drosophila piRNA community for technical interests.

      This reviewers expertise: Drosophila, piRNA pathway, heterochromatin, sRNA

      This reviewers limitations: nuclear-cytoplasmic trafficking, cytoskeleton

    1. Author response:

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

      eLife Assessment

      This important study deepens our understanding of how populations of a given species may diverge in their molecular and physiological patterns as a result of adaptation to different thermal regimes. By approaching this question from multiple directions, the authors provide solid evidence for adaptive changes in three strains of the diamondback moth after only three years of experimental evolution, and support the causal involvement of the PxSODC gene in thermal adaptation to both cold and hot temperatures. This work would benefit from more sophisticated phylogenetic analyses, better statistical support, and a more detailed discussion of the differences in the three strains at the pathway level.

      We sincerely thank the editors for this positive and constructive assessment. In the revised manuscript, we have addressed the highlighted points by: (1) re-inferring the phylogenetic tree of the PxSODC gene using a model-based Maximum Likelihood method (IQ-TREE) to ensure a robust evolutionary analysis; (2) substantially expanding the description of our statistical methods across all data types to ensure reproducibility and clarify multiple-testing corrections; and (3) adding a more detailed discussion of the pathway-level differences between the hot and cold strains, particularly integrating how their distinct transcriptomic responses align with their shared metabolic adjustments and phenotypic traits.

      Reviewer #1 (Public review):

      (1) The authors identify pathways that are enriched in different strain comparisons (Figure 3E), but do not provide a detailed interpretation of these results. It would be great if the authors could explain in more detail how the physiological processes of a cold-adapted strain of this species may differ from those of a warmer-adapted strain.

      We agree. We have addressed this by directly integrating our pathway enrichment results (Figure 3E) with the observed life-history phenotypes (concurrently addressing Reviewer 2's Comment 36a). We expanded the Discussion to explain that while both strains share convergent adjustments in core pathways (e.g., lipid metabolism for energy reallocation), their specific physiological strategies differ. The cold-adapted strain relies on broader transcriptional reprogramming to maintain homeostasis and support extended longevity/cold hardiness, whereas the hot-adapted strain utilizes broader metabolic rewiring to actively fuel its accelerated development and higher fecundity.

      (2) The authors reconstruct a phylogenetic tree of the PxSODC gene using the neighbor-joining algorithm. The limitations of this algorithm have been known for many years now, especially for sequences separated by long evolutionary distances. According to Wang et al. (2016), the last common ancestor of the species shown in Figure S4C occurred 392-350 million years ago. Given this, I would strongly recommend that the authors infer a phylogenetic tree using model-based methods, such as those implemented in RAxML-NG or IQ-TREE. Also, in the absence of a valid outgroup sequence, I would show the gene tree as unrooted or rooted based on the corresponding species tree.

      Agree. We have re-inferred the phylogenetic tree of the PxSODC gene using the model-based Maximum Likelihood (ML) method implemented in IQ-TREE. As recommended, in the absence of a valid outgroup sequence, the revised tree is now presented as unrooted. Supplemental Figure S4C (Figure 5-figure supplement 1C) and the corresponding text in the manuscript have been updated.

      (3) There is a key piece of the puzzle that is currently missing: the structural mechanism behind the mutational effects described in this study (e.g., Figure 5). The authors could leverage AlphaFold to generate structural models of different mutants and conduct molecular dynamics simulations to examine their conformational dynamics.

      We thank the reviewer for this excellent suggestion. We generated AlphaFold structural models of the wild-type (WT) and mutant (MU) PxSODC proteins and conducted 100 ns molecular dynamics (MD) simulations using GROMACS 2022.3 at three physiologically relevant temperatures: 15°C (cold stress), 26°C (favorable baseline), and 32°C (heat stress). Using 26°C as the physiological baseline, three key structural parameters support enhanced thermostability of the mutant protein (Figure 5–figure supplement 3). First, RMSD analysis revealed that under heat stress (32°C), the WT underwent severe conformational drift (RMSD increased from the 26°C baseline of 1.62 to 2.49, an increase of 0.87), while MU remained remarkably stable (from 1.59 to 1.66, an increase of only 0.07). Second, MU possessed a significantly more compact structure, with lower SASA values at 15°C (118.39 vs. 127.29 nm²) and 26°C (113.82 vs. 125.61 nm²), indicating optimized hydrophobic core packing. Third, the intramolecular hydrogen bond network of MU demonstrated dual stress resistance: under cold stress, MU actively increased hydrogen bonds from its baseline (113→119), whereas WT lost bonds (117→112); under heat stress, MU fully maintained its bond count (113→113). These results provide a direct structural mechanism for the enhanced catalytic efficiency of the mutant SOD at lower expression levels.

      Reviewer #1 (Recommendations for the authors):

      (4) The experimental evolution component of this study is described in the text as lasting for three years. It would help if the number of generations per strain were also reported.

      We have added the number of generations per strain. Over the three-year period, the hot strain completed ~75 generations and the cold strain ~15 generations. The ancestral strain was continuously maintained at 26°C throughout this period. The revised text has been updated in both the Introduction and Materials and Methods.

      (5) In Figure 3B: There is a typo in the word “Statistics”.

      Corrected. The typo in “Statistics” in Figure 3B has been fixed.

      (6) In Figure 3D: “CS” appears twice.

      Corrected. The duplicated “CS” label in Figure 3D has been replaced with the correct label.

      (7) Figure 4: This is not accessible to colorblind readers, who will clearly not be able to tell each color apart. As a non-colorblind person, I, too, have trouble figuring out which color label in panel B corresponds to which color in panel A. For example, I do not know off the top of my head how 'blue' differs from 'midnightblue', 'royalblue', or 'skyblue'. I recommend that the authors replace colors with identifiers, such as 'g1' for group 1 and so on.

      We appreciate this suggestion. We have replaced all color-based module labels with alphanumeric identifiers (M1, M2, M3, etc.) and added a corresponding legend. The main text and supplementary materials have been updated accordingly.

      (8) Lines 246-247: "Its secondary structure mainly consisted of strands, helices and coils." This sentence is redundant. These three are the only possible secondary structural elements, according to most bioinformatics tools such as PSIPRED, which the authors used. This sentence would be more useful if the authors could report the percentage breakdown of each secondary structural element.

      We have removed the redundant sentence and updated the text to report the specific percentage breakdown of the secondary structural elements based on our PSIPRED predictions (approximately 55.24% random coils, 16.19% alpha helices, and 28.57% extended strands). The revised text has been updated in the Results section.

      (9) Lines 260-261: "This suggests that the PxSODC gene can alter its expression pattern and function in response to environmental change...". I find this sentence a bit imprecise. Would it not be more precise to mention that the expression of this gene is regulated by temperature triggers?

      We agree that the original phrasing was imprecise. We have revised the sentence in the manuscript to state: “This suggests that the expression of the PxSODC gene is regulated by temperature triggers, and its altered function contributes to temperature-adaptive evolution in P. xylostella.”

      (10) The data points in Figures S1 and S7 are very small and hard to tell apart without zooming in a lot. Perhaps the authors could change the orientation of those pages to landscape and increase the size of the figures.

      Done. We have changed the orientation of Supplemental Figures S1 (Figure 1-figure supplement 1) and S7 (Figure 5-figure supplement 4) to landscape and increased the size of the figures and individual data points to improve visibility.

      (11) In Figure S2, the panel labeled as 'C' should be 'B' (based on the caption) and vice versa.

      Corrected. The panel labels ‘B’ and ‘C’ in Supplemental Figure S2 (Figure 2-figure supplement 1) have been swapped. The Supplementary Materials have been updated accordingly.

      Reviewer #2 (Public review):

      (1) The paper in its current form is hard to digest and would benefit from improved clarification of the storyline, as well as a tighter integration between the phenotypic, omics, and functional validation data. Currently, it is not always clear what the relevance is of all the reported results, nor why certain decisions were made, or how all the different methods the authors used fit together. For example, the authors functionally validated a second gene, PxDnmt1, but it is unclear why this particular gene was chosen, nor how it relates to their selection regimes when looking at the results obtained with the phenotyping and omics data collection. Seeing how much work the authors did, this makes the paper overwhelming and difficult to read.

      We sincerely appreciate this constructive feedback. In the revised manuscript, we have made significant structural revisions to improve the storyline and logical flow. We have streamlined the Results section (moving extensive descriptive data like life table curves and detailed metabolomics of mutant strains to the Appendix 1-3) to focus on the key findings. Furthermore, we have clarified the logical transitions between experiments. For instance, regarding the choice to validate PxDnmt1, we now explicitly explain in the Results that our untargeted metabolomic analysis of the PxSODC mutant strains revealed consistent alterations in 5-hydroxymethyluracil (involved in DNA demethylation) and 5'-deoxyadenosine (a precursor to the primary methyl donor S-adenosylmethionine) across all developmental stages. This specific metabolic signature provided a strong, data-driven hypothesis linking PxSODC function to epigenetic regulation via DNA methylation, prompting us to functionally validate PxDnmt1. By explicitly stating these rationales, the narrative is now much clearer and cohesive.

      (2) The authors at times stretch their results too far, as the ecological relevance of their study design and results is not clear, limiting the generalizability and value of the results for understanding species' adaptive potential under climate change. For example, the selection regimes used present the minimum and maximum known temperatures at which the species can survive and develop, but it is unclear how the temperatures relate to the natural environment of the source population, to what extent wild populations might experience these temperatures, and whether they would experience them at the extended duration used (12h at max/min temperature). Moreover, I wonder whether the comparisons made would identify the genes that matter under natural conditions, as unevolved populations were kept under constant conditions compared to 12h:12h temperature regimes for the evolved populations, and the metabolic and transcriptomic profiling was done under a constant favorable 26°C rather than under thermal stress in a, as far as I can tell, randomly chosen life stage (larval stage).

      We appreciate the reviewer raising these important points regarding ecological relevance and experimental design. In the revised manuscript, we have added context and acknowledged these limitations in the Methods and Discussion sections. First, regarding ecological relevance: The source population is from Fuzhou, a subtropical region where summer high temperatures frequently exceed 32°C and winter lows can drop below 10°C, making our selection temperatures ecologically relevant extremes for this population. The 12h:12h cycling temperatures were designed to simulate severe but natural diurnal fluctuations.

      Second, regarding constant control vs. cycling regimes: The constant 26°C represents the established optimal developmental temperature and standard laboratory condition for P. xylostella. We acknowledge that comparing cycling selection regimes against a constant control might conflate adaptation to absolute temperature extremes with adaptation to thermal fluctuation itself. We have added this as a caveat in the Discussion. Third, regarding omics profiling conditions: The transcriptomic and metabolomic profiling was conducted under common garden conditions (26°C) specifically to identify constitutive, genetically fixed adaptations resulting from evolutionary selection, rather than immediate physiological plasticity under stress. We have clarified these rationales in the text.

      (3) The paper in its current form does not adequately describe the statistical analyses underlying the results, nor do the authors share their code, making it very hard to judge whether the analyses used are appropriate and the results trustworthy. I have concerns about the inappropriate use of t-tests, the lack of correcting for confounding variables, and the need for multiple testing corrections.

      We sincerely appreciate this concern. In the revised manuscript, we have made substantial improvements to the description of statistical analyses throughout the Methods section:

      (1) Statistical methods for each data type are now described separately and in detail, specifying the tests used, the number and type of comparisons, and sample sizes.

      (2) For metabolomic data, we have clarified that FDR correction was applied alongside multi-criteria thresholds (|log<sub>2</sub>Fold Change| ≥ 1, VIP ≥ 1, FDR < 0.05). For transcriptomic data, FDR correction (Benjamini and Hochberg, 1995) was applied via DESeq2.

      (3) For WGCNA, we have specified the total number of correlation tests (29 modules × 30 metabolites = 870) and the stringent dual threshold (|r| > 0.8, P < 0.05) used to control for false positives, following standard practice.

      (4) For life table parameters, the paired bootstrap method with 100,000 replications was used for all pairwise comparisons among strains.

      (5) For all other experimental data (qRT-PCR, SOD activity, O<sub>2</sub><sup>-</sup> levels, survival rates, supercooling/freezing points, etc.), we have specified that t-tests were used only for two-group comparisons, while one-way ANOVA with Tukey's or Tamhane's T2 test was used for three or more groups, with non-parametric alternatives applied when normality assumptions were not met.

      (6) The raw data have been deposited in public repositories (see Data availability), and all statistical procedures are now described in sufficient detail to enable independent reproduction of the results.

      Reviewer #2 (Recommendations for the authors):

      Title

      (4) I don't feel the title adequately captures the work, I would instead of 'adaptive evolution' use 'experimental evolution' and I would not use the word 'underpins' but instead 'indicates', as it is not clear from your work whether the adaptations to the lab conditions you used would be ecologically relevant nor whether they are involved in thermal adaptation in wild populations.

      Accepted. The title has been revised to: “Experimental evolution to thermal stress indicates climate resilience in a cosmopolitan arthropod.”

      Abstract

      (5a) Please add the phenotype results to the abstract.

      We have added key phenotype results to the abstract. The revised text now reads: “The hot strain showed accelerated development, higher fecundity, and increased survival under extreme heat, while the cold strain exhibited lower supercooling and freezing points, indicating enhanced cold hardiness.”

      (6b) The Abstract doesn't really detail the answer to your research question yet: so what insights into the genetic mechanisms underlying thermal adaptation did you gain that are novel?

      We agree. We have revised the Abstract to explicitly highlight the novel genetic and molecular mechanisms we discovered. Specifically, we now detail that thermal adaptation is driven by a coordinated mutational, metabolic, and epigenetic (1) an energy-efficient genetic mechanism where non-synonymous mutations in PxSODC enhance superoxide scavenging efficiency, enabling effective oxidative stress management at lower gene expression levels; (2) convergent metabolic adjustments, notably a reduction in lipid metabolism to conserve energy; and (3) epigenetic regulation of thermal tolerance via DNA methylation. The revised text has been updated in the Abstract accordingly.

      (7c) Line 3: replace 'ectotherms' with 'arthropods' to match the title?

      Done. “Terrestrial ectotherms” has been replaced with “terrestrial arthropods” in the abstract.

      (8d) Line 9: replace 'demographic' with 'life history'?

      Done. “Demographic” has been replaced with “life history” in the abstract.

      Introduction

      (9a) The storyline is a bit unclear. Do you want to focus on the increased threat from insect pests under climate change or on the threat of climate change on insect persistence? Please pick one and adapt your storyline accordingly. I would suggest focusing on the first and talking more about the range extension of pest species under climate change (which would also require adaptation to cold extremes).

      We agree and have refocused the Introduction on the increased threat from insect pests under climate change, emphasizing that range expansion into new regions requires adaptation to both heat and cold extremes. Both the first and second paragraphs have been revised accordingly.

      (10b) Line 31-33: What do you mean by 'shows a positive relationship between the thermal tolerance range and the level of climatic variability'? Are they able to tolerate a larger range of temperatures?

      This sentence has been revised as part of the restructured Introduction, which now focuses on the range expansion of pest species under climate change. The revised text reads: “Such range expansion requires adaptation not only to warmer conditions in existing habitats but also to cold extremes encountered during colonization of higher latitudes or elevations (Harvey et al., 2020).”

      (11c) Line 33-35: Is this information relevant here?

      Agreed. This sentence has been removed as part of the restructured Introduction, which now focuses on the threat of pest range expansion under climate change.

      (12d) Line 55-56: What exactly do we not know yet about the mechanisms that enable thermal adaptation that you aim to fill in this paper? Please rephrase your knowledge gap to be more concrete (e.g., "but we do not yet know how...").

      We have rephrased the knowledge gap to be more concrete and aligned with the revised storyline. The revised text now reads: “...we do not yet know how long-term thermal selection drives coordinated changes across gene function, metabolic networks, and life history traits to enable thermal adaptation and range expansion in pest species.”

      (13e) Line 57: Also, here, the storyline is unclear. Why did you use the diamondback moth as your model species? You provide many different reasons, but it would help if you emphasized one reason that is in line with whichever storyline you want to focus on: is it because it is an insect pest that can tolerate a wide range of temperatures?

      We have streamlined this paragraph to focus on the primary rationale: P. xylostella is a globally distributed pest that thrives across a wide range of thermal environments, making it an ideal model for studying the genetic mechanisms of thermal adaptation. Supporting details on genomic resources are retained briefly as they enable the multi-omics approach used in this study.

      (14f) Line 65: Demonstrated how? Please give a short summary of the evidence for their genetic capacity to tolerate future climates.

      We have added a brief summary of the evidence. Specifically, genome-wide SNP analysis of field populations from 114 locations across diverse biogeographical zones revealed climate-adaptive genetic variability, indicating that P. xylostella can tolerate projected future climates in most regions (Chen et al., 2021).

      (15g) Line 72: What does 'Age-stage' mean? Should it read 'Aged-staged'?

      “Age-stage, two-sex life table” is an established demographic method developed by Chi (1988) that simultaneously accounts for both age and developmental stage in both sexes. This is a standard term in the field (Chi et al., 2020), so we have retained the original wording but added a brief clarification upon first use.

      (16h) Line 78-80: This needs a bit more explanation. Why does an increased ability to scavenge superoxide anions affect adaptability under extreme temperature environments?

      We have added a brief explanation. Extreme temperatures induce oxidative stress by elevating intracellular reactive oxygen species (ROS), including superoxide anions, which can damage cellular structures. Enhanced scavenging capacity thus helps maintain cellular homeostasis under thermal stress.

      (i) Line 82-86: Please be more precise. What novel insights did you gain about the genetic mechanisms underlying thermal adaptation?

      We have revised this sentence to more precisely summarize the novel insights, encompassing both the multi-omics findings and the functional validation of PxSODC.

      Results

      (18a) The results section is very long and presents an overload of information at the moment, overwhelming the reader. Consider moving some sections to the Supplements (for example, a large part of the phenotypic data that cannot be linked to the omics data and the metabolic profiling of the mutant strains) or leave them out of the paper altogether.

      We agree that the Results section was too dense. We have streamlined it by moving the following content to the Supplementary Materials:

      (1) Detailed age-stage survival and fecundity curve data for the ancestral, hot and cold strains (Supplementary Text S1).

      (2) Detailed life table analysis of the PxSODC mutant strains (Supplementary Text S2).

      (3) Detailed untargeted metabolomic profiling of the SODC-MU mutant strains across developmental stages (Supplementary Text S3).

      The main text now retains only the key life history comparisons, extreme temperature tolerance results, omics-based evidence linking transcriptomics and metabolomics, functional validation of PxSODC, and the DNA methylation findings, with brief summaries and cross-references to the Supplements for supporting details.

      (19b) Please also provide the effect sizes for the different effects you report, for example, how many degrees difference was there between ancestral and cold strains in the supercooling/freezing points, and what was the variation?

      We have added specific effect sizes (mean ± SEM and between-group differences) for all key comparisons throughout the Results section, including preadult duration, stage-specific survival rates under extreme heat, supercooling/freezing points, and SODC-MU mutant strain comparisons. For example, the supercooling points of CS pupae (-23.99 ± 0.18°C) were 0.90°C lower than AS (-23.09 ± 0.26°C), and the freezing points were 2.66°C lower (-14.24 ± 0.61°C vs. -11.58 ± 0.52°C). Please refer to the revised manuscript for all updated values.

      (20c) Line 93-94: "Intrinsic and finite rate of increase" of what?

      Clarified. These are population growth parameters. The revised text now specifies “intrinsic rate of increase (r) and finite rate of increase (λ) of the population.”

      (21d) Line 98-99: Please start the paragraph with this summary of the results and then further detail them.

      We have restructured this paragraph by moving the summary sentence to the beginning, followed by the supporting details.

      (22e) Line 100-109: Why did you look at daily survival and fecundity rates? Please add why this is relevant.

      As part of the overall streamlining of the Results section, this paragraph on detailed age-stage survival and fecundity curves has been moved to Supplementary Text S1. A brief justification for their relevance has been added there, noting that these curves capture stage-specific variation in survival and fecundity that summary life table parameters alone may obscure.

      (23f) Line 106: What do HS, AS, and CS stand for? And please provide the statistics for comparison of daily survival rates between the strains.

      We have defined the abbreviations (HS = hot strain, AS = ancestral strain, CS = cold strain) at their first appearance in the Results section. This paragraph on daily survival and fecundity has been moved to Supplementary Text S1, where the abbreviations are also defined. The survival rates reported are the maximum daily survival rates derived from the age-stage specific survival rate curves (s<sub>xj</sub>), and the statistical comparisons among strains are presented in Supplemental Table S1.

      (24g) Line 144-146: Why are these differential metabolites likely to play a crucial role?

      We agree this statement was speculative. It has been removed from the revised manuscript.

      (25h) Line 159-161: Why is a reduction of lipid metabolites evidence for adaptive evolution?

      We have revised this sentence to clarify the reasoning. The reduction in lipid metabolites in both independently evolved hot and cold strains suggests a convergent metabolic response, indicating that lipid metabolism adjustment is a shared adaptive strategy rather than a random change.

      (26i) Line 184-185: It is difficult to judge from Figure 3E the extent of overlap in KEGG pathways between the hot and cold strains. Can you adjust the figure to emphasize that overlap more?

      Agree. To intuitively emphasize the extent of overlap in KEGG pathways between the hot and cold strains, we have completely redesigned Figure 3E. Instead of presenting two separate panels with unaligned vertical axes, we have consolidated the data into a single back-to-back (mirrored) bar chart with a shared central y-axis.

      (27j) Line 211: Not only the red module, but also the blue and green module correlates with many of the shared differential metabolites.

      We agree. We have revised the text to acknowledge that the blue and green modules also showed strong correlations with shared differential metabolites, while noting that the red module had the highest number of significantly correlated metabolites and was therefore selected for further analysis.

      (28k) Line 215: I would rephrase this as genes being interesting candidates for being involved in thermal adaptation or 'seem to be important for the adaptation of...', as you don't know from these results whether these genes play a critical regulatory role.

      Agreed. We have toned down the language to reflect the correlative nature of these results.

      (29l) Line 233: Do you mean that you further analyzed 15 genes of the 79 identified candidate genes in the previous paragraph?

      Yes, exactly. From the 79 candidate genes, we selected 15 that were both annotated in the genome and had high expression levels (FPKM > 10) for further analysis. We have clarified this in the revised manuscript.

      (30m) Line 238: What does SOD stand for?

      We have spelled out the abbreviation upon first use in this section.

      (31n) Line 254-255: Please provide the stats for this result.

      We have added the specific allele frequencies for each strain. The Leu194-Met194 mutation frequency was determined by direct sequencing of 10 individuals per strain, and the frequencies are now reported in the revised text.

      (32o) Line 303-304: How did you test for enhanced stability to temperature fluctuations? And enhanced compared to what?

      This observation was based on the survival rate data in Figure 5C, where mutant pupae at 43°C showed no significant difference from the ancestral strain, whereas other life stages (eggs, larvae, adults) at 42°C showed significantly reduced survival in the mutant strains. We have revised the text to clarify the comparison.

      (33p) Line 324-326: Why do decreased expression levels demonstrate increased O₂⁻ scavenging capacity? And why is that beneficial for adaptation to thermal stress? Please explain.

      We have revised this sentence to clarify the logic. The non-synonymous mutations in the hot and cold strains likely alter the protein conformation of SOD enzymes, increasing their catalytic efficiency per molecule. This allows effective O<sub>2</sub><sup>-</sup> scavenging at lower expression levels, which is energetically favorable under thermal stress where energy conservation is critical for survival.

      (34q) Line 404-406: I'm confused. Is there a direct link between the gene you knocked out here and the results you presented up until now? How do the reduced levels of 5-methylcytosine relate to the metabolite results you present at the beginning of the paragraph, other than that both could be involved in DNA methylation?

      We have revised this paragraph to clarify the logical chain. Among the three metabolites consistently altered across all developmental stages in the SODC-MU strains, 5-hydroxymethyluracil is involved in dynamic DNA demethylation and 5'-deoxyadenosine is a precursor to S-adenosylmethionine (the methyl donor for DNA methylation). This suggested a link between PxSODC deletion and DNA methylation. To test this, we examined PxDnmt1 expression and activity in the thermally adapted strains and found both were significantly reduced. We then used RNAi to silence PxDnmt1 and confirmed that reduced DNA methylation (lower 5-mC levels) directly impaired thermal tolerance. Thus the connection is: PxSODC deletion → altered methylation-related metabolites → reduced DNA methyltransferase activity → decreased thermal tolerance.

      (35r) Line 410: Saying that your knockdown of a gene that did not directly pop up in any of your other analyses confirms that DNA methyltransferase is associated with the response to thermal selection is a stretch. Please rephrase.

      We agree this was overstated. We have toned down the language to reflect that the RNAi results provide preliminary evidence for a potential role of DNA methylation in thermal tolerance, rather than confirmation.

      Discussion

      (36a) The phenotype data are currently not discussed at all. Please add it to the discussion and try to integrate it more with the omics data you collected.

      We agree. To provide a cohesive narrative and avoid redundancy, we have addressed this comment in conjunction with our pathway interpretation (please see our response to Reviewer 1, Comment 1). In the revised Discussion, we explicitly integrated our specific phenotypic findings (e.g., accelerated development, increased fecundity, and heat survival in the hot strain; prolonged lifespan and lowered supercooling points in the cold strain) with the distinct transcriptomic and metabolomic profiles. This integration demonstrates how molecular and metabolic rewiring directly underpins the divergent life-history traits without engaging in unwarranted speculation.

      (37b) Line 433-434: I don't think this adequately represents the relevance of your particular study. I would suggest changing it to be more in line with the storyline of understanding the capacity for global dispersal in insect pests under climate change.

      We agree. We have revised this sentence to align with the storyline of pest range expansion under climate change.

      (38c) Line 476: This is a very odd statement; don't all species' genomes have genes encoding proteins involved in thermal adaptation? The reference also doesn't seem to be appropriate. I would suggest deleting this sentence.

      Agreed. This sentence has been removed.

      (39d) Line 483: Please write out SOD the first time you use it in a new section.

      Done. SOD has been spelled out at its first use in the Discussion.

      (40e) Line 544-548: This is a bit too specific to be the last sentence of the discussion. Try to formulate it more broadly in terms of what future research should focus on in general, not just your specific research.

      We agree. We have broadened the final sentence to address future research directions more generally.

      Figures

      (41a) Figure 1A: I don't think t-tests are appropriate here since you are not simply comparing two treatments, but testing for the effects of 5-6 different temperatures. And how did you correct for replicate populations in your analysis?

      Clarified. In Figure 1A, our comparisons are independent pairwise tests between exactly two strains (HS vs. AS) at each specific temperature and time point, making t-tests statistically appropriate. We were not testing for a continuous effect across temperatures. Regarding replicate populations, the individuals used in these assays were drawn from across the six replicate populations per treatment, with each biological replicate (n = 6, with 20 individuals per replicate) comprising individuals pooled from across the replicate populations to account for inter-population variation. We have clarified this in the revised figure legend.

      (42b) Figure 1B, Figure 5D, Figure 7: bar graphs are used for count data, so do the data represent the number of individuals with a certain trait value? If they are instead showing the mean of the population/treatment group, please use mean points ± standard errors instead.

      Accepted. The data in these figures represent continuous physiological traits (e.g., supercooling/freezing points) showing the mean of the populations, rather than count data. To align with current data visualization standards for continuous variables and to provide full transparency of the underlying data distribution, we have replaced the bar graphs in Figures 1B, 5D, and 7 with scatter plots. These revised figures now display the mean ± SEM overlaid with all individual biological replicate data points.

      (43c) Figure 3B: There is a typo in the graph, it reads 'Stattistics' instead of 'Statistics'.

      Corrected. The typo ‘Stattistics’ in Figure 3B has been fixed.

      (44d) Figure 3C: I don't understand what the colors of the graph mean here. Is it the average differential expression of each replicate compared to the ancestral?

      Clarified. We have updated the figure legend to explain that the colors represent the Pearson correlation coefficient (r) between pairs of biological replicates, indicating the degree of transcriptomic similarity among samples.

      Methods

      (45a) Please start each new methods paragraph with the purpose of the method/analysis, for example, "To investigate XX, we used method X to measure X". It is at the moment hard to understand why certain things were done.

      We agree. We have revised each Methods paragraph to begin with a clear statement of purpose, so that the rationale for each analysis is immediately apparent. All changes are shown in the revised manuscript.

      (46b) Line 575-578: Why were the selection regimes with cycling temperatures and the control with constant?

      The cycling temperatures in the hot (32°C/27°C) and cold (15°C/10°C) regimes were designed to simulate diurnal temperature fluctuations (12h light/12h dark) that more closely reflect natural thermal environments. The control was maintained at a constant 26°C, which is the established optimal developmental temperature for P. xylostella (Liu et al., 2002) and represents the standard laboratory rearing condition. We acknowledge this asymmetry and have added a justification in the revised manuscript.

      (47c) Line 581: How many generations was the ancestral population kept in the lab before the start of the selection experiment? And for how many generations were the populations selected?

      The ancestral population was maintained in the laboratory for approximately ~170 generations (from July 2012 to the start of the selection experiment) before the thermal selection began. The hot strain was selected for ~75 generations and the cold strain for ~15 generations over the three-year experiment. We have added this information to the revised manuscript.

      (48d) Line 585-586: I don't understand what you mean by randomly selecting six replicate populations per treatment for downstream experiments when you only had six replicate populations per treatment to begin with (as detailed in Line 574)?

      We apologize for the confusion. All six replicate populations per treatment were used for downstream experiments. We have corrected this sentence to remove the misleading “randomly selected” wording.

      (49e) Line 590: Were these 90 eggs also randomly selected, like for the individual life tables? And were these kept at the baseline temperature conditions?

      Yes, the 90 eggs were randomly selected and maintained under the baseline favorable temperature (26°C). We have clarified this in the revised manuscript.

      (50f) Line 606: Which life history and population fitness parameters were calculated?

      We have specified all parameters calculated in the revised manuscript.

      (51g) Line 609: Link to software doesn't work.

      We have updated the software link to the current working URL.

      (52h) Line 611: Please spell out what 'BT' stands for.

      Done. “BT” has been spelled out as “bootstrap” upon first use.

      (53i) Line 612-613: How many tests did you do? Did you correct for multiple testing? Using what method?

      The paired bootstrap method implemented in TWOSEX-MSChart inherently accounts for multiple pairwise comparisons through 100,000 bootstrap replications. We have clarified the scope of comparisons in the revised manuscript.

      (54j) Line 620-621: What does biological replicate mean here? Individual eggs / larvae / pupae / adults, or were all or some life stages pooled? Also, you now only detailed which samples were collected for metabolomic profiling, were the same samples used for transcriptomic profiling, or a subset?

      Each biological replicate consisted of pooled individuals at the same developmental stage. The same sample collection strategy was used for both metabolomic and transcriptomic profiling, but from independent biological replicates (six for metabolomics, three for transcriptomics). We have clarified this in the revised manuscript.

      (55k) Line 637: Also here, how many tests did you do? Were p-values corrected for multiple testing? Using what method?

      Differential metabolites were identified through pairwise comparisons using Student's t-test with FDR correction for multiple testing. A multi-criteria threshold of |log<sub>2</sub>Fold Change| ≥ 1, VIP ≥ 1, and FDR < 0.05 was applied. This approach was used for all metabolomic comparisons, including HS vs. AS, CS vs. AS, and SODC-MU vs. AS. We have clarified this in the revised manuscript.

      (56l) Line 662: And here: how many tests did you do? Did you correct for multiple testing? Using what method?

      In the WGCNA analysis, Pearson correlations were calculated between each module eigengene and each of the 30 common differential metabolites, resulting in a total of 29 × 30 = 870 correlation tests. Following standard WGCNA practice, rather than applying FDR correction, we used a stringent dual threshold of |correlation coefficient| > 0.8 and P < 0.05 to identify significant module-metabolite associations, which effectively controls for false positives (Langfelder and Horvath, 2008). We have clarified this in the revised manuscript.

      (57m) Line 663: How did you select these modules? The ones that significantly correlated with differential metabolites? Why did you not use the phenotype data here?

      Modules were selected based on significant correlations (|correlation coefficient| > 0.8, P < 0.05) with differential metabolites shared between the hot and cold strains. We chose metabolites rather than phenotype data as the trait input for WGCNA because metabolites serve as intermediate molecular phenotypes that bridge gene expression and organismal phenotypes, providing a more direct link to the underlying regulatory mechanisms. This approach allowed us to identify gene modules most closely associated with the metabolic changes driven by thermal adaptation, which could then be connected to the observed life history and fitness divergence.

      (58n) Line 666: move RNA extraction details to before RNAseq methods description.

      Done. The “RNA extraction and cDNA synthesis” section has been relocated to before the “Transcriptomic profiling” section for better logical flow.

      (59o) Line 836: This paragraph describing the statistics is very short, and it is unclear to what data the described analyses apply. As the different types of data are very different, I expect the analyses to differ as well. Please describe the statistical analyses for each data type in more detail, specifying what tests you used, which, and how many comparisons were performed.

      We agree. The statistical methods for life table analysis, metabolomics, and transcriptomics have been detailed in their respective method sections. We have expanded the Data analysis section to specify the statistical tests for the remaining experimental data.

      (60p) Line 837: Please include your SPSS scripts to ensure the reproducibility of your results.

      The statistical analyses in SPSS were performed using the graphical user interface. As all statistical tests, parameters, and comparison groups have been described in detail in the revised Methods section, and the raw data have been deposited in public repositories (see Data availability), we believe the analyses are fully reproducible. We are happy to provide additional details if needed.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Reviewer #1

      Minor comments 1) The authors suggest that the weak 4th protomer in the HCMV UL52 3-mer map is a consequence of flexibility. This may be the case, but it may also be the case that the class is polluted with 4-mer particles leading to reduced occupancy. Erasing the weak density and running a multi-model 3D classification providing the erased 3-mer and a 4-mer starting map may separate these.

      We performed additional analysis (i.e., 3-mer and 4-mer particles were combined into a multi-class ab initio reconstruction followed by multi-class heterogenous refinement) and found that the original 3-mer map was a mixture of 3-mer and 4-mer states.

      We have updated Fig. 2a, Supplementary Fig. 2, Supplementary Fig. 3, Supplementary Table 1, Supplementary Movie 1, and removed the discussion of the weak protomer in the 3-mer map from the results section. We have updated our EMDB and PDB depositions accordingly.

      • 2) I found the supplemental figure to show the DNA in the tripentamer map too small, this is an interesting finding and should be shown more clearly.*

      We have increased the size of Supplementary Fig. 6 and moved the figure caption to another page to accommodate this enlargement.

      Reviewer #2

      *Major issues 1) There is a high probability that the tripentamer is an artifact of the cross-linking. Because of this, it'd be great to know more about the cross-linking reaction, ideally mass spec identification and quantification of cross-links. This would also address the authors' speculation of contacts that stabilize the tripentamer. *

      Crosslinking is a commonly used technique to stabilize complexes that are observed through other means but do not survive the cryo-EM vitrification process. In an EMSA experiment (Supplementary Fig. 4a), UL32 binds 30 bp DNA and migrates slower than when bound to a 10 bp probe, consistent with formation of a supra-pentameric complex. The samples in the EMSA gels are not crosslinked. Additionally, an SDS-PAGE gel of the crosslinked product used for cryo-EM showed tight bands at molecular weights expected for oligomers, supporting specific crosslinking (Supplementary Fig. 4b). These results suggest that crosslinking stabilizes a species that can form but is relatively unstable in solution.

      Moreover, the author's claim "However, mutation of K532A/C535A reduced infectious virion production by half (Fig. 4b), suggesting that the tripentamer interface may play a role in the viral life cycle." Seems to be an overreach. Perhaps this is semantics but the data just show that these residues play a role in viral replication (albeit not a huge role based on the modest effect).

      We have modified the title of the results section (Line 216-217) to state that "Residues at the tripentamer interfaces contribute to infectious virion production in HSV-1" as well as Line 234 and 241 to indicate that the residues play a role in the viral life cycle.

      2) The density for the potential DNA does not look very convincing, although it still remains the strongest hypothesis. The authors should try to strengthen their argument. Does this putative DNA contact residues that they show are necessary for viral replication? Showing seq conservation on the structure could help their argument for the shared function of DNA-binding.

      The DNA likely contacts conserved residues at the base and midsection of the central channel (residues R302, R301, R293, K289, R580, R579, R572; see Fig. 6a). We have shown that these residues are important for the production of infectious virions (Fig. 6c): even a single point mutation (R572A) decreased production of infectious virus particles by more than 90%, and double and triple point mutants (R579A/R580A, K289A/R293A/R301A) eliminated production of infectious virus. Sequence conservation of these charged residues in the central channel regions is shown in Supplementary Fig. 1d, f.

      3) My last major issue is stylistic and concerns the descriptions of cryoEM structures. I found that the paper was a bit of challenge to read when the authors would introduce each structure. It was a bit of a slog to get through. Descriptions of the structures veered off into overly detailed comparisons that required constant comparison with the figure and didn't really advance my understanding past "the outer surfaces of the three orthologs are different." This masked the more interesting aspects of the authors' findings. Perhaps this could be summarized in supplementary figures or a table. Because this is a stylistic suggestion, the authors should feel free to ignore this request.

      We appreciate the reviewer's concerns about accessibility, but we are excited that these structures allowed us to thoroughly describe the convergent and divergent structural features across the Herpesviridae and hope that our in-depth analysis will allow for detailed mechanistic follow-up.

      *Minor comments 1) The descriptions of structure determination in the text were often unclear. For example, "In the 3-mer map, a poorly-resolved fourth protomer is visible at low contour levels, suggesting that an additional protomer is present but highly flexible in this class (Supplementary Fig. 3a)." Alternatively, it could be that the classification algorithm wasn't able to fully separate particles that were 3-mers from the 4mers. *

      The reviewer is correct. As described above (Reviewer #1 comment 1), we performed additional analysis and found that the original 3-mer map was a mixture of 3-mer and 4-mer states. We have updated Fig. 2a, Supplementary Fig. 2, Supplementary Fig. 3, Supplementary Table 1, Supplementary Movie 1, the EMDB and PDB depositions, and removed the discussion of the weak protomer in the 3-mer map from the results section.

      *When describing the structure determination of the HSV1 accessory factor, the authors describe no other particles other than the tripentamer. Were there other particles observed? It'd be a bit surprising that all of the protein adopted the tripentamer state. *

      We agree that this result is striking. We picked particles using a 'blob picker' to avoid introducing template bias and found that the tripentamer is the predominant species. Below we show the results of 2D classification of blob picked particles (classes sorted by particle number; obvious junk classes excluded for clarity). There is one class that suggests a pentamer, but template picking with a pentamer template (based on ORF68) did not yield a pentamer class.

      Additionally, as we describe in the results section and show in Supplementary Fig. 6a, further processing of the consensus UL32 map showed that 60% of particles formed a complete tripentamer (i.e., 15-mer) while other the remaining 40% formed incomplete tripentamers, missing one or more protomers (e.g., 17% of particles formed a 14-mer).

      Was symmetry applied, particularly for the tripentamer that appears to have C-3 symmetry? This is in materials and methods but not clear why it isn't mentioned when describing the structure determination and results.

      No symmetry was applied in the reconstruction for either UL32 or UL52. While we previously noted this in the methods section and in Supplementary Table 1, we have added this information to the results section (Line 169-170), the Fig. 3 legend, and cryo-EM processing figures (Supplementary Figures 2, 5, 6) for clarity.

      2) Throughout the paper, the authors use the word "remodel" to describe structural differences between orthologs. However, this word usually carries the implication of conformational rearrangement within a protein, and not across orthologs. Please consider a different description.

      We agree with the reviewer and have removed the term "remodel" throughout the manuscript text (i.e., Lines 116, 118, 120, 122, 302, 306) and from Supplementary Figures 1, 3, and 5.

      3) Figure 2F is confusing and difficult to interpret. It seems that the main point is that these interfaces are conserved, which might be more easily displayed as a standard sequence conservation score mapped onto the structure. I'm also not sure that this figure is necessary as a main figure and could be supplemental.

      We agree that the conservation could also be shown this way and have added labels to universally conserved residues of the protomer interface to Supplementary Fig. 1b, c. We have also moved Fig. 2f to the supplement (now Supplementary Fig. 2g).

      • 4) The authors write "UL32 bound to the shortest probe tested (10 bp, Supplementary Fig. 4a)." This implies that ONLY the shortest probe is bound and that others are not bound. Consider rephrasing.*

      We have rephrased to clarify at all probes tested, included the shortest, bound DNA (Line 153).

      • 5) Frustum is misspellt. ;)*

      Thank you. Spelling has been corrected (Line 185).

      6) In the discussion, the authors speculate that the variability of the outer surface is due to "virus- or host-specific interactions". I'm confused by "host-specific interactions", because the host is the same for all three viruses. Perhaps the authors mean that the different accessory factors could interact with different host factors? If so, are the authors making a Red Queen argument? If so, it'd be pretty cool to do dN/dS analysis to test that hypothesis.

      The reviewer is correct in that all three viruses (HSV-1, HCMV, KSHV) infect the same host; however, they replicate in different cell types, which could potentially express different host factors. We have no evidence to support this hypothesis and intended to propose that UL32 and UL52 may be interacting/co-evolving with other viral factors required for genome packaging. We have clarified Line 308 to generalize that "these regions are involved in virus-specific interactions".

      To me, this window into evolution of this factor is the biggest advance of the work, and tbh I felt that the authors could lean into this a bit more in the discussion section. Are there any differences in the packaging mechanisms of the different herpes families that can be related to their different behavior? Any other molecular evolution analyses (e.g. dN/dS ratio analysis) that could inform their study?

      We agree that understanding the evolution of the packaging accessory factor is an interesting future area of research. There are differences in capsid structure and occupancy of capsid-associated factors across the herpesvirus family (PMID: 34696343). However, we lack a mechanistic (or structural) understanding of viral genome packaging components across the herpesviruses, raising the possibility that there are differences in packaging mechanisms.

      Interestingly, the further diverged alloherpesviruses and malacoherpesviruses (other families in the order Herpesvirales) do not appear to encode a factor with similar predicted structure to the Herpesviridae packaging accessory factor (PMID: 41902279). It is unclear how the mechanism of packaging differs in the Orthoherpesviridae and whether replication in mammalian/avian/reptilian cells places additional evolutionary pressure on the viral genome packaging mechanism.

      Reviewer #3

      Major comments

      *1) [I]t is not clear whether the structures presented in the manuscript reflect those produced during HCMV or HSV-1 infection. *

      We agree with the reviewer that it is important to consider to what extent purified biomolecules resemble their in vivo counterparts. This criticism can be applied to any ex situ structural analysis. However, our experimental structures allowed us to make testable observations, including the correct assignment of structurally important zinc fingers and the identification of functionally important residues in the central channel.

      2) HCMV UL52 was presented to form two distinct structures, a 3-mer and a 4-mer (Fig. 2a). However, the authors acknowledge that the 3-mer is actually a 4-mer when the threshold for the cryo-EM map is lowered. The density is also visible in the PDB validation report for the 3-mer; EMD-74418.

      Reviewers #1 and #2 were also curious about the 3-mer. As described above, we performed additional analysis that showed that the original 3-mer map was a mixture of 3-mer and 4-mer states. We have updated Fig. 2a, Supplementary Fig. 2, Supplementary Fig. 3, Supplementary Table 1, Supplementary Movie 1, EMDB and PDB depositions, and removed the discussion of the weak protomer in the 3-mer map from the results section.

      *Given that ORF68, BFLF1, and UL32 (Didychuk et al., 2021) form complete pentamer rings, with BFLF1 forming stacked rings, it would seem odd for a protein with conserved function to deviate from a pentamer configuration, suggesting that the structures reported do not reflect the natively produced and functional protein. *

      We agree that this is a surprising finding; we initially anticipated that UL32 and UL52 would also form stable pentameric rings. While this study does not resolve a complete mechanism for this factor, it does provide the first structural evidence for the implications of their poor sequence conservation and lack of complementarity.

      Furthermore, this is not the first example of a conserved herpesvirus factor that possesses different oligomeric states across different subfamily homologs. As mentioned in the discussion, herpesvirus encode a sliding clamp processivity factor (HSV-1 UL42/HCMV UL44/KSHV ORF59) that shares a common PCNA-like fold, but which has varied oligomeric state across these herpesviruses.

      *3) Unlike ORF68 (Didychuk et al., 2021) and UL32 (Suppl. Fig. 4), dsDNA binding experiments were not performed with UL52. Could the partial pentamers simply be poorly formed due to expression in insect cells (mammalian cells were used for protein purification in Didychuk et al., 2021), absence of dsDNA, or inappropriate buffer conditions? Moreover, were the EM grid and vitrification parameters optimized? Grid geometries and chemistries can have profound effects of protein stability especially in the context of the air-water interface, leading to degradation of protein complexes (Glaeser, 2018; D'Imprima et al., 2019). Does UL52 form complexes with dsDNA? Data are shown for the HSV-1 packaging accessory factor. Perhaps dsDNA would stabilize the UL52 pentamer. *

      We have purified ORF68 and homologs from both human and insect cell expression systems, and do not observe changes in oligomeric behavior. We find that ORF68 purified as a stable pentamer from human cells (Didychuk eLife 2021) and from insect cells (this work). We have also recombinantly expressed and purified UL32 from human cells. UL32 was largely monomeric after strep affinity purification (chromatogram below, unpublished), as we report from insect cells (this work, Fig. 1c). We switched to insect cell expression systems because of the easier scalability.

      Our SEC-MALS data (Fig. 1d) shows that purified UL52 does not oligomerize into a pentamer in solution, so the observed sub-pentameric (3-mer/4-mer) assemblies are unlikely to be an artifact of cryo-EM freezing conditions or the air-water interface. We have not tested if UL52 forms complexes with dsDNA, although it likely does; it is possible that this interaction would stabilize a pentamer.

      4) In Didychuk et al., 2021, HSV UL32 is shown to form pentameric rings; negative stained 2D class averages were generated from tagged protein (twin strep tag), produced in mammalian cells (HEK293T), and not purified using size exclusion chromatography. In the present study HSV UL32 was not observed to form pentameric complexes "We first attempted to visualize the pentameric species by negative stain electron microscopy but were unable to identify particles of the expected dimensions." However, it is not clear why this was the case. If the pentameric structures were readily produced in previous experiments, why was cross-linking needed in the current study? As such, the tripentamer complexes seem artifactual in nature.

      While a sufficient number of particles were observed in a pentameric state to do 2D class averages in the eLife paper, this was not the dominant state. The results we report in this work are consistent with those reported in the eLife paper. Reviewer #2 (comment #1) was also concerned about the possibility of a crosslinking artifact: we reproduce our response below:

      "Crosslinking is a commonly used technique to stabilize complexes that are observed through other means but do not survive the cryo-EM vitrification process. In an EMSA experiment (Supplementary Fig. 4a), UL32 binds 30 bp DNA and migrates slower than when bound to a 10 bp probe, consistent with formation of a supra-pentameric complex. The samples in the EMSA gels are not crosslinked. Additionally, an SDS-PAGE gel of the crosslinked product used for EM showed tight bands, supporting specific crosslinking (Supplementary Fig. 4b). These results suggest that crosslinking stabilizes a species that can form but is relatively unstable in solution."

      We have updated Line 148 to clarify this. We have also included a negative stain micrograph, below, in which UL32 pentamers (purified from insect cells) are visible in the absence of crosslinking.

      5) Although the data presented in Fig. 4b suggest that interface residues, K532 and C535, might play a role in the formation of the tripentamer and have a minor role in HSV-1 replication, these experiments are incomplete. Single mutations are needed for each residue to assess their individual contribution to tripentamer formation, evidence for a loss of tripentamer formation is needed, and evidence for protein expression is needed.

      We agree that we have not unambiguously defined the role of the tripentamer, the precise contributions of residues K532 and C535, or defined the contribution of the tripentamer to HSV-1 viral replication. We seek to report this novel structure to lay the basis for future mechanistic work. Reviewer #2 (comment 1) also questioned the role of these residues in HSV-1 replication, and we addressed this by modifying the title of the results section (Line 216) to state that "Residues at the tripentamer interfaces contribute to infectious virion production in HSV-1" as well as Line 246 and 253 to indicate that the residues play a role in the viral life cycle.

      Please refer to Supplementary Fig. 7e for a western blot showing that these mutants do not impact UL32 expression. We included explicit references to UL32 expression on Lines 239 and 288.

      *6) In the previous negative stain electron micrographs reported by Didychuk et al., 2021, were the higher order tripentamer complexes seen? *

      We did not observed tripentamers in the Didychuk et al. 2021 negative dataset. Tripentamer formation may be concentration dependent. Negative stain EM carried out at nanomolar concentrations would likely cause dissociation of tripentamers, but cryo-EM and EMSA in our work were carried out at micromolar concentrations and were able to capture the higher order tripentamer.

      • 7) Formation of disulphide bonds between cysteine residues in vitro is not indicative of complexes forming in vivo during replication. What evidence is there for disulphide bond formation between packaging accessory factor pentamers for KSHV, EBV, and LCMV? In the present study, the disulphide bond could form due to proximity as a result of the cross-linking and the presence of molecular oxygen rather than a bona fide enzyme catalysed reaction during herpesvirus replication to generate packaging accessory factor tripentamers. *

      We agree that it is unlikely that disulfide bonds form during infection and have removed this speculation from the manuscript (Line 343-346).

      8) The DNA densities in Suppl. Fig. 6e to 6g are curious. As noted by the authors, the 30mer dsDNAs do not traverse through the central cavity of the pentamer. They appear to make contact with neighboring pentamers, again suggesting that these complexes are artefacts from cross-linking. This should be discussed more thoroughly.

      Please refer to above discussion of crosslinking and Supplementary Fig. 4.

      9) Previously proposed functional roles for ORF68 include a scaffold for terminase assembly, association of the terminase with the portal, generation of initial free ends, or coordination with other replication machinery (Didychuk et al., 2021). Presuming that the new structures for HCMV UL52 and HSV-1 UL32 occur naturally, how do they fit with the previously proposed functional roles of the herpesvirus packaging accessory factor? A more in-depth discussion of this would be valuable.

      The common core fold and pentamer/pentamer-like assemble are common features, as is the conserved, positively-charged central channel. We have added additional discussion of this.

      *Minor comments A lack of page numbers and line numbers made reviewing this manuscript more challenging than necessary. *

      We have included page numbers and line numbers in the revised manuscript.

      *As noted in the 'General comments' section above, ORF68 (3.37Å) and BFLF1 (3.60Å) both form pentamers (Didychuk et al., 2021) and were produced in mammalian systems HEK293T cells. Protein purification in the present study was performed in insect (SF9 or High Five) cells. Does this affect complex stability. Also, the tag was retained for UL32 in Didychuk et al., 2021; could this provide stability of the pentamer in the original studies? *

      As discussed above, we have no evidence to suggest that expression in human vs. insect cell expression systems dramatically changes oligomerization behavior (Reviewer #3, comment 3). N-terminal purification tags were also retained in this study for structural work but were removed for SEC-MALS, which shows that UL32 is likely in concentration dependent equilibrium between (unstable) pentamers and monomers.

      Suppl. Fig. 3 is missing.

      We apologize for this oversight and have included Supplementary Fig. 3.

      *"UL52 has two regions remodeled" The use of the word 'remodeled' is not appropriate in this context as it implies a single protein can form two shapes under different conditions rather than distinct structures between two disparate proteins; UL52 compared to ORF68. This should be rephrased. *

      This was also noted by reviewer 2, and we have removed the term "remodel" throughout the manuscript text (i.e., Lines 134, 138, 140, 337, 341) and from Supplementary Figures 1, 3, and 5.

      *What is the density in the central core of UL52 (Fig. 2a; Suppl. Fig. 2e)? Was any form of focused classification performed to establish the identity of the density within the central pseudocavity? *

      As noted in the manuscript, this density could be which could be attributed to co-purified protein or nucleic acid, or part of the unresolved, negatively charged loop (residues 82-181) interacting with the positively charged central channel. We have done additional analysis of the central channel density (3D classification with a focus mask) and do not resolve any distinct densities, suggesting that the density is very dynamic.

      *Does UL52 bind to dsDNA? To support the hypothesis that the herpesvirus packaging accessory factor has conserved functions across the three subfamilies dsDNA binding experiments should be performed. *

      We have not done this experiment. We think that demonstrating this finding for two of the three herpesvirus subfamilies is sufficient.

      There is no discussion about how these data relate to the previous functional model for ORF68 presented in Didychuk et al., 2021. Do the new data alter the previous functional models?

      The precise mechanistic contribution of the packaging accessory factor remains unknown, and our data do not delineate between the proposed potential roles described in Didychuk et al. 2021. Importantly, our structural information, demonstration of pentameric ring formation, and significance of the positively charged central channel show that the core function of this factor is likely conserved across the virus family. This was not known before our work.

      *There are some interesting grammatical phrases; please address throughout the manuscript. One example - "...a notable shared aspiration..." Proteins do not have aspirations. Please use a more formal scientific statement. *

      We have updated the language on Line 327.

      *Fig. 4b - Statistical analyses missing. Please provide. *

      Fig. 6c - Statistical analyses are missing. Please provide. Protein folding/expression data missing; see Fig. 5C showing mutations that result in poor protein expression.

      Suppl. Fig. 7f - Statistical analyses absent.

      Statistical analysis of the viral complementation in Figs. 4b and 6c has been included. Note that the viral yields reported in Supplementary Fig. 7f were used to calculate complementation efficiency in Figs. 4b and 6c. Protein expression of mutants shown in Fig. 6c was previously included in Supplementary Fig. 7e and is referenced on Lines 288 and 293.

      *Suppl. Fig. 2 and 5 - FSC curves have oddities, especially in the corrected curves. The cryo-EM resolution estimates calculated by CryoSPARC for the UL52 '3-mer' and 4-mer, and UL32 tripentamer are likely overestimated. In the PDB validation files each of the deposited structures has a warning for the resolution estimate "The value from deposited half-maps intersecting FSC 0.143 CUT-OFF 4.31 differs from the reported value 3.32 by more than 10 %", suggesting that the resolution estimates are inaccurate. The authors should provide a resolution estimate using loose masks and generate FSC curves using another software program such as RELION's postprocess to provide resolution estimates. *

      Thank you for bringing this to our attention. The differences in the resolution estimates are a known issue and are highly influenced by the tightness of the mask. In the revised manuscript we have updated the FSC curves to not include auto-tightened masks and revised our resolution estimates. This slightly changed the resolution to 3.29 Å for both UL52 3-mer and 4-mer and to 3.09 Å for the UL32 consensus map. Please also see the local resolution estimation maps in Supplementary Figures 2e and 5e for an illustration of the range of resolutions in each map.

      Suppl. Fig. 6f and 6g - Is there any visible density that might resemble the EGS crosslinking reagent?

      We do not expect to observe density for EGS due to the long flexible linker (~16 Å) between the two reactive groups.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      In this manuscript, the authors investigate the relationship between genetic codes and their robustness to single-point mutations. They construct ten alternative genetic codes by reassigning nine codons to Leu, Ser, or Ala, and assess mutational robustness using three reporter proteins subjected to error-prone PCR. This represents an interesting experimental approach to addressing the hypothesis that the standard genetic code is optimized for mutational robustness.

      We sincerely thank the reviewer for the positive evaluation of our experimental approach. We are encouraged that the reviewer recognizes the value of constructing multiple non-standard genetic codes in vitro and using them to experimentally examine the relationship between genetic code arrangement and mutational robustness. In the revised manuscript, we have further clarified the scope of our experimental system and the interpretation of the results, particularly emphasizing that our conclusions concern the mutational robustness of individual reporter protein activity measured in an in vitro translation system.

      Major comment:

      While I find the experimental design valuable, I am not fully convinced by the authors' conclusion that "alterations of the genetic code within the ranges explored in this study have no significant effect on mutational robustness". The current analysis is based on the functional output of three individual reporter proteins. Given that cellular systems involve far more complex interactions, it would be more appropriate to limit this conclusion to mutational robustness at the level of individual protein activity, rather than making broader generalizations.

      We thank the reviewer for this important comment. We agree that our original wording was broader than what can be directly supported by the present experiments. Because our analysis is based on the functional outputs of three individual reporter proteins translated in a reconstituted in vitro system, the results do not directly address mutational robustness at the level of the cellular system, protein interaction networks, or organismal fitness.

      Accordingly, we have revised the manuscript to limit our conclusion to the mutational robustness of individual reporter protein activity. In the revised Abstract, Results, and Discussion, we now state that within the experimentally tested range of non-standard genetic codes, we did not detect a dependence of the mutation-induced decrease in reporter protein activity on mutational cost. We have also added a statement in the Discussion noting that cellular systems involve many additional layers, including protein–protein interactions, metabolic networks, quality-control systems, and growth selection, and that whether genetic code arrangement affects robustness at these higher biological levels remains an important question for future work.

      Specifically, we have added this explanation and the new experiment to the revised manuscript as follows.

      Abstract

      “This result provides direct experimental evidence that mutational robustness does not significantly change in individual reporter protein activity when the genetic code is altered within the range of mutational cost tested in this study…”

      Introduction

      “Random mutations decreased reporter protein function at similar levels across all genetic codes examined, implying that alterations of the genetic code within the ranges explored in this study have no significant effect on mutational robustness of individual protein activity.”

      Result

      “Taken together, these results indicate that mutational robustness of individual reporter protein function did not substantially differ among the genetic codes…”

      Discussion

      “…suggesting that mutational robustness of protein activity remained largely unchanged within at least the ranges of mutational cost tested in this study. It should be noted that this conclusion is limited to the activity of individual reporter proteins translated in a reconstituted in vitro system. Therefore, whether similar trends would be observed at the level of cellular fitness or long-term evolution remains an open question.”

      Specific comments

      (1) tRNA modification and expression efficiency (Page 5, line 131)

      The authors attribute the observed inefficiency to the lack of chemical modifications in the tRNAs used. However, gene expression efficiency can also be strongly influenced by DNA sequence design. To better support this claim, it would be helpful to compare luciferase activity when expressed using native E. coli tRNAs. This comparison could clarify whether the observed effects are due to tRNA modification status or other sequence-dependent factors.

      We thank the reviewer for this important suggestion. We agree that the translation efficiency of NanoLuc templates with 21-, 32-, and 46-codons may be affected not only by the chemical modification of tRNAs but also by sequence-dependent factors, such as codon context and mRNA structure.

      To examine this possibility, we performed an additional comparison using native E. coli tRNAs in the tfPURE system. When the NanoLuc templates encoded with 21, 32, or 46 codons were translated using native E. coli tRNAs, the observed luminescence values were 1.2 × 10<sup>10</sup>, 0.78 × 10<sup>10</sup>, and 0.60 × 10<sup>10</sup>, respectively. Thus, the 46-codon NanoLuc template showed lower activity than the 21- and 32-codon templates even with native tRNAs, indicating that sequence-dependent effects indeed contribute to translation efficiency.

      However, the difference among these templates with native E. coli tRNAs was within approximately two-fold. This effect was much smaller than the marked decrease observed when the 46-codon template was translated using the in vitro prepared 46 tRNAs SGC system. Therefore, while sequence-dependent effects cannot be excluded, the inefficient translation in the reconstructed 46 tRNAs SGC is likely to be mainly attributable to the limited functionality of unmodified tRNAs decoding NNA codons.

      We have revised the manuscript to clarify this interpretation and have added the new comparison using native E. coli tRNAs.

      “We also examined whether the lower translation efficiency of the 46-codon NanoLuc template could be explained by sequence-dependent effects, such as codon context or mRNA structure. When the 21-, 32-, and 46-codon NanoLuc templates were translated using native E. coli tRNAs in the tfPURE system (Figure 1–figure supplement 2), the 46-codon template showed lower activity than the 21- and 32-codon templates; however, this difference was within approximately two-fold. Accordingly, we decided to use only the 32 codons used in near-SGC (i.e., excluding NNA codons) in the subsequent construction of non-standard genetic codes.”

      (2) Discrepancy between expression level and activity (Figure S7 vs Figure S8).

      Although GAL expression levels appear similar across different genetic codes (Figure S7), their activities differ substantially (Figure S8), even in the low-mutation library. This discrepancy warrants further investigation. Possible explanations include differences in protein folding efficiency or translational error rates, as mentioned by the authors in the main text.

      To address this, the authors could analyze the protein products using mass spectrometry. If this is not feasible due to low expression levels, alternative approaches such as SDS-PAGE (e.g., with radiolabeling or Western blotting) would still provide valuable information. Additionally, comparing activity after in vitro refolding could help distinguish between folding defects and sequence-level errors. While I understand that the primary aim of this study is to compare mutational robustness across genetic codes, discussing these observations would significantly enhance the mechanistic insight of the work.

      We agree that the discrepancy between similar GAL expression levels and different GAL activities across genetic codes is important for interpreting the results.

      In our experiment, GAL protein amounts were quantified using a C-terminal HiBiT tag. Because the HiBiT tag was fused to the C-terminus of GAL, this assay indicates that the amount of C-terminally completed GAL products did not differ substantially among genetic codes. However, we agree that this assay does not evaluate the sequence fidelity, amino acid misincorporation patterns, or folding state of the translated products. Therefore, the observed differences in GAL activity despite similar HiBiT signals may reflect genetic code-dependent differences in translational error rates, amino acid misincorporation, protein folding efficiency, or other effects on the fraction of catalytically active protein.

      We have revised the Discussion to explicitly describe this interpretation and to clarify that detailed mechanistic dissection of these baseline activity differences, for example by mass spectrometry, SDS-PAGE/Western blotting, or refolding analysis, is an important future direction but beyond the scope of the present study. We also clarified that the main analysis in this study uses the ratio of activity from the high-mutation library to that from the corresponding low-mutation library within each genetic code.

      We have added this explanation to the revised manuscript as follows.

      “Although protein amounts quantified by the HiBiT tag were comparable among genetic codes, GAL activities differed substantially. This indicates that the activity differences among genetic codes were not primarily attributable to differences in the amount of C-terminally completed translation products. The HiBiT assay does not provide information on the fraction of catalytically active protein, including sequence fidelity or folding state, and therefore cannot distinguish among these possibilities. Detailed characterization of translated products by mass spectrometry would provide further mechanistic insight into how individual non-SGCs affect protein quality. However, the primary objective of the present study was to compare mutation-dependent activity loss across genetic codes. Therefore, we evaluated this effect by normalizing the activity of the high-mutation library to that of the corresponding low-mutation library within each genetic code.”

      (3) Protein expression analysis for additional reporters.

      Since protein expression levels are critical for interpreting reporter activity, similar analyses should also be performed for luciferase (Luc) and mSG in both high- and low-mutation libraries. This would ensure that differences in activity are not confounded by variations in protein abundance.

      We agree that protein abundance is an important factor for interpreting reporter activity. In this study, we performed HiBiT-based protein quantification for GAL because GAL showed the largest variation in absolute activity among genetic codes, even in the low-mutation library. This analysis showed that the amount of C-terminally completed GAL products was broadly comparable among genetic codes and between low- and high-mutation libraries, indicating that the observed GAL activity differences were not primarily attributable to differences in total protein abundance.

      For all three reporters, our main analysis was based on the ratio of activity from the high-mutation library to that from the corresponding low-mutation library within each genetic code. This normalization was intended to evaluate mutation-dependent activity loss while reducing the influence of code-specific baseline differences in expression level or protein quality. We believe that the data are sufficient to evaluate the effect of mutations on protein activities. Nevertheless, we agree that protein quantification for Luc and mSG would provide useful information regarding variation in the baseline levels of reporter activity, and this is an important direction for future work.

      Reviewer #2 (Public review):

      Summary:

      The study addresses the long-standing question in molecular biology and genetics: why has nature selected the current genetic code (SGC, or standard genetic code)? The authors have tested 'error minimization theory', one of the prevailing hypotheses to explain this. Their approach is to create a minimum genetic code (MGC) and its variants (3^9 theoretical possible codes). Using three parameters to quantify the effect of mutations (Polarity, volume, and hydropathy), they computationally test the cost of these genetic codes (3^9) by simulations. Finally, they test this cost experimentally using an in vitro translation system with 10 select genetic code variants with a range of costs (low to high). They use three randomly mutated reporter genes for this purpose - beta-galactosidase, luciferase, and mSG. They find no correlation between the cost of the genetic code and the reporters' output. Based on these observations, they suggest that error-minimization theory may not explain the current egocentric code.

      The question they are asking is very exciting, and their approach is solid. The authors are very careful in their analyses and conclusions.

      We sincerely thank the reviewer for the positive assessment of our study and for the helpful suggestions. We are encouraged that the reviewer found the question exciting and the approach solid. In the revised manuscript, we have clarified the rationale for using the MGC/near-SGC framework, added further analyses and explanations of the mutational cost calculations, and revised the wording of our conclusions to more explicitly define the scope and limitations of the present experimental system.

      (1) The rationale for using MGC instead of SGC: It is unclear why the authors rely on the MGC for this analysis when the central question concerns the SGC. If the goal is to evaluate whether the SGC minimizes mutational cost, a more direct approach would be to generate alternative variants of the SGC itself and compare their mutational cost distributions. At present, it is difficult to assess whether conclusions drawn from this comparison are fully relevant to the stated biological question.

      We thank the reviewer for this important comment. We agree that directly constructing alternative variants of the SGC by changing amino acid assignment from SGC would be the most straightforward approach to testing whether the SGC minimizes mutational cost. However, this approach is currently not feasible in our reconstituted translation system for two reasons.

      First, our attempt to construct a 46-tRNA SGC-like system revealed that translation using the 46-codon NanoLuc template was approximately 100-fold less efficient than translation using the MGC or near-SGC (Fig. 1). This low activity likely reflects inefficient decoding of NNA codons by in vitro-prepared tRNAs, which lack native post-transcriptional modifications. Because this system did not provide sufficient translational activity for systematic reporter assays, we restricted subsequent experiments to the 32-codon near-SGC framework, excluding NNA codons. We now describe this technical limitation more explicitly in the revised manuscript.

      Second, the MGC framework provides vacant codons that can be reassigned by adding anticodon-variant tRNAs. This feature is essential for constructing multiple genetic code variants in parallel under controlled in vitro conditions. We, therefore, constructed the near-SGC-based non-SGC by adding each tRNA variant to the MGC as an experimentally tractable model system to verify whether differences in genetic code arrangement affect mutation-induced decreases in reporter protein activity.

      We have added this explanation to the revised manuscript as follows.

      “We first established a minimal genetic code, composed of 21 tRNAs with vacant codons, which allows multiple alternative codon assignments to be introduced under otherwise comparable translation conditions.”

      Despite this technical limitation, we believe that the central conclusion of this study—that mutational robustness in individual reporter protein activity does not change significantly when the genetic code is altered within the range of mutational costs tested here—remains well-supported by the present results.

      (2) The mutational cost analysis appears biologically oversimplified because all amino acid substitutions are treated equivalently. The analysis assumes that all mutations contribute equally to fitness consequences, which does not reflect biological reality. In natural proteins, the impact of an amino acid substitution depends strongly on its structural and functional context. For example, substitutions affecting catalytic residues, ligand-binding interfaces, phosphorylation sites, or other regulatory motifs can severely impair protein function even when associated changes in polarity, hydropathy, or volume are minimal. Conversely, substitutions in structurally permissive or functionally dispensable regions may have little or no measurable effect despite larger physicochemical differences. Therefore, changes in polarity, hydropathy, and volume alone do not necessarily predict functional consequences.

      We agree that the mutational cost used in this study is a simplified measure and does not capture the full biological complexity of amino acid substitutions. As the reviewer pointed out, the functional consequence of a substitution depends strongly on its structural and functional context, including whether the affected residue is involved in catalysis, ligand binding, protein–protein interactions, regulatory motifs, folding, or structurally permissive regions.

      In this study, we used physicochemical-property-based mutational costs because this type of definition has been widely used in classical formulations of the error minimization theory. Our aim was therefore not to construct a comprehensive predictor of protein fitness effects, but to experimentally test whether the conventional theoretical cost metrics used to discuss genetic code optimality are reflected in the average mutation-induced decrease in reporter protein activity. We have now clarified this rationale in the revised manuscript.

      “It should be noted that this conclusion is limited to the activity of individual reporter proteins translated in a reconstituted in vitro system. Therefore, whether similar trends would be observed at the level of cellular fitness or long-term evolution remains an open question.”

      (3) It is not clear why they increased the concentration of the two tRNAs in near-SGC. Have they maintained the same tRNA concentrations in experiments explained in Fig 5 for all 10 genetic codes tested?

      We apologize that the rationale for increasing the concentrations of tRNA<sup>Val</sup><sub>CAC</sub> and tRNA<sup>Arg</sup><sub>CCU</sub> was not sufficiently clear in the original manuscript. As we wrote in the previous manuscript, “To improve translation efficiency with near-SGC, we focused on two tRNA concentrations (tRNA<sup>Val</sup><sub>CAC</sub> and tRNA<sup>Arg</sup><sub>CCU</sub>), which were suggested to have low activities in a previous study (Iwane et al., 2016),” we tested whether increasing their concentrations would improve translation efficiency. As shown in Figure 1–figure supplement 1, NanoLuc activity increased as the concentrations of these two tRNAs were raised and used at 100 ng/µL for tRNA<sup>Val</sup><sub>CAC</sub> and tRNA<sup>Arg</sup><sub>CCU</sub> in the optimized near-SGC, referred to as near-SGC (RV), and in all subsequent experiments. Additional anticodon-variant tRNAs required for each non-SGC were used at optimized concentrations determined from Figure 2–figure supplement 1. For each genetic code, the same tRNA composition and concentrations were used for the low- and high-mutation libraries (See Supplementary Table S7). To clarify this point, we added the sentence, “The increased concentrations of these two tRNAs were used in all the subsequent experiments,” in the corresponding part.

      Reviewer #3 (Public review):

      In this manuscript, Miyachi and Ichihashi investigate whether the arrangement of the genetic code affects mutational robustness. Using an in vitro minimal genetic code with vacant codons, they constructed 10 non-standard genetic codes by reassigning Ala, Ser, and Leu, generating codes with replacement costs that were generally higher than those of the standard genetic code across several amino acid property measures. They then tested how random mutations affected the activity of reporter proteins translated under these altered codes. Although error minimization theory predicts that higher-cost codes should make mutations more harmful, the authors report that protein function declined to a similar extent across all codes examined, suggesting that mutational robustness remains largely unchanged within the range of genetic code alterations tested here.

      Strengths:

      This is an interesting study that investigates one of the most fundamental and intriguing questions in molecular evolution: the emergence of the genetic code, which is nearly universal across nature. The in vitro approach is a powerful aspect of the work and provides an opportunity to examine this phenomenon experimentally at a depth that has previously been inaccessible.

      Weaknesses:

      However, the authors' use of random mutation libraries has certain limitations that prevent the study from realizing its full potential to uncover the mechanisms governing the molecular evolution of the genetic code.

      We sincerely thank the reviewer for the positive evaluation of our study and for recognizing the strength of the in vitro approach. We are encouraged that the reviewer considers this system a powerful way to experimentally address the emergence of the genetic code.

      We also appreciate the reviewer’s constructive comments regarding the limitations of random mutation libraries. We agree that pooled random libraries do not allow us to assign functional effects to individual mutations or to fully uncover the molecular mechanisms underlying mutational robustness. In the revised manuscript, we therefore clarify that our conclusions concern the library-averaged effects of random mutations on individual reporter protein activity, rather than the effects of specific mutations or cellular-level fitness. To address this limitation, we have added explanations of the scope and limitations of the present approach.

      (1) Statistical analyses are missing for several of the manuscript's main claims. This issue applies throughout the paper, including, but not limited to, Figures 1D, 2B, 4B-D, and 5B.

      We thank the reviewer for this important comment. We agree that statistical analyses are necessary to support the major claims of the manuscript. We have therefore added statistical analyses appropriate for the purpose and experimental design of each figure.

      For Fig. 1D, we performed one-way ANOVA followed by Tukey’s post hoc test on NanoLuc activity to compare translation efficiencies among the MGC, near-SGC, near-SGC (RV), and SGC conditions. This analysis showed a significant overall difference among conditions (one-way ANOVA, p < 0.0001). Tukey’s post hoc test showed that near-SGC was significantly lower than MGC, that near-SGC (RV) significantly improved near-SGC translation, and that near-SGC (RV) was not significantly different from MGC. In contrast, the 46-tRNA SGC remained significantly less efficient than near-SGC (RV). We have summarized the major comparisons in Supplementary Table S8.

      For Fig. 2B, we compared NanoLuc activity between the 21-code control and the corresponding 21+1-code condition for each codon reassignment using Welch’s t-test on luminescence. This analysis was added to statistically support whether each anticodon-variant tRNA increased NanoLuc translation from the corresponding reassigned template. The statistical results are summarized in Supplementary Table S9.

      For Fig. 4B–D, we converted mutation rates per base to estimated numbers of mutations per gene and performed Spearman’s rank correlation analysis to evaluate whether reporter activity decreased monotonically with increasing mutational load. This analysis showed strong negative monotonic trends between mutation rate (estimated mutation number) and reporter activity for all three reporters (ρ = −0.90 to −1.00), supporting that the random mutation libraries reduced protein activity in a mutation-load-dependent manner.

      For Fig. 5B, replicate-level data were available for GAL, and we therefore performed two-way ANOVA using genetic code and mutation level as factors. This analysis detected significant main effects of genetic code and mutation level, indicating that GAL activity differed among genetic codes and decreased in the high-mutation library. However, no significant interaction between genetic code and mutation level was detected, indicating that the magnitude of mutation-induced activity reduction was not strongly code-dependent under the conditions examined.

      Finally, because the central claim of Fig. 5C, 5E, and 5G is that mutational cost does not systematically predict mutation-induced activity loss, we performed Spearman’s rank correlation analysis between each mutational cost metric and the high-/low-mutation activity ratio. No significant correlations were detected for any reporter or cost metric (Spearman’s ρ = −0.23 to 0.25), supporting the conclusion that mutational cost did not show a detectable monotonic relationship with mutation-induced activity loss within the tested range.

      We have added these statistical analyses to the revised manuscript. The following sentences were added to the figure legends:

      Fig. 1

      “Statistical comparisons in (D) were performed using one-way ANOVA followed by Tukey’s post hoc test on NanoLuc activity; major comparisons are summarized in Table S8.”

      Fig. 2

      “For each template, NanoLuc activity in the 21-code and corresponding 21+1-code conditions was compared using Welch’s t-test on luminescence. Statistical results are summarized in Table S9.”

      Fig. 4

      “Spearman’s rank correlation coefficients were ρ = −0.90 for GAL, ρ = −1.00 for Luc, and ρ = −1.00 for mSG”

      Fig. 5

      “For GAL activity in (B), two-way ANOVA was performed using genetic code and mutation level as factors. Significant main effects of genetic code and mutation level were detected (both p < 0.0001), whereas their interaction was not significant. For (C), (E), and (G), Spearman’s rank correlation analysis was performed between each mutational cost metric and the high-/low-mutation activity ratio. Statistical details are summarized in Table S10.”

      (2) In Figure 2A, the authors modify the NanoLuc gene by reassigning Ala, Leu, or Ser to new codons and elegantly show that the in vitro availability of the corresponding tRNAs is important for protein function. However, the functional importance of the specific modified positions within NanoLuc is not clear. As a result, it is difficult to determine what the expected consequences of these codon changes should be, which in turn limits the interpretation of the observed changes in protein activity. To improve the interpretability of this experiment, the authors should report exactly how many codons were modified in each variant and, ideally, examine the effect of progressively increasing the number of reassigned codons.

      We agree that the exact positions and numbers of codon replacements should be clearly reported. In the revised manuscript, we have added a list of the modified amino acid positions. In brief, two Ala codons, three Ser codons, or four Leu codons were replaced with the target vacant codon; the modified positions were Ala16 and Ala120, Ser31, Ser49, and Ser150, and Leu32, Leu67, Leu144, and Leu170, respectively.

      We also agree that progressively increasing the number of reassigned codons would provide additional mechanistic insight. However, the purpose of Fig. 2 was to test whether each vacant codon could be decoded by the corresponding anticodon-variant tRNA to produce functional NanoLuc, rather than to analyze the positional contribution of each replacement. We previously performed such progressive codon replacement analysis for one reassigned codon, ACG, in a related study (Miyachi et al., 2025), and the results supported the same qualitative interpretation. Although we did not repeat this progressive analysis for all codons in the present study, we expect that the qualitative interpretation of Fig. 2 would not be substantially changed.

      We have revised the figure text to clarify the scope of the experiment and added the detailed codon replacement information.

      “(A) Schematic illustration of reassignment experiments. Translation with the original MGC and NanoLuc template is shown at the top for comparison. An example of Ala reassignment to the UUG codon is shown at the bottom. In this example, three Ala codons in the NanoLuc sequence were replaced with one type of vacant codon (e.g., UUG), generating a 21 + 1 (UUG-Ala) codon set. Similar reassignment experiments were performed for three amino acids (Ala, Ser, and Leu) and nine vacant codons. Specifically, two Ala codons (Ala16 and Ala120), three Ser codons (Ser31, Ser49, and Ser150), or four Leu codons (Leu32, Leu67, Leu144, and Leu170) were replaced.”

      (3) The calculations presented in Figure 3 raise an interesting conceptual question: why does the near-standard genetic code not exhibit the lowest cost? One possible explanation is that the standard genetic code evolved under multiple competing constraints and is therefore not expected to be optimal for any single cost metric, while still achieving strong overall performance. In this context, it would be informative if the authors combined the three cost measures into a single integrated index and examined whether the near-SGC performs more favorably when all three dimensions are considered together. Such an analysis could add important depth to the study.

      We agree that the near-SGC is not necessarily expected to minimize each individual cost metric, because the standard genetic code may reflect multiple competing physicochemical, translational, biosynthetic, and evolutionary constraints rather than optimization of a single property.

      To address this point, we added an integrated cost analysis combining the three physicochemical cost metrics, Cost<sub>PR</sub>, Cost<sub>MV</sub>, and Cost<sub>HI</sub>. Because these three metrics have different numerical scales, we normalized each metric before integration. We used two types of integrated indices.

      First, for each metric m 𝛜 {PR, MV, HI}, we calculated a min–max normalized cost,

      Where G denotes the set of 19,683 candidate non-SGCs generated by assigning Ala, Ser, or Leu to the nine vacant codon boxes. We then defined the integrated min–max cost as

      Second, we calculated a z-score-normalized cost for each metric,

      Where µ<sub>m,G</sub> and 𝜎<sub>m,G</sub> are the mean and standard deviation of Cost<sub>m<sub>norm</sub></sub> across the candidate non-SGCs. The integrated z-score cost was then defined as

      Using both integrated indices, the near-SGC ranked first when compared with all 19,683 candidate non-SGCs; in other words, no candidate non-SGC showed a lower integrated cost than the near-SGC. The integrated min–max cost of the near-SGC was 0.01525, whereas the lowest value among candidate non-SGCs was 0.12301. Similarly, the integrated z-score cost of the near-SGC was −2.47947, whereas the lowest candidate value was −1.90838.

      We have added this integrated cost analysis as Supplementary Figure 5–figure supplement 7. We have also revised the Discussion to note that the near-SGC does not necessarily minimize every individual physicochemical cost, but performs most favorably when PR, MV, and HI are considered comprehensively. This result is consistent with the idea that the standard genetic code may represent a compromise among multiple constraints rather than optimization of a single physicochemical property.

      “We consider that the cost ranges examined in this study represent substantial fractions, especially for MV and HI. Although the near-SGC did not necessarily exhibit the lowest cost for each individual physicochemical metric, this does not mean that it is unfavorable in the multidimensional cost space. Because the SGC may reflect a balance among multiple physicochemical constraints rather than optimization of a single property, we also calculated integrated cost indices by combining Cost_PR, Cost_MV, and Cost_HI after min–max normalization or z-score normalization. In both integrated indices, the near-SGC showed the lowest overall cost when compared with all 19,683 candidate non-SGCs (Figure 5–figure supplement 7), indicating that no candidate non-SGC exhibited a lower combined cost than the near-SGC when the three physicochemical properties were considered comprehensively.”

      (4) It is difficult to assess the consequences of the random mutations presented in Figure 4 on reporter gene function based solely on the reported "error rate/base" parameter. In particular, the x-axis in Figure 4B should be converted into the estimated number of mutations per gene. This would make the results more intuitive and would allow the reader to better evaluate the expected degree of disruption to protein function.

      We agree that the mutation rate per base alone does not provide an intuitive sense of the expected mutational burden for each reporter gene. We therefore added a second x-axis to Fig. 4B–D showing the estimated number of mutations per gene. This value was calculated by multiplying the mutation rate per base by the coding sequence length of each reporter gene.

      We retained the original mutation rate per base axis to preserve the direct link to the sequencing-based mutation rate measurement, while adding the estimated mutations per gene axis to improve interpretability. We have revised the figure and figure 4 legend accordingly.

      “The lower x-axis indicates the estimated number of mutations per gene, calculated by multiplying the mutation rate per base by the coding sequence length of each reporter gene.”

      (5) A central limitation of the random mutagenesis libraries used in Figure 5, which also underlie one of the manuscript's main claims, is that the exact mutations and their distribution across the reporter genes are not reported. In addition, protein activity is measured only at the level of the entire library, without directly linking individual mutations to their functional consequences. This substantially limits mechanistic interpretation. In my view, this issue can only be addressed convincingly if the authors test a set of defined variants carrying specific mutations and directly evaluate their functional effects.

      (6) Related to the previous point, in Figures 5C, 5E, and 5G, the authors present the ratio between low-mutation-rate and high-mutation-rate libraries. However, because each library contains a different collection of mutations, it is unclear what can be inferred from these comparisons. To overcome this limitation, the authors should assess the effects of altered genetic codes on specific, defined mutations rather than on heterogeneous mutation pools alone.

      (7) Along the same lines, in Figures 5C, 5E, and 5G, it is unclear why the effects of random mutations would be expected to correlate with the three calculated cost metrics, given that the positions, identities, and functional relevance of the mutations within the genes are not known. Without this information, the biological meaning of these correlations remains difficult to evaluate.

      We agree that using pooled random mutation libraries does not allow us to directly link individual mutations to their functional consequences. We also agree that testing defined variants carrying specific mutations would provide a more direct and mechanistic understanding of how each genetic code affects the functional impact of particular amino acid substitutions. However, the purpose of the present study was different from such a defined-variant analysis. Our aim was to experimentally test whether the conventional mutational cost metrics used in error minimization theory predict the average effect of random mutational loads on protein activity. Because these theoretical costs are themselves defined as average expected physicochemical effects over many possible single-nucleotide substitutions, we reasoned that pooled random mutation libraries provide an appropriate first experimental framework to evaluate whether such average-cost metrics are reflected in the average functional output of translated proteins.

      We agree that low- and high-mutation libraries do not contain identical sets of mutations. Therefore, the high-/low-mutation activity ratio should not be interpreted as the effect of the same individual variants before and after additional mutations. Rather, it represents the relative reduction in average activity caused by increasing the mutational burden in a heterogeneous mutation pool under each genetic code. We have revised the text to clarify this interpretation.

      We also agree that the positions, identities, and functional relevance of individual mutations are not resolved in this pooled assay. This limitation prevents us from assigning mechanistic effects to specific substitutions. At the same time, using a small set of defined variants would introduce its own selection bias, because the conclusions could strongly depend on which mutations and which protein positions were chosen. Therefore, we consider the random-library approach to be a useful first step for testing library-averaged effects, whereas systematically defined variant analysis or genotype-resolved activity assays will be necessary to reveal mutation-specific mechanisms in future studies.

      In response to the reviewer’s concern, we have revised the Discussion to explicitly limit our conclusion to library-averaged effects on individual reporter protein activity. We now state that this approach does not identify the functional effects of individual mutations and that future studies using defined variants or high-throughput genotype–phenotype mapping will be required to determine how specific substitutions contribute to genetic code-dependent mutational robustness.

      Result

      “To estimate the average activity reduction associated with increased mutational burden under each genetic code, we calculated the ratio of activity obtained from the high-mutation library to that from the corresponding low-mutation library and plotted this ratio against each of the three mutational costs (Fig. 5C).”

      Discussion

      “A further limitation of this study is that the reporter activities were measured at the level of pooled random mutation libraries. Therefore, the high-/low-mutation activity ratio used in this study should be interpreted as the relative reduction in average activity caused by increasing the mutational burden in a heterogeneous mutation pool, rather than as the effect of identical variants before and after additional mutations. This library-averaged approach was chosen because the mutational costs considered here are also defined as average expected physicochemical effects over many possible single-nucleotide substitutions. In addition, because the non-SGCs constructed in this study were generated by reassigning only Ala, Ser, and Leu, the detectable effects may depend on how frequently mutations involving these amino acids occur in each reporter gene and whether the affected positions are functionally important. If genetic code dependent effects are restricted to a small subset of deleterious variants, such effects may be masked in pooled activity measurements. Future studies using defined variants or high-throughput genotype–phenotype mapping assays will be required to determine the mutation-specific and position-specific mechanisms underlying genetic code dependent effects on protein function (Rozhoňová et al., 2024).”

      (8) For each mutagenesis library, the number of variants, the average number of mutations per variant, and the distribution of mutation positions should be reported clearly and transparently. These details are important for evaluating the strength of the conclusions.

      We agree that a more transparent characterization of the random mutagenesis libraries is necessary for evaluating the strength and limitations of our conclusions.

      In the revised manuscript, we have added the estimated number of mutations per gene to the Results section. This value was calculated by multiplying the mutation rate per base by the coding sequence length of each reporter gene. For the high-mutation libraries used in Fig. 5, the estimated numbers of mutations per gene were approximately 8.0 for GAL, 4.5 for Luc, and 3.3 for mSG. We also added position-wise mutation profiles along each reporter gene (Figure 4–figure supplement 2), in addition to the heatmap shown in the original manuscript. These analyses clarify the mutational burden of each library and show that mutations were broadly distributed across the analyzed regions (approximately 300 nt in the middle of each gene) of the reporter genes.

      Regarding the number of variants, the translation reactions were performed using 5 nM DNA template in a 5 µL reaction, corresponding to approximately 1.5 × 10<sup>10</sup> DNA molecules. However, this value represents the total number of DNA molecules introduced into the reaction and does not directly indicate the number of unique full-length sequence variants, because multiple molecules can share the same genotype, and our sequencing analysis was designed to quantify mutation frequencies and positional distributions rather than to reconstruct full-length genotypes of individual library members. Therefore, we do not infer the exact number of unique variants in each library. Instead, we report the average mutation burden and position-wise non-reference rate distributions.

      We have revised the Results and added Supplementary Figure 4–figure supplement 2 accordingly.

      “For this experiment, two random mutation libraries were used: a low-mutation library prepared using the high-fidelity polymerase and a high-mutation library prepared using Taq DNA polymerase at a Mn<sup>2+</sup> concentration that yields mutation rates of 0.002 – 0.005 per base (0.0026 for GAL, 0.0027 for Luc, and 0.0048 for mSG, corresponding to approximately 8.0, 4.5, and 3.3 mutations per gene). We also plotted position-wise non-reference rates along the analyzed regions of each reporter gene, confirming that mutations were broadly distributed across the amplicons (Figure 4–figure supplement 2).”

      (9) Because only three amino acids were manipulated in the non-standard genetic codes, it remains unclear whether these particular amino acids occupy positions in the reporter proteins that are especially important for function and therefore likely to generate strong phenotypic effects. More broadly, it is not clear whether the assay is sufficiently sensitive to detect the effects of only a subset of deleterious variants within a pooled library. This point should be addressed more explicitly.

      We agree that this is an important limitation of the present study. Because our non-SGCs were constructed by reassigning only Ala, Ser, and Leu, the mutation-dependent effects that can differ among genetic codes are limited to mutations involving these reassigned codons or amino acid substitutions affected by these assignments. Therefore, the sensitivity of the assay depends on how frequently such substitutions occur in the reporter genes and whether the affected Ala, Ser, and Leu-related positions are functionally important.

      We have revised the Discussion to address this point more explicitly. In the revised manuscript, we now state that the absence of a detectable cost-dependent effect may reflect not only the limited cost range examined, but also the limited set of reassigned amino acids, the position-dependent importance of Ala/Ser/Leu residues in the reporter proteins, and the sensitivity limit of pooled activity measurements. We further note that future studies using genotype-resolved activity assays (defined variants) will be required to determine whether specific amino acid substitutions or specific protein positions exhibit stronger genetic code-dependent effects.

      “A further limitation of this study is that the reporter activities were measured at the level of pooled random mutation libraries. Therefore, the high-/low-mutation activity ratio used in this study should be interpreted as the relative reduction in average activity caused by increasing the mutational burden in a heterogeneous mutation pool, rather than as the effect of identical variants before and after additional mutations. This library-averaged approach was chosen because the mutational costs considered here are also defined as average expected physicochemical effects over many possible single-nucleotide substitutions. In addition, because the non-SGCs constructed in this study were generated by reassigning only Ala, Ser, and Leu, the detectable effects may depend on how frequently mutations involving these amino acids occur in each reporter gene and whether the affected positions are functionally important. If genetic code-dependent effects are restricted to a small subset of deleterious variants, such effects may be masked in pooled activity measurements. Future studies using defined variants or high-throughput genotype–phenotype mapping assays will be required to determine the mutation-specific and position-specific mechanisms underlying genetic code-dependent effects on protein function (Rozhoňová et al., 2024).”

      Recommendations for the authors:

      Reviewing Editor Comments:

      While we suggest that you address all the technical points raised by the reviewers, you may specifically want to limit the conclusion of the study to mutational robustness at the level of individual protein activity, rather than making broader generalizations. Also, the statistical analysis needs to be strengthened, as indicated in the reviews.

      We thank the Reviewing Editor for these important suggestions. We agree that the conclusion of the original manuscript was broader than what can be directly supported by the present experiments. In the revised manuscript, we have therefore limited our conclusion to mutational robustness at the level of individual reporter protein activity measured in a reconstituted in vitro translation system. We now explicitly state that our results do not directly address robustness at the level of cellular fitness, protein interaction networks, or long-term evolution.

      We have also strengthened the statistical analyses throughout the manuscript. Specifically, we added one-way ANOVA followed by Tukey’s post hoc test for Fig. 1D, Welch’s t-tests for Fig. 2B, Spearman’s rank correlation analyses for Fig. 4B–D and Fig. 5C/E/G, and two-way ANOVA for GAL activity in Fig. 5B. These analyses have been incorporated into the revised Results, figure legends, and supplementary information.

      Reviewer #2 (Recommendations for the authors):

      (1) Discuss other alternative hypotheses if the error minimization theory is unlikely.

      We thank the reviewer for this helpful suggestion. We think that the absence of a detectable relationship between mutational cost and reporter protein activity in our assay should not be interpreted as excluding all possible roles of error minimization in the evolution of the genetic code. Our results specifically address one aspect of the error minimization theory: whether physicochemical-property-based mutational cost predicts the average effect of random point mutations on individual reporter protein activity within the experimentally accessible range of non-SGCs tested here.

      In the revised Discussion, we have clarified that the organization of the SGC may have been shaped by multiple factors, including robustness to translational errors, historical constraints associated with genetic code expansion, biosynthetic or coevolutionary processes, stereochemical interactions, and the evolvability of proteins. Our results suggest that the contribution of mutational robustness at the level of individual protein activity may be limited within the range examined here, but they do not exclude the possibility that the SGC provides advantages under other forms of error, at the level of translation fidelity, cellular fitness, or long-term evolution.

      We have added a short discussion to clarify this point without expanding the scope of the manuscript beyond the present experimental results.

      “It should be noted that this conclusion is limited to the activity of individual reporter proteins translated in a reconstituted in vitro system. Therefore, whether similar trends would be observed at the level of cellular fitness or long-term evolution remains an open question. Moreover, our results do not exclude other possible roles of SGC organization. The SGC may have been shaped by multiple factors, including robustness to translational errors, historical constraints during genetic code expansion, biosynthetic or coevolutionary relationships among amino acids, stereochemical interactions, and effects on protein evolvability (Katoh and Suga, 2023; Koonin and Novozhilov, 2017, 2009; Novozhilov et al., 2007; Wong, 2005).”

      (2) A brief description of the PURE translation system can be provided for people from outside the field.

      We have added a brief description of the PURE system in the Introduction to make the experimental platform more accessible to readers outside the field. Specifically, we now explain that the PURE system is a reconstituted cell-free translation system composed of purified translation factors, ribosomes, aminoacyl-tRNA synthetases, tRNAs, amino acids, and energy-regeneration components. We also clarify that, in this study, we used a tRNA-free version of the PURE system, in which defined synthetic tRNA sets were supplied externally to reconstruct each genetic code.

      Introduction

      “A representative platform for such reconstitution is the PURE system (Shimizu et al., 2001), a reconstituted cell-free translation system composed of purified translation components, including ribosomes, translation factors, aaRSs, amino acids, and energy-regeneration components. In particular, a tRNA-free PURE system (Miyachi et al., 2022), in which endogenous tRNA activity is minimized and defined tRNA sets are supplied externally, enables genetic codes to be reconstructed by controlling the supplied tRNAs.”

      (3) Figure 5D and F - Technical replicates are provided only for GAL. A similar approach should be taken for LUC and mSG.

      We agree that replicate-level measurements for Luc and mSG would further improve reliability. However, repeating the full translation experiments for these reporters was not feasible in the current revision, as each experiment requires large amounts of freshly prepared tRNA-free PURE system and multiple defined tRNA mixtures for every genetic code variant tested. Given these material and technical constraints, we were unable to perform additional biological replicates within the scope of this revision. We would like to emphasize, however, that the GAL replicates shown in Fig. 5D and F are fully consistent across independent experiments, providing direct evidence for the reproducibility of the assay itself. Furthermore, the key metric in our analysis, the activity ratio between high- and low-mutation groups within each genetic code, is an internally normalized measure that is inherently less sensitive to between-experiment variability than absolute activity values. The correlation analyses further showed no significant relationship between mutational cost and this ratio across all three reporters, and this conclusion is consistent regardless of which reporter is examined. Together, we believe these results provide a robust basis for the conclusions drawn, even in the absence of full replication for Luc and mSG.

      (4) Provide statistical analysis wherever it is relevant (e.g, to support a lack of correlation).

      We have strengthened the statistical analyses throughout the revised manuscript. In particular, to support the lack of detectable correlation between mutational cost and mutation-induced activity loss, we performed Spearman’s rank correlation analyses between each mutational cost metric and the high-/low-mutation activity ratio for all three reporters. No significant correlations were detected for any reporter or cost metric. In addition, we added statistical analyses for other relevant figures, including one-way ANOVA followed by Tukey’s post hoc test for Fig. 1D, Welch’s t-tests for Fig. 2B, Spearman’s rank correlation analyses for Fig. 4B–D, and two-way ANOVA for GAL activity in Fig. 5B.

      Reviewer #3 (Recommendations for the authors):

      (1) In line 122, the phrase "as evenly as possible" is ambiguous and should be explained more precisely.

      We thank the reviewer for pointing this out. We have revised the phrase “as evenly as possible” to describe the codon design more precisely. Specifically, we now state that the NanoLuc coding sequences were designed so that the codons available in each genetic code were used with minimal differences in codon counts, while preserving the amino acid sequence of NanoLuc.

      “For near-SGC and SGC, the NanoLuc coding sequences were designed so that the codons available in each genetic code were used with minimal differences in codon counts, while preserving the amino acid sequence (Fig. 1B, 32 codons and 46 codons).”

      (2) For Figure 1D, a Western blot or another protein gel-based assay would be helpful to exclude the possibility that the observed differences arise from variation in translation efficiency rather than differences in protein activity.

      We agree that a protein gel-based assay such as Western blotting would in principle allow us to distinguish differences in translated protein amount from differences in specific activity, and we understand why such data would be informative. However, we would like to clarify that the primary purpose of Fig. 1D was to evaluate the overall functional translation output of each reconstructed genetic code, rather than to determine the mechanistic basis of any observed differences. In this context, NanoLuc luminescence serves as an integrated readout of the entire translation process, encompassing both translational efficiency and protein folding/activity. Crucially, regardless of whether the observed differences in NanoLuc luminescence reflect lower protein yield, reduced specific activity, or a combination of both, the conclusion of Fig. 1D remains the same. Although we did not perform Western blotting in this study, we believe that such an analysis would not change this interpretation and that the current data are sufficient to support this conclusion.

      (3) The number 3^9 is not immediately intuitive. It would be helpful if the authors also stated that this corresponds to approximately 20,000 possible non-standard genetic codes.

      We have revised the text to state both the exact number and the approximate value: 3<sup>9</sup> = 19,683, approximately 20,000 possible non-standard genetic codes.

      (4) The rationale for using the three cost parameters (PR, MV, and HI) should be explained in greater detail. Because these parameters are central to the manuscript, a citation alone is not sufficient. A concise explanation of their biological relevance would improve the clarity and accessibility of the study.

      We agree that the biological relevance of the three cost parameters should be explained more clearly. In the revised manuscript, we have added a concise explanation of why polar requirement (PR), molecular volume (MV), and hydropathy index (HI) were used.

      These parameters were selected because they have been widely used in theoretical studies of genetic code optimality and represent distinct physicochemical aspects of amino acid substitutions. PR reflects polarity-related interactions and has been a classical metric in error minimization analyses of the genetic code. MV represents side-chain size and steric volume, which could influence packing and structural stability in proteins. HI reflects hydrophobicity, which is closely related to protein folding and hydrophobic core formation. We have also clarified that these metrics are simplified descriptors and do not capture residue-specific structural or functional context, which we now discuss as a limitation of the study.

      “PR reflects polarity-related interactions of amino acids and has been used as a classical measure of amino acid similarity in error minimization analyses. MV represents side-chain size and steric volume, which could affect protein packing and structural stability, whereas HI reflects hydrophobicity, which could be closely related to protein folding or hydrophobic core formation.”

      (5) In Figure 3, the experimental framework would be easier to follow if the authors included a schematic and data for one representative non-SGC, explicitly illustrating how it differs from the near-SGC with respect to each of the three cost measures.

      We agree that showing one representative non-SGC would make the experimental framework and cost calculation more intuitive.

      In the revised manuscript, we added a new panel to Fig. 3 comparing the near-SGC with a representative non-SGC. We selected the PR<sub>max</sub> code as the representative example because it clearly illustrates how reassignment of vacant codon boxes can increase one mutational cost metric relative to the near-SGC. In this panel, we first show the codon assignment schemes of the near-SGC and PR<sub>max</sub> code in the same genetic-code format used in Fig. 1. We then show the corresponding heatmap representations for the three physicochemical properties used in the cost calculation: polar requirement, molecular volume, and hydropathy index. The Cost<sub>PR</sub>, Cost<sub>MV</sub>, and Cost<sub>HI</sub> values are shown for each code.

      This new panel illustrates how changes in codon assignment are translated into different physicochemical cost landscapes and clarifies how the representative non-SGC differs from the near-SGC with respect to each of the three cost measures.

      “To make the design of non-SGCs more explicit, we show one representative non-SGC together with the near-SGC in Fig. 3B. This comparison illustrates how assignment of Ala, Ser, or Leu to the vacant codon boxes changes the three mutational cost metrics, Cost<sub>PR</sub>, Cost<sub>MV</sub>, and Cost<sub>HI</sub>.”

      (6) In line 329, the phrase "similar pattern" is ambiguous and should be explained more explicitly.

      We have revised the ambiguous phrase “similar pattern” to describe the observation more explicitly. Specifically, we now state that the relative differences in GAL activity among genetic codes observed in the low-mutation library were broadly retained in the high-mutation library, although overall activity decreased.

      “For the high-mutation library, GAL activity decreased overall, while the relative differences in activity among genetic codes observed in the low-mutation library were broadly retained.”

      (7) Figure S7 appears to be an important control for the experiments shown in Figure 5, and I recommend moving it to the main figures.

      We thank the reviewer for this helpful suggestion. We agree that the HiBiT-based quantification of GAL protein amount is an important control for interpreting the GAL activity measurements in Fig. 5, and we appreciate the recommendation to increase its visibility. This analysis shows that the amount of C-terminally completed GAL products was broadly comparable among genetic codes, indicating that the large differences in GAL activity were not primarily attributable to differences in total translated protein amount.

      After careful consideration, we have opted to retain this analysis in the supplementary figures because the main focus of Fig. 5 is the relationship between mutational cost and mutation-induced activity loss, quantified by the high-/low-mutation activity ratio. The HiBiT experiment addresses a related but distinct question: whether differences in absolute GAL activity among genetic codes can be explained by differences in protein abundance, and we felt that including it in the main figures might shift the emphasis away from the central message of Fig. 5. Nevertheless, we have added a clear reference to Figure 4–figure supplement 1 in the main text and the figure legend to ensure that readers are directed to this control when interpreting Fig. 5.

    1. our learned paper signalas the observable relaxation p(Z | Xreb) of the ideal p(Z | X)

      i think we want more setup. I think we want to state: "As mentioned in the problem formulation, papers are transformed into reviews before reaching the decision. Given a paper (X), over decisions (D) and reviews (R) ( aka p(D,R|X)). While the flow indicates that reviews precede the decision, now that we have built a shortcut that predicts the decisionwithout the review, we question whether we can generate more \italics{decision-calibrated} reviews. This is valid by simply rearranging the joint distribution like so:

      then the formula.

      then the both factorizations are vlaid. then we can give a more conceptual understanding: if the conjecture is correct, that much of the decision can be determined by overall presentation quality, then perhaps reviews are simply a means-to-an-end to justify the reviewer's inital recaction.

      heres more context about sources that we can cite for this behavior: The strongest terms to search are:

      motivated reasoning, post hoc rationalization, biased assimilation, affect heuristic, halo effect, and in peer review specifically prestige bias, reviewer bias, or cognitive bias in peer review.

      Here are the most relevant scientific articles.

      1. Kunda — “The Case for Motivated Reasoning”

      Ziva Kunda, 1990, Psychological Bulletin

      This is probably the canonical article. Kunda argues that motivation can bias the cognitive processes people use to access, construct, and evaluate beliefs. In your case: a reviewer’s initial evaluation of a paper can shape which criticisms feel salient or persuasive.

      Best use: cite this for the general mechanism: people reason toward a conclusion they are already inclined to reach.

      1. Nisbett & Wilson — “Telling More Than We Can Know”

      Richard Nisbett & Timothy Wilson, 1977, Psychological Review

      This is highly relevant to the “reverse reasoning” part. They reviewed evidence that people often lack direct introspective access to the mental processes that caused their judgments, but still produce explanations for those judgments.

      Best use: cite this for the idea that reviewers may sincerely report reasons for a judgment without accurately knowing what actually caused the judgment.

      1. Haidt — “The Emotional Dog and Its Rational Tail”

      Jonathan Haidt, 2001, Psychological Review

      Haidt’s social intuitionist model is about moral judgment, not peer review, but the mechanism maps well: quick intuitive judgment is followed by slower post hoc reasoning. The article explicitly frames reasoning as often coming after intuition rather than causing judgment.

      Best use: cite this when you want the phrase “intuition first, reasoning second.”

      1. Lord, Ross & Lepper — “Biased Assimilation and Attitude Polarization”

      Charles Lord, Lee Ross & Mark Lepper, 1979, Journal of Personality and Social Psychology

      This is a classic study on how people evaluate evidence differently depending on their prior beliefs. People tend to accept congenial evidence more readily and scrutinize uncongenial evidence more harshly.

      Best use: cite this for the reviewer behavior where evidence supporting the reviewer’s initial take gets treated as decisive, while contrary evidence gets nitpicked.

      1. Slovic et al. — “The Affect Heuristic”

      Paul Slovic, Melissa Finucane, Ellen Peters & Donald MacGregor, 2007, European Journal of Operational Research

      This article argues that feelings of “goodness” or “badness” can rapidly guide judgments and decisions. That is very close to what people informally mean by a “paper gestalt”: an overall positive or negative feeling that then colors assessment of specific features.

      Best use: cite this for the gut reaction / affective global impression component.

      1. Tomkins, Zhang & Heavlin — “Reviewer Bias in Single- versus Double-Blind Peer Review”

      Andrew Tomkins, Min Zhang & William D. Heavlin, 2017, PNAS

      This is peer-review-specific. In a large conference-review setting, submissions were reviewed under single-blind and double-blind conditions. The study found that single-blind reviewing advantaged papers by famous authors and high-prestige institutions.

      Best use: cite this to show that manuscript judgments are not purely about the paper’s intrinsic content; contextual cues can bias reviews.

      1. Blank — “The Effects of Double-Blind versus Single-Blind Reviewing”

      Rebecca Blank, 1991, American Economic Review

      This was a randomized experiment at the American Economic Review. It found that reviewers were more critical when author identity was blinded, and acceptance rates were lower under double-blind review.

      Best use: cite this as older experimental evidence that review outcomes shift when identity/prestige cues are removed.

      1. Peters & Ceci — “Peer-Review Practices of Psychological Journals”

      Douglas Peters & Stephen Ceci, 1982, Behavioral and Brain Sciences

      Classic and brutal study: previously published psychology articles were resubmitted to the same journals with altered author/institution information. Most were not recognized, and many were rejected.

      Best use: cite this for the unreliability/context-sensitivity of peer review.

      1. Teplitskiy et al. — “The Social Structure of Consensus in Scientific Review”

      Misha Teplitskiy et al., 2018

      This study analyzed reviews of 7,981 neuroscience manuscripts submitted to PLOS ONE and found that reviewers favored authors closer to them in the co-authorship network. The authors interpret this not just as simple nepotism but as partly reflecting “schools of thought” and substantive evaluative differences.

      Best use: cite this if your point is that reviewers’ intellectual/social position can shape what they see as valid or flawed.

      1. Sordi et al. — “Halo Effect in Peer Review”

      José Osvaldo De Sordi et al., 2020

      This one is directly about the halo effect in peer review. It explores whether belonging to the same professional field or group can bias article evaluation during review.

      Best use: cite this for the closest peer-review-specific phrase to “paper gestalt”: halo effect in peer review.

      A good synthesis sentence would be:

      The phenomenon can be described as an interaction of affective first impressions, motivated reasoning, and post hoc rationalization: reviewers may form an early global evaluation of a manuscript and then selectively construct or emphasize criticisms that make that evaluation appear analytically grounded.

      For a paper or lit review, I’d probably cite Kunda 1990 + Nisbett & Wilson 1977 + Slovic et al. 2007 for the psychology mechanism, then Tomkins et al. 2017 + Peters & Ceci 1982 + Teplitskiy et al. 2018 for peer-review-specific evidence.

      the key is that based off this realization, we sought to see whether conditioning frontier coding agents for reviews can 1) improve their decision-prediction and 2) improve their generated reviews' alignment to human reviews.

    Annotators

    1. Author response:

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

      Joint Public Review

      This manuscript puts forward the provocative idea that a posttranslational feedback loop regulates daily and ultradian rhythms in neuronal excitability. The authors used in vivo long-term tip recordings of the long trichoid sensilla of male hawkmoths to analyze spontaneous spiking activity indicative of the ORNs' endogenous membrane potential oscillations. This firing pattern was disrupted by pharmacological blockade of the Orco receptor. They then use these recordings together with computational modeling to predict that Orco receptor neuron (ORN) activity is required for circadian, not ultradian, firing patterns. Orco did not show a circadian expression pattern in a qPCR experiment, and its conductance was proposed to be regulated by cyclic nucleotide levels. This evidence led the authors to conclude that a post-translational feedback loop (PTFL) clockwork, associated with the ORN plasma membrane, allows for temporal control of pheromone detection via the generation of multi-scale endogenous membrane potential oscillations. The findings will interest researchers in neurophysiology, circadian rhythms, and sensory biology. However, the manuscript has limited experimental evidence to support its central hypothesis and is undermined by several questionable assumptions that underlie their data analysis and model builds, as well as insufficient biological data, including critical controls to validate and/or fully justify the model the authors are proposing.

      We thank the reviewers for their thorough and thoughtful comments and believe that the manuscript is much stronger now after the revision which incorporates the requested changes. We added results of new experiments and additional analyses. Although these new insights did not change the previous conclusions, we significantly reworked the Discussion and added further references to clarify the conclusions we want to make.

      Please note that we used ORN as acronym for “olfactory receptor neuron” throughout the manuscript. ORNs contain odorant receptors (ORs), and in insects these ORs associate with the olfactory receptor co-receptor (Orco) to be trafficked to the membrane of the cilium of the ORN, where they can be contacted by pheromones and odorants. In Manduca sexta, evidence is accumulating for G-protein coupled metabotropic pheromone transduction and not for OR-Orco dependent ionotropic transduction, as shown for Drosophila melanogaster. In both insect species, besides its chaperone function, Orco can form leaky cation channels, which can regulate the spontaneous spiking activity of ORNs. In this study, we explored this role of Orco.

      Strengths:

      The study is notable for its combination of long-term in vivo tip recordings with computational modeling, which is technically challenging and adds weight to the authors' claims. The link between Orco, cyclic nucleotides, and circadian regulation is potentially important for sensory neuroscience, and the modeling framework itself - a stochastic Hodgkin-Huxley formulation that explicitly incorporates channel noise - is a solid and forward-looking contribution. Together, these elements make the study conceptually bold and of clear interest to circadian and olfactory biologists.

      Major weaknesses:

      At the same time, several limitations temper the conclusions. The pharmacological evidence relies on a single antagonist and concentration, without key controls. The circadian analysis is based on relatively small numbers of neurons, with rhythms detected only in subsets, and the alignment procedure used in constant darkness raises concerns of bias. The molecular evidence is sparse, with only three qPCR timepoints, and the model, while creative, rests on assumptions that are not yet fully supported by in vivo data.

      Please see our responses to the detailed comments.

      Detailed comments are provided below:

      (1) The role for Orco proposed in the authors' model largely stems from the effects seen following the administration of (a single dose) of the Orco antagonist, OLC15. However, this hypothesis is undercut by the lack of adequate pharmacological controls, including a basic multipoint OLC15 dose-response series in addition to the administration of blockers for the other channels that are embedded in their model, but which were ruled out as being involved in the modulation of biological rhythms. In addition, these studies would (ideally) also benefit from the inclusion of the same concentration (series) of an inactive OLC15 analog to better control for off-target effects.

      The Orco agonist VUAA1 (Jones et al., 2011) binds directly to Orco and increases the channel open time probability. In M. sexta hawkmoths, we have already published that VUAA 1 increases the low spontaneous activity of ORNs in a dose-dependent fashion (Nolte et al., 2013). Chen and Luetje (2012) systematically varied the chemical structure of VUAA1 to identify new Orco ligands and discovered 22 Orco ligand candidates (OLCs) that either activated or inhibited Orco. In their heterologous expression system, Orco was most sensitive to inhibition by OLC15. Based on these results, we published a dose-response curve of OLC15 inhibition (1-100 µM) using in vivo tip recordings of pheromone-sensitive long trichoid sensilla of M. sexta (Nolte et al., 2016). There, we also demonstrated that OLC15 dose-dependently antagonizes the VUAA1-dependent activation of Orco.

      Furthermore, we tested other published Orco antagonists, which were characterized in heterologous assays, in primary cell cultures of hawkmoth ORNs, as well as in in vivo assays in intact hawkmoths. We focused on amiloride-derived antagonists, because we previously identified an amiloride-sensitive cation channel in hawkmoth ORNs. We found that, in contrast to OLC15, the amilorides HMA and MIA were not Orco-specific antagonists but instead affected different ion channel targets depending on the time of day (Nolte et al., 2016). Based on those experiments and the dose-response curves we determined that the Orco agonist VUAA1 (Jones et al., 2011) and the Orco antagonist OLC15 (Chen and Luetje, 2012) worked best in hawkmoth ORNs to target Orco pharmacologically. Due to those results and other comparative tests with other published Orco antagonists we settled since then in all further experiments on a dose of 50 µM OLC15 as most adequate to antagonize Orco functions in Manudca. In the current study, we focus on Orco without excluding the possibility that other ion channels in the ORNs contribute to the control of membrane potential rhythms.

      We have clarified the Methods section accordingly.

      (2) The expression pattern of Orco was assessed using qPCR at only three timepoints. Rhythmic transcripts can easily be missed with such sparse sampling (Hughes et al., 2017). A minimum of six evenly spaced timepoints across a 24-hour cycle would be required to confidently rule out circadian transcriptional regulation. In addition, the use of the timeless mRNA control from another study is not acceptable. Furthermore, qPCR analysis measures transcript abundance, not transcription, as the authors repeatedly state. Transcriptional studies would require nuclear run-off or, more recently, can be done with snRNAseq analysis. Taken together, these concerns undermine the authors' desire to rule out TTFL-based control that directly led them to implicate a PTTF-based model.

      We agree with the referees that more time points and a direct comparison between timeless and Orco mRNA levels should be included in this manuscript. We included these additional qPCR experiments and edited the manuscript to make clear that we measure transcript abundance, but we will not perform snRNAseq analysis due to time- and financial constraints.

      (3) The modelling presented is based on Orco as a ZT-dependent conductance tied to the cAMP oscillations that were reported by this group in the cockroach and from the presence and functionality in Manduca of homomeric Orco complexes that are devoid of tuning ORs. While these complexes have been generated in cell culture and other heterologous expression systems, as well as presumably exist in vivo in the Drosophila empty neuron and other tuning OR mutants, there is no evidence that these complexes exist in wild-type Manduca ORNs. While this doesn't necessarily undermine every aspect of their models, the authors should note the presence of Orco/OR complexes rather than Orco homomeric complexes.

      Our ELISAs found circadian oscillations in cAMP levels not only in antennae of the Madeira cockroach (Schendzielorz et al., 2014, 2012), but also in hawkmoth antennae (Schendzielorz et al., 2015). For clarification, we added the 2015 citation to the Modeling chapter in the Methods section.

      We agree with the referees that we cannot distinguish between Orco homo- and heteromers in the different compartments of our hawkmoth ORNs but we know that both are expressed in the pheromone-sensitive ORNs. Thus, as the referee suggests, we added text regarding the presence and localization of OR-Orco heteromers. Consistent data collected across different experiments (heterologous expression systems, primary cell cultures of hawkmoth ORNs, in vivo/in situ studies) support that Orco homomers are present in hawkmoth ORNs. In addition to co-expression of MsexOrco and MsexSNMP-1 with either MsexOr-1 or MsexOr-4 in a heterologous expression system, MsexOrco expression alone was already sufficient to increase intracellular Ca<sup>2+</sup> levels spontaneously as a result of its property as leaky, non-specific cation channel, and in response to VUAA1 application (Nolte et al., 2013). Both in developing hawkmoth pupae and differentiating primary cell cultures of hawkmoth ORNs, Orco expression started during a developmental time window where ORNs did not yet express pheromone receptors but where Orco affected spontaneous activity and intracellular Ca<sup>2+</sup> levels dependent on VUAA1 (Nolte et al., 2016). In vitro patch clamp studies of differentiating cultured hawkmoth ORNs during this time window of pupal development characterized ion channels/currents with properties of Orco as a leaky, non-specific cation channel/current that depends on protein kinase C and cyclic nucleotides (Dolzer et al., 2021, 2008; Krannich and Stengl, 2008; Stengl, 1993). Thus, Orco homomers are present in developing hawkmoth ORNs during a time window where ORNs already express spontaneous activity but they do not heteromerize with pheromone receptors. However, we do not know whether and in what ratio homo- and heteromers of Orco and ORs are present in the respective sensillum compartments of adult hawkmoths because all OR-specific antibodies tested did not work in immunocytochemical studies of hawkmoth antennae (Nolte et al., 2013; Stengl, 1994; Stengl and Hildebrand, 1990). Our hypothesis of differential distribution of Orco homomers in the some and dendrite compartment, and OR-Orco heteromers in the cilia is based on differential immunocytochemical localization of Drosophila ORs mainly in the cilia compartment (Benton et al., 2006).

      We clarified our manuscript accordingly.

      (4) Some aspects of the authors' models, most notably the decision to phase align/optimize their DD and OLC15 recordings, are likely to bias their interpretations.

      It is consensus that insects display daily and circadian rhythms in pheromone-dependent mating, odor-gated feeding, and egg-laying behavior that phase-locks to environmental rhythms, corresponding with daily/circadian rhythms of sensory neuron physiology (e.g., Merlin et al., 2007; Rymer et al., 2007; Schendzielorz et al., 2015, 2012). However, circadian rhythms can be easily masked by stress, like the disturbances during an experimentally very challenging long-term recording experiment over several days. In addition, we observed over the years in our animal raising facility that in 17:7 light-dark cycles the originally nocturnal hawkmoths M. sexta distribute their activity patterns over the course of the day, finding nocturnal as well as diurnal hawkmoths. Thus, light-dark cycles were not enough to ensure phase-synchronized behavioral rhythms, and it is very likely that the nocturnal hawkmoths, next to stress signals, rely heavily on pheromone/odor dependent synchronization as also found in other moth species (Ghosh et al., 2024). Because we focus on spontaneous activity and not on pheromone-dependent physiology in this study, we used isolated males that were never exposed to the female pheromones, taking phase dispersal into account. Therefore, it became necessary in free-running conditions to first determine the respective behavioral rhythm for each animal, and then to phase-align their activity patterns to allow for statistical analysis. Otherwise, circadian differences would average out in a phase-dispersed free-running population. As requested by the referees in point (7), we added RAIN to test for rhythmicity in each of our recordings and revised the manuscript accordingly.

      Furthermore, in preliminary experiments we briefly exposed hawkmoths to pheromone the night before the start of the experiment. However, we failed to obtain phase-synchronized spiking rhythms. Most likely, a circadian pattern of pheromone exposure would have been necessary as zeitgeber, which could not be used here due to long-term pheromone-dependent effects in spiking activity. These results are added as supplementary figure to Fig 3.

      (5) The tip recordings from long trichoid sensilla are critical aspects of this study. These recordings were carried out on upper sensillar tips located on the distal-most second annulus. Since there are approximately 80 annuli on the Manduca antennae, it is unclear whether the recordings are representative of the antennal response.

      We think the reviewers might have misinterpreted our description of the recording site. In the Methods, we state that we clip off the 20 most distal annuli (leaving a stump of about 60 annuli) and insert the reference electrode into the flagellum up to the second annulus from the cut end, i.e., the recording sites are located at 2/3 – 3/4 of the antenna length as seen from the head of the animal. We clarified this in the Methods section.

      In addition, our lab did show with antibody stainings against Orco that apparently all ORNs that innervate long and short trichoid sensilla along the whole flagellum express the same staining pattern (Nolte et al., 2016). Lee and Strausfeld (1990) mapped all types of antennal sensilla, and together with pheromone-dependent tip-recordings of Kaissling et al. (1989) it was shown that most of the male antennal sensilla are pheromone-sensitive long trichoid sensilla, with one of the two innervating ORNs always responding to bombykal, ensuring high sensitivity to pheromone detection. Furthermore, our patch clamp recordings of primary cell cultures of whole male antennae found largely overlapping ion channel populations across ORNs (review: (Stengl, 2010)). This would indicate that all ORNs, whether they express ORs sensitive to pheromone or general odorants, could potentially share the same Orco-dependent spontaneous activity rhythms. Furthermore, in our lab, different experimenters from different years that recorded from long trichoid sensilla on different annuli did not detect obvious differences in neither the spontaneous activity nor the pheromone responses (c.f., Dolzer et al., 2003; Gawalek and Stengl, 2018; Schneider et al., 2025). Thus, it is very likely that we are reporting a general encoding mechanism that is not locally restricted along the antennal flagellum and is very likely shared by all types of OR-Orco expressing ORNs.

      (6.1) The authors do not provide any data in support of their cAMP/cGMP-based Orco gating…

      There are publications supporting cyclic nucleotide gating of Orco in Drosophila, but only after previous phosphorylation via protein kinase C (PKC; review: (Wicher and Miazzi, 2021)). Since Orco is very conserved among insect species, it is likely that PKC- and cGMP/cAMP-dependent regulations are present for Orco in other insect species. To test this, we are currently characterizing second messenger-dependence of spontaneous spiking activity, which is the focus of a follow-up manuscript. Nevertheless, to provide more evidence for our hypothesis of the current manuscript, we added a new set of tip-recording experiments that demonstrate cAMP-dependent gating of Orco. Because of the addition of this figure, we merged figures 8-10 into Figure 8 and added the cAMP data as Figure 9.

      (6.2) … and the PTTF model proposed is somewhat disappointing.

      For a detailed introduction of our PTFL membrane clock hypothesis please see our opinion paper that we refer to in the manuscript (Stengl and Schneider, 2024). We added clarification of how Orco activation can influence cAMP levels. A more elaborate PTFL clock model including many more of the identified ion channels in hawkmoth ORNs is the focus of another manuscript to come.

      (6.3) The model seems to be influenced by their long-held proposal that insect olfactory signaling has a critical metabotropic component involving cyclic nucleotides, PKC, etc, a view that may be influenced by the use of Orco homomeric complexes generated in HEK cells.

      Indeed, we propose a metabotropic pheromone-transduction cascade, which in moths and cockroaches is based on G-protein-mediated activation of phospholipase C but not on adenylyl cyclase activation. Our hypothesis is not influenced by HEK cell heterologous expression studies of Orco but is supported by our own work comparing in vivo tip recordings of intact hawkmoths with patch clamp experiments on hawkmoth primary cell cultures of olfactory receptor neurons, which are able to respond to their species-specific pheromones in vitro (Schneider et al., 2025; Stengl, 2010; Stengl and Funk, 2013; Wicher and Miazzi, 2021). In addition, a multitude of publications by other laboratories with in vivo and in vitro studies using physiological, genetic, and immunocytochemical assays all support a metabotropic signal transduction cascade in insect olfaction (Stengl, 2010; Stengl and Funk, 2013; Takagi et al., 2025; Wicher and Miazzi, 2021). In contrast, the hypothesis suggesting a solely ionotropic pheromone- and general odor-dependent transduction cascade for all insect species is based on very sparse experimental evidence, based primarily on heterologous expression studies such as HEK cells that lack the insect’s WT molecular surroundings, and thus, cannot predict OR-Orco function in vivo. Furthermore, the ionotropic hypothesis is heavily based upon the argument that an inverse 7TM receptor cannot couple to G-proteins, which lacks careful backup via biochemical and structural studies. In addition, the ionotropic hypothesis lacks support via carefully performed physiological in vivo studies in different insect species that paid attention to analysis of the distinct kinetic components of ORN´s odor/pheromone responses and that employ physiological concentrations and durations of odor/pheromone stimuli (please see our most recent publication by Schneider et al. (2025)). We added references to the possible odor transduction mechanisms to the introduction.

      (6.4) Nevertheless, structural studies on Orco do not support a cyclic nucleotide binding site, although PKC-based phosphorylation has been implicated in the fine-tuning/adaptation of olfactory signaling.

      While structural studies did not find evidence for conserved known cyclic nucleotide binding sites on Orco, this does not exclude the presence of indirect cAMP effects via e.g., Orco subunits complexing with other molecules under direct cAMP control, such as other ion channel subunits. Furthermore, it does not exclude so far unknown binding sites, or via sites that fold out only after a specific sequence of previous phosphorylations of the many phosphorylation sites on Orco. Indeed, physiological studies in Drosophila presented evidence for cyclic nucleotide dependence of Orco after previous PKC-dependent phosphorylation (Getahun et al., 2013). Our ongoing in vivo experiments in hawkmoths further corroborate a zeitgeber time-dependent PKC- and cyclic nucleotide-dependent modulation of Orco. These detailed studies will be published in a follow-up publication. In the revised version of this manuscript, we added tip-recording experiments that indicate cAMP involvement in Orco gating (new Figure 9).

      (7) Because only 5/11 LD and 7/10 DD animals showed daily rhythms, with averages lacking clear daily modulation, the methods are not sufficiently reliable enough to reveal novel underlying mechanisms of circadian rhythm generation. The reported results are therefore not yet reliable or quantifiable. To quantify their results, the authors should apply tests for circadian rhythmicity using methods such as RAIN, JTK CYCLE, MetaCycle, or Echo. The use of FFT and Wavelet is applauded, but these methods do not have tests of significance for rhythms and can be biased when analyzing data in which there could only be 1-3 circadian cycles. Because the conclusions appear to be based on 11-12 neurons that were recorded for 2-4 days, the reader is concerned that the methods are not yet perfected to provide strong evidence for circadian regulation of spontaneous firing of ORNs. The average data (e.g., Figure 3Bii and 3Cii) highlight the apparent lack of daily rhythms. In summary, the results would be more compelling if more than 50% of the recordings had significant circadian amplitudes and with similar periods and phases.

      The long-term tip-recordings of intact hawkmoths are very challenging and take a very long time to accomplish, thus, we are very happy that we succeeded in obtaining so many of them (N=40). We are thankful to the reviewers’ suggestion to use RAIN since this analysis revealed circadian rhythms in 7 of 11 LD recordings, 8 of 12 DD recordings, and 2 of 12 OLC15 recordings. Please see also our response to (4) above, commenting the phase-dispersal of activity rhythms observed in our experiments, as well as in the behavior of hawkmoth males in the mating cage.

      (8) The statement that circadian patterns of ORN firing are lost with the Orco antagonist (OLC15) is not strongly supported. The manuscript should be revised to quantify how Orco changed circadian amplitude in the 12 recorded neurons. Measures of circadian amplitude can avoid confusing/vague statements like Line 394 “low and high frequency bands appeared to merge during the activity phase around ZT 0 in the animals that showed clear circadian rhythms (N = 5 of 11 in LD)”. The conclusion that Orco blocks circadian firing appears to be contradicted by Figure 6, which indicates that ~6 of these neurons had circadian periods detected by wavelet. The manuscript would be strengthened with details about the specificity and reproducibility of the Orco antagonist. The authors quantify the gradual decrease in firing with the slope of a linear fit to estimate how the “effectiveness [of OLC15] increased over time.” They conclude that the drug “obliterated circadian rhythms and attenuated the spontaneous activity in several, but not all experiments (N = 8 of 12).” The report would be greatly strengthened with corroborating data from additional Orco antagonists and additional doses of OLC15 (the authors use only 50 uM OLC15).

      According to the valuable suggestions of the referees, we used RAIN to detect circadian rhythms in the spiking attributes in each individual animal. Since only 2 of 12 animals displayed a circadian rhythm in OLC15, statistical comparison of circadian amplitudes is not possible. We revised the results section accordingly and added to the figure legend to make it clearer that the heat maps in Fig 5 are representative from one animal each and not averages across animals.

      As the reviewer states correctly in (7), wavelet results of circadian rhythmicity must be interpreted carefully because of the low number of circadian cycles in ~3-4 day recordings. Since the heatmaps in Figure 5 visually revealed the presence of ultradian rhythms, the main focus of the wavelet analysis in Figure 6 is in the detection and quantification of ultradian periods up to 20 h.

      We revised the Methods section to include references to previous experiments that characterized the effect of different doses of OLC15 and other Orco antagonists and agonists in M. sexta antennae (Nolte et al., 2016). Please see also our response to (1).

      (9) The manuscript includes several statements that are more speculation than conclusion. For example, there is no evidence for tuning or plasticity in this report. Statements like the following should be removed or addressed with experiments that show changes in odor response specificity or sensitivity: "ORN signalosomes are highly plastic endogenous PTFL clocks comprising receptors for circadian and ultradian Zeitgebers that allow to tune into internal physiological and external environmental rhythms as basis for active sensing." (Discussion Line 622). The paper concludes that (line 380) "mean frequency of spontaneous spiking and the frequency of bursting expressed daily modulation, and are both most likely controlled via a circadian clock that targets the leak channel Orco." This is too bold given the available results.

      We revised the manuscript accordingly and clarified which statements are supported via published evidence and which are predictions based upon our novel hypothesis published in our opinion paper (Stengl and Schneider, 2024).

      (10.1) Because Orco conductance is modulated by cyclic nucleotides, it remains highly plausible that circadian regulation occurs upstream at the level of signaling pathways (e.g., calcium, calcium-binding proteins, GPCRs, cyclases, phosphodiesterases).

      We agree with the referees that it is very likely that there are multiple layers of interconnected feedback cycles that control Orco localization and activity. Our novel hypothesis suggests interlocked TTFL and PTFL control of physiological circadian rhythms, not strictly hierarchical TTFL control, which would require a daily turnover of membrane proteins and transcriptional control via the established TTFL clock in insect ORNs. We are currently searching for TTFL control at all levels of odor/pheromone transduction using ZT-dependent transcriptomics in combination with qPCR and single-nucleus transcriptomics, involving also all the molecules suggested by the referees. These studies are ongoing, are very time- and money-consuming, and are beyond the scope of this manuscript. However, we added a set of experiments to this manuscript in which we demonstrate that the effect of increased cAMP on the spontaneous spiking activity is mediated by Orco (new Figure 9).

      (10.2) The possibility that circadian oscillations of cyclic nucleotides are generated by the canonical TTFL mechanism has not been excluded. In fact, extensive work in Drosophila has demonstrated that the TTFL-based molecular clock proteins are required for circadian rhythms in olfaction.

      Our experiments that test circadian TTFL control at different levels of the cAMP transduction cascade in hawkmoth antennae are on the way and are part of another publication. In section 6.2 we already stated that our experiments do not exclude that Orco is under indirect control of the TTFL. We revised our discussion accordingly.

      The experiments published for TTFL dependent control of Drosophila olfaction that we are aware of (Krishnan et al., 1999; Tanoue et al., 2004) do not exclude interlinked PTFL and TTFL clocks. Krishnan et al. (1999) demonstrated that the TTFL clock in antennal olfactory receptor neurons correlates with circadian rhythms in odor responses measured in electroantennogram (EAG) recordings, not in single sensillum recordings as in our experiments. EAG recordings comprise not only voltage responses of the olfactory sensory neurons but also voltage changes generated in non-neuronal antennal cells such as trichogen and tormogen cells that built the transepithelial potential gradient via vATPases that generates the high K<sup>+</sup> concentration in the sensillum lymph (Jain et al., 2024; Klein, 1992; Thurm and Küppers, 1980). In addition, EAG recordings most likely contain responses of afferent neurons originating from somata in the brain that maintain central control of the antennae. Thus, EAG recordings are difficult to interpret.

      (11) A defining feature of circadian oscillators is the feedback mechanism that generates a time delay (e.g., PERIOD/TIMELESS repressing their own transcription). While the authors describe how cyclic nucleotides can regulate Orco conductance, they do not provide a convincing explanation of how Orco activity could, in turn, feed back into the proposed PTFL to sustain oscillations. For these reasons, the authors should consider:

      (a) Providing a broader discussion of non-TTFL models of circadian rhythms (e.g., redox cycles, post-translational modifications).

      We revised the discussion accordingly.

      (b) Reassessing Orco expression using a higher-resolution temporal sampling ({greater than or equal to}6 timepoints per 24 h).

      We added those experiments to the revised version of the manuscript (see our response to (2)).

      (c) Clarifying or revising the PTFL model to explicitly address how feedback would be achieved. Alternatively, the data may be more consistent with Orco conductance rhythms being regulated by post-translational mechanisms downstream of the canonical TTFL oscillator, as suggested by the Drosophila olfactory system literature.

      We added possible negative feedback elements to the Discussion to explain how our proposed PTFL could in principle work independent of TTFL clock.

      Minor weaknesses:

      (1) The authors should compare the firing patterns of ORN neurons to the bursts, clusters, and packets of retinal efferent spikes reported in Liu JS and Passaglia CL (2011; JBR). By comparing measures in moths to measures in Limulus, the authors might be able to address the question: Is the daily firing pattern of ORN neurons likely a conserved feature of circadian control of sensory sensitivity?

      We have revised the discussion accordingly.

      (2) The methods need further details. For example, it is unclear if or how single neuron activity was discriminated and whether the results were compromised by the relatively large environmental fluctuations in temperature (21-27oC), humidity (35-60%), or other cues known to modulate spontaneous firing.

      These large fluctuations stem from doing experiments at different seasons (higher temperature and humidity in the summer months, lower temperature and humidity in winter). Throughout each individual experiment, conditions were stable. We clarified the Methods section accordingly.

      Recommendations for the authors:

      The authors should post the code for their computational model to a repository like GitHub.

      The code for the computational model is now available at https://github.com/a-c-schneider/VijayanForlinoEtAl2025_Model.git

      References

      Benton R, Sachse S, Michnick SW, Vosshall LB. 2006. Atypical Membrane Topology and Heteromeric Function of Drosophila Odorant Receptors In Vivo. PLOS Biology 4:e20. DOI: https://doi.org/10.1371/journal.pbio.0040020

      Chen S, Luetje CW. 2012. Identification of New Agonists and Antagonists of the Insect Odorant Receptor Co-Receptor Subunit. PLOS ONE 7:e36784. DOI: https://doi.org/10.1371/journal.pone.0036784

      Dolzer J, Fischer K, Stengl M. 2003. Adaptation in pheromone-sensitive trichoid sensilla of the hawkmoth Manduca sexta. Journal of Experimental Biology 206:1575–1588. DOI: https://doi.org/10.1242/jeb.00302

      Dolzer J, Krannich S, Stengl M. 2008. Pharmacological Investigation of Protein Kinase C- and cGMP-Dependent Ion Channels in Cultured Olfactory Receptor Neurons of the Hawkmoth Manduca sexta. Chemical Senses 33:803–813. DOI: https://doi.org/10.1093/chemse/bjn043

      Dolzer J, Schröder K, Stengl M. 2021. Cyclic nucleotide-dependent ionic currents in olfactory receptor neurons of the hawkmoth Manduca sexta suggest pull–push sensitivity modulation. European Journal of Neuroscience 54:4804–4826. DOI: https://doi.org/10.1111/ejn.15346

      Gawalek P, Stengl M. 2018. The Diacylglycerol Analogs OAG and DOG Differentially Affect Primary Events of Pheromone Transduction in the Hawkmoth Manduca sexta in a Zeitgebertime-Dependent Manner Apparently Targeting TRP Channels. Frontiers in Cellular Neuroscience 12:218. DOI: https://doi.org/10.3389/fncel.2018.00218

      Getahun MN, Olsson SB, Lavista-Llanos S, Hansson BS, Wicher D. 2013. Insect Odorant Response Sensitivity Is Tuned by Metabotropically Autoregulated Olfactory Receptors. PLOS ONE 8:e58889. DOI: https://doi.org/10.1371/journal.pone.0058889

      Ghosh S, Suray C, Bozzolan F, Palazzo A, Monsempès C, Lecouvreur F, Chatterjee A. 2024. Pheromone-mediated command from the female to male clock induces and synchronizes circadian rhythms of the moth Spodoptera littoralis. Current biology 34:1414-1425.e5. DOI: https://doi.org/10.1016/j.cub.2024.02.042, PMID: 38479388

      Jain K, Prelic S, Hansson BS, Wicher D. 2024. Expression of Drosophila melanogaster V-ATPases in Olfactory Sensillum Support Cells. Insects 15:1016. DOI: https://doi.org/10.3390/insects15121016

      Jones PL, Pask GM, Rinker DC, Zwiebel LJ. 2011. Functional agonism of insect odorant receptor ion channels. Proceedings of the National Academy of Sciences 108:8821–8825. DOI: https://doi.org/10.1073/pnas.1102425108

      Kaissling KE, Hildebrand JG, Tumlinson JH. 1989. Pheromone receptor cells in the male moth Manduca sexta. Archives of Insect Biochemistry and Physiology 10:273–279. DOI: https://doi.org/10.1002/arch.940100403

      Klein U. 1992. The insect V-ATPase, a plasma membrane proton pump energizing secondary active transport: immunological evidence for the occurrence of a V-ATPase in insect ion-transporting epithelia. Journal of Experimental Biology 172:345–354. DOI: https://doi.org/10.1242/jeb.172.1.345

      Krannich S, Stengl M. 2008. Cyclic Nucleotide-Activated Currents in Cultured Olfactory Receptor Neurons of the Hawkmoth Manduca sexta. Journal of Neurophysiology 100:2866–2877. DOI: https://doi.org/10.1152/jn.01400.2007

      Krishnan B, Dryer SE, Hardin PE. 1999. Circadian rhythms in olfactory responses of Drosophila melanogaster. Nature 400:375–378. DOI: https://doi.org/10.1038/22566

      Lee JK, Strausfeld NJ. 1990. Structure, distribution and number of surface sensilla and their receptor cells on the olfactory appendage of the male mothManduca sexta. Journal of Neurocytology 19:519–538. DOI: https://doi.org/10.1007/BF01257241

      Merlin C, Lucas P, Rochat D, François M-C, Maïbèche-Coisne M, Jacquin-Joly E. 2007. An Antennal Circadian Clock and Circadian Rhythms in Peripheral Pheromone Reception in the Moth Spodoptera littoralis. Journal of Biological Rhythms 22:502–514. DOI: https://doi.org/10.1177/0748730407307737

      Nolte A, Funk NW, Mukunda L, Gawalek P, Werckenthin A, Hansson BS, Wicher D, Stengl M. 2013. In situ Tip-Recordings Found No Evidence for an Orco-Based Ionotropic Mechanism of Pheromone-Transduction in Manduca sexta. PLOS ONE 8:e62648. DOI: https://doi.org/10.1371/journal.pone.0062648

      Nolte A, Gawalek P, Koerte S, Wei H, Schumann R, Werckenthin A, Krieger J, Stengl M. 2016. No Evidence for Ionotropic Pheromone Transduction in the Hawkmoth Manduca sexta. PLOS ONE 11:e0166060. DOI: https://doi.org/10.1371/journal.pone.0166060

      Rymer J, Bauernfeind AL, Brown S, Page TL. 2007. Circadian rhythms in the mating behavior of the cockroach, Leucophaea maderae. Journal of Biological Rhythms 22:43–57. DOI: https://doi.org/10.1177/0748730406295462, PMID: 17229924

      Schendzielorz J, Schendzielorz T, Arendt A, Stengl M. 2014. Bimodal Oscillations of Cyclic Nucleotide Concentrations in the Circadian System of the Madeira Cockroach Rhyparobia maderae. Journal of Biological Rhythms 29:318–331. DOI: https://doi.org/10.1177/0748730414546133

      Schendzielorz T, Peters W, Boekhoff I, Stengl M. 2012. Time of Day Changes in Cyclic Nucleotides Are Modified via Octopamine and Pheromone in Antennae of the Madeira Cockroach. Journal of Biological Rhythms 27:388–397. DOI: https://doi.org/10.1177/0748730412456265

      Schendzielorz T, Schirmer K, Stolte P, Stengl M. 2015. Octopamine Regulates Antennal Sensory Neurons via Daytime-Dependent Changes in cAMP and IP3 Levels in the Hawkmoth Manduca sexta. PLOS ONE 10:e0121230. DOI: https://doi.org/10.1371/journal.pone.0121230

      Schneider AC, Schröder K, Chang Y, Nolte A, Gawalek P, Stengl M. 2025. Hawkmoth Pheromone Transduction Involves G-Protein–Dependent Phospholipase Cβ Signaling. eNeuro 12:ENEURO.0376-24.2024. DOI: https://doi.org/10.1523/ENEURO.0376-24.2024, PMID: 39880675

      Stengl M. 2010. Pheromone Transduction in Moths. Frontiers in Cellular Neuroscience 4:133. DOI: https://doi.org/10.3389/fncel.2010.00133

      Stengl M. 1994. Inositol-trisphosphate-dependent calcium currents precede cation currents in insect olfactory receptor neurons in vitro. Journal of Comparative Physiology A 174:187–194. DOI: https://doi.org/10.1007/BF00193785

      Stengl M. 1993. Intracellular-Messenger-Mediated Cation Channels in Cultured Olfactory Receptor Neurons. Journal of Experimental Biology 178:125–147. DOI: https://doi.org/10.1242/jeb.178.1.125

      Stengl M, Funk NW. 2013. The role of the coreceptor Orco in insect olfactory transduction. Journal of Comparative Physiology A 199:897–909. DOI: https://doi.org/10.1007/s00359-013-0837-3

      Stengl M, Hildebrand JG. 1990. Insect olfactory neurons in vitro: morphological and immunocytochemical characterization of male-specific antennal receptor cells from developing antennae of male Manduca sexta. Journal of Neuroscience 10:837–847. DOI: https://doi.org/10.1523/JNEUROSCI.10-03-00837.1990, PMID: 2319305

      Stengl M, Schneider AC. 2024. Contribution of membrane-associated oscillators to biological timing at different timescales. Frontiers in Physiology 14:1243455. DOI: https://doi.org/10.3389/fphys.2023.1243455

      Takagi S, Abuin L, Mermet J, Lee D, Benton R. 2025. A GPCR signaling pathway in insect odor detection. DOI: https://doi.org/10.1101/2025.10.03.680299

      Tanoue S, Krishnan P, Krishnan B, Dryer SE, Hardin PE. 2004. Circadian Clocks in Antennal Neurons Are Necessary and Sufficient for Olfaction Rhythms in Drosophila. Current Biology 14:638–649. DOI: https://doi.org/10.1016/j.cub.2004.04.009, PMID: 15084278

      Thurm U, Küppers J. 1980. Epithelial physiology of insect sensilla. In: Locke M, Smith DS (Eds). Insect Biology in the Future. Academic Press. p. 735–763. DOI: https://doi.org/10.1016/B978-0-12-454340-9.50039-2

      Wicher D, Miazzi F. 2021. Functional properties of insect olfactory receptors: ionotropic receptors and odorant receptors. Cell and Tissue Research 383:7–19. DOI: https://doi.org/10.1007/s00441-020-03363-x

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This paper provides a novel method to improve the accuracy of predictions of the impact of ITN strategies, by using sub-national estimates of the duration of ITN access and use over time from cross-sectional survey data and annual country ITNs received.

      Strengths:

      The approach is novel, makes use of available data, and has considered all of the relevant components of ITN distributions.

      Weaknesses:

      (W1.1) The main message of the paper was not very clear, and did not seem to fit the title. The title focuses on sub-national tailoring of ITN, but the abstract did not feature results directly about SNT. It was not very clear what the main result of the paper was - there are several ITN observations in the results and discussion. Most did not seem to be directly about SNT, but rather sub-national differences in use and access were accounted for in the analyses. It was not clear if the same conclusions would be reached without accounting for sub-national differences, but the estimates and predictions could be expected to be more accurate.

      Thank-you for highlighting this. We agree the title could be improved to better reflect the main messages of the paper and have now updated it to “Heterogeneity of use, access and retention of insecticide-treated nets: implications for subnational tailoring to maximise malaria control”. All parameters are estimated at a subnational level; this is not always the case a national level. We therefore do not have national-level models without subnational differences that our results could be compared to.

      (W1.2) Some of the results seemed to me to be apparent even without a modelling exercise (eg high coverage could not be maintained between campaigns, use would be higher with 2-yearly distributions rather than 3-yearly) or were not in themselves new insights (eg estimates of the duration of use). It would be helpful to clearly state what the novel results are in the abstract, the first paragraph of the discussion and the conclusions, and to make sure that the title is consistent.

      It is our understanding assessments on ITN coverage are often made from infrequent surveys, for example from MIS. These are typically conducted six months postcampaign and may miss notable reductions in use and access beyond this. Comparisons on ITN use and access are also frequently made directly between DHS surveys, which can be misleading in isolation if the time between campaigns and surveys is not considered. We have tried to highlight this more clearly in relation to Burkina Faso with the following text:

      “The observed decrease in use and access across many regions in Burkina Faso may therefore be a by-product of DHS surveys being conducted at progressively later dates relative to the most recent campaign; this does not necessarily indicate an underlying trend in decreasing use or access over longer timescales.”

      We do believe modelling exercises, such as the methodology presented here, can help generate improved estimates of ITN use and access over time than estimates from surveys alone, which can be biased by the relative timings of campaigns. It is also our understanding previous studies have generated national estimates of ITN retention. We are not aware of any previous studies that have estimated the duration ITNs continue to be used for, which is arguably of greater epidemiological importance than retention time. To best knowledge, these have also not been estimated at subnational scales previously.

      We acknowledge the novelty of some results were not clearly presented previously and are grateful to the reviewer for highlighting this. We have now highlighted some of the novel findings more clearly in the abstract, with the following text:

      “However, subnational variation in ITN retention and the duration that ITNs remain in use have not previously been quantified.”

      “Our results highlight that although transmission intensity remains an important factor for subnational tailoring of malaria control interventions, other factors, such as ITN use given access, meaningfully influence optimal deployment strategies.”.

      We have also highlighted the novelty and relevance of our findings more clearly in the first paragraph discussion, with the following text:

      “Funding constraints have also increased the need for consideration of subnational tailoring, with many recommendations being made on the basis of transmission intensity in the World Health Organisation (2025) Subnational Tailoring Reference Manual. However, a key uncertainty in assessing the potential impact of different ITN interventions has been how long nets remain in use rather than how long they are retained, and how this varies between regions. Here, to our best knowledge, we present the first estimates of subnational variation in ITN retention and the duration that ITNs remain in use, and also quantify for the first time how ITN use, access and retention vary between subnational regions across multiple African countries. Our work supports the change in guidance to optimal coverage as it highlights ITN interventions have notable differences in impact between settings, and that distributing fewer but more effective ITNs, particularly pyrethroid-chlorphenapyr products, is likely to be more impactful than maximising long-term coverage through increased campaign frequencies with pyrethroid-only ITNs. Our work also broadly supports World Health Organisation (2025) recommendations for subnational tailoring, particularly the consideration of deprioritisation of ITN distribution in very low transmission settings. However, our results provide new indications that deprioritisation of areas with higher ITN use given access may lead to greater resurgences in cases, highlighting that subnational tailoring decisions could be optimised further by considering additional factors to transmission intensity alone.”

      The novelty and relevance of our results are also now highlighted in the following text, which has been incorporated into the concluding paragraph:

      “In conclusion, the work indicates that universal coverage targets of 80% are unlikely to be consistently met due to waning overall ITN use in the intervening years between triennial mass campaigns. Improved coverage can be achieved through more frequent biennial distributions, though this is unlikely to be feasible at scale given the current funding landscape. Indeed, when resources are constrained, deprioritisation of ITN mass campaigns in certain settings is being increasingly considered through subnational tailoring of malaria control interventions. Our work highlights that the relationship between transmission intensity (whether measured in terms of prevalence or clinical cases) and intervention impact is non-linear, and notable resurgences in cases may follow when campaigns are deprioritised in all but very low transmission settings. This broadly supports WHO subnational tailoring guidance, which suggests consideration of deprioritising distribution of ITNs in regions with PfPR<sub>2-10</sub> < 1% (World Health Organization, 2025). However, while the World Health Organization (2025) Subnational Tailoring Reference Manual proposes that the withdrawal of ITNs in favour of indoor residual spraying should be considered in areas with low ITN use, here we estimate that ITN use alone appears to be a notably poorer predictor of the impact of ceasing mass campaigns than use given access. Our findings suggest that regions with higher use given access may experience disproportionately greater resurgences in cases following deprioritisation. This implies that regions with low use given access may warrant consideration for cessation of ITN distribution, rather than decisions being based solely on low overall ITN use irrespective of whether communities have sufficient ITN access. However, subnational differences in ITN use, access and retention are key knowledge gaps in many settings, and when estimated from infrequent surveys they are highly sensitive to bias arising from the timing of surveys relative to when campaigns were conducted. To our knowledge, this study is the first to estimate subnational variation in ITN retention and the first to estimate the duration that ITNs remain in use, which is of greater epidemiological relevance than retention time. It also provides a novel framework to correct for biases in estimates of ITN use and access arising from when campaigns were conducted. Although campaigns have historically aided increasing ITN use and access over time, we estimate the mean duration of ITN use is consistently shorter than mean retention times in all regions. This raises questions about whether punctuated distribution of ITNs through campaigns is the optimal mechanism for maximising their effectiveness and cost-effectiveness. Maximising the cost-effectiveness of interventions has become increasingly pertinent in the current funding context, and consideration of alternative distribution strategies, such as increased distribution through continuous distribution channels, including school- or community-based distribution, may be warranted. Frameworks such as the one presented here, which take into account the potential for impact from different net types and the high variability of ITN duration and use, could support NMP decision making on how best to maximise impact from available funds. Whilst such frameworks may be a useful tool, local knowledge of factors impacting ITN access and use as well as operational decision making will be paramount for NMP-led tailoring of subnational strategies.”

      (W1.3) On L236, the link to SNT is stated: "the models indicate trends that can support subnational tailoring of ITNs". They could indeed, but SNT itself is not done in this paper. It seems to be about improving sub-national predictions of the impact of single ITN strategies, by taking into account sub-national variation in access and use duration. This is useful, and the model developed has novel aspects.

      Thank-you for highlighting this. We hope our updated title and response to W1.12 below help address this. Where relevant we have also framed our findings in relation to the World Health Organization’s Subnational tailoring of malaria strategies and interventions: refence manual which was published following our original submission; examples of this are highlighted in our response above to W1.2.

      (W1.4) Individual countries may have records on when nets were distributed to the regions rather than needing to use the annual country number of nets together with the DHS data. It could be helpful to say what the analysis steps would be in that case.

      We have now added the following text of appendix 3.2 to clarify how the methodology could be adapted:

      “In contexts where national malaria programmes or other stakeholders have knowledge of the timings of mass campaigns (i.e. when there is no uncertainty in ɸ<sub>ij</sub>), the methodology can be adapted by deterministically evaluating the time since the last campaign (equation S18) for each time point.”

      (W1.5) There were several assumptions that needed to be made in building the model. There is some validation of the timing of the distributions (L633 "verified where possible through discussion with interested parties nationally and internationally") and the fit of estimated access and use to survey data, and agreement between predictions of prevalence and MAP estimates. It would be helpful to say which assumptions are important for the results (and would be key knowledge gaps) and which would not make a difference. It might be possible to validate the net timing model using a country where net distributions are known reasonably well.

      Thank-you for raising this. We acknowledge that to investigate which assumptions are less likely to make a meaningful difference, we would ideally have conducted a full sensitivity analysis on these. This however would be challenging, since many of these are structural assumptions rather than numerical ones (for example, the assumption of an exponential decay in use and access) which would require the entire methodology to be adapted to conduct a sensitivity analysis. We did validate our estimated campaign timings against some known subnational campaign timings for Senegal. However, we could not source data on when all campaigns were conducted for all regions of Senegal to the nearest month to be able to conduct validation against this. We were also not able to source other use and access data from separate data sources to the DHS to be able to validate our discrete-time models of historical use and access. PfPR2-10 estimates are however fitted to equivalent MAP estimates. These were validated against DHS estimates of PfPR6-59mo, which were not used at any stage to fit our models. We have made slight changes to the original wording in relation to this at the end of appendix 5.2.

      (W1.6) What was assumed about what happens to old nets after a mass campaign was not clear. This assumption is likely to affect the predictions of access for the biennial distributions.

      To generate our initial estimates of the mean duration of use and retention time with our hierarchical model, we assume nets are only distributed to individuals who do not already have ITNs (appendix 2). This initial step is necessary for our methodology, but is relaxed later under our discrete-time model where we assume ITNs are distributed at random such that individuals with an ITN are equally likely to receive a new ITN (and replace their existing one) following a mass campaign (appendix 4). Much of the aforementioned sections has been rewritten and we hope this is now clearer.

      (W1.7) L312 and elsewhere: That use given access declines with net age is plausible. However, I wondered if this could be partly a consequence of the assumptions in the model (eg the two exponential decays for access and use, the possible assumption that new nets displace the current ones when there is a mass campaign).

      Declining use given access as nets age is not affected by model assumptions. Due to being fitted independently of each other, there are no constraints that would prevent a faster decay in access than use. Had the data supported this, this would have led to use given access increasing over time since the last campaign. The data did not support this. Further clarification that use and access are fitted independently of each other is has now been provided in the following text:

      “All subsequent analyses described are conducted independently for use and access”

      (W1.8) The Methods section on Estimating historical use and access seemed to be aimed at readers familiar with formulae, but I think it could lose other interested readers. It could be useful to explain a little more about what is happening at each step and also why.

      Thank-you for highlighting this. We have re-written this section in the main manuscript, now named ‘Historical use, access and retention times’, where we now only highlight key equations and provide a high-level overview of the methodological steps. We have sought to provide clearer explanations here behind the rationale for each step to ensure maximum accessibility for interested readers. The original wording was used as a basis for the newly provided series of appendices which provide further technical detail; this wording has also been heavily re-drafted to improve clarity of each step.

      (W1.9) The model was fitted to MAP estimates of PfPR2-10, which themselves come from a model. It may be that there is different uncertainty in the MAP estimates for different regions. I couldn't see this on the graph, but maybe the uncertainty is small. Was this taken into account in the fitting?

      We only used median MAP estimates of PfPR2-10 to calibrate the baseline EIR for each region in our model. We have clarified our rationale in appendix 5.2:

      “Since the relationship between baseline EIR and PfPR2-10 here is specific to malaria simulation, MAP uncertainty estimates were not propagated through to our estimates in baseline EIR since these would not faithfully represent its true uncertainty.”

      (W1.10) Was uncertainty from each estimated component integrated into the other components?

      Thank-you for highlighting this as this indicates we had failed to clearly indicate this. To confirm, we propagate uncertainty in each component through to our estimates of cases averted. New text has been provided to clarify this in the following text:

      “Region-specific uncertainty in ITN efficacy, use, retention, and the relative contributions of continuous and campaign channels is therefore propagated through to our estimates of cases averted.”

      Further details are also provided in the preceding text of the same paragraph. The central 95% credible intervals of cases averted shown in figures 5.C and 6 and associated figure supplements are reflective of this uncertainty.

      (W1.11) Eyeballing Figure 2 (Burkina Faso), there is a general pattern of decline in all the regions, some differences between the regions and some differences in how well the model fits between the regions. If possible, it could be helpful to say how much better the fit was when using regionspecific compared to countrywide parameter values for access and use, and how different the results would be.

      In the “Universal coverage: was it achievable under triennial mass campaigns” results section, we have now provided further emphasis that the observed decrease from DHS data may be driven by surveys being conducted progressively later in relation to the last campaign:

      “The observed decrease in use and access across many regions in Burkina Faso may therefore be a by-product of DHS surveys being conducted at progressively later dates relative to the most recent campaign; this does not necessarily indicate an underlying trend in decreasing use or access over longer timescales.”

      In the case of Burkina Faso (figure 2.A), aside from months when very small numbers of individuals were surveys where either 0% or 100% use or access was reported, no other data lie outside our 95% credible interval for any region.

      We are unable to generate comparisons with countrywide parameters as these are not generated when fitting our discrete-time model, even though they are a by-product of the initial hierarchical model used to generate initial estimates of region-specific ITN retention, which was a necessary methodological step. We hope the extensive revision of the text in the methods and appendices helps to improve the clarity on this. Where national estimates are provided, these are population-weighted means of the subnational median posterior estimates. New text is included in appendix 1 to clarify this:

      “National and continental values are reported as population-weighted summaries of the median subnational estimates generated from the discrete-time models”

      (W1.12) The question of moving from a campaign every three to every two years may not be the most pertinent question in the current funding landscape. I realise that a paper is in development for a long time, but it would be helpful to comment on what else the model could be used for when fewer rather than more nets are likely to be available.

      We acknowledge the funding landscape has changed substantially, but we still believe this work has important implications in the current context. We have emphasised this further in the following text:

      “If budget constraints necessitate the deprioritisation of campaigns, our results highlight that this should be avoided, if possible, in regions with moderate to high transmission intensity, particularly those with mean annual incidence exceeding 100– 150 clinical cases per 1,000 people. Shortening campaign intervals from three to two years in moderate- and high-transmission regions is projected to avert more cases than the additional cases that may arise from ceasing campaigns in some lower-transmission settings. Additionally, although pyrethroid–chlorfenapyr ITNs are more costly, the additional cases projected to be averted by them relative to pyrethroid-only and pyrethroid–PBO ITNs are substantial. In certain national contexts it may be more cost-effective for biennial pyrethroid-chlorfenapyr campaigns to be conducted in fewer subnational regions even under reduced budgets. However, more thorough economic analyses will be needed to understand this fully. Moreover, as ITNs remain one of the most cost-effective malaria control interventions, improving the impact of them could still be more cost-effective than the introduction of new untested interventions (Topazian et al., 2023; Schmit et al., 2024).”

      We have also related some of our findings to the WHO Subnational Tailoring Reference Manual (as highlighted in W1.2), which we hope better relates our findings to the current context.

      Reviewer #2 (Public review):

      Summary:

      The authors design a custom Bayesian model to estimate the probabilities of access, use and use given access of insecticide-treated nets in six African countries, providing sub-national estimates and inferring the average duration of ITN use and access. An individual-based model was employed to simulate malaria epidemics and estimate the effectiveness of different ITN distribution strategies. The study finds that the mean probability of use or access did not reach 80% (a universal coverage formely targeted by WHO) for any of the regions, even for biennial campaigns, demonstrates that switching from triennial to biennial distribution campaigns increases population use by 7.9%, and evaluates the impact of employing more efficient ITNs on P. falciparum prevalence.

      Strengths:

      The authors developed a data-driven model that accounts for data collection imperfections and sources of uncertainty while differentiating between ITN use and access. They developed a methodology to infer the timing of a mass campaign from publicly available data instead of assuming fixed dates. The probability of use given access allows for determining the regions where ITN distribution is least effective. This work can help better inform future interventions by identifying regions where increasing mass campaign frequency or employing better ITNs are most effective. Finally, in addition to insights on ITN access and use for the six countries analyzed, the paper contributes a methodological framework that can likely be extended to other countries.

      Weaknesses:

      Since the models employed are rather complex, the description of the methodology may be hard to follow for most readers. In addition, the models assume many hypotheses, including:

      (W2.1) Exponential decay of ITN use/access.

      We do acknowledge different modelling studies have typically assumed either an exponential decay or an “S-shaped” smooth-compact loss function, with many of these studies having been validated against cluster-randomised trial data for both functional forms. We believe the ITN age distribution data across the DHS surveys inspected provides reasonable evidence to support the use of an Exponential decay function here. We have now included a proof (appendix 2.1) demonstrating an exponentially distributed ITN age distribution will be yielded for an exponential decay function with the same rate parameter; this is true under periodic ITN distribution and becomes an approximation for a finite number of surveys. We now also included additional text (appendix 2.2) highlighting the empirical ITN age distributions appear to support our exponential decay assumption.

      (W2.2) The decay rates for the probability of the ITN repelling and killing a mosquito are the same.

      Although the same decay rate parameter (\gamma_N) is present in our expressions for the probability of repellency and mortality (equations (53) and (54)), the half-life of the latter is shorter, since repellency is assumed to decay towards a constant value. These structural forms are not unique to this paper but are shared among all malaria simulation-based studies with ITN interventions. This decay rate parameter has been estimated in previous studies (Sherrard-Smith et al., 2022; Churcher et al., 2024), and we carry through uncertainty estimates from those previous studies into the work presented here; additional text has been added to clarify this:

      “Uncertainty in ITN repellency and mortality parameters (equation (53) and (54)) is also propagated forward to this study by simulating random draws from previous posterior distributions (Sherrard-Smith et al., 2022; Churcher et al., 2024) across each distribution event and realisation.”

      (W2.3) Given a time instant, all individuals in the same administrative unit and have the same probability of using a net;

      Our discrete-time model estimates the proportion of the population with use and access at each time instant. We purposefully do not conflate this with the probability of use and access, which can vary between individuals within the same subnational unit of analysis (urban and rural regions of each administrative-one area). We are grateful this point has been raised as it indicates we had not communicated this sufficiently clearly before. We hope the extensive re-draft of the ‘Historical use, access and retention times’ methods section has helped address this, in particular in the following text preceeding equation (7):

      “We do not assume the probability of access is the same for all individuals in a region at a given point in time. Instead, we assume the probability any given individual has access to an ITN at time t<sub>j</sub> can be described by a Beta distribution”

      (W2.4) ITN use/access decay models do not depend on the distribution strategy (e.g. bienal vs trienal distribution).

      We may not have fully understood this point, but in terms of our historical models of use and access, assumptions are not imposed on the frequency of previous campaigns. Instead, historical campaign timings are estimated from data from DHS surveys and the AMP Net Mapping Project (now detailed in appendix 3.1); historical estimated intervals could be either two or three years (or indeed any interval) as informed by this data. In terms of the duration of use and retention time, these are estimates how long a net would continue to be used, or provide access, if an individual were not to replace it at earlier date; these estimates are therefore independent of campaign intervals, and we have now added addition text to provide additional clarity:

      “However, throughout this study, the durations of use and retention time are always estimates of how long an individual continues to use or have access to a net in the absence of future replacement; estimates of these are therefore reflective of behaviour or ITN durability and not distribution patterns themselves.”

      We do acknowledge under our approach, use immediately following a campaign is agnostic of campaign frequency; however, given an absence of data on how use changes following a switch from triennial to biennial campaigns, we believe this was a reasonably conservative assumption. Further confirmation is now provided in the following text, with additional preceding context:

      “Future campaigns, whether conducted every two or three years, are therefore assumed to achieve a consistent initial level of use.”

      (W2.5) The Bayesian model assumes some narrow prior distributions.

      Thank-you for highlighting this. We acknowledge the need for further justification for the choice of priors. We have provided this in depth for the hierarchical model of the mean duration of use and access (in appendix 2.2). Further justification for the choice of priors for the discrete-time model are also now provided in appendix 4.2).

      The impact of these hypotheses on the estimated parameters is not explored in the paper, and no sensitivity analyses are performed, although some limitations are discussed.

      We fully acknowledge we had not conducted sensitivity analyses for many of our assumptions, and we have now tried to provide better justification for our assumptions. The assumptions most likely to influence inference are structural components of the modelling framework rather than scalar parameters that can be varied independently in a conventional sensitivity analysis. Many of the assumptions highlighted above are structural, such as the assumption of an exponential decay (W2.1). In the case of our assumption of exponential decay, multiple elements of the methodology are restricted by this (for example, when correcting for biases that arise from nets being lost between campaigns and survey times when estimating the timing of campaigns in appendix 3.1). Investigating the sensitivity of this assumption over an assumed smooth compact function would require extensive adaptation of the methodology that would be beyond the scope of this paper. Some other assumptions, such the assumption of the same decay rate parameter for repellency and mortality (W2.2) have been estimated in the previous studies referenced and have been validated against cluster-randomised, controlled trials. We nevertheless recognise our justification of some assumptions could have been expanded upon previously, and we hope the changes highlighted above go towards addressing this.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (R1.1) I looked for the reference WHO 2024b for the recent optimal allocation guideline, but there were just three WHO 2024 references in the bibliography. In addition, what exactly the 80% rule applies to is not clear - this could be explained so it is clearer what result to compare to it (or explain that the rule itself is not clear).

      We have used the eLife LaTeX/BibTex template for citations throughout and acknowledge this doesn’t show letter suffixes in the reference list for multiple author-year entries. We unsure of how to address this given this is generated by the official template, though we note that when citations are clicked on in the document, the relevant citation is then shown at the top of the page on the web version.

      (R1.2) L24 'estimated', but this seems more like a prediction. The words 'estimated' and 'predicted' should be carefully used throughout when combining statistical and mechanistic modelling.

      This has now been changed.

      (R1.3) The point estimates should always have measures of uncertainty.

      The rationale for the omission of credible intervals for some point estimates has now been clarified in the manuscript (appendix 1). The following text has been added:

      “Additionally, in relation to uncertainty estimates, credible intervals are shown for all subnational quantities that are directly estimated in our models. National and continental values are reported as population-weighted summaries of the median subnational estimates generated from the discrete-time models (appendix 4) and therefore do not correspond to explicitly estimated model parameters, so credible intervals are not shown for these aggregated estimates.”

      (R1.4) It would be helpful to justify the choice of ADM1 as the geographical unit.

      We have clarified the rationale for this on the following text:

      “Here, (subnational) regions are defined as the first administrative unit below the country level and are further divided into rural and urban areas to align with DHS stratification”

      (R1.5) The terminology was slightly confusing: in some places, it sounded as if regions were the sub-national regions, in others as if they were different things (eg L74, L105). L45 'and' seems odd here.

      ‘Region’ is used interchangeably with ‘subnational region’ at points in the paper to aid the flow of the text. We hope the use of paratheses around (subnational) in the updated text quoted above (and on the following text) helps provide clarity:

      “here, the units of analysis are consistently referred to as (subnational) regions”

      (R1.6) Spurious accuracy in some estimates, e.g. L52.

      This was a result cited from Bertozzi-Villa et al. (2021) for which uncertainty estimates were not available. We hope the response to R1.3 above helps clarify the rationale for omitting credible intervals for some estimates generated here.

      (R1.7) L68 'lose' instead of 'loose'.

      Now corrected.

      (R1.8) L534. I suspect that the model was actually fitted in Stan via the R interface rstan.

      Language adjusted accordingly.

      (R1.9) L633 'through' rather than 'though'.

      This section has been heavily redrafted and we have checked for typos.

      Reviewer #2 (Recommendations for the authors):

      The paper is well-written and presents an important contribution to better aid interventions. The proposed models are reasonable, but because of their complexity, even readers who work with epidemic modelling might have issues understanding the methodology.

      We thank the reviewer for highlighting that the methodology may be difficult to follow. The methods section has now been substantially rewritten to provide a clearer conceptual description of the modelling framework, with detailed model specification and derivations moved to the appendices. We hope this restructuring will allow readers to follow the modelling approach at a high level in the main text with technical details contained in the appendices.

      To improve the clarity of the methods section, I suggest:

      (R2.1) Include a list of symbols with the meaning of each variable defined in the text.

      Definitions for symbols are now also shown in appendix 1 – tables 1-5.

      (R2.2) Include a centralized full description of each model, clearly stating the priors and likelihood (similarly to a Stan code).

      There are two models that are fitted with Stan (the hierarchical retention model and discrete-time use/access model). To improve clarity for the hierarchical model, priors are now presented in a single block (equations 11 – 17) in appendix 2.2, with the likelihood (equation 18). For the discrete-time model, we have split the presentation of the priors (equations 37 – 42) and the likelihood expressions (equations 43 – 45) into different subsections (respectively appendices 4.2 and 4.3).

      (R2.3) If needed, include additional data preprocessing in the form of an algorithm.

      Although we have not included an algorithm outlining the preprocessing steps, we have ensured sufficient detail has been provided to facilitate replicability. For example, in appendix 1, we now outline how use and access are inferred from DHS data:

      “ITN use is inferred from DHS data (ICF, 2025) on whether individuals slept under an ITN the previous night, while all individuals who used an ITN are assumed to have access; when fewer than two individuals used an ITN, the ITN is assumed to be able to provide access at random to up to two individuals in a household.”

      (R2.4) Mention the main hypotheses and limitations of the model in the main text.

      We have ensured key assumptions of the model are stated in the re-written ‘Historical use, access and retention times’ methods subsection; for example, in the following text:

      “Due to the sparsity and irregularity of DHS and MIS surveys, we were unable to investigate seasonal fluctuations in either access or use; we therefore assume that nets provide access or are used continuously over some period of time.”

      (R2.5) Including a flowchart or diagram that provides an overview of the proposed framework could be helpful.

      We have now included a flowchart of methodological steps in appendix 1 – figure 1.

      (R2.6) Line 89: Define NMP before presenting the acronym.

      We have ensured this is defined in the first instance on line 39.

      (R2.7) Equation (1): Explain why you chose the Exponential distribution (e.g. constant hazard), as this is one of the main hypotheses of the model.

      As highlighted in our response to W2.1, we have now included justification of this assumption in the final paragraph of appendix 2.2.

      (R2.8) Equation (2): Although Equation (2) passes a clear message of how alpha_i^x is distributed, I wonder if it is mathematically correct to express the limit this way, since the argument of the limit is a random variable. Maybe the limit should be applied to gamma_i^x instead.

      Thank-you for highlighting this. We acknowledge the limit behaviour was expressed in a short-hand manner that is not strictly mathematically correct. Indeed, the limit should be applied to the decay rate parameter gamma (now shown in equation 10). In appendix 2.1, we have now provided a proof demonstrating the rate parameter of the pooled ITN age distribution should tend to the same decay rate as the assumed exponential loss function.

      (R2.9) I think the difference between pho_i^x (Equation (1)) and alpha_i^x (Equation (2)) is not very clear in the text.

      In the context of access, rho_{i(l)} and alpha_{i(l)} are respectively the duration an ITN l is retained for and its age at the time of a survey. We hope the redrafted appendices make this clearer, in addition to the inclusion of the new parameter tables in appendix 1.

      (R2.10) Line 479: Typo (and or).

      Updated wording is now contained in appendix 2.

      (R2.11) Line 711: Typo (The limit is equal to infinity).

      This has now been corrected.

      (R2.12) Equation (15): I could not understand this equation. What is rho(s) and rho(s \in I), where I is one of the intervals mentioned in this equation?

      Rho(tau_ik) was introduced as simplified notation for the probability density of the timing of campaign k in region i (tau_ik) but we acknowledge this was not explained clearly. We also acknowledge this equation presented a lot of concepts at once. The equation attempted to describe the probability density of the last campaign in region i relative to time t_j, denoted phi_ij. We no longer make use of this previously notation (rho) for the probability density. This equation has been updated to equation (30), with incremental explanation of its construction now provided on lines in appendix 3.2.

      (R2.13) Line 642: What is t?

      The use of $t_j \ni t$ was previously used to indicate that the discrete time point t_j lies within continuous time t. We acknowledge this was a non-standard use of notation and was not clearly explained. This section (now in appendix 4) has been rewritten without this notation. The use of t and t_j to denote continuous time and discrete time points respectively is now defined in the core notation table (appendix 1 – table 1).

      (R2.14) The proposed model has narrow hyperhyperpriors because of convergence issues. Are the estimated parameters sensitive to the choice of hyperhyperpriors?

      We acknowledge limited justification was previously provided for the choice of hyperhyperpriors. We have now provided additional justification within appendix 2.2.

      (R2.15) Since the proposed Bayesian models are relatively complex, it might be useful to provide convergence diagnostic plots in the supplement.

      Convergence diagnostics were inspected using the ShinyStan packagxe. Chains showed satisfactory convergence based on standard diagnostics. We have not included diagnostic plots due to the large number of parameters in the fitted models. Under the hierarchical model (appendix 2) for ITN use, 146 region-specific parameters (one for each region), 12 country-level hyperparameters (two for each country), and four hyperhyperparameters were estimated. Under the discrete-time model (appendix 4), a further 876 parameters (six for each region) were estimated. In total, 1,038 parameters were fitted for the ITN use models. The same number of parameters were estimated for the ITN access models, giving a total of 2,076 estimated parameters.

    1. Author response:

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

      eLife Assessment

      This manuscript presents a useful computational framework for systematically characterising how heterogeneity in initial conditions or biophysical parameters shapes the dynamic behaviour of protein signalling networks, with potential relevance to understanding adaptive drug resistance. While the approach represents a significant methodological contribution, the extent to which its conclusions are biologically informative remains debated, as the model is not qualitatively or quantitatively validated against experimental data. As a result, the strength of evidence supporting the mechanistic claims is viewed as incomplete.

      We thank the editors and reviewers for their further assessment of the manuscript. The revised public review raises several issues that overlap with points addressed in our previous response, particularly around the intended scope of MDN modelling, the interpretation of parameter sampling, and the qualitative nature of the experimental comparison. In this final revision, we have made targeted clarifications in the main text, Methods, figure legends, and Supplementary Information to make these points more explicit for readers. We emphasise that the present work is intended as a theoretical and exploratory framework for mapping the qualitative dynamic behaviours accessible to a fixed network topology, rather than as a quantitatively calibrated model of a specific tumour or cell line.

      Joint Public Review:

      In this manuscript, the authors proposed an approach to systematically characterise how heterogeneity in a protein signalling network affects its emergent dynamics, with particular emphasis on drug-response signalling dynamics in cancer treatments. They named this approach Meta Dynamic Network (MDN) modelling, as it aims to consider the potential dynamic responses globally, varying both initial conditions (i.e., expression levels) and biophysical parameters (i.e., protein interaction parameters). By characterising the "meta" response of the network, the authors propose that the method can provide insights not only into the possible dynamic behaviours of the system of interest but also into the likelihood and frequency of observing these dynamic behaviours in the natural system.

      The authors study the Early Cell Cycle (ECC) network as a proof of concept, focusing on pathways involving PI3K, EGFR, and CDK4/6 with the aim of identifying mechanisms that may underlie resistance to CDK4/6 inhibition in cancer. The biochemical reaction model comprises 50 state variables and 94 kinetic parameters, implemented in SBML and simulated in Matlab. A central component of the study is the generation of large ensembles of model instances, including 100,000 randomly sampled parameter sets intended to represent intra-tumour heterogeneity. On the basis of these simulations, the authors conclude that heterogeneity in kinetic rate parameters plays a stronger role in driving adaptive resistance than variation in baseline protein expression levels, and that resistance emerges as a network-level property rather than from individual components alone. The revised manuscript provides additional clarification regarding aspects of the simulation and filtering procedures and frames the comparison with experimental data as qualitative. Nonetheless, the study is best interpreted as a theoretical and exploratory analysis of the model's behaviour under heterogeneous conditions. Consequently, questions remain regarding the biological grounding of the sampled parameter regimes and the extent to which the reported frequencies of resistance-associated behaviours can be directly interpreted in physiological terms.

      While the authors propose a potentially useful computational framework to explore how heterogeneity shapes dynamic responses to drug perturbation, a number of important conceptual and methodological concerns remain to be addressed:

      (1) The sampling of kinetic parameters constitutes the backbone of the manuscript, yet important concerns remain regarding its biological grounding and transparency. Although the revised version provides additional clarification on the exploration of "model instances", it is still not sufficiently clear how parameter values and initial conditions are generated, nor how the chosen ranges relate to biological measurements. The kinetic rates are sampled over broad intervals without explicit justification in terms of experimentally measured bounds or inferred distributions. As a consequence, it remains uncertain whether the ensemble of simulated behaviours reflects physiologically plausible cellular regimes or primarily the properties of the assumed parameter space. In this context, the large-scale sampling (100,000 parameter sets) resembles a Monte Carlo exploration of the model rather than a biologically calibrated representation of tumour heterogeneity.

      Parameters were sampled from a uniform distribution spanning values 10-5 to 104. Conserved totals were sampled from the range 100 to 104. Each of these is roughly in line with measured spans of orders of magnitude for parameter values and protein expression (REF). Again, we would like to point out that we intentionally kept our ranges broad, and sampled from uniform distributions, to assess upper bounds of heterogeneity, not biologically informed heterogeneity. We also comment on the likely effects of expanding these ranges in our response to (26) in our original rebuttal.

      Main text has been updated to include this information. LINES: 175-179

      Furthermore, the adequacy of the sampling strategy in such a high-dimensional space (94 free parameters) remains open to question. In the absence of biologically informed constraints, the combinatorial space of possible parameter configurations is vast, and it is unclear to what extent the sampled ensembles can be considered representative. This issue is particularly relevant because the manuscript interprets the frequency of resistance-associated behaviours as indicative of their likelihood.

      This was addressed extensively in our original rebuttal, response to point (3). A new section was added to the supplementary text, along with new figures demonstrating the validity of the claims.

      The validation presented in Figure 7 does not fully resolve these concerns. The comparison with experimental data is qualitative, and the simulations are performed in arbitrary time units, which complicates direct interpretation alongside time-resolved experimental measurements. Moreover, certain qualitative discrepancies between simulated and experimental trends (e.g., persistent versus decreasing CDK4/6 activity) are not thoroughly discussed. As this figure represents the primary empirical reference point in the manuscript, the extent to which the model captures experimentally observed dynamics remains uncertain.

      This was addressed in the original rebuttal, response to point (12). The actual time units are arbitrary in the sense that they are determined by the units of the parameters in our model. It is important to understand that the meta-dynamic analysis is not calibrated to data and so the meaning of time units is far less important than the distribution of behaviours. We have updated the figure to reflect the arbitrary units of time in our simulations.

      Finally, aspects of presentation continue to limit transparency. Parameter ranges are described at different points in the manuscript but are not consolidated clearly in the Methods, and the definition of initial conditions remains ambiguous - particularly whether these correspond to conserved quantities or to the dynamic variables used to initialise simulations. In addition, the exact number of model instances underlying specific analyses and figures is not always explicit. Greater clarity on these issues is essential for assessing reproducibility and for interpreting the quantitative claims of the study.

      (2) A central conclusion of the manuscript is that heterogeneity in protein-protein interaction kinetics is a stronger driver of adaptive resistance than heterogeneity in protein expression levels. To assess the latter, the authors fix a nominal set of kinetic parameters and generate 100,000 random initial concentrations for the 50 model species. However, according to the simulation protocol described in the manuscript, each trajectory includes three phases: (i) simulation under starvation conditions to equilibrium, (ii) mitogenic stimulation to a second ("fed") equilibrium, and (iii) application of drug treatment. The equilibrium concentrations reached in phases (i) and (ii) are determined by the kinetic parameters of the model and are independent of the initial concentrations, provided the system converges to a stable steady state. In dynamical systems terms, stable equilibria are defined by the parameter set and attract all initial conditions within their basin of attraction. Since the kinetic parameters are fixed in this experiment, the pre-treatment equilibrium that serves as the starting point for drug application should likewise be fixed. Under these conditions, it is therefore not unexpected that sampling a large number of initial concentrations has limited influence on the treated dynamics.

      This raises conceptual questions about the interpretation of the comparison between kinetic and expression heterogeneity. If the system converges to a unique stable steady state prior to treatment, then variability in initial concentrations does not propagate into variability in drug response, and the observed dominance of kinetic heterogeneity may partly reflect this structural property of the model rather than a biological principle. Clarification is needed regarding whether multiple steady states exist under the nominal parameter set, and if so, how basins of attraction are explored.

      More broadly, it remains unclear why initial protein concentrations can be sampled independently of the kinetic parameters. In biological systems, steady-state expression levels are typically determined by the underlying kinetic rates. A more consistent approach might require constraining initial concentrations to correspond to equilibrium states of the chosen parameter set, thereby introducing relationships between at least some of the 50 initial conditions and the 94 kinetic parameters. Finally, the manuscript employs a non-standard terminology regarding "initial conditions," which may further obscure interpretation of these results and would benefit from clarification.

      This was addressed in the original rebuttal, response to point (4). Text was modified to clarify what was meant by initial conditions to clarify that this meant the conserved total for the protein species. A supplementary figure (supp. fig. 4) was added to demonstrate that changes to the conserved totals of protein species does, in fact, shift the dynamics and steady state equilibria of protein species. Text was updated throughout the paper to ensure that our definition of ‘initial conditions’ was consistent throughout the text.

      (3) The technical implementation of the modelling and simulation framework remains difficult to evaluate due to insufficient methodological detail. Although the authors state that kinetic parameters are randomly sampled, the manuscript does not specify the distributions from which parameters are drawn, nor whether potential correlations between parameters are considered or explicitly ignored. Without this information, it is not possible to assess how implicit modelling assumptions shape the ensemble of simulated behaviours. Given that the conclusions rely on frequency-based interpretations across sampled parameter sets, greater transparency regarding the sampling procedure is essential.

      Updated the main text to clarify random sampling from a log transformed uniform distribution. LINES: 175-179

      A further concern relates to the parameter filtering step. The authors report that the "vast majority" of sampled parameter sets produced systems that were "too stiff," and that these were excluded on the grounds that stiff dynamics are not biologically plausible. However, the manuscript does not clearly define how stiffness is assessed, nor why stiffness is interpreted as biologically unrealistic rather than as a numerical property of the formulation. In standard practice, stiff systems are typically handled using appropriate implicit solvers rather than being discarded. Similarly, parameter sets that produce negative state values are excluded, yet such behaviour may arise from numerical artefacts rather than from intrinsic model inconsistency. The rationale for excluding these parameter sets, rather than adapting the numerical scheme, is not sufficiently justified.

      The reported rejection rate - approximately 90% of sampled parameter sets - is substantial and raises questions regarding the interplay between model structure, parameter ranges, and numerical methods. As currently described, the filtering step appears to select parameter sets based primarily on computational tractability rather than on experimentally motivated biological criteria. The manuscript would be strengthened by clarifying whether the retained parameter sets are representative of biologically meaningful regimes, and by distinguishing clearly between exclusions based on biological plausibility and those arising from numerical considerations.

      This was extensively addressed in the original rebuttal, response to points (6) and (7). Main text was updated to clarify that a solver specific for stiff systems was used. Furthermore, we addressed this issue but consequential analysis revealed that lack of drug response and not achieving steady state in the simulated time period now accounted for the majority of filtering. This had no effect on the distributions of behaviours identified in our analyses. Main text was updated to reflect these changes. Rejection rate was explicitly discussed in main text.

      Finally, important aspects of the simulation protocol require clarification. The model is simulated under "fasted" and "fed" conditions until equilibrium is reached, yet the criterion used to determine convergence is not specified. It would be important to describe how equilibrium is assessed (e.g., based on the norm of the time derivatives). Additionally, it remains unclear whether the mitogenic stimulus applied in the "fed" phase is assumed to be constant over time and, if so, how this assumption relates to biological experimental conditions. Greater detail on these implementation choices is necessary to ensure interpretability and reproducibility.

      This was addressed in the original rebuttal, response to point (8). Clarification about simulations were added to main text, including explicitly stating that mitogenic and drug inputs were continuous stepwise functions and how steady state equilibrium was defined/calculated.

      (4) The manuscript states that the modelling conclusions are strongly supported by existing literature; however, the validation presented does not fully substantiate this claim. As noted above, the comparison with CDK2 and CDK4/6 experimental data remains qualitative, and the use of arbitrary simulation time units complicates interpretation of temporal agreement. The extent to which the model quantitatively or mechanistically recapitulates experimentally observed dynamics therefore remains uncertain.

      This was addressed in the original rebuttal, response to points (13) and (14). Wording was changed to remove the suggestion of strong evidence and the tone was shifted to reflect reasonable qualitative support for our analysis, not strong evidence.

      The claim that the model reproduces known resistance mechanisms is also difficult to assess in light of Figure S10, where a large fraction of network nodes (~80%) appear implicated in resistance under some conditions. If most components of the network can, in at least some parameter regimes, be associated with resistance phenotypes, the resulting lack of selectivity weakens the strength of model-based validation. It becomes challenging to distinguish specific mechanistic insights from generic consequences of network connectivity.

      In addition, the Supplementary Information notes that certain components of the mitogenic and cell-cycle pathways were abstracted or excluded in order to maintain computational tractability. While such abstraction is understandable in a large ODE framework, it raises interpretative questions. Proteins identified as potential resistance drivers within the model may, in some cases, represent aggregated or simplified pathway effects. Clarifying in the main text how such abstractions may influence the attribution of resistance mechanisms would strengthen the biological interpretation of the results.

      This was addressed in the original rebuttal, response to points (15). The discussion was significantly revised to reflect our reasoning with respect to our conclusions. We completely understand that more work could be done to verify our claims, however, our intention is to demonstrate the generalised relationship between network heterogeneity and drug resistance, not to predict patient-specific resistance mechanisms.

      Drug inhibition is central to the manuscript's conclusions. The revised version clarifies that inhibition is implemented as a fixed fractional modification of specific kinetic rate laws. This abstraction is appropriate for exploring network-level responses, but it represents a stylised perturbation rather than a pharmacologically calibrated model of drug action. For full interpretability and reproducibility, the mathematical form of the modified rate laws, as well as the timing of inhibition relative to network equilibration, should be specified unambiguously. The biological implications of the findings depend critically on understanding this modelling choice.

      All equations were included in the supplementary model files, including typeset ODEs, as requested by the reviewers. R15 and R27 contain the relevant equations, which specify the exact implementation of the drug inhibition. Number of time units per simulation phase now included in main text. LINES: 166 – 168

      The one-at-a-time perturbation analysis presented in Figure 5 provides an interpretable ranking of first-order control points across the ensemble and offers mechanistic insight into primary sensitivities of the network. However, many targeted therapies act on multiple components, and resistance frequently arises through combinatorial mechanisms. The reported rankings should therefore be interpreted as identifying primary influences under isolated perturbations, rather than as a comprehensive account of multi-target drug behaviour.

      Overall, the manuscript succeeds in presenting a conceptual and exploratory framework for analysing how signalling network topology can shape the qualitative landscape of adaptive responses under heterogeneous kinetic conditions. Its principal contribution lies in establishing a systematic platform for large-scale in silico exploration. At the same time, the current limitations in biological calibration, parameter grounding, and validation constrain the extent to which the conclusions can be interpreted as predictive or quantitatively representative of specific tumour contexts. Addressing these issues would further strengthen the connection between the theoretical landscape described here and experimentally observed resistance dynamics.

      Joint Recommendations for the authors:

      (1) Supplementary Figure S4 is not sufficiently explained in its current form. The structure of the figure, the meaning of its colour coding, and the intended interpretation are not clearly described, making it difficult for readers to extract the key message without substantial inference. Given that the manuscript relies heavily on large-scale ensemble analyses, clear visual communication is essential. A more detailed legend, explicit definition of axes and colour scales, and improved visual labelling would substantially enhance clarity, accessibility, and reproducibility.

      Supp. Fig. 4 legend updated with additional detail. LINES: Supp. Text. 256 - 263

      (2) The approximately 90% rejection rate of sampled parameter sets should be reported explicitly in the main text of the manuscript rather than only in the Supplementary Information. Given the central role of large-scale parameter sampling in the study, this level of exclusion is a critical aspect of the modelling workflow and directly affects the interpretation of robustness and representativeness. Clear disclosure in the main text would allow readers to properly evaluate the effective size of the analysed ensemble and the implications of the filtering procedure for the generality of the conclusions.

      This was explicitly addressed in the original rebuttal.

      (3) The model would benefit from quantitative validation against experimental data. In Figure 7C, the authors note in the response letter that the simulations are performed in arbitrary time units. However, the figure itself labels the time axis in hours, which may lead readers to infer a direct quantitative correspondence between simulated and experimental time courses. If the simulations are not calibrated to real time, this labelling is potentially misleading and should be corrected. Either the model should be explicitly time-calibrated and quantitatively compared to experimental measurements, or the figure should clearly indicate that the time axis is dimensionless. Clarifying this point is essential to avoid overinterpretation of the agreement between model and data.

      Label updated.


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

      Joint Public Reviews:

      In this manuscript, the authors proposed an approach to systematically characterise how heterogeneity in a protein signalling network affects its emergent dynamics, with particular emphasis on drug-response signalling dynamics in cancer treatments. They named this approach Meta Dynamic Network (MDN) modelling, as it aims to consider the potential dynamic responses globally, varying both initial conditions (i.e., expression levels) and biophysical parameters (i.e., protein interaction parameters). By characterising the "meta" response of the network, the authors propose that the method can provide insights not only into the possible dynamic behaviours of the system of interest but also into the likelihood and frequency of observing these dynamic behaviours in the natural system.

      The authors studied the Early Cell Cycle (ECC) network as a proof of concept, specifically focusing on PI3K, EGFR, and CDK4/6, with particular interest in identifying the mechanisms that cancer could potentially exploit to display drug resistance. The biochemical reaction model consists of 50 equations (state variables) with 94 kinetic parameters, described using SBML and computed in Matlab. Based on the simulations, the authors concluded the following main points: a large number of network states can facilitate resistance, the individual biophysical parameters alone are insufficient to predict resistance, and adaptive resistance is an emergent property of the network. Finally, the authors attempt to validate the model's prediction that differential core sub-networks can drive drug resistance by comparing their observations with the knock-out information available in the literature. The authors identified subnetworks potentially responsible for drug resistance through the inhibition of individual pathways. Importantly, some concerns regarding the methodology are discussed below, putting in doubt the validity of the main claims of this work.

      While the authors proposed a potentially useful computational approach to better understand the effect of heterogeneity in a system's dynamic response to a drug treatment (i.e., a perturbation), there are important weaknesses in the manuscript in its current form:

      (1) It is unclear how the random parameter sets (i.e., model instances) and initial conditions are generated, and how this choice biases or limits the general conclusions for the case studied. Particularly, it is not evident how the kinetic rates are related to any biological data, nor if the parameter distributions used in this study have any biological relevance.<br /> (2) Related to this problem, it is not clear whether the considered 100,000 random parameter samples sufficiently explore parameter space due to the combinatorial explosion that arises from having 94 free parameters, nor 100,000 random initial conditions for a system with 50 species (variables).<br /> (3) Moreover, the authors filter out all the cases with stiff behaviour. This filtering step appears to select model parameters based on computational convenience, rather than biological plausibility.<br /> (4) Also, it is not clear how exactly the drug effect is incorporated into the model (e.g., molecular inhibition?), nor how it is evaluated in the dynamic simulations (e.g., at the beginning of the simulation?). Moreover, in a complex network, the results may differ depending on whether the inhibition is applied from the start or after the network has reached a stable state.<br /> (5) On the same line, the conclusions need to be discussed in the context of stability, particularly when evaluating the role of initial conditions. As stable steady states are determined by the model parameters, once again, the details of how the perturbation effect is evaluated on the simulation dynamics are critical to interpret the results.<br /> (6) The presented validation of the model results (Fig. 7) is only qualitative, and the interpretation is not carefully discussed in the manuscript, particularly considering the comparison between fold-change responses without specifying the baseline states.

      We thank the reviewers for their thoughtful and constructive comments. In response to their comments, we have undertaken a substantial revision to address all the comments, improve clarity, transparency, and robustness while preserving the paper’s core contribution: a principled, scalable framework (MDN) for mapping how molecular heterogeneity and network architecture shape adaptive drug-response dynamics. At a high level, we clarified the study design and analysis goals, tightened definitions, and added methodological detail where it most advances interpretability. Importantly, these updates leave the analytical pipelines and major conclusions unchanged.

      Conceptually, we now make explicit that our objective is coverage of the output space of qualitative dynamics supported by the network topology, not exhaustive enumeration of parameter space. To support this, we added a convergence analysis and clarified that “triplicates” refers to independent ensembles used to demonstrate reproducibility. We also refined how we describe and implement initial conditions (as conserved total abundances that encode expression heterogeneity) and reframed filtering as minimal numerical/feasibility checks, using rejection sampling to obtain the prespecified ensemble size. Solver choices and input modelling (constant step mitogen/drug) are now spelled out succinctly.

      We expanded the model specification and rationale (complete reaction list with rate laws and brief biological justifications in the Supplement) and unified terminology throughout. Figures and legends have been overhauled for readability and accuracy, with missing labels added and ordering corrected. For validation, we clarified the nature of the single-cell reporter readout, improved Figure 7’s presentation, and emphasised - consistent with our aims - that comparisons are qualitative.

      Finally, we have rewritten the Discussion to centre on interpretation, implications, and connect our findings to the literature. It now: (i) frames MDN as a systems-level framework that links molecular heterogeneity to qualitative signalling “meta-dynamics” and adaptive escape under constant drug pressure; (ii) highlights two key findings: an asymmetry in control (interaction kinetics exert stronger, more consistent influence than protein abundance) and a topology-driven convergence whereby a vast parameter space funnels into a finite set of recurrent behaviours; (iii) shows that resistance is a network-level property, with many possible routes but a small set of recurrent hubs/modules dominating; and (iv) provides a qualitative alignment with single-cell reporter data while clarifying the intent and limits of that comparison. Moreover, we now explicitly discuss limitations (rate-law simplifications, broad priors, determinism, and modular abstractions) and outline next steps for future research, including data-constrained priors and stochastic extensions.

      We believe these revisions materially strengthen the manuscript and fully address all the reviewers’ comments. A detailed, point-by-point response follows.

      Joint Recommendations for the Authors:

      (1) It is confusing exactly what are the different sets evaluated in each cases, e.g. "generated 100,000 model instances, each with the same set of ICs but a unique set of randomly generated parameter values" (lines 299-300), "generated 100,000 model instances (in triplicate), each with the same set of 'nominal' parameter values (see supplementary Table S1), and a unique set of ICs, and repeated the analysis as performed previously" (lines 366-368), "combined the 1000 IC sets with each parameter set to create 1000 model instances" (lines 382-383), "repeated for 1000 parameter sets, allowing us to observe how frequently IC variation induced adaptive resistance independent of the chosen parameter set" (lines 386-387). A small table or just a clearer explanation is needed.

      In response to these comments, we have revised the main text to clarify the process of model instance generation. Specifically, we have made changes at page 7: line 297 - page 8: line 302, page 8: lines 305 - 310, page 9: lines 372-378, and page 9: line 384 – page 10: line 399 in the revised main text.

      We have also added a new Figure (Figure S1) to the supplementary file to allow readers to visualise the model generation process for each relevant set of experiments. Supplementary figures are referenced in the main text where appropriate.

      (2) The authors mentioned performing each simulation in triplicate, which is puzzling as the model is based on deterministic ODEs with fixed parameters for each simulation. Under such conditions, one would anticipate identical results from multiple simulations with the same initial conditions and fixed parameters. Perhaps the authors expect the model to exhibit chaos or aim to assess the precision of the parameter estimates through triplicate simulations. Further clarification from the authors would be valuable to comprehend the rationale behind conducting triplicate simulations in a deterministic setting.

      We agree that repeating deterministic ODE simulations with identical inputs would be redundant. In our study, “triplicate” referred instead to generating three independent ensembles of 100,000 unique model instances each, where model parameters (or initial conditions) were randomly resampled. These ensembles were analysed separately to assess whether the inferred meta-dynamic distributions converged robustly. Indeed, the distributions from the three replicates were nearly indistinguishable, confirming that the results are reproducible and not artefacts of a particular random draw.

      We have revised the main text to clarify this distinction (page 8: lines 305 - 310) and added an extended explanation for meta-dynamic behaviour convergence in the new section Error Convergence in the supplementary text (page 6: lines 184 - 210).

      (3) While the lack of a connection between model parameters and biological data (mentioned in the public review) may not be a fatal flaw in the manuscript, the concern about the 100,000 random samples being insufficient to explore the parameter space is valid. In a thought experiment, considering the high and low rate for each parameter and the combinatorial explosion of possibilities (2^94), the number of simulations performed (100,000) represents only an extremely small fraction of the entire parameter space (~1/10^(23)). This limitation might not accurately capture the true heterogeneity present inside a solid tumour. One potential solution is to determine biological bounds on model parameters through data fitting, which can provide more meaningful constraints for the simulations. Alternatively, increasing the number of simulations and adopting more efficient sampling techniques can enhance the coverage of possible parameter sets.

      We thank the reviewer for this insightful comment. We agree that the 94-dimensional parameter space is vast, and that 100,000 simulations represent only a fraction of the total combinatorial possibilities. However, the objective of our study is not to exhaustively sample the entire parameter space, but rather to sufficiently sample the ‘output space’ - that is, the complete spectrum of qualitative dynamic behaviours the network topology can generate. The key question is whether 100,000 model instances are sufficient for the distribution of these output dynamics to converge.

      To formally address this, we have performed a convergence analysis, which is now detailed in the new supplementary section "Error Convergence" (Supplementary text page 6: lines 184 - 210) and illustrated in Supplementary Figure S12. This analysis demonstrates that the mean squared error (MSE) between dynamic distributions from N and 2N simulations exponentially decreases as N increases, and the distribution of protein dynamics changes negligibly well before reaching 100,000 instances. Furthermore, performing the entire analysis in triplicate with independent random seeds yielded nearly identical meta-dynamic maps (average standard deviation < 0.04%), giving us high confidence that we have robustly captured the network's behavioural repertoire.

      We believe this convergence occurs because the system is degenerate: many distinct parameter sets within the high-dimensional space map to the same qualitative outcome (e.g., 'rebound' or 'decreasing'). Our goal was to capture the set of possible outcomes, not every unique parameter combination that leads to them.

      Regarding the parameter range, we intentionally chose a broad, unbiased range (10<sup>-5</sup> to 10<sup4></sup>)as a proof-of-concept to delineate the theoretical upper limit of heterogeneity the network can support, thereby capturing even rare but potentially critical resistance dynamics. We agree with the reviewer that a future direction is to constrain these ranges using biological data. Such an approach would transition from defining what is possible (the focus of this manuscript) to predicting what is probable in a specific biological context. We have added this important point to the Discussion (page 16: lines 663-679) to highlight this avenue for future work.

      (4) One of the manuscript's main results indicates that protein interactions play a more significant role in driving adaptive resistance than protein expression. To explore the impact of protein expression, the authors fixed a nominal parameter set and generated 100,000 initial concentrations of the 50 proteins in the ODE model. However, the simulations' equilibrium concentrations in the "starvation" and "fed" phases, which form the initial condition for the treated phase, are uniquely determined by the nominal model's kinetic parameters and not the initial conditions, which remain identical for each simulation. From a dynamical systems perspective, stable steady states are determined by the model parameters and attract all initial conditions within their basin of attraction. As a result, a random sampling of the initial conditions has a limited impact on the model dynamics. The authors' conclusion that "the ability of expression to induce resistance also seems to be dependent on the master parameter set" can be explained by this dynamical systems perspective, where the resistance state corresponds to a stable steady state determined by the master parameter set. Considering this, the evidence presented in the manuscript may not fully support the authors' conclusion regarding the importance of protein expressions relative to protein dynamics. The discrepancy might be attributed to a possible misunderstanding of this point, and further clarification from the authors could be helpful.

      We thank the reviewer for the thoughtful perspective. We agree that, in a monostable system with fixed kinetic parameters and fixed conserved totals, varying only the initial split among moieties (e.g., X vs pX) will not change the final steady state; trajectories converge to the same attractor. In our analysis, however, “initial conditions” predominantly refer to total protein abundances (e.g., X_tot = X + pX + complexes), used as a proxy for expression heterogeneity. These totals are invariants on the simulated timescale (no synthesis/degradation in the pre-equilibration phases), and therefore alter the value of the steady state under a given parameter set. In other words, our IC sampling mostly varies conserved totals rather than merely redistributing a fixed total; hence the equilibrium reached after the starvation/fed pre-equilibrations depends on the sampled totals and the kinetics. This can be seen in the new Supplementary Figure S4, showing that changing the ICs does shift the eventual steady state even when kinetic parameters are fixed.

      We have revised the text to: (1) define ICs explicitly as total abundances for multi-state species, (2) distinguish “initial split” from “conserved totals,” and (3) clarify that expression effects are context-dependent rather than universally dominant (page 4: lines 139-141 and page 10: lines 413-416)

      (5) Additionally, it is important to note that the random sampling of 100,000 initial concentrations might not sufficiently explore the vast space of possible initial conditions. In the thought experiment mentioned earlier, where each protein can have high or low expression concentrations, there are approximately 2^(50) = ~10^(15) possible combinations of initial concentrations. Thus, the 100,000 random simulations only represent around ~1/10^(10) of the possible initial conditions in this simplistic scenario. Consequently, this limited sampling of initial conditions may not provide enough information to draw meaningful conclusions, even if the initial conditions were more directly linked to kinetic rates.

      Please see our response to Comment (3). Briefly, our ICs are continuous total abundances (conserved moieties), not binary high/low states; many IC configurations converge to the same qualitative attractors, so we estimate distributional properties rather than enumerate all combinations. Our convergence diagnostics (independent replicates and sample-size doubling) show that the meta-dynamic distributions stabilise well before N=100,000 (see Supplementary Figure S12). We have clarified this in the Supplementary Information (Error Convergence section) with the new convergence results.

      (6) The authors implement a parameter selection step in the manuscript, where they filter out parameter sets that lead to what they term non-biological simulations. However, the rationale for determining if a given parameter set results in a stiff system of ODEs remains unclear. The authors cite references [38,39] to support the claim that stiff equations are not biologically plausible. Still, upon review, it is evident that [38] does not include the term "stiff," and [39] discusses using implicit methods to simulate stiff ODE models without specifically commenting on the biological plausibility of stiff systems. The manuscript lacks direct evidence to justify the conclusion that filtering out parameter sets that result in stiff ODE systems is reasonable. Since the filtering step accounts for the majority of discarded parameter sets, a stronger foundation is required to support the statement that stiff equations are non-biological.

      We thank the reviewer for pointing out the issue in our original justification. The reviewer is correct: stiff systems are a common feature of biological models, and our claim that they are likely ‘biologically implausible’ was not well substantiated. The filtering of these model instances was, in fact, due to a computational limitation rather than a biological principle. The issue was that these parameter sets produced systems of ODEs that were so numerically stiff they were unsolvable within a reasonable timeframe by the SUNDIALS ODE solver suite, which is specifically designed for such systems.

      Following the reviewer's comment, we investigated the source of this prohibitive stiffness. We discovered it was not an intrinsic property of the parameter sets themselves, but rather an artifact of our simulation setup. The extreme stiffness occurred almost exclusively during the initial integration timesteps, caused by the large initial discrepancy between the concentrations of active and inactive protein forms. This large discrepancy created the conditions for overtly stiff solutions i.e. unsolvable with implemented ODE solve settings. To overcome this problem, we set a large maximum number of steps in the ODE solver for the first couple of time points, enabling the solver to overcome the excessively stiff portion of the solve. We found that the vast majority of the previously 'unsolvable' model instances could now be successfully simulated. Consequently, the number of parameter sets discarded due to solver failure is now negligible (< 1%), and this filtering step no longer accounts for the majority of discarded parameter sets. Most importantly, the distributions of dynamics were not significantly altered by this adaptation.

      We have revised the " Sampling and filtering of model instances (page 5: lines 174 – 189)" part in the Methods section to reflect this more accurate understanding. We have corrected our original claim regarding the biological plausibility of stiff systems and corrected our use of the references. Ref [38] was included to demonstrate that models of biological systems are stiff, which was a major conclusion of that paper, and [39] was originally included to demonstrate that solving ODEs is reliant on solvers that can integrate stiff systems. Upon review, ref [39] has been removed.

      Overall, this investigation has made our analysis more robust by allowing us to include a wider, more representative range of parameter sets, and has tangibly improved the quality of our study.

      (7) Additionally, it is important to consider the standard method for accounting for stiff systems, as presented in [39], which involves using implicit numerical methods for ODE simulation. The authors mention using numerical methods from the SUNDIALS suite, which includes implicit methods, but the specific numerical method used remains unclear. Furthermore, it would be valuable for the authors to disclose the number of parameter sets that were filtered to obtain the final set of 100,000 accepted parameter sets. This information would provide insights into the extent of filtering and the proportion of parameter sets that were excluded during the selection process.

      We apologise for the lack of specific detail and have now updated the text. To clarify, all ODE simulations were performed using the CVODE solver from the SUNDIALS suite. This solver employs an implicit, variable-order, variable-step Backward Differentiation Formula (BDF) method, which is robust and specifically designed for handling the stiff systems common in biological network modelling. We have now explicitly stated this in the "ODE model construction, modelling, and simulations (page 4: lines 162 – 164)" section of the Methods.

      Regarding the filtered parameters, we have included a revised and detailed discussion of this in the "Sampling and filtering of model instances (page 5: lines 174 – 189)" part in the Methods section (see our response to comment (6) above). Briefly, after applying the filters, ~40–45% of instances did not reach steady state within the simulation timeframe, and ~50–55% did not meet the minimum drug-response criterion. Approximately 10% satisfied all criteria and were retained for analysis. Importantly, we employed ‘rejection sampling’ and continued drawing until we had N = 100,000 accepted instances that satisfied all the criteria.

      (8) An important step in the simulation process described by the authors is the simulation of the "fasted" and "fed" states until an equilibrium is reached. However, it is not clear how the authors determine if the system has reached an equilibrium. It would be helpful if the authors could provide more information regarding the criteria used to assess equilibrium in the simulations. Regarding the "fed" state, it is not explicitly stated whether the mitogen stimulus is assumed to be constant throughout the "fed" experiment. Considering the dynamic nature of mitogen stimulation in biological systems, it would be beneficial if the authors could clarify this assumption and discuss its biological relevance.

      We apologise for the lack not specifying this in the original text. A simulation was considered to have reached equilibrium when the concentration of every protein species changed by < 1% over the final 100 time steps of the simulation phase. We have now added this criterion to the "Sampling and filtering of model instances (page 5: lines 177 – 179)" part of the Methods section.

      Regarding the second part of the comment, in our simulations, both the mitogenic and the drug inputs were modelled as constant, stepwise functions that, once turned on, remained at a fixed concentration for the remainder of the simulation. The biological rationale for this choice was to rigorously test for bona fide adaptive resistance. By maintaining a constant mitogenic and drug pressure, we can ensure that any observed recovery in the activity of downstream proteins is due to the internal rewiring and adaptation of the signalling network itself, rather than an artefact of the removal or decay of the external stimulus/drugs. We have now clarified this rationale in the "ODE model construction, modelling, and simulations (page 4: lines 168 – 171)" part of the Methods section.

      (9) The "Description of Model Scope and Construction" section in the Supplementary Information should include explicitly the model reactions and some discussion about their specific form (e.g., why is '(((kc2f1*pIR*PI3K) / (1 + (pS6K/Ki2))) + (kc2f2*pFGFR*PI3K))' representing the phosphorylation rate of PI3K, with pS6K in the denominator?).

      The reviewer is right to ask for model justification. We have expanded the Supplementary “Description of Model Scope and Construction” section (page 2: line 63 – page 5: line 185) to include a complete reaction list with rate laws and a brief rationale for each. We also explain the specific PI3K phosphorylation term: activation by pIR and pFGFR is attenuated by pS6K via a denominator, which captures the well-described S6K-mediated negative feedback that reduces activation (e.g., via IRS1 phosphorylation).

      (10) In line 349, the statement "Given that CDK46cycD is only strongly suppressed in just under 60% of the model instances (Figure 3C)" lacks clarity regarding where to look to interpret the 60% value. If this means that 4 out of the 7 model instances are resistant, and the other 2 proteins also have the same percentage of resistance, then there is no apparent reason to focus solely on CDK46cycD.

      The reviewer is correct; the figure reference was an error, which has been rectified in the main text (page 9: line 355). The actual figure reference was to Supplementary Figure 2A, which shows the heatmap of all the frequencies for each protein dynamics for all the active protein forms. CDK4/6cycD shows a sustained decreasing dynamic for 59.93% of model instances, which is where this number was derived. We have also now explicitly referenced this number in the supplementary Figure 2A legend.

      We focus on CDK4/6cycD because it is the direct pharmacological target of CDK4/6 inhibitors. Our point was to suggest that even when the target is suppressed in the majority of instances (~60%), this does not reliably propagate to uniform downstream inhibition across the network, thus highlighting emergent, network-driven adaptive responses.

      (11) We observed that in Fig. 5A, the authors show that multiple pathways are blocked. However, it is unclear whether they reduced the value of one parameter in the experiment or simulated multiple combinations of parameter inhibition. Considering the large number of parameters (94) in the model, if the authors simulated all possible combinations of parameter inhibition, the number of combinations would be significantly more than 94. An actual inhibitor typically has an inhibitory effect on multiple molecules. Therefore, it would be necessary to identify the parameters that lead to drug resistance when multiple molecules are inhibited. However, examining the inhibition patterns for all 94 parameters would be practically impossible. As a potential approach, we suggest using ensemble learning techniques, such as random forests, to handle this problem efficiently. With a dataset of binary outputs indicating the presence or absence of resistance for a sufficient number of inhibition patterns, ensemble learning can be applied to find the parameters that contribute to drug resistance. Popular feature selection algorithms like Boruta could be utilised to identify the most relevant parameters. The results obtained by ensemble learning are similar to the ranking in Fig. 5C, potentially providing a more robust validation of the authors' findings. By incorporating these additional analyses, the authors could strengthen the reliability and significance of their results related to parameter inhibition and drug resistance.

      We appreciate the suggestion and the opportunity to clarify. Figure 5A depicts multiple pathways were interrogated, but in the analysis, parameters were inhibited one at a time (OAT) - not in combination. We have revised the figure legend and added a section named “Protein knockdown perturbation analyses (page 6: lines 228 – 233)” in the Methods section to make this explicit. Moreover, some additional text in the main text has been slightly modified to make this clearer (page 11: lines 462-463, page 24: lines 856-857).

      We chose the OAT design intentionally to obtain causal, first-order attribution of control points across a broad parameter ensemble without confounding from simultaneous co-inhibition. This provides an interpretable ranking of primary drivers (Figure 5C) that is consistent with the paper’s mechanistic focus. We agree that a multi-target inhibition approach could be a useful next step; however, an exhaustive combinatorial screen is beyond the scope of this proof-of-concept. In such future studies, the ensemble learning, as suggested by the reviewer, could be layered onto our MDN framework to assess robustness of the ranking under co-inhibition.

      (12) In explaining the parameterization of the model, we find an implication of a quantitative model. However, upon examining the results in Fig. 7D, we observe that they are only qualitatively correct. When comparing Figs. 7A and 7C, we note that many model instances are immediately suppressed, and the time scale remains unknown. We believe it would be essential for the authors to explain how the model of this study maintains its quantitative nature despite the results in Fig. 7. If such an explanation cannot be provided, it raises concerns regarding the biological reliability of several findings within this study.

      While our framework is built on quantitative ODEs, the validation we present in Figure 7 is indeed qualitative. This is an intentional and key feature of our study's design. Our goal was not to build a calibrated, quantitative model of a specific cell line (e.g., MCF10A), but rather to establish a proof-of-concept theoretical framework that systematically explores the full spectrum of dynamic behaviours a given network topology can possibly generate. To achieve this, we intentionally sampled parameters from a very broad, unbiased range to delineate the theoretical upper limit of heterogeneity. This in silico population is therefore designed to be far more heterogeneous than any single isogenic cell line.

      The striking qualitative agreement seen between our meta-dynamic distributions and the single-cell data in Figure 7D is thus not a failure of quantitative prediction, but rather a strong validation of our core premise: that a significant degree of signalling heterogeneity exists in cell populations and that our framework can effectively capture its emergent properties.

      Regarding the specific comment on Figure 7C, we apologise for the lack of clarity. Nominally, we chose to simulate for 24 hours however, the x-axis in our simulations represents arbitrary time units, as the timescale is dependent on the meaning/units of the parameter values. The goal is to compare the qualitative shape of the response (e.g., rebound, sustained decrease), not the absolute time in hours. Moreover the rapid initial suppression seen in many of our model instances (Fig 7C) is a direct parallel to the rapid suppression seen in the experimental data (Fig 7A). This initial phase is followed by a wide variety of adaptive behaviours (or lack thereof) in both our simulations and the real cells, which is the key phenomenon we are studying.

      We have revised the text (page 14: lines 598-601) and Figure 7’s legend to state more explicitly that our validation is qualitative and to clarify the purpose of our broad, uncalibrated approach. We have also added a note in the Discussion (page 18: lines 744-747) that calibrating this framework with cell-line-specific data is a natural next step for generating quantitative, context-specific predictions.

      (13) Related to the previous point, the experimental data is presented as fold-change during CDK4/6 inhibition, and we notice that the initial fold-change at time 0 varies between 1 and 1.8. The difference in initial fold-change is unclear to us, as our understanding of fold-change typically corresponds to the change from baseline, typically represented by the protein concentration at time 0.

      Furthermore, while the experimental data exhibits uniformly decreasing CDK4/6 activity, a substantial number of simulations indicate constant CDK4/6cycD, showing a significant qualitative discrepancy between the simulations and experimental findings. This disparity makes it difficult for us to interpret the comparison between the two datasets effectively, given the complexities in comprehending the experimental fold-change figure.

      As Figure 7 serves as the primary validation of model simulations in the manuscript, we believe that the current presentation may not provide a compelling reason to believe that the model accurately captures experimental data. To enhance clarity and validation, we suggest overlaying the experimental data over the simulations or considering the median and 10/90% percentile of the experimental data, which may potentially offer improved readability and facilitate a more robust interpretation of the comparison.

      The experimental data from Yang et al. (ref 55, main text) measures kinase activity using a nucleus-to-cytoplasm translocation reporter system, wherein a bait protein is phosphorylated by the target kinase causing it to translocate from the nucleus to the cytoplasm. Hence, the y-axis represents the ratio of nuclear vs. cytoplasmic fluorescence, not a fold-change from a t=0 baseline. The variation in the starting value (between 1 and 1.8) reflects the inherent heterogeneity in the reporter's localization across individual cells even before the drug is added. We have updated the y-axis label and revised Fig. 7’s legend to state this explicitly.

      The most likely explanation for the discrepancy between experimental dynamics and our simulation dynamics is that the experimental data comes from an isogenic cell line that is largely sensitive to CDK4/6 inhibition. Our simulations are derived from a very wide parameter sweep, where the intent is to represent all possible cell states. It is quite striking that that there is such a high correlation between the experimental data and simulations, indicating that perhaps the heterogeneity of even isogenic cell lines is significantly greater than might be intuited; a point we now mention in the revised Discussion (page 17: lines 716-727).

      It is worth noting again, that our analysis is intentionally constructed to be as heterogeneous as possible, and is not trained on any biological data that might otherwise constrain the output-behaviour space. The isogenic cell line almost certainly represents a much more constrained output-behaviour space than our analysis.

      The y-axis label has also been updated accordingly. As mentioned in (12) this result is intended as a qualitative validation, showing that cell lines indeed have highly variable signalling dynamics. Given the range of parameters tested, we think it is surprising that the degree of agreement between the experiment and our analysis is as high as it is. Again, we believe this suggests that heterogeneity may be more prevalent than is intuited. We do not believe we have made any strong quantitative claims in the main text, and we certainly aim to work towards biological, quantitative validation in the future. Finally, we altered the wording of the results heading (page 14: line 562) to make it clear that we are only making qualitative claims and removed the claim that the evidence was strong.

      With these clarifications and corrections, we believe the validation is now much more compelling. The key point is not a perfect quantitative match, but the strong similarity in the distribution of heterogeneous behaviours.

      (14) The authors mention simulating treatment with 10nM of CDK4/6i or Ei, but specific details on how this treatment is included in the model simulations are not provided. This lack of information makes it challenging to fully evaluate the comparison between model simulations and experimental evidence in Figure 7. It would be highly appreciated if the authors could clarify how the treatment with CDK4/6i or Ei is incorporated into the simulations to facilitate a better understanding and interpretation of the results.

      To clarify, the effects of the inhibitors were incorporated directly into the kinetic rate laws of their respective target reactions.

      CDK4/6 inhibitor (CDK4/6i): This was modelled as an inhibitor of the formation of the active CDK4/6-cyclin D complex. We have now explicitly detailed this in the description for reaction R27 in the "Description of Model Scope and Construction" section of the Supplementary Information.

      Estrogen Receptor inhibitor (Ei): This was modelled as an inhibitor of the estrogen-dependent activation of the Estrogen Receptor. This is now explicitly detailed in the description for reaction R15 in the same supplementary section.

      It is however important to reiterate that our goal in Figure 7 is qualitative, shape-based comparison; therefore, we used a fixed fractional inhibition (reported in Methods) rather than a calibrated IC50/Hill model.

      (15) The authors state strong support for their modelling conclusions based on the literature. However, we still have concerns regarding the validation of the model against CDK2 or CDK4/6 data in Figure 7, as it appears less convincing to us. Furthermore, the authors list known resistance mechanisms that are replicated in their modelling. Nevertheless, we find the conclusion somewhat weakened by Figure S10, where approximately 80% of the nodes are implicated in some form of resistance pathway. This raises questions about the model's selectivity, as many proteins included in the model seem to drive resistance in some manner. In the Supplementary Information, the authors mention excluding or abstracting some protein species from the mitogenic and cell cycle pathways to manage computational resources effectively. This abstraction makes it difficult to determine if the proteins identified as potential drivers of resistance genuinely drive resistance or might represent abstractions of other potential drivers. To enhance the manuscript's clarity and address potential concerns about the model's selectivity and abstraction, we suggest providing more details and discussion in the main text.

      The reviewer's observation that a large number of nodes are implicated in resistance pathways in Figure S10 is correct. However, we argue this is not a weakness of the model's selectivity, but rather a key finding that reflects the biological reality of adaptive resistance. The literature is replete with a wide and growing number of distinct mechanisms of resistance even to a single class of drugs (1,2), which supports the idea that cancer can co-opt a wide variety of network nodes to survive.

      Figure S10 is not a binary map where every implicated node is equal, instead it is a likelihood map, where the colour and weight of the connections represent how often a particular interaction participates in driving resistance across the theoretical full range of possible network dynamics. The figure shows that while many nodes can contribute to resistance, they do so in a hub-like manner i.e. small subsets of nodes coordinate to drive resistance. This provides a rationalised, data-driven prioritisation of the most dominant and recurrent resistance strategies. We draw two important conclusions from this work 1) Resistance likely occurs due to resistance hubs, not individual proteins, and 2) that the frequency of a resistance hub in an MDN analysis is likely proportional to the frequency of that hub emerging as a resistance mechanism in a population of cells and patients.

      Regarding the issue of abstraction, the reviewer is correct that this is an inherent feature of any tractable systems model. In our case, several species in the mitogenic/cell-cycle pathways are module-level proxies to control model size. The highly implicated "hub" nodes in our model likely represent critical cellular processes that are themselves composed of several individual protein interactions.

      To address these concerns, we have significantly revised the Discussion (page 16: lines 681 – 694) to: (1) frame resistance as a network-level phenomenon; (2) show that our frequency-based ranking is selective, prioritising the most probable, recurrent mechanisms; and (3) clarify that - given model abstraction -our findings implicate critical processes (modules), not just single proteins, as the drivers.

      Overall, these changes do not alter our main conclusions: adaptive resistance is an emergent, network-level property; many routes exist, but a smaller set of nodes/modules consistently carry the largest influence across heterogeneous contexts.

      (16) We consider that the figures and legends, including the supplementary information, are inadequately explained. The information provided is insufficient for us to comprehend the figures fully, leading to the need for interpretation on our part as readers. This could potentially introduce biases when trying to understand the claims made by the authors. To improve our understanding, it would be essential for the authors to assign appropriate labels to the figures and provide comprehensive explanations in the legends. For example, in Fig 3, we suggest labelling the tree diagrams in panels A and B, as well as the colour bars. We also recommend applying the same approach to other figures, adding accurate axis labels and descriptions of colour gradients to enhance clarity.

      We thank the reviewer for this critical feedback. To address this comment, the figure legends have been revised where appropriate and greatly expanded to improve their comprehension. Moreover, we have added explicit labels to all previously unlabelled components, such as the cluster dendrograms and colour code bars in Figure 3A, B.

      (17) To enhance readability, we recommend interchanging the order of Figures 1 and 2 in the sequence they appear in the main text. Alternatively, the text can be adjusted to refer to the figures in the correct order. Additionally, attention should be given to the bottom of Fig 1, which appears to be cropped or cut off. Furthermore, the incorrect word spacing in some figure elements, such as Fig. 3A title, Fig. 5B title, and Fig. 6B y-label, should be corrected for improved visual presentation.

      Following the reviewer’s comment, the order of Figures 1 and 2 has been switched to reflect the order in which they are referred to in the main text. These Figures have been re-exported to fix unintentional word spacing errors.

      (18) We recommend that the language used to refer to the initial conditions in the manuscript is clarified and homogenised. Currently, the authors use different terms such as "basal expression," "protein expression," "state variable values," or "initial conditions" to refer to them. This variation in terminology can be confusing for readers. In particular, the use of "basal expression" is problematic, as it typically refers to the leaky value of a reaction in the absence of an inducer, making it another biophysical parameter of the system rather than an initial condition. To enhance clarity and consistency, we suggest the authors decide on a single term to refer to the initial conditions throughout the manuscript and provide a clear explanation of its meaning to avoid any confusion. This will help readers better understand the concept being discussed and prevent any potential misinterpretations.

      We thank the reviewer for this very helpful suggestion. To resolve this and improve clarity, we have homogenized the language throughout the manuscript. We now clarify the use the following 3 terms in their specific contexts:

      We use “protein abundances” exclusively for the conserved total abundances of multi-state species (e.g., Xtot = X + pX + complexes) that are sampled across instances to represent expression heterogeneity.

      We use ‘initial conditions’ to refer to initial values of the state variables in a model simulation. This term is related to protein abundance as the setting of initial conditions for conserved species sets the protein abundance. This is explicitly stated in the text (page 3: lines 87 - 91).

      We use “state variables” to refer to the time-dependent model species.

      We avoid the term “basal expression” in technical descriptions. Where a biology-facing phrase is helpful, we use “protein expression level”. This is used when referring to the biological concept that the initial conditions are intended to represent, i.e. the heterogeneity in protein amounts across a cell population.

      We have performed a thorough search-and-replace to ensure this new convention is applied consistently and have removed the potentially confusing term "basal expression" from the revised manuscript.

      (19) Why are saturable functions (e.g., Michaelis-Menten functions) ignored in the model? What are the potential consequences?

      The main objective of this work was to perform a large-scale, systematic exploration of a high-dimensional parameter space (94 parameters) to map the full repertoire of qualitative dynamic behaviours a network topology can support. Using saturable functions like Michaelis-Menten kinetics would have roughly doubled the number of parameters to be explored (from k to Vmax and Km for each enzymatic reaction), making a parameter sweep of this scale computationally intractable. We therefore prioritised the breadth of the parameter search over the depth of kinetic detail, which we believe is the appropriate choice for a proof-of-concept study focused on heterogeneity.

      This simplification has potential consequences. A major one is that our model cannot capture phenomena that arise specifically from enzyme saturation, such as zero-order kinetics or certain forms of ultrasensitivity (switch-like responses). However, we argue that this is an acceptable trade-off for two main reasons: (1) Our analysis is based on classifying broad, qualitative response shapes (increasing, decreasing, rebound, etc.). Mass-action kinetics are fully capable of generating this rich spectrum of behaviours; and (2) by varying the mass-action rate constants over nine orders of magnitude (from 10<sup>-5</sup> to 10<sup4></sup>), our parameter sweep effectively samples a vast range of reaction efficiencies. A very low rate-constant can approximate the behaviour of a saturated, low-efficiency enzyme, while a high rate-constant can approximate a highly efficient, non-saturated one. In this way, the broad sweep of the rate parameter partially reflects the effects that would be captured by varying Vmax and Km.

      For transparency, we have added a brief rationale to the “ODE model construction, modelling, and simulations” part of the Methods (revised main text, page 4: lines 153-155) and the "Description of Model Scope and Construction" section in the Supplementary file (Supplementary text page 2: lines 63-73).

      (20) Given the relevance of the concept of "heterogeneity" in this work, a short discussion about biochemical noise and its implications on the analysis (e.g., why it is not included, and if it will be a next step) would be appreciated.

      Our MDN modelling framework represents heterogeneity by creating an ensemble of deterministic models, where each model instance has a unique set of kinetic parameters and/or initial protein abundances. We propose that this is a powerful way to mechanistically represent the functional consequences of all sources of cellular variation. Over time, the effects of genetic mutations, epigenetic states, and even the time-averaged impact of intrinsic biochemical noise will manifest as changes in the effective interaction strengths and protein concentrations within a cell. Our large-scale parameter/IC sweep is designed to systematically explore the full range of dynamic behaviours that can emerge from this underlying biological variation. Therefore, our approach does not compete with stochastic modelling but is complementary to it. While stochastic simulations can capture the dynamic trajectories of single cells, our framework provides a panoramic view of the entire spectrum of possible stable phenotypes that can emerge at the population level. We agree that modelling intrinsic biochemical noise (stochasticity arising from finite copy numbers), e.g. using chemical Langevin or SSA, is a possible extension in future work but expected to be very computationally expensive. We have added a brief discussion on this as future direction in the revised Discussion.

      (21) We have noticed that the first four paragraphs of the Discussion section overlap with the Introduction, as they mainly reiterate the significance of the study itself rather than focusing on the specific results obtained. To avoid redundancy and provide a more cohesive and informative discussion, we recommend that the authors shift the focus of the Discussion section towards presenting potential interpretations, even if they are not definitive, of the results obtained. By doing so, the Discussion will serve as a valuable platform for deeper analysis and insightful observations, allowing readers to better comprehend the implications and significance of the research findings.

      We thank the reviewer for this structural feedback. Following the reviewer's feedback, we have significantly rewritten and restructured the Discussion section. The redundant introductory material has been removed.

      The rewritten Discussion centres on interpretation, implications, and connect our findings to the literature. It now: (i) frames MDN as a systems-level framework that links molecular heterogeneity to qualitative signalling “meta-dynamics” and adaptive escape under constant drug pressure; (ii) highlights two key findings: an asymmetry in control (interaction kinetics exert stronger, more consistent influence than protein abundance) and a topology-driven convergence whereby a vast parameter space funnels into a finite set of recurrent behaviours; (iii) shows that resistance is a network-level property, with many possible routes but a small set of recurrent hubs/modules dominating; and (iv) provides a qualitative alignment with single-cell reporter data while clarifying the intent and limits of that comparison. Moreover, we now explicitly discuss limitations (rate-law simplifications, broad priors, determinism, and modular abstractions) and outline next steps for future research, including data-constrained priors and stochastic extensions.

      We believe this substantial revision has transformed the Discussion into a much more insightful and valuable part of the manuscript that directly addresses the reviewer's concerns.

      (22) The supplemental text file containing the model equations can be a bit challenging to read and understand. It would be greatly beneficial if the authors could consider generating a file using a typesetting program.

      We have now included a typeset list of state variable equations and ODEs, along with the original model files.

      (23) The authors mentioned that some model parameterizations result in negative solutions, which is surprising. Access to the model equations would help understand why this happens and is crucial for researchers who may want to use this approach. Clarifying the model equations' presentation would enhance transparency and aid other researchers in applying this method for similar research questions.ach. Clarifying the model equations' presentation would enhance transparency and aid other researchers in applying this method for similar research questions.

      The reviewer is correct to be surprised by the mention of negative solutions, as negative concentrations are physically impossible. We clarify that these are not a result of any structural flaw in our model's equations but are a well-known, although rare, numerical artifact of floating-point arithmetic in computational solvers.

      Our model is constructed using standard mass-action and first-order kinetics, which structurally guarantee non-negativity. However, when a species' concentration approaches the limits of machine precision (i.e., becomes a very small number extremely close to zero), the ODE solver can, in rare instances, numerically undershoot zero, resulting in a small negative value. If this occurs, it can lead to instability in subsequent integration steps.

      This is not a biological phenomenon but a computational one. Therefore, the standard and appropriate procedure, which we follow, is to implement a filter that discards any simulation trajectory where such a numerical instability occurs.

      (24) The reference listed for the CDK4/6 and CDK2 measurements is Yang et al. [55] in the figure caption, but as Xe et al. in lines 559-561 of the manuscript.

      The text has been updated to match citation.

      (25) We suggest that the authors revise and cite a previous study conducted by Yamada et al. (Scientific Reports, 2018), which presents an approach to expressing cell heterogeneity as a probability distribution of model parameters.

      Following this suggestion, we have revised the Discussion (see response to comment (21)) to include and discuss Yamada et al. (Scientific Reports, 2018), which models cell heterogeneity as a probability distribution over parameter values.

      (26) In the manuscript, on line 677, the authors state, "This indicates that there is an upper limit to the degree to which parameter sets can influence the qualitative shape of a protein's dynamic within a given network topology." We wish to highlight that this finding may not be particularly surprising. Given that the parameters were randomly determined within a specific range, it is understandable that altering the number of parameter samples would not substantially impact the distribution of model instances.

      We thank the reviewer for this insightful comment, which allows us to clarify the significance of this finding. While it is true that any sampling from a fixed distribution will eventually converge statistically, our conclusion is not about statistics but about the intrinsic, constraining properties of the network's topology. The novelty is not that the distribution converges, but that it converges to a surprisingly limited and finite repertoire of qualitative dynamic behaviours. A complex, non-linear network with nearly 100 free parameters could theoretically generate an almost endless variety of complex dynamics. Our finding is that this specific biological topology acts as a powerful filter, robustly channelling the vast majority of the near-infinite parameter combinations into a small, recurring set of functional outputs (increasing, decreasing, rebound, etc.).

      The reason for this finite limit is mechanistic, as the reviewer's comment prompted us to investigate further. Our parameter sweep already covers an extremely wide, 9-order-of-magnitude range. As we pushed parameter values to even greater extremes in exploratory simulations, we found they do not generate novel, complex dynamic shapes. Instead, they tend to drive network nodes into saturated states- either permanently "on" (maximally activated) or permanently "off" (minimally activated). In both cases, the node becomes unresponsive to upstream perturbations.

      Therefore, further expanding the parameter range would be unlikely to uncover new behavioural categories; it would simply increase the proportion of model instances classified as "no-response." This demonstrates a fundamental principle: the network topology itself enforces an upper limit on its dynamic complexity. We think this inherent robustness is what allows for reliable cellular signalling in the face of constant biological variation. We believe this is a non-trivial finding, and we have revised the Discussion (page 16: lines 664 - 680) to state this conclusion and its implications more clearly.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      We thank all reviewers for the valuable feedback and critical insight on our study. We acknowledge the concern that the manuscript, in its initial form, appeared descriptive and did not provide the mechanistic insight inferred from the current data. In the revised manuscript, we will (i) more clearly delineate what mechanistic inferences can be drawn from the existing data, (ii) expand our discussion of the caspase-independent mechanisms, and (iii) incorporate additional experiments/analyses aimed at identifying downstream effectors that mediate the observed phenotypes. In this revision plan, we have included six new figures addressing some of the major issues raised by reviewers.

      1. Specifically, to address questions about mechanistic insight, we generated stable ACSL1:HaloTag expressing hESCs. Currently presented as Figure 1A for reviewers____. __ACSL1 is a critical enzyme that catalyzes the first step of fatty acid oxidation at the outer mitochondrial membrane. Our previous analysis and work from the Opferman lab demonstrated that ACSL1 contains a BH3-like domain. Thus, we examined the effects of MCL-1 inhibition on the mitochondrial localization of this enzyme. Our findings pinpoint that MCL-1 inhibition is causing the displacement of ACSL1 from the mitochondria (__Figures 1B-C for reviewers). Our interpretations of the effects of MCL-1 inhibition are 2-fold: 1) as we show in our data, MCL-1 inhibition causes disruption of the mitochondrial cristae, altering the microenvironment for fatty acid oxidation, and 2) as seen in cancer cells, the MCL-1 inhibitor may also displace ACSL1 from the mitochondria. In the new version of the manuscript, we will focus on these 2 mechanisms as mechanistic outcomes of MCL-1 inhibition.
      2. We have included data of cells treated with Perhexilin (CPT1/2 inhibitor), and Etomoxir (CPT1a inhibitor) (Figure 2 for reviewers). This experiment determines whether direct perturbation the FAO pathway mimics the effects of the MCL-1i.
      3. We have assayed the effects of MCL-1 inhibition on oxygen consumption rates in NPCs. Currently presented as Figure 3 for reviewers.
      4. We will perform MCL-1:MICOS proximity ligation assays and/or immunoprecipitation assays to determine whether MCL-1 inhibitors disrupt the association of MCL-1 with MICOS. Preliminary data suggesting an association (albeit, very weak) are shown in Figure 4 for reviewers. __Reviewer #1____ (Evidence, reproducibility and clarity (Required)): __

      Summary: This study claims that beyond its canonical anti-apoptotic function, MCL-1 has essential non-apoptotic roles in human neurodevelopment. Pharmacologic inhibition of MCL-1 in human neural stem cells disrupts mitochondrial inner membrane architecture by destabilizing cristae and the OPA1-MICOS complex, leading to swollen mitochondria with disorganized cristae. These structural defects impair fatty acid oxidation and lipid droplet homeostasis, linking cristae integrity to metabolic competence. Independently of apoptosis or proliferation, MCL-1 inhibition selectively depletes intermediate neural progenitors, indicating a direct role in lineage progression. Overall, the work positions MCL-1 as a key regulator of mitochondrial structure-metabolism coupling that instructs neural progenitor identity and human neurogenesis.

      Overall: The study does a good job of using (in most assays) caspase inhibition (e.g., QVD treatment) to block apoptotic responses induced by MCL-1 inhibition. As a result, many of the phenotypes caused by inhibition are likely to be independent of caspase activation. As a result, this manuscript would be of interest to researchers that study the topics of the BCL-2 family and cell death signaling, mitochondrial bioenergetics and dynamics, neurodevelopment, and cellular metabolism. However, as currently presented the manuscript is only descriptive and lacks mechanistic insight.

      We thank Reviewer 1 for the insightful evaluation of our work. We are encouraged that the reviewer finds the study relevant to investigators in the fields of BCL-2 family biology, mitochondrial dynamics and bioenergetics, neurodevelopment, and cellular metabolism. We also thank the reviewer for pointing out the need to increase the mechanistic insight of our findings. As mentioned above, in the revised manuscript, we are proposing to address this.

      Major Concerns:

      1) The authors only use a single MCL-1 inhibitor and never use other non-targeting BH3-mimetics (such as venetoclax) as negative controls. This seems like a missed opportunity to demonstrate that the phenotypes observed are MCL-1 dependent.

      This is an excellent point. We will include venetoclax (ABT-199) to examine their effect on intermediate progenitors (TBR2 +) and early born neurons (BIII tubulin +).

      2) There is no mechanism proposed in this study other than reliance upon QVD as not affecting the phenotypes. As submitted, the manuscript only can speculate that these phenotypes are due to non-apoptotic roles of MCL-1 inhibition. The authors have missed an opportunity to explore MCL-1's non-apoptotic functions directly.

      Mechanistically, we propose MCL-1 is acting in 2 ways: 1) as we show in our data, MCL-1 inhibition causes disruption of the mitochondrial cristae, altering the microenvironment for fatty acid oxidation, and 2) as seen in cancer cells, MCL-1 inhibitors may also displace ACSL1 from the mitochondria.

      In the past few weeks, since receiving the initial reviews, we have focused on testing the 2nd possibility, since the accumulation of lipids was also seen in cancer cells (see PMID: 38503284). We have successfully generated stable ACSL1:HaloTag expressing hESCs (Figure 1A for reviewers). Our findings included here, ACSL1 is displaced from the mitochondria by MCL-1 inhibition in NPCs (Figures 1B-C for reviewers).

      Other concerns exist that weaken the impact of the study.

      1. Figure 1 should include the fact that QVD inhibition (shown in Sup Fig 2) does not obviate the phenotype induced by pharmacological inhibition of MCL-1 on mitochondrial morphology. We would like to clarify that QVD does prevent the phenotypes induced by MCL-1 inhibition on mitochondrial morphology. In Fig1B, we report an increase in volume and surface area at 24h and 48h along with a decrease in mitochondrial content at 48h when NPCs were treated with MCL-1i only. However, NPCs co-treated with QVD in Supp Fig 2B did not exhibit any significant morphological phenotypes on average or at min/max values. Reviewer 1 may be referring to Fig 1B's corresponding min/max values presented in Supp Fig 2A where we reported an increase in __max __volume.

      Figure #

      Volume

      Surface Area

      Fig 1B (MCL-1i only, avg values)

      Increase (avg vol)

      increase (avg)

      Supp Fig 2B (MCL-1i+QVD)

      no change

      no change

      Supp Fig 2A (MCL-1i only, max/min values)

      increase (max vol)

      no change (max)

      For clarity, we will move Supplementary Fig 2A into Supplementary Fig 1.

      Figure 2 would benefit from evidence that caspase inhibition does not repress the phenotype on mitochondrial cristae morphology (volume and area). Furthermore, the FIB-SEM data are very hard to appreciate as the size precludes visualization of individual mitochondria.

      While we included the visualization of the segmented mitochondria and cristae (Figure 2C), as well as snapshots through the z-stack for segmented cristae only (Figure 2E) and segmented mitochondria separately (Supp Figure 3A) in the original manuscript, we are also now attaching the FIB-SEM 3D reconstruction videos (New Supplementary Videos 1-2 for reviewers) (1. Mito and cristae, 2. Cristae only, 3. Mito only) for ease of visualization purposes.

      Figure 3 reports that MIC60 and OPA1 appear to be downregulated in response to MCL-1 inhibition, but these appear to be more significant only when QVD is added. Why would the phenotype be obscured in the non-QVD setting (Fig. 2B&C). How does MCL-1 inhibition lead to changes in MIC60/MICOS/OPA1? This seems quite preliminary at this point.

      In Figures 3B and 3C, we report decreased protein levels of short-form OPA1 and MIC10 only, not MIC60. We argue that our data with QVD shows that the cell death function of MCL-1 (i.e., inhibiting cell death effectors from initiating the caspase cascade) is not the main trigger of the phenotypes we report (cristae dysregulation and fatty acid oxidation disruption), however, cells without a functional cristae and/or defects in FAO, may not be able to survive long-term. Thus, QVD treatment preserves these cells that may not survive the dismantling of such an essential structure. To confirm this, we have performed immunofluorescence of cleaved caspase 3 (Figure 5 for reviewers). These results show that indeed MCL-1 inhibition at the time points of our study doesn't result in increased activation of Caspase-3. We reported similar results of MCL-1 inhibition in oligodendrocyte precursor cells (Gil and Hanna et al., Glia, 2025, PMID: 41420072)

      The loss of MIC60 and OPA1 should repress electron transport chain function, are such impacts observed in the cultured cells? This could be shown by assessing oxygen consumption, etc. Such data would enhance the authors' conclusion that MCL-1 inhibition leads to defects in mitochondrial physiology*. *

      We completely agree with this comment by Reviewer 1. In our revision, we will include an assessment of mitochondrial oxygen consumption rate, using the Seahorse analyzer (mitochondrial stress test), of NPCs treated with MCL-1i. Preliminary data (n=3) are currently presented as Figure 3 for reviewers. Interestingly, these data show a more nuanced cellular response. Consistent with our conclusion that MCL-1 inhibition does not cause apoptotic cell death, MCL-1i did not affect mitochondrial respiration at baseline. The specific deficits appear in spare respiratory capacity and maximal respiration, meaning cells can sustain routine mitochondrial function but lose the ability to respond to increased energetic demand. This suggests MCL-1 loss creates a mitochondrial reserve deficiency rather than a generalized bioenergetic failure. The results with caspase inhibitors show a near-zero OCR across both 24h and 48h timepoints, and significant reductions in maximal respiration, spare respiratory capacity, and non-mitochondrial OCR. Remarkably, these conditions are not detrimental to newborn neurons, as shown in Figure 7. This is very interesting because it suggests that, under severe bioenergetic failure, neural stem cells (PAX6+) can differentiate into newborn neurons in a TBR2-independent manner. More relevant to this study, our results unequivocally demonstrate that TBR2-positive cells depend on the non-apoptotic function of MCL-1

      In Figure 4, the differences between transcripts (qPCR data) and protein (immunoblot) data are often confusing and not well explained. Why do the authors propose that mRNA expression is decreasing whereas the protein expression is increasing? Example CPT1. Furthermore, it is unclear what these data mean functionally? Is this reflective of enhanced lipid oxidation or simply a response to inhibition of fatty acid oxidation? Clarification of the impact of these findings is necessary.

      We agree with Reviewer 1 that the results could be hard to interpret. However, the effects of MCL-1 inhibitors on the transcription of fatty acid oxidation genes have been widely cited by the work of Opferman and Walensky (PMID: 36198266). We speculate that the effects on transcription are triggered by mitochondrial signaling. The mechanistic insight into this phenomenon would be an interesting next step.

      In the case of CPT1, we addressed this comment and found that the difference is due to differential expression of isoforms The RT-qPCR shown in Figure 4, is on CPT1c, whereas the western blot is on CPT1a. Unfortunately, after trying several products, we determined that there are no good antibodies for CPT1c. Thus, since we can't compare gene and protein expression, we will include CPT1a RT-qPCR data to complement the western blot.

      The increase in lipid droplet number induced by MCL-1 inhibition has been previously documented, but it is unclear whether this increase is related to an inability to oxidize lipid (defective fatty acid oxidation) that leads to increases in the cellular abundance or whether this indicates that MCL-1 inhibition leads to enhanced storage. Do other inhibitors of fatty acid oxidation lead to similar increases in lipid droplet size and abundance? Does QVD inhibition affect this phenotype?

      This is a great point raised by Reviewer 1, and one we have also wondered about. We conducted an experiment using C16 BODIPY to address this point (Figure 6 for Reviewers). We observed no changes in C16 lipid droplet accumulation in count, volume, or surface area when cells were treated with MCL-1 inhibitor for 24 hours total with or without a starvation period in the last 6 hours of treatment. However, we observed significant pan-lipid droplet accumulation in the same conditions. This contrast suggests that FAO of exogenous LC-fatty acids is not reliant on MCL-1. This finding does not discount from the requirement of MCL-1 for other FAO processes especially given the major limitation of how much C16 BODIPY (fluorescent palmitate) can be administered to the cells (10µM) which was 10-fold less than what we exogenously supplied to the cells for the pan-BODIPY experiment (100µM, see Figure 5). It is entirely possible that this small dose was not enough to detect any lipid droplet accumulation.

      We have now also included experiments using etomoxir and perhexiline to assess their effects on TBR2/PAX6 (Figure 2 for reviewers). The results indicate that inhibiting the FAO pathway does not fully mimic the effects of MCL-1i on TBR2. However, we show that MCL-1i displaces ACSL1 from the mitochondria, a step that is upstream of CPT1/2. We suggest a model in which the coordinated non-apoptotic function of MCL-1 at the outer mitochondrial membrane promotes ACSL1 activity and, in the inner mitochondrial membrane, regulates mitochondrial cristae morphology. While our data point to this model, we are limited by the tools to investigate it further, but it will be a great direction for future experiments.

      For Figure 6, while these data may be very meaningful, as presented they are very hard to appreciate. Insets that show the neuronal populations would help to convey the point that the differentiation is impacted. Also, are there other methods that could confirm these observations (qPCR to show changes in differentiation).

      We agree with Reviewer 1. In the new version of the manuscript, we will include panels that zoom into the cell populations we quantified. The current panels will go to a new Supplemental figure. We will also add the TUBB3 to the qPCR panel in the new version.

      Figure 7 is also very hard to appreciate. What is the reader to see? Can these be quantified? It seems that QVD may be rescuing in this figure, does this suggest that MCL-1 inhibition might be inducing death. All of this needs to be quantified.

      We will provide quantification of BIII tubulin branching, and it will be included next to the images provided.

      BCL-XL has also been implicated in affecting mitochondrial electron transport chain function (See PMID: 19255249, 21926988, 21987637). Can BCL-XL inhibitors affect any of the phenotypes associated here?

      We will include experiments to test the effect of BCL-2 and BCL-XL inhibitors on TBR2 cells to address this comment.

      Please be carefully avoid using the term "MCL-1 loss", when talking about pharmacological inhibition. Only genetic ablation (e.g. knockout, silencing, etc.) should be termed loss.

      We have now removed the reference to MCL-1 loss in line 199.

      __*Reviewer #1 (Significance (Required)):

      The study advances in human cells the impacts of MCL-1 inhibition. They replicate many impacts previously observed in mouse systems and refine analyses to impacts on MICOS complex, lipid droplet storage, and neuronal differentiation. While these findings are important and would be well received by a wide audience, the study fails to provide almost any mechanistic insight into how these phenotypes are being induced. The only common theme is that blocking caspase activation in many assays fails to block the phenotype.

      *__

      __Reviewer #2_ (Evidence, reproducibility and clarity (Required)): _*

      Summary: This manuscript by Hanna et al. investigates non-apoptotic roles of MCL-1 in human neural stem cells and connects MCL-1 inhibition to mitochondrial cristae formation and beta-oxidation. Connecting these roles to brain development, the authors also show a reduction in the number of progenitor cells upon MCL-1 inhibition, independently of caspase activity. Throughout their work, the authors make use of an impressive array of imaging techniques. While the methods used offer sufficient evidence to connect MCL-1 inhibition to cristae architecture, the mechanistic underpinnings of this effect remain unexplored. *__

      We thank Reviewer 2 for the thoughtful and positive assessment of our manuscript. We appreciate the reviewer's recognition that our study reveals non-apoptotic roles of MCL-1 in human neural stem cells. We are also grateful for the acknowledgment of the imaging approaches employed, which allowed us to connect MCL-1 function to cristae architecture with multiple complementary techniques. We acknowledge the reviewer's point that the mechanistic basis by which MCL-1 influences cristae structure remains insufficiently defined. In the revised manuscript, we will clarify the limitations of the current data, expand our discussion of potential mechanisms, and incorporate additional analyses to identify downstream effectors that mediate these structural and metabolic changes.

      Major comments:

      - In Fig. 1B, the very same representative images are shown for both conditions (DMSO and S63845) at 48 hours.

      We deeply appreciate Reviewer 2 for catching this unintentional duplication that occurred during figure preparation. We have now corrected this issue.

      - For Western Blot analysis, it looks like the authors only quantified the band density of their proteins of interest without considering varying levels of control protein (Actin) levels. Normalizing the protein levels to actin would account for any differences in loaded protein amounts (although a Ponceau staining might be preferable still to exclude this). This is especially relevant for Fig. 4E, where actin levels visibly differ between the conditions.

      All WB quantifications were normalized to Actin (this detail is now added to the y-axis of all band density graphs and figure legends). In addition, we will transform the data to a logarithmic scale to "normalize" for gel-to-gel variability.

      - The authors offer evidence that MCL-1 inhibition impedes proteolytic cleavage of OPA1-L into the OPA-1-S isoforms, yet do not explore the mechanism behind this. Since OPA1 is cleaved by both OMA1 and YME1L, determination of the levels of these proteases could help shed some light on the mechanism leading to cristae reorganization.

      We will follow up on Reviewer 2's comment with a WB analysis of OMA1 and YMEL in cells treated with an MCL-1 inhibitor.

      - Generally speaking, while the authors show all those effects (cristae defects, FAO dysfunction) upon MCL-1 inhibition, it would be interesting to see whether any of those effects can be rescued by blocking FA import e.g. through carnitine palmitoyl- transferase 1a (CPT1a) inhibition with etomoxir to understand if they are downstream of altered Fa supply. This could affect cristae morphology through altered Cardiolipin biogenesis.

      This is an excellent point, which was also raised by reviewer 1. We have now included experiments using etomoxir and perhexiline to assess their effects on TBR2/PAX6 (Figure 2 for Reviewers). As mentioned above, the results indicate that inhibiting the FAO pathway does not fully mimic the effects of MCL-1i on TBR2. However, we show that MCL-1i displaces ACSL1 from the mitochondria, a step that is upstream of CPT1 and 2. We suggest a model in which the coordinated non-apoptotic function of MCL-1 at the outer mitochondrial membrane promotes ACSL1 activity and, in the inner mitochondrial membrane, regulates mitochondrial cristae morphology. While our data point to this model, we are limited by the tools to investigate it further, but it will be a great direction for future experiments. The suggestion of Reviewer 2 that the effects on FAO could impact cardiolipin biogenesis is a very exciting possibility. However, difficult to test with the tools available.

      - In line 262 the authors discuss that mitochondria lose metabolic function upon MCL-1 inhibition. This claim would require additional experiments. While the authors look at lipid droplet accumulation and FAO enzymes, there are many more aspects to mitochondrial metabolic function that should be investigated. While measuring the oxygen consumption rate via Seahorse might require additional resources (optional), measurements of ATP production, ROS generation or determination of the mitochondrial membrane potential should be feasible.

      We fully agree with Reviewer 2's comment, which was also raised by Reviewer 1. In our revision, we will include an assessment of the mitochondrial oxygen consumption rate of NPCs treated with MCL-1i, measured using the Seahorse analyzer (mitochondrial stress test). These data are presented as Figure 3 for reviewers. Interestingly, these data show a more nuanced cellular response. While MCL-1i does not globally collapse mitochondrial respiration at baseline, the specific deficits appear in spare respiratory capacity and maximal respiration, meaning cells can sustain routine mitochondrial function but lose the ability to respond to increased energetic demand. This suggests MCL-1 loss creates a mitochondrial reserve deficiency rather than a generalized bioenergetic failure. The results with caspase inhibitors show a near-zero OCR across both 24h and 48h timepoints, and significant reductions in maximal respiration, spare respiratory capacity, and non-mitochondrial OCR. These conditions are detrimental for TBR2-positive NPCs (Figure 6) , but not for newborn neurons (Figure 7).

      - While the authors "propose a model in which MCL-1 associates with MICOS", they do not offer direct scientific to support this hypothesis. Co-immunoprecipitation experiments or e.g. proximity ligation assays would better support the proposed model.

      We agree with this statement. Preliminary, we have performed proximity ligation assays and immunoprecipitation analyses to test for this interaction (see below and ____Figure 4 for reviewers), and the results indicate an interaction, albeit very weak. In the revised version of the manuscript, we will attempt to repeat these experiments with MCL-1i.

      - While Fig. 7 shows representative images, quantification e.g. for the truncation of neuronal processes is missing.

      We will provide quantification of BIII tubulin branching, which will be included alongside the images provided.

      - In lines 219f. the authors state that they "observed a significant downregulation of PAX6 and EOMES at 24 hours that was not rescued by QVD co-treatment". While there is still a trend towards a downregulation, there is no statistical significance anymore. In fact, PAX6 levels almost mirror those of SOX2 which is not described as "downregulated" by the authors. In order to be more consistent, I would suggest rephrasing this part, or at least reword it to be less absolute.

      In the new version, we will clarify that while QVD rescued TBR2 and PAX6 transcript levels at 24h, it did not rescue them at 48h. We will also mention the downregulation of SOX2 at 48h that persists with co-treatment.

      - Brinkmann et al. (2025) also investigated cristae structure upon MCL-1 deletion in vivo and found no effect when MCL-1 was replaced with other Bcl-2 family members. It would be interesting to combine MCL-1 inhibition with overexpression of MCL-1 versus BCL-XL to reconsolidate some of the discrepant findings.

      While this is a great suggestion for future studies, there are some complications. Specifically, it is likely that the inhibitor may also target the overexpressed MCL-1 and thus, a mutant form is needed.

      To address this, we generated a Flag-tagged MCL-1 construct with a mutated BH3 domain, previously described by Kotschy et al. Nature 2016. We validated the construct in HeLa cells, but unfortunately the mutant protein appears to be significantly less stable than the WT construct, complicating analysis of this experiment.

      Minor comments:

      - In Supp. Fig. 1C the MCL-1 protein is shown both to run above 37kDa (upper panel) and below 37 kDa (lower panel). Could the authors please comment on why this is the case?

      The observed variation is caused by drift in the gel during electrophoresis. In Fig 1C, the protein ladder is on the edge of the gel, whereas in Fig 1E, the protein ladder is in the middle of the gel, and the last sample is on the edge and also exhibits edge drift.

      - In line 64 of the introduction the authors mention clinical trials yet do not give a citation for these trials making it hard to judge whether the content of these trials is actually related to the brain.

      This information is anecdotal, based on an Amgen press release.

      - MCL-1 as well as ACSL-1 are sometimes written without the hyphen both in the text and figures.

      We will carefully check the manuscript before submission.

      - Lines 92-94 and 106-108 essentially highlight the same existing knowledge gap. Maybe the content of these two paragraphs could be combined in order to avoid repetition.

      We thank Reviewer 2 for this suggestion. We will do this in the new version of the manuscript.

      - In Fig. 1A, the authors provide a schematic for their experimental design. While the figure legend is very thorough, some of this information (like the days of collection) could also be included in the figure itself. The same is true for schematics in the following figures.

      We agree with this and will incorporate the suggestion in the new version.

      - Fig. 2A includes a typo (analyze) but would maybe also be more suitable for the supplement figures or could even be combined with Fig. 1A as not much new content is added.

      We already incorporated these changes in the new version of the manuscript.

      - Regarding statistical analysis, could the authors please comment on why they did not consider one-sample t-tests suitable for the cases where control values were set at 1 (e.g. Fig. 4B, C for the relative expression).

      This is a valid suggestion. We will rerun RT-qPCR data using a one-sample t-test.

      - In lines 247f. the authors state that "inhibition of MCL-1 leads to [...] and disassembly of the MICOS complex as well as OPA1". This sounds like OPA1 is still cleaved upon MCL-1, which is not at all what the authors showed and further discuss. Rewording of the sentence would help in avoiding any misunderstandings.

      We agree with this comment and have now reworded the paragraph: "Inhibition of MCL-1 leads to structural collapse of the cristae likely due to the possible disassembly of the MICOS complex, as suggested by decreased MIC10 levels, and interruption of OPA1 cleavage, as suggested by decreased short-form OPA1, two scaffolds required for cristae maintenance."

      - In lines 210f. the authors state that "quantitative imaging increased the average and maximum volume of lipid droplets". While there is definitely a trend towards an increase for the maximum volume, the increase is in fact not statistically significant. This should be reflected in the wording.

      We have reworded this to "Quantitative imaging revealed a significant increase in average lipid droplet volume and a trending increase in maximum volume of lipid droplets."

      - In Fig. 6 the overlap between TBR2 and PAX6 is hard to judge when printed out. Including a zoom-in may make it easier to judge.

      We agree with Reviewer 2. In the new version of the manuscript, we will include panels that zoom into the cell populations we quantified. The current panels will go to a new Supplemental figure. We will also add the TUBB3 to the qPCR panel in the new version.

      - In Fig. 7 the color-coding is listed in the figure legend but is missing from the figure itself. If the authors could include this, as they did for the other figures, it would further improve this figure.

      We agree. We have specified the channel color in the new figure.

      - Line 238 should reference Fig. 7A, as Fig 7B does not exist.

      Thanks for catching this. It is already corrected

      - In the figure legends the authors state that biological replicates were used. Were technical replicates also performed?

      Yes, technical replicates were performed for RT-qPCR.

      Reviewer #2 (Significance (Required)):____ Significance

      The authors make use of a wide array of imaging techniques to further elucidate non-apoptotic roles of MCL-1. The study has the potential to offer new insights into mitochondrial biology on the level of basic research rather than translational. While the methods used offer sufficient evidence to connect MCL-1 inhibition to cristae architecture, the mechanistic underpinnings of this effect remain unexplored. Nevertheless, the study offers additional knowledge on the role of MCL-1 in human neural stem cells, whereas previous research mostly focused on cardiomyocytes or cancer cells.

      Reviewer #3____ (Evidence, reproducibility and clarity (Required)):

      Summary: ____ In this study, Gama et al. describe a non-canonical role for the anti-apoptotic protein Myeloid Cell Leukemia-1 (MCL-1) in mitochondrial cristae organization and suggest a role of MCL-1 in regulating metabolism and neuronal differentiation. Using fluorescence microscopy imaging and electron microscopy, the authors show changes to mitochondrial morphology upon treatment with MCL-1 inhibitor S63845. MCL-1 inhibition results in altered protein and transcript levels of some key proteins involved in mitochondrial cristae organization and fatty acid metabolism. While some of the findings are interesting and indeed point towards a non-canonical role of MCL-1, several key conclusions of the authors are not sufficiently supported by the data shown in the manuscript.

      We thank Reviewer 3 for the careful evaluation of our manuscript. We appreciate the reviewer's recognition that our study identifies a potential non-canonical role for MCL-1 in mitochondrial cristae organization, metabolism, and neuronal differentiation. As with Reviews 1 and 2, we are encouraged that the reviewer finds these observations interesting and suggestive of previously unappreciated functions for MCL-1. We agree that stronger evidence is required to firmly link MCL-1 inhibition to specific changes in MICOS organization and metabolic regulation. In the revised manuscript, we will (i) more clearly distinguish between observations and mechanistic inferences, (ii) temper conclusions where appropriate, and (iii) incorporate additional analyses and controls to better substantiate the proposed model.

      Major comments:

      1. The authors try to disentangle the apoptotic and non-apoptotic role of MCL-1 through addition of a caspase inhibitor. However, I am not convinced that phenotypes found under the addition of caspase inhibitor are necessarily caused by non-canonical functions independent of apoptosis. It could also be that the observed changes happen upstream of caspase activation. In addition, many of the described finding, such as CPT1 expression changes, only happen in the presence of the caspase inhibitor. If one follows the logic of the authors, changes associated by non-canonical MCL-1 functions should happen under MCL-1 inhibition and caspase inhibition, but not with MCL-1 inhibition only____. __ The reviewer is right that we expected non-canonical functions to happen under MCL-1 inhibition and caspase inhibition. Our data with QVD shows that the cell death function of MCL-1 (i.e., inhibiting cell death effectors from initiating the caspase cascade) is not the main trigger of the phenotypes we report (cristae dysregulation and fatty acid oxidation disruption), however, cells without a functional cristae and/or defects in FAO, may not be able to survive long-term. Thus, QVD treatment preserves these cells that may not survive the dismantling of such an essential structure. To confirm this, we performed immunofluorescence of cleaved caspase 3 (__Figure 5 for reviewers). These results show that, indeed, MCL-1 inhibition at the time points of our study doesn't result in increased Caspase-3 activation. We reported similar results of MCL-1 inhibition in oligodendrocyte precursor cells (Gil and Hanna et al., Glia, 2025, PMID: 41420072).

      The authors show no data on the viability of the cells in response to the MCL-1 inhibitor. To exclude secondary effects of the inhibitor, at least some of the results should be validated with an MCL-1 knock down.

      We will include this experiment in our revised manuscript. To check the effects of MCL-1 knockdown on TBR2 positive cells, we tested 5 different ASOs for MCL-1. Knockdown efficiency with ASOs was very low (on average In Figure 1, the authors show immunofluorescence data of mitochondria and nucleus staining and conclude that MCL-1 inhibition alters mitochondrial morphology. Based on the images shown in Fig. 1, I do not think that individual mitochondria can be segmentd to measure their volume and length. In addition, some metrics such as mitochondrial content are not explained in the text or methods.

      We can achieve mitochondrial segmentation with a SoRa Spinning Disk Confocal Microscope, which has a lateral (XY) resolution of approximately 120 nm to 150 nm and an axial (Z) resolution of approximately 300 nm-320 nm. All images are first denoised prior to sharpening using the Richardson-Lucy deconvolution algorithm. Additionally, the FIB-SEM data are consistent with the IF data (both show increase in mitochondrial volume and surface area).

      We agree with Reviewer 3 that we need to explain some metrics in the revised version. We will specify the meaning of mitochondrial content (count of all mitochondria in FOV, not normalized to Hoechst).

      In Fig. 2 B-D, the authors show TEM and FIB-SEM imaging to demonstrate alterations in the cristae architecture upon treatment with MCL-1 inhibitor. However, based on the images shown, it looks that cristae area and density is reduced under S63845 treatment in TEM images, while the FIB-SEM data come to the opposite conclusion. In addition, the quantification of cristae volume quantified as cristae volume in percentage is unclear to me.

      We apologize for the confusion. No conclusions about the cristae area and density were made using the TEM data, because TEM data represent a single snapshot section of a mitochondrion without a discernible orientation. Cristae from TEM were described as "aberrant" and preliminarily revealed changes in cristae and were followed up with FIB-SEM, 3D reconstruction of intact mitochondria, and quantification of volume.

      In the new version of the manuscript, we will specify that the cristae volume is normalized to the volume of its respective mitochondria (i.e., how much of the mitochondrial volume is attributed to cristae).

      The change in CPT1/2 protein levels (Fig. 4) is interesting but does not directly proof that fatty acid oxidation is altered, as concluded by the authors. For this, the authors would need to directly measure fatty acid oxidation for example using Seahorse or metabolic tracing experiments. Also, to prove that the MCL-1 inhibition affects neural differentiation through fatty acid oxidation, a rescue experiment should be performed through CPT1 overexpression.

      We agreed that this is an important point. We have optimized the fatty acid oxidation test using Seahorse and will make sure to include it in the revised version of the manuscript.

      In Figure 6, the authors show decreased intermediate progenitor cells after MCL-1 inhibition by immunofluorescence staining. I am not convinced that this can be concluded from the data shown, since the concentration of intermediate progenitor cells is very close to the noise levels. Since the MCL-1 treated cells look much less sparse, I don't think the percentages can be compared (total counts are between 2-20). Although this data might give some indication that differentiation could be impaired, the measured effect could be very well due to lower viability of the cells. The authors need to control for this or come up with a different method for measuring differentiation.

      The number of TBR2 is low, but we disagree with the reviewer's assessment of noise levels. We focused on cells expressing only TBR2 and rigorously examined this population of cells. The percentages are compared to account for the lower density of the MCL-1i-treated cultures, as the IPC counts are normalized to the Hoechst total cell count within the FOV. Moreover, the immunofluorescence images are complemented with RT-qPCR, which shows significant downregulation of EOMES (gene encoding TBR2).

      Figure 7 is missing quantification

      We will include this quantification in the revised version of the manuscript.

      Reviewer #3 (Significance (Required)):

      General assessment____: The manuscript reports an interesting finding, which suggest a non-canonical role of MCL-1 in mitochondrial remodeling, regulation of fatty acid oxidation and neuronal fate. While this finding would be highly interesting and relevant, the presented data do not sufficiently support this conclusion. Further experiments would have to be performed to proof causality. ____ Advance: Should the authors manage to proof their hypothesis by additional experiments, this would indeed advance the field on mitochondrial remodeling and its effect on neuronal differentiation by

      identifying a novel molecular player. ____ Audience: mitochondrial biology, cell biology, developmental neuroscience Own expertise: mitochondrial biology, cell biology, advanced imaging techniques

    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 investigate the impact of rare and extreme events on rodents' decisionmaking under risk, in gain and loss contexts. They describe the behavior of 20 rats performing a four-armed bandit task, where probabilistic gains (sugar pellets) and losses (time-out punishments) can - in some arms - incorporate extremely large - but rare - outcomes. They report that most rats are sensitive to rare and extreme outcomes despite their infrequent occurrence, and that this sensitivity is primarily driven by extreme loss events which they try to avoid, rather than extreme gains that they seek to obtain.

      They finally propose a modification of standard reinforcement-learning, which features a specific sensitivity to rare and extreme outcomes and can account for the observed behavior.

      Strengths:

      The manuscript really taps into a surprisingly neglected but very relevant aspect of decision-making: the effect of rare and extreme events (REE). The authors have developed an experimental setup that seemingly allows investigation of this aspect, which is not trivial given the idiosyncratic properties of rare and extreme events.

      The parameters of the experimental setup seem also to be well thought off: basically, in the absence of REE, some options are objectively better than others (because, in expectation, they overall deliver more food, or minimize time-out punishments), but this ordering reverses if REE are taken into account. This allows for a clean test of the integration of REE in the rodent's decision-making model.

      The data is presented and analyzed in a very descriptive but exhaustive and transparent way, down to the description of individual rodent's behavior.

      Weaknesses:

      While the description and analyses of the behavioral patterns are rigorously done under the economic lens of risky decision-making, the authors' interpretation heavily relies on the assumption that rodents have built the correct model of the task during the training. Extensive details are provided about the training procedure, and the observed behavior at the end of the training, but it remains virtually impossible to disambiguate choices due to imperfect learning to choices made due to intrinsic preferences for risk or REE.

      As detailed in Material and Methods, the animals were progressively overtrained following standard behavioral procedures. During this process, they experienced all available options, including both positive and negative REE. We assume that repeated exposure to these REE supported learning, as would be expected for any event occurring throughout such an extended training phase. The rats ultimately displayed an asymmetric pattern of choices: they consistently avoided the Black Swan, indicating that they had learned its negative consequences, yet they did not systematically seek the Jackpot. If their behavior were driven solely by incomplete learning or by an inherent preference for risk or REE, we would expect to see the opposite pattern systematic Jackpot seeking or inconsistent avoidance of the Black Swan.

      By nature, gains (food pellets) and losses (time-out punishments) are somewhat incommensurable so the interpretation of the asymmetry due to outcome valence is also subject to interpretation. There might be some additional subtleties due e.g. satiety that could come from gaining REE (i.e. the delivery of 80 pellets from the Jackpot).

      As described in Material and Methods, we used mouse pellets (20 mg) instead of rat pellets (45 mg) to prevent satiety during Jackpot delivery (80 pellets). We also selected gains (sweet pellets) and losses (delays) that we have successfully used in previous rat decision-making paradigms, such as the rat gambling task (Adams et al., 2017; doi: 10.1523/ENEURO.0094-17) and the loss-chasing task (Breysse et al., 2021; doi: 10.1111/ejn.14895). Notably, if the Jackpot induced satiety, one would expect animals to stop seeking it yet this was not systematically observed. Nonetheless, we added a sentence to the Discussion on page 18 of the manuscript to acknowledge that we cannot fully exclude the possibility that satiety contributed to the lack of systematic Jackpot Seeking.

      In its current form, the paper is quite hard to digest. This is naturally the case with interdisciplinary work (here mixing economists and neurobiologists). But I am afraid that with the current frame, the paper is going to miss its target, in terms of audience.

      We have rewritten entirely and the english was corrected thanks to ChatGPT. We hope that the paper is now easier to digest.

      The proposed model seems somewhat disconnected from the behavioral patterns: while the model suggests an effect of REE at the decision stage (i.e. with specific decision weights for those rare events), this formalism seems at odds with the observation that REE (notably in the loss domain) has an impact of subsequent behavior - (Black Swans tend to reinforce Total Sensitivity to REE) which rather suggests an effect at the learning stage.

      We agree with the referee that this may appear surprising at first glance. However, we would first like to emphasize that the general model allows REE to influence learning—that is, to contribute to the updating of the Q-subvalues. Moreover, even when REE are incorporated only as decision weights, as is the case for most rats, this does not imply that REE are unimportant during learning. In fact, the model assumes that REE are learned once and for all when they first occur during a trial of the corresponding option. Unreported simulation exercises indicate that a more gradual learning of maximal and minimal values would likely yield similar results.

      Second, the Before/After analysis shows that the behavioral response to Black Swans is locally small in terms of both total and one-sided sensitivities. This suggests that such effects are likely too subtle to be captured by this class of models for most rats. We have added this clarification to the revised version (page 17).

      Discussion:

      This study convincingly demonstrates that REEs are processed rather uniquely, which makes sense given their evolutionary relevance. REE has indeed been somewhat neglected in previous research, and this study therefore opens an interesting new front on the fundamental aspects of decision under risk. The authors have devised an original theoretical and empirical framework that will be useful for the community, and the combination of economics analysis and rodent behavior constitutes a thoughtprovoking ground to think about the nature of risk preferences. The interpretation and mechanistic account of these aspects, as well as their generalizability outside the specific context of this study, remain to be strengthened.

      We have modified the discussion to further insist on the translational aspect of the study and its interest for various populations (page 22). We hope that the generalizability is now strengthened.

      Reviewer #2 (Public Review):

      Summary:

      This paper attempts to examine how rare, extreme events impact decision-making in rats. The paper used an extensive behavioural study with rats to evaluate how the probability and magnitude of outcomes impact preference. The paper, however, provides limited evidence for the conclusions because the design did not allow for the isolation of the rare, extreme events in choice. There are many confounding factors, including the outcome variance and presence of less-rare, and less-extreme outcomes in the same conditions.

      Strengths:

      (1) The major strength of the paper is the significant volume of behavioural data with a reasonable sample size of 20 rats.

      (2) The paper attempts to examine losses with rats (a notoriously tricky problem with non-human animals) by substituting time-outs as a proxy for losses. This allows for mixed gambles that have both gain and loss possible outcomes.

      (3) The paper integrates both a behavioural and a modelling approach to get at the factors that drive decision-making.

      (4) The paper takes seriously the question of what it means for an event to be rare, pushing to less frequent outcomes than usually used with non-human animals.

      Weaknesses:

      (1) The primary issue with this work is that the primary experimental manipulation fails to isolate the rare, extreme events in choice. As I understand the task, in all the conditions with a rare extreme event (e.g., 80 pellets with probability epsilon), there is also a less-rare, less-extreme event (e.g., 12 pellets with probability 5). In addition, the variance differs between the two conditions. So, any impact attributable to the rare, extreme event could be due to the less rare event or due difference in the variance. The design does not support the conclusions. Finally, by deliberately confounding rarity and extremity, the design does not allow for assessing the impact of either aspect.

      We agree with the referee that both the REE and the rare (≈10% frequency) but non-extreme outcomes are present in the relevant options. However, the rare but non-extreme reward is not large enough to make the convex option attractive and to shift choice away from the concave option. In other words, unlike REE, these outcomes do not reverse stochastic dominance in our design (as noted in Material and Methods). We have explored modified designs for human subjects in which the rare but non-extreme outcomes are removed. Preliminary results indicate that the behavioral phenotypes observed in rats also emerge in humans under these modified conditions, suggesting that REE are the primary drivers. We have added a statement to the Discussion (page 22) to clarify this point.

      We elaborate further in our response to point (3) below on why analyses based solely on variance are insufficient when dealing with REE. To clarify the role of rare and extreme outcomes in distinguishing convex from concave options, we provide two new columns to Table 2 in the Materials and Methods, in our reply to point (3).

      Finally, although a detailed analysis of rare but non-extreme outcomes lies outside the scope of this paper, the symmetric treatment of extreme and frequent outcomes can be addressed straightforwardly using strong First-Order Stochastic Dominance. Classical decision-theoretic approaches indeed satisfy this property.

      (2) The RL-modelling work also fails to show a specific impact of the rare extreme event. As best as I can understand Eq 2, the model provides a free parameter that adds a bonus to the value of either the two options with high-variance gains (A and V in the paper) or to the two options with high-variance losses (F and V in the paper). This parameter only depends on whether this option could have possibly yielded the rare, extreme outcome (i.e., based on the generative probability) and was not connected to its actual appearance. That makes it a free parameter that just bumps up (or down) the probability of selecting a pair of options. In the case of the "black swan" or high-variance loss conditions, this seems very much like a loss aversion parameter, but an additive one instead of a multiplicative one.

      We agree with the referee that the additional parameters, compared to more standard Q-learning models, specifically capture the fact that some options deliver REE while others do not. In our estimation procedure, these parameters become nonzero as soon as REE are observed for the first time for a given option. Therefore, the first step is to estimate a baseline nested model in which REEs contribute only at the learning stage (i.e., they affect the updating of Q-subvalues), while the additional parameters are constrained to zero. The next step is to compare alternative models against this baseline, allowing REEs to enter through the additional parameters. In this respect, our specification is parsimonious, especially given that very little is known about REEs in computational neuroscience. More structural modeling is certainly a promising direction for future research, and this paper constitutes a first step toward that goal.

      We provide the BIC, in addition to the AIC, to account for the presence of additional parameters in model selection and to ensure that the observed improvement in fit is not merely driven by their inclusion.

      Unlike most of the existing literature, our results extend the notion of loss aversion to extreme losses. The negative decision weight on options yielding the Black Swan can be interpreted as a differential treatment of negative REE, an issue we discuss extensively in the Discussion (page 20).

      (3) The paper presented the methods and results with lots of neologisms and fairly obscure jargon (e.g., fragility, total REE sensitivity). That made it very hard to decipher exactly what was done and what was found. For example, on p. 4, the use of concave and convex was very hard to decipher; the text even has to repeat itself 3 times (i.e., "to repeat" and "in other words") and is still not clear. It would be much clearer (and probably accurate) to say that the options varied along the variance dimension, separately for gains and losses. Option A was low-variance gains and losses. Option B was low-variance losses and high-variance gains. Option C was high-variance losses and low-variance gains, and Option D was high-variance losses and gains. That tells much more clearly what the animals experienced without the reader having to master a set of new terminologies around fragility and robustness, which brings a set of theoretical assumptions unnecessarily into the description of the experimental design. In terms of results, "Black Swan" avoidance is more simply known as risk aversion for losses.

      Because our experimental design focuses on REE, outcomes cannot be summarized only by their variance. This is well known from the large literature on so-called fat-tailed statistical distributions. Unlike the Normal distribution that is entirely characterized by its expected value and variance, fat-tailed distributions have nonzero kurtosis. This implies that a fat-tailed distribution (e.g. exponential) with the same expected value and variance as the Normal differs importantly by possessing extreme values that are much more likely in terms of frequency. To illustrate, if the distribution of pellets was assumed to be Normal with expected value set at 3.89 and variance set at 9.37 as for the convex option, the probability of getting 80 pellets would be about 2.10<sup>-16</sup>, practically zero. In contrast, this probability is smaller than, but close to 1% in our design.

      In Material and Methods, we clearly explain how our novel approach in terms of convexity relates to the moments of the reward distributions, including but not limited to the variance. To clarify further, we provide two new tables (Author response table 2 and Author response table 3) to be compared to Table 2 of the manuscript in which we report the first four moments (mean, standard deviation, skewness and kurtosis) of the full concave and convex gain distributions, reproduced for convenience

      Author response table 1.

      In Author response table 2 we report the first four moments when REE are truncated. Comparing convex and concave gains shows that the convex option has a smaller but still close mean compared to the concave option. In contrast, the former has larger variance, skewness and kurtosis compared to the latter. Therefore, interpreting choosing the convex option as reflecting “preference” for variance is at best incomplete.

      Author response table 2.

      First four moments of concave and convex gains when REE are removed

      Author response table 2 further shows that REE alone goes a long way towards explaining the differences between convex and concave options in terms of the first four moments: removing the rare and extreme value results in the concave option having now a larger mean, while the convex option still has larger variance, skewness, and kurtosis but by a smaller margin.

      In Author response table 3 we report the first four moments when both RE and REE are truncated, which shows that the convex and concave options differ only with respect to their mean (which is here also larger for concave).

      Author response table 3.

      First four moments of concave and convex gains when both RE and REE are removed

      In addition, our focus on REE implies that we go beyond mean-variance preferences that apply mostly to Gaussian distributions. It is not clear theoretically what type of utility functions would reflect preferences that combine a taste for variance, skewness and kurtosis, even though all those moments affect expected utility. See for example Phelps, C.E. “A user’s guide to economic utility functions”. J Risk Uncertain 69, 235–280 (2024) for a recent overview (on page 242, Phelps states that “In situations where risk is not normally distributed, it is ill-advised to ignore statistical parameters beyond variance, unless the deviations from normality are relatively small”).

      More importantly, our proposed measure of the convexity of the reward distributions, the Jensen gap, further reveals how even restricting the analysis to the first four moments is incomplete in the sense that it fails to characterize the difference between options: the fifth moment of the concave contributes more the Jensen gap than even kurtosis, while one needs to look at much higher moments to find significant contributions to the Jensen gap for the convex option. In that sense, there is no reason to restrict the analysis to variance, and even to skewness and kurtosis, to compare options, in general and in our particular setup as well. Note that introducing REE would result in convex distributions even in simplified designs, e.g. with 3-value support. Studying REE implies the need to look beyond variance, and our proposal is to use the Jensen gap as a measure of convexity. In the Material and Methods section of the paper, we did not develop an in depth analysis of Jensen gap so as to spare the reader confronted with an already rather technical paper.

      We thank the referee for raising the issue of whether variance is a simpler explanation of our results. To keep the main text as short as possible, we chose to refrain from adding technical complexity. We hope we made clear in our reply that the analysis cannot be restricted to variance when studying REE. We believe that Jensen gap is a useful notion in this regard. As our replies will be made publicly available, we chose not to integrate the above discussion in the main text.

      (4) Were the probabilities shuffled or truly random (seem to be fixed sequences, so neither)? What were the experienced probabilities? Given the fixed sequences, these experienced ("ex-post") probabilities, could differ tremendously from the scheduled ("ex ante") probabilities. It's quite possible that an animal never experienced the rare, extreme event for a specific option. It's even possible (if they only picked it on the 10th/60th choices by chance), that they only ever experienced that rare extreme event. This cannot be known given the information provided. The Supplemental info on p.55 only gives gross overall numbers but does not indicate what the rats experienced for each choice/option-which is what matters here. A simple table that indicates for each of the 4 options, how often they were selected, and how often the animals experienced each of the 6-8 possible outcome would make it much clearer how closely the experience matched the planned outcomes. In addition, by restricting the rare outcome to either the 10th or 60th activations in a session, these are not random. Did the animals learn this association?

      Probabilities are not random and a limited number of fixed sequences has been used, as stated in Material and Methods. We have chosen sequences that satisfy our assumptions about ex-post stochastic dominance reversal of convex over concave options when REE are added. We have added in Table S4 the choice frequencies for all four options. If the animals had learnt the 10th and 60th activation, they would exhibit a strategy in their choice that would tend to be more optimized than what is observed. For example, the options offering the possibility to obtain the Jackpot are not optimal in terms of gains for the frequent events, therefore the animals should tend to select these options only around the 10th and 60th choice. Most of their other choices should favor the options delivering the larger gains in the frequent domain. This is not what is observed. We have added this important point in the discussion (page 18).

      (5) The choice data are only presented in an overprocessed fashion with a sum and a difference (in both figures and tables). The basic datum (probability/frequency of selecting each of the 4 options) is not provided directly, even if it can theoretically be inferred from the sum and the difference. To understand what the rats actually do, we first need to see how often they select each option, without these transformations.

      As described in Material and Methods, the 4 options are combinations of 2 convex and concave sub-options for gains and losses, which is why our analysis of the behavioral data focuses on convexityrelated total and one-sided sensitivities to REE. The third dimension needed to fully characterize rats’ behavior is simply 1−ff<sub>FF</sub>, the fraction of non-Fragile choices. In addition, we also provide in Table S4 of the Supplementary Material an alternative interpretation in terms of Black Swan Avoidance and Jackpot Seeking. We have added in Table S4 the choice frequencies for all four options. Finally, all the raw data will be made available with open access and no access codes.

      (6) There is insufficient detail provided on the inferential statistical tests (e.g., no degrees of freedom or effect sizes), and only limited information on exactly what tests were run and how (bootstrapping, but little detail). Without code or data (only summary information is provided in the supplement), this is difficult to evaluate. In addition, the studies seem not to be pre-registered in any way, leaving many researchers with degrees of freedom. Were any alternative analysis pipelines attempted? Similarly, there were many sub-groupings of the animals, and then comparisons between them - were these post-hoc?

      We understand the concern of the referee for pre-registration of the referee, as an epistemic safeguard to make empirical claims more falsifiable, more transparent, and less dependent on post hoc rationalization. But the contemporary push for preregistration is often presented as an “epistemic improvement,” but in practice it functions largely as a norm of moral regulation, not a scientific necessity. The rhetoric is moralistic: preregistered research is “clean,” “transparent,” “credible,” while non-preregistered work is viewed with suspicion—even when the methodology is sound. This language is not epistemologically neutral; it enforces ought to be done, irrespective of the diversity of legitimate scientific practices.

      From a philosophy of science perspective, this is historically and conceptually problematic. Scientific progress has never followed a uniform, rule-based method. As e.g. Feyerabend has argued, major discoveries have emerged precisely because researchers were not bound by predetermined plans: they followed anomalies, improvised, reinterpreted data, and revised methods and hypotheses in light of new evidence — practices that a rigid preregistration ethos can suppress and that are not aligned with how genuine discovery often occurs.

      Even from a statistical standpoint, preregistration is far from a panacea. It reduces some degrees of freedom (mainly in confirmatory statistics), but it does not eliminate flexibility; researchers can still choose models, transformations, exclusion rules, stopping rules, etc. And more importantly: reducing flexibility is not inherently epistemically virtuous. Flexibility is often necessary to understand data properly—especially in new paradigms or first-of-their-kind experiments, which is the case for this study. Science needs exploration, opportunism, and theoretical plasticity. Preregistration is compatible with these only if it is treated as one optional tool among many—not as a universal evaluative standard.

      As the referee pointed out, this study “taps into a surprisingly neglected but very relevant aspect of decision-making.” Our work is therefore mainly exploratory: the experimental paradigm reveals new behavioral patterns in how rats cope with rare and extreme events, and much of our analysis is necessarily descriptive. We conduct formal inference only where it is methodologically appropriate — the short-term behavioral response to rare events (for which we now provide more details in the Material & methods section p.35) and the estimation of augmented Q-learning models, which follow a standard econometric approach (documented in the Material & Method section–see also our response to recommendation 4). These inferential results support the descriptive patterns that motivate this new line of research.

      (7) On p. 17, there is an attempt to look at the impact of a rare, extreme event by plotting a measure of preference for the 10 trials before/after the rare, extreme event. In the human literature, the main impact of experiencing a rare, extreme event is what is known as the wavy recency effect (See Plonsky et al. 2015 in Psych Review for example). What this means is that there tends to be some immediate negative recency (e.g., avoiding a rare gain) followed by positive recency (e.g., chasing the rare gain). Using a 10-trial window would thus obscure any impact of this rare, extreme event. An analysis that looks at a time course trial-by-trial could reveal any impact.

      We thank the referee for drawing our attention to the wavy recency effect documented in human experiments. We have added the corresponding reference in the Discussion (page 20). Regarding rats, the Before/After analysis reported in the paper suggests that there is no sizeable immediate recency effect for Jackpots. Even for Black Swans, the immediate recency effect we report remains modest when using a 10-trial window, and the analysis of the choice immediately following a REE does not show evidence of immediate negative recency. This casts doubt on the presence of such an effect in rats.

      (8) As I understood the method (p. 31), the assignment of options to physical locations was not random or counterbalanced, but deliberately biased to have one of the options in the preferred location. This would seem to create a bias towards a particular option and a bias away from the other options, which confounds the preference data in subsequent analyses.

      We agree that the design incorporated an intentional bias toward the anti-fragile option as a proof of concept. Nevertheless, Figure 8 demonstrates that animals substantially altered their choices between training and final testing, with a median change of approximately 35% across sessions. This indicates that behavior was driven by the structure of possible outcomes rather than by a stereotyped location-based preference.

      (9) Are delays really losses? This is a big assumption. Magnitude and delay are different aspects of experience, which are not necessarily commensurable and can be manipulated independently. And, for the model, how were these delays transformed into outcomes for the model? Eq 1 skips over that. Is there an assumption of linearity? In addition, I was not wholly clear if the delays meant fewer trials in a session or if the delays merely extended the session and meant longer delays until the next choice period.

      Consistent with established rodent decision-making paradigms (Adams et al., 2017 doi: 10.1523/ENEURO.0094-17; Breysse et al., 2021 doi: 10.1111/ejn.14895), we employed sweet pellets as gains and imposed delays as losses. Delays are operationalized as losses because they preclude the animal from engaging in reward-generating behavior; thus, increasing the delay duration proportionally increases the magnitude of the opportunity cost.

      (10) The paper does not sufficiently accurately represent the existing literature on human risky decision-making (with and without rare events). Here are a few examples of misrepresented and/or missing literature:

      Most studies on decision-making do not only rely on p > 10% (as per p. 2). Maybe that is true with animals, but not a fair statement generally. Some do, and some don't. There is substantial literature looking at rarer events in both descriptions (most famously with Kahneman & Tversky's work), but also in experience (which is alluded to in reference 19). That reference is not only about the situation when choices are not repeated (e.g. the sampling paradigm), but also partial feedback and full-feedback situations.

      We have corrected that statement in the main text (page 3) and we thank the referee for pointing this out.

      The literature on learning from rewarding experiences in humans is obliquely referenced but not really incorporated. In short, there are two main findings - firstly people underweight rare events in experience; second, people overweight extreme outcomes in experience (both contrary to description). Some related papers are cited, but their content is not used or incorporated into the logic of the manuscript.

      One recent study systematically examined rarity and extremity in human risky decision-making, which seems very relevant here: Mason et al. (2024). Rare and extreme outcomes in risky choice. Psychonomic Bulletin & Review, 31, 1301-1308.

      There is a fair bit of research on the human perception of the risk of rare events (including from experience) and important events like climate. One notable paper is Newell et al (2015) in Nature Climate Change.

      We agree with the referee that the related literature on REE in animal Decision Making is scant and that it is more developed in humans. We thank the referee for pointing at Mason et al. (2024), who clarify where the literature on humans stands and why combining rarity and extremity, as we also do, is important and highly relevant. We have added a new statement and references in the Introduction and Discussion (pages 3, 20, 22).

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) As said above, I think the manuscript would really benefit from a rewriting, to replace some technical terms with more readable ones, and maybe rebalance the focus from the current focus on the framework (heavily loaded with economics concepts, which will be hard to digest for the eLife readership) to a higher weight on information that is critical to understand and interpret the behavior (e.g. information about training & training behavior, etc.).

      We have revised the entire manuscript to improve readability and have clarified in the main text: (1) why convexity of exposures to REE could, beyond variance, be useful for experiments in other settings that our own; (2) why the associated notion of antifragility may be applicable to other settings and therefore of broader interest; (3) what was done in the training sessions compared to the final sessions.

      (2) From Figure 8, it seems that rodent behavior is more clustered after the training (i.e. before the sessions) than after the sessions. Could that be a sign of imperfect learning?

      Figure 8 mostly suggests that there is some flexibility in the choices made and that the intended initial bias towards the antifragile choice in the design of the task could be over ridden by the rats.

      (3) The modelling section seems incomplete. I think the authors want to tease apart where REE enters the model and should propose an alternative where REE affects the learning rather than the decision.

      In fact, the general model allows REE to have an effect at the learning stage only (i.e. to contribute to the updating of the Q subvalues), when the specific decision weights attached to options delivering REE are both zero. However, our analysis shows that such a model is rejected by the behavioral data for all rats. We have clarified this point in the revised version.

      (4) Also, parameter and model recovery exercises seem mandatory (Wilson & Collins, 2019).

      We thank the referee for highlighting this valuable reference in computational modeling, particularly in the context of model identification and estimation in computational biology. In the present research, we adopted an econometric perspective on model identification—especially with regard to the integration of Q-values for gains and losses. The softmax choice function is formally equivalent to a multinomial logit model, and as is well known in econometrics, identification in such models presents non-trivial challenges. The standard approach in classical Q-learning is to multiply the Q-value by an inverse temperature parameter (also known as a precision parameter in random utility models). When extending the model to include separate Q-values for gains and losses, specifying the model in an identifiable way becomes more complex.

      To address this issue, we considered several alternative model specifications and conducted grid-based estimation of starting parameter values. This approach allowed us to examine the shape of the loglikelihood function and assess whether the parameters are globally identified, rather than only identifiable up to a linear combination. We found that the most parsimonious and empirically identified specification in our experimental paradigm is one in which Q-values for gains and losses are summed, each weighted by distinct decision weights (see our Equation 2 in the paper).

      The inclusion of decision weights for REE for each option (Equation 2) is then structurally equivalent to introducing constant terms in a logit model. The identification of these parameters follows standard econometric results on discrete choice models (e.g., Davidson & MacKinnon, 2003): since we model choices among four options, three free parameters can be estimated, leaving one degree of freedom in the specification. As mentioned in the "Modelling and Statistical Analysis" section, we further guarded against the presence of local maxima by applying a two-step estimation procedure, combining two optimization algorithms with multiple sets of starting values for the baseline model (i.e., the model without decision weights for REE). We also tested the addition of a global optimization method— simulated annealing—but found that it did not significantly improve upon our two-step procedure. This is not surprising, as our preliminary investigation of model identification, based on grid searches over starting parameter values, confirmed that all parameters were identified in our simple specification. Our intuition is that simulated annealing may yield different estimates than gradientbased methods primarily in cases where the model is not theoretically identified—suggesting that the need for such global optimization techniques can be indicative of underlying identification issues in Qlearning models.

      Regarding model comparison, we have used penalized information criteria to account for additional parameters. Although we do not report confusion or inversion matrices for our nested models, we verified that the estimated models replicate observed behaviors across all phenotypes, as shown in the main text (see bottom left panel of Figure 5 for the Total and One-Sided sensitivities). Most importantly, we conducted 100 additional simulations of 40 artificial sessions for each phenotype using the “winning” models and the median fitted parameters. These simulated rats—playing the task 100 times over 40 sessions—offer strong evidence that the selected models are valid: they quantitatively capture the behavior of all phenotypes in terms of our key metrics, Total and One-Sided sensitivities (see bottom right panel of Figure 5).

      Taken together, this methodical econometric approach to model specification and estimation gives us strong confidence in the identification and robustness of our model. Overall, while Wilson & Collins (2019) provide an interesting framework for model estimation in computational biology, we believe that a more formal theoretical analysis of model identification in Q-learning models would be a valuable addition to the field—though it lies beyond the scope of the present work. In our view, computational biologists should complement simulation-based validation and empirical fit with formal methods for assessing theoretical identifiability, particularly when estimating complex choice models.

      Davidson, R. and J.G. MacKinnon (2003) Econometric Theory and Methods. Oxford University Press (New York).

      Wilson, R. C., & Collins, A. G. (2019). Ten simple rules for the computational modeling of behavioral data. eLife, 8, e49547. https://doi.org/10.7554/eLife.49547

      Reviewer #2 (Recommendations For The Authors):

      (1) The paper confuses risk sensitivity and exploration in the opening lines. These are not the same.

      What we have in mind here is that uncertainty about outcomes is one of the main drivers of exploration, in the sense that there would be no need to explore in a counterfactual world with deterministic gains and losses. We have modified the opening lines of the paper to better reflect this dimension (page 2).

      (2) p. 9. "awfully long" is an unnecessary descriptor. Descriptions of methods should be more factual.

      The manuscript has been entirely rewritten.

      (3) p. 13. Most points lie on the left of the square (not right?).

      We thank the referee for pointing at this typo, that is now corrected in the text (page 8).

      (4) p. 13. Last line. "obviously" is patronizing to the readers.

      The manuscript has been entirely modified to address related points.

      (5) p. 23. The avoidance of black swans by not choosing that option sounds like a hot-stove effect (see Denrell & March, 2001). Is this evidenced here?

      To the best of our knowledge, the statement that “people tend to avoid activities they have had a negative experience of, resulting in a negativity bias” (from Jerker Denrell’s website) does not explicitly concern REE. Instead, it appears to refer broadly to reinforcement learning mechanisms driven by negative outcomes, irrespective of their magnitude or frequency. In our task, animals encounter both negative rare events (RE) and negative rare and extreme events (REE; Black Swans). Notably, the task design does not allow rats to completely avoid negative RE unless they cease performing the task altogether—a pattern typically seen in paradigms involving aversive stimuli such as electric foot shocks. The fact that all 20 rats maintained stable performance across the 41 sessions provides evidence against a pronounced hot-stove effect. This point has been incorporated into the revised discussion (page 20).

      (6) "menus" is an odd term. Better described as reward schedules?

      “Menu” has been replaced by “option” in the main text.

      (7) Why are they 20-minute sessions? I thought it was 120 trials per session? And 41 sessions? Or was this only in training?

      Each session ended after 20 minutes had elapsed, which led to approximately 120 trials (but not systematically). The choice of 20 minutes was made in order to limit the number of trials to prevent satiety. The total number of sessions ran with all 20 animals for the final testing was 41, an odd number but there was no justification to remove one session from the analysis. The training was much longer and is not included in the 41 sessions.

      (8) Really not clear why these Jensen inequalities were relevant or even calculated for these options? How is it relevant to what animals chose or experienced? They seem to be based on the generative probabilities for different options, which is not what happened in reality.

      We propose the Jensen gap as a general measure of convexity that relates to all moments of the probability distribution, as described in more detail in our answer to point (3) above. As such, we think it is a characterization of options with stochastic outcomes that could prove useful to other experimenters in alternative settings beyond our own.

      (9) Only some summary data in supplemental materials. No open data or code for recreating the experiment or analyzing the data.

      The data is available on Github (see page 38) and the code will be available upon request.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      We thank the reviewers for their time and constructive comments on our manuscript.

      Reviewer #1 recognizes the importance of the question we address (namely, the early consequences of Wilms' tumour inducing mutations on kidney development in two models for different Wilms' tumour initiating mutations) and provides useful suggestions for improvement of the manuscript.

      Reviewer #2 raises the concern regarding the novelty of the study. We appreciate these comments and this implies the necessity of mainly textual changes we have to do to highlight the novel aspects of our study and findings and their significance in the revision of the manuscript.

      Reviewer #3 offers a generally positive assessment of the data, while suggesting that the work may be interpreted primarily from a developmental perspective rather than a Wilms' tumour-focused one. In the revision there is need to better emphasize how these perspectives are closely interconnected in the context of Wilms' tumour biology.

      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      This manuscript addresses an important gap in Wilms tumor (WT) biology: what are the earliest pathogenic events following WT driver mutation induction, and how do these early developmental trajectories differ across genotypes? The authors provide a carefully staged and comparative analysis of two WT-associated genetic contexts-conditional Wt1 loss (using lineage-specific Cre drivers targeting nephrogenic (Six2-Cre) versus stromal (Foxd1-Cre) compartments, as well as a temporally controlled Wt1CreERT2 model targeting both lineages upon tamoxifen induction) and inducible LIN28B overexpression, and relate the resulting developmental phenotypes to two CSC marker paradigms derived from patient-based studies. A major strength is the precise, time-resolved description of the earliest initiating phenotypes (E12.5 and E18.5, with additional postnatal analysis for LIN28B) and the direct side-by-side comparison of how each genotype perturbs nephrogenesis. The authors conclude that Wt1 loss (especially in the nephrogenic lineage) leads to a severe developmental block accompanied by a disturbance of lineage identity ("lineage confusion"), whereas LIN28B overexpression causes a disturbed transition between uninduced and induced nephron progenitor cell (NPC) states, producing blastemal-like regions that persist postnatally. Using immunostaining for NCAM1, SIX2, CITED1, and ALDH1A2, the authors map marker combinations during normal kidney development and across mutant contexts, and propose that tumor-initiating alterations, most clearly in the LIN28B model, and more suggestively in the Wt1CreERT2 (Wt1CE) context, promote the emergence of a CSC-like population inferred to co-express all four markers (NCAM1+SIX2+CITED1+ALDH1A2+), a state not observed in normal kidneys.

      We thank Reviewer #1 for this correct and complete summary of our manuscript. This reviewer recognizes the current gap in our understanding of the origins of Wilms' tumors and appreciates the approach we have chosen to start filling this gap using two different mouse models.

      Overall, this study provides a particularly clear direct comparison of the earliest tumor-initiating events triggered by distinct WT-relevant driver alterations. While the manuscript does not yet offer a detailed molecular mechanistic framework explaining why these two mutations produce such divergent developmental and marker-state outcomes (which would further strengthen the work), the careful comparison and the conclusions drawn from it are meaningful and make an important contribution to our understanding of the developmental processes that can lead to Wilms tumor initiation.

      We thank this reviewer for recognizing the importance of a direct comparison of the early consequences of two different Wilms' tumour mutations. We agree we do not yet provide a mechanistic framework for these differences. Although these studies are on-going, they are outside the scope of this manuscript.

      *Major comment: 1. A central and highly emphasized conclusion of this manuscript is that tumor-initiating alterations induce a CSC-like population co-expressing all four markers (NCAM1, SIX2, CITED1, and ALDH1A2), and that this state is not observed during normal kidney development. Because this "quadruple-positive" population is a key mechanistic take-home message and closely linked to the overall conceptual model, the manuscript would be substantially strengthened by a direct, same-cell demonstration of co-expression of all four markers, rather than inference from consecutive sections. The authors state that they were unable to do so due to a technical limitation, namely, antibody host-species constraints that prevent co-detection of CITED1 and ALDH1A2 within the same section. *

      We agree that not being able to show co-expression of all 4 CSC markers is a serious limitation for the interpretation of our data. The reviewer suggests the following alternatives:

      *Several feasible approaches could address this limitation for example: - Identify an alternative antibody reagent from a different host species. *

      The 'problematic' antibodies are the ones staining for ALDH1A2 and CITED1, which are both Rabbit IgG. Alternative antibodies for ALDH1A2 are all raised in rabbit, so these will not solve this problem. For CITED1 we have now identified a biotin-conjugated antibody which could be used in additional co-staining. We propose to test this antibody for the revision of this manuscript.

      *- RNAscope / smFISH for in situ single-cell co-detection. *

      We are aware of these techniques as alternative for antibody staining. However, we have no experience with these techniques, nor do we have access to the required technologies. After discussions with collaborators with much experience in this technique, we realized the combination of the potential extensive optimization and costs does not make this a suitable alternative for the limited samples we have available.

      *- Single-cell RNA-seq (scRNA-seq) to test whether a bona fide quadruple-positive transcriptional state exists. *

      This could be an option but is itself a huge project and therefore outside the scope of this manuscript. We note that the known scarcity in single cell data might still complicate the detection of each marker in individual cells, especially for low-expressed TFs like Six2 and Cited1.

      *Overall, resolving this technical limitation would markedly increase confidence in one of the manuscript's most important claims and strengthen the proposed genotype-phenotype/CSC-marker framework

      *

      _As discussed above, we propose the t_ry the biotin-conjugated CITED1 antibody__

      • It is somewhat unexpected that the Six2-specific Wt1 deletion appears to produce a more severe phenotype than the tamoxifen-inducible Wt1CreERT2 approach, which is intended to target a broader Wt1-derived lineage (both nephrogenic and stromal). The Discussion offers several plausible, non-mutually exclusive explanations for this observation (e.g., timing, recombination efficiency/mosaicism, and the rescue contribution of "escaping" wild-type cells). It would be helpful to support at least one of these explanations experimentally. For example, the authors could quantify the extent of "escape" (percentage of non-recombined cells within the lineage) across embryos/timepoints to validate that mosaicism is indeed the cause of the milder phenotype. *

      We can address this experimentally by making use of the tdTomato Cre reporter that was included in our model which allows us to follow the fate of mutated and non-mutated cells in the lineage. We propose to combine Six2 antibody staining with the tdTomato signal to quantify the percentage of cells that has maintained Six2 expression and is therefore likely an escaping cell/nephron.

      Minor comments 1. Please clarify whether the difference shown in Fig. 2C is statistically significant, and report n, error bars/variation, the statistical test used, and p-values (if applicable).

      These details will all be added.

      • The authors note the presence of some SIX2+; tdTomato+ cells in Foxd1GC control kidneys. Given the expected stromal restriction of Foxd1 lineage labeling, please clarify the likely explanation and, if possible, indicate how frequent this is.

      *

      The reviewer here points to the important question regarding the origin and potential overlap between the stromal and nephrogenic lineages. This is not only an important but highly relevant question for origin and biology of Wilms' tumours, but also for normal kidney development. Kobayashi et al (2014) reported some contribution of the Foxd1 lineage in the Six2 lineage. Also Magella et al (2018) found some signs for this, as did a recent pre-print (Haghighitalab et al. 2026). There is even data suggesting that (part of) the renal stromal is derived from the paraxial instead of intermediate mesoderm in chicken (Guillaume et al. 2009) with some supportive data from mouse development as well (Levinson et al. 2005). The latter is especially interesting given the commonly found ectopic muscle differentiation in WT1-mutant Wilms' tumours (Miyagawa et al. 1998; Schumacher et al. 2003; Gadd et al. 2012). However, if a common, potentially Foxd1+/Six2+ double positive, progenitor exists, it will in the normal developing kidney be present before E11.5 and therefore the data in our current manuscript, or the unpublished scMultiome data, is not informative for this. We propose to discuss this in detail in the Discussion of the manuscript, and speculate on its relevance for Wilms' tumours.

      It is somewhat unexpected that Six2-specific Wt1 deletion appears to produce a more severe phenotype than the tamoxifen-inducible Wt1CreERT2 approach, which is intended to target a broader Wt1-derived lineage. The Discussion offers several plausible, non-mutually exclusive explanations (e.g., timing and/or recombination efficiency/mosaicism and the contribution of "escaping" cells). it would be helpful to support at least one of these explanations experimentally, for example by quantifying the extent of "escape" across embryos/timepoints and tamoxifen dosing.

      This was addressed above.

      *4. A careful proofreading pass is needed to ensure text-figure consistency, particularly for arrow annotations. For example, the Results text refers to "Fig. 1F, arrows," but arrows are not apparent in that panel. Likewise, the Results text mentions a "white filled arrow" in Fig. 2H, whereas the figure appears to show only open arrows. Please align the wording with the annotations actually shown in the figures. *

      We apologize for these errors and thank the reviewer for pointing them out. These, and all other textual and graphical errors, will be corrected in the new version of the manuscript.

      __Reviewer #1 (Significance (Required)): __

      Overall, this study provides a particularly clear direct comparison of the earliest tumor-initiating events triggered by distinct WT-relevant driver alterations. While the manuscript does not yet offer a detailed molecular mechanistic framework explaining why these two mutations produce such divergent developmental and marker-state outcomes (which would further strengthen the work), the careful comparison and the conclusions drawn from it are meaningful and make an important contribution to our understanding of the developmental processes that can lead to Wilms tumor initiation.

      We thank the reviewer for this comment, and like to emphasize that this is precisely the scope we intended with the current manuscript.

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      *Wilm's Tumor, a pediatric kidney cancer, is associated with gain or loss of activity of a number of genes including the loss of activity of the nucleic acid binding protein WT1 and gain of activity (enhanced expression at the mRNA level) of the RNA binding protein Lin28 which negatively impacts the maturation of the miicroRNA let-7, elevating levels of let-7 targets. Previous mouse studies have examined the impact of loss of Wt1 throughout within the nephron progenitor and interstitial cell compartments in capping mesenchyme that is thought to be the source of the tumor and of broad elevated expression in all kidney progenitors. *

      *In this manuscript, the authors have refined the loss of Wt1 to nephron or stromal progenitors and compared the phenotype to loss of Wt1 in both lineages examining cultured kidneys over a 72 hr period, in addition to uncultured kidneys examined at e18.5. A similar analysis was performed on Lin28 mutants. The analysis itself consisted of video imaging, limited immunostaining and histochemistry. *

      Reviewer #2 provides, in our opinion, a very limited overview of the contents of our manuscript. Our work presented here shows:

      • A detailed analysis of effects of Wt1 loss or activation of LIN28B in the following systems:
      • 5 embryonic kidneys
      • 5 embryo kidneys
      • P19 postnatal kidneys (for the LIN28B model)
      • In vitro cultured kidneys.
      • Time-laps analysis of in vitro cultured kidneys

      • In the case of the Wt1 knockout this was studied in nephrogenic, stromal, and the combination of nephrogenic and stromal lineages

      • Whereas our previous work (Berry et al. 2015) focused on different stages of nephron development, we now focus on the different lineages.
      • For the first time we study the different marker sets for Wilms' tumour cancer stem cells in their developmental context. Important take-home messages for this are:
      • The two published maker sets behave different in the normal developing kidney, and no cell types or developmental stages exist in the normal developing kidney that expresses all four markers
      • In contrast, after either of the two Wilms' tumour mutations are induced, we have strong, though not yet conclusive, evidence that this event induces cells that are positive for all four CSC markers, suggesting these quadruple-positive cells could be the functional CSCs. This mutation-dependent appearance of the CSCs would be a complete different mechanism for the origin of CSCs than believed for, for instance, leukemia and colorectal cancer, where an existing cell type with stem- or progenitor cell characteristics which already express the CSC markers picks up the tumour initiating mutations and thus starts behaving as CSC. The cascade our data suggests for the Wilms' tumour CSCs is much more complex.

      • To our knowledge this is the first direct and side-by-side comparison of the early effects of different Wilms' tumour mutations. This analysis clearly shows the differences in underlying biology for these two situations, and this can have important consequences for interpretation of patients data (which was historically almost always generated without knowing the initiating mutation) and opens the possibility of mutation-specific therapeutic possibilities and requirements. This is funcamentally different from the current patient stratification based on clinical outcome (favorable vs non-favorable histology) or very general molecular markers with clear biological consequences (like chr 1p status).

      • With respect to the mutation-dependent accumulation of CSC markers, although in both Wt1 and LIN28B models this seems to be happening, for the LIN28B model this seems to be the result of a simple developmental block, whereas for the Wt1 mutants this appears to be a lineage conversion phenotype. This is again something that has to our knowledge never been suggested for the origin of CSCs and even in the context of normal kidney development is almost unprecedented.
      • We optimize the use of the Wt1CreERT2 driver to target different lineages in the developing kidney using different timepoints for tamoxifen treatment. Not only does this have technical use, it also illustrates the complex role of Wt1 in the earliest stages of kidney development.

      Although the data presented are descriptive and do not yet provide a complete molecular mechanism, we believe they offer novel, unexpected and important insights that merit publication. We acknowledge that these aspects may not have been sufficiently clear in the original version of the manuscript, and therefore not being picked up by the reviewer. In response to Reviewer #2 comments, we propose a thorough rewrite of the Discussion of the manuscript to emphasize these aspects more.

      *While wholly qualitative and largely observational and descriptive, the limited data are of good quality and the conclusions drawn are reasonable. *

      We thank the reviewer for their compliments on the quality and conclusions of the data. While we acknowledge the reviewer's characterization of the study as quantitative and descriptive, we respectfully do not consider this to diminish its suitability for publication. We believe the dataset provides substantial and meaningful insights (definitely not limited), and we have clarified and expanded upon the novel aspects and significance of our findings as outlined above.

      *For the Wt1 study, most interesting would be in the loss of Wt1 from the NPC lineage. Clearly, there is already a significant phenotype at the time of study (E12.5) hence there is no strong insight into the earliest effects of Wt1 loss and how this might contribute to tumor formation. Quite what happens to these cells phenotypically is unclear given the limited set of markers used to look at the cells. Specific removal of Wt1 from the stromal lineage generates a milder phenotype, indicating a role for Wt1 there, but without a mechanistic analysis of the resultant products, the underlying mechanisms remain unclear. *

      As discussed in our response to reviewer #1, we agree on the lack of mechanism in the current study but emphasize here as well that although this is the topic of the on-going follow-up studies this is outside the scope of the current manuscript. We refer to the same response for our proposal for additional experiments for the revised version of the manuscript.

      *Wt1 removal from both lineages generated a phenotype less severe than removal from nephron progenitors (and previous data on "double lineage removal" with a Nestin1 cre), an indication that the genetic approach was not up to the task. *

      Respectfully, we would like to emphasize the practical challenges associated with the use of genetically modified mouse models for developmental (and other) studies. We doubt there are many Cre drivers that do exactly what they were intended to do, do only that, and at full 100% efficiency. Many Cre drivers are, when originally described, only described for the cell type they were intended for, and any other activities or limitations are missed or ignored. One could rightfully argue that is bad science, but unfortunately this is often the reality and the starting point for many in vivo analyses. And these are only the complications regarding the behaviour of the Cre driver, and does not even touch on issues like the biological processing of tamoxifen, and the stability of already existing mRNA and protein of the gene of interest in the context of, in this case, a rapidly developing organ. Simply dismissing technical complications as 'not up to the task' is in our opinion not the way forward for studying the origin of diseases.

      What is important, and what we demonstrate, is the realization of the limitations of a system, test them and where possible take them into account in the interpretation of data. In this case, instead of hiding the incompleteness of the Cre activity, we actually demonstrate this using retained staining of Wt1 and discuss this in the context of the different phenotypes. We have carefully tried not to overinterpret our data, and note that this reviewer does not give any specifics where this could be affecting our manuscript.

      We also like to stress that in the context of Wilms' tumour development the incomplete activity of this Cre driver could even increase the relevance of this model, since the early stages of Wilms' tumourigenesis in the (future) patient happen in a few mutant cells in the context of a further normal developing kidney. The effect of the normal cells in our model that we speculate about could also be important in the patient, we just don't have the technical possibilities to test this yet.

      *In some sense, one could regard this work as a pilot study, looking to optimize expensive and time-consuming mouse experiments to maximize insight (ie choose optimum model, address most informative time points, decide on analytical approaches). As a stand-alone paper, the work may not significantly advance our understanding of the topic. *

      As argued above, in our opinion this does not do justice to the work we describe in our manuscript.

      For example, can simple loss of Wt1 tells us anything about Wt? Yes Wt1 is lost in a subset, but even in these there are additional genetic mutations.

      Of course even in WT1-mutant tumours there will be additional mutations found in the tumour. In fact, it has been known for a long time that WT1-mutant Wilms' tumours select for oncogenic mutations in β-catenin with a surprising preference for specific mutations affecting Ser45. However, it is clear that in these tumours the loss of WT1 is the first, rate-limiting step (Fukuzawa et al. 2004; Li et al. 2004; Zirn et al. 2006; Uschkereit et al. 2007). These β-catenin mutations are selected for in an already WT1-mutant context. If we want to understand the full biology of the WT1 mutant tumours including the β-catenin mutation, we will first need to understand the effect of only losing WT1 because that is what provide the selective pressure for the next step (oncogenic mutation in β-catenin). The work described here is an essential first step in that.

      • For Lin12, there is no significant advance beyond the studies of the Daly lab. *

      As argued above, this is not correct. The following aspects were not covered in the original paper describing this model:

      • The in vitro analysis of control and LIN28B embryonic kidneys, including the time-lapse analysis demonstrating how the phenotype develops over time
      • The expression of the Wilms' tumour cancer stem cell markers and how these change as a result of the LIN28B activation
      • The direct comparison to the Wt1 loss phenotypes, and the demonstration these different mutations lead to fundamentally different biological phenotypes despite both eventually being classified as Wilms' tumours.

        I have no useful suggestions for improvement which would require a completely different approach to the problem from the start.

      We respect this reviewer's opinion, but based on the above we do not agree and maintain a different interpretation.

      Reviewer #2 (Significance (Required)):

      *The authors set out the goal in the introduction - to obtain a better understanding of the origins of Wilm's tumor. There doesn't appear to be an insight of cancer relevant significance beyond earlier studies. *

      Our work studies the very first steps in the development of Wilms' tumours. It will never be possible to study this in the (future) patient as these happen around wk 8-10 of pregnancy. By instead analyzing this in mouse models we show fundamental biological differences between different Wilms' tumour inducing mutations which is for sure relevant for patients, the interpretation of patient data (or more the difficulties with interpreting patient data if the initiating mutation or tumour class is not known). Moreover, the data provides new insights in the Wilms' tumour cancer stem cells, a preferred target for any therapy, and suggests the combination of all four known markers might be required to identify and study the true WT CSC. In our opinion such findings provide extremely relevant insights for the field.

      *To a readership now/too used to analysis at genome scales (genomic, transcription), this study might appear modest. *

      While we agree that genome-wide approaches can provide valuable insights, this doesn't mean that work that doesn't use them cannot provide important insights nor does it mean that every piece of work that does use them provides any new insights. We respectfully emphasize that the merit of a study should be assessed based on the data presented and their interpretation, rather than on the techniques that were used to obtain them.

      The target audience is unclear.

      Our target audience for this manuscript is everybody who is interested, for whatever reason, in the biology of Wilms' tumours.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      *Wilms tumor arises from disrupted kidney development. Progenitor-like populations and cancer stem cell (CSC) fractions have been described in patient tumors, but how specific mutations alter embryonic programs to generate these states remains unresolved. *

      *Pop et al. model genotype-phenotype relationships during kidney embryogenesis. Using Six2- and Foxd1-driven Cre lines, they test the effects of Wt1 loss-of-function and Lin28b gain-of-function in nephron and stromal progenitors. Through explant imaging, histology, and immunofluorescence, they define mutation-specific effects on ureteric branching, cap mesenchyme organization, stromal composition, and nephron differentiation. *

      *Lineage-restricted Wt1 deletion produces distinct outcomes depending on whether nephron progenitors, stromal progenitors, or both are targeted. Lin28b overexpression causes delayed nephrogenesis and lobular organization resembling human Wilms tumor morphology, with expansion of blastemal-like populations. *

      This is a correct summary of this part of our data.

      These genetic removals of Wt1 and overexpression of Lin28b are useful for the field in understanding where and how Wt1 functions and whether Lin28b could be a model for Wilms' tumor.

      We agree that our data on Wt1 loss focusses on the role of Wt1 in normal kidney development, how its loss disrupts normal kidney development and how this could be important for Wilms' tumourigenesis. This includes but goes beyond being only relevant for the function of Wt1, it informs on the biology of WT1-mutant Wilms' tumours.

      There is in our mind no doubt whether the LIN28B model is a model for Wilms' tumours. Activating mutations in LIN28B are found in human patient tumours, and already in the original publication of this model (Urbach et al. 2014) it was convincingly shown that the phenotype in the kidneys after less than 3 weeks (when the animals have to be culled animal welfare reasons) represents early stages of Wilms' tumours. Our data presented here confirms this, and extends it with respect to the behavior of the CSC markers and the comparison to the Wt1 loss phenotypes.

      Whether the use of previously defined markers NCAM and Aldeflour serve the authors well or is a distraction is to be determine but it is unclear how useful these have been for understanding WT biology thus far. The authors describe these in the developing kidney in explants and in vivo.

      *Overall, the data support the view that distinct mutations generate different forms of lineage derailment but it is unclear how this links to Wilms tumor. It is better suited to dsescribe the role of an interesting protein Wt1 in kidney development and lineages therein. Connecting it to tumor biology would require further scrutiny of tumors. *

      Since CSCs are, according to the cancer stem cell model, the cells in a tumour that should preferentially be targeted, the exact identification of the CSC markers is directly important for the treatment of tumours. Our data analyzes two different sets of CSC markers, we show these cells label non-overlapping cell types in the normal kidney but that after mutation induction their expression changes and potentially become co-expressed in a single cell type (see our response to Reviewer #1 for more details on this). Identifying the developmental origins of CSCs in a tumour that is the direct result of disturbance of normal embryonic development (Hohenstein et al. 2015; Li et al. 2021) can be used as an entry point into understanding the biology of these tumours. Based on this we argue that although our analysis is on embryonic kidneys, their implications are highly relevant for the actual tumours and their treatment. We propose to further emphasize this in the Introduction and Discussion of our manuscript.

      *The study shows that removal of Wt1 in the stromal compartment has distinct phenotypes, which could be important for Wilms tumor biology as this is an poorly understood part of this tumor. *

      As already discussed in our response to Reviewer #1, we agree this is a potential important and poorly understood part of Wilms' tumours, directly for WT1 mutant tumours which are stromal-predominant, but potentially also for other tumours. We propose to further address this in the Discussion of the manuscript.


      *Major comments: *

        • This manuscripts uses elegant genetics to scrutinize the role of Wt1 and Lin28b. These stand out as difficult to conduct experiments and are of high value. *

      We thank this Reviewer's appreciation for the design, challenges and value of our data.

      In contrast, the section on ALDH1A2 and ALDEFLUOR activity is less integrated with the developmental framework.

      We discussed our reasons for focusing on the normal developmental context of the cells expressing the CSC markers in the previous section. Since the originally described CSC marker was activity for the AldeFluor enzymatic assay (Pode-Shakked et al. 2013) which we could not use on sections or kidney rudiments, we had to conclusively identify which ALDH isozyme is responsible for this signal in this context. There is much inconsistency about this in the literature, and whichever isozyme is important in these tumours might not be the causative factor in other tumours where AldeFluor labels the CSCs. We therefore use previously published microarray data from the group that originally identified the NCAM1/ AldeFluor combination as Wilms' tumour CSCs to identify ALDH1A2 as the culprit in this cancer type. With this knowledge we could move our analyses to antibodies, allowing co-staining with the other markers. Note that if the signal in these CSCs would have been the result of ALDH1A1 or ALDH1A3 which we show are expressed in the developing ureteric bud, the implications of this for the biology of the tumours would be totally different. We propose to discuss this aspects and its importance in more detail in the revised manuscript.

      *Much is unclear here e.g, antibody validation, rationale for performing these assays in explants rather than in vivo tissue, and the shift in Aldh1a2 staining pattern between E12.5 and E18.5, including reported nuclear localization.

      *

      We need to correct the reviewer on this remark, part of our data is using in vivo samples (E12.5 and E18.5) as well as cultured kidney rudiments. We will clarify which technique we use in the legends of the figures. We prefer to use this combination of techniques for several reasons: 1) the additional 3D information obtained from kidney rudiments can help with identifying specific developmental stages in the developing kidney; 2) due to the different fixation more antibodies work reliably in cultured rudiments than on paraffin frozen sections; 3) this is an important extra factor in the validation of antibodies; and 4) the possibility of culturing kidney rudiments on a time-lapse imaging system allows us to study phenotypes over time (this also greatly reduces the number of animals we need to study multiple timepoints in a developing system, an important aspect for the 3Rs). A good example of this in the timelapse data shown for the nephrogenic Wt1 knockout. The extreme outwards migration of the mutant cells (we show this using the tdTomato reporter) could only be identified in timelapse experiments, but is fully consistent with the sections of the corresponding E12.5 and E18.5 in vivo sections.

      We have no explanation for the shift to nuclear localization for ALDH1A2. We are not aware of any other publications showing this. We cannot rule out this is a technical artifact but based on all other expression data obtained with this antibody and their consistency with other publication we don't think this is very likely.

      *It is unclear how the manuscript is strengthened by this component. NCAM1 is referenced in the context of Wilms tumor CSCs, but unlike the rest of the manuscript which is mechanistic, it is unclear whether NCAM1 represents a mechanistic node in tumor initiation or merely a surface marker used for cell isolation? If NCAM1 functions just as a proxy for a progenitor-like state rather than a driver of tumor biology surely Wilms tumors will be full of progenitors or blastemal cells and many surface markers. It is unclear what strong evidence shows NCAM1 to be useful, this distinction should be stated. *

      Cancer stem cells are defined based in functional characteristics, i.e. the capability of reconstituting a complete tumour with all of its complexity after transplantation in immune-compromised mice. The markers are usually, indeed, merely proxy markers for a specific cell type in the tumour with this functional capacity. The same can be said in this case for the AldeFluor activity, it is used as CSC marker for many cancer types but we are not aware of any data on a functional role for this pathway in any of them. It would be a really interesting experiment to combine our models with an additional conditional knockout for Ncam1 or Aldh1a2 to see if the phenotype we describe here changes. The genetics of such an experiment with so many alleles are however horrendous, would come with an enormous surplus of animals and would take too long for the average project.

      The developmental framework presented argues that mutation-specific lineage derailment underlies tumor formation. Marker identity alone does not define pathogenesis. Perhaps reorganize this section to align it with the lineage-confusion model or removing it altogether would make the manuscript punchier?

      • *

      We propose to rewrite these parts to make this more clear.

      • *
      • The manuscript is highly focused on the nephrogenic compartment yet removes Wt1 from the stroma as part of one of the main lines of experiments. At several occasions, stromal changes are described qualitatively but using quantitative terms. As such, the manuscript currently comes across as having a bit of a black box where we cannot see the stroma beyond H&E stains. Could there additional antibody stains for stromal markers e.g., Pdgfra, Pdgfrb, or Meis1 to better visualize this compartment and perhaps enable quantification of changes?*

      We agree this lack of additional stromal markers is a limitation of the current manuscript. Our reason for so far not including these was our doubts on the usefulness and relevance for the complete renal stroma of many commonly used markers. The scarceness of detailed studies on the developing stroma was a big part of this doubt. Some preliminary tests show that Meis1 is not exclusively found in the developing stroma of the mouse kidney but is also expressed in early stages of the nephrogenic lineage, and is therefore not a good marker for this purpose. Pdgfra and Pdgfrb however seem to be expressed throughout the complete stroma and not in the other lineages. __We propose to analyze these two additional markers for the revised manuscript. __

      *Minor comments: *

      *Page 4, Lines 89-95: Remove the repeated sentence beginning "Although best known as a transcription factor...". *

      *Page 8, Line 164: Arrows referenced in Figure 1F are not visible. *

      *Page 8, Lines 164-166: The sentence may refer to Figure 1G; this figure is not otherwise cited. *

      *Page 18, Lines 413-414: (Pode-Shakked et al., 2013) is cited twice. *

      *Figure 2C: Error bars are missing. Indicate number of biological replicates. *

      *Gene nomenclature should be consistent throughout the manuscript. A mouse protein/gene is Six2/Six2. *

      *Use precise language when referring to protein detection rather than "expression." *

      *Standardize corticomedullary orientation across figures. *

      *Page 7, Lines 160-161: Provide immunostaining supporting WT1+/Tdtomato− stromal identity. Co-staining with Foxd1 would clarify lineage assignment. *

      *At E18.5 in the Six2-driven Wt1 mutant, WT1 signal is absent despite earlier stromal WT1+ cells. Clarify the fate of these cells. *

      *Comment on the lower recombination efficiency observed in Wt1CE at E11.5. *

      *Page 14, Lines 321-322: Determine how long CITED1 persists in WTCE mice. Co-staining with later differentiation markers would clarify whether progenitor retention coexists with nephron maturation. *

      Page 15, Lines 352-353: Clarify whether the sentence describing blastemal-like regions should reference Figure 5D.

      We thank the reviewer for these correction and other minor comments. We will address them in the revised manuscript. With respect to the remark regarding the gene nomenclature, until recently we were also under the assumption that mouse proteins only have the first character as capital. However, to our surprise we recently realized the official mouse nomenclature states that the protein (but not the gene) is in fact in all capitals. We refer for this to section 1.5.2 at https://www.informatics.jax.org/mgihome/nomen/gene.shtml.

      References.

      Berry RL, Ozdemir DD, Aronow B, Lindstrom NO, Dudnakova T, Thornburn A, Perry P, Baldock R, Armit C, Joshi A et al. 2015. Deducing the stage of origin of Wilms' tumours from a developmental series of Wt1-mutant mice. Dis Model Mech 8: 903-917.

      Fukuzawa R, Breslow NE, Morison IM, Dwyer P, Kusafuka T, Kobayashi Y, Becroft DM, Beckwith JB, Perlman EJ, Reeve AE. 2004. Epigenetic differences between Wilms' tumours in white and east-Asian children. Lancet 363: 446-451.

      Gadd S, Beezhold P, Jennings L, George D, Leuer K, Huang CC, Huff V, Tognon C, Sorensen PH, Triche T et al. 2012. Mediators of receptor tyrosine kinase activation in infantile fibrosarcoma: a Children's Oncology Group study. J Pathol 228: 119-130.

      Guillaume R, Bressan M, Herzlinger D. 2009. Paraxial mesoderm contributes stromal cells to the developing kidney. Dev Biol 329: 169-175.

      Haghighitalab A, Nosrati F, Dehghani-Ghobadi Z, Sayed M, Ahn C, Hu Y-C, Chung E, Lim H-W, Park J-S. 2026. A knock-in Six2Cre line reveals transient interstitial potential in nephron progenitors. bioRxiv: 2026.2002.2004.703893.

      Hohenstein P, Pritchard-Jones K, Charlton J. 2015. The yin and yang of kidney development and Wilms' tumors. Genes Dev 29: 467-482.

      Kobayashi A, Mugford JW, Krautzberger AM, Naiman N, Liao J, McMahon AP. 2014. Identification of a Multipotent Self-Renewing Stromal Progenitor Population during Mammalian Kidney Organogenesis. Stem Cell Reports 3: 650-662.

      Krishna A, Meynert A, Dolt KS, Kelder M, Mesropian A, Ewing A, Brouwers C, Claassens JW, Linssen MM, Sheraz S et al. 2026. Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signaling. Nat Genet 58: 366-375.

      Levinson RS, Batourina E, Choi C, Vorontchikhina M, Kitajewski J, Mendelsohn CL. 2005. Foxd1-dependent signals control cellularity in the renal capsule, a structure required for normal renal development. Development 132: 529-539.

      Li CM, Kim CE, Margolin AA, Guo M, Zhu J, Mason JM, Hensle TW, Murty VV, Grundy PE, Fearon ER et al. 2004. CTNNB1 mutations and overexpression of Wnt/beta-catenin target genes in WT1-mutant Wilms' tumors. Am J Pathol 165: 1943-1953.

      Li H, Hohenstein P, Kuure S. 2021. Embryonic Kidney Development, Stem Cells and the Origin of Wilms Tumor. Genes (Basel) 12.

      Magella B, Adam M, Potter AS, Venkatasubramanian M, Chetal K, Hay SB, Salomonis N, Potter SS. 2018. Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf. Dev Biol 434: 36-47.

      Miyagawa K, Kent J, Moore A, Charlieu JP, Little MH, Williamson KA, Kelsey A, Brown KW, Hassam S, Briner J et al. 1998. Loss of WT1 function leads to ectopic myogenesis in Wilms' tumour. Nat Genet 18: 15-17.

      Pode-Shakked N, Shukrun R, Mark-Danieli M, Tsvetkov P, Bahar S, Pri-Chen S, Goldstein RS, Rom-Gross E, Mor Y, Fridman E et al. 2013. The isolation and characterization of renal cancer initiating cells from human Wilms' tumour xenografts unveils new therapeutic targets. EMBO Mol Med 5: 18-37.

      Schumacher V, Schuhen S, Sonner S, Weirich A, Leuschner I, Harms D, Licht J, Roberts S, Royer-Pokora B. 2003. Two molecular subgroups of Wilms' tumors with or without WT1 mutations. Clin Cancer Res 9: 2005-2014.

      Urbach A, Yermalovich A, Zhang J, Spina CS, Zhu H, Perez-Atayde AR, Shukrun R, Charlton J, Sebire N, Mifsud W et al. 2014. Lin28 sustains early renal progenitors and induces Wilms tumor. Genes Dev 28: 971-982.

      Uschkereit C, Perez N, de Torres C, Kuff M, Mora J, Royer-Pokora B. 2007. Different CTNNB1 mutations as molecular genetic proof for the independent origin of four Wilms tumours in a patient with a novel germ line WT1 mutation. J Med Genet 44: 393-396.

      Zirn B, Samans B, Wittmann S, Pietsch T, Leuschner I, Graf N, Gessler M. 2006. Target genes of the WNT/beta-catenin pathway in Wilms tumors. Genes Chromosomes Cancer 45: 565-574.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors generated mouse and zebrafish models for DeSanto-Shinawi Syndrome, caused by loss-of-function variants in the WAC gene. Using these vertebrate systems, they demonstrate conserved craniofacial and social-behavioral phenotypes that parallel human clinical features, along with deficits in GABAergic markers. They observe increased seizure susceptibility and male-biased brain volumetric changes in Wac mutant mice. Together, these findings begin to define the biological consequences of Wac haploinsufficiency and provide valuable resources for future mechanistic studies.

      Strengths:

      WAC is a high-confidence neurodevelopmental disorder gene and one of the genes identified by large-scale exome sequencing efforts, including the Satterstrom et al. (2020) autism spectrum disorder cohort. This study establishes the first vertebrate Wac models, addressing a major gap in the understanding of DeSanto-Shinawi Syndrome, and provides a framework for studying other syndromic forms of autism. The models generated will be impactful and useful to the community to study and understand DeSanto-Shinawi Syndrome.

      The cross-species analysis is important and well executed, and reveals both conserved and divergent phenotypes. The behavioral and anatomical assays are rigorously executed and well-controlled, and the inclusion of RNA-sequencing analyses adds valuable insights into the mechanisms underlying brain function in Wac mutants. Notably, the RNA-seq data reveal upregulation of several clustered protocadherins, genes central to neuronal identity and cell-cell interactions, which are known to be regulated by dynamic developmental regulation of chromatin architecture. This observation provides an intriguing hint that could link Wac function to higher-order chromatin organization and neuronal connectivity.

      Weaknesses:

      The evidence is solid, but the study remains incomplete in its mechanistic depth and molecular interpretation. The authors compellingly describe behavioral, anatomical, and transcriptomic phenotypes associated with WAC loss, yet do not explore how WAC mechanistically regulates chromatin or transcription. Given prior evidence that WAC interacts with the RNF20/40 ubiquitin ligase complex and promotes histone H2B ubiquitination and transcriptional elongation, the paper would benefit from a discussion of these functions as a potential link between Wac haploinsufficiency and the observed changes in neuronal gene expression. Similarly, the authors mention WAC's WW and coiled-coil domains but do not consider how these domains could mediate nuclear interactions or recruitment of transcriptional cofactors that shape gene regulation and chromatin organization in neurons.

      We agree that many mechanisms underlying how both animal model phenotypes and human symptoms that are caused by the Wac gene still need to be worked out. Due to the need to generate a great deal of data to first describe these models in this manuscript this will be expanded upon later. In lieu of this, we plan to follow up with mechanistic papers later to fully address the gap that remains. We have now added a paragraph in the discussion to bring up these important points regarding the roles of Wac during transcription and how its protein domains might be involved in these processes.

      The transcriptomic analysis is rich but largely descriptive. Although the upregulation of clustered protocadherins is particularly intriguing, these findings are not validated or localized to specific neuronal populations. The study would be strengthened by independently validating the most significant RNA-seq changes, such as protocadherin gamma genes, using in situ hybridization methods to confirm the spatial and cellular specificity of expression changes.

      We have greatly expanded the analyses of the bulk RNA-seq data, including a more rigorous look into the differences in gene expression between sexes, which has additionally revealed males to be more impacted by Wac loss of function. We have also added new western blot data for pan protocadherin alpha, which is now validated to be upregulated in the cortex (new Figure 7I and 7J). We are holding back any additional data from this report as we have single nucleus RNA-seq data that will be reported on in follow-up papers with targeted conditional deletion models.

      Finally, while the behavioral and MRI results add valuable breadth, their interpretation would be improved by clearer reporting of sample sizes, statistical corrections, and effect sizes to support claims of sex-specific and regional brain volume differences.

      Some additional details have been added to the methods section. In addition, we have now provided sample sizes assessed in each figure legend.

      Reviewer #2 (Public review):

      The authors describe the first deep neurological characterization of WAC mutation in two vertebrate species (zebrafish and mouse). They examine these at various levels, guided by the work in humans that has associated a heterozygous WAC mutation with DeSantos Shinawi Syndrome (DESSH). Therefore, they investigate the animals for a variety of phenotypes, following a template for what is seen when characterizing a new mouse/fish model of a developmental disability gene. Investigations include analysis of skull and jaw for abnormalities(both species), MRI of brain structure(in mice), electrophysiology(mice), assessment of signaling pathways (by Western blot, in mice), cell counts (both, more in mice), transcriptomics (mice), and behavior (both).

      Generally, this describes an important first characterization of the consequences of the mutation. Most of the studies appear well-conducted and reasonably powered, thus solid or convincing. However, there are a few places where the data presentation could be improved for clarity, and a few concerns about some choices in analytical approach for a couple of the experiments, where improved statistical approaches could improve their sensitivity and/or better rule out false positives, and thus the support of some of these claims is currently incomplete. There is also some lack of clarity about the rationale for some decisions regarding the fish genetics. Nonetheless, this is an important and useful first characterization of many phenotypes of these lines. Such experiments form a baseline for future mechanistic studies in the same lines and a platform to test approaches to reverse phenotypes.

      Individual claims and their strength & weaknesses:

      (1) The authors developed mouse and zebrafish models of WAC deletion

      They used the existing KOMP floxed WAC line to generate a null allele. For the mouse, there is a Western showing that it is indeed null for the protein. The fish data is less robustly validated - they don't confirm the allele in null at the protein or RNA level, and fish have two paralogs (waca and wacb), and this paper only characterizes one of these. So this evidence is less clear. The evaluated mice are heterozygous (Het), similar to patients, while the fish appear to be evaluated as homozygous mutants.

      We agree with the reviewer’s comments on zebrafish genetics. Since antibodies against zebrafish Wac proteins are not available, we could not examine protein levels in zebrafish. We predicted frameshift mutations due to DNA analyses in waca and wacb KO zebrafish. We made waca KO, wacb KO, and waca/wacb double KO zebrafish. waca/wacb double KO zebrafish showed a lethal phenotype, similar to homozygous mice mutants. Since wacb KO zebrafish did not show any detectable phenotype we do not report those here. However, we now show examples of the wacb and dKO zebrafish in Figure S1. Since waca KO zebrafish showed craniofacial and behavioral phenotypes that are comparable to mice Het and human patients, they are focused on in this report.

      (2) The authors show that both species show altered craniofacial features

      These data appear well powered, and the findings are robust.

      We appreciate this confirmation.

      (3) Each model altered GABAergic neurons

      In mice, the authors stained with PV antibodies and saw a decrease in cells positive for this staining. A second marker, Lhx6, does not show a difference, suggesting this might be a change in PV expression rather than cell number. They could maybe look into the literature to see if this loss of just the protein also occurs in other models. Overall, the sample size here is a bit smaller than other parts of the paper (n=3), and the methods on the cell counts were less clear, so it is not as clear that this finding is as robust. The authors counted several other broad classes of cells, and those appear normal. Interestingly, there might also be some TBR1 mislocalization in layer 6 that might be significant with added power.

      Thank you for these suggestions. Yes, other models also show this lack of PV expression even when MGE-lineage interneurons are present at normal levels. We mention in the discussion a previous study on the ASD gene CTNNAP2 that showed this. We also agree that there is a trend going on in the Tbr1 population. We assessed another WT and Het pair for Tbr1 laminar distribution and were able to determine that these changes held up and are now significantly different; the person counting these numbers was blind to the genotypes. Finally, we added more details to the methods to describe how the counting was performed.

      The fish data is based on an in situ hybridization for GAD. The measure shown is the width of the positive area in the forebrain. This measure is not one I have seen much before, and has potential to be driven by something unrelated to GABA (e.g., if the whole forebrain were simply a bit smaller). So this analysis could use a couple of other approaches (density of signal?) and/or a control probe for some other brain gene showing the measure is normal, and thus it is not just a size issue.

      To compare altered GABAergic neurons in mice and zebrafish, we tried to isolate zebrafish PV genes and examined their expression by whole-mount in situ hybridization, now included Figure S3 but found no differences. However, we could not find any zebrafish PV gene useful for GABAergic neurons. We chose to examine gad1b expression in the positive area of the forebrain in WT and waca KO zebrafish and then found differences in the brain area with gad1b expression. Since WT and waca KO brain sizes are generally the same we believe this measurement is reasonable to make this conclusion and have added text to the results section to justify.

      (4) Mice were more susceptible to the seizure-inducing agent PTZ

      These data appear well powered, and the findings are robust. The authors also did a fair amount of useful electrophysiology that was all normal, but appeared to be well executed.

      Thank you, we appreciate this confirmation.

      (5) Mice had changes in brain volume that interact with sex

      The authors conducted an MRI on a good number of mice and reported a slight increase in global volume just in males. Sample size is fair, but the statistical approach here may be better if it puts males and females in the same model (to boost power and explicitly test for sex by genotype interaction that they report), and there is some chance that the brain region level differences that they report could include some false positives. They tested many regions, and it is not clear whether or not they corrected for the number of tests. Often, an FDR correction would be used in such imaging studies. It may be that only the most robust regional findings will survive those corrections. It is interesting data either way, but the analysis could be improved.

      Given the 80 regions (bilaterally) that we used and the number of mice, i.e. 6-7, we are underpowered to robustly undertake FDR types of corrections. In the data presented we used t-tests between sex and regions to illuminate putative regional changes. However, we did revisit our MRI data and found three data sets where the results were not normally distributed. We thus changed our statistical test to Mann Whitney for male retrosplenial cortex, male parietal cortex and female corpus callosum, which are now reflected in the figures and differential statistics noted in figure legends.

      (6) Several behaviors are altered in the mice as well

      These studies were fairly well-powered (n=15,16), and they found several positive and negative results, including alterations in memory and sociability in both species. There is a minor statistical flaw in the three-chamber analysis (they don't actually compare the Hets directly to the wildtypes in their statistical testing - a common mistake in neuroscience that should be addressed. But the data look like they will probably still be significant when correctly analyzed. In the supplement, the authors could do a bit more with the data they have to look at hyperactivity (i.e., show total motion in open field, not just time in center vs. periphery), and adding sex to their model might improve sensitivity for genotype effects.

      Thank you for these suggestions. We have done several things to address this behavioral paradigm. First, we added more n’s and also switched from comparing the mouse vs. object to just comparing genotypes as a variable. In addition, we switched to quantifying a discrimination index, described in Phiilips et al., 2019 PMID: 31112129 for our measurement. These new data are shown in Figure 3A. Open field total distance traveled has now been added to Figure S2A. For all other measurements, we did first assess for sex differences but found none and thus compiled both sexes for the graphs.

      (7) Some biochemical signaling pathways are altered in the brain

      These are n=4 immunoblots, and show altered phospho ERK, but no changes in other signaling events predicted from prior WAC literature like H2B ubiquitination. They appear well done, and the authors share the full blots in the supplement.

      Thank you, we appreciate this confirmation. Since Wac is an adaptor protein we needed to test these reported molecular changes in neurons that were previously only reported in cell lines and drosophila. We were not surprised that some of these previously reported changes would not be the same in brain cells. However, it is possible that these changes might arise in more discrete brain regions or at different times during development, which will be tested in our future conditional knockout models.

      (8) WAC deletion also alters gene expression in the brain

      These studies were well-powered for RNAseq, with 10 and 14 samples, using neonates (P2), just the forebrain. The sequencing quality metrics all looked good, and the approach to analysis was okay. It would be stronger to again include sex in the model, rather than separate by sex. There were some typos in this part of the paper that made part of the conclusions unclear, but the RNAseq nicely confirmed the mutation of the mice, and discovered many differentially expressed genes, consistent with the role of this gene as a regulator of transcription. The presentation could be expanded to make more use of the data. Overall, though, this is a useful first characterization of the transcriptome in the line.

      Thank you for the suggestions. We have greatly expanded our assessments of the RNA-seq data. Upon analyzation of the data we found many differences between males and females and now show combined and sex-separated data. Our new data isolate several more extreme and some unique changes in males that are better shown as stand alone figure panels. In addition to these edits, we have also reworked all the text in this section of the results for better reading.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The cause and timing of lethality in the homozygous Wac knockout should be reported or discussed. Investigating Wac homozygous knockout embryos, if viable at early stages, could provide valuable insight into the developmental origins of the neuroanatomical and behavioral phenotypes described in the heterozygous animals. Even a brief histological or transcriptomic characterization of embryonic brains would strengthen the mechanistic understanding of Wac function during neurodevelopment.

      We agree and have collected embryos as early as embryonic day 12.5 from multiple litters but never detected a knockout. We have added this text to the animal methods sections to let readers understand effort had been done to determine when death occurs. While we don’t currently explore this further in mice we now include zebrafish waca; wacb double knockouts. Notably, while we were able to generate a few of these mutants, most died. However, some zebrafish were aged long enough to observe lethal deficits in heart formation and swim bladder development, suggesting that early loss of Wac could impact these critical organs that leads to death.

      (2) A better description of the data reported in Supplementary Tables 3 through 5 is needed. Supplementary Table 3 does not report any statistically significantly differentially expressed genes in the FDR column, and Supplementary Table 5 reports only two, and the reader should understand what the columns are indicating.

      We have now added figure legend text to the supplementary file to explain each Table mentioned here.

      Reviewer #2 (Recommendations for the authors):

      (1) Page 3, last paragraph. The description of wacb is confusing. I recommend that the authors provide the unshown data they mention and also further explanation of the breeding scheme and result. Indeed, if wacb is homozygous lethal, does that make it more like the mouse WAC gene, and thus potentially the more relevant paralogue to study? Are both waca and wacb expressed in the same tissues? How does that compare to mouse and human WAC expression? Such figures about gene expression (even when adapted with permission from public resources like Allen brain atlas or GTEX) are common in this sort of paper, as they can be helpful to understand when and where the gene is thought to act. For waca vs. wacb, they may help determine which gene is more relevant to the brain (for example, if only one is expressed in the brain).

      First, this is a great question and we have now added whole mount in situ for the waca and wacb genes as Figure S1. These data show low to no wacb expression in brain regions while waca is highly expressed there. Since the waca mutants showed phenotypes relevant to DESSH but wacb mutants did not, this correlates with observed expression patterns without fully excluding wacb from any role. Thus, we also made waca/wacb double KO zebrafish that showed a lethal phenotype, similar to homozygous mice mutants. Only a few waca; wacb double knockouts survived a little through development and are now shown in Figure S1. Since wacb KO zebrafish did not show any detectable phenotype on their own, we did not include the data since there are already several figures/tables in this manuscript. However, the waca KO zebrafish did show phenotypes similar to humans with DESSH and are the ones we focused on.

      (2) Why did the authors cross the mice into the outbred CD1 background? Usually, most labs keep the lines on an inbred background. Was there a particular rationale here? I am not saying that they could not outcross them. It is just a bit puzzling why. Perhaps a sentence of explanation in the methods section would be warranted.

      This is a great question and we have now added text to the animal methods section. Many labs that study development, especially on genes critical for survival/life like the Wac gene, use a more robust strain like CD-1. By doing this, we have a better chance of evaluating mutants at more mature ages and getting enough progeny to do more reproducible studies.

      (3) A typical first experiment in a new knockout (fish or mouse) is to establish that the deletion does indeed result in a loss of RNA and protein. In the absence of this, the rest of the paper cannot be as confidently interpreted.

      We did this for the mouse model and found reduced protein expression in the constitutive Het, however this datum is part of the western blots in figure 5. We now mention this in the early results section that protein levels were reduced in the Hets but maintain that the presentation of the western blot is better suited in Fig. 5 to compare to the other western blots. For zebrafish this was attempted but was more difficult. Available antibodies don’t work in zebrafish. RNA expression was attempted in both models and due to Wac being a critical gene for life, there are checks in place to upregulate faulty and normal RNA in the waca model. We screened for frameshift mutations in multiple KO lines and confirmed it by genomic DNA sequencing. In making many KOs and large-scale mutagenesis in zebrafish, we usually depend on phenotype-genotype segregation in Mendelian inheritance for many generations.

      (4) Are these new lines indeed knockouts? I did find a WAC western as part of a later figure for the mouse. The authors may want to mention that earlier, or present at least that data right away. What about in the fish? Is there a way to confirm at the RNA or protein level that it is indeed a null allele?

      Yes, as mentioned in the above response we have now mentioned our Wac western blot results early when introducing the mouse mutants and the issues with doing this in fish are presented above as well.

      (5) Why are fish used that are KO while mice are Hets? Are WAC homozygous mice not viable? This should be mentioned. Regardless, the rationale for examining heterozygous mice and homozygous mutant fish should be provided. Each kind of experiment is useful, but they are interpreted in different ways. Hets will genocopy the patients, who are generally hets, while KOs are often useful for a study of the essential roles of the genes, even if they are not really modeling the patient gene dose.

      Wac homozygous mice in our hands are embryonic lethal, now mentioned in the animal methods section, but we found early on that the Hets mimic several human DESSH patients. In zebrafish it is more complicated. We analyzed waca and wacb hets in zebrafish but found no phenotypes. This could be in part due to some complementation between the waca and wacb genes. It is also possible that a full waca KO could resemble a human DESSH individual since wacb may complement somewhat, even though deleting wacb entirely does not have a measurable phenotype. We have added more text to the discussion to explore these complexities. We also made waca/wacb double KO (dKO) zebrafish but they showed lethal phenotype, similar to homozygous mice mutants and suggesting some complementation by the wacb gene even though alone it did not exhibit phenotypes.

      (6) Figure 3A: It does not appear that the authors are directly statistically comparing the two groups (genotypes) that they are drawing conclusions about. This is an unfortunately common mistake in the neuroscience literature across papers. There is a nice older review about it here. https://pubmed.ncbi.nlm.nih.gov/21878926/. To draw conclusions about the differences between the mouse genotypes, they need to compare the two genotypes directly with a statistical test. See Nygard et al for a recommended approach, like comparing social preference indexes

      (https://onlinelibrary.wiley.com/doi/abs/10.1002/aur.2154).

      Thank you for this information. Previous reviewers at a different journal asked for this particular evaluation. We have now made changes to address the assessment, and graphs now reflect comparisons of genotypes instead of a single genotype between time with a mouse or object. We have also moved to using a social discrimination index to compare the genotypes, similar to the study mentioned.

      (7) MRI - it is a bit weird to separate the male and female brains just for the MRI. Was there a premise from human data to do so? If not, the authors should probably pool them. If they are concerned there are sex effects (or, more likely, a sex by genotype interaction) I recommend that they use a two-factor ANOVA and simply put both sex and genotype into the model. This will also have the advantage of increasing their statistical power for genotype effects a bit. If their current results are robust, they will still show up as a significant sex x genotype interaction.

      All data in the manuscript initially compared the sexes to each other. We have now added this text to the animal section of the methods: For MRI, some zebrafish behaviors and now the RNA-seq data, sex was a difference and due to this observation, sex was (or now is) presented independently for these measurements. We now state that if no sex differences were observed the data were pooled.

      (8) Also, did the authors correct for multiple testing in the MRI analysis? Since they are testing many regions, there is a risk of false positives if they do not. This could be confounded further by their splitting the data by sex, thus doubling the number of tests.

      As noted above we did not do multiple corrections given the large number of regions and low number of replicates.

      (9) How many images per animal were analyzed for the cell counts? This detail is absent from the methods and would help with evaluating the robustness of these findings. What other approaches were used to make sure the counting was unbiased?

      We analyzed 3-4 images per animal for counts and counted hundreds of cells per image. In addition, the person counting was blinded to avoid any bias. These details have now been updated in the methods.

      (10) As with the MRI, for the DEG analysis, I recommend the authors simply put sex and genotype into the same model as two factors (with an interaction), to increase their sensitivity to genotype effects, as well as be able to report on robust genotype x sex differences, if there are any. They may also consider testing the model with and without excluding the three outlier animals on their PCA. It may be that the noise of those outliers is detracting from their sensitivity for DEGs somewhat.

      We greatly expanded our analyses and found more robust and unique changes in males that are now added to Figure 7 and supplemental files. After considering the data, decided to highlight the sex differences separately.

      (11) A few more relatively simple things could readily be done with the RNAseq data to add some depth and interpretation. For example, do the hits here overlap other published IDD/autism DEG lists from mouse knockouts studies of genes like FoxP2, Chd8, Dnmt3a, Myt1l, Tcf4, etc? Do autism genes show up in the lists of hits here? And if so, more than expected by chance? Can they provide some visualization of their GO results in the main figure?

      When we looked into the sex differences more we found that only the males showed significant upregulation of other autism risk genes increase that was previously unappreciated when the sexes were assessed together. Yes, several autism genes do show up but is heavily biased to males. Our main Figure 7 and new supplemental files show new GO term analyses and provide additional data looking not only autism but other factors.

      (12) It appears the IMPC has phenotyped this mouse somewhat, including craniofacial abnormalities. They also report on some blood cell differences. Anyway, if no one has written about that data yet (as it was generated in the context of a big consortium effort), their guidelines may allow you to include some of their data as Supplementary Figures here with proper attribution. It might help to at least summarize useful findings from there in your discussion.

      Due to the large number of figures/tables already in this report we don’t think this will be helpful. However, we do refer readers to the consortium in the animal methods section so they can explore data already generated by the IMPC.

      (13) Minor/Typos:

      (a) Figure 2K: I am confused by the description of three genotypes in the legend, but only two in the panel?

      Corrected.

      (b) I found it a little distracting that some results figures were embedded in the introduction.

      We have moved the figures further in the manuscript to start in the results section.

      (c) I don't understand this sentence: "Due to reduced sample size, sex-stratified DE was performed without model corrections at FDR < 0.1, 7 and found genes significantly upregulated and downregulated, respectively;" The sample size here seemed robust, so I am not sure what they were referring to? Are there missing numbers form this sentence? What is the 7? I think there are enough typos here that I am not sure how to evaluate this claim. Thus, the writing and clarity of this part could be improved.

      This section had several typos that have now been corrected.

      (d) "Marwan Shinawi, (unpublished results)" is a bit atypical of a citation. Are these results being reported with his permission? If so, then it should say 'personal communication' (if the journal permits this - some do not). If not, they should not report someone else's unpublished results without their explicit permission. It might upset some people to have their results presented this way.

      We have changed unpublished results to personal communication. Marwin Shinawi is an author on this manuscript and has approved of everything we have reported.

      (e) In all figures, consider shape or color coding for sex, even when pooling the data (e.g, the data points in the behavior figures).

      This is a good idea but since we found no difference when analyzing the data we don’t see how this extra work will make a difference. Since we now mention that sex differences were only presented as separate graphs when observed in the methods we think this should be acceptable.

    1. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #1

      Evidence, reproducibility and clarity

      Summary

      Alshamsi et al. investigate the role of Drosophila neurotrophins (DNTs) and their Toll receptors in regulating neuronal apoptosis during optic lobe development.

      The authors provide compelling evidence that different DNTs and their Toll receptors are expressed in optic lobe neurons, and their activity regulates neuronal survival during optic lobe development. They further show that disruption of DNT/Toll signaling impacts neuronal morphologies.

      Comments

      ABSTRACT

      "Over-expression of DNT-3 (spz-3) and DNT-2 (spz-5) could rescue natural occurring cell death, whereas their loss of function caused cell death, showing that DNT-3 and DNT-2 can, and are required to, promote cell survival during optic lobe development."

      I find it more appropriate to say that OE prevents naturally occurring cell death because it inhibits a normal physiological process."rescue" would only be correct if there were an experimental or genetic loss (e.g., deletion of a survival factor) and you are restoring normal survival levels

      "Importantly, DNT-2 is expressed in Mi1 neurons and Toll-2 in connecting L1 neurons. We show that DNT-2 functions in concert with Toll-2, as Toll-2 RNAi knock-down prevented the rescue of apoptosis by DNT-2 over-expression and all Toll-2+ neurons were lost in DNT-2 mutants."

      I find this sentence very difficult to follow

      i suggest moving "Importantly, DNT-2 is expressed in Mi1 neurons and Toll-2 in connecting L1 neurons."

      to the next sentence. "by specifically investigating the Mi1 (DNT-2+) and L1 (Toll-2) synaptic partners", alterations in DNT-2 or Toll-2 expression levels impaired connectivity of L1 neurons at the M1 medulla layer and altered dendritic morphology of L1 neurons

      "As DNT-3 (spz-3) and DNT-2 (spz-5) are expressed in the medulla and they could influence both lamina and medulla neurons, this suggests that their function maintaining cell survival could enable the stabilisation or alignment of connected neurons across medulla columns."

      influence what? this is very vague and needs a temporal understanding of when neurons die, synapses are formed, and consider the phenotypes of the mutants and RNAi experiments.

      INTRODUCTION

      "Neuronal survival is maintained by neurotrophic factors secreted in limited amounts by target cells, leading to the survival of only those neurons that receive trophic support (Levi-Montalcini, 1987, Davies, 2003)."

      Perhaps the authors can be more precise, e.g. One mechanism by which Neuronal survival is regulated is through neurotrophic factors secreted in limited amounts by to be synaptic partners and adjacent cells

      "In this context, if neurotrophism is fundamental for nervous system development, it could have been enabled by evolutionarily conserved molecular mechanisms."

      I think the authors want to suggest that given the fundamental and widespread role of neurotrophism in nervous system development, it remains unknown if it relies on evolutionarily conserved molecular players.

      "Neurotrophins - NGF, BDNF, NT3, NT4 - are the main growth factors maintaining neuronal survival in the vertebrate nervous system (Levi-Montalcini, 1987, Lu et al., 2005). Importantly, they can also promote cell death, depending on context (Lu et al., 2005). They can promote cell survival via their Trk receptors and ERK and AKT downstream and via p75NTR and NFB downstream, or cell death via p75NTR, Sortilin, and JNK signalling instead (Lu et al., 2005). mechanisms."

      The authors should avoid the repeated use of "they"

      "There are six spz and nine Toll paralogous genes in Drosophila, which could play distinct functions. In fact, at least full-length DNT-1 and Toll-1 can promote cell death instead, and at least Toll-6 can promote either cell survival or cell death, depending on context (Foldi et al., 2017, Singh et al., 2025, Zhu et al., 2008) . Importantly, mature DNT-1 and DNT-2 with Toll-6 and Toll-7 are required for and can promote neuronal survival during circuit formation in the embryonic ventral nerve cord (McIlroy et al., 2013, Zhu et al., 2008)."

      I find this paragraph difficult to follow. I suggest the following editing, which the authors might want to consider:

      "There are six spz and nine Toll paralogous genes in Drosophila, which could play distinct functions. In fact, at least full-length DNT-1 and Toll-1 can promote cell death instead, while and at least Toll-6 can promote either cell survival or cell death, depending on context (Foldi et al., 2017, Singh et al., 2025, Zhu et al., 2008) . Importantly, mature DNT-1 and DNT-2 with Toll-6 and Toll-7 are required necessary and sufficient to promote for and can promote neuronal survival during circuit formation in the embryonic ventral nerve cord (McIlroy et al., 2013, Zhu et al., 2008).

      "During this time (24-50h APF), connectivity between photoreceptors, lamina and medulla neurons is established; this is followed by medulla neurons connecting to lobula neurons;"

      I find this sentence misleading, if not incorrect. If by connectivity the authors mean synaptogenesis, for all that is known, synaptogenesis has been shown to occur from from mid-pupal development (P50) onwards If by connectivity, the authors mean the targeting of specific neuropiles and layer organization, it is also incorrect that lamina and medulla organization precedes the connectivity between medulla and lobula neurons. These processes are all concurrent. Can the authors please clarify?

      "and by 72h APF cell death has greatly diminished and synaptogenesis completes connectivity patterns, in preparation for adult eclosion at 96h APF (Millard and Pecot, 2018, Melnattur and Lee, 2011, Hadjieconomou et al., 2011, Kurmangaliyev et al., 2020) "

      Kurmangaliyev et al., 2020 is probably not an appropriate citation here as it mostly deals with transcriptional programs of circuit assembly in the developing optic lobe

      "Thus, 24-48h APF is a critical period to maintain necessary lamina and medulla neurons alive in the optic lobe."

      Perhaps the authors want to revisit this sentence and explicitly say that 24-48h APF is a period where apoptosis defines cell numbers

      "The development of the Drosophila visual system has been well described (Holguera and Desplan, 2018, Melnattur and Lee, 2011, Millard and Pecot, 2018, Hadjieconomou et al., 2011, Behnia and Desplan, 2015)."

      I find that Behnia and Desplan, 2015 is not appropriate, as it is a review that describes the characterization of neuronal circuits underlying visual modalities in the fly brain, and not their development. The following reviews dealing with different aspects of neurogenesis, neuropile development and circuit formation are likely more relevant: Bakshi et al Current Opinion in Neurobiology 2025 Malin et al PNAS 2021 Ngo Dev Bio 2017

      "R7 and R8, together with lamina neurons target to medulla layers M6 and M3, respectively, organizing into medullar columns that respond to the same point in visual space and maintain retinotopy."

      I find this sentence misleading because lamina neurons do not target M6 and only L3 targets M3.

      "Medullar interneurons also form connections across multiple layers, where each layer represents different visual features (Fischbach and Hiesinger, 2008, Millard and Pecot, 2018)."

      Here, Behnia and Desplan, 2015, Matsliah et al Nature 2024, Borst and Groschner , Annu. Rev. Neurosci. 2023, and even Schnaitmann et al J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2020 are better references that review feature detection and circuit organization in the optic lobe.

      "Neurons within the lobula complex integrate signals from the medulla and project to the optic glomeruli in the central brain and motor outputs to enable appropriate behavior (Behnia and Desplan, 2015, Borst et al., 2020, Courgeon and Desplan, 2019b)."

      I find Courgeon and Desplan, 2019b is not very appropriate here, as it reviews the coordination of neural patterning in the Drosophila visual system. More adequate and relevant manuscripts and reviews are Wu et al. elife 2016, Tanaka and Clark, 2022, Lapoetke et al. Neuron 2022 , even Zhao et al. elife 2024

      "Spz-5 is well known as Drosophila neurotrophin-2 (DNT-2), and as Spz-3 has been proposed to have neurotrophin functions which we expand on and demonstrate here, we refer to Spz-3 as DNT-3 (Zhu et al., 2008, Coutinho-Budd et al., 2017, Sun et al., 2024, Ballard et al., 2014, Ulian-Benitez et al., 2017)."

      This last paragraph of the introduction seems out of place, and partly redundant with page 3. Perhaps the authors would like to finish the introduction with a paragraph highlighting the major findings and conceptual advance of the manuscript? This seems to be a good and natural way of following their previous sentence "Here, we asked whether neurotrophin family ligands encoded by DNTs (spzs) and their Toll receptors could regulate cell survival during neural circuit formation, in the Drosophila pupal optic lobe."

      RESULTS

      I suggest the following edit: To ask whether DNTs (spzs) are expressed in the pupal optic lobe, we generated T2A-Gal4 driver lines for spz-1,3,4,5 fly lines , crossed them to 10xUASmyrGFP or 20UAS6xmCherry reporter flies, and analysed resulting progeny optic lobes during development and in the adult with anti-GFP antibodies, as required (Figure 1A).

      Also, If the lines were also crossed with mcherry, mentioning anti-GFP antibodies is incomplete.

      "spz-1MIO2318-T2A>myrGFP and spz-1MIO2318-T2A>6xmCherry revealed expression in a few centrifugal neurons in the lobula complex that projected to the lamina,"

      At which stage?

      "subsequently medulla neurons and abundant arborisations into the lobula complex and medulla."

      Subsequent to what? I am sorry, but I don't understand this description.

      "Expression from spz4MI5678 -T2A->myrGFP was not detected until 72h APF" Data before 72h APF is missing Where was it expressed? Which cell types? Which neuropiles?

      "And then was found in the medulla and lobula complex and followed by the trachea." At which stage? What was followed by the trachea? I think the authors mean that at later staged (in the adult) expression was restricted to the trachea in both medulla and lobula

      "spz-3-T2A>6xmCherry (hereby named DNT-3) was highly expressed in non-neuronal retinal cells and medulla neurons;"

      At what stage?

      "And subsequently in the trachea and possibly glia."

      The authors could and should explain how they reach this conclusion. Given that no cell type specific markers were used, this identification was likely based on morphological features.

      "Finally, DNT-2-T2A>6xmCherry (spz-5) was found in medulla neurons, which could be tentatively identified as Mi1 medulla neurons (Nern et al., 2025) by 48h APF, and this pattern was maintained."

      The authors suggest these neurons are Mi1 based on what? Also, Fischbach's Cell Tissue Res (1989) seminal paper is probably worth mentioning.

      "Abundant cells expressed spz-1 in the lobula complex (Figure 1B, left) and medulla (Figure 1B, right), and DNT-3 (spz-3) and DNT-2 (spz-5) in the medulla (Figure 1B) during optic lobe development. DNT-3 (spz-3) and DNT-2 (spz-5) were expressed in distinct non-neuronal cells in the retina, seen in Multi Colour Flip Out (MCFO) clones (Figure 1C)."

      This sentence is misleading. These experiments allow the authors to conclude that spz+ neurons innervate these neuropiles. It does not allow the authors to conclude that spz molecules localize to the neuropiles. The authors should revise these claims in the main text and relevant figure legends

      "To visualize the distribution of Tolls in the optic lobes during pupal development, we used the GAL4 lines previously described (Li et al., 2020), driving expression of the reporter myrGFP (Figure 2A)."

      Same comment as above

      "Using MCFO clones as well as myrGFP, we could identify some of the Toll-8+ neurons as Lawf1, feedback neurons projecting from the medulla to the lamina (Figure 2B), and L2 and L4 lamina neurons (Figure 2B, C); Toll-6+ cells to include L3 and L4 lamina neurons (Figure 2B,D); and Toll-2+ neurons as L1 lamina neurons which target to M1 and M5 medulla layers and L3 lamina neurons that project to M3 (Figure 3B,E) (Hakeda-Suzuki and Suzuki, 2014, Behnia et al., 2014)."

      Hakeda-Suzuki and Suzuki, 2014, Behnia et al., 2014 are not the most appropriate references. Instead, I suggest the authors should cite Fischbach's Cell Tissue Res (1989).

      "Overall, the expression in the scRNAseq dataset (Kurmangaliyev et al., 2020) of the spz ligands and Toll-8 (also known as Tollo) data were less consistent with the cell biology data, whereas the expression of Toll-1, -2 and -6 confirmed cells seen with the cell-biology based reporters"

      It is perhaps more accurate to refer to the cell-biology based reporters as translation reporters, which is what T2a based Gal4 drivers are.

      "Most particularly, Toll-2 mRNA (synonym 18w) was found in L1 and L3 lamina neurons over time, plus also in L5 at 24h APF, and Toll-6 mRNA was found in L2, L3, L4 over time, plus also in L1 at 24h (Supplementary Figure 1-6)."

      This sentence is difficult to read and could be considered poorly written for several reasons including: - "plus also" is repetitive. "Plus" and "also" serve the same function. - Inconsistent punctuation. The lack of commas before "and Toll-6 mRNA..." makes the sentence feel unbalanced. -Vague time reference. "Over time" is imprecise. It's unclear whether it means during development, at multiple timepoints, or something else. Also regarding scRNAseq analysis: - the authors mention "We compared our reporter-based profiles with published scRNAseq datasets of the optic lobe through development (Kurmangaliyev et al., 2020, Ozel et al., 2021)" however the Ozel dataset doesn't seem to be used.

      Also, from the Material and Methods section:

      "The data were imported as a Seurat object, and cells corresponding to specific timepoints (e.g., 24 h, 36 h) were subsetted based on the provided metadata. Dimensionality reduction was carried out using principal component analysis (PCA), followed by Uniform Manifold Approximation and Projection (UMAP) embedding computed on the first 30 principal components. Cluster annotations provided by the original authors were used for all cluster-level analyses and visualisations."

      The Kurmangaliyev dataset is already processed. I am probably missing something here, but is not obvious to me why the authors performed PCA again

      "To conclude, at the time of naturally occurring cell death (0-48h APF), Toll-1 is highly expressed throughout the optic lobe; Toll-2, -6 and -8 are expressed in the medulla; Toll-8 and Toll-6 are prominently expressed in the lobula complex, and Toll-6 and Toll-2 are prominent in the lamina."

      This is misleading. These experiments allow the authors to conclude that toll+ neurons innervate these neuropiles. It does not allow us to conclude that toll molecules localize to the neuropiles. The authors should revise these claims in the main text and relevant figure legends

      "To ask whether DNTs can promote cell survival in developing optic lobes, we over-expressed DNT-2 (spz-5) and DNT-3 (spz-3) and visualized dying cells with the apoptotic marker anti-Dcp1 at the peak of naturally occurring cell death (24h APF)."

      These experiments were done using Toll8-Gal4 and nsyb-Gal4 drivers. What's nsyb-Gal4 expression during development? Is the expression of this driver consistent with the conclusions drawn from these experiments?

      "To test whether DNT-2 could promote cell survival during optic lobe development, we over-expressed full-length DNT-2FL or cleaved DNT-2CK in all neurons with nsybGAL4. This reduced the incidence of Dcp1+ apoptosis in the lamina and outside the lamina too (Figure 3C-D and Supplementary Figure S9C,D)."

      How do the authors explain that DNT-2CK reduced the number of Dcp1+ cells?

      "We generated DNT-3 (spz-3) loss of function mutants by P-element mobilization. DNT-2 and DNT-3 loss of function mutants caused considerable cell debris in the medulla and lobula complex, which compromised the analysis in this region, so we focused on the lamina."

      Perhaps, rather than stating that the mutants caused considerable cell debris, the authors could say that the mutants displayed considerable cell debris

      More importantly, I have concerns with the data from these experiments (Figure 3). Dcp1 signal volume intensity using Imaris. In all panels (A,C,E) the segmented images do not match the raw DCP1 staining, raising concerns on how much can one rely on this quantification. Could this be because the Dcp1 staining shown is a single z plane and the segmentation is a 3d rendering? The authors should carefully and robustly explain this discrepancy which is present in all images where Dcp1 signal volume intensity was quantified.

      Also, could the authors explain why the quantifications in Figure 3B and 3C differ by an order of magnitude (10×) from those in panel 3D? Please look at the WT control, there is a 10X difference in signal volume intensity.

      "Toll-2pTVGAL4 flies are heterozygous mutant for Toll-2, and, remarkably, in combination with DNT-2 homozygous mutants resulted in semi-lethality, revealing a functional interaction between these two genes.

      I cannot entirely follow this conclusion. I understand the authors propose that the combination of partial loss of Toll-2 and full loss of DNT-2 affects viability, more than either mutation alone. Is this what they mean? Can the authors comment on the viability of DNT-2 mutants?

      "Macrophages loaded with HisYFP and distributed mostly between the retina and lamina could be observed across these samples (Figure 4C), suggesting they had engulfed dead cells" How do the authors identify these YFP+ cells as macrophages?

      "Together, these data show that DNT-2 functions as a ligand for Toll-2 to maintain the survival of neurons in the lamina, medulla and lobula complex during optic lobe development." While the results from Figure 4 showing that DNT-2 acts as a ligand for Toll-2 to support neuron survival are solid ( in particular panels C-F), it doesn't necessarily mean all neurons die directly due to loss of Toll-2 signaling. It is plausible that Neurons that express Toll-2 die because they lose critical survival signals. The death of these Toll-2-expressing neurons could then cause a cascade effect, where neighboring or connected neurons die indirectly due to loss of trophic support, disrupted circuits, or secondary damage. So, the observed cell death in multiple regions may be a combination of direct effects on Toll-2-positive neurons and indirect effects on other neurons. "In the Drosophila pupa, connectivity of lamina to medulla neurons takes place at 30-48h APF, and between medulla and lobula complex at 60-70h APF (Kurmangaliyev et al., 2020, Millard and Pecot, 2018, Pecot et al., 2014, Hadjieconomou et al., 2011)." I have the same comment as mentioned above regarding the timing of connectivity. If by connectivity, the authors mean the targeting of specific neuropiles and layer organization, it is incorrect that lamina and medulla organization precedes the connectivity between medulla and lobula neurons. These processes happen concurrently. Can the authors please clarify?

      "Importantly, the expression of synaptic markers starts at 24h, peaks at 60h APF and spontaneous neuronal activity takes place at 48h APF, meaning that at least some neural circuits are already connected by this point (Kurmangaliyev et al., 2020)."

      The correct placement of the reference to Kurmangaliyev et al. is after "peaks at 60h APF " A reference to Akin et al and Bajar et al when referring to PSINA is missing.

      "Thus, the period of naturally occurring cell death overlaps with connectivity" I think the authors mean that the period of cell death is concurrent with the development of synaptic connectivity.

      "L1 neurons normally project along columns that can be labelled with mAb24B10, and target to layers M1 and M5 of the medulla." The authors should mention that 24b10 labels the photoreceptors, providing a spatial reference to identify medulla columns

      "Interestingly, Toll-2RNAi knock-down did not alter the phenotype caused by DNT- 112FL overexpression, and impaired targeting to the same extent as each genetic manipulation alone (Figures 5B,D)."

      How do the authors interpret these results? And perhaps the authors would like to explain the rationale of overexpressing DNT-2fl in L1 neurons, that do endogenously express it.

      "To conclude, these data show that DNT-2 and Toll-2 are required for appropriate connectivity of L1 neurons to target Mi1 medulla neurons at M1 medulla layer."

      The authors characterize neuronal morphologies but do not directly assess connectivity using synaptic markers. While defective morphologies are likely to impact connectivity, the conclusion that DNT-2 and Toll-2 are required for appropriate connectivity should be tempered. The authors should revise their wording to reflect that their data support morphological defects rather than direct evidence of altered synaptic connectivity.

      DISCUSSION

      "In fact, throughout animal development, between 50% (e.g. in Drosophila) and 80% (e.g. in vertebrates) are lost to naturally occurring cell death"

      "of neurons" is missing before "are lost"

      "Consistently with these findings, we have shown that the survival of L1 neurons depends on DNT-2 functioning together with Toll-2."

      The authors state that "the survival of L1 neurons depends on DNT-2 functioning together with Toll-2." It seems that what they intend to convey is that DNT-2 acts as a ligand for Toll-2. The text should be clarified to explicitly indicate this ligand-receptor relationship rather than implying a cooperative function.

      "These data demonstrate that DNT-2 and Toll-2 function together in visual system development."

      Since the authors did not use tub-GAL80 or another temporal control to restrict gene expression specifically to development, the observed phenotypes could reflect combined developmental and adult effects. Throughout the text, the authors should revise their wording to acknowledge this limitation.

      "Finally, interference with the normal levels of DNT-2 and Toll-2 also impaired axon targeting and dendritic morphology, consistently with the coupling between cell survival with connectivity."

      The authors state that interference with normal levels of DNT-2 and Toll-2 "impaired axon targeting and dendritic morphology, consistently with the coupling between cell survival and connectivity." This statement seems tautological, as neurons that die cannot form connections. The authors should clarify whether they are referring to a specific mechanistic link beyond this obvious consequence.

      "Our findings are consistent with prior reports that had shown the maintenance of cell survival to be required during neural circuit formation."

      This statement seems tautological. It is generally expected that neurons must survive in order to contribute or be part of neural circuits. The authors should clarify if they are highlighting a specific mechanistic insight beyond this obvious requirement.

      "In the medulla, Dm8 medulla neurons are produced in excess and are eliminated during connectivity to their R7 inputs (Courgeon and Desplan, 2019a). This is enabled by the cell surface molecular tags DIP in yDm8 binding Dpr11 in yR7, during synaptic matching (Courgeon and Desplan, 2019a)."

      The statement that "Dm8 medulla neurons are produced in excess and are eliminated during connectivity to their R7 inputs" is both unclear and inaccurate. It is not evident what is meant by "during connectivity." Moreover, Courgeon and Desplan (2019a) show that Dm8 neurons undergo cell death before or by P40, prior to synaptogenesis. The authors should correct this statement and clarify the timing and mechanism of Dm8 neuron elimination.

      "Importantly, the maintenance of cell survival takes place during connectivity, and enables synaptic matching between connecting neurons."

      It is unclear what is meant by "during connectivity." Moreover, both Courgeon et al. (2019a) and Xu et al. (2018, 2022) show that these neurons (e.g., Dm8, Dm12, Dm14) undergo cell death before or by P40, prior to synaptogenesis. The authors should clarify the timing and mechanism of cell survival and revise this statement accordingly.

      "By contrast, it has also been proposed that apoptosis plays a minor role in cell number control during visual system development, depending instead on cell proliferation and spatial patterning through Dpp/BMP signalling (Malin et al., 2024). However, those findings were based on events taking place at the larval third instar wandering stage, when proliferation and spatial patterning are prevalent, whereas apoptosis peaks in pupa."

      It seems that the authors are trying to suggest that different mechanisms control cell numbers at different developmental stages: during larval neurogenesis (L3), cell numbers are regulated primarily by proliferation and spatial patterning, whereas in the pupal stage, neuronal survival via apoptosis plays a key role. If this is the intended point, it should be stated more clearly, as the current comparison to Malin et al. (2024) is confusing and does not make this distinction explicit.

      "However, Toll-2 mutant MARCM clones generated in the pupa result in a dramatic loss of lamina neuron dendrites and aberrant axonal navigation in the medulla, as well as widespread neuronal loss (Li et al., 2020)." This statement is puzzling. Neurogenesis occurs during the larval stage until P15, and MARCM requires progenitor cell division. The authors should clarify how MARCM clones were generated during pupation and provide the relevant experimental details in the Materials and Methods. "Importantly, connectivity between L1 and medulla neurons takes place between 20-48h APF, during the period of naturally occurring cell death, and spontaneous activity in the optic lobe takes place at 48h, meaning at least some circuits are connected by then (Kurmangaliyev et al., 2020)."

      The authors state that "connectivity between L1 and medulla neurons takes place between 20-48h APF," but no reference is provided for this timing. To my knowledge, no study has directly demonstrated this, so the authors should either provide supporting evidence or revise this statement. Additionally, citing Kurmangaliyev et al. (2020) for spontaneous activity in the optic lobe is not appropriate for this point, as PSINA was originally described by Orkun Akin.

      "When altering DNT-2 or Toll-2 levels, L1 axonal terminals in the medulla were misrouted, rather than being confined to a single column. This is reminiscent of the phenotypes caused by alterations in Dscam and Fez levels (Millard et al., 2007, Peng et al., 2018)."

      The authors note that altering DNT-2 or Toll-2 levels causes L1 axonal terminal phenotypes reminiscent of phenotypes caused by changes in Dscam and Fez levels (Millard et al., 2007; Peng et al., 2018). However, they only reference these previous studies without discussing whether there could be a shared mechanism. While these comparisons are interesting, the manuscript would benefit from either a deeper discussion of potential mechanistic links or a clear statement that the comparison is purely phenotypic.

      "As DNT-2 is secreted in medulla neurons and Toll-2 is expressed along neurons that connect in the medulla (e.g. L1, Mi1, Tm3, Dm9, T4), DNT-2 could help keep connecting neurons together during dynamic cellular events in development."

      This sentence is poorly written and vague. It is unclear what "keep connecting neurons together" means mechanistically. Likely, DNT-2 is secreted by postsynaptic medulla neurons (e.g., Mi1), whereas Toll-2 is expressed in neurons innervating the medulla (e.g., L1, Mi1, Tm3, Dm9, T4). The authors should rephrase this sentence to clearly convey their mechanistic and cellular interpretation.

      FIGURES

      Figure 1 Arrowheads point to what? OL orientations should be described in the figure captions

      Figure 5 The title of Figure 5 ("Altering the levels of DNT-2 and Toll-2 modifies L1 axon targeting at medulla M1 layer") is misleading. The correct layer targeting is preserved; what changes is the pattern of unicolumnar innervation. When DNT-2 or Toll-2 levels are altered, L1 neurons innervate multiple columns rather than maintaining their normal single-column specificity. The title should be revised to reflect that the defect is in columnar specificity rather than layer targeting.

      Supplementary Figures S1 to S6 Combined UMAPs showing the expression of spz-1, -3 (DNT-3),-4 and -5 (DNT-2) and Toll-1, -2 (18w), -6 and -8 (Tollo) in distinct cells over time.

      Information about which UMAP corresponds to which time point is missing

      MATERIALS AND METHODS Genetics. Please see S1 Table for the list of the stocks used and Table S3 for full genotypes for each experiment. Table S3 is not the full genotypes for each experiment. This information is partly available in the Source Data excel file

      Significance

      During development, neurons are initially produced in excess. One mechanism by which the final neuronal numbers are refined relies on trophic support, which maintains the survival of necessary neurons, while excess neurons are eliminated.

      In the Drosophila optic lobe, a wave of apoptosis occurs during pupation, peaking at a critical period thought to be essential for establishing final neuronal numbers and supporting proper neural circuit formation. However, the mechanisms underlying this developmental process remain poorly understood. In this manuscript, Alshamsi et al. investigate this wave of apoptosis by examining the role of Drosophila neurotrophins (DNTs), which are encoded by spätzle (spz) paralogous genes and signal through Toll receptors to regulate neuronal survival during brain development.

      The authors use translation reporters to demonstrate that DNTs and Toll receptors are differentially expressed across various neuronal types innervating all optic lobe neuropils during development. They then focus on DNT-3 and DNT-2, which they show to be necessary for controlling neuronal numbers, likely by maintaining neuronal survival during pupal stages.

      Notably, the results reveal a previously uncharacterized interaction between DNT-2 and Toll-2. The findings suggest that DNT-2 acts as a neurotrophic factor produced by medulla intrinsic neurons, binding to the Toll-2 receptor expressed in other neurons innervating the medulla. By examining Toll-2+ L1 neurons, which are postsynaptic in the lamina and presynaptic in the medulla, the authors provide compelling evidence that DNT-2/Toll-2 signaling regulates L1 neuronal numbers.

      Interestingly, the authors also show that disruption of DNT-2/Toll-2 signaling affects L1 axonal and dendritic morphologies. However, the extent to which changes in neuronal survival and neuronal morphology are mechanistically or cellularly linked is not addressed. These findings are consistent with previous reports showing that DNTs and Toll receptors regulate neuronal survival in embryonic, larval, and pupal ventral nerve cords, as well as in the adult. Importantly, DNTs and Tolls can also promote cell death, highlighting their dual role in controlling neuronal number and circuit formation.

      While the data is for the most part solid, I have concerns regarding the execution, interpretation of certain results and the conclusions drawn. Additionally, references to previous work are often incorrect or incomplete; I provide several examples below along with non-exhaustive suggestions for improvement. Finally, the manuscript would benefit from careful text revision and improvements to figure presentation, for which I also offer non-exhaustive guidelines.

      Overall, I would recommend this manuscript undergo revision before its publication and I would be happy to reassess a revised version that addresses the comments above.

    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 set out to define how arginine availability regulates lipid metabolism and to explore the implications of this relationship in pancreatic ductal adenocarcinoma (PDAC), a tumor type known to exist in an arginine-poor microenvironment. Using a combination of rigorous genetic and metabolomic approaches, they uncover a previously underappreciated role for arginine in maintaining lipid homeostasis. Importantly, they demonstrate that arginine deprivation sensitizes PDAC cells to ferroptosis through lipidome perturbations, which can be exploited therapeutically via co-treatment with aESA and ferroptosis inducers (FINs). These findings have meaningful implications for the field. They not only shed light on the metabolic vulnerabilities created by nutrient restriction in PDAC, but also suggest a practical avenue for combination therapies that exploit ferroptosis sensitivity. This is particularly relevant in the context of pancreatic cancer, which is notoriously resistant to conventional treatments. The methods employed are broadly applicable to other nutrient-stress contexts and may inspire similar investigations in other solid tumor types.

      Strengths:

      One of the major strengths of the study is the use of complementary and well-controlled approaches-including metabolomic profiling, genetic perturbations, and in vivo models-to support the central hypothesis. The experiments are thoughtfully designed and clearly presented, and the conclusions are, for the most part, well supported by the data. The findings provide mechanistic insight into nutrient-lipid crosstalk and identify a potential therapeutic strategy for targeting arginine-deprived tumors.

      We thank the reviewer for their positive assessment of our manuscript.

      Weaknesses:

      A key weakness of the study lies in the mechanistic connection between arginine levels and SREBP1 activation. While the authors show that arginine restriction leads to reduced SREBP1 expression, the magnitude of this effect appears modest relative to the substantial changes observed in the lipidome. The study would benefit from a deeper analysis of SREBP1 regulation-particularly whether nuclear translocation or activation is affected. This could be addressed by examining the nuclear pool of SREBP1, using either subcellular fractionation or improved immunofluorescence imaging in both cell lines and tissue samples.

      We thank the reviewer for this comment and in our revised manuscript have undertaken several new studies to assess how the nuclear pool of SREBP1 is regulated by arginine starvation. We further identified one mechanism by which arginine starvation suppresses SREBP1 protein levels, namely GCN activation. We believe these additional studies strengthen the manuscript and appreciate the reviewer suggesting these studies.

      Another area where additional context would strengthen the manuscript is in the transcriptomic profiling of PDAC cells cultured in a tumor interstitial fluid mimic (TIFM). While the study emphasizes lipid-related pathways, highlighting the most significantly upregulated and downregulated pathways in Figure 1B would give readers a broader perspective on how arginine restriction reprograms the PDAC transcriptome. For instance, because polyamines are downstream of arginine and are known to influence lipid metabolism, it would be worth discussing whether these metabolites contribute to the phenotypes observed. Similarly, an evaluation of whether Dgat1/2 expression is altered could help delineate the full scope of lipid metabolic rewiring.

      We thank the reviewer for suggesting this change to our manuscript and we now provide much more extensive analysis of our transcriptomic analyses in Figure 1 – Figure supplement 1, which we think will make our manuscript more useful to readers.

      Finally, it is worth noting that the KPC mouse model used in this study is based on conditional deletion of p53, which leads to faster-growing tumors and a distinct tumor microenvironment compared to models harboring the p53^R172H point mutation. Including a brief discussion of this distinction would help readers contextualize the translational relevance of the findings.

      We have revised the manuscript to include a discussion of this point.

      Reviewer #2 (Public review):

      This study by Jonker et al. examines how the metabolic adaptations to the microenvironment by pancreatic ductal adenocarcinomas (PDAC) present vulnerabilities that could be used for therapeutic purposes. The evidence supporting the claims of the authors is mostly solid, and the multiplicity of models used, as well as the combination of in vitro and in vivo work, are appreciated, but some conclusions would benefit from additional substantiation. This work would be of interest to biologists working on the impact of microenvironment and metabolism in cancer, and especially those investigating pancreatic cancer.

      We thank the reviewer for their positive assessment of our manuscript.

      In this study, the authors use mostly "doublings per day" as an indicator of cell death, notably for Figures 4 to 6. However, proliferative arrest (or a decrease in the proliferative rate) is not necessarily synonymous with cell death. It might be nice to complement these experiments with a true measure of cell death (e.g., PI uptake).

      We thank the reviewer for this important comment and have performed extensive additional experiments to measure cell death directly via viability markers in addition to our indirect measurements of cell number at the start and end of experiments. We believe these additions strengthen our claims that PUFAs cause arginine starved PDAC cells to undergo ferroptotic cell death.

      The composition of Tumor Interstitial Fluid Medium (TIFM) was published previously, but nonetheless a reminder of the composition of this medium in a Supplemental file of this study might be helpful. In particular, at the start of the Results section, the nature of serum/lipids in the different media should be specifically noted, especially given that the subsequent focus of the work is on lipids/SREBP. It is known that differences in the extracellular availability of lipids can profoundly alter de novo lipid biosynthesis pathways.

      We thank the reviewer for this comment. We have edited the text to provide additional context on the composition of TIFM, especially lipid availability. We further have provided a supplemental file with the composition of TIFM. We hope this will make the manuscript more useful and readily interpretable for readers.

      Reviewer #3 (Public review):

      This important study investigates the impact of nutrient stress in the tumor microenvironment (TME), focusing on lipid metabolism in pancreatic ductal adenocarcinoma (PDAC).

      Understanding TME composition is crucial, as it highlights cancer vulnerabilities independent of intracellular mutations, particularly because PDAC tumors are often exposed to limited nutrient availability due to reduced perfusion.

      By utilizing a medium that mimics the nutrient conditions of PDAC tumors, the authors convincingly show that TME nutrient stress suppresses SREBP1, leading to reduced lipid synthesis, with low arginine levels identified as a key driver of this suppression. Importantly, mice with arginine-starved pancreatic tumors respond to a polyunsaturated fatty acid-rich diet. This discovery uncovers a synthetic lethal interaction in the tumor microenvironment that could be leveraged through dietary interventions.

      The conclusions of this paper are mostly well supported by data; however, below are some aspects that could be further clarified.

      We thank the reviewer for their positive assessment of our manuscript.

      This study uses PDAC cells from the LSL-Kras G12D/+ ; Trp53 ; Pdx-1-Cre PDAC model. The authors convincingly demonstrate that the cell-extrinsic stimuli of low arginine availability suppress lipid synthesis and thus exert a dominant effect over the cell-intrinsic oncogenic Ras mutation, which is known to enhance fatty acid synthesis. Could the effect of low arginine on lipid synthesis be specific for certain mutations in PDAC? It would be interesting to investigate or discuss whether different mutations show the same SREBP1 reduction caused by low arginine levels, and whether these low SREBP1 levels can be ameliorated by arginine re-supplementation. Here, Jonker et al. show that human PDAC cells cultured in TIFM have reduced SREBP1 levels (Figure 1 - Figure supplement 1C). It would be further supportive of their conclusions if the authors could show that arginine re-supplementation is sufficient to restore SREBP1 levels in human PDAC cells.

      We thank the reviewer for this comment. In response, we have now shown that arginine supplementation increases SREBP1 levels and fatty acid synthesis in human PDAC cells (Figure 2 – Figure supplement 2). Further, we have also updated the manuscript to discuss that using the LSL-Kras G12D/+; Trp53; Pdx-1-Cre PDAC model limits our ability to assess how genetic differences influence the response to arginine starvation. We additionally discuss the genetic diversity of the human PDAC cell lines used in these studies, which do include different oncogenic mutations. We believe that these results provide some data that the findings we have made regarding arginine deprivation and SREBP in our genetically defined murine PDAC cell line are applicable to human PDAC cells with more diverse oncogenic lesions.

      The authors demonstrate that mPDAC cells cultured in RPMI and subsequently implanted into an orthotopic mouse model exhibit reduced expression of SREBP target genes when compared to in vitro cultured mPDAC-RPMI cells. This finding is in line with the observation that culturing PDAC cells in TIFM downregulates SREBP target genes compared to PDAC cells cultured in RPMI. However, caution is needed when directly comparing mPDAC-RPMI cultured cells to those in the orthotopic model, as the latter may include non-tumor cells and additional factors that could confound the results. The authors should explicitly acknowledge this limitation in their study.

      We thank the reviewer for this important caveat and we have revised to text to address this point. Importantly, we note that for all comparisons between in vitro and in vivo cultures, we carefully sort malignant cancer cells from orthotopic tumors prior to analysis. We believe this approach mitigates the impact of stromal contamination on our analyses.

      The in vivo evidence demonstrating that PUFA-rich tung oil reduces tumor size is compelling. However, the specific in vitro findings regarding its impact on doubling rates per day, particularly in the context of arginine-dependent PUFA supplementation, require further explanation. To enhance the robustness of their data and conclusions, the authors could consider conducting additional cell viability and proliferation assays. Moreover, it would be valuable to assess whether the observed effects on doubling rates per day remain significant after normalizing the data to the initial doubling time prior to PUFA supplementation. This is in particular important regarding the statement that "Addition of arginine significantly decreases sensitivity to a-ESA" as these cells already start with a higher doubling rate prior to a-ESA treatment.

      We thank the reviewer for this important comment and have performed additional experiments to measure cell death directly via viability markers in addition to our indirect measurements of cell number at the start and end of experiments. Furthermore, to address the issue of different rates of cell growth in cultures affecting the response to perturbations, we also used growth rate corrected metrics (PMID: 27135972) to ensure that affects of perturbations on cell growth and viability are not confounded by the baseline proliferative kinetics of the cells under various media conditions. We believe these additions strengthen our claims that arginine starvation sensitizes PDAC cells to PUFAs.

      Overall, this paper presents a compelling study that significantly enhances our understanding of the PDAC tumor microenvironment and its complex interactions with the tumor lipid metabolism.

      We again thank the reviewer for their positive assessment of our manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In this study, the authors employ rigorous genetic and biochemical (metabolomic) approaches to uncover a previously unappreciated role for arginine in regulating lipid homeostasis. They further demonstrate the relevance of this pathway in pancreatic tumors, a solid tumor type often characterized by limited access to extracellular arginine. The authors present compelling evidence that arginine deprivation creates a metabolic liability, rendering tumors more susceptible to lipidome perturbations. This vulnerability can be therapeutically exploited through co-treatment with aESA and FIN to induce ferroptosis. Overall, the conclusions are convincing, the manuscript is well-written, and the figures are clearly presented.

      We again thank the reviewer for their positive assessment of our manuscript.

      The key weakness of the study lies in the mechanistic link between arginine levels and SREBP1 expression. While the data support the authors' argument, the observed changes in SREBP1 expression following arginine restriction appear modest relative to the more pronounced changes in the lipidome. To strengthen this connection, the authors may consider performing cellular fractionation to focus their analysis on the nuclear (active) pool of SREBP1. Improved immunofluorescence imaging and quantification of nuclear SREBP1 levels in tissues would also provide additional support for their model.

      We thank the reviewers for this helpful comment. To strengthen this study, we both examined the nuclear levels of SREBP1 in TIFM cultured cells and worked to identify the mechanistic link connecting arginine levels of SREBP1 expression.

      First, we found that arginine starvation does not lead to nuclear exclusion of SREBP1. We believe this finding strengthens our conclusion that arginine starvation regulates SREBP1 at the level of protein expression. We do agree with the reviewer that the change in SREBP1 protein level is modest, but we do show the effects of arginine on PDAC cell lipid metabolism are SREBP1 dependent (Figure 3O-P, Figure 5F, Figure 5 – Figure supplement 2D). Thus, we interpret these data that even the relatively modest change in SREBP1 protein levels are sufficient to cause large changes in the output of this transcription factor and the cellular lipidome.

      Second, we determined if the arginine-responsive GCN2 signaling pathway, which is known to regulate SREBP1, could contribute to the suppression of SREBP1 observed in PDAC cells. We found that GCN2 signaling is activated in PDAC cells in TIFM culture by arginine starvation and is active in animal tumors. We further found that activation of GCN2 is in part responsible for suppression of SREBP1, which is consistent with prior literature describing a role for GCN2 activation in suppressing SREBP1 translation (PMID: 17276353). Thus, while other mechanisms are at play in transducing arginine starvation to reduced SREBP1 protein levels, we have identified one mechanism (activation of GCN2) by which arginine starvation suppresses SREBP1, leading to the lipidomic changes we observed upon starvation of this amino acid.

      In addition, it would be helpful for the authors to highlight the most significantly upregulated and downregulated pathways in Figure 1B to give a more comprehensive view of transcriptomic changes in PDAC cells cultured under TIFM conditions. For example, since polyamines are downstream of arginine and known to regulate lipid metabolism, could some of the observed effects be attributed to changes in polyamine levels? Similarly, do arginine levels affect the expression of Dgat1 or Dgat2?

      We have added an additional Figure supplement to Figure 1 that include a comprehensive list of up- and downregulated gene sets in PDAC cells cultured in TIFM via GSEA analysis. We also added additional KEGG metabolic pathway analysis via GATOM (PMID: 35639928). We hope these additions will be useful for readers and point their attention to other metabolic pathways that are significantly altered by nutrient stress, such as the TCA cycle and oxidative phosphorylation, beyond those related to lipid metabolism that we investigated here.

      From this analysis, we did not specifically note strong changes in the expression of polyamine metabolic enzymes or DGATs.

      Finally, the KPC model used in this study involves conditional deletion of p53, which is known to produce tumors with a faster progression and a distinct tumor microenvironment compared to the more commonly used p53^R172H knock-in model. Including this point in the discussion would help contextualize the findings.

      We thank the reviewers for mentioning this limitation of our study. In the results section of the test, we now included a discussion of the limitations of the mouse model used in the discussion of the work. We also highlight in the text now that in addition to our studies using the murine p53 deletion model that our studies make use of human PDAC lines that contain p53 mutations. We believe that these results provide some data that the findings we have made regarding arginine deprivation and SREBP in our genetically defined murine PDAC cell line are applicable to human PDAC cells with more diverse oncogenic lesions.

      Minor comments to improve clarity:

      (1) In Figure 3C, it would be helpful to annotate the PE-linked TG for clarity.

      We do not understand exactly what PE-linked TGs refers to. We note in Fig. 3C that ether-linked triglycerides are labeled in orange and annotated as O-TG and vinyl ether-linked triglycerides are labeled in grey and annotated as P-TG.

      (2) Is Figure 3P mislabeled? Both conditions are labeled as +Arg / -lipid.

      We thank the reviewers for pointing out this mistake in the figure and have updated it to correctly label these samples as sgSREBP1 and sgNTG transduced PDAC cell lines.

      Reviewer #2 (Recommendations for the authors):

      (1) Figure 1B: Misspelling in Y axis "Normalized enrichment score".

      We thank the authors for catching this mistake and have corrected this error.

      (2) Figure 1B: Could the authors elaborate on why they decided to focus specifically on these three hits, which are not the most downregulated genes (the "top hits") appearing in the GSEA?

      We chose to focus on lipid metabolism as multiple transcriptomic analysis tools, namely GSEA and GATOM, which specifically focuses on enrichment in KEGG annotated metabolic pathways, highlighted lipid synthesis as being the most transcriptionally regulated metabolic pathway in TIFM. To make this apparent to readers, we added an additional Figure supplement to Figure 1 that includes a comprehensive list of up- and downregulated gene sets in PDAC cells cultured in TIFM from GSEA and GATOM analysis. We hope these additions will make the logic for our focus on lipid synthesis clear and will be useful for readers in highlighting other metabolic pathways that are significantly altered by nutrient stress, such as the TCA cycle and oxidative phosphorylation.

      (3) Figure 1: It might improve the clarity of the text if the three pairs of murine cell lines (mPDAC1, mPDAC2, mPDAC3) were introduced in a bit more detail in the main text and not just in the figure legend.

      We have added more detail describing the three mouse cell lines used in the main text.

      (4) Figure 1E: The authors may wish to comment on why they chose to perform transcriptomic analyses with the mPDAC3 derived models, and not mPDAC1 or mPDAC2, given that mPDAC3 appears to exhibit the most distinct phenotype of the three, according to the results presented in Figure 1 J-L.

      The transcriptional analysis described in Fig. 1E was performed on a previously acquired dataset using mPDAC3 cell lines (PMID: 37254839), which is why this line was used. We have revised the text to make it clear that this transcriptional analysis uses pre-existing data from a previous publication.

      (5) Figure 1L: The authors may wish to clarify why they only show relative palmitate to assess global fatty acid biosynthesis in these cell lines. There is a decrease in labeled palmitate of mPDAC3 cells cultured in TIFM in comparison to the cells cultured in RPMI media, showing a decrease in the lipid biosynthesis of these cells in these conditions. However, there also seems to be lower palmitate levels in the TIFM-cultured mPDAC3 cells specifically, in comparison to their mPDAC1 and mPDAC2 counterparts. Why is that? Could the authors comment on this result?

      We thank the reviewers for this helpful observation. In Figure 1L (now Figure 1N), we wanted to show how culture conditions (RPMI/TIFM) affected both the total amount of palmitate in PDAC cells but also the fraction that is labeled (i.e. arising from de novo synthesis). We think this provides more information for readers by allowing them to assess both changes in pool size of palmitate and changes in the fraction of palmitate that is synthesized. We like this presentation as it shows clearly that while total palmitate levels behave differently across cell lines (with TIFM culture reducing levels in mPDAC1-2 but increasing levels in mPDAC3) the amount of palmitate that is synthesized de novo is decreased in all three cell lines when cultured in TIFM. To highlight this, we also present the fraction of palmitate that is labeled in Fig. 1O.

      We are unsure why TIFM culture reduces total palmitate levels in some PDAC cell lines, while others are able to maintain total palmitate pools. We assume that TIFM cultures increase lipid uptake to compensate for lack of synthesis, and potentially differences in lipid scavenging capacity between the lines could explain this difference. We are currently working on experiments to test these hypotheses and will present the results in a future study.

      (6) Figure 2 - Figure Supplement 1A: It would be informative and appreciated to know which nutrients are actually represented and correspond to certain points on the graph, in particular for the ones that are the most differentially present in the two different media.

      We have now updated this graph to highlight key metabolites that are most differentially abundant between the two media. We also now provide as a Supplementary file the composition of TIFM, which provides readers with all the information needed to understand which metabolites are differentially abundant in TIFM and any media they wish to compare.

      (7) Figure 2 - Related to Figure supplement 1D: It would be useful to know how or why arginine was selected for further investigation from the subset of amino acids. The authors could elaborate on this, by showing or highlighting the data that drew attention to this amino acid initially.

      We thank the reviewers for this note. We have tried to make Figure 2 – Figure supplement 1 more clear as to how arginine was selected for further investigation. We have updated the figure to improve clarity for the comparisons of different media that enabled us to identify differences in amino acids between RPMI and TIFM as driving the difference in lipid metabolism. We have also highlighted in Figure 2 – Figure supplement 1A that arginine is the most differentially abundant amino acid and editing the text to explain the logic that this high degree of differential abundance is why we focused on arginine amongst all the amino acids as a likely candidate for regulation of SREBP1.

      (8) The legends for Figures 2G and 2H could be improved, i.e., making clearer that 2H shows incorporation in the circulating fatty acids, unlike 2G.

      We have updated the figure with improved labeling as the reviewer suggested to denote which panels correspond to which sample type.

      (9) Figure 3E and 3G: The heatmaps displayed here show that the addition of arginine to TIFM culture medium restores fatty acid synthesis; however, it appears that the nature of the lipids synthesized in this condition may differ from the ones synthesized in RPMI cultured conditions.

      We have added additional text highlighting that arginine supplementation to TIFM and RPMI culture led to induction of different SREBP1-target genes, but that both lead to activation of fatty acid synthesis and desaturation genes, which contributes to the focus of our study on de novo synthesis of saturated and monounsaturated fatty acids in the study.

      (10) Figure 3O: The SREBP1 immunoblot still seems to show some residual bands for the cells transduced with SREBP1 targeting sgRNAs, therefore, the authors may want to be more nuanced and present this model as a KD, instead of a KO, as mentioned in the text?

      We agree with the reviewer’s suggestion, and we have changed the text to describe these as knockdowns rather than full knockouts.

      (11) Figure 3P: Is it possible that there is an error in the legend of the figure (Lipids + for the first bar and - for the second one?). The figure could also be improved by a legend that explains what the different colored bars represent.

      We thank the reviewers for pointing out this mistake in the figure and have updated it to correctly label these samples as sgSREBP1 and sgNTG transduced PDAC cell lines.

      (12) Figure 4: The authors are stating in Figure 4 - Figure supplement 1A-F, that argininerestricted mPDAC cells are not sensitized to xCT or GPX4 inhibitors that trigger ferroptosis and that therefore SREBP1 suppression by arginine restriction in the TME does not sensitize PDAC cells to ferroptosis inducers. However, this does not appear to be so clear with the data shown. This might be due to the limitations associated with the population doubling measurements instead of the lethality measures noted above. Likewise, later it is proposed that arginine restriction sensitizes both mPDAC cells and human PDAC cells to α-ESA induced ferroptosis. These results would benefit from a direct measure of cell death. Related to the above point, it would be useful to better understand why cells cultured in arginine-deprived TIFM do not appear to be sensitized to ferroptosis inducers, but these same cells die from ferroptosis when treated with α-ESA. It would be useful to present some thoughts.

      We thank the reviewers for bringing up this important point. To the reviewers first point, we repeated xCT and GPX4 inhibitor treatment experiments to include both growth corrected (PMID: 27135972) proliferation assays and Sytox-based viability assays. In both cases, we did not find consistent sensitization to xCT or GPX4 inhibitors across multiple PDAC lines when cultured in TIFM. In contrast, we found consistent sensitization to PUFA treatment across multiple murine and human PDAC cell lines cultured in TIFM. Together, this analysis suggests that arginine starvation specifically sensitizes PDAC cells to PUFAs, but not other ferroptosis inducers.

      We agree with the reviewer that this is an interesting and unexpected observation. We do not have a mechanistic understanding as to why this is the case. However, we believe this is quite interesting and suggests that PUFAs maybe a better method of inducing ferroptosis in certain conditions than other ferroptosis inducing approaches. We have added text to the discussion to highlight this interesting and unexplained observation.

      (13) Figure 6: The authors mention that α-ESA is used here at sublethal doses, which do not affect viability or proliferation, but this is not shown in either the main or supplementary data. These data should be provided somewhere. It might also be nice to mention in the main text (not just in the legend) the dose of α-ESA used for the combination treatments.

      We thank the reviewers for this helpful suggestion. To illustrate that α-ESA is used at a sublethal dose, we altered each panel to be on a linear rather than logarithmic x-axis, therefore including the DMSO control arm for each ferroptosis inducer in combination with α-ESA. We hope this now clearly illustrates that this dose α-ESA is not perturbing cell growth or viability in these assays.

      (14) Figure 6B: Fer-1 treatment does not seem to rescue the phenotype very clearly. This could again be because cell death is being conflated (to degree) with effects on proliferation, and Fer-1 is not expected to affect cell proliferation. Again, measuring cell death directly would be better than measuring population doublings.

      We thank the reviewers for this helpful comment. To address this concern, we have added Sytox-based viability assays to figure 6. These assays indicate that Fer-1 treatment rescues the viability of PDAC cells treated with ferroptosis inducers, α-ESA, or the two in combination.

      Reviewer #3 (Recommendations for the authors):

      General notes:

      (1) It would be easier for the reader if one condition were consistently placed in the same position throughout the graphs. For example, RPMI results should always appear first and TIFM second. Currently, this is inconsistent throughout the manuscript (e.g., Figure 1 - Figure Supplement 1: RPMI is first and TIFM second; Figure 2 - Figure Supplement 1: TIFM is first and RPMI second).

      We thank the reviewers for this note. We have updated the figures to remain consistent in their ordering throughout the manuscript.

      (2) Please briefly explain the differences between PDAC1-3 and clarify why most follow-up experiments were conducted using PDAC1. Presumably, this was because PDAC1 showed the most robust effect on fatty acid synthesis.

      We have added additional text in the results section of the manuscript describing the different murine PDAC lines used in this study. We performed most studies with mPDAC1 as this line has robust differences in fatty acid synthesis between culture conditions. However, murine PDAC lines recapitulate the transcriptional subtype diversity of PDAC (PMID: 29364867), so we critically repeat key experiments in multiple mPDAC lines to determine if a given finding is translatable to other PDAC subtypes.

      (3) Are only SREBP1 protein levels affected or are SREBP1 RNA levels also decreased in low arginine TME?

      We appreciate this important comment. We have added SREBP1 RNA levels to Figure 1 to show that RNA levels do not differ between conditions, whereas protein levels of SREBP1 change significantly.

      (4) What was the rationale for investigating lipid metabolism even though it was not the top changed metabolic gene signature? It would be interesting to briefly discuss which pathways were the most enriched.

      We chose to focus on lipid metabolism as multiple transcriptomic analysis tools, namely GSEA and GATOM, which specifically focuses on enrichment in KEGG annotated metabolic pathways, highlighted lipid synthesis as being the most transcriptionally regulated metabolic pathway in TIFM. To make this apparent to readers, we added an additional Figure supplement to Figure 1 that includes a comprehensive list of up- and downregulated gene sets in PDAC cells cultured in TIFM from GSEA and GATOM analysis. We hope these additions will make the logic for our focus on lipid synthesis clear and will be useful for readers in highlighting other metabolic pathways that are significantly altered by nutrient stress, such as the TCA cycle and oxidative phosphorylation.

      Further comments:

      (1) Figure 1 Supplement 1A: It is not clear which SREBP target genes are significant. Please indicate this more clearly.

      The analysis in this section was done on expression level of all the indicated genes between groups (tumor/normal) rather testing for significance of individual genes between the two groups. We have updated both the text and the figure legend to clarify this as the statistical analysis that was performed.

      (2) Figure 1J and 2C: The Western blot loading control (Actin) does not appear equal across all samples. It would be helpful to include a quantification normalized to the Actin loading control.

      We have included quantification of each western blot to help interpret these immunoblots.

      (3) Supplementary Figure 2: How often has this experiment been performed? The TIFM results appear to consistently show the same values. If this is the case, it needs to be labeled appropriately.

      Thank you for pointing out that how we presented the data was confusing as to how the experiment described was performed. Initially, we performed multiple separate experiments to identify arginine starvation as the TIFM-driver of SREBP1 suppression. To compare across all the separate media conditions, we performed one experiment with all the relevant media conditions together, which is the experiment that is described in the manuscript. Thus, there was one set of control TIFM/RPMI conditions to which we compared all of the different media conditions. As we initially presented the data, it appeared as if we had performed multiple experiments in which the TIFM/RPMI controls had exactly the same behavior, which is not the case. We have updated the data presentation in this figure to make it clear that this was the experimental design for the data presented.

      (4) Figure 3P: Please add a legend for this panel.

      We thank the reviewers for point out this mistake in the figure and have updated it to correctly label these samples as sgSREBP1 and sgNTG transduced PDAC cell lines.

      (5) Figure 4 - Figure Supplement 1: Please review the legend carefully. The legend currently includes only circles, but some of the graphs (A and F) display squares.

      Thank you for catching this mistake. We have updated the panels and legends for this figure so they are concordant.

      (6) Figure 4D: The effect of a-ESA treatment on the doubling delta of arginine-treated versus non-treated TIFM cells looks similar. It looks like the difference is because cells treated with arginine start at higher doubling values from the beginning. I would suggest looking at the delta and subsequently tone down the statement: "Addition of arginine significantly decreases sensitivity to a-ESA."

      Thank you for this helpful comment. To avoid any confounding effects of differences in basal growth rate between mPDAC cells grown in different media, we have converted all of our data to GR values as described in (PMID: 27135972) which enables us to take into account the basal growth rates of cultures when calculating the effects of treatments/perturbations on culture growth and viability. We hope this addition makes the effect that arginine has on α-ESA sensitivity clear beyond the impact that arginine has on basal growth rate.

      In addition, we also measured the viability of α-ESA treated mPDAC cells with and without supplemental arginine (current Fig. 5E) by Sytox-exclusion assay. We believe this new data supports the claim that arginine makes PDAC cells resistant to the addition of exogenous PUFAs.

  2. May 2026
    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Ducrocq et al. present research exploring the genetic link between simple multicellular group formation (ace2Δ/ace2Δ) and its interaction with cell-cycle progression mutants (e.g., cln3Δ/cln3Δ), demonstrating that this combination can provide fitness benefits during fluctuating resource conditions, resulting in a rapid increase in the fraction of multicellular cell-cycle mutants over unicellular yeast without selection for multicellular size. Because both the multicellular phenotype and the regulatory link enabling faster escape from the stationary phase are controlled by the Ace2 transcription factor, this work demonstrates that multicellularity can arise as a side-effect of a completely independent fitness advantage unrelated to the benefits of group formation itself. As a "passenger phenotype," multicellularity could thus emerge for other selective reasons, potentially facilitating a later transition to more entrenched multicellularity if novel conditions arise where group formation becomes directly beneficial.

      Strengths:

      This work is novel and exciting for research exploring the very first steps of the transition from unicellularity to simple multicellularity. This is particularly significant because the formation of multicellular groups is almost always assumed to come at a cell-level fitness cost due to reduced reproductive fitness compared to remaining unicellular. This cell-level fitness cost generally needs to be outweighed by the benefits of multicellular group formation (e.g., large size escaping predation) for the multicellular phenotype to be stable, which is true for a large number of cases studied in the literature, where the multicellular phenotype can only evolve over unicellular competitors under strong selection for multicellular groups. However, this study presents an interesting case of a genetic and environmental condition under which individual cells (forming simple multicellular clusters) can actually have higher reproductive fitness than unicellular yeast. This demonstrates that the assumed cost at the single-cell level does not always apply. In summary, this work represents a unique example contrary to common assumptions regarding the costs of multicellular phenotypes, showing that simple multicellular phenotypes can evolve and remain stable without requiring strong selection for multicellular size or other benefits of group formation.

      The claims and interpretation of the results align well with the data presented. This is due to the careful and straightforward experimental design testing predictions with a clear, stepwise methodology, ruling out alternative explanations and providing support for the proposed link between the mutations (ace2, cln3, and others), their impact on faster exit from quiescence, and thus earlier entry into reproduction in fresh media, resulting in higher fitness in the snowflake yeast phenotype compared to unicellular yeast.

      Weaknesses:

      The authors show that the same multicellular phenotype with higher cell-level fitness due to faster exit from the stationary phase can also be observed with alleles found at other loci in non-laboratory yeast strains, implying that the results are likely not specific to a peculiar case genetically engineered in laboratory strains, but that similar phenotypes may be present in nature. However, this remains to be explored further by examining the natural ecology of commercially available or wild yeast isolates and their genomes. This is by no means a weakness of this study and, therefore, not necessarily something the current work can improve. It does mean, however, that the relevance of these findings for early multicellularity in yeast, and even more so for nascent multicellularity in distinct taxa, remains to be explored in the future. Until then, it is difficult to make strong claims about how applicable these results would be for non-laboratory yeast and other taxa. Regardless, this work does its part by representing a very exciting finding.

      Reviewer #2 (Public review):

      Summary:

      Here, the authors attempt to demonstrate that a simple model of multicellularity - snowflake yeast - exhibits key ecologically relevant changes in the regulation of the cell cycle. By examining the effects of the ace2 mutation in environments where multicellularity is not directly selected for or against, and combining it with mutations in key cell cycle regulators, they hope to show that mutations driving simple multicellularity can be selectively favored due to their effects on the release from quiescence rather than their effects on multicellularity itself.

      Strengths:

      The experiments performed are extensive and thorough. The yeast genotypes examined are judiciously chosen, so as to map out a functional model of the relationship between alterations to cell cycle control and changes to multicellularity phenotypes. Multiple possible interactions are examined, with the causal link and model of the relationship between the multicellular passenger phenotype and the selectable quiescence-release phenotype being well-supported. There are extensive controls demonstrating the separation between the 'passenger' multicellular phenotype and the cell cycle regulation phenotypes examined, including haploid/diploid strains with different multicellular phenotypes but similar cell cycle regulation phenotypes, and phenocopy strains in which downstream enzymes are deleted rather than key central regulators.

      Weaknesses:

      My only concerns about these results relate to the focus on selection on cell cycle control being examined in a model of multicellularity with key core cell cycle mutations rather than in a wild-type background, as this is a somewhat artificial system.

      I believe, however, that the authors convincingly make their case that this work on the multicellular phenotypes of yeast represents a potent proof-of-concept that simple multicellularity can be driven into existence or selected for as a passenger phenotype due to pleiotropic effects of mutations under selection from real-world ecological pressures. They are able to connect this phenotype back to known mutations of particular cell cycle regulators (RB) in other multicellular lineages and demonstrate that ecologically relevant changes to the cell cycle are connected to multicellular phenotypes. As a proof of concept of the connection between these phenotypes, rather than a study of a particular event in the past of a living lineage, it makes a strong case.

      A longstanding question in the field of multicellularity is the selective pressures that can drive simple multicellularity into existence and then act on simple multicells to drive their increased size and complexity. This work brings to the table tangible evidence of the possibility that, instead of being selected for on its own, simple multicellularity can be a side-effect of selection on other key phenotypes.

      This separates the question of the origins of multicellularity and the forces that drive its further evolution. This separation can reframe how the field is studied, especially in the context of the apparent dichotomy between dozens of origins of 'simple' multicellularity across the tree of life and a few origins of 'complex' multicellularity in the history of Earth. Especially in light of other evidence that multicellularity is connected to changes in cell cycle regulation, I believe that this is an important insight that will alter the way we think about the origins of this key evolutionary transition.

      We thank the reviewers for their insightful comments on our work.

      We agree with reviewer #1 that further experiments would be needed to figure out how the observations done on lab strains can apply to yeast in various ecological conditions and particularly in the wild. We here provide a proof of principle that multicellularity selection can arise as a side-effect. It obviously does not prove that it took place during yeast evolution, but we would like to emphasize that resource fluctuations are very common in ecological conditions, making it highly likely that the environmental conditions necessary for the selection of the side effects described have arisen.

      We agree with reviewer #2 that our work on yeast strains is “somewhat artificial” as often the case with model organisms under laboratory conditions. Importantly though, we showed that the effect found with the cln3 knock-out mutation can be phenocopied by overexpression of WHI5 (encoding the yeast equivalent of Rb). We propose that variations in the levels of cell cycle regulators during evolution may have played a role in multicellularity selection as a side effect. We agree that this is merely a hypothesis to explain the selection of multicellularity (just like predator escape) and that there is no direct evidence that this occurred in the history of the lineage. Nevertheless, our work provides a first evidence that such a selection of multicellularity as a side effect could be possible, and gives a framework to understand how multicellularity can persist in the wild, even when it is not the primary target of selection.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      As mentioned in my public review, I very much appreciate this work, its interpretation for early multicellularity as an example opposite to the assumed cost of multicellular phenotypes, and the robust design behind the premise and claims. Therefore, my suggestions below are mostly aimed at improving the readability and data presentation.

      (1) In the abstract, Lines 24-27 (the last sentence): This statement is worded too generally and therefore reads as too strong. I think the authors' work provides an example that multicellularity itself does not need to be beneficial all the time - this is really exciting and makes sense! However, there is a substantial body of work showing the origin and maintenance of multicellularity for its direct benefits. Relative to that body of work, this represents a special case, and therefore, while we should definitely reconsider the view that "multicellularity always comes at a cell-level fitness cost," we cannot overgeneralize these findings. Please consider reframing this statement.

      Done, now line 25 (addition of “in some cases”)

      (2) Line 48 (Introduction): "This mostly concerns two major regulators, RB and Cyclin D." Which organisms are you referring to? Please specify.

      Done.

      (3) In the Introduction, there are at least three sentences that need citations: L57-58, L59-60, and L65. For instance, I do not know what makes CLN3 the yeast functional equivalent of RB, and I wanted to verify this claim, but no references are cited. Please ensure citations are provided throughout the manuscript.

      Done: ref 11,12 and 13 were added

      (4) This is my main request regarding data collection and presentation. The authors share some microscopy images of mutant strains in Figure 2 for different purposes (e.g., Figure 2B compares the fraction of budded cells between two genotypes). However, I would appreciate seeing a collected microscopy figure showcasing the phenotypes of all genotypes that went into competition experiments, including the planktonic (WT lab strain) yeast, either where they appear or in a supplementary figure, all presented with the same magnification and scale to make them comparable. Because cell size, shape, and multicellular phenotype are all key aspects of the competition experiments, being able to see all those genotypes/phenotypes would prepare the reader to make predictions about the fitness assays and other experiments.

      Done Supplementary Figure 1 B-E were added

      (5) Related to my previous point, I would appreciate seeing cell size measurements for the different genotypes (both single cells of planktonic genotypes and single cells forming multicellular clusters). Cell size is a key trait that directly impacts the results shown in the paper, and summary statistics comparing them would be helpful for interpreting the results.

      Done Supplementary Figure 1 F was added

      (6) In competition experiments, the authors mix unicellular and multicellular yeast clusters at 50/50 and measure the fraction of a phenotype of interest (usually the % of snowflake). It took me a while to understand what is being counted under the "% snowflake yeast" category. This is because, while each cell in unicellular yeast should be counted as one unit, one can count a snowflake yeast composed of 50 cells as 50 units or as 1 unit. Please clearly state what is being counted for the Y-axis labeled "% of snowflake yeast" (or relabel those Y-axes in plots to make this clear).

      Done: Added in figure legend 1A and Y-axes of competition figures

      (7) I recommend editing the genotype labels in figures (see, for instance, Figure 1B, C, D). In Figure 1B, the bars are labeled as "CLN3/CLN3 co-culture" or "cln3Δ/cln3Δ co-culture," etc. These are actually co-cultures of SF vs. PK (with or without a CLN3 copy). Please consider using more representative labels that will be easier for readers to understand.

      Done: this has been changed in all concerned figures

      (8) In the Results, L225, you begin referring to AMN1368D as AMN1. I suggest using the full allelic form throughout the text so it will be clear each time that you are referring to that specific allele, as I was confused about whether you were discussing the allele or the gene AMN1 itself.

      This has been changed throughout the text.

      (9) Discussion, Lines 250-252, states that this is a "situation that is likely to happen very often under ecological conditions." Are there any examples you can cite?

      Done, as also requested by reviewer #2 (now line 256-7)

      (10) Lines 272-275 contain a strong, general statement suggesting that co-evolution of cell cycle regulation and multicellularity could be more general (which is acceptable as speculation). However, the suggestion that this co-evolution could have "started very early in the evolution of eukaryotic cells" is too speculative. I would recommend sticking with the alternative, suggesting that the link between the two phenotypes may be a case of convergent evolution.

      Done

      (11) Lines 278-279 are both vague and too bold. The text mentions a link between cancer and multicellularity and then extends this link through cell cycle regulators. Without explaining the connection between cancer and multicellularity and then trying to link it to cell cycle regulators, all in a few words without background, this sentence is too vague. Please consider deleting this or spending more time clearly explaining the link, which would at best still be speculative.

      These speculative sentences were removed.

      (12) First, I wanted to note that I highlighted Lines 284-287, as this passage is clearly written and provides a nice argument. I also wonder if you could mention that your work shows simple multicellular cluster formation should not always come at a cost, contrary to the general assumption in the literature, and add a few citations to support that claim. This would highlight how significant this work is within the broader multicellularity literature.

      Changed in discussion (now line 242-4 with additional references 30 and 31)

      (13) I recommend labeling the genotype of your "quintuple mutant" in Figure 3. You can refer to it as the quintuple mutant in the text, but I had to go back and forth to see what those mutations were when trying to think about potential genetic interactions. Even the legend of Figure 3 does not specify the genotype and refers to it only as the "quintuple mutant."

      Now explicitly stated in the title of the figure

      Reviewer #2 (Recommendations for the authors):

      I find the presented research to be of high quality, with very important implications. I have suggestions for improvement of the manuscript, but they are largely stylistic, with one paper that I believe deserves citation regarding the proteins involved. I see little need for additional experiments or analysis, just a clearer description of the results and their significance.

      (1) Line 62: Yeast CLN3 definitely performs the same role as cyclin D in the cell cycle, but has an unclear phylogenetic relationship with the rest of the cyclins. See Cross, Buchler, & Skotheim 2011 ("Evolution of networks and sequences in eukaryotic cell cycle control"). This reference also covers the functional relationship between RB and Whi5, referred to in nearby sentences, as does Medina, Walsh, and Buchler 2019 ("Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain").

      The reference has been added

      (2) Line 69: Is the question whether the evolution of G1/S regulation favoring multicellularity the question, or the two of them being connected such that the evolution of one can affect the other?

      It is clearly the first of the two questions.

      (3) Line 73: Comma after Ace2.

      Done

      (4) Line 76: It would be clearer to specify that snowflake and ACE2 yeast were co-cultured without settling selection or other selection that explicitly favors multicellularity, unlike in experiments where multicellular evolution is observed, as in Ratcliff publications.

      This is now specified.

      (5) Line 80: Specify which phenotypes observed for ace2 mutants are observed, specifically, both the multicellularity and the release from quiescence.

      Done

      (6) Line 146: This observation should be noted as another indication that the multicellular phenotype is not behind the selective pressure, because it is so different between unicells and multicells.

      Overall, you have very strong evidence that this is the case, and emphasizing this would benefit the paper!

      Done.

      (7) Line 151: specify that you are maintaining yeast in proliferation in coculture.

      Done.

      (8) Line 181: This is another key experiment showing that the multicellular phenotype is not the causal reason for the change in quiescence. It might make things clearer to bring all these confirmatory experiments together, particularly the haploids and the sonicated single cells.

      This is now clearly stated line 195.

      (9) Line 225: The choice of referring to the non-laboratory strain as the 'AMN1' wild type default may be confusing to readers, who may treat the genetic background you are using as the ground truth wild type. I recommend throughout the paper always specifying the allele's amino acid to avoid any confusion.

      The genotype is now clearly presented throughout the text.

      (10) Line 238: I would continue to specify that the multicellular phenotype has no selective advantage, specifically when no selection for size is applied.

      See added sentence Line 242-4 (revised version)

      (11) Line 243: I would say that the evolution of cell cycle regulation may interact with the multicellular phenotype.

      This was changed (now line 248)

      (12) Line 244: Strike 'indeed' and the 'the' before AMN1 and ACE2.

      Done

      (13) Line 252: Suggest some ecological conditions under which quiescence exit is likely, such as boom and bust or moving from rotting fruit to rotting fruit.

      Done

      (14) Line 267: Are you suggesting that the specific genes AMN1 and ACE2 had particular effects on actual organisms in the past, or that it represents a broad pattern of evolution in which multicellularity could be more broadly related to exit from quiescence? I believe it is the latter, and I think that should be clearer.

      Modified as suggested

      (15) Line 280: In this paragraph, I think that the point being made could be slightly clearer - if I am not mistaken, you are making the distinction between the appearance of multicellularity and its refinement under selection, and that the former may be more common than previously believed, given this proof of concept. I think this can be made clearer. Furthermore, it is worth noting that all experiments that show effects of the multicellular phenotype are in mutant backgrounds, and explaining why this is still relevant to wild organisms. It might be taken by some as indicating that the multicellular phenotypes are not relevant to a wild population, but the connection to known RB mutations in known multicellular lineages and the fact that it is connected to a very key aspect of cell cycle regulation, I think, overcomes this issue, and this should be made clear.

      Our study reveals a genetic link between multicellularity and Whi5 and Cln3, two important G1/S cell cycle regulators. Similar genetic interactions have been observed in phylogenetically distant species, reinforcing the idea that the interplay between cell cycle regulation and multicellularity is a general feature and not a mere artifact of mutant background.

      The neutral fitness effect of multicellularity in wild-type backgrounds is particularly of interest. By being maintained as a side effect of selection on fundamental cellular processes, the neutral effect of multicellularity may have provided “an evolutionary scheme” for its repeated emergence throughout the tree of life. As such, the "passenger selection" hypothesis fits well with the observations of phenotypic reversibility and facultative multicellularity, despite varying and specific selective pressures. Our work thus gives a framework to understand how multicellularity can persist in the wild, even when it is not the primary target of selection.

      (16) Line 314: What promoters are they driven by?

      Specified

      (17) Line 336: What was the culture volume, and the volume transferred?

      Specified

      (18) Line 362: How was the proportion of blue-stained cells scored? Manually, or with an imaging software cutoff?

      Specified

      (19) Figure 1: I think that the full genotypes of each strain should be specified, either in the legend or the key of the figure, rather than always specifying the ACE2 genotype and other mutations separately.

      Done as requested by reviewer #1

      (20) Figure 2E, 2F: Same as Figure 1, regarding genotypes.

      Done

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript has several strengths, including a technically comprehensive approach that combines mouse genetics, electrophysiology, live imaging in assembloids, and human organoid models, providing a rich and multifaceted dataset. Cross-species validation through the parallel use of mouse and human systems strengthens the generality of the observed phenotypes and increases relevance to human neurodevelopment.

      Consistent phenotypic observations across systems show that ARHGEF6 loss affects migration, neurite morphology, growth cone structure, and neuronal survival, supporting a coherent role in cytoskeletal regulation.

      There is clear evidence for developmental defects, including reduced interneuron numbers, increased apoptosis in the ganglionic eminences, and migration deficits, all well supported by quantitative analyses. Also, there is a high-quality electrophysiological characterization that demonstrates reduced firing in interneurons, providing a well-controlled functional phenotype.

      Strengths:

      The manuscript has several strengths, including a technically comprehensive approach that combines mouse genetics, electrophysiology, live imaging in assembloids, and human organoid models, providing a rich and multifaceted dataset. Cross-species validation through the parallel use of mouse and human systems strengthens the generality of the observed phenotypes and increases relevance to human neurodevelopment.

      Consistent phenotypic observations across systems show that ARHGEF6 loss affects migration, neurite morphology, growth cone structure, and neuronal survival, supporting a coherent role in cytoskeletal regulation.

      There is clear evidence for developmental defects, including reduced interneuron numbers, increased apoptosis in the ganglionic eminences, and migration deficits, all well supported by quantitative analyses. Also, there is a high-quality electrophysiological characterization that demonstrates reduced firing in interneurons, providing a well-controlled functional phenotype.

      We thank the reviewer for their positive and thoughtful assessment of our manuscript. We appreciate their recognition of the technical breadth of the study, including the integration of mouse genetics, electrophysiology, live imaging in assembloids, and human organoid models. We are also grateful that the reviewer highlights the value of our cross-species approach, as a major goal of the study was to determine whether ARHGEF6 loss produces convergent developmental and cellular phenotypes in both mouse and human systems.

      Weaknesses:

      Despite the strengths mentioned above, the study has some conceptual and experimental weaknesses that reduce its impact. The mechanistic insight is limited, as the research does not directly establish how ARHGEF6 regulates downstream signaling pathways.

      We appreciate the reviewer’s constructive comment. We agree that, although our data establish a phenotypic link between ARHGEF6 loss and interneuron development, they do not directly dissect the molecular mechanisms underlying the observed defects. Our interpretation that the mutant phenotype involves dysregulation of cytoskeletal dynamics is based on the directly observed defects in actin polymerization and organization in neural progenitor cells and neuronal growth cones respectively, and is consistent with the abnormalities observed in neurite morphology and neuronal migration. This interpretation is further supported by the established role of Arhgef6 as a regulator of the small Rho GTPases Rac1 and Cdc42. Previous evidence shows that Arhgef6 loss reduces the activity of both GTPases and deregulates the expression of the cytoskeletal regulators Pak1–3, Limk1, and Cofilin in the mouse brain (Ramakers et al., 2012). Moreover, spine abnormalities in Arhgef6-knockdown ex vivo slice cultures can be rescued by expressing the active form of Pak3, a downstream effector of Rac1 and Cdc42 (Node-Langlois et al., 2006). Together, these findings support a model in which the loss of the protein affects development through cytoskeletal dysregulation, likely involving altered Rho GTPase signalling. We nevertheless agree that further experiments would be required to establish a direct causal relationship between ARHGEF6 loss, Rho GTPase activity, cytoskeletal dysregulation, and the interneuron phenotypes described here. We will therefore revise the manuscript to clarify that this mechanistic link remains an interpretation supported by our data and the literature, rather than a direct demonstration within the present study.

      Also, there is insufficient evidence for interneuron specificity; although the central claim is that ARHGEF6 plays a selective role in interneurons, the data do not adequately exclude the possibility that the observed effects reflect broader neuronal defects. The study lacks critical controls across cell types, as several phenotypes observed in organoids and progenitors, including apoptosis, reduced neuronal output, and altered morphology, could also affect multiple neuronal populations without being directly tested.

      We agree that the current data do not exclude the possibility of alterations in other neuronal lineages, specifically the excitatory lineage. With regard to this, we would like to emphasize that the investigation of excitatory cell phenotypes was beyond the scope of the present study, as this aspect has previously been examined by Ramakers et al., 2012 and Node-Langlois et al., 2006, particularly in the context of hippocampal pyramidal cells, which are among the few cell types showing consistent expression of the gene in the adult mouse brain (Allen Brain Atlas; Yao et al., 2021). In this context, it is interesting to note that, in Ramakers et al., 2012 (Figure S1), MAP2 immunostaining of hippocampal formations revealed comparable distribution and intensity of neuronal cell bodies and dendrites throughout the hippocampus of both wild-type and Arhgef6-KO animals. With regard to morphological maturation of excitatory cells, whereas we observe a simplification of interneuron morphology in both mouse and human models, Ramakers et al., 2012 reported increased dendritic arborization complexity in hippocampal pyramidal cells. With regard to migration, a direct comparison with excitatory neurons would be intrinsically difficult, as excitatory and inhibitory neurons undergo highly distinct migratory processes and are therefore not directly comparable. We greatly appreciate the reviewer’s comment, as it gives us the opportunity to better discuss the relationship between our findings and previous studies in the Discussion. We will revise the manuscript and avoid implying that the phenotype observed is exclusive to interneurons.

      Furthermore, the data are predominantly descriptive, with many results remaining correlative and failing to establish causal relationships.

      We agree that our study primarily establishes a phenotypic framework and does not fully resolve the causal hierarchy among altered survival, migration, cytoskeletal morphology, and intrinsic excitability. We will revise the manuscript to make this limitation explicit, avoiding statements that imply direct causality beyond the data presented.

      Some more comments:

      (1) Given that ARHGEF6 is a guanine nucleotide exchange factor for Rac1 and Cdc42, the absence of direct measurements of GTPase activity or downstream signaling represents a significant gap. The interpretation that the observed phenotypes are mediated through specific cytoskeletal pathways, therefore, remains inferential.

      We appreciate the comment. The interpretation that our phenotype involves dysregulated cytoskeletal dynamics is based on the observed defects in actin polymerization and F-actin organization in neuronal growth cones and is consistent with the abnormalities in neurite morphology and neuronal migration. We will explicitly state in the Discussion that, since we did not directly measure Rac1 and Cdc42 activity levels in our models, our hypothesis regarding the involvement of this molecular pathway in the establishment of the observed phenotype therefore remains inferential, despite being supported by the current literature.

      (2) The manuscript repeatedly interprets the findings as interneuron-specific. However, several key observations are not demonstrated to be restricted to IN. Without direct comparison to excitatory neurons or other cell types, it is difficult to conclude that ARHGEF6 plays a selective role in interneurons rather than a more general role in neuronal development. The well-done analysis of the transcriptomic dataset is not sufficient to claim IN specificity. This issue is particularly important for the interpretation of the human organoid experiments, where reductions in SOX2⁺ progenitors and NEUN⁺ neurons, as well as increased apoptosis, could reflect global developmental defects. Similarly, in the mouse experiments, the reduction in GAD67⁺ cells is compelling, but it is not shown whether other neuronal populations are also affected.

      As previously mentioned, we understand the reviewer’s concern regarding the specificity of the observed phenotypes in interneurons and agree that the claims should be tempered. However, it is important to note that the interpretation of the human organoid experiments should be reconsidered. The use of specifically ventralized MGE-like organoids allowed us to assess the cell-autonomous nature of defects such as the reduction in inhibitory progenitors’ neuronal output, the increased apoptosis, and the morphological abnormalities of inhibitory neurons. We will acknowledge in the Discussion the limitations of the study with regard to assessing the cell-autonomous nature of the observed migration defects.

      (3) The study provides a strong phenotypic description but limited causal resolution. For example, migration defects, altered growth cone morphology, and reduced branching are all consistent with impaired cytoskeletal regulation, but the links between these phenotypes are not directly established. Likewise, while the electrophysiological data convincingly show reduced firing in interneurons, the connection between altered cytoskeletal dynamics and intrinsic excitability is not explored.

      The observed migration defects, altered growth-cone morphology, and reduced branching are consistent with impaired cytoskeletal regulation. However, we acknowledge that the mechanistic links among these phenotypes remain to be directly demonstrated. Similarly, although our electrophysiological data show reduced firing in ARHGEF6-KO interneurons, the present study does not provide direct evidence linking impaired excitability to altered cytoskeletal dynamics. In the latter case, we think that the underlying mechanisms should be further investigated at the subcellular level, particularly with respect to cytoskeleton-mediated intracellular trafficking and localization and distribution of ion channels. One limitation of the present study, which may have masked electrophysiological alterations associated with differences in membrane composition (current Figure S1D–H), is that different interneuron subtypes with distinct intrinsic properties were pooled together in the analysis. We will expand the Discussion to address these limitations.

      (4) Several aspects of data presentation could be improved. In multiple figures (e.g., Figure 1A, D; Figure 4 and Video S1, 2), the images are difficult to interpret due to high cellular density, limited magnification, or lack of clear annotation. In some cases, it is not fully clear how quantifications were performed or which regions were analyzed. Improving the visual clarity with arrows, boxes, and high-magnification inserts of the data would strengthen confidence in the conclusions.

      We would like to thank the reviewer for pointing this out. We agree that some images and videos would benefit from clearer annotation. In the revised manuscript, we will add high-magnification insets, arrows or boxes highlighting the relevant regions/cells, and clearer descriptions of the quantified regions. We will also improve legends and video labels to indicate genotype, region, and tracked cells.

      Reviewer #2 (Public review):

      The authors investigate the impact of the deletion of the small GTPase regulator ARHGEF6 on the development and physiology of interneurons. Using public databases, they first show that ARHGEF6 is enriched in interneurons or in areas that give rise to them, both in development and adulthood, in humans and mice. Using a complete KO mouse previously reported, and using a GAD67-GFP reporter mice line, they show that in the adult mouse cortex and hippocampus, there is a notorious reduction GFP+ cells. These mice show increased apoptotic cells at different timepoints and areas of the brain during development. In the developing cortex of ARHGEF6-KO mice, there are fewer IN in all layers of the developing cortex, and cells present processes not correctly oriented. IN from the hippocampus in culture show reduced excitability and impaired neurite branching. The authors then established isogenic hiPSCs lines to study ARHGEF6 deletion in human cells and differentiated ventral forebrain neurons, to find interneuron-related and non-related phenotypes. Most importantly, human interneurons grown in organoids show reduced branching and altered growth cone morphology. The authors claim that the novel interneuron phenotypes found in these models can explain, in part, the human intellectual disabilities associated with mutations in this protein. The study is well conducted and opens new avenues of research not only for the role of small GTPases regulation in early nervous system development, but also for how interneuron deficiencies impact a wider range of intellectual disability syndromes found in humans.

      We appreciate the reviewer’s positive evaluation of our manuscript and their recognition of this work’s potential to expand the focus of intellectual disability research on the development and function of the inhibitory system. We are particularly encouraged that the reviewer highlights the strength of our combined mouse and human cellular models, as well as the relevance of the interneuron-related phenotypes we identify across systems.

      However, most conclusions of the present version would be strengthened after considering the following comments:

      Major comments:

      (1) The reported biological processes evaluated at different developmental stages may be directly or indirectly related to ARHGEF6 function itself. As a model of a hereditary disease, full organism gene deletion is valid, since the human patients suffer from that condition as well. However, to investigate the roles of a protein, complete deletions may not be very accurate since they can give rise to phenotypes that are only indirectly related to the protein function itself. Most conclusions of the present manuscript should either be discussed in this regard or add evidence for a direct role of the protein. One such evidence is typically performed with acute knockdowns in culture, or in developing brains by in utero electroporation. For example, Figure 1C shows that the principal excitatory neurons in the hippocampus do not express ARHGEF6. However, most electrophysiological and behavioral evidence of defects in ARHGEF6-KO mice arises from evaluating these cells (Ramakers et al., 2012). I am not suggesting that either previous or actual evidence is wrong. But I believe readers would benefit from a clear distinction (or add caution notes) between a functional consequence of the deletion (that can be months away and in other cells than the actual molecular defect) and a true cell biological function of the protein under study. In favor of the authors, this is a concern with most conclusions derived from KO organisms.

      We agree with the reviewer that phenotypes observed in constitutive knockout models may, in some contexts, reflect indirect or compensatory consequences of long-term gene loss. Conditional and/or inducible knockout or knockdown approaches can certainly help dissect the nature of the observed defects and better define the effects of gene ablation at different developmental stages or in specific cell types. However, in the context of our study, it is important to note that the experiments performed in ventralized MGE-like organoids allowed us to assess the cell-autonomous nature of very early developmental defects in the inhibitory lineage, in isolation from other cell types. These defects include reduced neuronal output from inhibitory progenitors, increased apoptosis, and morphological abnormalities in inhibitory neurons. Therefore, the phenotypes reported here are less likely to reflect effects originating in, or indirectly caused by, cell types that do not express Arhgef6.

      With regard to Figure 1C, we state in the Results that “among excitatory populations, only CA3 pyramidal neurons and mossy cells exhibited expression levels comparable to those observed in inhibitory clusters (Figure 1D, Table S2),” thereby not neglecting the potential effect of the lack of a functional protein in these populations.

      (2) Figure 1E-G H I. All conclusions are made with a GAD67-GFP reporter, which is a very powerful and reliable tool for large-scale screening. All the conclusions of the paper would be strengthened if some immunohistochemical staining in the same areas of specific markers for interneurons would be added as supporting complementary evidence.

      We appreciate the insightful comment of the reviewer. Additional validation using established interneuronal markers will further strengthen the GAD67-eGFP analysis. We will perform complementary stainings (e.g., PVALB and CCK) and quantifications and include these data as a Supplementary Figure.

      (3) Cell death in development: It is surprising that the high amount of TUNEL staining during development does not translate into gross histological changes in the adult brain (studied elsewhere). Can authors discuss possible explanations?

      We appreciate the thoughtful consideration of our findings. We think that possible explanations include partial compensatory mechanisms during development, which may mitigate the long-term anatomical consequences of increased cell death. In addition, the phenotype may be restricted to specific neuronal populations or developmental windows, thereby producing functional alterations without necessarily resulting in overt macroanatomical defects. Thus, although increased developmental cell death may contribute to altered circuit assembly and neuronal output, it may not be sufficient to produce gross histological changes detectable at the adult brain level.

      (4) Section 4 (Figures 2F-J) - The authors present this staining as an analysis of migration. Normally, migration studies are performed with a "pulse-chase" paradigm, where a single cohort is labeled and then followed over time (normally by in utero electroporation of a fluorescent protein). Tissue is then fixed at different time points, and migration can be followed. On the contrary, the evidence is from a single point, in an experimental setting in which all Gad67 IN are stained, and hence, one cannot imply a defect in migration. The differences between WT and ARHGEF6-KO are obvious and interesting; it is just that they cannot be solely attributed to a problem in migration.

      Also, a true phenotype of migration in the current setting should have found that the cells that failed to migrate are accumulated in deeper layers. My impression is that the changes in IN per layer are easier explained by total cell number, rather than migration. Perhaps evaluating earlier timepoints could clarify this.

      We appreciate the reviewer’s suggestion to implement an additional time point in the in vivo migration analysis. Since an earlier in vivo time point would most likely not reveal migration-related defects, as most cells would still be confined to the ganglionic eminence (Liaci et al., 2022), we will include analyses performed at a later developmental time point as supplementary evidence. We will also revise the wording to clarify that the fixed-tissue data show altered distribution and orientation of GAD67-eGFP-positive interneurons, which are consistent with impaired migratory behavior when considered together with the in vitro live-imaging data. At the same time, we will acknowledge that reduced interneuron survival and/or neuronal output may also contribute to the observed phenotype.

      (5) It is known that ARHGEF6 deletion produces severe F-actin phenotypes in neurons. Have the authors confirmed in their hippocampal cultures GAD67 cells ALSO have these phenotypes? Stress fibers in somas, growth cones, and actin patches along neurites.

      We did not directly assess F-actin organization in GAD67-eGFP murine primary cultures. Direct analyses of F-actin organization, growth-cone morphology, and cytoskeletal organization were performed only in the human system. To further assess this phenotype, we will perform phalloidin staining on GAD67-eGFP brain sections to evaluate F-actin organization in interneurons in vivo.

      (6) Section 4. The authors present data for deficient migration of the GFP-labeled interneurons. Is it possible to assess, in the same sections, whether other cell types are also affected? Although the hypothesis that ARHGEF6 deletion will have an impact in IN is well rooted in expression data, by assessing other cell types, one can even include a positive control or evidence for a cell-autonomous phenotype.

      We thank the reviewer for their thoughtful suggestions. We agree that extending the analysis to additional cell types would provide further insight into the specificity of the phenotype; however, a comprehensive evaluation of all neuronal populations falls beyond the scope of this research. The use of ventralized MGE-like organoids enabled us to examine whether key defects were cell-autonomous, including the reduced neuronal output of inhibitory progenitors, increased apoptosis, and abnormal inhibitory-neuron morphology.

      (7) ARHGEDF6 deletion has an important impact on organoid development (size, shape, etc). Have the authors analysed whether these organoids produced fewer interneurons?

      We would like to clarify that the organoids analyzed in the study are ventral MGE-like organoids and therefore the reduction in neuronal output (current Figure 4K) primarily reflects the ventral/interneuron lineage in this model.

      (8) In assembloids, the differences in migration parameters are very small between WT and ARHGEF6-KO, which reinforces that perhaps what is observed in the different layers of cortex during mouse development is likely not entirely due to migration, as concluded.

      We agree that the migration parameters in assembloids should not be interpreted in isolation. We will revise the text to emphasize that the reduction in the number of interneurons observed in the adult brains is part of a broader pattern that also includes altered neuronal output and reduced viability.

      (9) To properly weigh the present evidence -interneuron deficits- using the ARHGEF6-KO model, authors should include a deeper discussion in light of much work that has been done using these mice. How does the finding of a diminished IN population in the brain of these mice explain the large amount of electrophysiological and behavioral evidence produced before with these animals? Perhaps the most important work to discuss these aspects is the initial ARHGEF6-KO report by Ramakers and colleagues (2012), but there are others.

      We appreciate the reviewer’s emphasis on the importance of framing our findings within the broader context of the existing literature. We will expand the Discussion to better integrate previous work on ARHGEF6-KO mice. Specifically, we will discuss how reduced interneuron number and altered interneuronal function may contribute to previously reported electrophysiological and behavioral phenotypes, acting in concert with previously described alterations in excitatory neurons and synaptic plasticity (Ramakers et al., 2012).

      Minor comments:

      (1) Figure 1A. It looks clear that the GE shows the highest expression of ARHGEF6; however, the reader needs the reference levels where the log2 expression is calculated. What are the reference levels?

      We would like to thank the reviewer for pointing this out. We will clarify in the caption that the log2(RPKM+1) expression values are shown as absolute values and are not relative to a reference condition.

      (2) Have the authors compared the number of GAD67-eGFP cells in the hippocampal cultures between WT and ARHGEF6-KO mice?

      We did not rely on total GAD67-eGFP counts in dissociated hippocampal cultures because differences could reflect initial plating composition, survival, and maturation. In our experience, the MGE-like organoid system provides a more controlled in vitro context to assess neuronal output in the ventral lineage.

      (3) Section 3, as a caution note, authors should mention that it is not possible to know from the evidence provided which cells are dying.

      We agree with the reviewer and will add a cautionary statement noting that TUNEL staining alone does not identify the precise dying cell type. We will clarify that increased cell death in the ganglionic eminence and MGE-like organoids is consistent with a prominent involvement of the ventral/inhibitory lineage, while acknowledging the limits of the assay.

      (4) In the dorsal-ventral assembloids, it is expected that the ventral organoid would contain lots of GFP expression compared to the dorsal, but in the image shown (Figure 5A) both parts of the assembloid seem to have the same amount and distribution of GFP. How is that possible?

      We appreciate the thoughtful comment of the reviewer. After two weeks of fusion, a considerable number of interneurons are expected to have migrated from the ventral to the dorsal compartment of the assembloid (Birey et al., 2017; Sloan et al., 2018). In terms of distribution, we think that current Figure 5A shows a gradient of eGFP-positive cells within the dorsal compartment, with the number of labeled cells decreasing as the distance from the fusion interface between the two organoids increases. By contrast, a comparable gradient is not evident in the ventral compartment, where several labeled neurons remain present even in regions distal to the fusion site.

      Reviewer #3 (Public review):

      Summary:

      ARHGEF6 is a RAC1/CDC42 guanine nucleotide exchange factor that has been proposed to be associated with X-linked intellectual disability, but its relevance to the pathology is not well established. ARHGEF6 has been assigned a role in spine density and plasticity of hippocampal pyramidal neurons, but nothing is known about its role in interneuron development. Here, the authors show that ARHGEF6 is expressed early in development in the inhibitory lineage during the peak of interneuron generation and migration. The aim of the study is therefore to investigate whether, in addition to its role in pyramidal neurons, ARHGEF6 could play a role in inhibitory neuron development. Using both ARHGEF6-KO mice and organoids from ARHGEF6-KO hiPSCs, the authors show that ARHGEF6 plays a critical role in interneuron development and function

      Strengths:

      The major strength of the paper is the very detailed analysis of the role of ARHGEF6 using two different systems: ARHGEF6-KO mice and deletion of ARHGEF6 in human iPSC-derived organoids. Strikingly, deletion of ARHGEF6 in both systems induces similar defects such as an increase in apoptosis, reduced neuronal output, impaired neuronal morphology, and disrupted migratory dynamics. This compelling evidence demonstrates that ARHGEF6, in addition to its already well-described role in spine formation and plasticity, is playing a crucial role during embryonic development through its function in interneurons.

      We thank the reviewer for this positive assessment of our work and for highlighting the strength of our combined in vivo and human iPSC-derived organoid approaches. We are pleased that the reviewer recognizes the consistency of the phenotypes observed across both systems and acknowledges that our findings support a crucial role, during early stages of embryonic development, for a protein previously thought to be relevant primarily in the synaptic context.

      Weaknesses:

      (1) In Figure 1, the authors show that ARHGEF6 is expressed in different regions of the brain, including the interneuron lineage, and that depletion of ARHGEF6 reduces the number of GABAergic neurons in the adult cortex and hippocampus. To try to better characterize this defect, the authors in Figure 2 investigate whether deletion of ARHGEF6 affects interneuron migration and survival during embryonic development. To do so, ARHGEF6 ko mice were crossed with the GAD67-eGFP reporter line to follow the inhibitory lineage. The authors analyse apoptosis using TUNEL staining, and show that it is significantly increased in the ganglion eminence of ARHGEF6-KO E14.5 embryos. The authors claim that this is not the case in the cortex. However, the image shown in Figure 2A really suggests that staining is increased. Which part of the neocortex is analysed for quantification? This should be clarified.

      We would like to thank the reviewer for pointing this out. The region analyzed was the same as that used to assess GAD67-eGFP-positive cells in Figure 2F. We will clarify the exact neocortical region used for TUNEL quantification and revise the figure and legend to make the analyzed area explicit. We will also analyze additional animals to improve the accuracy of the analysis.

      (2) In Figure 2F-J, the authors investigate the migration of interneurons by analysing the GAD67-eGFP staining, and clearly show that the migratory abilities of the depleted neurons are reduced. However, the authors do not discuss the fact that, because depletion of ARHGEF6 increases apoptosis, there are fewer neurons available for migration. This is important for the interpretation of the data. This point should be clarified.

      We appreciate this comment and believe that it is particularly relevant to the interpretation of the data shown in Figure 2F–G. We will clarify the limited interpretation of this specific analysis in the Results section. The altered directionality observed in vivo, together with evidence of impaired migratory behavior obtained through in vitro live imaging, supports the possibility that altered migratory dynamics contribute to the phenotype, although increased apoptosis and reduced neuronal output may also contribute.

      (3) In Supplementary Figure S2, the authors describe the establishment of the ARHGEF6-KO human iPSC line and test the ability of these cells to undergo correct development, especially for the generation of neural progenitor cells. I was wondering why the authors do not present the data of both control and ARHGEF6-KO cells.

      We thank the reviewer for pointing this out. All staining reported in the organoids and assembloids in this paper shows that the WT ATCC-DYS0100 cell line, as well as the mutant, efficiently differentiates into neuronal tissue. The Supplementary Figure was intended to validate the impact of the mutation on the ability of the iPSC line to retain its differentiation capacity as a preliminary step before proceeding with organoid differentiation. We will integrate stainings for NPC markers on the WT line in the Supplementary Figure.

      (4) At the molecular level, how ARHGEF6 depletion could affect neuronal survival is missing. In addition, as ARHGEF6 is a GEF for RAC1 and Cdc42 amongst other GEFs, I would have expected that the authors test how RAC1 activity (and Cdc42) is affected in ARHGEF6-depleted brains and in ARHGEF6-KO organoids. The measure of phalloidin staining and the anisotropy index are not really meaningful.

      We appreciate the thoughtful comment of the reviewer. Previous evidence already shows that Arhgef6 loss reduces the activity of both GTPases and deregulates the expression of the cytoskeletal regulators Pak1–3, Limk1, and Cofilin in the mouse brain (Ramakers et al., 2012). Regarding organoids, we agree that direct RAC1/CDC42 activity measurements would have strengthened the molecular mechanism. We will revise the manuscript to avoid implying that our phalloidin-based measurements alone establish the underlying dysregulated molecular pathway.

      (5) The authors show that ARHGEF6-KO forebrain organoids were markedly smaller compared to their isogenic controls, and their study suggests that ARHGEF6 expression impacts progenitor maintenance and neurogenesis. Despite representing only a minority of the total neuronal population, I was wondering whether ARHGEF6-KO mice present brain morphology defects such as microcephaly.

      We appreciate the comment. We did not perform a morphometric analysis for microcephaly in the present study. We will add this limitation to the Discussion and note that gross brain morphology changes were not reported in the previously published ARHGEF6-KO mouse characterization (Ramakers et al., 2012). We will also clarify that the smaller organoid phenotype may reflect developmental defects that may reflect developmental defects that are not fully compensated in a reductionist in vitro model and therefore do not necessarily imply overt microcephaly in vivo.

      References

      Allen Institute for Brain Science. Allen Mouse Brain Atlas: Arhgef6 ISH data. Available from: Allen Brain Map.

      Birey, F., Andersen, J., Makinson, C. D., Islam, S., Wei, W., Huber, N., Fan, H. C., Metzler, K. R. C., Panagiotakos, G., Thom, N., O’Rourke, N. A., Steinmetz, L. M., Bernstein, J. A., Hallmayer, J., Huguenard, J. R., & Pașca, S. P. (2017). Assembly of functionally integrated human forebrain spheroids. Nature, 545(7652), 54–59. https://doi.org/10.1038/nature22330

      Liaci, C., Camera, M., Zamboni, V., Sarò, G., Ammoni, A., Parmigiani, E., Ponzoni, L., Hidisoglu, E., Chiantia, G., Marcantoni, A., Giustetto, M., Tomagra, G., Carabelli, V., Torelli, F., Sala, M., Yanagawa, Y., Obata, K., Hirsch, E., & Merlo, G. R. (2022). Loss of ARHGAP15 affects the directional control of migrating interneurons in the embryonic cortex and increases susceptibility to epilepsy. Frontiers in Cell and Developmental Biology, 10, 875468. https://doi.org/10.3389/fcell.2022.875468

      Nodé-Langlois, R., Muller, D., & Boda, B. (2006). Sequential implication of the mental retardation proteins ARHGEF6 and PAK3 in spine morphogenesis. Journal of Cell Science, 119(23), 4986–4993. https://doi.org/10.1242/jcs.03273

      Pelkey, K. A., Chittajallu, R., Craig, M. T., Tricoire, L., Wester, J. C., & McBain, C. J. (2017). Hippocampal GABAergic inhibitory interneurons. Physiological Reviews, 97(4), 1619–1747. https://doi.org/10.1152/physrev.00007.2017

      Ramakers, G. J. A., Wolfer, D., Rosenberger, G., Kuchenbecker, K., Kreienkamp, H.-J., Prange-Kiel, J., Rune, G., Richter, K., Langnaese, K., Masneuf, S., Bösl, M. R., Fischer, K.-D., Krugers, H. J., Lipp, H.-P., van Galen, E., & Kutsche, K. (2012). Dysregulation of Rho GTPases in the αPix/Arhgef6 mouse model of X-linked intellectual disability is paralleled by impaired structural and synaptic plasticity and cognitive deficits. Human Molecular Genetics, 21(2), 268–286. https://doi.org/10.1093/hmg/ddr457

      Sloan, S. A., Andersen, J., Pașca, A. M., Birey, F., & Pașca, S. P. (2018). Generation and assembly of human brain region-specific three-dimensional cultures. Nature Protocols, 13(9), 2062–2085. https://doi.org/10.1038/s41596-018-0032-7

      Yao, Z., Nguyen, T. N., van Velthoven, C. T. J., Goldy, J., Sedeno-Cortes, A. E., Baftizadeh, F., Bertagnolli, D., Casper, T., Chiang, M., Crichton, K., Ding, S.-L., Fong, O., Garren, E., Glandon, A., Gouwens, N. W., Gray, J., Graybuck, L. T., Hawrylycz, M. J., Hirschstein, D., … Zeng, H. (2021). A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. Cell, 184(12), 3222–3241.e26. https://doi.org/10.1016/j.cell.2021.04.021

    1. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Evidence, reproducibility and clarity):

      Summary

      Sheidaei and colleagues report a novel and potentially important role for an early mitotic actomyosinbased mechanism, PANEM contraction, in promoting timely congression of chromosomes located at the nuclear periphery, particularly those in polar positions. The manuscript will interest researchers studying cell division, cytoskeletal dynamics, and motor proteins. Although some data overlap with the group's prior work, the authors extend those findings by optimizing key perturbations and performing more detailed analyses of chromosome movements, which together provide a clearer mechanistic explanation. The study also builds naturally on recent ideas from other groups about how chromosome positioning influences both early and later mitotic movements.

      In its current form, however, the manuscript is not acceptable for publication. It suffers from major organizational problems, an overcrowded and confusing Results section and figures, and a lack of essential experimental controls and contextual discussion. These deficiencies make it difficult to evaluate the data and the authors' conclusions. A substantial structural revision is required to improve clarity and persuasiveness. In addition, several key control experiments and more conceptual context are needed to establish the specificity and relevance of PANEM relative to other microtubule- and actin-based mitotic mechanisms. Testing PANEM in additional cell lines or contexts would also strengthen the claim. I therefore recommend Major Revision, addressing the structural, conceptual, and experimental issues detailed below.

      Major Comments

      A. Structural overhaul and figure reorganization

      The Results section is overly dense, lacks clear structure, and includes descriptive content that belongs in the Methods. Many figure panels should be moved to Supplementary Materials. A substantial reorganization is required to transform the manuscript into a focused, "Reports"-type article.

      Move methodological and descriptive details (e.g., especially from the second Results subheading and Figure 2) to the Methods or Supplementary Materials.

      In these parts, we define four phases of kinetochore motion in early mitosis. Without such a description in the main text, readers would be confused about subsequent analyses. Figure 2 is also important to show examples of how the four phases develop. Although we respect this suggestion from the reviewer, we would like to keep these parts in the main text and main figure.

      Remove repetitive statements that simply restate that later phenotypes arise as consequences of delayed Phase 1 (applicable to subheadings 3 onward).

      As suggested, we have removed the statement for the delayed start of Phase 2 for peripheral kinetochores in azBB-treated cells (Page 9, second paragraph). We have also simplified the statement for the delayed start of Phase 3 and Phase 4 to avoid repetition (Page 9, third paragraph; Page 10, second paragraph).

      Figure 4I: This panel is currently unclear and should be drastically simplified.

      Following this suggestion, we simplified Figure 4I by removing the column of ‘Start’, which is easily deduced from the ‘Duration’ results and therefore does not provide much new information.

      I recommend to reorganize figures as follows:

      Figure I: Keep as single figure but simplify. Figure 1D and 1E could be combined, move unnormalized SCV to supplementary materials. Same goes for 1F.

      We have reorganized Figure 1, as suggested, and moved unnormalized data to supplemental materials.

      New Figure 2: Combine current Figures 2A, 3A, 3C, 3D, 4C, 4F, and 4H to illustrate how PANEM contraction facilitates initial interactions of peripheral chromosomes with spindle microtubules which increases speed of congression initiation.

      If we were to follow this suggestion, we would lose Figure 2B, D, Figure 3B and Figure 4A, where examples of kinetochore motions are shown in images and 3D diagrams. The new Figure would mostly consist of only graphs. Without examples of images and 3D diagrams, readers would have difficulty understanding the study. Although we respect this suggestion from the reviewer, we would like to keep Figures 2, 3 and 4, as they are (except for making Figure 4I simpler; see above).

      New Figure 3: Combine current Figures 5A, 5C, 5D, 5F, 6B, 6C, and lower panels of 4H to show how

      PANEM contraction repositions polar chromosomes and reduces chromosome volume in early mitosis to enable rapid initiation of congression.

      If we were to follow this suggestion, we would lose Figure 5B and Figure 6A, where examples of kinetochore/chromosome dynamics are shown in images and 3D diagrams. For the same reason as above, we would like to keep Figure 5 and 6 as they are, although we respect this suggestion from the reviewer.

      New Figure 4: Combine Figures 7A, 7B, 7D, 7E, 7F, expanded Supplementary Figure S7, and new data to demonstrate that PANEM actively pushes peripheral chromosomes inward which is important for efficient chromosome congression in diverse cellular contexts.

      We have conducted new experiments to demonstrate the role of PANEM in diverse cellular contexts, as detailed below. We have combined the new results with the original Figure S7 to create Figure 8 in line with this suggestion.

      On the other hand, in our view, combining Figure 7A-E and the extended Figure S7 would be confusing because the two parts address different topics. Although we respect this suggestion from the reviewer, we would like to keep Figure 7 and the extended Figure S7 (i.e. Figure 8) separate.

      B. Specificity and redundancy of actin perturbation

      To establish the specificity and relevance of PANEM, the authors should include or discuss appropriate controls:

      Apply global actin inhibitors (e.g., cytochalasin D, latrunculin A) to disrupt the entire actin cytoskeleton. These perturbations strongly affect mitotic rounding and cytokinesis but only modestly influence early chromosome movements, as reported previously (Lancaster et al., 2013; Dewey et al., 2017; Koprivec et al., 2025). The minimal effect of global inhibition must be addressed when proposing a localized actomyosin mechanism. Comment if the apparent differences in this approach and one that the authors were using arises due to different cell types.

      We did experiments along this line, using a dominant-negative LINC construct, in our previous study (Booth et al eLife 2019). LINC-DN should more specifically remove/reduce PANEM than the global actin inhibitors mentioned above. LINC-DN attenuated the reduction of CSV soon after NEBD and increased the number of polar chromosomes (Booth et al eLife 2019); i.e. in this regard, the outcome was similar to azBB treatment in the current study. One can expect that global actin inhibitors would also inhibit the PANEM formation and show effects similar to LINC-DN. By contrast, the indicated references reported that global actin inhibitors strongly affect mitotic rounding and cytokinesis but only modestly influence early chromosome movements, as the reviewer noted. One possibility is that such differences may have arisen from different cell types – this could be important, especially given that some cells form the PANEM and others do not (Figure 8A). A second possibility is that cytokinesis, mitotic rounding and PANEM formation may rely on actin polymerization to different extents. For example, the same concentration of global actin polymerization inhibitors may affect cytokinesis, but may still allow PANEM formation to proceed without observable effects on early chromosome movements. As suggested, we discussed this topic in the Discussion (page 16, third paragraph).

      Clarify why spindle-associated actin, especially near centrosomes, as reported in prior studies using human cultured cells (Kita et al., 2019; Plessner et al., 2019; Aquino-Perez et al., 2024), was not observed in this study. The Myosin-10 and actin were also observed close to centrosomes during mitosis in X.laevis mitotic spindles (Woolner et al., 2008). Possible explanations include differences in fixation, probe selection, imaging methods, or cell type. Note that some actin probes (e.g., phalloidin) poorly penetrate internal actin, and certain antibodies require harsh extraction protocols. Comment on possibility that interference with a pool of Myo10 at the centrosomes is important for effects on congression.

      As the reviewer implies, we cannot rule out that we could not detect actin associated with the spindle or centrosomes because of the difference in methods or cell lines between the current study and the literature mentioned by the reviewer. We have therefore moderated our claim in the Discussion that ‘we did not detect any actin network inside the nucleus, on the spindle or between chromosomes’ by adding ‘at least, using the method and the cell line in the current study’ to this statement (Page 14, second paragraph). We have also cited the three references mentioned by the reviewer in the Discussion (Page 14, second paragraph). Regarding Myosin10, azBB (blebbistatin variant) should have negligible effects on class-X myosin, including Myosin-10 (Limouze et al 2004 [PMID 15548862]). It is therefore unlikely that the effects of azBB that we observed in the current study are due to the inhibition of Myosin-10. We have cited Woolner et al 2008 and another paper and discussed this topic in the Discussion (Page 14, second paragraph).

      C. Expansion of PANEM functional analysis

      To strengthen the conclusions and broaden the study beyond the group's previous work, PANEM function should be tested in additional contexts (some may be considered optional but important for broader impact): [underlined by authors]

      Test PANEM function in at least one additional cell line that displays PANEM to rule out cell-line-specific effects.

      As suggested, we have studied the effect of PANEM contraction in cell lines other than U2OS. We have found that when PANEM contraction was inhibited, the reduction in chromosome scattering was diminished in RPE1 cells (new Figure 8B, C). Moreover, we have found that inhibition of PANEM contraction increased polar chromosomes during prometaphase/ metaphase in RPE1 and HCT116 cells (which form PANEM), but not in HeLa cells (which do not form PANEM) (new Figure 8D, E). These results suggest that the effects of PANEM contraction, originally observed in U2OS cells, are also present in other cell lines (RPE1 and HCT116) that form PANEM.

      Examine higher-ploidy or binucleated cells to determine whether multiple PANEM contractions are coordinated and if PANEM contraction contributes more in cells of higher ploidies or specific nuclear morphologies.

      This is an interesting suggestion, but it takes lots of time to conduct such a study, and it goes beyond the scope of this paper.

      Investigate dependency on nuclear shape or lamina stiffness; test whether PANEM force transmission requires a rigid nuclear remnant.

      This is an interesting suggestion, but it takes lots of time to conduct such a study, and it goes beyond the scope of this paper.

      Analyze PANEM's contribution under mild microtubule perturbations that are known to induce congression problems (e.g., low-dose nocodazole).

      In the current study, we found that PANEM contraction affects chromosome motions in Phase 1 and Phase 3 but not Phase 2 or Phase 4. Mild microtubule perturbation itself could affect chromosome motions in all four Phases. We do not think it would be so informative to study what additional effects the reduced PANEM contraction shows when combined with mild microtubule perturbation.

      Evaluate PANEM contraction role in unsynchronized U2OS cells, where centrosome separation can occur before NEBD in a subset of cells (Koprivec et al., 2025), and in other cell types with variable spindle elongation timing.

      Following this suggestion, we first investigated the timing of spindle elongation, relative to NEBD, in asynchronous U2OS cells (Figure 8 – figure supplement 3). We imaged cells every 5 min (it was difficult to reasonably observe enough mitotic cells using a shorter interval). Most of the cells showed no significant change in the spindle length (distance between two spindle poles) after (or around) NEBD [e.g. Cell 1 in A] or a mild reduction in it [e.g. Cell 2 in A]. Only a small number of cells (2-3 out of 26) showed a mild increase in the spindle length after (or around) NEBD [e.g. Cell 3 in A]. Because the spindle elongation after NEBD was rare and mild, it was difficult to address how the timing of spindle elongation affects the effect of PANEM on reducing chromosome scattering and on chromosome relocation from polar regions. We explained this result and discussed this topic in the Discussion section.

      Quantify not only the percentage of affected cells after azBB but also the number of chromosomes per cell with congression defects in the current and future experiments.

      It is tricky to count the number of chromosomes because they frequently overlap. Counting kinetochores is more feasible, but kinetochore signals show some non-specific background (e.g. those outside of the nucleus in prophase). We therefore quantified the chromosome volume at polar regions in azBB-treated cells (Figure 6C).

      D. Conceptual integration in Introduction and Discussion

      The manuscript should better situate its findings within the context of early mitotic chromosome movements:

      Clearly state in the Introduction and elaborate in the Discussion that initiation of congression is coupled to biorientation (Vukušić & Tolić, 2025). This provides essential context for how PANEM-mediated nuclear volume reduction supports efficient congression of polar chromosomes.

      It has been a widely accepted view in the field that chromosome congression precedes biorientation, since the publication in 2006 (Kapoor et al Science 2006). Very recently, this view has been challenged by the new publication (Vukušić & Tolić, Nat comm 2025), as indicated by this reviewer. We have mentioned this new model and discussed the new interpretation of our results based on this new model, in the Discussion (page 15; ‘It has been a widely accepted view…’).

      To explain the new interpretation of our results more clearly, we have a new diagram as a supplemental figure (Figure 9 – figure supplement 1) in the revised manuscript.

      Explain that PANEM is most critical for polar chromosomes because their peripheral positions are unfavorable for rapid biorientation (Barišić et al., 2014; Vukušić & Tolić, 2025).

      We have included such a statement in the Discussion, as a part of the new interpretation of our results based on the new model that chromosome biorientation precedes congression (see above). We have also cited the indicated two papers.

      Discuss how cell lines lacking PANEM (e.g., HeLa and others) nonetheless achieve efficient congression, and what alternative mechanisms compensate in the absence of PANEM. For example, it is well established that cells congress chromosomes after monastrol or nocodazole washout, which essentially bypasses the contribution of PANEM contraction.

      Following this suggestion, we discussed three possible mechanisms that could compensate for a lack of PANEM and facilitate kinetochore-MT interaction and chromosome congression, based on previous literature (Page 17): 1) the enhanced assembly rate of spindle MTs may facilitate kinetochore-MT interactions in N-CIN+ cancer cells, 2) chromosome biorientation may precede congression more frequently to promote the congression towards the spindle midplane, and 3) the balance between CENP-E, Dynein and chromokinesin’s activities may incline to greater chromosome-arm ejection forces towards the spindle midplane.

      Minor Comments

      These issues are more easily addressable but will significantly improve clarity and presentation.

      Introduction

      Remove the reference to Figure 1A in the Introduction. The portion of Figure 1 and related text that recapitulates the authors' previous work should be incorporated into the Introduction, not the Results.

      As suggested in the second sentence of this comment, we have moved most of the second paragraph of the first section of Results to Introduction (Page 4) and cited Figure 1A and 1B in Introduction. We would like to keep the reference to Figure 1A in the Introduction, because showing the PANEM images at the beginning of the manuscript would help readers’ understanding of our study. In addition, citing Figure 1A in the Introduction is more consistent with the suggestion in the second sentence of this comment.

      Results (by subheading)

      First subheading: When introducing the ~8-minute early mitotic interval, cite additional studies that have characterized this period: Magidson et al., 2011 (Cell); Renda et al., 2022 (Cell Reports); Koprivec et al., 2025 (bioRxiv); Vukušić & Tolić, 2025 (Nat Commun); Barišić et al., 2013 (Nat Cell Biol).

      As suggested, we cited these references at the indicated part of the first section of the Results (page 5).

      Second subheading: Cite key reviews and foundational research on kinetochore architecture and sequential chromosome movement during early mitosis: Mussachio & Desai, 2017 (Biology); Itoh et al., 2018 (Sci Rep); Magidson et al., 2011 (Cell); Vukušić & Tolić, 2025 (Nat Commun); Koprivec et al., 2025 (bioRxiv); Rieder & Alexander, 1990 (J Cell Biol); Skibbens et al., 1993 (J Cell Biol); Kapoor et al., 2006 (Science); Armond et al., 2015 (PLoS Comput Biol); Jaqaman et al., 2010 (J Cell Biol).

      Rieder & Alexander, 1990 (J Cell Biol) and Kapoor et al., 2006 (Science) have already been cited in the second section of the Results in the original manuscript. We agree that all other references should be cited in this manuscript, and they are now cited in the Introduction and/or Discussion where they fit best (e.g. Mussachio & Desai 2017 reviews the kinetochore in general and is therefore best cited in the Introduction).

      Third subheading: Clarify why some kinetochores on Figure 3A appear outside the white boundaries if these boundaries are intended to represent the nuclear envelope.

      We interpret that these are background signals in the cytoplasm, which do not come from kinetochores, because 1) before NEBD, they were outside of the nucleus, and 2) after NEBD, they did not show any characteristic kinetochore motions such as those towards a spindle pole (Phase 2) and the spindle mid-plane (Phase 4). We have commented on these background signals in the legend for Figure 3A.

      Fourth subheading: Note that congression speed is lower for centrally located kinetochores because they achieve biorientation more rapidly (Barišić et al., 2013, Nat Cell Biol; Vukušić & Tolić, 2025, Nat Commun).

      Relevant to this comment, there was an error regarding the congression speed of central kinetochores (original Figure 4H). The congression speed of peripheral kinetochores was shown correctly, but for central kinetochores it was shown incorrectly with µm per time interval (30s) shown, rather than µm per minute. We amended this error in the revised manuscript (new Figure 4H). Based on the corrected data, the speed of congression is similar between peripheral and central kinetochores. The original Figure 3G (the speed of poleward motion for central kinetochores) had a similar error, which we have also corrected in the revised manuscript. We apologize for these errors and the confusion it may have caused.

      Regarding this comment, if biorientation is achieved more rapidly for central kinetochores, Phase 3 (rather than congression speed) would be shorter for central kinetochores. Indeed, Phase 3 is slightly shorter for central kinetochores (control) than for peripheral kinetochores (control) (Figure 4C), but the difference is not statistically significant (t test; p\=0.21).

      Fifth subheading: Cite studies on polar chromosome movements: Klaasen et al., 2022 (Nature); Koprivec et al., 2025 (bioRxiv). Clarify that Figure 5F displays only those kinetochores that initiated directed congression movements.

      These two references have already been cited and discussed in this Result section of our original manuscript. However, considering this suggestion, we have discussed more about polar chromosome movements reported by Koprivec et al (page 11). Meanwhile, the reviewer is correct about Figure 5F, and we have clarified this point in the Figure 5F legend.

      Sixth subheading (currently in Discussion): Move the final paragraph of the Discussion into the Results and expand it with preliminary analyses linking PANEM contraction to congression efficiency across untreated cell types or under mild nocodazole treatment.

      As suggested, we have moved the final paragraph of the Discussion in the original manuscript to make a new final section in the Results in the revised manuscript. Moreover, as suggested, we have studied the outcome of inhibiting PANEM contraction in cell lines other than U2OS (Figure 8 B–E), and have described the new results to the new final section in the Results.

      Discussion

      1. When discussing cortical actin, cite key reviews on its presence and function during mitosis: Kunda & Baum, 2009 (Trends Cell Biol); Pollard & O'Shaughnessy, 2019 (Annu Rev Biochem); Di Pietro et al., 2016 (EMBO Rep).

      As suggested, we have cited all these review papers in the Discussion (page 17), and mentioned the role of the cortical actin on the spindle orientation and positioning (Kunda & Baum, 2009; Di Pietro et al., 2016), as well as the function of the actomyosin ring on cytokinesis (Pollard & O'Shaughnessy, 2019).

      Significance

      Advance

      This study's main strength is its novel and potentially important demonstration that contraction of PANEM, a peripheral actomyosin network that operates contracts early mitosis, contributes to the timely initiation of chromosome congression, especially for polar chromosomes. While PANEM itself was previously described by this group, this manuscript provides new mechanistic evidence, improved perturbations, and detailed chromosome tracking. To my knowledge, no prior studies have mechanistically connected this contraction to polar chromosome congression in this level of detail. The work complements dominant microtubule-centric models of chromosome congression and introduces actomyosin-based forces as a cooperating system during very early mitosis. However, the impact of the study is currently limited by major organizational issues, insufficient controls, and incomplete contextualization within existing literature. Addressing these issues will substantially improve clarity and credibility. [underlined by authors]

      We have addressed the underlined criticisms as detailed above.

      Audience

      Primary audience of this study will be researchers working in cell division, mitosis, cytoskeleton dynamics, and motor proteins. The findings may interest also the wider cell biology community, particularly those studying chromosome segregation fidelity, spindle mechanics, and cytoskeletal crosstalk. If validated and clarified, the concept of PANEM could be integrated into textbooks and models of chromosome congression and could inform studies on mitotic errors and cancer cell mechanics.

      Expertise

      My expertise lies in kinetochore-microtubule interactions, spindle mechanics, chromosome congression, and mitotic signaling pathways.

      Reviewer #2 (Evidence, reproducibility and clarity):

      In this manuscript, Sheidaei et al. reported on their study of chromosome congression during the early stages of mitotic spindle assembly. Building on their previous study (ref. #15, Booth et al., Elife, 2019), they focused on the exact role of the actin-myosin-based contraction of the nuclear envelope. First, they addressed a technical issue from their previous study, finding a way to specifically impair the actomyosin contraction of the nuclear membrane without affecting the contraction of the plasma membrane. This allowed them to study the former more specifically. They then tracked individual kinetochores to reveal which were affected by nuclear membrane contraction and at what stage of displacement towards the metaphase plate. The investigation is rigorous, with all the necessary controls performed. The images are of high quality. The analyses are accurate and supported by convincing quantifications. In summary, they found that peripheral chromosomes, which are close to the nuclear membrane, are more influenced by nuclear membrane contraction than internal chromosomes. They discovered that nuclear membrane contraction primarily contributes to the initial displacement of peripheral chromosomes by moving them towards the microtubules. The microtubules then become the sole contributors to their motion towards the pole and subsequently the midplane. This step is particularly critical for the outermost chromosomes, which are located behind the spindle pole and are most likely to be missegregated.

      Significance

      While the conclusions are somewhat intuitive and could be considered incremental with regard to previous works, they are solid and improve our understanding of mitotic fidelity. The authors had already reported the overall role of nuclear membrane contraction in reducing chromosome missegregation in their previous study, as mentioned fairly and transparently in the text. However, the reason for this is now described in more detail with solid quantification. Overall, this is good-quality work which does not drastically change our understanding of chromosome congression, but contributes to improving it. Personally, I am surprised by the impact of such a small contraction (of around one micron) on the proper capture of chromosomes and wonder whether the signalling associated with the contraction has a local impact on microtubule dynamics. However, investigating this point is clearly beyond the scope of this study, which can be published as it is. [underlined by authors]

      The suggested topic (underlined) is intriguing. However, we agree with the reviewer that it is beyond the scope of this paper. The reviewer recommends publication of our manuscript as it is.

      Reviewer #3:

      Sheidaei et al., report how chromosomes are brought to positions that facilitate kinetochore-microtubule interactions during mitosis. The study focusses on an important early step of the highly orchestrated chromosome segregation process. Studying kinetochore capture during early prophase is extremely difficult due to kinetochore crowding but the team has taken up the challenge by classifying the types of kinetochore movements, carefully marking kinetochore positions in early mitosis and linking these to map their fate/next-positions over time. The work is an excellent addition to the field as most of the literature has thus far focussed on tracking kinetochore in slightly later stages of mitosis. The authors show that the PANEM facilitates chromosome positioning towards the interior of the newly forming spindle, which in turn facilitates chromosome congression - in the absence of PANEM chromosomes end up in unfavourable locations, and they fail to form proper kinetochore-microtubule interactions. The work highlights the perinuclear actomyosin network in early mitosis (PANEM) as a key spatial and temporal element of chromosome congression which precedes the segregation process.

      Major points

      (1) The complexity of tracking has been managed by classifying kinetochore movements into 4 categories, considering motions towards or away from the spindle mid-plane. While this is a very creative solution in most cases, there may be some difficult phases that involve movement in both directions or no dominant direction (eg Phase3-like). It is unclear if all kinetochores go through phase1, 2, 3 and 4 in a sequential or a few deviate from this pattern. A comment on this would be helpful. Also, it may be interesting to compare those that deviate from the sequence, and ask how they recover in the presence and absence of azBB.

      To respond to this comment, we would like to first clarify how we selected kinetochores for our analysis. We selected kinetochores that can be individually tracked. If kinetochore tracking was difficult (before the start of Phase 4 in control and azBB-treated cells or before observing the extended Phase 3 in azBB-treated cells) because of kinetochore crowding, we did not choose such kinetochores. For example, related to the next comment of this Reviewer, we did not include kinetochores close to spindle poles (within 4 µm) at NEBD in our analysis for the following two reasons: First, these kinetochores often did not show clear and rapid movements towards a spindle pole, which we used to define Phase 2. Second, although we referred to kinetochore co-localization with a microtubule signal for the start of Phase 2, this was difficult for kinetochores close to spindle poles because of a high density of microtubules. As requested, we have added this comment to the Method section (page 25).

      With the above selection, all selected kinetochores without azBB treatment (control) showed the poleward motion (Phase 2) and congression (Phase 4) in this order, though their extents were varied among kinetochores. All selected kinetochores with azBB treatment also showed the poleward motion (Phase 2), and some of them showed congression (Phase 4) after Phase 2. Then, Phase 1 and Phase 3 were defined as intervals between NEBD and Phase 2 and between Phase 2 and Phase 4, respectively. If no Phase 4 was observed with azBB, we judged that Phase 3 continued till the end of tracking. We have added this comment to the Method section (page 25-26).

      (2) Would peripheral kinetochore close to poles behave differently compared to peripheral kinetochore close to the midplane (figure S4)? In figure 3D, are they separated? If not, would it look different?

      Since we did not include kinetochores close to spindle poles (at NEBD), for which it was difficult to define Phase 2 (see our response to the above major point 1), in our analysis, the suggested comparison is not feasible.

      (3) Uncongressed polar chromosomes (eg., CENPE inhibited cells) are known to promote tumbling of the spindle. In figure 5B with polar chromosomes, it will be helpful to indicate how the authors decouple spindle pole movements from individual kinetochore movements.

      In contrast to CENPE-inhibited cells, azBB-treated cells did not show much tumbling of the spindle, though both cells showed uncongressed polar chromosomes. The reason for this difference may be fewer uncongressed polar chromosomes in azBB-treated cells. There were still modest spindle motions in azBB-treated cells. However, because kinetochore motions were assessed relative to a spindle pole (and other reference points on the spindle) in our study (Figure 2A, C), the modest spindle motions were offset in our analyses of kinetochore motions. We have clarified the underlined part in the Method section (page 24).

      (4) The work has high quality manual tracking of objects in early mitosis- if this would be made available to the field, it can help build AI models for tracking. The authors could consider depositing the tracking data and increasing the impact of their work.

      As suggested, we have included kinetochore tracking data as supplemental data in the revised manuscript (Figure 3 – source data 1–4; Figure 5 – source data 1, 2).

      Minor points

      (1) It will be helpful for readers to see how many kinetochores/cell were considered in the tracking studies. Figure legends show kinetochore numbers but not cell numbers.

      As suggested, we have now mentioned the number of cells, where the kinetochore motions were analyzed, in the legends for Figures 3, 4, 5, and supplemental figures.

      (2) Discussion point: If cells had not separated their centrosomes before NEBD, would PANEM still be effective? Perhaps the cancer cell lines or examples as shown in Figure 6A have some clues here.

      Following this suggestion, we first investigated the timing of spindle elongation, relative to NEBD, in asynchronous U2OS cells (Figure 8 – figure supplement 3). We imaged cells every 5 min (it was difficult to reasonably observe enough mitotic cells using a shorter interval). Most of the cells showed no significant change in the spindle length (distance between two spindle poles) after (or around) NEBD [e.g. Cell 1 in A] or a mild reduction in it [e.g. Cell 2 in A]. Only a small number of cells (2-3 out of 26) showed a mild increase in the spindle length after (or around) NEBD [e.g. Cell 3 in A]. Because the spindle elongation after NEBD was rare and mild, it was difficult to address how the timing of spindle elongation affects the effect of PANEM on reducing chromosome scattering and on chromosome relocation from polar regions. We explained this result and discussed this topic in the Discussion section.

      (3) Figure 7 cartoon shows misalignment leading to missegregation. It may be useful to consider this in the context of the centrosome directed kinetochore movements via pivoting microtubules. Is this process blocked in azBB-treated cells?

      We understand that the Reviewer refers to the kinetochore pivoting mechanism around a spindle pole, which was recently reported by the Tolic group (Koprivec et al., 2026). Such a pivoting mechanism would work only when the spindle elongates (i.e. the distance between spindle poles is enlarged) after NEBD. Therefore, to address this Reviewer’s question, we tried to assess how PANEM contraction contributes to relocating polar chromosomes when the spindle elongates before or after NEBD in asynchronous U2OS cells (i.e. in the situation where the kinetochore pivoting mechanism is applied or not), as we noted above in response to Point 2. However, spindle elongation after NEBD was rare and mild, and we were unable to address this issue (see our response to Point 2). We discussed this matter in the Discussion section.

      (4) Are all the N-CIN- lines with PANEM highly sensitive to azBB? In other words, is PANEM essential for normal congression in some of these lines.

      Because blebbistatin could kill cells by inhibiting cytokinesis, the blebbistatin sensitivity of cell growth may not necessarily reflect how essential the PANEM contraction is for chromosome congression.

      Instead, we addressed more directly how essential the PANEM contraction is for chromosome congression. We analyzed chromosome congression in RPE1 and HCT116 cells (both are NCIN-) in the presence and absence of pnBB, the inhibitor of PANEM contraction (new Figure 8D, E). With pnBB, these cells showed congression defects, suggesting that the PANEM contraction is essential for chromosome congression in these N-CIN- cells.

      (5) Are congression times delayed in lines that naturally lack PANEM?

      For example, it takes 10-20 min for HeLa cells (lacking PANEM) to complete chromosome congression after the NEBD (Bancroft et al 2025: https://doi.org/10.1242/jcs.163659). This is not significantly different from the time (8-18 min) for chromosome congression we observed in U2OS cells (which form PANEM). We assume that cells lacking PANEM have developed a compensatory mechanism for efficient chromosome congression – we have discussed possible compensatory mechanisms in the last paragraph of the Discussion (page 17).

      (6) Page 23 "we first identified the end of congression" how does this relate to kinetochore oscillations that move kinetochores away from the metaphase plate?

      The start of kinetochore oscillation was defined as the end of Phase 4 if we could track the kinetochore until that point. In some cases where the kinetochore became close to the midplane (< 2.5 µm), it was not possible to track it further due to kinetochore crowding around the spindle mid-plane – in such cases, the end of Phase 4 was assigned as the end of tracking. These definitions were not necessarily clear in the original manuscript. Moreover, in the original manuscript, it was not clearly stated that the end of Phase 4 was defined in the same way for both non-polar and polar kinetochores. We have now clarified these points in the Method section (page 25).

      (7) Are spindle pole distances (spindle sizes) different in early and late mitotic cells (4min vs 6min after NEBD) in control vs azBB-treated cells? Please comment on Figure S2E (mean distance) in the context of when phase 4 is completed. Does spindle size return to normal after congression?

      In Figure S2E (Figure 1 – figure supplement 6 in the revised manuscript), we did not observe a significant difference in the spindle-pole distance (the spindle size) between control and azBBtreated cells at any individual time points. The smallest p-value was 0.094 at 6.0 min. As suggested, we have explained this in the legend for this supplementary figure. Completion of Phase 4 is highly variable across different kinetochores within the same cell; thus, a general comment on its completion timing in cells is not feasible.

      Significance:

      The current work builds upon their previous work, in which the authors demonstrated that an actomyosin network forms on the cytoplasmic side of the nuclear envelope during prophase. This work explains how the network facilitates chromosome capture and congression by tracking motions of individual kinetochores during early mitosis. The findings can be broadly useful for cell division and the cytoskeletal fields.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Renard, Ukrow et al. applied their recently published computational pipeline (CHROMAS) to the skin of Euprymna berryi and Sepia officinalis to track the dynamics of cephalopod chromatophore expansion. By segmenting each chromatophore into radial slices and analyzing the co-expansion of slices across regions of the skin, they inferred the motor control underlying chromatophore groups.

      Strengths:

      The authors demonstrate that most motor units of cephalopod skin include a subregion of multiple chromatophores, creating "virtual chromatophores" in between the fixed chromatophores. This is an interesting concept that challenges prevailing models of chromatophore organization, and raises interesting possibilities for how chromatophore arrays may be patterned during development.

      This study introduces new analyses of cephalopod skin that will be valuable for the quantitative study of cephalopod behavior.

      Weaknesses:

      The authors chose to image spontaneous skin changes in sedated animals, rather than visually-evoked skin changes in awake, freely-moving animals. Spontaneous chromatophore changes tend to be small shimmers of expansion and contraction, rather than obvious, sizable expansions. This may make it more challenging to distinguish truly co-occurring expansions from background activity. The authors don't provide any raw data (videos) of the skin, so it is difficult to independently assess the robustness of the inferred chromatophore groupings.

      The patch-clamp experiments in E. berryi are used to test the validity of their approach for inferring motor units. The stimulations evoke expansions of sub-regions of each chromatophore, creating "virtual chromatophores" as predicted from the behavioral analysis. However, the authors were not able to predict these specific motor units from behavioral analysis before confirming them with patch-clamp, limiting the strength of the validation. It would be informative to quantify the results of the patch-clamp experiments - are the inferred motor units of similar sizes to those predicted from behavior?

      The authors report testing multiple experimental conditions (e.g., age, size, behavioral stimuli, sedation, head-fixation, and lighting), but only a small subset of these data are presented. It is difficult to determine which conditions were used for which experiments, and the manuscript would benefit from pooling data from multiple experiments to draw general conclusions about the motor control of cephalopod skin.

      The authors use a different clustering algorithm for E. berryi and S. officinalis, but do not discuss why different clustering approaches were required for the two species.

      Impact:

      The authors use their computational pipeline to generate a number of interesting predictions about chromatophore control, including motor unit size, their spatial distribution within the skin, and the independent control of subregions within individual chromatophores by putatively distinct motor neurons. While these observations are interesting, the current data do not yet fully support them.

      The CHROMAS tool is likely to be valuable to the field, given the need for quantitative frameworks in cephalopod biology. The predictions outlined here provide a useful foundation for future experimental investigation.

      We thank the reviewer for the thoughtful and detailed evaluation of our work and for recognizing the potential of the CHROMAS pipeline for studying chromatophore control.

      We agree that some aspects of the manuscript required clarification and additional explanation, and we have revised the text accordingly. We also now provide access to representative raw video recordings in the Data Availability section. In the E. berryi patch-clamp experiments, single motor neurons evoked expansions of sub-regions of chromatophores, consistent with the “virtual chromatophore” concept. We have now quantified the size of motor units across patch-clamp sessions, and the results show that the inferred motor-unit sizes broadly match those predicted from behavioral recordings, supporting the validity of our approach.

      We agree that pooling data across individuals would provide valuable insight into variability across animals. In practice, we recorded chromatophore activity from several animals (14 Euprymna berryi and 12 Sepia officinalis) under different experimental conditions during development of the experimental pipeline. However, acquiring long, stable, artifact-free recordings suitable for motor unit analysis is technically challenging. We now clarify this point in the manuscript. Specifically, we explain that multiple animals were recorded during pipeline development, while the analyses presented focus on recordings with the highest signal quality. We anticipate that the framework introduced here will enable future studies to collect larger datasets and compare motor unit organization across individuals, developmental stages, and species.

      HDBSCAN was used for E. berryi during initial exploratory analyses, and Affinity Propagation was adopted for S. officinalis because it better captured the correlation structure of those recordings. We did not re-analyze the E. berryi data with Affinity Propagation, and the implications of algorithm choice are now discussed in the Discussion.

      Reviewer #2 (Public review):

      Summary:

      Overall, this is an excellent paper, making use of a newly developed system for monitoring the behaviour of chromatophores in the skin of (mostly) free-swimming bobtail squid and European cuttlefish. The manuscript is very well-written, clearly presented and very well-structured. The central finding, that individual chromatophores are connected to multiple motor neurones, is not new. Novelty instead comes from the ability to measure the actuation of chromatophore sections across wide areas of skin in free-swimming animals, showing the diversity of local motor units and reinforcing the notion that individual chromatophores are not necessarily the individual units of colour change, but rather local motor units that cover multiple neighbour and near-neighbour chromatophore muscles. This is an excellent finding and one that will shape our understanding of the neural control of cephalopod skin colour.

      Strengths:

      The methodological approach to collecting large amounts of data about local variations in the expansion of sections of chromatophores is exciting, and the analysis pipeline for clustering sections of chromatophores whose spontaneous activity correlated over time is powerful and exciting.

      Weaknesses:

      Some minor edits and typographical errors need correcting. I also had some concerns that the preparation for the electrophysiological section of the manuscript complies with the journal's ethical requirements, so I would urge that this be carefully checked.

      We thank the reviewer for the positive evaluation of our work and for recognizing the value of the methodological approach and the clarity of the manuscript.

      We have carefully reviewed the manuscript and corrected minor typographical errors.

      Regarding the ethical considerations raised for the electrophysiological experiments, we have carefully verified that the experimental procedures comply with the journal's ethical requirements and relevant institutional guidelines.

      Reviewer #3 (Public review):

      Summary:

      This study uses high-resolution videography and a custom computer-vision pipeline to dissect the motor control of cephalopod chromatophores in Euprymna berryi and Sepia officinalis. By quantifying anisotropic chromatophore deformations and applying dimensionality reduction methods, the authors infer that individual chromatophores can be a part of multiple motor units. Clustering analyses reveal putative motor units that often span multiple chromatophores, with diverse and overlapping geometries. Chromatophore expansion dynamics are faster and more stereotyped than relaxation, consistent with active neural contraction followed by passive recoil. Together, the results show that chromatophores function not as uniform pixels but as fractionated, coordinately controlled elements that enable flexible pattern generation

      Strengths:

      The authors present compelling, direct evidence that a). chromatophore deformations are anisotropic, and indirect evidence that b) individual chromatophores can be split across multiple putative motor units. This evidence is provided through data collected over large spatial scales, but also at a sub-chromatophore resolution. This combination of scale and resolution is not possible using traditional neuroanatomical and physiological approaches alone.

      The authors also develop a new non-invasive, image analysis approach to extract information about chromatophore deformation across large spatial scales on the organism's body. In principle, this approach is applicable across species and may allow for further comparative characterization of chromatophore motor control. It is therefore a promising new tool and useful resource for the community.

      Weaknesses:

      An important weakness of the work is that the methods the authors develop can only be applied during resting, spontaneous 'flickering' activity of chromatophores. The inability to reliably apply their technique during any kind of realistic camouflage is a large limitation, as it means this method cannot be used to study the dynamics of motor control during realistic camouflage behaviors.

      Another weakness of this paper is the rather limited electrophysiological validation of the computational findings. The authors present only one electrophysiology experiment in E. berryi, the species that they used only for 'methodological development' and not for detailed characterization. A complementary electrophysiological experiment in S. officinalis, or some visualization of neuron morphology confirming that motor neurons do indeed project to multiple chromatophores, would strengthen the generalizability of their computational analysis. This would be particularly pertinent to validate the author's claim that some motor units contain chromatophores that are quite distant from one another on the animal.

      Overall, the authors' technical contributions and method development are an important advance. This work serves as an excellent proof of concept that their method can extract useful information about chromatophore motor control. Further validation of their method is needed to fully trust the fine-scale conclusions drawn about the distribution and composition of multi-innervated chromatophores. Furthermore, the authors raise many interesting ideas about developmental constraints on circuit wiring and potential adaptive significance of multi-innervated chromatophores for certain features of camouflage patterning. Their method may be able to help resolve some of these questions in the future if it is refined and applied across developmental stages, regions of the animal, and across species

      We thank the reviewer for their thoughtful evaluation and for recognizing the potential of the computational approach introduced in this study.

      Regarding the focus on spontaneous chromatophore activity, we have clarified earlier in the Results section why these events are necessary to isolate individual muscle activations. While large camouflage patterns are visually striking, they involve the coordinated activation of many groups of chromatophores by premotor circuits simultaneously, making the identification of individual motor units, our goal here, impossible. Our approach can, however, also be applied during active behavior, including camouflage; the questions addressed there would be different, focusing on how multiple motor units are coordinated to generate the resulting skin patterns, rather than resolving the structure of single motor units. This could be challenging if the patterns of premotor control are highly variable, thus making the detection of meaningful or interpretable motion correlations difficult. This remains to be tested.

      We also acknowledge that electrophysiological validation remains limited. Patch-clamp experiments were performed in Euprymna berryi to test predictions generated by the computational analysis, and these experiments confirmed that activation of single motor neurons can produce anisotropic expansion of chromatophore subregions. We now provide the associated datasets in the Data Availability section. We agree that complementary electrophysiological or anatomical experiments in Sepia officinalis would further strengthen the conclusions. Such experiments represent an important direction for future work.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      General points:

      (1) Given all the experimental conditions and animals tested, the manuscript would be much stronger if the figures represented pooled data from many animals and experiments (e.g. Figure 1C).

      We agree that pooling data from multiple animals would strengthen the manuscript. In practice, we tested these experimental conditions across several animals (14 Euprymna berryi and 12 Sepia officinalis), but we selected the segments shown in the figures for their minimal artifacts and errors. Acquiring high-quality, stable recordings of this type is extremely challenging, and the presented data represents the clearest examples suitable for analysis and visualization. We hope that in the future these methods will enable not only the collection of a larger, high-quality dataset, but also comparisons across individuals, ages, species, and different regions of the mantle.

      (2) It's very unclear what animals were used for each experiment:

      (a) E. berryi: L677 states that 14 animals were filmed, and L684 implies that non-sedated individuals were used in addition to sedated animals, but it appears all the data is from a single E. berryi with sedation?

      The original wording was unclear, so we modified the sentence for clarity. The Methods now specify that 14 animals were filmed to refine the experimental pipeline and explore different conditions, while the data presented in the Results are from a single lightly sedated individual chosen for quality and stability of chromatophore activity.

      (b) S. officinalis: L692 onwards states that lots of different conditions and animals were explored, but only minimal data from a couple of animals is described in the figures. L156 states that all (?) the data comes from one head-fixed animal and one sedated and head-fixed animal. L549: The conclusion states that the pipeline was used in freely moving animals, but it appears that all of the S. officinalis were head-fixed? This is very confusing. Rather than describing the conditions of every experiment ever performed, the manuscript would benefit from explicitly stating the experimental conditions used for each figure.

      The original text was unclear. We have clarified in the manuscript which animals and experimental conditions were used for the analyses in each figure. To clarify, E. berryi was recorded without head fixation, whereas S. officinalis data were obtained under head-fixed conditions. We did film 11 S. officinalis without head fixation, and data can in principle be extracted from these recordings. Head fixation was used both to minimize visual artifacts and to enable longer, stable recordings, which was important for capturing the highest level of apparent noise in motor unit activation—information that is critical for our analyses of motor-unit organization, though not necessary for studies of broader camouflage patterns. Our computational pipeline enables large-scale analyses that would be very difficult or impossible with traditional electrophysiology, not that all data were acquired from freely behaving animals. While fully unconstrained recordings remain technically challenging due to optical and logistical constraints, we maintain that our approach provides a valid framework for analyzing freely behaving animals.

      (c) Additionally, there is a claim that the sedated condition represents the unsedated one (e.g. L151 and L643), but no data is shown to support this. L173 references Figure 6d as evidence, but 6d doesn't exist. Only L210 provides sedation/no sedation statistics for the number of components per motor unit. However, in L643 it says "and motor unit organization remained unchanged". This data needs to be shown to include that statement.

      Reference to the inexistant 6d figure was removed. L170 provides statistics for the number of principal components per chromatophore, and L210 provides statistics for the number of components per MU. We do not think a sub-figure is necessary. We, however, agree that L643 “motor unit organisation” is potentially misleading as we only compared the number of chromatophores belonging to a single MU and not the MU shape or distribution. Changed “organization” to “size (in chromatophores)”.

      (3) The text needs considerable revision. There are many typos (including multiple instances of "refs" instead of the actual references being inserted). These issues make the manuscript much more difficult to evaluate.

      Our apologies. We have now added the missing refs.

      (4) It is not clear how convincing the chromatophore groups are. For instance, Figure 4h could alternatively be interpreted as a group of 5 chromatophores in a motor group that happen to co-vary with a sixth one at a great distance. Without seeing some of the raw data (videos), it's difficult to assess how convincing it is that these chromatophores belong to the same group. I recommend analyzing: when multiple chromatophores expand together, what is the likelihood that other chromatophores also happen to expand at the same time (given the frequency that they're all changing shape spontaneously)?

      We appreciate the reviewer’s concern. Chromatophores are assigned to the same cluster because their activity, or that of their slices, covaries consistently over time. It is, of course, possible that what appears as a single motor unit may reflect two or more motor neurons acting simultaneously during the recording. Longer video segments increase confidence in the integrity of inferred motor units, but in the absence of a ground truth for motor unit spatial organization in this species at this age, it is difficult to quantify the likelihood that two motor units are being conflated. Raw video data is provided in the Data Availability section. We note, however, that most of the time motor units cannot be readily discerned by eye, because individual chromatophores and their constituent slices fluctuate continuously, and motor-unit correlations are subtle and distributed across multiple chromatophores.

      (5) The rationale for focusing on spontaneous activity is introduced relatively late in the manuscript and would benefit from being stated earlier. Examples should be provided of what this looks like (as opposed to regular chromatophore expansion). It would be valuable to see measurements across many experiments of how expanded the chromatophores are - what is the change in surface area? And what is the frequency of expansion for each chromatophore?

      Thank you for the remark. This is true. We have added a paragraph at the beginning of the Results section to clarify the rationale for focusing on spontaneous activity.

      This section now reads:

      “Because our primary aim was to describe the composition and coordination of chromatophore motor units, it was important to examine animals in the absence of the descending commands that occur during active behavior. Spontaneous activity, typically mild and “noisy” was thus ideal to enable measurements of the motion correlations between chromatophores that reflected shared motor neuron drive, rather than shared correlations due to upstream motor neuron groupings by premotor circuits.”

      We added an example of video recording of spontaneous activity in our Data Availability section.

      While quantifying expansion magnitude and frequency across experiments would indeed be valuable, these questions fall outside the primary focus of the present study, which centers on resolving motor unit organization. In the section “Dynamics of chromatophore expansion and contraction,” we analyze the speed of expansion and contraction to demonstrate that such kinetic features can be reliably detected with the temporal resolution of our video imaging approach. By isolating single muscle activations, we establish a methodological framework that can be used in future work to quantify expansion amplitude, rate of change and frequency across preparations.

      (6) Chromatophore expansion was only measured in anesthetized E. berryi, and L679 states that chromatophore expansion was triggered by shining light on the skin. However, light-mediated chromatophore expansion may be mediated by a different mechanism, so chromatophore correlations do not necessarily reflect the underlying motor control.

      We agree that there is, in principle, a theoretical risk of direct light-mediated activation of chromatophores. Yet, the kinetics of this light mediated activation are very different, and are the object of a separate, on-going investigation by our groups. In our experiments, the illumination was applied to the whole animal rather than locally to the skin, ensuring that all chromatophores and the eyes were exposed to the same light source. By transitioning from darkness to light, we created a window in which chromatophores were partially expanded—both fully contracted and fully expanded states would show little to no decorrelation. Within this window, we observed spontaneous fluctuations in chromatophore activity, which formed the basis for our correlation analyses. To our knowledge, direct light-mediated expansion of chromatophores has not been reported in E. berryi although it may exist there. Finally, the size, shape, and orientation of the inferred motor units align with electrophysiological evidence, supporting the validity of our motor unit inferences.

      (7) Some figures might be better suited for the supplement. For instance, it's not clear what the significance of Figure 5 is (it's not currently sufficiently justified in the text).

      We have clarified the purpose of Fig. 5 in both the Results and Discussion sections. In the Results, we now explain that events are separated by amplitude to show that expansion–contraction kinetics can be reliably measured across a full range of chromatophore events, validating the precision of our videographic approach. In the Discussion, we highlight that this precision allows measurement of radial muscle speeds and opens avenues to study chromatophore biomechanics, including the contributions of intertwined forces such as radial muscles, elastic pigment sacs, and intercellular coupling.

      (8) Multiple chromatophores can belong to multiple clusters - this study reveals that this is because subsections of a chromatophore are controlled separately. But do the same sections (slices) of chromatophores ever belong to multiple clusters?

      Yes, it is possible. Dubas (1985) used videographic recordings to show that the same chromatophore muscle fibers could be activated by stimulation of different nerve bundles, supporting Florey’s (1969) electrophysiological evidence for polyneuronal excitatory innervation. From Dubas: "Usually, different muscle fibres were recruited by each nerve but sometimes a single muscle fibre responded to stimulation of each nerve. Variations of the stimulus voltage also produced gradation of the amplitude of shortening of individual muscle fibres. This supports the evidence above for multiple innervation of single muscle fibres."

      The petal-like distribution of motor-neuron influence shows overlapping territories, suggesting that some chromatophore sections may be influenced by multiple neurons. However, this overlap could arise from polyinnervation of individual muscles, the presence of gap junctions between muscles, or passive mechanical coupling due to the elastic properties of the pigment sac.

      The petal-like distribution of motor-neuron influence shows overlapping territories, suggesting that some chromatophore sections may be influenced by multiple neurons. However, this overlap could arise from polyinnervation of individual muscles, the presence of gap junctions between muscles, or passive mechanical coupling due to the elastic properties of the pigment sac.

      With the present approach, it is not possible to disentangle the relative contributions of these mechanisms, which will require targeted physiological or anatomical experiments. For this reason, we adopted a hard clustering approach for individual chromatophore slices.

      (9) All time should be labeled in seconds, not in frames, and all distances should be measured in um or mm, not in pixels.

      We chose to present figures in pixels and frames to reflect the native units of our recordings and analyses, which preserves fidelity and reproducibility of the computational pipeline. For biological interpretation, corresponding values are converted to µm in the main text, providing the relevant real-world scale. A scale for conversion is provided in the figure legend.

      Specific comments:

      (1) L36: I'm not sure the description of virtual chromatophores here is clear enough to make sense to a more general audience.

      Addressed. We retained the concept of ‘virtual chromatophores’ in the abstract and added a brief clarifying phrase to indicate that these are functional groupings of adjacent chromatophore territories that act as single units.

      (2) L50: "Rimmed by" - consider rephrasing.

      Addressed. Replaced with “surrounded”.

      (3) L64: "refs" - actual references aren't inserted. There are multiple other examples of this.

      Addressed. Added missing references.

      (4) L100: This section could use rewriting. Some of the text reads more like a figure legend.

      Addressed. We have streamlined the main text to reduce redundancy with the figure legend.

      (5) L101: Consider the opening sentence/s providing a more general introduction to the question and approach.

      Addressed.

      (6) L104: This implies that the data presented are from 14 animals of many ages. This is only relevant if the pooled data is analyzed and presented.

      We agree that the original phrasing was ambiguous. We have modified the sentence for clarity, and explain in the Methods that 14 animals were filmed to refine the pipeline and explore experimental conditions, while the analyses shown are from a single animal.

      (7) L111: HDBSCAN should be defined.

      Addressed. The acronym has been expanded.

      (8) L173: Figure 6D doesn't exist.

      Addressed. Reference to the inexistent 6d figure was removed.

      (9) L193: "excluding negative (contraction) phases" This phrase requires clarification.

      Addressed. Added “see Methods” in the legend and added clarification on the reasoning in Methods.

      (10) L204: Should explain why the switch to affinity-propagation clustering was made when a different method was used for E. berryi.

      Addressed in discussion.

      (11) Figure 3: I recommend including a diagram or image of a whole cuttlefish and showing what the corresponding imaging area was in relation to the animal so the reader gets an intuitive sense of scale.

      Thank you. We have added a supplementary figure to give the reader a sense of scale.

      (12) L221/Fig 3b: These colors are supposed to represent clusters of 3 to 5 chromatophores? The clusters look much bigger.

      The figure shows clusters of 3 to 5 chromatophores, but many adjacent clusters were assigned the same color. We have changed the colors to remove this ambiguity.

      (13) Figure 3c: This would be more powerful if it represented the combined data of many experiments to draw a general conclusion. Also, shouldn't these cluster sizes match those in 2e, e.g. they get as big as 40?

      We assume the reviewer is referring to a comparison between Figures 3c and 2e. For visualization purposes, the graph in 3c was truncated to display over 90% of the data, which explains why the largest clusters appear smaller than in 2e. We modified the legend accordingly. We agree that the results would be strengthened by pooling data from additional experiments; however, acquiring high-quality, artifact-free recordings suitable for motor unit analysis is extremely challenging. We hope that our framework will enable future studies to extend this analysis.

      (14) Figure 4: I would show some of these examples earlier, to give the reader an intuitive sense of the data and claims (though it doesn't need its own figure - provide a couple of examples, and the diagram of how much of the mantle you're sampling) then put the rest in the supplement, and include some videos too.

      We agree that providing spatial context is important for readers to develop an intuitive understanding of the dataset. However, introducing examples of motor units earlier in the manuscript would, in our view, interrupt the logical progression of the Results, where motor unit identification builds on prior analyses. To address the reviewer’s concern, we have added a new supplementary figure (Fig. S1) illustrating the size and location of the sampled mantle region. In addition, we now provide representative videos in the Data Availability section to give readers direct visual access to the underlying dynamics.

      (15) Figure 4f: Is the location of the split color in each dot accurate? It's surprising that each one is split down the middle, and the pink side is always on the right - this is unintuitive given where the motor neuron is likely to be located.

      The dots and half dots represent the membership of a chromatophore to a particular cluster.

      (16) Figure 5: I didn't find this figure sufficiently justified in the text. I would move this to the supplement.

      Addressed in General point #7.

      (17) L350: States that 12 animals were patched, but the data isn't shown. It's important to show all of this data (some of which can be in the supplement).

      Addressed. We provided the data in the Data Availability Section.

      (18) Figure 5: I would quantify how many chromatophores were in each motor group across all the recording sessions, and compare this to the equivalent behavioral analysis.

      We assume the reviewer means Fig. 6. We calculated and stated the size of motor units across patching sessions.

      (19) Figure 5c: I recommend labeling each panel with a different number so you can refer to specific data.

      We assume the reviewer means Fig. 6c. We consider the figure layout clear enough to allow readers to follow the data without additional panel numbers.

      (20) L379: Typo: repeat of "quantitative"

      Addressed.

      (21) L576: Salinity should be 33-36 ppt, not %

      Addressed.

      (22) L877: The salinity units are sg? That should be stated. Though I would use the same units for salinity throughout.

      Addressed.

      Overall, this work introduces a potentially valuable quantitative framework for studying chromatophore dynamics. Addressing the points above would substantially strengthen the manuscript and clarify the scope and support for its conclusions.

      We thank the reviewer for these many helpful comments.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 64 - missing references for chromatophore colour with age.

      Addressed. Added missing refs.

      (2) Line 64-65 - would be good to have a little more detail about what is meant by 'migrating through the skin'. Is this a lateral process, or depth in the skin?

      Addressed. Changed “migrating in the thickness..” with “through the thickness..” to emphasize verticality.

      (3) Line 72 - typo, should read '...individual and groups...'

      Addressed.

      (4) Remove 'In Fig 1, ...' from line 104.

      Addressed.

      (5) Figure 1 - It's unclear why some chromatophores are uncoloured with a red dot in the centre. Are these chromatophores that do not share a cluster with neighbours? If so, wouldn't it make more sense to colour the chromatophore with a unique colour of its own? Or, at the very least, make a note in the caption to indicate that all white chromatophores are not clustered with neighbours.

      Segmented chromatophores are shown in white, with coloured slices highlighting cluster membership. Uncoloured slices represent outliers. Addressed in the figure legend.

      (6) Line 119 - the concept of a 'closed virtual chromatophore' needs a few more words of explanation. The way I interpret the text as it is, is that the motor units driving colour change are not necessarily the individual chromatophores, but a motor region containing a mixture of whole and partial chromatophores innervated by the same motor neuron. If this is the case, a few extra words of description would help here to remove any ambiguity as I think this is an important concept for the paper.

      Addressed. We added a sentence clarifying the concept.

      (7) Line 173 - Figure 6d doesn't exist in the paper. Was a different panel intended? If so, please make sure to number the figures in order of appearance in the manuscript.

      Reference to the inexistent figure 6d was removed.

      (8) Figure 3b is very difficult to see. Perhaps consider lightening the background image. Please also indicate whether the individual colours refer to individual clusters. If this is the case, then some of these clusters look much larger than the 3-5 suggested in the caption.

      This issue has been corrected.

      (9) Line 210 - remove the bold type.

      Addressed.

      (10) Line 211 - please specify which 'two groups' you are referring to here. Presumably, this is anaesthetised and non-anaesthetised.

      Addressed.

      (11) I think that the text is missing any indication of the pixel sizes involved in extracting slice metrics, particularly from the S. officinalis data. It would be great to include some data on how many pixels span the radius of an expanded chromatophore. There is some small indication of this in Figure 2a, but a panel or two with details about the pixel size of S. officinalis chromatophores and their slices would be welcome. This would help with the judgment of the robustness of the resolution of the analysis. Looking at the y-axis in Figure 5a, there is some indication that the chromatophore radius is only 1 to 8 pixels. Is this the case?

      Figure 5a doesn’t show chromatophore radius but instead the relative change in peak amplitude during an expansion event. At that point the chromatophore has likely a larger radius as you sum the baseline radius of the chromatophore + the size of the peak.

      (12) Line 246-7 - reword this sentence to avoid referring to Figure 3d in the narrative. Include it in parentheses instead.

      Addressed.

      (13) Lines 408 and 409 - missing references.

      Addressed.

      (14) Line 576 - salinity should be reported in parts per thousand, not per cent.

      Addressed.

      (15) Line 593 - how were animals <50mm fed?

      Animals smaller than 50 mm were fed Neomysis spp. or small Palaemonetes spp., as noted a few lines above the description for animals larger than 50 mm.

      (16) Line 847 - typo - '...putative motor units' ramifications...'

      Addressed.

      (17) Line 854 - better to write out the [chrom_id, label] info as narrative text rather than using the variable names.

      Addressed.

      (18) Line 876 - two typos '...were reared in an artificial...'

      Addressed.

      (19) Line 877 - please use the same salinity metric as used in the earlier part of the methods.

      Addressed.

      (20) Section 898-910 - equipment details would ideally include the location of the company. E.g. (BX51W1, Olympus, Tokyo, Japan).

      Addressed.

      Reviewer #3 (Recommendations for the authors):

      I am left with a number of questions that arise from the authors' work, some of which the authors themselves briefly mention in the technical limitations section.

      (1) In relation to the first weakness, do the authors know if the recruitment patterns they identify are likely to be the same when octopi perform visually-mediated camouflage to their environment?

      Thank you for this comment. We assume the reviewer is referring to S. officinalis. There seems to be a misunderstanding: our approach is designed to reveal the smallest independent functional units—motor units—that together generate skin patterns. The technique is fully applicable to an animal displaying camouflage, but the results would necessarily differ. Camouflage patterns are composed of relatively large shapes compared to individual motor units and arise from the coordinated activation of multiple units. Disentangling motor units requires decorrelated activity, whereas visually-evoked camouflage inherently drives correlated motor-unit activation by premotor control. To use an analogy, if our goal were to map the distribution and wiring of pixels on a screen, it would be more informative to broadcast a noise signal rather than display coherent images, as the noise produces decorrelated activity that allows the underlying structure to be resolved. We have clarified this important point in the early results section.

      (2) The authors provide indirect evidence that motor neurons innervate multiple chromatophores. Can sets of radial muscles within a chromatophore be innervated by multiple motor neurons? Is there neuroanatomical evidence or experiments that could perhaps shed light on this?

      Addressed above. Same question as #1(8).

      (3) Are multi-innervated chromatophores evenly distributed across the octopus's body? For instance, could the authors compare chromatophore recruitment over multiple patches on the animal from multiple regions?

      At present, we do not have sufficient data to quantitatively compare motor-unit structure or the distribution of multi-innervated chromatophores across different body regions of cuttlefish. However, we would not necessarily expect uniformity across the skin, as distinct body regions are associated with characteristic pattern elements (e.g., the white square on the central mantle or the thicker zebra stripes along the sides). It is therefore plausible that different motor-unit geometries and densities are differentially represented across regions to support these region-specific patterns. Future recordings spanning multiple patches and body locations will be required to test this question directly.

      (4) Relatedly, is there any idea of whether chromatophore size or age corresponds with the number of motor units within a single chromatophore?

      At present, our analyses are limited to single developmental time points, and we therefore cannot directly assess whether chromatophore size or age correlates with the number of motor neurons innervating an individual chromatophore. However, this is a question that our analysis framework is explicitly designed to address. Our custom pipeline, CHROMAS, (Ukrow, Renard et al., 2025) includes tools for longitudinal image alignment that allow chromatophores to be tracked within the same animal across development. Applying these scripts to developmental datasets enables future analyses linking chromatophore growth or age to changes in the motor innervation of single chromatophores.

      I understand that a full resolution to the issues raised above may require substantial additional experiments. At a minimum, further discussion of these points with integration of existing literature would elevate the paper.

    1. Author response:

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

      Reviewer #1 (Public review):

      (1) The rationale behind averaging sentence embeddings across multiple transformer models (with different architectures and training objectives) is unclear. These transformer-based models have different training paradigms and model architectures, which may result in misaligned semantic spaces. The averaging operation may dilute the distinct sentence representations learned by each model, potentially weakening the overall semantic encoding for sentences. Please clarify this choice or cite supporting methodology.

      The reviewer questions the rationale for averaging sentence embeddings across different models. However, our method involves computing correlations separately for each model, then averaging the correlations. We apologize for the confusion. We have clarified this on page 3:

      “Results for the ‘Transformers’ model are computed by computing correlations separately for five different transformer models and then taking a simple average of these correlations. Results for each individual transformer are presented in Supplementary Information Figure S2.”

      (2) All structure-sensitive models discussed incorporate semantics to some extent. Including a purely syntactic baseline, such as a model based on context-free grammar, would help confirm the importance of syntactic structures.

      Following the suggestion, we have implemented two syntactic models and discuss the results on page 10:

      “We also found that purely syntactic models based on constituency parses (see Benepar and CFG) show poor correlations with brain activity (see Supplementary Information Figure S2). Examining the corresponding RSA matrices (see Figure S1), this seems to be due to such models being overly sensitive to syntactic form, and relatively insensitive to which words are assigned to different nodes within the syntactic tree. This is most evident for the edit-distance similarity metric, and to a lesser extent also for the subtree similarity metric. This finding highlights the value of hybrid approaches designed to appropriately balance sensitivity to lexical, syntactic, and compositional information in representing semantic information at the sentence level.”

      (3) In Figure 2, human behavioral judgments show weak correlations with neural data, and even fall below those of computational models, suggesting the behavioral judgments may not reflect the sentence structures in a brain-like way. This discrepancy between behavioral and neural data should be clarified, as it affects the interpretation of the results.

      While the behavioural judgements are made by different participants and involve a different task than the neuroimaging results, nonetheless we agree the difference is surprising and warrants more detailed consideration. We have included a more detailed discussion of this issue on page 11:

      “Our study has several limitations. First, we found a surprisingly low correlation between behavioural ratings and brain activations (see Figure 2). This may be partly explained by differences in task structure. In the behavioural experiment, participants viewed many pairs of related sentences, and were explicitly asked to pay attention to differences in the words of each sentence. In contrast, in the fMRI task, participants read one sentence at a time without an explicit comparison. In addition, we suspect that presentation of so many sentence pairs with highly similar structures may have biased the way in which participants rated sentence similarity. Modifications to the behavioural task to mitigate these aspects may reduce the divergence between behavioural and brain findings.”

      (4) To better contextualize model and neural performance, sentence similarity should be anchored to a notion of semantic "ground truth", such as the matrix shown in Figure 1a. Comparing this reference with human judgments, brain responses, and model similarities would help establish an upper bound.

      While our design matrix served as the basis for constructing a set of stimuli with systematic modifications, we respectfully suggest that it should not be regarded as a ‘semantic ground truth’. Sentence pairs within each category will not have the same degrees of semantic similarity since the words and context differ across sentences in a graded manner. Furthermore, while we anticipated ‘different’ sentence pairs would be less similar than ‘swapped’ sentence pairs, and that within each of the six block diagonals the ‘modified’ or ‘substituted’ sentence pairs would be the most similar, we did not have any prediction about the magnitude of these differences. Our goal was to construct a set of sentence pairs which spanned a range of semantic similarities, and allowed for dissociation between lexical similarity and overall similarity in meaning. The design matrix is not intended to represent a ‘ground truth’ that human judgements or brain representations would be expected to conform with.

      (5) The structure of this paper is confusing. For instance, Figure 5 is cited early but appears much later. Reordering sections and figures would enhance readability.

      We agree that placement of figures was not ideal in the previous draft. We have reworked the manuscript so that all figures appear closer to their mention in the text, and the figure (now Figure 3) appears in the correct order. We have also substantially revised the discussion, and included subheadings to help guide the reader through the various different issues we include.

      (6) While the analysis is broad and comprehensive, it lacks depth in some respects. For instance, it remains unclear what specific insights are gained from comparing across brain regions (e.g., whole brain, language network, and other subregions). Similarly, the results of simple-average and group-average RSA appear quite similar and may not advance the interpretation.

      We included both analyses in line with our preregistration, and also because we believe the fact that two distinct approaches to analyzing the data yield similar results strengthens our conclusions.

      (7) While explaining the grid-like pattern due to sentence length is important, this part feels somewhat disconnected from the central question of this paper (word order). It might be better placed in supplementary material.

      We believe that the grid-like pattern in the RSA results is an important unexpected finding that warrants discussion in the main manuscript.

      Reviewer #1 (Recommendations for the authors):

      (1) Consider including a purely syntactic baseline model. For instance, parse each sentence into a constituency tree and compute tree edit distances between pairs of trees. This would allow you to construct a sentence similarity matrix based solely on syntactic structure, and may clarify the role of syntax in sentence representations.

      See our response to Public Review comment 2.

      (2) Instead of averaging embeddings across different transformer-based models, I recommend reporting RSA results for each model individually. For instance, compare one sentence-level model (e.g., SentBERT or SimCSE) and one general-purpose language model (e.g., GPT-2 or Llama).

      See our response to Public Review comment 1.

      (3) I suggest revisiting the structure of the Results section to improve the clarity and impact of your key findings. Consider which results are most central to the paper's claims and ensure they are presented in the main text. Less central analyses (e.g., the analysis on the grid-like pattern) might be better suited for the supplementary information. Presenting behavioral results prior to neuroimaging results could also improve logical flow by first validating model similarity estimates behaviorally.

      As mentioned in our response to Public Review comment 5, we have revised the ordering of the figures to improve the flow of the main manuscript. We believe that the grid-like pattern in the RSA results is an important unexpected finding that warrants discussion in the main manuscript. In addition, we believe that presenting the neuroimaging results first is appropriate as this is the primary and most important contribution of our study.

      Reviewer #2 (Public review):

      (1) The stimuli are not fully controlled for lexical content across conditions. Residual lexical differences between sentences could still influence both brain and model similarity patterns. To more cleanly isolate syntactic effects, it would be useful to systematically vary only a single structural element while keeping all other lexical content constant (e.g., the boy kicked the ball / the ball kicked the boy). It would be better to engage more with the minimal pair paradigm, which is widely used in large language model probing research.

      The reviewer rightly argues that our stimuli do not fully control for lexical content across conditions, and that a more appropriate paradigm may be to utilise minimal pairs in which only a single variable of interest (such as sentence structure) is modified. We agree that most of our sentence pairs do not constitute minimal pairs; however, this was not our objective. Our study design aimed to synthesise traditional minimal pair approaches with more recent research paradigms using naturalistic stimuli. As such, we selected stimuli which are more complex and contain more variable features than traditional minimal pair studies, but which also are tailored to highlight differences which are of particular theoretical interest.

      Because we are interested in comparing the effects of multiple sentence elements and semantic roles, a systematic pairwise comparison of minimal pairs is not necessarily optimal. Instead, we designed our stimuli to leverage the advantage of fMRI in that we can measure the brain representations corresponding to each sentence, and hence can conduct a full series of pairwise comparisons of sentence representations. We do not claim this approach to be universally superior to a minimal pair approach, but we do believe our novel approach provides additional insights and a new perspective on semantic representation relative to minimal pair studies.

      We have added the following paragraph on pages 9-10 contrasting our approach to previous minimal-pair studies:

      “Another approach that has seen widespread use is the presentation of minimal sentence pairs that differ only in one specified aspect, for example, interchanging subject and object in a sentence (Frankland 2015, Wang 2016, Frankland 2020, Giglio 2024), or altering adjective-noun phrases to influence composition (Graves 2010, Schell 2017, Fyshe 2019, Ciapparelli 2025). Our approach is an extension of these approaches utilising more naturalistic and complex sentences, designed to facilitate comparison of a wider range of structural manipulations (see Table 1). In more completely characterising the representational structure of various computational models in response to different structural contrasts, we can more comprehensively evaluate their adequacy as models of semantic processing in the brain.”

      (2) The comparisons are done across fundamentally different model types, including static embeddings, graph-based parsers, and transformers. The inherent differences in dimensionality and training objectives might make the conclusion drawn from RSA inconclusive. Transformer embeddings typically occupy much higher-dimensional, anisotropic representational spaces, and their similarity structure may reflect richer, more heterogeneous information than models explicitly encoding semantic roles. A lower RSA correlation in this study does not necessarily imply that transformers fail to encode syntactic information; rather, they may represent additional aspects of meaning or context that diverge from the narrow structural contrasts probed here.

      The reviewer notes that low RSA correlations do not necessarily imply that transformers fail to encode syntactic information. We acknowledge this in our discussion (page 10), where we also highlight that our focus is not on whether transformers encode such information, but rather what transformer representations can tell us about how sentence structure is represented in the brain. Our results indicate that transformer embeddings do not have the same geometric properties as brain representations of sentence meaning, at least for certain types of sentences where lexical information is insufficient to determine overall meaning.

      The reviewer also notes that transformer embeddings are highly anisotropic; however, we adjust for this by normalising each feature as discussed on page 14. Finally, the reviewer notes that the transformers we examine differ in architecture and training objectives. This is not critical for our study because we are not seeking to determine which architecture or training objectives are best. Our goal is simply to compare a range of approaches and see which, if any, have similar sentence representations to those formed by the brain. In fact, our results indicate that architecture and training regime make relatively little difference for our stimuli, as shown by the pattern of results for all models in Figure S2.

      (3) The interpretation of the RSA correlation largely depends on the understanding of models. The authors suggest that because hybrid models correlate better than transformers, this implies that transformers are inferior at representing syntax. However, this is not a direct test of syntactic ability. Transformers may encode syntactic information, but it may not be expressed in a way that aligns with the RSA paradigm or the chosen stimuli. RSA does not reveal what the model encodes, and the models might achieve a good correlation for non-syntactic reasons (e.g., length of sentence, orthographic similarity, lexical features).

      The reviewer argues that RSA correlations do not measure the extent to which a model encodes syntactic information. This is very similar to the previous point. We do not claim that our results show that transformers do not encode syntactic information. Rather, our claim is that sentence embeddings derived from transformers have different geometric properties to brain representations, and that brain representations are better described by models explicitly representing key semantic roles. From this we conclude that, at least for the sentences we present, the brain is highly sensitive to semantic roles in a way that transformer representations are not (at least to the same extent). We have clarified this in a modified paragraph on page 11:

      “We emphasise that our results do not show that transformers fail to represent syntactic or semantic role information. Indeed, large language models show clear capabilities of correctly interpreting sentence structure (Chang 2024), and probing studies have found that transformers represent information about syntax and word order (Clark 2019, Manning 2020). This is consistent with our finding that directly prompting GPT-4 to rate sentence similarity yields very high correlations with human judgements (see Supplementary Information Figure S3). Nonetheless, the fact that transformers can encode and utilise structural information to perform linguistic tasks does not mean that they effectively utilise this information to construct a brain-like representation of sentence meaning.”

      We also respectfully disagree with the reviewer’s suggestions that sentence length and orthographic or lexical similarities may drive model correlations with brain activity. As we discuss on page 19, we explicitly control for differences in sentence length when computing correlations. Our process for constructing our sentence set also controls for lexical similarity by generating pairs of sentences with all or mostly the same words but different orderings. We did not explicitly address orthographic similarity, but this will be strongly correlated with lexical similarity.

      Reviewer #2 (Recommendations for the authors):

      (1) Model dimensionality: the interpretability of cosine similarity diminishes as the dimensionality increases, and there are some math tricks to work around it. To make a fair comparison among models with different dimensionalities, it would be better to apply some dimensionality-insensitive distance metrics.

      We thank the reviewer for this suggestion. We repeated all vector-based similarity calculations using the Dimension Insensitive Euclidean Metric (DIEM). As shown in Figure S9, the results are broadly similar, though with overall somewhat lower brain correlations for most transformers compared to cosine similarity.

      (2) Depending on the scope of the current study, if the authors would like to establish whether transformers are inferior to graph-based models in representing syntax, a linear classifier using the model embeddings would be sufficient. I think this would be a more direct assessment of model syntax ability than correlation with brain data.

      As we discuss in our previous responses, our objective in this study was not to assess how well transformers can represent syntax. Rather, the goal was to assess whether internal transformer representations have similar geometric properties to patterns of brain activation. Our results indicate that transformers do represent sentence structure, but in a different manner to the human brain.

      Reviewer #3 (Public review):

      (1) The interpretation of findings is nuanced. Although Transformers underperform as brain models on the critical subsets of controlled sentences, a Transformer outperforms all other models when evaluated on the union of all sentences when both word-level content and structure vary. Transformers also yield equivalent or better models of human behavioral data. Thus, although Transformers have demonstrable flaws as human models, which are pinpointed here, in the general case, (some) Transformers are more human-like than the other models considered.

      The reviewer argues that we overstate some of our conclusions, as several transformers achieve higher brain correlations than the hybrid model when computed over all sentence pairs, as well as on the behavioural data. In response, we first note that our primary interest in this paper is on the block diagonal sentence pairs, as these were specifically designed to interrogate how different models represent sentence structure. The comparison with all sentence pairs is presented for comparison but is not our primary focus on this paper, as also reflected in the pre-registered prediction that our VerbNet-CN hybrid model would show higher brain correlations than transformers over this block diagonal subset.

      Second, we have included a new analysis in the revised manuscript (Figure S9) where we compute brain correlations controlling for the pattern of similarities observed in the primary visual cortex (averaged over participants), as a way to control for visual similarity. This added control substantially reduces the brain correlations of the transformers, such that they all have lower correlations than VerbNet-CN and AMR-smatch even over the set of all sentence pairs. We provide interpretation of this result in the discussion.

      Third, we would like to note one of the disadvantages of transformers as a model of mind or brain representations is that they are largely a ‘black box’ whose workings are poorly understood. One advantage of hybrid models like our simple semantic role model is that they can be much easier to interpret, thereby enabling them to be used to determine which features are most important for brain representations of sentence meaning, and what mechanisms are used to combine individual words into a full sentence. Given their relative simplicity and interpretability, we believe hybrid models have considerable value as scientific tools, even in cases where they achieve comparable correlations to transformers. We have added a short discussion of this issue in the revised manuscript (page 10).

      (2) There may be confounds between the critical sentence structure manipulations and visual representations of sentence stimuli. This is inconvenient because activation in brain regions that process semantics tends to partially correlate with visual cortex representations, and computational models tend to reflect the number of words/tokens/elements in sentences. Although the study commendably controls for confounds associated with sentence length, there could still be residual effects that remain. For instance, the Graph model correlates most strongly with the visual cortex despite these sentence length controls.

      We agree with the reviewer that this is a potential confound. As noted in the previous response, we have implemented a new control analysis in which we directly control for visual similarities as reflected in participant-averaged similarities of primary visual cortex activations in response to all stimuli. These results are shown in Figures S8-S11 in the SI. We show that transformer correlations are reduced much more than graph and hybrid models with this control. Also, we note that the AMR-smatch graph model shows high correlations with other brain regions even after removing correlations with the visual cortex (Figure S10). This indicates that the model represents a range of sentence features, including both superficial visual or length-related features, as well as semantic features that are represented in common with language and other cortical regions.

      (3) Sentence similarity computations are emphasized as the basis for unifying comparative analyses of graph structures and vector data. A strength of this approach is that correlation is not always the ideal similarity metric. However, a weakness is that similarity computations are not unified across models. This has practical consequences here because different similarity metrics applied to the same model produce positive or negative correlations with brain data.

      The reviewer notes that the method for computing similarities differs between the vector-based (mean and transformer) models, and the hybrid and syntax-based models, thereby potentially adding an additional confound to our results. We agree that this is a potential limitation, and our correlations should always be understood as applying to a model paired with a similarity metric. However, we believe that this is mostly unavoidable when comparing different formalisms. In the revised manuscript we have incorporated an entirely new similarity metric for vector-based models (DIEM similarity), as well as an extended discussion of the effect of different similarity metrics for graph and hybrid models.

      Reviewer #3 (Recommendations for the authors):

      (1) Compute separate RSAs on each sentence pair type (especially Swapped), to quantify how each sentence type manipulation contributed to the divergence between model and brain. Although the manuscript is already brimming with analyses, I think squeezing this in would be helpful because the results currently rely on qualitative inspection of group-average scatter plots to interpret how sentence pair manipulations contributed to the divergence between Transformers and humans. The Swapped condition would appear to be the centrepiece of the title and manuscript, and potentially the only condition for which confounds associated with the surface form of sentence are controlled for (because sentences should be the same words in different orders). Thus, this analysis might see to the inconvenient visual cortex correlations in Figures 3d/e.

      We respectfully disagree that computing separate RSA for each sentence pair type would be a useful additional analysis. The motivation for the construction of our stimulus set was to provide a range of variants of a given base sentence that alter the semantic meaning and lexical content (somewhat) independently. The purpose of the ‘modified’ sentences, for instance, is to construct sentences with a similar overall meaning but lower lexical similarity due to the inclusion of many modifier words. It is precisely the comparisons across the different pair types that provide information about how each model represents sentence semantics, so restricting an analysis to only a single subset would not be very informative. Another problem with this approach is that it would dramatically reduce the number of sentence pairs analysed, thereby decreasing statistical power. In the revised manuscript we have provided additional details regarding the motivation and rationale for how our stimulus set of 108 sentences was constructed, which should help to elucidate this point more clearly. The following excerpt is from page 3:

      “Within each of the six subsets, we begin with a base sentence such as `the cameraman brought the equipment to the director', which we then systematically modified in various ways to create different combinations of lexical and compositional similarity, in order to dissociate these two aspects of meaning (see Table 1 for further details).”

      (2) Explaining the motivation for the sentence stimulus types. I appreciated the careful design of the dataset, but I couldn't immediately work out the motivation for all the different sentence types, and why this selection was ideal to identify divergences with Transformers. For instance, given the goal of (approximately) controlling for lexical similarity whilst varying sentence meaning, I couldn't immediately see why stimulus blocks weren't all built from rearranging the same content words (as in the Swapped condition). The negative RSA correlation with the Mean model also made me stop and think - it seems like the more similar the words in a sentence, the more different their structure, and vice versa, but I wasn't clear that this was a design feature. Thus, a few extra words motivating the conditions could be helpful for the reader, and these might helpfully lead them to anticipate the negative RSA correlation.

      As noted in the previous response, in the revised manuscript we have expanded our explanation of the rationale for the construction of our 108 sentences. In particular, Table 1 in the methods section now includes two additional columns which summarise the intended combinations of lexical and overall sentence similarity which our sentence pairs are intended to satisfy.

      (3) Explanation for why different implementations and similarity computations between variants of ostensibly equivalent Graph / Hybrid models yielded widely divergent positive vs negative brain correlations, despite both positively capturing behavioural ratings. This might incorporate a brief intuitive explanation of how Graph model similarities were computed (e.g., what SMATCH and WWLK do). In light of the above, why do different similarity algorithms applied to the Graph model yield positive and negative correlations on the same brain (e.g., Figure S2 - Graph / Graph-WL a,b, diag-pairs). Same goes for why Hybrid and Hybrid-AMR yielded positive vs negative correlations (e.g., Figure S2 - Graph / Graph-WL a,b, diag-pairs). Acknowledge that the brain results are sensitive to similarity computations in the Discussion.

      We appreciate this suggestion. We have added an extended consideration of these issues to the discussion (pages 10-11), as well as some additional details regarding the differences between the Smatch and WWLK metrics in the methods section (page 17).

      (4) Acknowledgement and explanation of why the human similarity ratings were poor at explaining brain data in Figure 2a,b (right column diag-pairs). The poor behaviour vs brain match is indirectly implied in the Discussion as "the comparison between behavioural and fMRI data is somewhat difficult owing to the difference in task structure." However, I would suggest being upfront and explicitly mentioning and explaining the poor brain match in Figures 2a and b, because the reader will notice and wonder - especially because the models correlate strongly with the behavioural data without the models doing the human behavioral task (though this could be a possibility, see later).’

      As suggested, we have included a passing reference to this in the presentation of our main results in page 5, and a lengthier discussion on page 11:

      “Our study has several limitations. First, we found a surprisingly low correlation between behavioural ratings and brain activations (see Figure 2). This may be partly explained by differences in task structure. In the behavioural experiment, participants viewed many pairs of related sentences, and were explicitly asked to pay attention to differences in the words of each sentence. In contrast, in the fMRI task participants (who were not the same as the behavioural task participants) read one sentence at a time without an explicit comparison. In addition, we suspect that presentation of so many sentence pairs with highly similar structures may have biased the way in which participants rated sentence similarity. Modifications to the behavioural task to mitigate these aspects may reduce the divergence between behavioural and brain findings.”

      (5) Brief explanation of why model vs brain correlations tended to be strongest in the visual cortex (Figure 3d,e). Currently, this issue is only mentioned in passing, however, it seems worthy of further comment.

      We appreciate the reviewer for highlighting this issue. We have added discussion of the potential for visual confounds to several points in the revised manuscript, including the ‘Neuroscience of semantics’ subsection on page 11. As noted, we have also added a new analysis in which we compute correlations controlling for the average RSA similarities of the primary visual cortex. We find that this additional control significantly reduces correlations for most transformer models, but only has a more modest reduction on the correlations for most of the graph and hybrid models, particularly VerbNet-CN (see Figures S8-S11).

      (6) Softening/clarifying some statements that could be misconstrued as suggesting Transformers were universally inferior models. Statements made in the Abstract/Discussion initially came over to me as implying that Transformers were universally inferior models when compared to the Graph/Hybrid models - but this appears only to be true when one looks at analyses conducted within block diagonal sentence subsets. Otherwise, when analyses are conducted on all sentences (between and within blocks, Figure 5) Llama 3 L2 provides by far the strongest brain model. Transformers also appear to yield the strongest accounts of the behavioural data, whether tested on block diagonal or all sentence pairs (Figure S3). To remedy this, I would suggest softening some statements in the Abstract/Discussion that could be misconstrued as suggesting that Transformers were universally inferior. I would also suggest explicitly acknowledging that when the entire dataset was analyzed, Transformers were most accurate, and that (some) Transformers best accounted for the behavioural data.

      We agree that there was some lack of precision in certain sections of the previous draft regarding the conclusions to be drawn regarding the representational capacities of transformers. We have revised the abstract and conclusion to better reflect our intended message, which is that transformers certainly can represent sentence structure and semantic roles, but that the way in which they do this (through vector representations in their hidden layers) is significantly different to how such features are represented in the human brain. In particular, we have included this new text on page 10:

      “We emphasise that our results do not show that transformers fail to represent syntactic or semantic role information. Indeed, large language models show clear capabilities of correctly interpreting sentence structure, and probing studies have found that transformers represent information about syntax and word order. This is consistent with our finding that directly prompting GPT-4 to rate sentence similarity yields very high correlations with human judgements (see Figure S3). Nonetheless, the fact that transformers can encode and utilise structural information to perform linguistic tasks does not mean that they effectively utilise this information to construct a brain-like representation of sentence meaning.

      (7) Given that GPT-4 was already deployed to parse semantic roles for the hybrid model, and GPT-4 should be able to generate reasonable similarity ratings between sentence pairs, it struck me that an interesting addendum could be to use GPT-4 similarities derived from the human behavioral task to interpret both brain and human behavioral data. This might also help support the case for conducting analyses within a similarity-based framework.

      We appreciate this suggestion. We have added this model (GPT-4 ratings of sentence similarity) to the revised manuscript (see Figures S1-S3).

      Other changes

      As noted by reviewer 3, the full set of sentence pairs was missing from the previous draft. They have been added to the SI of the revised manuscript.

      We have renamed the Graph and Hybrid models in the manuscript to AMR-Smatch and Verbnet-CN respectively, for greater clarity as to which models these terms refer to, and also to better differentiate from the newly added constituency parse graph models.

      We have thoroughly revised the discussion section, incorporating feedback from all reviewers regarding areas needing additional depth.

      We have added subsections to the discussion to aid the reader navigating the now lengthier section.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      This rigorous and creative study uses an elegant combination of metabolomics, transcriptomics, and budding yeast molecular genetics to discover that (i) activating AMPK to maintain mitochondrial respiration fueled by cytosolic Acetyl CoA and (ii) increasing fatty acid synthesis independent of respiration drive independent pathways that increase the fitness of replicatively-aged budding yeast cells, albeit without increasing their lifespan. This work will be of interest to scientists in the field of aging and metabolism. Some clarifications in the text would address the following concerns, which would increase the impact of the study:

      (1) What does activation of AMPK (via PGDP-Sak1 expression) do to the replicative lifespan? How many bud scars, in general, do the subpopulations that are older - yet have less Tom70 (increased mitochondrial fitness) - have, after the 48 hrs time point that they are examining? How many divisions occurred in this 48hr time period - i.e. is it long enough to have all cells reach the end of their replicative lifespan? This information is important to rule out that a subset of the mutant cells just divided faster and hence had more divisions within 48 hrs (growing faster and living longer are different things). Having identical growth curves doesn't indicate per se that they all divide at the same rate, as there may be a subpopulation that divides faster and a subpopulation that doesn't grow so well.

      Increasing AMPK activity increases replicative lifespan [PMID: 25869125], but given our finding that AMPK activation splits the population, such replicative lifespan assays are hard to interpret. Bud scar counts have a similar issue. Hence we restricted the lifespan and bud scar analyses to wt and A2A which are more homogenous (Figures S2 B and E). A2A cells at 48h have ~25% more bud scars than wt cells. Yes, by 48h most of the cells have lost viability (Figure 2E). The reviewer is correct that you can't properly compare the lifespan curves if the cells divide at different rates, hence our follow-up test of wt at 48h vs A2A at 40h viability after we had confirmed that these timepoints captured cells at equivalent replicative ages (Figure 2D,E). This shows that viability of A2A is slightly lower than wt at matched age, indicating a slightly shorter lifespan.

      (2) A2A cells do not have an extended replicative lifespan (RLS) but show an increase in the "low senescence" population (Figure 2). If the cells are not becoming senescent, why don't they have longer RLS? Not having a longer lifespan seems inconsistent with the statement that "bud scar counting confirmed that A2A cells reach a higher age than wild type", which comes back to how many times the cells can divide in the 48hr timepoint studied and their rate of cell division? Also, the lifespan curve shown is plotted against time, not cell division number, which does not take into account different division times of cells within the population (described above). It would be much more useful to show standard lifespan curves showing cell division numbers per lifespan per cell.

      Our observation that cells can reach the end of life without senescing is consistent with other studies that have studied the life course of individual cells by microscopy [PMID: 31291577, 32675375]. These studies always highlight some proportion of the cells that reach the end of life with no or minimal senescence, though this fraction varies with the experimental system. The question of why cells lose viability without senescing is a complete unknown in the field, but reflects a wider lack of consensus as to why yeast lose viability with replicative age.

      We are wary about making strong statements on lifespan for exactly the reason the reviewer picks out. In liquid culture we can only assess viability over time, and it is clear from the comparison of liquid and solid media lifespans performed by the Gottschling lab [PMID: 19652178] that culture system has a huge effect on lifespan, with cells in classical microdissection-based lifespan assays living far longer than they do in liquid. This of course means that classical microdissection assays are not very useful for A2A so we are left with an unsatisfactory approximation. We have therefore restricted our conclusion on lifespan to simply say that lifespan of A2A cells is not extended which our data in Figures 2D,E,S2B does support (see also answer to Q1), and therefore with the majority of A2A cells showing low senescence marks and high fitness at 48h we can conclude that lifespan and fitness loss must be separable.

      We will note these limitations of lifespan measurements in the manuscript.

      (3) Increased "fitness" of the old cells is implied from the increased size of the colonies that the old cells can make. However, this is a measure of the fitness of the daughters per se, not the old mother cells. Are the old mothers just passing on healthier mitochondria and more lipids to the daughters, such that they can divide more times? If the aged cells have an "increased fitness", why don't they divide more times themselves (i.e. live longer?).

      Yes, colony growth speed is defined by daughter cell replication, and as long as the daughters and subsequent generations divide at the same rate irrespective of whether they come from a young or old mothers then the size of the colony after 24 hours varies based on the time it took the initial mother to produce a daughter. This is what the assay really measures. We note that aged wildtype mothers often do not divide at all in the first 24 hours after being put on an agar plate (hence the tiny reported colony size), even though they do eventually produce a daughter which then forms a colony, whereas A2A cells tend to produce the first daughter rapidly whether young or old. It is known that daughters of aged wildtype mothers also divide slower, which will also contribute to differences in colony size, and this may well result from a lipid and/or mitochondrial contribution, but the primary driver of colony size in 24 hours is the time the mother took to initially divide. We will add this detail to the manuscript.

      As noted above, the mechanistic basis of lifespan is unknown, but although senescence can shorten lifespan, our work and that of others shows that lifespan is still limited in the absence of senescence.

      (4) The statement is made that "these experiments define two classes of aging cells with distinct metabolic needs, coherent with the model of two aging trajectories previously proposed (referencing Nan Hao's work)". However, the big difference here is that in Nan Hao's work, their two aging trajectories influenced the length of lifespan, but that does not appear to be the case here. That distinction should be made clear. Perhaps the authors could also speculate as to why the A2A yeast stops dividing after presumably the same number of cell divisions, even though they have an activated AMPK and activated fatty acid synthesis pathway.

      We will add this distinction. As noted above, we are wary of making strong statements regarding lifespan as the assays we can do in liquid culture are limited. We are therefore similarly wary about speculating about causes for the lack of lifespan difference because in reality all we can do is rule out a big effect. We would love to speculate on why the A2A cells don't have an extended lifespan, but at this point we don't have any good ideas on this point!

      (5) I am a bit confused by the use of the word "senescence" by this lab here and in their previous growth on galactose studies. If yeast don't senesce, which is usually defined as an irreversible arrest of the cell cycle where cells stop dividing, shouldn't the yeast that do not senesce still be dividing and hence have a longer lifespan? Should a different term be used rather than senescence? Such as "fitness late in life". The authors giving their definition of senescence may help reduce this apparent contradiction.

      We completely agree, this is confusing and noted this distinction in the Introduction. Use of the term senescence to mean a loss of fitness late in life in yeast stems from the classical definition of senescence as applied to whole organisms. However, the term senescence as applied to cells has a more specific meaning in terms of the cell cycle as the reviewer notes. As an individual S. cerevisiae is both a cell and an organism, the terminology clashes. However, the marker we largely employ (Tom70-GFP) which in our hands is a very good proxy for fitness was originally defined as marking the senescence entry point (SEP), so overall we feel we can't avoid the term.

      Reviewer #2 (Public review):

      Summary:

      In this study, the authors investigate how cytosolic acetyl-CoA metabolism influences replicative aging in budding yeast. They propose that acetyl-CoA regulates aging through three major pathways: (1) mitochondrial transport to support mitochondrial function, (2) fatty acid synthesis, and (3) global protein acetylation. The data show that AMPK activation promotes mitochondrial import of acetyl-CoA and partially mitigates mitochondrial decline in a subset of aging cells.

      Furthermore, the engineered A2A strain, which enhances mitochondrial acetyl-CoA utilization while relieving inhibition of fatty acid synthesis, increases the proportion of cells exhibiting a "low senescence" phenotype.

      Overall, this is a thoughtful and potentially impactful study that advances our understanding of metab to olic control of aging. Addressing the points below, particularly by refining interpretations and, where feasible, incorporating additional analyses, will further strengthen the manuscript and its conclusions.

      Strengths:

      The study has several notable strengths. It addresses an important question by shifting the focus from lifespan to preservation of late-life fitness, which is highly relevant to aging biology. The work integrates metabolic, genetic, and functional analyses to link cytosolic acetyl-CoA flux with distinct aging outcomes, and the engineering of the A2A strain provides a clear and elegant demonstration of how coordinated pathway modulation can improve cellular fitness.

      Weaknesses:

      (1) While the manuscript focuses on mitochondrial transport and fatty acid synthesis, cytosolic acetyl-CoA is also a key regulator of histone acetylation and chromatin silencing. It would strengthen the study to consider whether acetyl-CoA depletion contributes to improved fitness through enhanced rDNA silencing. Given the well-established role of rDNA instability in yeast aging, additional experiments examining rDNA silencing and stability would be valuable. For example, monitoring rDNA copy number changes (not necessarily ERCs) under AMPK activation, oleic acid supplementation, and in the A2A strain, similar to approaches used in the authors' prior work, would help clarify whether chromatin regulation contributes to the observed phenotypes.

      We have data addressing this point that we will add to the manuscript. In short, we see no difference in gene expression from Sir2-repressed sub-telomeric regions or MAT loci, but the genome-wide gene expression dysregulation associated with age is partially suppressed in PGPD-SAK1. However, A2A does not suppress this further, so it is not critical for the suppression of senescence in A2A though we are following this up. ERC accumulation is higher in A2A at 48h, consistent with the cells being older, meaning that ERCs are unlinked to senescence onset as we have previously reported. There is a strong upregulation of transcripts from Sir2-repressed rDNA intergenic spacers with age in all genotypes, but we attribute this simply to the copy number increase of these regions on ERCs rather than a defect in silencing. We have previously looked for heritable changes in rDNA copy number arising during ageing and found (to our surprise) absolutely nothing, so we don't expect any changes under these conditions.

      (2) The current data do not fully distinguish whether AMPK activation and oleic acid supplementation act on distinct subpopulations of aging cells. An alternative explanation is that oleic acid supplementation enhances mitochondrial function and acts additively with AMPK activation, thereby increasing the fraction of cells in the "low senescence" state. Since this distinction is not central to the main conclusions, I suggest softening the language around subpopulation specificity. Emphasizing instead that the A2A strain coordinately modulates multiple branches of acetyl-CoA metabolism to improve late-life fitness would maintain the strength of the central message without overinterpretation.

      We agree that oleic acid and the lipids produced downstream of Acc1 in A2A may improve late life fitness via enhanced mitochondrial function, and in support of this Oxygen Consumption Rate is marginally (though significantly) higher in A2A than PGPD-SAK1. We will add this data to the manuscript. However, we disagree with the interpretation of an additive effect as we report throughout the study that AMPK activation and lipid biosynthesis/supplementation affect different sub-populations of cells. We do not observe populations of intermediate senescence cells, rather by flow cytometry and fitness assays we observe individual cells in binary low senescence or high senescence states.

      (3) The manuscript proposes that lipid starvation and excess acetyl-CoA are major drivers of senescence in distinct subpopulations of wild-type aging cells. This conclusion is not yet fully supported by the presented data. Direct measurements of age-dependent divergence in acetyl-CoA and fatty acid levels at the single-cell level would be needed to substantiate this model. Based on the current evidence, a more conservative interpretation would be that aging cells exhibit differential sensitivity to perturbations in acetyl-CoA and lipid metabolism. Accordingly, I recommend revising the statement in the Abstract ("We further implicate lipid starvation and excess acetyl coenzyme A availability as major drivers of senescence...") and the corresponding discussion text to better align with the data.

      We agree and will adjust the abstract to make it clearer that the lipid starvation / excess acetyl coA interpretation is a model.

      Reviewer #3 (Public review):

      Summary:

      These findings suggest that PGPD-SAK1 yeast show a subpopulation with lowered TOM70-GFP expression in high bud scar staining aged cells. Deletion of CAT2 or MLS1 reduces this effect. A PGPD-SAK1 acc1S1157A double mutant (called "A2A" here) shows an even larger effect of lowered tom70 expression in high bud scar staining aged cells. Utilization of various additional mutants involved in acetyl-CoA transport, carnitine shuttle, respiration, etc., leads the authors to conclude that these shifts in TOM70-GFP in aged cells are linked to the AMPK-fatty acid metabolic regulatory system.

      Strengths:

      These extensive and clearly described experiments reveal interesting changes in TOM70-GFP intensity in subsets of aged yeast in several mutants eventually identified as linked to the AMPK-fatty acid metabolic regulatory system.

      Weaknesses:

      (1) 3 biological replicates for mRNASeq is low.

      Thank you for pointing this out. We performed another replicate after posting the initial preprint but didn’t update the figure in the eLIFe-reviewed version. We will add this to the scatter plots and analysis in Figure 1, the findings have not changed.

      (2) While "Traditional conceptions of ageing implicate a progressive accumulation of damage leading to systemic degradation in performance until death, with evolutionary pressures acting to maximise early life fitness and fecundity at the expense of ageing health." is tangential perhaps to the data and conclusions of the study, both claims of this sentence are at best controversial, and the manuscript is no weaker for their omission.

      We actually feel that this sentence is very important to the message of the manuscript, which is that ageing does not necessarily have to involve a loss of fitness before death. Ageing is often described as the progressive wearing out of components leading to decline and death (with an old car often used as an analogy); in the ageing field this is certainly controversial, but outside the field this remains the normal understanding. We think it is important to state this widely held viewpoint with which our findings are hard to reconcile.

      Our interpretation that yeast are bet-hedging as a population growth strategy and this drives ageing in the long term is a classic antagonistic pleiotropy - we will add this term (from the citation that is already in the manuscript) and clarify in the discussion to make it obvious why we are introducing this concept in the introduction.

      (3) The statement that "Here, we determine the basis of senescence and fitness loss in replicatively ageing yeast" is a bit strong as a summary of the present careful work presented here. If the authors had created yeast mutants that retained fitness indefinitely, this would be a more appropriate strength of claim to summarize the work.

      Indeed - we will refine this sentence.

    1. Teleshuttle ucm.teleshuttle.com › 2018 › 11 › as-we-will-think-legacy-of-ted-nelson.html Smartly Intertwingled: "As We Will Think" -- The Legacy of Ted Nelson, Original Visionary of the Web Why Nelson matters A fuller explanation of why Nelson matters is in my post from a few years ago, Digital Camelot - The Once and Future Web of Engelbart and Nelson, but here I caption its core message: If you care about modern culture and how technology is shaping it, this is worth thinking about -- A powerful eulogy for where the Web might have gone, and still may someday, and the friendship of the two people most responsible for envisioning the Web* -- Ted Nelson's eulogy for his friend Doug Engelbart, as reported by John Markoff in The Times -- with Nelson's inimitable flair.

    2. Medium rreisman.medium.com › as-we-will-think-the-legacy-of-ted-nelson-original-visionary-of-the-web-f4f69a60bd6 “As We Will Think” — The Legacy of Ted Nelson, Original Visionary of the Web | by Richard Reisman | Medium 26 November 2018 - A fuller explanation of why Nelson ... about — A powerful eulogy for where the Web might have gone, and still may someday, and the friendship of the two people most responsible for envisioning the Web* — Ted Nelson’s ...

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      This study investigated how visuospatial attention influences the way people build simplified mental representations to support planning and decision-making. Using computational modeling and virtual maze navigation, the authors examined whether spatial proximity and the spatial arrangement of obstacles determine which elements are included in participants' internal models of a task. The study developed and tested an extension of the value-guided construal (VGC) model that incorporates features of spatial attention for selecting simpler task mental representation.

      Strengths:

      (1) Original Perspective:

      The study introduces an explicit attentional component to established models of planning, offering an approach that bridges perception, attention, and decisionmaking.

      (2) Methodological Approach:

      The combination of computational modeling, behavioral data, and eye-tracking provides converging measures to assess the relationship between attention and planning representations.

      (3) Cross-validated data:

      The study relies on the analysis of three separate datasets, two already published and an additional novel one. This allows for cross-validation of the findings and enhances the robustness of the evidence.

      (4) Focus on Individual Differences:

      Reports of how individual variability in attentional "spillover" correlates with the sparsity of task representations and spatial proximity add depth to the analysis.

      We thank the Reviewer for their overall positive assessment of our work and their helpful comments. We have addressed each point below.

      Weaknesses:

      (1) Clarity of the VGC model and behavioral task:

      The exposition of the VGC model lacks sufficient detail for non-expert readers. It is not clear how this model infers which maze obstacles are relevant or irrelevant for planning, nor how the maze tasks specifically operationalize "planning" versus other cognitive processes.

      The method for classifying obstacles as relevant or irrelevant to the task and connecting metacognitive awareness (i.e., participants' reports of noticing obstacles) to attentional capture is not well justified. The rationale for why awareness serves as a valid attention proxy, as opposed to behavioral or neurophysiological markers, should be clearer.

      We thank the reviewer for urging further clarity here. Our work builds closely on the previous maze navigation paradigm and VGC model developed and reported by Ho et al. Nature (2022). We directly adopted variants of their maze stimuli, computational model and obstacle awareness measures, and married these with an investigation of the role of visuospatial attention. We agree that it would be useful for the reader to have a more in-depth description of the paradigm and model, and how it operationalises planning, without needing to refer back to the original Ho et al. paper. We have now added additional explanatory sections to the Introduction and Methods as follows:

      On page 4:

      “One elegant approach to forming such a simplified representation is to adaptively select the granularity of information required to complete the task (Ho et al., 2022), known as value-guided construal (VGC). Unlike previous accounts, which model human planning as a search over all items (e.g.., tube lines), the VGC model predicts that a cognitively limited decision-maker selects a manageable subset of information over which to plan— i.e., a task representation—balancing utility and complexity (Ho et al., 2022). In our example, the VGC algorithm would plan over a few relevant tube lines rather than planning over all possible stations. To select the representation that achieves the best balance between utility and complexity, the model searches across all possible combinations of tube lines, computing the value (i.e., the plan’s utility minus its cost) of each representation for planning a specific journey. The algorithm then selects the representation with the highest value, which ensures that an ideal observer selects a representation which only includes the items (i.e., tube lines) that lead to successful planning while excluding as many items as possible to keep the plan as simple as possible. For our purposes, items included in the representation are considered taskrelevant, while items that are not represented are considered task-irrelevant. This algorithm, therefore, provides a normative standard of an efficient plan to which we can compare people’s actual plans.”

      On page 6:

      “We operationalized planning using a maze navigation paradigm, akin to our tube-related example, where participants were required to plan a route through the maze, avoiding obstacles that blocked their path. Obstacles predicted by the sVGC model to be included in the representation were considered task-relevant.”

      “At the end of every trial, participants reported their awareness of specific obstacles (see Methods for details). The level of awareness reported for different obstacles provides a read-out of what features of the environment individuals were subjectively representing while solving a particular maze. While other markers of attention and awareness (for instance, behavioural or neurophysiological variables) could also be used, here we focused on direct awareness reports in order to relate our findings both to those of Ho and colleagues and to the subjective awareness reports used in consciousness science (e.g. the Perceptual Awareness Scale (Barnett et al., 2024; Overgaard & Sandberg, 2021; Ramsøy & Overgaard, 2004; Samaha et al., 2015)). Participants were instructed to maintain central fixation while planning (see dataset dSC 1), in line with previous empirical work using this task (Ho et al., 2022).”

      To visualize our effects, we binarized the predictions of the sVGC model such that obstacles with a marginalized probability greater than 0.5 were considered taskrelevant, while other obstacles were considered task-irrelevant (e.g., Figure 2b). We now clarify this point in the caption of Figure 2.

      (2) Attention framework:

      The account of attention is largely limited to the "spotlight" model. When solving a maze, participants trace the correct trail, following it mentally with their overt or covert attention. In this perspective, relevant concepts are also rooted in attention literature pertaining to object-based attention using tasks like curve tracing (e.g., Pooresmaeili & Roelfsema, 2014) and to mental maze solving (e.g., Wong & Scholl, 2024), which may be highly relevant and add nuance to the current work. This view of attention may be more pertinent to the task than models of simultaneously tracking multiple objects cited here. Prior work (notably from the Roelfsema group) indicates that attentional engagement in curve-tracing tasks may be a continuous, bottom-up process that progressively spreads along a trajectory, in time and space, rather than a "spotlight" that simply travels along the path. The spread of attention depends on the spatial proximity to distractors - a point that could also be pertinent to the findings here.

      Moreover, the tracing of a "solution" trail in a maze may be spontaneous and not only a top-down voluntary operation (Wong & Scholl, 2024), a finding that requires a more careful framing of the link to conscious perception discussed in the manuscript.

      Conceptualizing attention as a spatial spotlight may therefore oversimplify its role in navigation and planning. Perhaps the observed attentional modulation reflects a perceptual stage of building the trail in the maze rather than a filter for a later representation for more efficient decision making and planning. A fuller discussion of whether the current model and data can distinguish between these frameworks would benefit readers.

      We thank the reviewer for highlighting relevant findings in the attention literature that were missing from our discussion. We fully agree that a complete account of the interplay of planning, navigation, and attention is likely to recruit the kind of curvetracing processes highlighted by the reviewer. However, we emphasise that our current focus is not on the process of navigation through a maze, but on the process of construing the maze itself. In other words, we are focused not on how people represent their path from A to B, but how they represent the maze itself, which they then use as a basis for planning between A and B. The VGC model predicts that a subset of obstacles will be included in this construal. We think that a spotlight model is a good starting point for this work, because attention is being deployed across the whole maze stimulus, and then becomes attached to particular objects located in particular positions. This is a distinct process from that involved in navigating the path itself. Accordingly, our stimuli were designed such that task-relevant obstacles could be presented either proximally or distally to the optimal path (e.g., Figure 1a and Supplemental Figures S1-6). An obstacle that blocks any possible path on one side of the maze is task-relevant but located a long way from the optimal path. The results of Ho and colleagues’ (2022) third experiment demonstrate how task-relevant yet distal obstacles are better remembered than task-irrelevant proximal obstacles (see Figure 4 of Ho et al., 2022). We also observed that obstacles further away from the navigation path were often represented by participants (see Figures S1-6), which cannot be explained by curve tracing alone.

      While these results cannot definitively rule out the possibility that participants automatically trace the path while also construing the maze, they suggest that the value-guided construal process is an independent predictor of participants’ representations beyond proximity to the navigated path. To make this distinction clearer, we now cite the papers alluded to by the reviewer, in the Discussion on pages 28-29, while also acknowledging the potential for investigating attention during the navigation process itself:

      “Future work may also wish to examine the relevance of visuospatial attention for the navigation process itself in this task. While our present findings speak to how individuals perceive the maze while planning, it remains unclear how attention is deployed during navigation along a path, such as how object-based attention progressively spreads along trajectories in time and space(Pooresmaeili & Roelfsema, 2014; Wong & Scholl, 2024).”

      There is also one additional nuance to the current spotlight model that we were inspired to consider by the reviewer’s comment. This is the idea that attentional effects may spread within or along the obstacles themselves. We cannot explore this in the current data because we asked for awareness of the entire obstacles, not parts of obstacles, but it may be possible to explore this in future work, for instance, with eye tracking measures.

      More generally, the growth-cone (i.e., zoom lens) model of attention for curve tracing proposed by Roelfsema and colleagues shares considerable similarities with the spotlight of attention model. Both models argue for the grouping of spatially proximal items based on attention. While the growth-cone model argues for varying sizes of zoom lenses (i.e., receptive fields of neurons) that facilitate the tracing of proximal items, both models predict that spatially proximal items are preferentially processed together because of attention. Indeed, the spotlight model could model these varying zoom lenses by altering the width of the attentional spotlight dynamically across the visual scene based on the spatial proximity of obstacles. Following related comments by Reviewer 2, we now investigate inter-individual differences in the attentional spotlight of participants and observed that these differences significantly predict participants’ mental representations (see Attentional spotlight model of task representations). We have now updated the Discussion to include consideration of these alternative model frameworks:

      On page 27:

      “Second, in the current work we were unable to distinguish whether these attentional effects are driven by a fixed spotlight of attention, or whether attention operates akin to a zoom lens, shifting the ‘width’ of the focus of attention according to the task demands (Eriksen & St. James, 1986; Müller et al., 2003; Schad & Engbert, 2012). The latter view would be consistent with growth-cone models of attention in which the focus of attention expands and contracts in accordance with task demands, mirroring the various receptive field sizes in the visual hierarchy (Pooresmaeili et al., 2014; Pooresmaeili & Roelfsema, 2014). In partial support of this idea, we found significant inter-individual differences in the width of participants’ attentional spotlight (Figure S11). It is also possible that attention is deployed within or along parts of obstacles, rather than on entire obstacles. Future work using naturalistic measures of eye movements may be able to address these questions.”

      (3) Lateralization of attention:

      The analysis considers whether relevant information is distributed bilaterally or unilaterally across the visual display, but does not sufficiently address evidence for attentional asymmetries across the left and right visual fields due to hemispheric specialization (e.g., Bartolomeo & Seidel Malkinson, 2019). Whether effects differ for left versus right hemifield arrangements is not made explicit in the presented findings.

      We thank the reviewer for this suggestion. To address this point, we fitted a three-way interaction model between VGC model prediction, lateralization index, and side (left vs right hemifield). We did not find evidence for the three-way effect (β= 0.01, SE= 0.02, 95% CI [-0.03, 0.04], p = 0.738; ΔBIC = 58.30 in favour of the null effect; see table below), suggesting that the side to which participants lateralized their attention did not influence their task representations. This result is now reported on page 12:

      “This effect did not vary significantly as a function of the specific hemifield (i.e., left vs right) in which task-relevant information was presented (β= 0.01, SE= 0.02, 95% CI [-0.03, 0.04], p = 0.738; ΔBIC = 58.30 in favour of the null effect; see table S14).”

      We also explored inter-individual differences in participants’ tendency to lateralize their attention (see also the next point). We observed that participants tended to lateralize their attention slightly more to the right-hand side for non-lateralized maze stimuli, despite the normative sVGC model predicting that participants should not lateralize their attention for these stimuli (Figure 3c). These results may speak to potential asymmetries in lateralization, but given the exploratory nature of these analyses, they should be verified and replicated in future work.

      (4) Individual differences:

      Individual differences in attentional modulation are a strength of the work, but similar analyses exploring individual variation in lateralization effects could provide further insight, and the lack of such analyses may mask important effects.

      Thank you for this suggestion. In new analyses, we explored whether i) participants exhibited differences in their tendency to lateralize their awareness reports, and ii) whether the degree to which they tended to lateralize their awareness predicted their performance on a separate set of maze stimuli. In short, we observed substantial variation in participants’ tendency to lateralize their awareness (Figure S11) and found that this tendency reflected an inter-individual difference which was stable across maze types. We report these new findings on pages 14-16.

      “Inter-individual variation in lateralization of attention

      Next, we investigated participants’ tendency to pay attention to obstacles within a single hemifield (left vs right) regardless of the sVGC model predictions. To do so, we computed an awareness lateralization index (ALI) based on participants’ self-reported awareness reports of obstacles on each trial (Figure 3a). Large positive values indicate that participants were preferentially aware of the right hemifield, whereas negative values indicate preferential awareness of the left hemifield. Values close to zero indicate that participants paid attention to both hemifields equally (see Methods for details). We observed that participants’ tendency to lateralize their awareness varied greatly across the Ho datasets 1 and 2 (Figure 3b); some participants preferentially paid attention to a single hemifield, regardless of whether the sVGC model predictions were lateralized. For the dSC1 dataset, we observed that on some trials, participants significantly lateralized their awareness (|ALI| > 0.5; Figure 3c) even though the sVGC model predictions were non-lateralized. These findings suggest that participants’ tendency to pay attention to a single hemifield may represent an observable inter-individual difference in how they allocate their awareness to form task construals.”

      “To further explore these inter-individual differences, we tested whether participants’ tendencies to lateralize their attention to a single hemifield was consistent across trials and maze stimuli. We observed that participants’ tendency to lateralize their attention to a single hemifield was similar for left and right lateralized maze stimuli (Spearman ⍴= 0.72, Figure 3d). This suggests that participants who preferentially attended to a single hemifield did so regardless of which hemifield they should attend to. More consequentially, the tendency for participants to lateralize their awareness on maze stimuli whose model predictions were also lateralized linearly correlated with participants’ tendency to lateralize their attention on non-lateralized maze stimuli (Spearman ⍴= 0.88, Figure 3d). Taken together, these findings emphasize that some individuals tend to preferentially attend to a single hemifield when planning. This tendency, importantly, represents an inter-individual difference in how participants allocate their attention across various maze types.”

      (5) Distinction between overt and covert attention:

      The current report at times equates eye movement patterns with the locus of attention. However, attention can be covertly shifted without corresponding gaze changes (see, for example, Pooresmaeili & Roelfsema, 2014).

      We fully agree, and thank the reviewer for prompting further reflection on this distinction. In the online experiments run by Ho and colleagues (i.e., datasets Ho1 and Ho2), participants’ eye movements were not tracked, and therefore, they could not disambiguate whether participants were engaging in covert or overt attention to sample maze obstacles. In our third experiment (i.e., dataset dSC1), we both recorded eye movements and explicitly instructed participants to fixate centrally while viewing the maze. This ensured that participants oriented their attention only covertly during planning (see Figure S13-14).

      We now elaborate on this important distinction in the Results section of the manuscript, page 12:

      “In addition, we monitored participants’ eye movements in dataset dSC 1 to ensure that attention shifts would be covert as opposed to overt—a distinction which could not be determined in the online samples of datasets Ho 1 and 2.”

      On page 28:

      “Importantly, while the visuospatial attention effects observed in the Ho 1 and 2 datasets are likely driven by both covert and overt shifts in attention, the findings presented in experiment 3 (i.e., dSC1 dataset) rule out the contribution of overt shifts in attention through the use of eye tracking (see Figure S13-14)(Carrasco, 2011; Pooresmaeili & Roelfsema, 2014).”

      The implications for interpreting the relationship between eye movement, memory, and attention in this setting are not fully addressed. The potential dynamics of attention along a maze trajectory and their impact on lateralization analysis would benefit from further clarification.

      We thank the reviewer for urging more clarity here. The attentional dynamics we document in our study concern how people perceive / construe the maze itself, rather than how they deploy their attention to guide active navigation. We have now sought to make this distinction clear at a number of points in the paper. The core idea is that attention acts as an early filter to select which obstacles are part of a task construal, which then affects both awareness and memory.

      We have now clarified the focus of our study in the introduction on pages 5-7:

      “Our focus in this study was to examine how participants perceive and represent their environment (the maze stimulus). This is a distinct process to how participants orient their attention during navigation itself, which is not part of our current study. To do so, we harness classical signatures of attentional selection to characterise how visuospatial attention shapes awareness of maze obstacles during planning.” … “Our focus in the present study was to examine attentional effects on participants’ perception of the maze stimulus. We did not quantify how individuals deploy their attention in the phase in which they were navigating through the maze.”

      We did not explicitly test for memory effects in our new experiments, but Ho and colleagues demonstrated that the sVGC model predicted not only awareness reports, but also participants’ memory of obstacles (see Ho et al., 2022). Indeed, task representations computed from memory or awareness reports were strikingly similar in their experiments (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness). In relation to eye movements, we refer the reviewer back to our previous response, which details how eye movements were measured and controlled during maze construal.

      Figure 1 legend (b) --> (c)

      We have corrected this typo in the figure caption.

      Reviewer #2 (Public review):

      Summary:

      Castanheira et al. investigate the role of spatial attention for planning during three maze navigation experiments (one new experiment and two existing datasets). Effective planning in complex situations requires the construction of simplified representations of the task at hand. The authors find that these mental representations (as assessed by conscious awareness) of a given stimulus are influenced by (spatially) surrounding stimuli. Individual participants varied in the degree to which attention influenced their task representations, and this attentional effect correlated with the sparsity of representations (as measured by the range of awareness reports across all stimuli). Spatially grouping taskrelevant information on either the left or right side of the maze led to mental representations more similar to optimal representations predicted by the valueguided construal (VGC) model - a normative model describing a theoretical approach to simplifying complex task information. Finally, the authors propose an update to this model, incorporating an attentional spotlight component; the revised descriptive model predicts empirical task representations better than the original (normative) VGC model.

      Strengths:

      The novelty of this study lies in the proposal and investigation of a cognitive mechanism through which a normative model like value-guided construal can enable human planning. After proposing attention as this mechanism, the authors make concrete hypotheses about mismatches between the VGC predictions and real human behavior, which are experimentally validated. Thus, not only does this study describe a possible mechanism for simplification of task information for planning, but the authors also propose a descriptive model, revising VGC to incorporate this attentional component.

      A strength of this paper is the variety of investigative approaches: analysis of existing data, novel experiment, and a computational approach to predict experimental findings from a theoretical model. Analyzing pre-existing datasets increases the size of the participant cohort and strengthens the authors' conclusions. Meanwhile, comparing the predictions of the existing normative model and the authors' own refined model is a clever approach to substantiate their claims. In addition, the authors describe several crucial controls, which are key to the interpretability of their results. In particular, the eye tracking results were critical.

      In summary, this paper constitutes an important step toward a more complete understanding of the human ability to plan.

      We thank the Reviewer for their thoughtful and positive assessment of our findings. We also appreciate the constructive feedback on our methodology, which we believe has substantially improved our manuscript.

      Weaknesses:

      (1) There is a critical conceptual gap in the study and its interpretation, mainly due to the reliance on a self-report metric of awareness (rather than an objective measure of behavioral performance).

      a. Awareness is tested by a 9-point self-report scale. It is currently unclear why awareness of task-irrelevant obstacles in this task would necessarily compromise optimal planning. There is no indication of whether self-reported awareness affects performance (e.g., navigation path distance, time to complete the maze, number of errors). Such behavioral evidence of planning would be more compelling.

      We thank the reviewer for prompting further reflection on the connection between construal and navigation performance. We wish to emphasise that the primary focus of our study was on measuring and modeling participants’ task construals using perceptual awareness judgments, building on the methods developed by Ho and colleagues, rather than on navigation performance itself. However, as the reviewer points out, there is a natural relationship between construal and performance – if you represent the wrong obstacles, plans may be disrupted.

      To explore the relationship between task construals and performance on the navigation task we first regressed out the effects of the sVGC model on participants’ awareness reports and computed the mean squared residuals for each trial. We then used these values to predict participants’ navigation response times on each trial. We observed a significant negative relationship, suggesting that on trials where participants’ representations showed greater deviations from the normative model, they were in fact faster at navigating the mazes. This relationship was surprising, and at odds with the initial idea that adhering to normative VGC aids in task performance. However, we think that this direction of effect may make sense if one considers that a large part of the actual construal (rather than the normative prediction) in our data was in fact driven by effects such as lateralisation which are not accounted for by the sVGC model. If one is faster at harnessing inductive biases such as lateralisation, then one may be faster to complete the maze but also show a greater deviation from the predictions of the original model.

      To further explore these effects, we next focused on the distinction between lateralised and non-lateralised mazes. Here, we reasoned that the initial phase of lateralised attentional selection would lead to lateralised mazes being easier to navigate than nonlateralised ones. We conducted new analyses to determine whether participants navigated lateralized maze stimuli faster and with fewer moves than maze stimuli with non-lateralized model predictions. As detailed in Methods, we excluded trials in which participants significantly deviated from the optimal number of moves (9 or more moves) and took longer than 20 seconds to solve the maze. In line with our interpretation that attention operates as an inductive bias, participants were faster and deviated less from the optimal path on lateralized compared to non-lateralized mazes.

      We now report these new results on navigation performance on pages 20-21:

      “Maze navigation performance

      The previous analyses focused on participants’ task representations during planning. We next sought to explore links between participants’ task representations and maze navigation performance. Participants performed the maze navigation task near-ceiling: they solved 95% of maze stimuli in under 20 seconds, with minimal deviation from the optimal path (i.e., 9 moves or fewer). Notwithstanding this limited variance in task performance, we explored whether participants’ task construals may have impacted their navigation speed. To do so, we first regressed out the effects of the sVGC model from participants’ awareness reports and used the mean squared residuals for each trial to predict response times (see Methods for details). Surprisingly, we observed a negative relationship between mean squared residual variance and response times (β = -0.31, SE = 0.05, 95% CI [-0.41, -0.21], p < 0.001), indicating that participants were faster on trials where the sVGC model explained less variance in their awareness reports. In other words, trials in which participants deviated more from the sVGC model predictions were solved faster. We note that one reason for this may be the strong influence of the lateralisation effect on navigation performance (see paragraph below), which itself is not part of the sVGC model prediction.”

      “We then explored whether participant performance differed between lateralised and nonlateralised mazes. Here, we reasoned that the initial phase of lateralised attentional selection would lead to lateralised mazes being easier to navigate than non-lateralised ones. Consistent with this hypothesis, participants were faster (β = -0.04, SE = 5.91*10<sup>3</sup>, 95% CI [-0.06, -0.03], p< 0.001) and followed the optimal path more closely (β = -0.59, SE = 0.09, 95% CI [-0.78, -0.40], p< 0.001) when maze stimuli were more lateralized.”

      And in the Discussion section, on page 23:

      “Mental representations and task performance

      We observed that participants were faster and deviated less from the optimal path on maze stimuli that were lateralized. This effect is not predicted by the original sVGC model but dovetails with the interpretation that early visuospatial attention operates as an inductive bias to guide the formation of simplified task representations. Surprisingly, we also observed that participants were faster to navigate mazes on trials where their simplified task representation deviated from the sVGC model prediction. We interpret this seemingly contradictory finding in the following way: there are several factors beyond the sVGC model – including, for instance, maze lateralisation – that predict both construal and performance on the maze navigation task. Further work is needed to understand how inductive biases such as lateralisation shape both construal and performance, and the real-world benefits that such strategies might afford for naturalistic stimuli.”

      b. Relatedly, it would have been more convincing to have an objective measure of awareness, for instance, how the presence or absence of a "task-irrelevant" obstacle affects performance (e.g., change navigation path distance or time to complete the maze), or whether participants can accurately recall the location of obstacles.

      We thank the reviewer for prompting further reflection on the validity and robustness of our awareness measures. We emphasise however that our focus is not (primarily) on maze navigation performance, but on task construal, which as noted in our previous response may come apart from navigation performance for a variety of reasons. Our primary goal is to measure participants’ subjective awareness of the maze as a marker of their idiosyncratic (conscious) mental representation on each trial. In doing so, we build on a rich tradition of measuring subjective awareness in consciousness and perception science (for instance, work using the Perceptual Awareness Scale, or detection judgments). In this sense, we think our awareness scale (following Ho et al.) represents a valid and straightforward way of assessing our target psychological construct. However, we also agree with the Reviewer that convergent evidence from other measures is always valuable. In Ho and colleagues’ original paper, they developed a variant of the maze task where participants had to recall the location of obstacles, as well as rate their awareness (Exp 3) and a variant in which participants could hover their mouse over hidden obstacles in the maze to reveal their location – an online metric of attentional deployment (Exp 4). These data afforded us the opportunity to validate the awareness reports against an objective measure of recall, as suggested by the Reviewer. In reanalysing these data, we observed that the obstacle awareness and memory/hover measures were strikingly correlated within two independent samples of participants (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness; ⍴ = 0.76 between the probability of hovering over the obstacle and awareness; ⍴ = 0.65 between the duration of the mouse hovering and awareness). These re-analyses are now reported on page 22 of our manuscript, to highlight the convergent validity of the awareness metric:

      “Finally, we examined the convergent validity of participants’ awareness reports by reanalyzing the memory recall data reported in Ho and colleagues’ experiment(Ho et al., 2022). We reasoned that participants should demonstrate similar task representations regardless of the measure used to probe the construal. In line with this prediction, we observed that the obstacle awareness reports and memory/hover measures were strikingly correlated within three independent samples of participants (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness; ⍴ = 0.76 between the probability of hovering over the obstacle and awareness; ⍴ = 0.65 between the duration of the mouse hovering and awareness; see Tables S18 and S19).”

      c. Consequently, I'm not sure that we can conclude that the spatial context does impact participants' ability to plan spatial navigation or to "incorporate taskrelevant information into their construal". We know that the spatial context affects subjective (self-reported) awareness, but the authors do not present evidence that spatial context affects behavioral performance.

      Following the line of argument above, we think it’s important to separate out task construal (the simplified representation of the maze, measured by awareness reports), and the impact of this on navigation and other aspects of behaviour. The awareness reports (and other convergent measures) show that task-relevant information (as predicted by the VGC) is incorporated into the construal, a process which is modulated by spatial context. These are the key targets of our modeling. Whether this impacts performance is a distinct question, and one that we now address in our response to point a above.

      d. Another concern that may complicate interpretation is the following: Figure 3c shows improved VGC model predictions (steeper slope) for mazes with greater lateralization. However, there are notable outliers in these plots, where a high lateralization index does not correspond to good model performance. There is currently no discussion/explanation of these cases.

      The Reviewer astutely points out some outliers in our analysis. While on average lateralized maze stimuli are represented more closely to the sVGC model, there are indeed some noticeable outlier mazes. These mazes represent stimuli in which participants tended to lateralize their attention to the ‘wrong hemifield’—e.g., participants were more aware of obstacles in the right hemifield despite sVGC model predicting that obstacles on the left hemifield were task-relevant. We believe this explains the poor sVGC model fits on these trials. We note, however, that on average participants were capable of attending to the correct hemifield without explicit instructions (i.e., 9 out of 12 mazes).

      We have now included a discussion of these outliers in the results section of the paper on page 12:

      “We note that for three maze stimuli whose model predictions were lateralized there was nevertheless a poor fit to the sVGC model (see Figure 2c, right panel). These outliers correspond to maze stimuli where participants, on average, lateralized their attention to the incorrect hemifield (i.e., the opposite hemifield to that predicted by the sVGC model).”

      (2) I noticed an issue with clarity regarding task-relevance. It is currently not fully clear which obstacles are "task irrelevant". Also, the term is used inconsistently, sometimes conflating with "awareness". For example, in the "Attentional spotlight model of task representations" section, the authors state that "taskrelevant information becomes less relevant when surrounded by task-irrelevant information". But they really mean that participants become less aware of those task-relevant obstacles. I assume task-relevance is an objective characteristic related to maze organization, not to a participant's construal. Indeed, the following paragraph provides evidence of model predictions of awareness.

      We apologize for any confusion regarding the terminology of our manuscript. We indeed use the terms task-relevant and task-irrelevant to refer to obstacles that are objectively predicted by the normative sVGC model or the attentional spotlight model to be included in (>0.5) or excluded from (<0.5) task construals, respectively. This designation reflects the predictions from the computational model and does not reflect participants’ reported awareness. We then ran linear hierarchical models to predict participants’ awareness reports from these model predictions. The Reviewer is correct that the task-relevance of obstacles is indeed related to the maze’s organization, and not related to participants’ subjective reports of awareness. We have now clarified this point throughout the manuscript to better emphasize the difference between the model predictions of taskrelevance and participants’ subjective reports.

      On page 17:

      “To achieve this, we computed the predictions of the existing VGC model for each obstacle’s task relevance in a given maze, and averaged these predictions within an attentional spotlight of 3 squares (Figure 4a & S8, see Methods for details). This process yielded novel model predictions, whereby some obstacles which were once predicted as task-irrelevant by the normative sVGC are now predicted as task-relevant by the attentional spotlight model. We depict the effects of this spatial spotlight in Figure 4a: task-irrelevant stimuli (plotted in grey; see middle left obstacle) neighbouring taskrelevant obstacles (plotted in orange) become more task-relevant, whereas taskrelevant information becomes less relevant when surrounded by task-irrelevant information (see bottom right orange obstacle). This deviation in model predictions from the normative sVGC model was used to predict participants’ awareness reports. We hypothesized that this spotlight-VGC model would predict participants’ reports better than the original VGC model, which does not account for spatial attention.”

      (3) The behavioral paradigm has some distinct disadvantages, and the validity of the task is not backed up by behavioral data.

      a. I understand the need for central fixation, but it also makes the task less naturalistic.

      The fixation cross was required on every trial such that participants could maintain central fixation for our eye tracking experiment. While this design is less naturalistic, it allows us to examine the eye movements of participants. Requiring participants to fixate during the ‘planning’ phase of the experiment allowed us to isolate the effects of covert attention from changes in awareness due to overt shifts in attention. In other words, differences in participants’ awareness reports in the 3rd experiment cannot be explained by longer fixation times to specific obstacles.

      b. The task with its top-down grid view does not seem to mimic real human navigation. Though this grid may be similar to mental maps we form for navigation, the sensory stimuli corresponding to possible paths and to spatial context during real-life navigation are very different.

      We agree with the reviewer that while our task is engaging for participants and simple to follow, it does not mimic naturalistic navigation in humans. There is a natural tension in computational / experimental work in cognitive science in wanting to build closely on previous results and paradigms, while ensuring that results can generalise to real-world contexts. Here, our choice of paradigm and measures was closely built on previous papers using this task from Ho and colleagues (2022, 2023). While preparing this response, we learnt that the MIT group had also harnessed this same task to develop a novel dynamic variant of the VGC model (Chen et al., 2026) called the Just in Time model (JIT). The advantage of building on this prior work is that we are able to iteratively refine and expand the VGC approach, and (in our case) bring it into closer contact with work on modeling the deployment of spatial attention in human vision. The top-down aspect of the maze notably facilitated the study of the spatial deployment of attention. We now discuss the novel dynamic variant of the VGC model in our paper on page 27:

      “We close by reflecting on opportunities for further work in this area. First, an important next step is to explore the process by which task representations are formed, and how inductive biases might affect the process of task construal. The sVGC model is a normative model of the optimal task representation. Since it’s construction involves an exhaustive calculation over possible paths, it is not a plausible basis for a model of the psychological process by which participants actually construct task representations. More recently a process model of task construal has been proposed, the Just in Time model (JIT). The hypothesis of the JIT model is that participants’ task representations are built up over time by iteratively simulating possible paths through the maze, affording insight into the construal process (Chen et al., 2026). In future work, it would be of interest to ask whether the attentional effects we observe in our experiments could be meshed with a dynamic JIT account of construal. We speculate that visuospatial attention may operate as an early filter, limiting the space of potential construals based on coarse spatial features of the environment, constraining a dynamic selection of obstacles. Brain imaging techniques with high time resolution, such as M/EEG, may be able to shed further light on how task representations are formed as participants plan.”

      c. Behavioral performance is not reported, so it is unknown whether participants are able to properly complete the task. The task seems pretty difficult to navigate, especially when the obstacles disappear, and in combination with the central fixation.

      Behavioural performance is now reported in response to point 1a above.

      d. There is no discussion of whether/how this navigation task generalizes to other forms of planning.

      We fully agree that an important next step would be to generalise our results on construal to naturalistic forms of planning – for instance, using immersive VR mazes, and or investigating cognitive rather than perceptual construals. We have now added a line to this effect to the Discussion on page 28.

      “An important next step to further our understanding of task representations would be to extend the current paradigm to other forms of planning and more naturalistic tasks, such as navigating immersive virtual reality (VR) environments, planning over cognitive rather than perceptual representations (e.g. planning over an abstract space), or internallyguided planning based on working memory.”

      Reviewer #2 (Recommendations for the authors):

      (1) There are, of course, benefits to simple tasks like the ones described, but it would be interesting to compare the results to a possible experiment in which a top-down grid/map is used for planning, but then task execution is carried out in a simulated environment corresponding to the map. Also, perhaps beyond the scope of the questions addressed in this paper, but I am curious how unexpected obstacles affect representations. For instance, if participants plan based on a topdown map and then begin "real" navigation but encounter an unexpected obstacle that was not indicated on the map, does this modulate representations/awareness of future obstacles (near vs. far)?

      We fully agree that all of these lines of investigation would be super interesting to pursue in future studies, and we have added a line to the discussion to that effect on page 28:

      “An important next step to further our understanding of task representations would be to extend the current paradigm to other forms of planning and more naturalistic tasks, such as navigating immersive virtual reality (VR) environments, planning over cognitive rather than perceptual representations (e.g.. planning over an abstract space), or internallyguided planning based on working memory.”

      (2) Regarding self-reported awareness as a metric, an additional experiment could ask participants to recreate the maze (identify locations of obstacles after they disappear). This would be a more objective measure of awareness.

      Yes indeed, and as described above, this was a metric used by Ho and colleagues in their previous experiment. As we describe in more detail above, the task representations obtained via memory or awareness reports demonstrated striking similarity (⍴ = 0.86).

      (3) What is meant by "all possible orientations of the maze" in this Methods sentence: "For dataset dSC 1, participants solved each of these 24 mazes four times (i.e., all possible orientations of the maze)"?

      We thank the Reviewer for prompting more clarity here. We vertically and horizontally reversed mazes (i.e., left-right flipped) such that participants could not predict the location of the goal or start location. In this way, each maze stimulus had four potential orientations. This resulted in 96 trials of 24 unique mazes. We have clarified this point in the Methods section on page 30:

      Maze stimuli were vertically and horizontally reversed (i.e., left-right flipped) such that participants could not predict the location of the start or goal location. This resulted in four potential orientations of each maze across all 24 mazes, 96 trials in total.

      (4) For lateralization, it was unclear until reading the Methods that the lateralization index was calculated using the VGC-predicted level of taskrelevance. From the main text and Figure 2, I assumed you were just counting the number of task-relevant obstacles on each side, rather than also quantifying relevance. I understood after reading the Methods, but this could be clarified further.

      We agree with the Reviewer that this was not evident from the text. We have now updated the Results section of the manuscript to clarify this point on page 11:

      “To test this hypothesis, we derived a measure of task-relevant lateralization inspired by the attention literature (Ghafari et al., 2024; Keefe & Störmer, 2021; Vollebregt et al., 2015) (Figure 2a). Specifically, we separated maze stimuli across the vertical meridian and computed the ratio of task-relevant information presented on the left versus right side derived from the sVGC model. For example, the maze shown in Figure 2a has twice the amount of task-relevant information presented in the left hemifield than in the right (lat. Index= 1/3). A lateralization index of 0.0 indicates that both hemifields contain equal amounts of task-relevant information (i.e., non-lateralized). The lateralization index was computed using the continuous VGC predictions for each obstacle (see Methods).”

      (5) The explanation in the Methods of how the width of the attentional spotlight was chosen references Figure 1b and Supplementary Figure S2, but it seems that Supplementary Figure S8 explains this more in the caption. Also, I don't see how Figure S2 supports this.

      We apologize for this typo. The explanation of how we selected the width of the attentional spotlight should indeed reference supplemental Figure 15 (previously Figure S8). We have now corrected this and elaborated on this choice in the Methods section on page 35:

      “We fixed the ‘width’ of the attentional spotlight to a distance of 3 squares based on the observation that the two neighbouring obstacles positively predicted the awareness of a probe. We observed that the mean and median distance between neighbouring obstacles of the 2nd rank (i.e., second closest) was 3 squares away for all mazes (Figure S15). We therefore opted to fix the value of the attention spotlight to 3 squares based on these observations. Future work utilizing this model should consider the statistics of their maze stimuli when deciding on the ‘width’ of the attentional spotlight.”

      (6) The attentional spotlight width was assumed to be 3 squares, based on the linear regression predictions of the effect of neighboring obstacles on stimulus awareness. Given the individual differences across participants, it would be interesting to choose a different attentional spotlight size for each participant. Would a participant-specific attentional spotlight width improve the predictions of the spotlight-VGC model?

      The Reviewer highlights a very interesting question: do individuals vary in terms of their attentional spotlight? To test this hypothesis, we first estimated the size of the attentional spotlight for each individual based on lateralized maze stimuli, and then used this to generate personalized attentional spotlight model predictions for each subject based on these values (Figure S11). We restricted this analysis to the dSC1 dataset, where we had substantially more trials (96 in total).

      In brief, we observed that indeed the personalized spotlight model fit participants’ awareness reports better than both a normative sVGC model and a group-level attentional spotlight model. We interpret these findings with some caution as i) a subset of individuals had flat attentional slopes and therefore were excluded from these analyses, and ii) we believe we require additional trials to ensure a robust model fit at the individual level. While our results are encouraging, we hope future investigations into inter-individual differences will extend these findings.

      We have included these additional analyses in the main text.

      On page 18:

      “To further explore inter-individual differences in task construal, we tested whether adjusting the attentional spotlight width to each participant’s awareness reports improved the predictions of the attentional spotlight model. To do so, we first determined the width attentional spotlight of each individual in the dSC1 dataset based on lateralized maze stimuli. We then generated person-specific attentional spotlight model predictions for the non-lateralized maze stimuli to avoid overfitting the data (Figure S11). We note that 7 participants had either flat attentional slopes or negative beta coefficients, which prevented the selection of an appropriate attentional spotlight width (see Methods for details). We observed a significant improvement in model fit for the person-specific attentional spotlight model relative to both the group-level attentional spotlight model (ΔBIC= -1487.39) and the normative sVGC model (ΔBIC= -1655.29). While the limited trial numbers per participant in our current dataset warrants caution in interpreting these findings, these findings do encourage further research on inter-individual differences in attentional deployment during planning.”

      On pages 23-24:

      “Inter-individual differences in attention

      We also observed considerable inter-individual differences in attentional effects across participants (Figure 1c). While some participants were strongly influenced by the spatial context of neighbouring stimuli, others showed more limited evidence for an attentional effect (Figure 1b). Inter-individual differences in attention predicted the sparsity of participants’ simplified representations: participants with larger attention effects exhibited sparser representations. Moreover, these inter-individual differences in effects of spatial proximity could be incorporated into the attentional spotlight model by varying the width of the spotlight, resulting in better model predictions.”

      “Beyond these spatial proximity effects, we also observed that participants varied in their tendency to lateralize their attention to a single hemifield (Figure 3). This tendency was observed across all three datasets, including on maze stimuli whose value-guided model predictions were not lateralized. This suggests that although a strategy of allocating attention is sub-optimal for these maze stimuli, some individuals preferentially attend to a single hemifield in a heuristic-like fashion. This tendency to attend to a single hemifield was a robust inter-individual difference across maze stimuli (Figure 3d), and dovetails with individual-level variation in spatial proximity effects. Taken together, these findings offer novel insights into how people vary in the ways they allocate spatial attention to solve complex problems. Future research could explore how these individual differences constrain performance on other tasks that require planning and search in highdimensional spaces.”

      On page 17 of the Supplemental Materials:

      (7) The supplementary text about lateralization effects, above Supplementary Table S8, references Table S6, but it is Table S6 does not seem to display lateralization results.

      We thank the Reviewer for pointing out this typo: we now refer to the correct supplementary table (S9).

      (8) Why does it matter that "the maze stimuli were not designed to test horizontalmeridian lateralization effects"? What is the effect on power? Is it because there is not a good enough range in lateralization indices? It would be good to clarify, or just remove that explanation, since the cortical retinotopy explanation seems more convincing.

      We did not specifically design the maze stimuli such that there is an equal number of obstacles above and below the horizontal meridian. As such, the lateralization index derived along the horizontal meridian does not control for the number of obstacles in each hemifield, which may influence participants’ awareness reports. In contrast, we designed maze stimuli such that this would not be a concern for the vertical meridian. We have clarified this point in the discussion on page 27.

      “Third, while we observed clear lateralization effects along the vertical meridian (i.e., left vs right hemifield), effects along the horizontal meridian were less clear (i.e., above vs below; see Table S15-16). One potential explanation of this asymmetry is the retinotopic organization of the cortex, in which spatially adjacent stimuli can be retinotopically distant if presented on the opposite side of the vertical (but not horizontal) meridian, facilitating distractor inhibition. Importantly, while the visuospatial attention effects observed in the Ho 1 and 2 datasets are likely driven by both covert and overt shifts in attention, the findings presented in experiment 3 (i.e., dSC1 dataset) rule out the contribution of overt shifts in attention through the use of eye tracking (see Figure S13-14)(Carrasco, 2011; Pooresmaeili & Roelfsema, 2014).”

      (9) For Figure 2c, it would be helpful to directly state what each dot and line mean.

      We updated the caption of Figure 2c to clarify what we are plotting: each point represents an obstacle, and each line the linear fit for a maze stimulus.

      “Each point represents an obstacle in a maze, and each line represents the model fit for that specific maze stimulus.”

      (10) Figures and wording imply there is only a single probe obstacle per trial, but methods and model imply that participants are asked to report awareness for every obstacle. This should be clarified.

      We apologize for any confusion regarding the methodology of our study. The Reviewer is correct that participants reported their awareness of every obstacle presented on a given trial. We have clarified this in the Results section of the manuscript on page 7:

      “Note, participants reported their awareness of every obstacle presented on a given trial.”

      We have also updated the caption of Figure 1 to clarify this point:

      “Once participants finished navigating the maze, they were asked to report their awareness of every obstacle presented on a given trial in a random order.”

      (11) What is the reason for the exclusion of participants (33 for experiment 1 and 26 for experiment 2)?

      Participants were excluded from the Ho et al. datasets 1 and 2 based on their preregistered exclusion criteria, as detailed in the Methods section of their paper. In short, trials were excluded if participants took longer than 20 seconds to complete the trial, or if they spent longer than 5 seconds in the initial state. Participants were excluded if less than 80% of trials remained after reaction time exclusions or if they failed 2 out of 3 comprehension checks. We have elaborated on this point in the Methods section on page 31.

      “Participants were excluded from analyses based on pre-registered exclusion criteria as detailed in (Ho et al., 2022). In short, participants were excluded if 20% or more of their trials were removed based on reaction times, or if they failed 2 out of 3 comprehension checks.”

      (12) The supplemental figures are not referenced in order, and some are not referenced at all; this should be fixed.

      We thank the Reviewer for pointing this out and have reorganized our Supplementary materials accordingly.

      Reviewer #3 (Public review):

      Summary:

      The authors build on a recent computational model of planning, the "value-guided construal" framework by Ho et al. (2022), which proposes that people plan by constructing simple models of a task, such as by attending to a subset of obstacles in a maze. They analyze both published experimental data and new experimental data from a task in which participants report attention to objects in mazes. The authors find that attention to objects is affected by spatial proximity to other objects (i.e., attentional overspill) as well as whether relevant objects are lateralized to the same hemifield. To account for these results, the authors propose a "spotlight-VGC" model, in which, after calculating attention scores based on the original VGC model, attention to objects is enhanced based on distance. They find that this model better explains participant responses when objects are lateralized to different hemifields. These results demonstrate complex interactions between filtering of task-relevant information and more classical signatures of attentional selection.

      Strengths:

      (1) The paper builds on existing modeling work in a novel manner and integrates classic results on attention into the computational framework.

      (2) The authors report new and extensive analyses of existing data that shed light on additional sources of systematic variability in responses related to attentional spillover effects

      (3) They collect new data using new stimuli in the original paradigm that directly test predictions related to the lateralization of task-relevant information, including eye tracking data that allows them to control for possible confounds.

      (4) The extended model (spotlight-VGC) provides a formal account of these new results.

      We thank the Reviewer for their positive assessment of our manuscript and their insightful comments, which has improved the clarity of our findings.

      Weaknesses:

      (1) The spotlight-VGC model has a free parameter - the "width" of the attentional spotlight. This seems to have been fixed to be 3 squares. It would be good if the authors could describe a more principled procedure for selecting the width so that others can use the model in other contexts.

      Our choice for this parameter was informed by the spatial effects reported in Figure 1b. We observed that the two closest neighbouring obstacles to a probe had similar awareness (i.e., positive beta weights). We therefore compute the mean and median distances between obstacle pairs that were the second closest obstacle to a probe. This distance was 3 squares away, as depicted in Figure S15. We fixed the width of the attentional spotlight across all studies based on this observation. We agree that future research utilizing this model may need to tune this hyperparameter depending on the mean distance between a probe and its neighbours.

      We have clarified this point in the methods section on page 35:

      “We fixed the ‘width’ of the attentional spotlight to a distance of 3 squares based on the observation that the two neighbouring obstacles positively predicted the awareness of a probe. We observed that the mean and median distance between neighbouring obstacles of the 2nd rank (i.e., second closest) was 3 squares away for all mazes (Figure S15). We therefore opted to fix the value of the attention spotlight to 3 squares based on these observations. Future work utilizing this model should consider the statistics of their maze stimuli when deciding on the ‘width’ of the attentional spotlight.”

      Following the suggestion of Reviewer 2 point 6, we now also explored inter-individual differences in this parameter. To do so, we first used the lateralized mazes in the dSC1 dataset to determine the optimal width of the attentional spotlight for each individual.

      Then, we used this spotlight to derive model predictions for each person. We observed that these personalized attentional spotlight model predictions fit participants’ awareness reports on non-lateralized mazes better than the fixed-width spotlight model. We believe this preliminary result suggests the importance of modelling inter-individual differences in attentional deployment during planning. We report these effects on page 17.

      (2) Have the authors considered other ways in which factors such as attentional spillover and lateralization could be incorporated into the model? The spotlightVGC model, as presented, involves first computing VGC predictions and only afterwards computing spillover. This seems psychologically implausible, since it supposes that the "optimal" representation is first formed and then it gets corrupted. Is there a way to integrate these biases directly into the VGC framework, perhaps as a prior on construals? The authors gesture towards this when they talk about "inductive biases", but this is not formalized.

      We thank the reviewer for bringing up this very important point. We think that a full computational treatment of the inductive bias would be a distinct project, but now seek to expand our discussion on the mechanisms by which representations could be formed. In this context, we specifically highlight novel computational work from the MIT group that was published as a preprint in the time since we submitted our paper, and which proposes a new process account of construal, the “Just in Time” (JIT) model. We also elaborate on a possible mechanism by which visuospatial attention may aid the dynamics of the construal process. In short, we agree with the reviewer that spatial attention may bias individuals to search over a subset of potential representations based on low-level spatial characteristics of the obstacles (e.g., their spatial spread in the visual field), prior to (or in concert with) a dynamic JIT-like selection process. We now elaborate on these possibilities on pages 27-28:

      “We close by reflecting on opportunities for further work in this area. First, an important next step is to explore the process by which task representations are formed, and how inductive biases might affect the process of task construal. The sVGC model is a normative model of the optimal task representation. Since it’s construction involves an exhaustive calculation over possible paths, it is not a plausible basis for a model of the psychological process by which participants actually construct task representations. More recently a process model of task construal has been proposed, the Just in Time model (JIT). The hypothesis of the JIT model is that participants’ task representations are built up over time by iteratively simulating possible paths through the maze, affording insight into the construal process (Chen et al., 2026). In future work, it would be of interest to ask whether the attentional effects we observe in our experiments could be meshed with a dynamic JIT account of construal. We speculate that visuospatial attention may operate as an early filter, limiting the space of potential construals based on coarse spatial features of the environment, constraining a dynamic selection of obstacles. Brain imaging techniques with high time resolution, such as M/EEG, may be able to shed further light on how task representations are formed as participants plan.”

      […]

      “Fourth, it will also be necessary to elaborate on how bottom-up and top-down aspects of attentional selection are combined to guide complex task representations and plans. Foundational questions remain unanswered, for instance: can multiple spatial locations be preferentially selected at once, i.e. are there multiple spotlights (Awh & Pashler, 2000; McMains & Somers, 2004; Pylyshyn & Storm, 1988; Shaw & Shaw, 1977)? There is also discourse on how spatial attention may move from one location to another: are the intervening visual regions between attended locations similarly selected (Dubois et al., 2009; Kr & Np, 1999; McMains & Somers, 2004, 2005)? Our findings tentatively suggest that individuals are able to attend to disparate spatial regions to form sparse task representations, yet there is substantial variability in how individuals orient their attention during the task. The present paradigm and computational modelling, in conjunction with carefully designed stimuli, may help resolve these outstanding questions.”

      (3) Can the authors rule out that the lateralization effects are the result of memory biases since the main measure used is a self-report of attention?

      We thank the reviewer for bringing up this important point. In our experiments, we sought to measure participants’ subjective awareness of the maze stimuli as a readout of their conscious task representation on each trial. This approach marries an extensive literature on measures of perceptual awareness in consciousness science (e.g., using the Perceptual Awareness Scale) with computational models of planning. Participants’ memory of (their awareness of) the obstacles is inherent to this approach, but just as with similar approaches in consciousness science (e.g. measures of iconic memory in the Sperling paradigm), we think it provides a reasonably “online” measure of awareness. It’s important of course to ensure that results obtained with awareness reports are not idiosyncratic, and generalise to other approaches to quantifying task representations.

      To further bolster the convergent validity of our awareness measure, we reanalyzed the data from Ho and colleagues. In their original paper, they developed a variant of the maze-navigation task where participants were asked to recall the location of obstacles as well as report their awareness (Exp 3) and a third variant of the task where participants could hover their cursors over hidden obstacles to reveal their locations (Exp 4). These data allowed us to validate the awareness reports against objective measures of recall and mouse-tracking data. We observed that the subjective awareness reports of participants were strikingly correlated with recall/hover measures across two independent samples of participants (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness; ⍴ = 0.76 between the probability of hovering over the obstacle and awareness; ⍴ = 0.65 between the duration of the mouse hovering and awareness). We believe these findings validate participants’ awareness reports. These findings are now reported on page 22 of the manuscript.

      “Finally, we examined the convergent validity of participants’ awareness reports by reanalyzing the memory recall data reported in Ho and colleagues’ experiment (Ho et al., 2022). We reasoned that participants should demonstrate similar task representations regardless of the measure used to probe the construal. In line with this prediction, we observed that the obstacle awareness reports and memory/hover measures were strikingly correlated within three independent samples of participants (Spearman ⍴ = 0.86 between memory accuracy and awareness; ⍴ = 0.86 between confidence in memory and awareness; ⍴ = 0.76 between the probability of hovering over the obstacle and awareness; ⍴ = 0.65 between the duration of the mouse hovering and awareness; see Tables S18 and S19).”

    1. Author response:

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

      Reviewer #1 (Public review)

      Summary:

      In this manuscript the authors derive a mean-field model for a network of Hodgkin-Huxley neurons retaining the equations for ion exchange between the intracellular and extracellular space.

      The mean-field model derived in this work relies on approximations and heuristic arguments that, on the one hand, allow a closed-form derivation of the mean-field equations, and on the other hand restrict its validity to a limited regime of activity corresponding to quasi-synchronous neuronal populations. Therefore, rather than an exact mean-field representation, the model provides a description of a mesoscopic population of connected neurons driven by ion exchange dynamics.

      Strengths:

      The idea of deriving a mean-field model which relates the slow-timescale biophysical mechanism of ion exchange and transportation in the brain to the fast-timescale electrical activities of large neuronal ensembles.

      Weaknesses:

      The idea underlying this work is not completely implemented in practice.

      The derived mean field model do not show a one-to-one correspondence with the neural network simulations, except in strongly synchronous regimes. The agreement with the in vitro experiment is hardly evident, both for the mean-field model and for the network model. The assumptions made to derive the closed-form equations of the mean field model have not been justified by any biological reason, they just allow for the mathematical derivation. The final form of the mean-field equations do not clarify whether or not microscopic variables are used together with macroscopic variables in an inconsistent mixture.

      Comments on revisions:

      The main weaknesses I listed in the first report are still present, since the authors did not answer my questions on a solid basis. I report the list for completeness:

      (1) It seems that the reduction methodology that is employed is not the most suitable one for the single-neuron model they are considering.

      (2) The formulation of the mean-field derivation is unnecessarily complicated. It could be heavily simplified by following previously published approaches to derive biologically realistic neural masses.

      (3) The model seems to work only for highly synchronized situations and not for the standard asynchronous evolution usually observed in neural circuits.

      Therefore, my statement remains unchanged.

      Reviewer #2 (Public review)

      Summary:

      The authors aiming in developing a neural mass model characterized by few collective variables mimicking the dynamics of a network of Hodgkin - Huxley neurons encompassing ion-exchange mechanisms. They describe in details the derivation of the mean-field model , then they compare experimental results obtained for the hippocampus of a mice with the neural network simulations and the mean-field results. Furthermore, they report a bifurcation analysis of the developed model and simulation of a small network containing various coupled neural masses, somehow moving towards the simulation of an entire connectome.

      Strengths:

      The author attempts to develop a mean-field model for a globally coupled network of heterogeneous Hodgkin-Huxley neurons with explicit ion exchange mechanism between the cell interior and exterior.

      Weaknesses:

      (1) They do not employ the reduction methodology more suited for the single neuron model they consider.

      (2) Their derivation of the neural mass model is based on several assumptions, and not all well justified.

      (3) Their formulation of the mean-field derivation is unnecessary complicated, it can be strongly simplified by following previously published approaches to derive biologically realistic neural masses.

      (4) Their model seems to work only for highly synchronized situations and not for the standard asynchronous evolution usually observed in neural circuits.

      General Statements:

      The authors honestly declared the many limitations of their approach, once assumed this the results of the mean-field are somehow inconsistent with the neural network simulations as expected.

      The authors suggest to employ this model for the simulations on the whole connectome to follow seizure propagation, however I believe that a simpler model, as the Epileptor, remains superior in this respect to this model. That indeed includes biophysical parameters but their correspondence with the ones employed in the network dynamics remain elusive, due to the many assumptions required to derive this mean field model. Furthermore it is more complicated than the Epileptor, I do not think that the present model will be largely employed by the community.

      Comments on revisions:

      The authors have corrected mistakes present in the manuscript and put a correct list of references.

      However, they refuse

      (1) To simplify the formulation of the model, the model contains unnecessary complications, as I have clearly written in my report, the authors agree, but they do not want to change the formulation;

      (2) To derive the mean field model in a simpler way, as possible, and as I asked many times in my Referee report, this would help the readers to understand the important aspect of the derivation, without not needed and confusing complicated formulations;

      (3) To compare direct simulations of the network with neural mass results in sub-section "Bifurcation analysis: emergent network states and multistability" to show bistability, as I asked.

      As a matter of fact the performed modifications do not solve my previous doubts on the validity of the results reported in the manuscript.

      Therefore, my previous assessments remain valid.

      We thank the editors and the two reviewers for their continued engagement with our manuscript. The three weaknesses retained from the first round are essentially identical between the two public reviews:

      (i) The reduction methodology is not the most suitable for the single-neuron model we consider;

      (ii) The mean-field derivation is unnecessarily complicated;

      (iii) The model works only in highly synchronous regimes and does not reproduce the asynchronous evolution typical of neural circuits.

      Both reviewers explicitly note that their assessments remain unchanged and we have decided not to alter the formulation of the model. We use this response to state—on the public record—exactly where we agree with the reviewers, where we disagree, and why.

      On point (i): the reduction methodology.

      We fully agree with the reviewers' technical observation: the Ott–Antonsen / Lorentzian-ansatz reduction in the form introduced by Montbrió, Pazó and Roxin (2015) is exact for canonical Type I neurons (QIF), whose membrane-potential equation is quadratic, and is not directly applicable to a Type II / Hodgkin–Huxley-type neuron whose voltage dynamics is cubic-like. On this point there is no disagreement.

      Where we differ is in the conclusion the reviewers draw from this observation. The reviewers read our work as applying an inappropriate reduction methodology to an inappropriate neuron model. We instead positioned our work, from the outset, as an extension of that methodology: we keep the biophysically detailed Hodgkin–Huxley substrate (because it is the only level at which extracellular ion concentrations, depolarization block, bursting and seizure-like events are biophysically grounded), and we adapt the reduction by approximating the cubic voltage nullcline as a piece-wise quadratic with two parabolas of opposite curvature. This is explicitly an approximate, not exact, mean-field. The Lorentzian ansatz is then applied on each branch of the piece-wise quadratic, with the limitations of this construction analyzed in the manuscript.

      The reviewers' alternative—starting from a Type I canonical model and grafting on biophysical features—would indeed yield an exact mean-field, but it would forfeit precisely what motivates our work: a tractable mesoscopic description in which the slow variables are physiologically interpretable ion concentrations rather than phenomenological parameters. The trade-off is that we give up exact rigour in order to construct a bridge between the Montbrió-style next-generation neural mass models on one side and the Epileptor on the other, with the additional benefit that the parameters of the resulting neural mass retain a biophysical correspondence (e.g., [K<sup>+</sup>]_bath, Δ[K<sup>+</sup>]_int, [K<sup>+</sup>]_g, the gating variable n) that the Epileptor does not afford.

      We therefore respectfully maintain our position: the methodology is not "the wrong reduction for a Type II neuron"; it is an extended reduction designed to be applicable beyond the Type I case, with explicitly characterized validity.

      On point (ii): the formulation is unnecessarily complicated.

      We agree with the reviewers that, given the assumptions we ultimately adopt, namely that the gating variable n and the potassium concentrations Δ[K<sup>+</sup>]_int and [K<sup>+</sup>]_g are treated as collective (mesoscopic) variables shared by the population, with n a function of the average membrane potential, the closed neural mass equations could be reached by the more direct path used by Guerreiro et al. (2022) and the related literature (R1–R7). In the revised manuscript we now state this explicitly, and we note that the same five-dimensional system arises under either derivation.

      Our choice to follow Chen and Campbell (2022) is motivated by the fact that it makes each approximation visible at the point where it is invoked. In particular, it exposes the moment-closure step (Eq. 19), the vanishing-flux boundary condition (Eq. 28), and the locations where microscopic and mesoscopic variables enter the description. We believe that for a reader trying to extend our framework, for instance to a setting with partial heterogeneity in the slow variables, or with stochastic gating, this is the more useful presentation. We have added a remark stating that the simpler Guerreiro-type derivation reaches the same equations under our assumptions, so that readers can take whichever route they find clearer.

      On point (iii): the model only works in highly synchronous regimes.

      Here we partially agree and partially disagree, and we would like the partial disagreement to appear on the public record.

      We agree that the Lorentzian ansatz is, strictly, valid in regimes where the population's membrane potential distribution is unimodal, that is, when essentially all neurons sit on the same side of the threshold V*. Where we disagree is with the implication that the mean-field model fails outside the strongly synchronous regime. The supplementary analysis in Fig. S2, added in the previous round, quantifies the error introduced by the first-moment approximation of n as a collective variable across the full range of [K<sup>+</sup>]_bath values, spanning quiescent, bursting, seizure-like, sustained ictal and depolarization-block dynamics. The fraction of neurons whose gating variable deviates from the population mean is below 2% for the parameters used throughout the manuscript, and the error becomes appreciable only during the brief transitions between sub- and supra-threshold states. These are precisely the moments at which the population is genuinely bimodal and the single-Lorentzian assumption is theoretically expected to leak. In other words, the error peaks coincide with the moments where our derivation tells us in advance that the assumption is locally invalid; the model "knows where it fails." Away from these transitions, the mean-field tracks the population average across all dynamical regimes shown in Fig. 3, not only in the most strongly synchronized ones.

      This is, in our view, the strongest argument we can make: we are not claiming exactness, and we are not unaware of the limitations. We have characterized them analytically (the construction of the piece-wise Lorentzian, and the theoretical reason a closed solution exists only when the two branches collapse onto one), and we have characterized them numerically (Fig. S2). The deviations are bounded, their location in parameter space is well identified, and they coincide with transitions where the underlying assumption is locally violated. We believe this constitutes a controlled approximation rather than an uncontrolled one, and we would like this distinction to be visible to readers of the Reviewed Preprint.

      We note, in this connection, that the reviewers' preferred reference point, the next-generation neural mass model of Montbrió et al. (2015), which is exact and one-to-one with its underlying network, is exact precisely because the underlying network is a network of QIF neurons. The corresponding statement for a network of Hodgkin–Huxley-type neurons with explicit ion exchange does not, to our knowledge, exist in closed form, and may not exist at all. The relevant question is therefore not whether our model matches the exactness of the QIF case, but whether the controlled approximation we provide is useful. Given the qualitative agreement with neural-network simulations across the full range of [K<sup>+</sup>]_bath, the qualitative agreement with the in vitro recordings, and the recovery of the expected bifurcation structure with new emergent regimes, we believe the answer is yes.

      Other outstanding points in the review.

      Reviewer 2 reiterates the view that the Epileptor remains superior for whole-connectome seizure-propagation simulations because it is simpler and better characterized. We do not dispute that the Epileptor is more thoroughly analyzed and more parsimonious. The complementarity we propose is not a replacement but a parameter-grounding, as the Epileptor's phenomenological parameters (excitability, slow permittivity) acquire, in the present framework, an interpretation in terms of measurable biophysical quantities (extracellular potassium, intracellular potassium variation, glial buffering).

      We thank the reviewers and editors once again for their careful reading, and we are grateful that the points of disagreement have been sharpened to a state where readers can judge them transparently.


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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, the authors derive a mean-field model for a network of Hodgkin-Huxley neurons retaining the equations for ion exchange between the intracellular and extracellular space.

      The mean-field model derived in this work relies on approximations and heuristic arguments that, on the one hand, allow a closed-form derivation of the mean-field equations, and on the other hand restrict its validity to a limited regime of activity corresponding to quasi-synchronous neuronal populations. Therefore, rather than an exact mean-field representation, the model provides a description of a mesoscopic population of connected neurons driven by ion exchange dynamics.

      We agree with the reviewer's characterization. Our manuscript describes the derivation as relying on "approximations and heuristic arguments" and states that "the derivation is not exact"; what we provide is a controlled, approximate mesoscopic description in which the slow variables are physiologically interpretable ion concentrations rather than phenomenological parameters. An exact closed-form thermodynamic limit is, to our knowledge, available only for canonical Type I (QIF) networks (Montbrió, Pazó and Roxin, 2015) and a few of their extensions; it is not currently known for a Hodgkin–Huxley-type network with explicit ion-exchange dynamics. We acknowledge that the original description of the regime of validity may have caused confusion on this point, and in the revised manuscript we have therefore replaced the looser formulation "strongly synchronous regimes" by the more accurate "regimes where the membrane-potential distribution is unimodal and can be reasonably approximated by a Lorentzian" throughout the manuscript.

      Strengths:

      The idea of deriving a mean-field model that relates the slow-timescale biophysical mechanism of ion exchange and transportation in the brain to the fast-timescale electrical activities of large neuronal ensembles.

      We thank the reviewer for recognizing the motivation behind our work. This explicit coupling between slow biophysical ion dynamics and fast electrical activity is precisely the feature we tried to preserve in the reduction, even at the cost of giving up exactness.

      Weaknesses:

      The idea underlying this work is not completely implemented in practice.

      We address this general statement through the four specific sub-points the reviewer raises in the paragraph that follows.

      The derived mean field model does not show a one-to-one correspondence with the neural network simulations, except in strongly synchronous regimes.

      We partially agree and partially disagree. We agree that the Lorentzian ansatz is strictly valid where the membrane-potential distribution is unimodal, i.e. when essentially all neurons sit on the same side of the threshold V*. We disagree with the implication that the mean-field fails outside this regime. To make this claim quantitative, we added a new supplementary figure (Fig. S2) that quantifies the deviation of individual neurons' gating variables from the population mean across the full range of [K<sup>+</sup>]_bath values—quiescent, bursting, seizure-like, sustained ictal and depolarization-block dynamics. The fraction of deviating neurons is below 2% for the parameters used in the manuscript, with localized peaks only during the brief, genuinely bimodal transitions between sub- and supra-threshold states—precisely the moments at which the theory predicts the assumption to be locally invalid. Away from these transitions, the mean-field tracks the population average across all dynamical regimes shown in Fig. 3, not only in the strongly synchronized ones.

      The agreement with the in vitro experiment is hardly evident, both for the mean-field model and for the network model.

      We acknowledge that the experimental and simulated traces in the original Fig. 4 did not match quantitatively; this was never our intention. The figure and its caption have been reorganized in the revised manuscript to frame the comparison as qualitative: we aim to demonstrate the shared structure i.e., the slow modulation of fast population activity by extracellular potassium fluctuations, rather than to claim a quantitative fit.

      We also added two clarifications that account for the residual differences: (i) the network simulations were intentionally run with rescaled biophysical parameters (membrane capacitance, gating time constants) to keep the computational cost feasible, a standard practice when the goal is to validate dynamical mechanisms rather than absolute timescales; (ii) the in vitro LFP recordings were AC-coupled, so the slow DC components visible in the mean-field traces are filtered out at acquisition.

      The assumptions made to derive the closed-form equations of the mean-field model have not been justified by any biological reason, they just allow for the mathematical derivation.

      We agree that the modelling assumptions were scattered through the original derivation. In the revised manuscript, the three core assumptions are stated explicitly at the point of derivation: (i) the gating variable n is treated as a collective, population-averaged variable; (ii) the potassium concentrations Δ[K<sup>+</sup>]_int and [K<sup>+</sup>]_g are homogeneous across the population, biophysically justified by the rapid redistribution of ions through diffusion and electrochemical gradients, which enforces near-instantaneous equilibration at the mesoscopic scale; (iii) no heterogeneity is assumed at the level of ion dynamics. The meaning of "locally homogeneous" is now defined explicitly.

      On the biophysical motivation of the in vitro perturbation used in the experiment, we have added a new Methods subsection that explains how low extracellular Mg<sup>2+</sup> unblocks NMDARs and abolishes the divalent-cation stabilisation of the resting membrane potential, depolarising hippocampal neurons and increasing the driving force for outward K<sup>+</sup> currents. This provides a biophysical link between the experimental perturbation and the model's main control parameter, the extracellular potassium concentration. We also added a reference to the well-established model of epileptic discharges that underpins the experiment.

      The final form of the mean-field equations does not clarify whether or not microscopic variables are used together with macroscopic variables in an inconsistent mixture.

      We now explicitly acknowledge that in the spiking-network simulations the gating variable n is microscopic (each neuron has its own n_i), whereas in the mean-field derivation it is treated as mesoscopic and shared by the population. This asymmetry between modalities is discussed both in the Results and in the Limitations sections, and is identified as a likely source of some of the discrepancy between the two modalities.

      We have also made the notation in Eqs. (36)–(37) consistent (firing rate r used throughout, full current-based dV/dt̄ restored) and fixed the typos and broken equation/reference labels that contributed to the impression of inconsistency (Eqs. 18, 28, 29; the Fig. 2(c) [K<sup>+</sup>] bath label; the lost reference at line 696).

      Reviewer #2 (Public review):

      Summary:

      The authors aim to develop a neural mass model characterized by a few collective variables mimicking the dynamics of a network of Hodgkin – Huxley neurons encompassing ion-exchange mechanisms. They describe in detail the derivation of the mean-field model, then they compare experimental results obtained for the hippocampus of a mouse with the neural network simulations and the mean-field results. Furthermore, they report a bifurcation analysis of the developed model and simulation of a small network containing various coupled neural masses, somehow moving towards the simulation of an entire connectome.

      We thank the reviewer for the accurate summary of the manuscript's structure and aims.

      Strengths:

      The author attempts to develop a mean-field model for a globally coupled network of heterogeneous Hodgkin-Huxley neurons with an explicit ion exchange mechanism between the cell interior and exterior.

      We thank the reviewer for recognizing this objective. The retention of Hodgkin–Huxley dynamics with explicit ion exchange is precisely the feature that distinguishes our framework from QIF-based reductions, and it is what enables the slow variables of the resulting mean-field to retain a direct biophysical interpretation.

      Weaknesses:

      (1) It seems that the reduction methodology that is employed is not the most suitable one for the single-neuron model they are considering.

      We agree, on technical grounds, with the observation: the Ott–Antonsen / Lorentzian-ansatz reduction is exact for canonical Type I neurons (QIF) and is not directly applicable to a Type II Hodgkin–Huxley-type neuron with a cubic-like voltage nullcline. Where we differ is in the conclusion. We did not apply an inappropriate reduction to an inappropriate neuron; we deliberately extended the methodology by approximating the cubic nullcline as a piece-wise quadratic with two parabolas of opposite curvature, and then applying the Lorentzian ansatz on each branch. The result is an explicitly approximate, biophysically grounded mean-field, with its regime of validity stated and quantified (Fig. S2).

      To make this positioning explicit, we have added a paragraph to the Introduction that situates our work within the next-generation neural mass literature (Byrne et al. 2020; Montbrió, Pazó & Roxin 2015; Guerreiro et al. 2022; Forrester et al. 2024; Perl et al. 2023; Gerster et al. 2021; and works on short-term plasticity, adaptation, conductance-based reductions,

      spike-timing-dependent plasticity, random connectivity and noise) and clarifies that we see our contribution as complementary to these approaches, not as a competitor to the exact QIF reductions.

      (2) The authors' derivation of the neural mass model is based on several assumptions, and not all well justified.

      We agree that, in the original submission, the modelling assumptions were scattered through the derivation. In the revised manuscript, the three core assumptions are stated explicitly at the point of derivation: (i) the gating variable n is treated as a collective population-averaged variable; (ii) the potassium concentrations Δ[K<sup>+</sup>]_int and [K<sup>+</sup>]_g are homogeneous across the population, biophysically justified by the rapid redistribution of ions through diffusion and electrochemical gradients, which enforces near-instantaneous equilibration at the mesoscopic scale; (iii) no heterogeneity at the level of ion dynamics is assumed. The meaning of "locally homogeneous" is now defined explicitly. In addition, we have added Fig. S2, which quantifies numerically the error introduced by the moment-closure assumption (deviation below 2% for the parameters used in the manuscript).

      (3) The formulation of the mean-field derivation is unnecessarily complicated. It could be heavily simplified by following previously published approaches to derive biologically realistic neural masses.

      We agree that, under the assumptions ultimately adopted in our model—namely that n, Δ[K<sup>+</sup>]_int and [K<sup>+</sup>]_g are mesoscopic—the final five-dimensional system can be reached by the more direct path used by Guerreiro et al. (2022) and the related literature. We now state this explicitly in the revised manuscript and note that the same system arises under either derivation, so that the reader can take whichever route they find clearer. Our choice to retain the Chen and Campbell (2022) formalism is pedagogical: it exposes the moment-closure step (Eq. 19), the vanishing-flux boundary condition (Eq. 28), and the locations where microscopic versus mesoscopic variables enter the description, which is the more useful presentation for a reader wishing to extend the framework (e.g. to partial heterogeneity in the slow variables or to stochastic gating). We also made the notation in Eqs. (36)–(37) consistent (firing rate r used throughout, full current-based dV/dt̄ restored) and fixed a number of typos and broken equation/reference labels.

      (4) The model seems to work only for highly synchronized situations and not for the standard asynchronous evolution usually observed in neural circuits.

      We partially agree and partially disagree. We agree that the Lorentzian ansatz is strictly valid where the membrane-potential distribution is unimodal; we have replaced "strongly synchronous regimes" by this more accurate formulation throughout the manuscript. We disagree, however, with the implication that the mean-field is useful only in those regimes. Fig. S2, added in this revision, explicitly quantifies the deviation across all dynamical regimes (quiescent, bursting, seizure-like, sustained ictal and depolarization-block dynamics): it remains below 2% for the parameters used in the manuscript, with localized peaks only during the brief sub-to-supra-threshold transitions where the population is genuinely bimodal. Away from these transitions, the mean-field tracks the population average across all dynamical regimes shown in Fig. 3.

      General Statements:

      The authors honestly declared the many limitations of their approach. It is assumed that the results of the mean-field are somehow inconsistent with the neural network simulations as expected.

      We thank the reviewer for acknowledging that the limitations are honestly declared. As detailed above and quantified in Fig. S2, the deviation from the network simulations is bounded and well characterized; it is not assumed but measured.

      The authors suggest employing this model for the simulations on the whole connectome to follow seizure propagation, however, I believe that the Epileptor remains superior in this respect to this model. That indeed includes biophysical parameters but their correspondence with the ones employed in the network dynamics remains elusive, due to the many assumptions required to derive this mean-field model. Furthermore, it is more complicated than the Epileptor, I do not think that the present model will be largely employed by the community.

      We do not propose our model as a direct replacement for the Epileptor and we do not dispute that the Epileptor is more thoroughly analyzed and more parsimonious. The complementarity we propose is not a replacement but a parameter-grounding: the Epileptor's phenomenological parameters (excitability, slow permittivity) acquire, in our framework, a concrete interpretation in terms of measurable biophysical variables (extracellular potassium, intracellular potassium variation, glial buffering). Retaining the Hodgkin–Huxley substrate is essential to ground these variables biophysically.

      To make this complementarity more visible, the Limitations and Discussion section has been expanded to discuss the choice of a purely excitatory network as a first step (with excitatory–inhibitory generalizations available via the synaptic reversal potential) and to point to additional biological ingredients (calcium and other ions, plastic synapses, random connectivity and noise, adaptation, spike-timing-dependent plasticity) that the framework can accommodate, with reference to the next-generation neural mass literature.

      We thank the reviewers and editors for their careful reading. We hope this public response makes our reasoning, the limits of our approach, and the concrete revisions made in this round transparent.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In general, the writing is scattered. Every time a model is introduced, one starts from the general formulation only to find that a very simplified case is used with respect to that formulation, which is very confusing. Authors need to reduce unnecessary formulations that confuse the reader and make it clear which formulations are actually used.

      We thank the reviewer for this comment and understand the concern regarding the balance between general formulations and specific approximations. Our intention in including the more general equations and derivations (e.g., Eq. 7 and others) was pedagogical — to ensure completeness and transparency in the modeling steps, especially for readers less familiar with mean-field reductions of biophysically detailed models. These general forms also serve to clarify the assumptions underlying the simplifications we employ. In the latest version, we improved the clarity of core equations (e.g., Eq. 37), which form the basis of all simulations presented (see details below, in the answer to question 14).

      (2) The Introduction would benefit from a wider view of the literature. The literature on exact mean field models (i.e. derived from the Lorentzian Ansatz) has flourished in the last years. In particular, it would be worth considering the following papers, where exact neural mass models are applied to perform whole-brain and large-scale brain simulations:

      Forrester, M., Petros, S., Cattell, O., Lai, Y. M., O'Dea, R. D., Sotiropoulos, S., & Coombes, S. (2024). Whole brain functional connectivity: Insights from next generation neural mass modelling incorporating electrical synapses. PLOS Computational Biology, 20(12), e1012647.

      Perl, Y. S., Zamora-Lopez, G., Montbrio, E., Monge-Asensio, M., Vohryzek, J., Fittipaldi, S.,

      Campo, C. G., Moguilner, S., Ibanez, A., Tagliazucchi, E., Yeo, B. T. T., Kringelbach, M. L., & Deco, G. (2023). The impact of regional heterogeneity in whole-brain dynamics in the presence of oscillations. Network Neuroscience, 7(2), 632-660.

      Byrne, Aine, James Ross, Rachel Nicks, and Stephen Coombes. "Mean-field models for EEG/MEG: from oscillations to waves." Brain topography 35, no. 1 (2022): 36-53.

      Gerster, M., Taher, H., Skoch, A., Hlinka, J., Guye, M., Bartolomei, F.,... & Olmi, S. (2021). Patient-specific network connectivity combined with a next generation neural mass model to test clinical hypothesis of seizure propagation. Frontiers in Systems Neuroscience, 15, 675272.

      Byrne, Aine, Reuben D. O'Dea, Michael Forrester, James Ross, and Stephen Coombes. "Next-generation neural mass and field modeling." Journal of neurophysiology 123, no. 2 (2020): 726-742.

      Benitez-Stulz, Sophie, Samy Castro, Gregory Dumont, Boris Gutkin, and Demian Battaglia. "Compensating functional connectivity changes due to structural connectivity damage via modifications of local dynamics." bioRxiv (2024): 2024-05.

      We have added the following paragraph:

      “Recently, a class of these models, called next-generation neural mass models [42], has been developed based on an analytical approach introduced by [25] that allowed for the exact derivation of mean field parameters for a population of quadratic integrate-and-fire (QIF) neurons. These can be linked to EEG/MEG oscillations [43], including epipeltic seizures [43], and have been used to study various aspects of the whole-brain dynamics such as the low-dimensional manifold of the resting state [45,46], aging [47] and neural signatures of consciousness [48].”

      We have also modified the preceding paragraph of the introduction that now reads:

      “At the mesoscopic level, the observable properties of a neuronal ensemble are generally explained by statistical physics formalism of mean-field theory [19-22]. Mean-field models demonstrated a predictive value for studying the mesoscopic dynamics of neuronal populations [23], providing statistical descriptions of neuronal networks [2, 19, 24-29], which can be used to address questions related to network-level mechanisms [12, 24, 30].

      In general, neural mass models have a low enough number of parameters to be tractable and provide general intuitions regarding mechanisms underlying complex neuronal activity [31-36]. For example, statistical population measures, such as the firing rate, can be used to assess mesoscopic dynamics [1, 7, 31, 36-41].”

      (3) Moreover, conductance-based models have been already implemented in neural mass models not only in references [69, 71, 95], but also in:

      Guerreiro, I. C., Di Volo, M., & Gutkin, B. (2023). A new generation of reduction methods for networks of neurons with complex dynamic phenotypes.

      Capone, C., Di Volo, M., Romagnoni, A., Mattia, M., & Destexhe, A. (2019). State-dependent mean-field formalism to model different activity states in conductance-based networks of spiking neurons. Physical Review E, 100(6), 062413.

      We have added the following sentence:

      “Moreover, conductance-based couplings between the spiking neurons have been already implemented in neural mass models [58, 59, 91, 93, 121], but without an extracellular exchange mechanism.”

      (4) Sec. 1.1 As previously established in the literature, a system of all-to-all coupled neuronal equations can be solved exactly in the thermodynamic limit (i.e., infinite neurons limit) if the single neuron membrane potential equation is a quadratic function and if the instantaneous distribution of membrane potentials of neurons in a population is described by a Lorentzian [Montbrió, E., Pazó, D. & Roxin, A. Physical Review X 5 (2), 021028 (2015)]. This means that the thermodynamic limit can be performed for a Canonical Type I model like the quadratic integrate-and-fire.

      What is the biological justification and the reason to approximate a different neuron type (a type II neuron model), whose membrane potential equation resembles a cubic function, with a quadratic function? The fact that it can be solved in the quadratic approximation is not, in my opinion, a sufficient justification. It would be more correct to start from a type I neuron at the microscopic level with a quadratic function and then provide additional biological features.

      We thank the reviewer for raising this important point. We respectfully disagree with the notion that starting from a canonical Type I model (such as the quadratic integrate-and-fire neuron) would be a more biologically grounded approach. While the quadratic form is analytically convenient, it does not capture certain key features of neuronal excitability particularly those related to bursting, seizure-like events, and depolarization block which are closely tied to the cubic-like nullcline geometry arising in Hodgkin–Huxley-type models, especially in the presence of slow ion dynamics.

      Our work seeks to bridge biophysical realism with analytical tractability. The step-wise quadratic approximation we employ is specifically designed to mimic the cubic membrane potential profile that emerges from the full ion-exchange dynamics. While the Lorentzian Ansatz is not strictly justified in this case from first principles, we show that it yields a workable and biologically interpretable mean-field description, which aligns with single-neuron dynamics, population simulations, and even in vitro observations. To our knowledge, this is a novel contribution that extends mean-field modeling beyond currently available approaches, which are often restricted to simplified or phenomenological neuron models.

      In this context, using a quadratic approximation is not merely a mathematical convenience — it is a means to retain key dynamical features of more realistic (non-Type I) neurons within a tractable framework, enabling insights into complex behaviors like multistability and pathological bursting.

      (5) Sec. 1.2 As shown in Figure 3, the mean-field equations do not show a one-to-one correspondence with the neural network simulations, except in strongly synchronous regimes. This represents a strong limitation in the model, especially because exact neural mass models (as shown in Reference [23]) perfectly fit the dynamics of the underlying network model both in the asynchronous and in the synchronized regime.

      We appreciate the reviewer’s observation and acknowledge that our original description may have caused confusion. The model's validity is not strictly limited to strongly synchronous regimes, but rather to regimes where the distribution of membrane potentials across the neuronal population remains unimodal and can be reasonably approximated by a Lorentzian. This includes but is not restricted to—highly synchronized states.

      We agree that this distinction is important and have clarified it in the revised manuscript (e.g., “in strongly synchronous regimes” —> “in regimes where the membrane potentials' distribution is unimodal and can be reasonably approximated by a Lorentzian”).

      In contrast to exact mean-field reductions based on quadratic integrate-and-fire neurons (e.g., [23]), our model originates from a biophysically grounded HH-type neuron with ion exchange dynamics, and necessarily involves heuristic approximations to achieve a closed-form mean-field description. While this results in a less exact correspondence with network simulations in more heterogeneous or bimodal states, our goal was to retain biological interpretability and account for phenomena such as ion-driven bursting and seizure-like transitions, which are not captured by standard QIF-based neural masses.

      We see our contribution as complementary to existing exact reductions — offering a biophysically grounded alternative that remains tractable and informative in a relevant class of unimodal, mesoscopic dynamical regimes.

      (6) Sec. 1.3 In this section the authors show the comparison between in vitro experiments and simulations with both the network model and the neural mass model (Figure 4, panels a,b,c). The qualitative agreement that is supposed to be shown is hardly evident. The shape of the signals is different as is the type of bursting. The only agreement results in the fact that there are repeated spiking events at successive times in a periodic manner. However, the time scale of the simulations is different for neural network simulation and mean-field experiment, making it difficult to compare them. While the period of the bursting event is around 2 min for mean field simulation (in according with experiments), the time scale of the network simulation is 60 times smaller, thus meaning that we are considering completely different mechanisms and phenomena. The justification given by the authors, that "the parameters were modified to simulate shorter fluctuations (in the network of Hodgkin-Huxley neurons) for computational efficiency" is inappropriate.

      The poor agreement turns out to be even worse in the comparison between experiments and mean-field simulations shown in panels d and e of Figure 4. While the mean field simulation is characterized by a periodic behaviour both in the mean membrane potential and in the external potassium concentration, the in-vitro traces are not periodic and show an increasing irregular activity of the extracellular LFP in correspondence with increasing external potassium concentration.

      How it is possible to justify the implementation of this model if the working hypotheses are not supported by the results? The worst agreement of the network simulations with the experiments reinforces the doubt raised in the previous point: what is the reasoning underlying the choice of Hodgkin-Huxley as a single neuron model?

      We thank the reviewer for this detailed critique. We acknowledge that the comparisons in Figure 4 involve limitations and we now provide a clearer rationale and context in the revised manuscript. First, we emphasize that our intention is not to claim a quantitative match between the experimental and simulated traces, but rather to demonstrate that our model grounded in biophysical mechanisms such as ion exchange is capable of qualitatively reproducing a key feature observed experimentally: the slow modulation of neuronal activity by extracellular potassium concentration. For example, both in vitro (Fig. 4a, 4d) and in our simulations (Fig. 4b, 4e), bursts of activity ride on slower oscillations of potassium, and the interplay of fast and slow dynamics is central to both.

      Regarding the discrepancy in timescales between the neural network and mean-field simulations: the network simulations were intentionally run with accelerated dynamics by rescaling biophysical parameters (e.g., membrane capacitance and gating time constants) to keep the computational cost feasible. We now clarify in the manuscript that this choice is standard practice in computational modeling when the primary goal is to validate dynamical mechanisms rather than replicate absolute timescales.

      On the shape of LFP signals: the experimental recordings were AC-coupled, and the DC components associated with slower shifts in membrane potential such as those modeled in the mean-field simulations are not captured in those recordings. This limits the visibility of key features like the underlying potential jumps. Additionally, no claim is made regarding a specific bursting classification in either data or simulation.

      We agree that the experimental trace in Fig. 4d shows more complex, non-periodic dynamics (e.g., slowing burst frequency and irregularity), which are not captured by our current deterministic model. These differences could plausibly arise from additional physiological processes (e.g., stochastic transitions between metastable regimes or variability in ion regulation) that are not modeled here. In future work, such phenomena may be captured by introducing noise or parameter variability (see, e.g., Saggio et al., A taxonomy of seizure dynamotypes , elife 2020), or by allowing the parabola coefficients in the nullcline approximation to vary dynamically.

      Finally, regarding the choice of a Hodgkin–Huxley-type neuron: this model allows us to incorporate a biophysical description of ion exchange, which is central to the phenomena we study. While modeling the spiking mechanisms explicitly precludes certain mathematical simplifications available to very simplified neuron models with reset, it enables direct links between mesoscopic dynamics and measurable quantities such as extracellular potassium an essential objective of our work. To summarize, we rearranged Fig4:

      Potassium can have periodic behavior with V bursting riding on top (Fig.4 a). The model also shows this behavior at different timescales (Fig. b,c,e).

      AC LFP recording is filtered so we might not see the V jump during the bursts (because we do not have DC recordings). No claim about bursting class here.

      Potassium can also have more complex behavior (e.g., slowing down of burst frequency Fig.4.d), that the deterministic model do not show, but maybe exploring dynamical parameters (e.g., from parabolas or K_bath) or with added noise allowing to jump between regimes (reference Saggio et al. eLife 2020).

      (7) Sec. 1.5 Here six neural masses are coupled via long-range structural connections with random weights. Simulations of the system are shown for two different values of the global coupling parameter (G = 0 and G = 100). How many realisations of the network have been considered?

      We thank the reviewer for pointing this out. The presented simulation was intended as a proof-of-concept demonstration to illustrate the model’s capacity to support network-level propagation of pathological activity. For this purpose, we considered a single representative realization of the structural connectivity with random weights. Given the deterministic nature of the model and the qualitative focus of the demonstration, additional realizations do not qualitatively change the observed behavior — namely, the transition from localized to network-wide bursting as coupling strength increases. We have now clarified this in the revised manuscript.

      “This simulation serves as a proof of concept to illustrate how local pathological activity can propagate through a network depending on the strength of coupling. We used a single representative realization of randomly weighted structural connectivity. While we did not perform a systematic exploration of different realizations or coupling strengths, we observed that the qualitative behavior namely, the emergence of network-wide bursting beyond a critical coupling threshold remains robust across similar setups. The model is compatible with empirical connectome data and can be readily extended to simulations using realistic brain network architectures.”

      In future applications involving data-driven network architectures or variability analyses, we agree that exploring multiple realizations or empirical connectomes will be valuable.

      How do the results depend on the different choices of the random weights? What is the dependence of the emergent dynamics on G? What kind of dynamics can be observed varying smoothly the parameter G (e.g. from 0 to 100)?

      This section serves as a proof of concept to show that pathological activity in one node can propagate through the network when coupling is strong. We used a single random weight configuration and did not systematically explore variations in G or connectivity. While richer dynamics likely emerge across intermediate values of G, a full parameter sweep is beyond the scope of this study. We clarify this in the revised text (see answer above).

      (8) Sec. 2.1 In the description of the experiment it is mentioned that only Mg^{2+} is varied. What is the role played by Mg^{2+} variation in influencing the external potassium concentration variation? How the experiment can be linked to the model? How the hypothesis of introducing an equation for the potassium concentration current in the microscopic model is supported by the experiment and vice-versa?

      We thank the reviewer for this question. We have added a new subsection in the Methods explaining the.agnesium removal as a mean to influence the external potassium dynamics:

      “The membrane of hippocampal neurons is equipped with N-methyl-D-aspartate type glutamate receptors (NMDARs). These receptors have a very high affinity for glutamate and can, in principle, be activated by ambient glutamate present at low concentrations in the brain extracellular fluid (ECF). Under normal physiological conditions, this activation does not occur because extracellular magnesium ions (Mg<sup>2+</sup>) block the NMDAR channel at membrane potentials more negative than about –50 mV; this voltage-dependent block prevents receptor activation at rest. When extracellular magnesium is removed, the block is relieved, allowing NMDARs to be activated, leading to neuronal depolarization toward the action potential threshold [117].”

      “In addition, as a divalent cation, Mg<sup>2+</sup> interacts with the negatively charged neuronal membrane, contributing to the stabilization of the resting membrane potential. Lowering extracellular magnesium concentration disrupts this effect, resulting in membrane depolarization [118].”

      “Consequently, magnesium removal not only facilitates NMDAR-dependent depolarization, but also directly depolarizes neurons. This depolarization increases the driving force for outward potassium currents through K<sup>+</sup> channels, meaning that variations in Mg<sup>2+</sup> can indirectly influence external potassium dynamics during neuronal activity.”

      (9) Sec. 2.6 The modified version of the continuity equation has been derived following Reference [95], where the authors consider a network of Izhikevich neurons, and each neuron is modelled by a two-dimensional system consisting of a quadratic integrate and fire equation plus an equation that implements spike frequency adaptation. In particular, in [95] the authors achieve a closed set of mean-field equations with the inclusion of the mean-field dynamics of the adaptation variable by using a Lorentzian ansatz combined with the moment closure approach. The moment closure condition is also assumed in the present manuscript (Eq. 19). Under which assumptions is the implementation of the moment closure condition justified?

      We are thankful to the reviewer (and also to the R2) for pointing out to the validity of the justification of the assumptions that we have used in our formalism. We hence agree that the moment closure is not a sufficient justification for assuming that V depends on the mean n, which is neccessary for the derivation of Eq. 20, but in addition we need the assumption that n can be treated as a collective variable as it is done in the works mentioned by the reviewer 2. In addition we have performed numerical simulations of the full system to calculate the error term introduced by this approximation, and the results in the new Fig. S2 show that this is below 2% for each of the different dynamical regimes.

      We have hence modified the justification for Eq. (19) reading:

      “Next we assume a first-order moment closure condition for the variable n [59], justified by the numerical simulations of the full network (see Fig. S2) which show that for most of the neurons (close to 99 \% for the value of ∆ same as in the other simulations) the mean of the population is well capturing the behavior of the single neurons [122]. Finally, putting together these factors and assuming that n can be treated as a collective variable for each neuron (see Limitations of the model} section) we arrive to ” and also

      “The validity of the first moment closure, Eqs. (19), as in [59], is supported by the numerical simulations, which show that, both, during the silent regime and when seizure-like events occur, n<sub>i</sub> for most neurons track the network averaged ⟨n | V, η⟩. In particular, it is less than 2% of the neurons that fire while the mean is low, and vice-versa, Fig. S2. In less synchronized scenarios (larger ∆ or smaller J), however, this value would increase, but the mean would always capture the qualitative behaviour of the population.”

      This is also now explicitly mentioned in the following paragraph:

      “Unlike the mean membrane potential ⟨V⟩ and the firing rate (r), which can be explicitly derived from the continuity equation under the Lorentzian assumption, the expression for ⟨n(t)⟩ in Eq. (26) is formal. In our mean-field model, the gating variable (n) is treated as a global population variable, evolving deterministically as a function of the average membrane potential. Therefore, ⟨n(t)⟩ corresponds to the collective gating variable assumed to be shared by all neurons, and is not computed by averaging distinct microscopic (n<sub>i</sub>) values.”

      (10) Considering also the comments reported above, I think that it would make more sense to start from an Izhikevich neuron model as microscopic model and add the equations for the ionic currents as mesoscopic variables (i.e. written as population average variables), instead of starting from the Hodgkin-Huxley single neuron model and trying to make hardly justifiable approximations and simplifications.

      We respectfully disagree. While the Izhikevich model is computationally efficient, it lacks the biophysical detail required to capture key ion-driven mechanisms such as depolarization block, slow ion accumulation, and specific burst-initiation dynamics all of which are central to our study. The Hodgkin–Huxley framework, despite requiring approximation, provides the necessary physiological grounding to link microscopic ion exchange with emergent population behavior.

      (11) Sec. 2.7 What is the advantage of using six more parameters to fit, like R-,R+,c-,c+,I-,I+?

      This is in contradiction with the spirit of deriving a mean-field model, where the number of parameters should be reduced. What is the advantage of this mean-field derivation with respect to other mean-field derivations of Hodgkin-Huxley neurons, like the one in Reference [9]?

      The additional parameters (R±, c±, I±) are not arbitrary they compactly parametrize the cubic-like nonlinearity of the membrane potential dynamics in our stepwise-quadratic approximation. This trade-off allows us to preserve essential biophysical features of HH neurons (e.g., bursting regimes, depolarization block) within a tractable analytic framework. Compared to alternative approaches like in ref. [9], which focus on phenomenological reductions and do not yield an ODE system, our model offers more direct interpretability in terms of ion dynamics, providing a closer link between microscopic mechanisms and mesoscopic activity patterns.

      (12) Sec. 2.11 The derivation of the mean-field dynamics for the gating variable is rather heavy and difficult to follow. This section could be simplified, whilst also better explaining the underlying approximations and the validity of these approximations, which is currently missing.

      We agree that the derivation is technical, but we chose to retain it for transparency, as it follows the Chen and Campbell approach and makes key approximations such as moment closure explicit. We have now added a clarification that n is treated as a collective variable We hope that the current level of detail helps readers understand the assumptions underlying the gating variable dynamics.

      (13) Sec. 2.12 The derivation of Eqs. (36) is quite confusing and needs to be re-written in a clearer form. Why are both the variables x and r present in these equations, since they are proportional according to Eq. (25)?

      We thank the reviewer for pointing this out. We have adjusted the equations to improve clarity and now consistently express the firing rate in terms of a single variable. This removes the redundancy and simplifies the presentation.

      (14) Sec. 2.13 The derivation of Eqs. (37) is quite confusing and needs to be rewritten in a clearer form.

      Both the auxiliary variable x and the firing rate r are present in this equation, the same as in Eq. (36). Therefore it is presented as a set of equations for the auxiliary variable x and for the physical variable V. Moreover in the equation for dV/dt, the quadratic term in V has disappeared and it is not clear to me which are the variables corresponding to I- and I+. In particular, in Eqs. (36) there are two different current terms I-,I+ for the two equations related to dy/dt. In Eqs. (37) there is a single term (I_{cl} +I_{Na}+I_K+I_{pump})/C_m which is identical for both equations related to dV/dt. I was expecting two different terms also in Eqs. (37).

      We appreciate the reviewer’s close reading. To improve clarity, we now express the dynamics in terms of the firing rate r, replacing \dot{x} with \dot{r} in both Eq. (36) and Eq. (37) to avoid confusion.

      As for the current terms: in Eq. (37), we reverse the stepwise quadratic approximation and reintroduce the original ionic currents from Eq. (16). This is why the expressions involving I_{\text{cl}}, I_{\text{Na}}, I_K, and I_{\text{pump}} appear as a single summed term in \dot{V}, rather than the split I_-,I_+ terms used in the stepwise approximation. We now clarify this in the text.

      We also write V as \bar{V} to clarify that it refers to the average membrane potential for the neuronal population. Finally, we wrote the final equation in a more compact form to improve clarity (new Eq.38).

      (15) Moreover, while the equation for the gating variable n can be considered as a differential equation for a mesoscopic variable since n depends on average values only, it is not clear to me if the remaining variables 𝛥[K+]_{int}, [K+]_g can be considered mesoscopic or not. Since Eqs. (37) represent a mean-field model, I expect every variable to be a mean-field variable. This could be easily achievable for the extracellular potassium concentration, but I do not understand how a site-specific microscopic variable like the intracellular potassium concentration variation can be automatically inserted in a set of mean-field equations without any averaging or intermediate steps. This is a crucial point to be clarified for the validity of the neural mass equations.

      We thank the reviewer for raising this important point. In our model, we assume spatial homogeneity at the mesoscopic scale, meaning that ion concentrations — both intra- and extracellular — are uniformly distributed across the population. As a result, variables such as \Delta[K^+]_{\text{int}}, Δ[K+]int and [K+]g are treated as population-level averages, consistent with the mean-field framework.

      Moreover, the rate of change of intracellular potassium is tightly coupled to extracellular dynamics via ion exchange mechanisms, justifying its inclusion as a slow, mesoscopic variable. We now clarify this modeling assumption explicitly in the text.

      “By locally homogeneous, we mean that all neurons in the population are assumed to share the same extracellular and intracellular ionic environment and are connected with identical coupling rules, allowing us to treat the population as uniform with respect to ion dynamics and connectivity.”

      “These slow variables are in addition considered to be mesoscopic, meaning they are identical for every neuron in the population.”

      Minor points:

      (1) Figure 2, panel d. Please detail the variable on the y-axis, which is not reported in the figure.

      Done

      (2) Eq. (15) is cited in many parts of the manuscript, while it seems to me it would be more appropriate to reference Eq. (2). Is this a mistake or is there a reason to cite Eq. (15)?

      The reviewer is correct, we have had a wrong equation label, which we have now corrected.

      (3) Figure 4 Would it be possible to show enlargements of the mean membrane potential traces to directly compare the different bursting types shown by the simulation of the different models?

      The panel d already contains enlarged part of the membrane potential traces. For the rest, going back to the Q6, we want to stress again that our intention is not to claim a quantitative match between the experimental and simulated traces.

      (4) Figure 5 In the caption the author refers to "the generic model, single neuron model, and epileptor model". Could you please better explain the models referred to and why they are mentioned? Are the generic model and the single neuron model those that are presented in the Materials and Methods section? Or do you refer to completely different models, as for the epileptor?

      We have removed the reference to the generic model (we had in mind the canonical model for seizures by Saggio et al. 2017), since it is not mentioned in the paper, and we have clarified that the single neuron model and epileptor model, which were used to simulate seizure like events.

      (5) Sec 2.5 As already stated above, the authors need to reduce unnecessary formulations that confuse the reader. Here, for example, Eqs. (6) and (7) are unnecessary, in view of the fact that delta spikes are used (Eq. 8).

      We thank the reviewer for the suggestion, but we disagree, and we think it is better to start the derivations from the more general case, as done with Eqs. 6-7.

      (6) Sec. 2.6 Could you please better explain why in Eqs. (15) and (16), the variable V0 is introduced, while before and after this, the variable V is used?

      We thank the reviewer for the comment. In Eqs. (15) and (16), \dot{V}_0 denotes the free term of the membrane potential equation, i.e., the component driven solely by the intrinsic ionic currents and excluding the synaptic input I_syn. Only this \dot{V}_0 term (a function rather than an independent variable) is approximated by the piece-wise quadratic expression in Eq.(21). In contrast, the variable V represents the membrane–potential variable, which dynamics is obtained by combining \dot{V}_0 with the synaptic current contribution I_syn. In summary, there is no independent variable V_0; only the function \dot{V}_0 is introduced to represent the intrinsic (non-synaptic) component of the membrane–potential dynamics. We have now clarified this in the text.

      (7) In the square brackets of the r.h.s. of Eq. (18), for all the intermediate steps, it appears G^n(V,n) ϱ^V, while there should be G^n(V,n) ϱ^n.

      We thank the reviewer for catching this typo. We have corrected this in the revised manuscript.

      (8) Sec. 2.8 Here the authors affirm that "a double-Lorentzian (or a piece-wise Lorentzian) could be a suitable form for ρ^V (t, V | η). However, it is not clear under which conditions such an assumption would allow a solution to the continuity equation". What are the problems underlying the implementation of the double Lorentzian? It seems to be a more correct form than the single Lorentzian actually implemented.

      We thank the reviewer for this thoughtful question. In principle, a double-Lorentzian ansatz for \rho^V can indeed be implemented in several reasonable ways–for example, by enforcing that the combined area of the two Lorentzian components is normalized to one (to preserve the probabilistic interpretation) and by imposing smoothness constraints at their boundaries. However, despite exploring these implementations, we were unable to obtain non-trivial solutions of the continuity equation under this parametrization. The only solvable case we found is the degenerate one in which the two Lorentzians collapse onto each other (i.e., (x_- = x_+) and (y_- = y_+)), which reduces the ansatz to the single-Lorentzian form used in the manuscript. For this reason, although the double-Lorentzian is conceptually appealing, it did not yield practically useful solutions within our framework.

      (9) Eq. (28). The symbols used for the flux (especially those used in the second-to-last step once the inner integration is performed) are confusing and it is difficult to understand what they mean.

      We thank the reviewer for noting this issue. The problem was due to a LaTeX typo that prevented the vertical lines—indicating that the flux is evaluated at specific points—from rendering correctly. We have now corrected this.

      (10) Eq. (29) In the third step there are some misprints that impair comprehension.

      We thank the reviewer for noting this. We have corrected these misprints in the revised version.

      (11) Line 696. The reference is not displayed.

      Fixed.

      Reviewer #2 (Recommendations for the authors):

      As a really general remark, this manuscript is written in a confusing manner, the authors present their model in a general formulation and their analysis in a complicated way that in the end is not needed, as I will explain in detail in the following.

      Another general question is why the authors want to employ the neural mass reduction methodology developed in [23] to obtain exact mean-field evolution for quadratic neurons (like the quadratic integrate and fire (QIF)) for a model that reveals a cubic dependence on the membrane potential, as the FizhHugh-Nagumo neuron (that indeed is a 2d reduction of the Hodkgin-Huxley model), to obtain an approximate neural mass model that somehow works qualitatively only for synchronized dynamics? Why not use another approach more suited to derive the neural mass model for cubic nonlinearity, as the one suggested in [33] and [69] by Di Volo and co-authors? What is the rationale behind the choice of the authors?

      We appreciate the reviewer’s critical feedback and the opportunity to clarify our methodological choices. Our decision to base the mean-field model on Hodgkin–Huxley-type neurons stems from the need to retain ion channel dynamics, which are essential to capture the coupling between membrane activity and extracellular ionic concentrations. This biophysical link is central to our study and cannot be achieved using more abstract neuron models such as QIF or FitzHugh-Nagumo alone.

      Regarding the mean-field reduction method: while the Ott-Antonsen/Lorentzian framework is indeed exact for QIF neurons, we adopted a stepwise quadratic approximation to apply a similar formalism to the cubic-like dynamics of the HH model. This choice enables us to analytically capture a rich set of behaviors, including bursting, depolarization block, and seizure-like dynamics, in a tractable mean-field system.

      We considered the approach of Di Volo and colleagues [33, 69], but their methodology is tailored to asynchronous irregular regimes, whereas our model is specifically designed to capture dynamics in quasi-synchronous or bursting regimes — including epileptiform activity — which are not covered by the assumptions of the Di Volo framework.

      We now clarify these modeling choices more explicitly in the revised manuscript.

      "Unlike phenomenological or reduced models, the Hodgkin–Huxley framework allows us to retain explicit ion exchange dynamics, which are essential for linking membrane behavior to extracellular potassium fluctuations. This level of biophysical detail is crucial for modeling pathological regimes such as seizure onset and propagation."

      Furthermore, the derivation of the neural mass equations is unnecessarily complicated, as a matter of fact, they approximate all the variables (except the membrane potentials of the single neurons) as collective variables (i.e. the gating variable and the potassium concentration) common to all the neurons. The neural network model for which they derive the neural mass model presents microscopic evolutions of the membrane potential cubic-like plus other global variables equal for all neurons, that depend on collective variables such as the mean membrane potential or the mean firing rate. Once clarified, the derivation of the neural mass model is much simpler, and it is not necessary to follow the approach reported in Reference [95] [Chen, L. & Campbell, S. A. Exact mean-field models for spiking neural networks with adaptation. Journal of Computational Neuroscience 50 (4), 445-469 (2022)] which is unnecessarily complicated. The authors can follow a much simpler methodology as explained by Guerriero et al in Reference [R6] (cited below) where the authors consider the same model studied in [95]. Such a methodology has been applied in many cases already, to introduce realistic aspects in the neural mass model [23] (see References [R1-R7] below). I strongly encourage the authors to reformulate their approach in a simpler and clearer manner, by following the approach reported in [R1-R7]. The manuscript will become more readable and it will gain in comprehension.

      We thank the reviewer for this helpful suggestion. We agree that, given the assumptions made in our derivation (i.e., shared gating and ion concentration variables across neurons), the mean-field equations could alternatively be obtained using the simpler methodology proposed by Guerriero et al. [R6] and related works [R1–R7]. However, we chose to follow the derivation presented by Chen and Campbell [95] because it makes the approximations (e.g., moment closure, flux boundary assumptions) explicit and generalizable to future extensions. However, we also acknowledge that the assumption of n to be treated as a collective variable is needed, and for clarity, we have now added a remark in the manuscript indicating that the same result could be recovered more directly using the approach of Guerriero et al.

      “We note that, under the assumption of globally shared gating and ion concentration variables across the neuronal population, the resulting mean-field equations can also be derived using simpler methods as proposed by Guerriero et al [58]. In this work, we follow the more general formalism of Chen and Campbell [59], which makes the role of key approximations (e.g., moment closure, vanishing flux at boundaries) explicit. This also facilitates potential generalizations to settings with partial heterogeneity or dynamic gating distributions.”

      “Finally, putting together these factors and assuming that n can be treated as a collective variable for each neuron”

      “Unlike the mean membrane potential ⟨V⟩ and the firing rate (r), which can be explicitly derived from the continuity equation under the Lorentzian assumption, the expression for ⟨n(t)⟩ in Eq. (26) is formal. In our mean-field model, the gating variable (n) is treated as a global population variable, evolving deterministically as a function of the average membrane potential. Therefore, ⟨n(t)⟩ corresponds to the collective gating variable assumed to be shared by all neurons, and is not computed by averaging distinct microscopic (n<sub>i</sub>) values.”

      Now I will examine in detail all the manuscript and report comments/remarks/suggestions numbered as (Q#) on how to improve the present manuscript to render it easier to read and more comprehensible, these are not minor remarks, just detailed ones.

      Introduction

      (Q1) The Introduction section needs a part devoted to the reduction methodology developed in [23] for QIF neurons and a presentation of previous works dealing with the introduction of biologically realistic aspects in the neural mass model derived in [23]. Here is a non exhaustive list of such papers concerning the introduction of the following realistic aspects in the neural mass developed in [23]:

      (I) short-term synaptic plasticity :

      [R1] Exact neural mass model for synaptic-based working memory H Taher, A Torcini, S Olmi, PLOS Computational Biology 16 (12), e1008533 (2020)

      [R2] Bursting in a next generation neural mass model with synaptic dynamics: a slow-fast approach H Taher, D Avitabile, M Desroches, Nonlinear Dynamics 108 (4), 4261-4285 (2022)

      [R3] Mean-field approximations of networks of spiking neurons with short-term synaptic plasticity R Gast, K Thomas R, H Schmidt, Physical Review E 104 (4), 044310 (2021)

      (II) spike frequency adaptation:

      [R4] Gast, Richard, Helmut Schmidt, Thomas R. Knösche. "A mean-field description of bursting dynamics in spiking neural networks with short-term adaptation." Neural computation 32.9 (2020): 1615-1634.

      [R5] Population spiking and bursting in next-generation neural masses with spike-frequency adaptation, A Ferrara, D Angulo-Garcia, A Torcini, S Olmi, Physical Review E 107 (2), 024311 (2023).

      (III) conductance-based neuron with a slow current (Izekievic model):

      [R6] A new generation of reduction methods for networks of neurons with complex dynamic phenotypes,IC Guerreiro, M Di Volo, B Gutkin, preprint arxiv: 2206.10370 (2022)

      (IV) spike timing-dependent plasticity:

      [R7] Mean-field approximations with adaptive coupling for networks with spike-timing-dependent plasticity, B Duchet, C Bick, Á Byrne, Neural computation 35 (9), 1481-1528 (2023).

      (V) random connectivity and noise:

      [R8] Mean-field models of populations of quadratic integrate-and-fire neurons with noise on the basis of the circular cumulant approach

      DS Goldobin Chaos: An Interdisciplinary Journal of Nonlinear Science 31 (8) (2021)

      [R9] A reduction methodology for fluctuation-driven population dynamics DS Goldobin, M Di Volo, A Torcini, Phys. Rev. Lett. 127, 038301 (2021)

      [R10] Shot noise in next-generation neural mass models for finite-size networks VV Klinshov, SY Kirillov Physical Review E 106 (6), L062302 (2022)

      I think the authors should refer in the introduction to these previous papers, where realistic biological aspects have been already introduced in the neural mass model developed in [23].

      We have added a whole pragaraph devoted to the next-generation neural mass models and in particular to the other works introducing biological realism in this class of models:

      “Recently, a class of these models, called next-generation neural mass models [42], has been developed based on an analytical approach introduced by [25] that allowed for the exact derivation of mean field parameters for a population of quadratic integrate-and-fire (QIF) neurons. These can be linked to EEG/MEG oscillations [43], including epipeltic seizures [44], and have been used to study various aspects of the whole-brain dynamics such as the low-dimensional manifold of the resting state [45, 46], aging [47] and neural sig natures of consciousness [48]. Number of works dealt with the introduction of biologically realistic aspects in the mostly phenomenological neural mass model derived in [25]. These included short-term synaptic plasticity [49–51], spike frequency adaptation [52, 53], spike timing-dependent plasticity [54], synaptic delay [29], random connectivity and noise [55–57], as well as an extension of the conductance-based neurons with a recovery variable [58–60].”

      (Q2) Line 117 - Please specify what you mean by locally homogeneous, here.

      Thank you for allowing us the opportunity to clarify this. We now report:

      "By locally homogeneous, we mean that all neurons in the population are assumed to share the same extracellular and intracellular ionic environment and are connected with identical coupling rules, allowing us to treat the population as uniform with respect to ion dynamics and connectivity."

      (Q3) In this sub-section the authors should clarify all the hypotheses they employ to derive the neural mass models, not only the Lorentzian approximation they did for a cubic model, but also the fact that they assume that the gating variable n is a global variable as well as that the potassium concentration are assumed to be the same for all neurons, that they assume no heterogeneity at this level. This is a fundamental aspect that should be clarified at this stage already.

      We thank the reviewer for this important observation. We agree and have revised the text in the derivation section to explicitly state all key assumptions. Specifically, we now clarify that:

      (1) The gating variable n is treated as a population-average (global) variable;

      (2) The potassium concentrations Δ[K+]int and [K+]g are assumed to be homogeneous across the neuronal population; and (3) No heterogeneity is assumed at the level of the ion dynamics.

      This assumption is biophysically motivated: ion concentrations — particularly extracellular potassium — tend to redistribute rapidly due to diffusion and electrochemical forces, leading to an effectively well-mixed environment at the mesoscopic scale. As such, assigning separate compartments to individual neurons is not justified in this modeling context. We now explicitly note this in the manuscript to avoid ambiguity.

      “3) We assume that the potassium concentrations, both intracellular(\( \Delta[K^+]_{\text{int}} \)) and extracellular (through the buffering variable \( [K^+]_g \)), are homogeneous across the neuronal population. This is justified physiologically by the rapid redistribution of ions through diffusion and electrochemical gradients, which enforce near-instantaneous equilibration at the mesoscopic scale. As such, assigning separate compartments to each neuron is neither practical nor biologically meaningful in this context. We assume that the potassium concentrations, both intracellular (\( \Delta[K^+]_{\text{int}} \)) and extracellular (through the buffering variable \( [K^+]_g \)), are homogeneous across the neuronal population. This is justified physiologically by the rapid redistribution of ions through diffusion and electrochemical gradients, which enforce near-instantaneous equilibration at the mesoscopic scale. As such, assigning separate compartments to each neuron is neither practical nor biologically meaningful in this context; 4) We assume that the gating variable n, which governs potassium conductance, can be treated as a population-averaged variable. This allows us to describe the neuronal ensemble using a reduced set of collective (mean-field) variables.”

      Comparison with neural network simulations

      (Q4) The comparison the authors perform between the microscopic model and the neural mass is misleading, From what the authors wrote it seems that you are considering 4 variables for each neuron in the network model (this is unclear from how the model is written in Eq (9)), I guess one for the membrane potential, one for the gating variable and two for the potassium concentration. However, this is not the network model for which the neural mass has been developed, the neural mass has been obtained for a network made of N + 3 variables (N membrane potentials and 3 collective variables for gate, and potassium concentrations) this is a sort of mesoscopic network models, analogously to what done previously in references [R1,R3,R4] above and others. If the authors would compare their neural mass with this mesoscopic model the agreement among the two would be improved.

      We agree with reviewer’s observation and we now acknowledge this issue in the Results and in the Limitations. We have already modified the text to explicitly state that for the mean filed derivations n is treated as a collective variable and we have added the following statements:

      “Also note that the gating variable n is treated as microscopic in the neural network, while in the derivations for the mean-field it is considered as a mesoscopic and identical for the whole population. This is likely responsible for some of the discrepancies between the two modalities.”

      “Moreover, the discrepancy between the two modalities would have likely been smaller if for the neural network we also adopted a gating variable that is mesoscopic and identical across the spiking neurons, as in similar works [49–51]. However, here we demonstrate the validity of the mean-field approximation even for the more natural, microscopic representation of the gating variable in the neural network.”

      Comparison with in vitro experiments

      (Q5) Experiment -- The experiment is performed in vitro on the intact Hippocampus of mice between postnatal days P5-P7. It is known [R1] that neuronal activity at an early developmental stage is provided in the Hippocampus by a network primarily driven by synchronized GABA_A that provides an excitatory action and generates giant depolarizing potentials (GDPs) [R11]. However, GDPs have frequencies in the range of 1 Hz - 0.1 Hz, not matching the oscillation frequencies reported by the authors. I have several questions here:

      (E1) At this stage P5-P7 are the interactions among neurons essentially excitatory? Or not, please explain why, Are the oscillations reported by the authors somehow related to GDPs? The depolarizing action of GABAergic transmission and the presence of GDPs during early rodent brain development, as described by Ben-Ari and some others researchers, are characteristics commonly observed in ex vivo brain preparations, but are not evident under physiological in vivo conditions (see doi: 10.3389/fphar.2012.00065).

      In our preparation—intact mouse hippocampus—GABAergic synaptic transmission is not depolarizing. This is evidenced by the fact that inhibition of ionotropic GABA_A receptors with bicuculline triggers interictal-like discharges, which are routinely used as a model of epileptiform activity (see doi: 10.1016/j.nbd.2014.12.013). Therefore, in our experiments at P5–P7, neuronal interactions are not purely excitatory, and the observed low Mg2+ induced oscillations are not related to GDP.

      (E2) What is the nature of the oscillations reported by the authors in Figure 4 ? Which is their origin, please explain in the text of the paper clearly.

      The model of epileptic discharges presented in our study was first introduced over 20 years ago and has since become a well-established paradigm for screening potential antiepileptic drugs and research on the mechanism of epileptic seizure. A detailed description of this model can be found in doi: 10.1046/j.1460-9568.2002.02143.x, and its pharmacological properties are reviewed in doi: 10.1046/j.1528-1157.2003.19503.x. These references have now been added to the manuscript for clarity.

      We have added the following:

      “The model of epileptic discharges presented in our study was first introduced over 20 years ago [115] and has since become a well-established paradigm for screening potential antiepileptic drugs and research on the mechanism of epileptic seizure [116].”

      (E3) How exactly does the concentration of extracellular potassium ions change, this is not clear even in Methods, please clarify.

      [R11] Excitatory actions of GABA during development: the nature of the nurture Y Ben-Ari, Nature Reviews Neuroscience 3 (9), 728-739 (2002).

      We have now added a new Subsection in the methods explaining how we use Mg2+ variation to influence the external potasium variation.

      “The membrane of hippocampal neurons is equipped with N-methyl-D aspartate type glutamate receptors (NMDARs). These receptors have a very high affinity for glutamate and can, in principle, be activated by ambient glutamate present at low concentrations in the brain extracellular fluid (ECF).Under normal physiological conditions, this activation does not occur because extracellular magnesium ions (Mg<sup>2+</sup>) block the NMDAR channel at membrane potentials more negative than about –50 mV; this voltage-dependent block prevents receptor activation at rest. When extracellular magnesium is removed, the block is relieved, allowing NMDARs to be activated, leading to neuronal depolarization toward the action potential threshold [117]. In addition, as a divalent cation, Mg<sup>2+</sup> interacts with the negatively charged neuronal membrane, contributing to the stabilization of the resting membrane potential. Lowering extracellular magnesium concentration disrupts this effect, resulting in membrane depolarization [118]”

      “Consequently, magnesium removal not only facilitates NMDAR-dependent depolarization, but also directly depolarizes neurons. This depolarization increases the driving force for outward potassium currents through K<sup>+</sup> channels, meaning that variations in Mg<sup>2+</sup> can indirectly influence external potassium dynamics during neuronal activity.”

      (Q6) Lines 187-191 and Figure 4 -- The authors wrote : "In Figure 4.c we show the membrane potential and external potassium for a simulation of N = 3000 coupled HH-like neurons showing a similar behavior, although the parameters were modified to simulate shorter fluctuations for computational efficiency." This sentence is unclear. What is clear from Figure 4 is that the network simulations gave rise to collective oscillations on a completely different scale seconds with respect to minutes and also the profile of the potassium concentration has a clearly different evolution. From Figure 4 one can conclude that network simulations have nothing to do with the neural mass evolution and the experiment. I think the authors should better clarify and describe the results reported in Figure 4.

      We thank the reviewer for the observation. We have revised the relevant section of the manuscript to clarify the interpretation of Figure 4 and avoid any implication of quantitative matching. As stated in our response to Reviewer 1 (comment 6), the comparison is intended to highlight the shared qualitative structure across experimental data, the neural mass model, and the network simulation — specifically, the modulation of fast bursting by slow extracellular potassium fluctuations. The difference in timescale in the network simulation arises from rescaled parameters used for computational efficiency. We now explicitly state this and have updated the figure caption and accompanying text accordingly to reflect these points.

      (Q7) Why do the authors consider a purely excitatory network to describe the experimental results? What is the reason for this choice? Why they do not consider as usual balanced excitatory- inhibitory networks? Please clarify this point.

      We thank the reviewer for raising this point. We chose to model a purely excitatory network as a first step in isolating the role of extracellular potassium dynamics in generating population-level bursting. This allows us to focus on the ion-driven modulation mechanisms without introducing additional complexity from inhibitory feedback. Similar modeling choices have been made in previous studies of bursting and seizure-like dynamics (e.g., Gutkin et al.,), where inhibition is omitted to emphasize intrinsic or modulatory mechanisms. We acknowledge that incorporating inhibitory populations is an important next step for capturing a broader range of dynamics, but for the current study, the excitatory-only network provides a minimal and interpretable framework aligned with our focus.

      (Q8) By comparing Figures 4 (a) and (b) it seems that the bursting activity observed in the experiment and in the mean-field simulations seem quite different, originating from different mechanisms and bifurcations, Can the authors comment on this?

      We thank the reviewer for this important observation. We have reorganized the presentation of Figure 4 and revised the accompanying text to better clarify the nature of the comparison (see also our response to Reviewer 1, point 6). Our aim is not to claim that the experimental and simulated bursts arise from identical bifurcation mechanisms, but rather to highlight shared qualitative features — in particular, slow modulation of population activity by extracellular potassium. We now also comment on the potential role of more complex or noise-driven bifurcations (see Saggio et al. 2020) in shaping experimental bursting dynamics, which are not fully captured by the current deterministic model.

      Bifurcation analysis: emergent network states and multistability

      (Q9) This sub-section will gain interest by reporting simulations of the network and of the neural mass model presenting bistable dynamics.

      We agree with the reviewer that this would be an important addition, but we believe that it goes beyond the scope of this work (for the computational reasons among others) and it remains for future work. We have however updated the bifurcation analysis section.

      Limitations of the model

      (Q10) Lines 276- 280 -- I think that the parameters c+,c_,R+,R_ depend not only on the slow variables, potassium concentrations but also on the actual value of the gate variable n. This should be stressed.

      We thank the reviewer for this helpful observation. We agree and have clarified in the revised manuscript. This reflects the mean-field assumption that n is treated as a collective variable, and we now make this dependency explicit in the text.

      “Furthermore, the parabola coefficients c_-,c_+, R_-, R_+ were fixed as constants, however, these coefficients could be made functions of the slow variables and the gating variable, which might unveil new dynamical regimes and extend the validity of the thermodynamic limit beyond the regimes described in this work. Also, in the case of constant values, an in-depth exploration of the parameter space is required to fully characterize the model and its bifurcation structure.”

      (Q11) The authors wrote: " Other limiting assumptions are the moment closure condition (19) and the assumptions that the functions (3) averaged across the neuronal population can be expressed as functions of the average membrane potential V and gating variable n (which is only true in the cases where the functions (3) can be reasonably approximated as linear functions in a range of V and n." Apart from that a parenthesis is lacking, I think that this last aspect has been already taken into account when performing the fit with 2 parabolas to the sum of the currents, or not? In case, please specify.

      We thank the reviewer for catching the missing parenthesis — this has been corrected in the revised manuscript. Regarding the modeling point: the two-parabola fit applies specifically to the membrane potential dynamics and captures the nonlinear dependence of the total current on V (eq.16). In contrast, the moment closure assumption involves approximating averages of nonlinear functions of both V and n, such as those appearing in the gating dynamics (e.g., n∞(V)). This is not directly accounted for by the parabola approximation, but is handled separately via the mean-field approximation of G^n as a function of the average variables (eq.15).

      (Q12) A limitation that should be stressed is that the authors in the neural mass model consider the gate variable and the potassium concentrations, as global variable equal for all neurons, and where n depends on the mena membrane potential, to write that the moment closure (19) is a limiting assumption is honestly too clear, please be explicit here.

      We have now the following two statements:

      “These slow variables are in addition considered to be mesoscopic, meaning they are identical for every neuron in the population.”

      “In our mean-field model, the gating variable (n) is treated as a global population variable, evolving deterministically as a function of the average membrane potential. Therefore, ⟨n(t)⟩ corresponds to the collective gating variable assumed to be shared by all neurons, and is not computed by averaging distinct microscopic (n<sub>i</sub>) values.”

      Discussion

      (Q13) The authors could discuss in this section the further biological ingredients they can introduce in their neural mass based on the previous works [R1-R9] that have already shown how to include plastic synapses, random connectivity, noise, adaptation, spike-timing-dependent plasticity, etc and which of these ingredients they consider more relevant for the whole brain dynamics.

      In order not to repeat the same statements from the Introduction, we have now addded the following sentence:

      “This approach, taking into account key biophysical details, offers a first step in considering the role of the glia in neural tissue excitability. Following this direction, other ions, such as calcium should be taken into consideration, as well as other effects such as plastic synapses, random connectivity, noise, adaptation, spike-timing-dependent plasticity, as already discussed in the Introduction.”

      (Q14) The authors should also discuss why they limited their analysis to purely excitatory networks, and what would change by including excitatory-inhibitory interactions in each single mass and across neural masses, if this makes sense or not.

      As stated in our response to Q7, we chose to focus on purely excitatory networks as a first step to isolate and study the core role of extracellular potassium dynamics in driving bursting behavior. This modeling choice allows for a minimal system where the interaction between intrinsic ionic mechanisms and network coupling is most transparent.

      We also note that excitatory and inhibitory effects can be modeled within the same formalism by adjusting the synaptic reversal potential — for example, $E_{syn}=0$mV for excitatory, and $E_{syn}=-80$mV for inhibitory interactions. Including inhibitory populations would introduce additional complexity and richer dynamical regimes (e.g., oscillatory instabilities, balance states), which are certainly of interest but beyond the scope of this study.

      Materials and Methods

      (Q15) Fig.2 - I think a plus is lost in panel (c) where it should be [K+bath];

      Thank you. We corrected the figure.

      (Q16) Caption of Figure 2- the authors wrote: "In the case where the derivative of the membrane potential is zero for V > V ⋆ (e.g., if the cubic function is shifted up by adding a constant current to the membrane potential derivative), the population is described by the red distribution in the steady state, and the continuity equation is governed by the negative parabola equation." This sentence is unclear, the authors mean in the case where the derivative of the membrane potential crosses zero at V > V*? Please clarify.

      We thank the reviewer for pointing this out. Yes, we refer to the case where the membrane potential derivative crosses zero at a point V>V∗. We have clarified this in the revised figure caption.

      (Q17) Lines 558-562 -- Eqs (6) and (7) are examples of unnecessary complications of which this manuscript is full of. Since the authors do not consider any synaptic dynamics and homogenous (equal) couplings, these equations are not needed, I strongly recommend removing Eqs (6) and (7) and limiting to the expression reported in Eq (8), which indeed should also be corrected see next remark.

      We appreciate the reviewer’s concern regarding clarity. As mentioned in our response to Reviewer 1, the inclusion of Eqs. (6) and (7) was intentional and serves a pedagogical purpose — to present the general structure of the network interactions before introducing simplifying assumptions. While we agree that Eq. (8) suffices for the simulations considered in this manuscript, we believe that showing the more general form helps clarify the model’s extensibility, for instance to cases with heterogeneous coupling or synaptic dynamics.

      (Q18) Eq (8) - line 562 - Since the authors assume no synaptic evolution, i.e. instantaneous post-synaptic potentials, they can clarify that Eq (8) represents the population firing rate that later will be one of the fundamental variables of the neural mass model and call it r, as in the following. Furthermore, $s_i$ does not depend on the neuron index $i$ in a fully coupled network with homogenous coupling, as in the present case, this quantity is the same for all neurons. Please drop the index and call it r since it is the population firing rate.

      We thank the reviewer for this useful suggestion. We now clarify in the text that under the assumptions of all-to-all homogeneous coupling and no synaptic dynamics, s_i is identical for all neurons and can be interpreted as the population firing rate r. This connection is made explicit in the revised manuscript.

      “Under the assumption of instantaneous synaptic transmission and homogeneous all-to-all coupling, the synaptic activation variable (s<sub>i</sub>) is the same for all neurons and corresponds to the population firing rate, which we denote by (r)”

      (Q19) Line 564-567 - Here the network model is incomplete, it is not sufficient that the authors report the evolution equation for the membrane potential Eq (9). They should report the evolution equation for the gate variable n and for the potassium concentration as done in Eq (1). This request is fundamental because it is unclear from the present formulation which are the variables that are microscopic (associated with the single neuron evolution) and which are global (common to all the neurons). This is a fundamental aspect and it should be clarified. I guess that n will depend on the neuron index $i$, while the potassium concentration it is unclear how the authors will consider them, global or local. I guess that the internal density should depend on the neuron index $i$ or not ? Anyway, I would like to know exactly which network model has been simulated e.g. to obtain the results reported in Figure 3.

      We thank the reviewer for this essential clarification request. In the revised manuscript, we now explicitly state the full network model, including the evolution equations for the gating variable n_i and potassium variables. While in some simulations we consider the full microscopic model involving 4N variables (where each neuron has its own V_i ,n_i ,Δ[K+]int_i ,[K+]g_i), for the mean-field reduction and mesoscopic comparisons we assume that the gating and potassium variables are shared across neurons. This assumption is consistent with prior work (e.g., Chen & Campbell) and is biophysically justified in the case of potassium due to its fast spatial equilibration in extracellular space. We also now mention this explicitly in the Limitations.

      (Q20) Continuity equation - Lines 568 - 597 - This part can be largely simplified and rewritten, as a matter of fact, the authors consider the gate variable n, the potassium concentrations as global (collective variables) depending on mean field values of <V> they can directly start from eq 20, by stating that they assume that the other variables (n, $\Delta[K^+]_{int}$, $[K^+]_g$) are collective variables, common to all the neurons, and that depends only on mean field variables as <V> or r. This has been done in many previous cases since the Ott-Antonsen Ansatz can be applied whenever the potential evolution is driven by quadratic terms and in the presence of mean field variables, the first indication of this was reported in 1993 by Watanabe and Strogatz for phase oscillators :

      [R12] Watanabe, Shinya, and Steven H. Strogatz. "Integrability of a globally coupled oscillator array." Physical review letters 70.16 (1993): 2391.

      Anyway, this approach has been previously employed to derive a neural mass model for networks of QIF neurons in the presence of various further neuronal variables (ranging from slow currents to plastic evolution of the couplings) describing more biologically realistic situations, see references [R1-R7] above. I strongly encourage the authors to reformulate their approach in a simpler and clearer manner, particularly interesting is for them the article [R6] by Guerriero et al, the authors examine exactly the same model as in Ref [95] [Chen, L. & Campbell, S. A. Exact mean-field models for spiking neural networks with adaptation. Journal of Computational Neuroscience 50 (4), 445-469 (2022)]. However, they solve the problem in a much more simple way, I encourage the authors to follow this approach.

      We thank the reviewer for the constructive suggestion. We acknowledge that, under the assumption that n, Δ[K+]int , and [K+]g are collective variables shared across the neuronal population, one could directly begin from Eq. (20) and proceed using the simpler approaches found in Guerriero et al. [R6] or related works [R1–R7]. However, we chose to retain the Chen & Campbell formalism, with additional clarification regarding the mesoscopic nature of the gatin variable, as it explicitly highlights the key approximations used in the derivation, which may be beneficial for readers seeking to extend the method. See also general response to reviewer 2 at the beginning.

      (Q21) Eq (26) -- I do not think the authors can estimate explicitly <n(t)> from the equation (26), as they do for the mean membrane potential and the firing rate. This is just a formal expression representing a collective variable, I do not think that <n> will coincide with the average of the values of n_i for each neuron. Please discuss this point, and in this case show that <n> indeed coincides with the average of all of the values of the single neuron gate variable n_i.

      We thank the reviewer for raising this important point. We agree that Eq. (26) is more formal than operational, as ⟨n(t)⟩ is not directly derived from the continuity equation in the same way as ⟨V⟩ or the firing rate r. Rather, it reflects our mean-field assumption that the gating variable evolves as a collective population-averaged quantity, governed by the dynamics of the average membrane potential. In our formulation, n is treated as a global variable shared across neurons, and thus ⟨n(t)⟩ effectively is the gating variable in the neural mass model — rather than the result of averaging heterogeneous n_i. We have clarified this distinction in the text to avoid suggesting that Eq. (26) provides an explicit estimate of microscopic gating dynamics.

      “Unlike the mean membrane potential ⟨V⟩ and the firing rate (r)>, which can be explicitly derived from the continuity equation under the Lorentzian assumption, the expression for ⟨n(t)⟩ in Eq. (26) is formal. In our mean-field model, the gating variable (n) is treated as a global population variable, evolving deterministically as a function of the average membrane potential. Therefore ⟨n(t)⟩ corresponds to the collective gating variable assumed to be shared by all neurons, and is not computed by averaging distinct microscopic (n<sub>i</sub>) values.”

      (Q22) Mean-field dynamics for the gating variable - All this sub-section is in my opinion not useful, if the authors assume from the beginning that <n(t)> is a global variable. Indeed in the end they write for <n(t)> the evolution equation Eq (30) which is the same equation as for the single neuron gate variable (1) but for the mean values of n and <V>. I suggest removing this sub-section.

      We thank the reviewer for this suggestion. We agree that, under the assumption that n is a global collective variable, the resulting equation for ⟨n(t)⟩\langle n(t) \rangle⟨n(t)⟩ is equivalent in form to the single-neuron gating equation, driven by the average membrane potential. However, we chose to retain this subsection to explicitly demonstrate how the gating dynamics enter into the mean-field formulation, especially for readers less familiar with this type of reduction. This step also mirrors the structure of the derivation used for other state variables in the model and maintains clarity for potential extensions where n may not be strictly global.

      (Q23) Line 696 - here an equation reference is lost.

      Thank you for pointing this out. We have corrected the text and restored the missing equation reference in the revised manuscript.

      (Q24) Eqs (36) -(37) -- Since the variables r and x entered in Eq (36) are essentially the same as Eq (25), apart from a constant R/pi, the use of two different names complicated in a useless manner an already complicated expression, Please decide to use everywhere r or x and then proceed consequently this applies also to Eq (37). This will also allow us to rewrite the equation in x or r in a more compact form.

      As noted in our response to Reviewer 1, point 14, we have revised Eq. (37) to ensure consistency in notation by replacing x with r throughout.

      (Q25) Eq (37) - This equation is written in a manner that is not careful enough, apart from that the authors are passed now from (x,y) to (pi*r/R,V) , therefore they should substitute everywhere x with r. Furthermore, the equation for the derivative of V is confusing, the authors should use the same approximate expression employed in eq (36) that makes explicit the quadratic dependence on V itself, otherwise, I believe that the equation is incorrect.

      In the same response to Reviewer 1, point 14, we also clarified the expression for \dot{V} in Eq. (37), we reintroduced the full current-based formulation (as in Eq. 16), reversing the quadratic approximation used earlier. This is now explicitly stated in the text, and we have improved the equation presentation to avoid confusion.

      (Q26) Eq (37) below line 708 - From this expression, it is clear that the gate variable n and the potassium variables are ruled exactly by the same equations as for the single neuron Eq (1) and that the Lorentzian Ansatz enter only in the rewriting of the evolution of the membrane potentials of the neurons in the network. In the end, the authors are doing exactly the same approximation made by many other authors [R1-R7], that these variables are collective, i.e. they are the same for all neurons, and in particular n=n(V) is a function of the mean membrane potential V. The mean field model that the authors derive corresponds to a microscopic model where the single neurons are heterogenous only in the intrinsic currents $\eta_i$, but they are all driven by collective variables, like n(V) and the potassium variables that are identical for all neurons. This should be clarified.

      We agree with the conclusion by the reviewer, and as seen through the previous responses, we now explicitly acknowledge the fact that n and the two slow variables are considered as a mesoscopic variables for the mean-field derivation, while for the spiking network, n remains microscopic.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Manuscript number: RC-2026-03407

      Corresponding author(s): Laura Cantini, Julio Saez-Rodriguez

      [The "revision plan" should delineate the revisions that authors intend to carry out in response to the points raised by the referees. It also provides the authors with the opportunity to explain their view of the paper and of the referee reports.

      • *

      The document is important for the editors of affiliate journals when they make a first decision on the transferred manuscript. It will also be useful to readers of the reprint and help them to obtain a balanced view of the paper.

      • *

      If you wish to submit a full revision, please use our "Full Revision" template. It is important to use the appropriate template to clearly inform the editors of your intentions.]

      1. General Statements [optional]

      This section is optional. Insert here any general statements you wish to make about the goal of the study or about the reviews.

      We thank both reviewers for their thorough and constructive evaluation of our manuscript.

      Reviewer 1 highlighted that the manuscript would benefit from 1) a stronger positioning of ReCoN within the existing literature on multicellular modelling and network exploration, 2) a justification of our methodological choices, including the use of Random Walk with Restart (RWR), 3) the choice of input datasets for GRN inference and an assessment of the robustness of ReCoN's predictions to noise in these networks, 4) a more systematic exploration of ReCoN's parameter space (restart probability, layer transition probabilities, filtering thresholds).

      Reviewer 2 raised concerns about 1) the generalisability of the α parameter value (by default, 0.8) across independent datasets, 2) the expected contribution of the indirect effect in prediction performances, 3) the robustness of GRN across datasets and systems, and 4) the need for more quantitative validation in the spatial/microenvironment showcase. They also pointed out an unsupported claim regarding gene knockout prediction in the abstract.

      Several clarifications on figures, methods, and writing were also requested by both reviewers.

      As the main addition to the manuscript, we propose a new showcase based on the recently published Human Cytokine Dictionary (Oesinghaus et al., 2025). This showcase will simultaneously address several reviewer concerns by allowing us to 1) test the robustness and performance of α = 0.8 in an independent dataset, 2) evaluate the impact of different GRN inference methods (HuMMuS, SCENIC+, CellOracle, GRNBoost2) and noise on ReCoN's predictions..

      We will conduct a systematic parameter exploration on the Heart Atlas showcase, covering restart probability and inter-layer transition probabilities. We will additionally strengthen the validation of the microenvironment showcase by providing additional comparison to matched single-cell fibroblast data.

      Regarding the manuscript, we will substantially expand the discussion to better contextualise ReCoN within existing multicellular modelling approaches and the methods to justify our methodological choices (RWR/MultiXrank, dataset selection). We will remove the unsupported gene knockout claim from the abstract and reframe it as a future direction. In addition, we will clarify the distinction between ReCoN variants and rename them for clarity in the results section 1.2., improve figure legends. Finally, we will also work on the tool's documentation, including new tutorials on using spatial data and on running ReCoN with scRNA-seq-only GRN inference.

      We believe these revisions will substantially strengthen the manuscript and address the reviewers' concerns regarding method's robustness, generalisation, and contextualisation.

      2. Description of the planned revisions

      Reviewers' comments are in blue

      Authors' answers are in black

      Proposed text modifications are in green

      Reviewer #1

      R1.1. This is a very well-written paper; the methods used are adequate, and the use cases are relevant and broad, exploiting state-of-the-art datasets and tools.

      The author's claims are mostly justified. The authors could make an effort to more explicitly cite other efforts in similar directions. The claim 'We envision ReCoN as an extension to prior multicellular modelling, offering an interesting compromise between prediction of cell type responses and understanding of their molecular coordination.' is very general and could be better substantiated. In fact, the authors do not really give examples of alternative approaches to study systems of interacting cells, other than mechanistic agent-based models, which are clearly very different.

      Response:

      We thank the reviewer for pointing out the lack of contextualisation for ReCoN in this closing discussion.

      We wanted to remind that ReCoN builds notably on multicellular factor decomposition methods. We also want to emphasise the interest in completing cell communication methods that describe the big picture in multicellular interactions.

      • *

      We proposed to *explicitly state these two points with such rephrasing: *

      • *

      Network-based representations of multicellular systems have been an active field for many years, from early conceptual cytokine networks (Frankenstein, Alon, and Cohen 2006) to curated ligand-receptor cascades of hematopoietic tissue (Kirouac et al. 2010, Qiao et al. 2014). In parallel, and from bulk RNA-seq, the consideration of tissue specificities in GRN inference has been another way to consider the importance of the context in molecular mechanisms reconstruction (Sonawane et al. 2017). Single-cell analysis allowed decomposing tissue composition and quantifying gene expression, opening the possibility of scaling the inference of these networks and the inference of multicellular mechanisms in general, to large sets of molecules. Several methods have been developed to recover multicellularity. A first direction extends ligand-receptor interaction inference into the receiver cell response through curated signalling cascades, yielding ligand to target cascades (Browaeys, Saelens, and Saeys 2020, Jin et al. 2021, Zhang et al. 2021, Yan et al. 2025). A second direction leverages spatial context through explainable multi-view models that decompose marker variation in both intra- and intercellular contributions (Arnol et al. 2019, Tanevski et al. 2022), without considering the mediating cascades. Finally, the more recent family of multicellular factor decomposition methods focuses on the coordinated aspect of cellular programs rather than on the mechanisms. ReCoN's methodology proposes a network-based approach based on single-cell data and the philosophy of this last group of methods. Indeed, ReCoN aims to retrieve links between molecular drivers and such coordinated multicellular programs by bridging and exploring CCC inference and GRN modelling (Badia-i-Mompel et al. 2023) within large and coherent heterogeneous multilayer network.

      Arnol D, Schapiro D, Bodenmiller B et al. Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis. Cell Rep 2019;29(1):202-211.e6. https://doi.org/10.1016/j.celrep.2019.08.077.

      Badia-i-Mompel P, Casals-Franch R, Wessels L et al. Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data. Preprint, bioRxiv, 21 Dec. 2024, 2024.12.20.629764. https://doi.org/10.1101/2024.12.20.629764.

      Badia-i-Mompel P, Wessels L, Müller-Dott S et al. Gene regulatory network inference in the era of single-cell multi-omics. Nat Rev Genet 2023;24(11):739-54. https://doi.org/10.1038/s41576-023-00618-5.

      Browaeys R, Saelens W, Saeys Y. NicheNet: modeling intercellular communication by linking ligands to target genes. Nat Methods 2020;17(2):159-62. https://doi.org/10.1038/s41592-019-0667-5.

      Frankenstein Z, Alon U, Cohen IR. The immune-body cytokine network defines a social architecture of cell interactions. Biol Direct 2006;1(1):32. https://doi.org/10.1186/1745-6150-1-32.

      Jin S, Guerrero-Juarez CF, Zhang L et al. Inference and analysis of cell-cell communication using CellChat. Nat Commun 2021;12(1):1088. https://doi.org/10.1038/s41467-021-21246-9.

      Kirouac DC, Ito C, Csaszar E et al. Dynamic interaction networks in a hierarchically organized tissue. Mol Syst Biol 2010;6(1):MSB201071. https://doi.org/10.1038/msb.2010.71.

      Oesinghaus L, Becker S, Vornholz L et al. A single-cell cytokine dictionary of human peripheral blood. Preprint, bioRxiv, 15 Dec. 2025, 2025.12.12.693897. https://doi.org/10.64898/2025.12.12.693897.

      Qiao W, Wang W, Laurenti E et al. Intercellular network structure and regulatory motifs in the human hematopoietic system. Mol Syst Biol 2014;10(7):MSB145141. https://doi.org/10.15252/msb.20145141.

      Radig J, Droit R, Doncevic D et al. Tracking biological hallucinations in single-cell perturbation predictions using scArchon, a comprehensive benchmarking platform. Preprint, bioRxiv, 27 June 2025, 2025.06.23.661046. https://doi.org/10.1101/2025.06.23.661046.

      Sonawane AR, Platig J, Fagny M et al. Understanding Tissue-Specific Gene Regulation. Cell Rep 2017;21(4):1077-88. https://doi.org/10.1016/j.celrep.2017.10.001.

      Tanevski J, Flores ROR, Gabor A et al. Explainable multiview framework for dissecting spatial relationships from highly multiplexed data. Genome Biol 2022;23(1):97. https://doi.org/10.1186/s13059-022-02663-5.

      Yan L, Cheng J, Nie Q et al. Dissecting multilayer cell-cell communications with signaling feedback loops from spatial transcriptomics data. Genome Res published online 12 May 2025. https://doi.org/10.1101/gr.279857.124.

      Zhang Y, Liu T, Hu X et al. CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication. Nucleic Acids Res 2021;49(15):8520-34. https://doi.org/10.1093/nar/gkab638.

      R1.2. Moreover, the exploration of the multilayer networks with RWR is a very reasonable choice but could there be other approaches? I think the authors could discuss this issue to briefly support their choice of this method.

      Response:

      It is a very relevant comment, as this choice has not been discussed in the paper; we propose extending the method section about ReCoN's networks exploration with a justification about this choice.

      • *

      There is currently a limited set of network exploration methods that have been implemented for multilayer networks. It includes notably pymnet (Nurmi et al., 2024), natively adapted to heterogenous multilayer networks, and multinet (Bagavathi et al., 2019) and muxviz (De Domenico et al., 2015), initially developed for multiplexed networks (e.g. social network where the same set of nodes is present in each layer) but adaptable to more complex multilayer networks. However, to our knowledge, only MultiXrank proposes a robust measurement of proximity between each pair of nodes.

      Indeed, pymnet does not propose implementation for pairwise distance, similarly for muxViz, which focuses on community and motif detection. Multi-net does propose pairwise distance based on shortest paths, but implements it only for nodes of the same multiplex (e.g. in our network, it would only be two genes, or two receptors, respectively). https://www.rdocumentation.org/packages/multinet/versions/4.3.2/topics/multinet.distance

      • *

      We provide the additional justification for choosing RWR and MultiXrank over a reimplementation of another method or an extension of another method.

      • *

      • The total complexity of the RWR is O(δm) - when the number of nodes is negligible compared to the number of edges, with m the number of edges and δ the number of iterations in the walk (Baptista et al., 2022 - Supp Notes 2.A; Jin W. et al, 2019). This linear increase with the number of edges is particularly interesting for large networks, such as ReCoN ones that can contain several million* edges. The number of iteration δ and the computational time increases inversely to the restart probability, which is an important factor to keep this probability high. *

      • *

      • *MultiXrank is particularly interesting for its flexibility as it allows to easily attribute different weights to the different layers and to precise the direction of the exploration easily. *

      • *

      • It also produces deterministic results by prolonging exploration until convergence.

      • *

      • Additionally, in the context of ReCoN, the indirect effect of each cell is run independently. We previously extended the implementation of multiXrank for running RWR in parallel in a previous work (Trimbour et al., 2024), making it already adapted for optimising ReCoN's explorations.

      • *

      For all these reasons MultiXRank implementation seemed to be the best choice for robust and efficient exploration of ReCoN's HMLN.

      • *

      Bagavathi, A., Krishnan, S. (2019). Multi-Net: A Scalable Multiplex Network Embedding Framework. In: Aiello, L., Cherifi, C., Cherifi, H., Lambiotte, R., Lió, P., Rocha, L. (eds) Complex Networks and Their Applications VII. COMPLEX NETWORKS 2018. Studies in Computational Intelligence, vol 813. Springer, Cham. https://doi.org/10.1007/978-3-030-05414-4_10

      Manlio De Domenico, Mason A. Porter, Alex Arenas, MuxViz: a tool for multilayer analysis and visualization of networks, Journal of Complex Networks, Volume 3, Issue 2, June 2015, Pages 159-176, https://doi.org/10.1093/comnet/cnu038

      Nurmi et al., (2024). pymnet: A Python Library for Multilayer Networks. Journal of Open Source Software, 9(99), 6930, https://doi.org/10.21105/joss.06930

      Jin, Woojeong, Jinhong Jung, and U. Kang. "Supervised and extended restart in random walks for ranking and link prediction in networks." PloS one 14.3 (2019): e0213857

      R1.3. Generally the discussion should provide the reader the context in the existing literature in which the work can be set, detailing its impact. I think this could be improved.

      Response:

      • *

      We hope that the correction on the context proposed for comment R1.1 offers a first clarification on the context in the literature.

      • *

      We also propose to extend the description of ReCoN's impact with the following sentences in the discussion: "Unlike purely data-driven approaches, ReCoN contextualizes prior knowledge balancing both robustness through literature data, and specificity through new measurements. This mechanistic approach opens new possibilities for understanding how cellular coordination shapes tissue-level responses and for designing targeted molecular interventions."

      • *

      R1.4. Regarding the choice of datasets, it is clear that the method is quite demanding, requiring single cell and different omics to build the model, in addition to the expression dataset that is used as a use case. This inevitably leads to using a mix of datasets.

      For example in the mouse experiments the gene regulatory network was inferred from both a lymph node scRNA-seq dataset and a splenic scATAC-seq dataset, presumably due to the lack of multiome data in this setting. However the cell-cell communication network was inferred from the control case of the Immune Dictionary. Why can't the authors use the control data also for inferring GRNs?

      Is atac-seq really necessary in the inference of the GRN? What is the impact of the fact that lymph node and spleen samples might be different?

      :

      • *

      Is it a very *interesting comment, and we propose to add both 1) an explanation about our dataset choice to generate the GRN as a Supplementary text, and 2) a new experiment about the effect of GRNs built from multi-omics and scRNA-seq alone. *

      • *

      • Dataset choice

      • *

      We decided to infer a GRN using multiomics data, as these methods seem to perform better and are becoming the state of the art (Badia-i-Mompel et al. 2023, Trimbour, Deutschmann, and Cantini 2024, Yuan and Duren 2025).

      As scATAC-seq data was not produced for the Mouse Immune dictionary, we tried to find an external dataset, used HuMMuS, the method we previously developed, as it is also based on RWR and performs well on unpaired data.

      • *

      scATAC-seq

      Our first criteria was to match the mouse model used in the immune dictionary dataset, which reduced importantly the number of multicellular immune cell datasets available. We extended our research to a splenic dataset, as spleen is itself classified as a high specialised lymphatic structure, (check) and contains notably the same cell types than classical lymph nodes.

      • *

      scRNA-seq

      While we could technically use the control mice of the Immune Dictionary single-cel RNA-seq data with the spleen scATAC-seq data, the Immune Dictionary only provides 100 or less cells for each cell types per stimulation, which would results in a low number of cells. As GRN quality seems to depend a lot on the number of cell used, we favoured choosing a larger dataset.

      • *

      Our choice to use single-cell multiomics methods was driven by the novelty of these methods over scRNA-seq based ones, the performance improvement that they seemed to offer in several benchmarkings, and the will of developing a pipeline integrating the most complete data available for contextualization (Badia-i-Mompel et al. 2024).

      • *

      • GRN impact over the Human Immune Dictionary

      • *

      While it does not relate directly to this showcase, we will also add a new dataset analysis, detailed in the the comment R1.12. In the Human Cytokine Dictionary showcase,, we propose exploring the effect of choosing different GRNs, built from external multi-omics data or from the control scRNA-seq data of the dataset itself. We hope it can partially help users to decide in general wether to use external datasets of higher quality or sample-specific datasets.

      • *

      Finally, we propose to add in the documentation of the tool, a section showing how to use ReCoN with only scRNA-seq for the GRN inference, and the performance of different GRNs for the Human Cytokine Dictionary dataset directly in the paper.

      • *

      R1.5. The code is very clear, we were able to install and run it and it is quite well-documented. However, a few more details should be given in the text regarding how the evaluation of the performance is carried out.

      For example: If I understand correctly, when predicting the impact of cytokine perturbations the ReCoN predictions of genes impacted are compared to differentially expressed genes identified through traditional DEG analysis. What is compared is the ranking of these genes from ReCoN with the ranking provided by DEseq2. There is no description of how this comparison of ranking gives rise to AUROC values. Also, is it just the ranking that is predicted or can they also estimate how well they can predict the effect size?

      Response:

      • *

      We are thankful for pointing out the unclear technical details. DEG results were binarised, to obtain the list of differentially genes using the thresholds indicated in the section 4.4.4. We considered a gene as perturbed in each cytokine treatment if the comparison of control and treated cells had a t-test p-value below 0.1 and if the log-fold change was above 1.

      • *

      The second, and more general point of the reviewers, ReCoN scores should be considered to provide ranking on the possible regulations, but cannot be considered proportional to the effect size. As they are represent a likelihood more than a score, the binarisation should be the most appropriate transformation for the validation

      • *

      *Moreover, as the scores can be seen as the probability to end up the exploration on each node, they are always summing to one. This also prevents interpreting the scores as the amplitude of change. As an illustration example: if a receptor regulates three genes identically, they would (hopefully) all be having a score of (1 - R)/3, R being the restart probability in ReCoN, whether their expression doubles or is multiplied by 10. *

      • *

      While it can legitimately be seen as a downside, we believe it is similar in practice to most methods inferring GRN methods in practice, where trying to predict the true amplitude of gene perturbations usually results in very low performances (Badia-i-Mompel et al. 2024).

      • *

      We propose changes related to this comment.

      • *

      • We would modify the section 4.4.4. of the method with the following paragraph to explicit that it consists in a binary selection: "For each cytokine-cell type pair, differentially expressed genes were binarised: genes passing the significance thresholds (FDR P-val 1) were labelled as positives, and all remaining genes as negatives. ReCoN scores were then used to rank all genes, and AUROC values were computed from this ranking against the binary labels."

      • *

      • We will also include a section "ReCoN scores interpretation" on the documentation website, as score interpretation precisions will be particularly useful for users.

        R1.6. When describing the use cases, I think a bit more detail would help.

      For example 'To identify the cell-type-specific genes associated with HF, we used the MOFAcell scores of the multicellular factor 1 (MCP1) reported in ReHeat236' I supposed the explanation is on the dataset but for the sake of clarity it would be good to expand this sentence to give at least an idea of the approach.

      Response:

      • *

      We completely agree that more explanations should be provided, to avoid for the reader having to switching between articles to understand the concepts behind this showcase. As suggested by the reviewer, we propose a general description of the approach with the short paragraph, and to remove the term "loading":

      • *

      "In the ReHeat2 study, the first multicellular factor (MCP1) was associated with heart failure. We used the gene loadings of MCP1 as a proxy for the cell-type-specific transcriptomic changes associated with heart failure, ranking genes by their absolute loading values."

      • *

      We also propose to complete the method section: "MOFAcell is a multicellular factor analysis method that decomposes multi-sample single-cell data into latent factors representing coordinated gene expression patterns across cell types. Each factor is characterised by cell-type-specific gene scores, reflecting their individual contribution to the coordinated program. In this showcase, we use the first multicellular program (MCP1), as it was associated with heart failure"

      R1.7. Regarding the calculation of the R matrix from the NichNet matrices L and G, I gather that the R matrix is calculated once and is thus fully data-independent and available just like the L and G matrices from NichNet. This was not very clear in the tutorials.

      Response:

      • *

      We are very thankful for the reviewers' involvement in testing the tools itself and its documentation. First, we propose a new website page explaining the pre-computed resources available for receptor - gene links, and added a descriptive paragraph in the tutorial themselves.

      *Second, we notice a typo in the equation, where it should actually be L = R * G with the current definition. We corrected it in the next version, and precised that R is fully data independent and solely inferred from prior knowledge. *

      R1.8. Also, this might just be a typo in the tutorial: 'The default α = 0.8 gives more weight to direct effects, which has been empirically validated. You can adjust this based on your biological question." I believe the manuscript says alpha>0.5 refers to indirect effects dominating.

      Response:

      • *

      We corrected the saying in the tutorials. Indeed, a high alpha represents a stronger indirect effect. Additionally, a similar typo was in the first equation of the paper, we are correcting it too.

      R1.9. Same for the pre-processing of the spatial data for the third use case, a little more details on how this was done would help the users and readers.

      Response:

      • *

      We propose adding a specific section about the spatial pre-processing and analysis in the methods.

      We are also adding a tutorial on spatial data. Since spatial data processing is computationally intensive without GPUs, we will also provide the data already processed, in order to allow anyone to test this tutorial too.

      • *

      R1.10. I don't see issues with the statistical power of the analysis.

      Rather, I think the authors should provide some examination of the parameter space for their model. Whereas ana analysis of the impact of the Alpha parameter is provided, I believe there are several more parameters that have a crucial impact and choices for their values should be discussed.

      For example 'In the GRN reconstruction only the links with a score above 1.5e-7 were retained in ReCoN's gene regulatory layer. How was this chosen?

      We have identified the following parameters that are somehow justified but could be explored to have a better feel for how they impact the results

      Restart probability: How often the walker goes back to the starting seed/molecule

      Layer transition probability: How often the walker stays in the same layer - different cell? - different layers? Gamma

      Node transition within a layer: How often one jumps to a different layer

      Response:

      This is a very valid point raised by the reviewer about parameters explorations.

      • *

      We focused on exploring the alpha (direct/indirect effect) parameter, as its value was the incertitude when designing the model.

      • *

      We would like to address this comment by adding new explorations for the restart probability and the transition probability between layers. The probability to transition between specific nodes inside a layer directly depends itself on 1) the restart probability, 2) the transition probabilities, and 3) the weights of the edges, that are determined before and independently to ReCoN's exploration.

      • *

      The Heart Atlas showcase allows to evaluate each set of parameters in around 10 min instead of 10h for the Immune Dictionary. We thus propose to evaluate restart probability and layer transition probabilities on the data of this showcase.

      • *

      • We would explore the restart probability of 0.1 * N, with N between 1 and 9.

      • *

      • For transitions probabilities we propose varying GRN, receptor, and cell communication importance with the following configurations: - Staying in CCC probabilities (- not jumping to receptor layer) among (0.1, 0.3, 0.5, 0.7, 0.9), staying in receptor layer (- not jumping to GRN) of (0.25, 0.5, 0.75), staying in GRN layer (- not jumping to CCC) of (0.25, 0.5, 0.75). It would result in 9 intracellular variations combined with 5 intercellular variations.

      • *

      We envision an evaluation by measuring the correlation between the results of the different configurations, and the time before convergence of the results, as it could potentially increase drastically when decreasing the restart probability. If correlations below 0.9 are observed between some results, we will compare their absolute performances.

      • *

      We would include the figures related to these explorations in the supplementary data. We would highlight the main findings in the method section dedicated to the random walk with restart. Finally, we would briefly describe the parameter exploration design in the first section of the results, for curious readers who would like to verify parameter choice before reading the showcases.

      • *

      R1.11. Weighting parameters: How much weight for direct or indirect effect to account for the combined effect - alpha - this is the only one that is explicitly explored.

      Response:

      We are very thankful for this comment, and we decided to modify our tutorial guidelines to make this choice more intuitive and general.

      • *

      Indeed, 1.5e-7 would hardly make sense for most methods, which would not produce such low scores. We now propose to select the first 2 million connections of GRNs, in order to keep a complete or a large portion of the network if other methods than HuMMuS are applied.

      • *

      In our case, 1.5e-7 was empirically determined from the distribution of HuMMuS scores, to keep the 2 million top connections as HuMMuS networks are generally almost fully connected, which is a particularity for classical GRN inference methods, and keeping it entirely would make exploration time much longer.

      • *

      R1.12. Finally, this might be considered OPTIONAL but would greatly improve the work in our opinion:

      The method crucially depends on the networks that are used in the different layers and to connect layers and cell types. As we know, biological data is noisy and incomplete (FP and FN) at each level and in each datatype. It would be really useful to estimate what is the robustness of the results to this noise. Particularly, from personal experience, we think the GRNs reconstructed from data are often almost fully connected and it is exceedingly difficult to validate them in specific contexts. This means that some 'errors' are likely to be present.

      Since several methods exist for inferring GRNs one could simply compare the results using different methods for this part of the network.

      A related point involves the characteristics of the RWR algorithm, that will be quite impacted by the presence of hubs in these networks (either in single layers or across several) that is likely to impact the exploration. If proteins that are hub are effectively important, that is not a problem, but in some layers, for example, the receptor-receptor layer that presumably will contain PPIs, there might be biases in hubs being just better studied proteins, and these hubs might have an 'unjustified' weight in the walks.

      One potential approach to assess the robustness of the method to these issues could be an empirical one that just randomly perturbs the networks in ReCoN to see to what extent similar predictions are achieved.

      *Response: *

      • *

      We are thankful for this relevant comment on GRN and prediction stability, and would like to take it as an opportunity to support the hypothesis that different GRN methods can be used in ReCoN.

      • *

      When developing our previous HMLN-based tool, HuMMuS (Trimbour et al. 2024 - Supp Figure 6), we observed that its multilayer structure provided more robust results than individual layers. We would like to reproduce such an analysis, verifying that ReCoN results have less variability than the GRN layers individually.

      We propose to integrate a new showcase on the Human Cytokine Dictionary (Oesinghaus et al. 2025), trying to predict cytokine downstream effects similarly to the Mouse Immune Dictionary showcase.

      This showcase would be useful to confirm the contribution of the indirect effect and test the impact of different GRN on the results.

      We would generate different GRN with several other GRNs methods: SCENIC+, CellOracle, and GRNBoost2 - the latest using only the scRNA-seq of the control samples in the Human Cytokine Dictionary.

      • *

      The GRN methods produce generally output with very low overlap (Badia-i-Mompel et al. 2024)*. *

      *If we observe high correlations between the ReCoN predictions associated with the different GRNS, it would provide already a validation of ReCoN's robustness to GRN noise. *

      If lower correlations between ReCoN's predictions are obtained, we will add a specific permutation experience over the HuMMuS GRN, creating different level of artificial noise and assessing more precisely the robustness of ReCoN to GRN stochasticity.

      • *

      Regarding PPI hub justification, our *applications did not use receptor PPI and are not affected by bias at this level in the showcases. This bias could specifically be present in the receptor-gene links, as we derive it from the ligand-gene connections of Nichenet which was itself partially based on prior knowledge. It is thus possible that some receptor are reached more often due to this bias and not a stronger effect. It seems however, hard to control in this context, as ReCoN currently relies on this prior knowledge. Currently, we hope that the combination of personalised, literature-agnostic GRN with literature-based receptor - gene can provide an interesting trade-off. In future development, we could imagine a receptor-gene network based solely on perturbations, but it would require controlling also the bias of ligand - receptor binding couples, which limits even the use of ligand-based experience. *

      We propose adding a short point in the discussion about hub effects from RWR-based methods.

      • *

      R1.13. Please add page numbers.

      *Response: *

      • *

      We will add the page numbers.

      • *

      R1.14. Figures are nice and clear.

      Some specific minor points are listed here below.

      Define hMLN on first appearance fig1 caption (no page numbers..

      2nd appearance heterogeneous multilayer structure (HMLN) ...

      Response:

      • *

      We updated the legend of the figure to include the definition of the acronym, as it arrives before first text occurrence. (Or define at both positions ?)

      R1.15. Bi_j not so clear to what it refers when first mentioned

      Response:

      • *

      *Bi_j represents a weight that can be attributed to favour some cell-to-cell transitions. It is usually not necessary to use them.

      *

      *It is of interest notably to model 1) known spatial patterns in situ and hypothesis/design where cell types favour some connections. *

      • *

      E.g.: for modelling the skin, a user might notably want to increase connections between epidermic and dermic cells, and between dermic and hypodermic cells.

      • *

      We propose a new explanation of Bi_j to both explain it's meaning in the modelling, and illustrates situations for using it: "The coefficient B_{i,j} modulates the influence of cell type i on cell type j in the indirect effect computation. By default, all B_{i,j} are set to one, weighting each cell type's contribution equally per cell. However, it can be adjusted to encode additional biological knowledge, such as spatial proximity between cell types or known cooperation patterns. For instance, when modelling the skin, a user might increase B_{i,j} between epidermal and dermal cells, and between dermal and hypodermal cells, to reflect their spatial organisation."

      R1.16. personalized interaction specificity. - maybe better word than personalised (contextualised?)

      Response:

      • *

      We agree that contextualised explicits better the meaning behind this model. Personalised might notably lead to expect patient-specific data, which is not the case here.

      • *

      We propose to rephrase all the model names to : Receptor-matrix, ReCoN-no-CCC, ReCoN-no-context, ReCoN-complete.

      R1.17. ReCoN-genetic and ReCoN, ( generic?)

      Response:

      • *

      We will correct this typo.

      R1.18. responses. It is expected to observe common behaviors in-between cell-type, that the GRN

      and the generic CCC network already contribute captures.

      • not very clear

      Response:

      • *

      We aimed here to provide an explanation to the already good performance of the "ReCoN-no-context" (or its name updated according to comment R1.16), which could be surprising as no cell-type specific information is used. The explanation proposed is the good prediction of several properties shared by all immune cell types, such as similar metabolic pathways, despite their specific roles. If we adopt a quantitative view on their transcriptome like in this showcase, it can be expected that the cell type responses are relatively well predicted through the common properties only.

      • *

      As this is a very relevant comment, and that several comments pre-submission we received were also related to this result, we would like to keep an explanatory sentence.

      • *

      R1.19. Figure 2b the icon of cells with double arrows might suggest phenotype shift when instead this is just communication

      Response:

      (left side) We are very thankful for paying attention to the details of the paper and fully agree with this analysis. We propose to represent ligand emission instead of arrows, reusing the convention of the Figure 1.

      R1.20. eTACs explain acronym and what they are

      Response:

      • *

      We update the first occurrence of eTACS to extrathymic Aire-expressing cells (eTACS).

      R1.21. Due to very few genes being differentially

      expressed, only cDC1 was conserved and evaluated for IL22,

      Not so clear

      Response:

      • *

      As we are commenting on IL22 stimulation results, we reorganised the sentence to make it less convoluted: "For IL22 stimulation, only cDC1 presented enough genes being differentially expressed."

      R1.22. In this showcase (not very clear, use case?)

      Response:

      • *

      We perceive "use case" as describing a type of use for the method, while a show case is a specific example of a use case. We thus find showcase more appropriate here. We will however go over all use of the word, to be sure it is only used for the precise examples we provided, and not to describe "use cases".

      R1.23. different fibroblast specializations - maybe phenotypes?

      Response:

      • *

        • It is a very good suggestion, as specialisation would involve functional aspects (that we can't really be sure of), and a chronological evolution*
      • Phenotype generally includes numerous properties, such as morphology, that we cannot validate here. We think the use of phenotype might be stronger than specialisation here. To simplify, phenotype can work, to be more precise: transcriptomic specialisation? I am honestly not sure of the best change here.

      R1.24. Figure 4b

      1. b) Schematic view of the deconvolution process and cell type-specific count inference from the spatial niches.

      Not so clear what the heatmap shows, rows and columns

      Spots heatmap : label niche on rectangles in cols

      And each col is a spot

      Rows are cell types or cells?

      In the cell types x spot

      Response:

      This figure can indeed benefit strongly from legend modifications. On both matrix, lines represent the genes, while columns represent the spot / individual cells deconvoluted per spots

      • *

      • We would annotate the niche legend (here the colour surroundings) by a symbolic drawing instead of writing it on the matrix

      • *

      Legend "genes" on the first matrix

      • *

      Write deconvolution ON the figure directly

      R1.25. Cell2location. Add reference, maybe explain basic functionality?

      Response:

      • *

      Cell2location was not referenced in the results section, and was only referenced in the section 4.6.2 of the methods, as the 72th citation. We corrected this oversight, and propose 1) a brief explanation of deconvolution right before, 2) a brief explanation of Cell2location particularity in inferring individual cell profiles - which is not common in spatial deconvolution.

      R1.26. reconstructing different patients, tissues, and microenvironments to predict

      context-specific molecular treatments.

      Unclear

      fibrosis in different - at

      molecular levels

      Response:

      • *

      We will modify this section title according to the reviewer's citation and the different reformulation.

      R1.27. Figure 5d myeloid and endothelial colour code inversed from 5 BC

      Response:

      • *

      The legends are individually correct, but there is no reason to not make them coherent across panels. We will update the legend of the panel 5.d..

      • *

      R1.28. 5d indicate important pathways in organe should not change the colour of the nodes (purple=common, blue or green specific). Use border colour maybe?

      Response:

      • *

      We had forgotten to precise the colour code of this panel, where the choice of orange highlighted here the gene set related to molecular pathways instead of functional annotations. As the name already explicits pathway, we now think that the orange background is redundant informations and may create some confusion. We thus would like to update Wnt and TNFA pathways backgrounds to ___ (more enriched in cell type), and purple (significantly enriched in all cell types).

      R1.29. 5e is not a venn diagram

      1. e) Venn diagram showing the overlap between transcription factors (TFs) predicted by ReCoN (green) and those previously

      implicated in fibrosis (orange) or cardiac diseases (violet). Only the top 10 TFs were annotated from literature

      sources; full sizes of fibrosis- and cardiac disease-related receptor sets can therefore not be represented.

      1. f) also not a venn diagram e/f now in supp

      the "NABA ECM collagens" gene set. Nodes are

      grouped by molecular type (e.g., transcription factors, receptors, ligands), and links represent the weighted,

      direct regulatory interactions present in the ReCoN-constructed

      Response:

      • *

      As the diagrams do not indicate the total number of receptor/TF that are in the literature, it cannot be Venn diagrams. We updated the legend to :Venn diagram showing the Overlapp between [...]

      • *

      As we reorganised the paper, these plots are now only in supplementary; we removed the duplicate occurrence in the figure 5 legend.

      R1.30. Why Sankey plot? Normally sankey plot represents flow (of regions changing from 1 state to another) but here this is just a weighted network?

      No communication from firbos back to other cell types? No communication between ventricular/myeloid/lymphoid?

      Response:

      • *

      We are thankful for this useful feedback which helped us realising interesting details were missing from the paragraph.

      • *

      *This is only intended for visualising regulatory cascade, so users have to decide on one receiving cell, a set of target genes, and sending cells. It includes a specific subset of regulatory cells, and only their interactions with the target cells. Here, we illustrated the regulation of some ECM genes produced by fibroblast. *

      • *

      Sankey Diagram might indeed not be the clearest representation, as we are not modelling the all diffusion, and not a flow per se. We propose to replace by another representation that we hope will be more intuitive for biologists (and more aesthetic), such as illustrated below:

      R1.31. as a extension to - an

      underrepresented in the current. - current framework?

      Response:

      • *

      framework works perfectly to fill the missing word in the sentence

      • *

      R1.32. However, it can't represent more - cannot

      Borrowing representation from hypergraphs, which introduces

      The network exploration implementation of ReCoN also present some limitations.

      limitations. While random walks

      with restarts offer a stable and fast exploration workflow for multilayer networks, it

      currently only considers positive weights to predict regulation strengths. It involves that the

      nature of the regulation, as activation or inhibition, has to be identified a posteriori.

      • check concordance/grammar

      Response:

      • *

      We will update the raised grammatical errors

      • *

      R1.33. Only the nodes that are included in one of the layers are present in the

      final results, ignoring the ones present only in bipartites.

      Unclear

      Response:

      • *

      Layers and bipartites are treated differently by the algorithm, and layer presence is necessary to appear in the results.

      • *

      In practice, it just means that receptors/ligands not paired in the CCC, or genes not regulated by any TF in the GRN, won't appear.

      • *

      We propose clarifying with this second explanation

      • *

      "In practice, a node must have at least one connection in its layer to appear in the final results. It thus means that receptors or ligands absent from the CCC network and genes not targeted by any transcription factor in the GRN will not receive a score from the random walk exploration."

      • *

      R1.34. a scATAC - an

      • *

      Barsi et al is published https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013188

      Response:

      • *

      We updated the reference with the published article.

      R1.35. effects, allowing for modulating in a second

      time their contribution. - word order

      Response:

      • *

      We propose to formulate "allowing in a second time to modulate their contribution"

      R1.36. others. However, it is possible to adjust the Beta coefficient to

      represent it based on the available information for each dataset.

      Represent- adjust?

      Response:

      • *

      We agree with the reviewer's suggestion to use adjust.

      R1.37. We use the latter to compare the different models. - what is the latter?

      Response:

      • *

      The latter referred to the 25 cytokines of the Immune Dictionary which had at least one connection in the inferred cell communication network with CellPhoneDB. We propose clarifying this formulation to "..."

      R1.38. It resulted in the scRNA-seq in 1,789 cells with 13,167

      genes, and for the scATAC-seq in 3,759 cells with 254,545 regions.

      Check english

      Response:

      • *

      We propose replacing this sentence by the following: "It resulted in a scRNAseq dataset of 1,789 cells with 13,167 genes, and a scATACseq dataset of 3,759 cells with 254,545 regions."

      R1.39. GRETA pipeline.- reference

      Response:

      • *

      We added the citation to the paper of the GRETA pipeline in the section 4.5 of the methods: "Badia-i-Mompel et al., 2026"

      R1.40. We kept all the cells whose annotations through unsupervised clustering,

      followed by marker gene annotations, through scANVI were coherent.

      Word order

      Response:

      • *

      We propose the following reformulation to correct the sentence: "We kept all cells whose annotations were coherent between unsupervised clustering with marker-gene labelling and scANVI-based label transfer"

      R1.41. In parallel, pairs of ligands and receptors with both associated with scores above

      an absolute gene loading of 0.1 were considered potential driver interactions in HF.

      Unclear

      Response:

      • *

      In the MOFAcell results, factors correspond to linear combination of genes that explain a large part of the data variance; the contribution of each gene is called loading. We chose the factor that classified the best patient with and without fibrosis, and kept all the top genes, all of those with a score above 0.1.

      • *

      We propose reformulating this sentence as the word "loading" could overcomplicate here for most readers: "To identify the ligand and receptors driving heart failure, we considered all of those with an absolute contribution to the multicellular factor of 0.1."

      R1.42. gseapy Python - reference?

      Response:

      • *

      The gseapy package was indeed not cited, we now include the citation : "Zhuoqing Fang, Xinyuan Liu, Gary Peltz, GSEApy: a comprehensive package for performing gene set enrichment analysis in Python, Bioinformatics, 2022;, btac757, https://doi.org/10.1093/bioinformatics/btac757"

      R1.43. and to calculate average for each spatial context the average cell type expression.

      Unclear

      Response:

      • *

      we propose to reformulate the sentence to: "These cell-type-spot profiles were used later for each spatial context to create a specific cell-cell communication networks and to calculate cell type average expressions."

      R1.44. We only used the loadings of all cell

      types but the fibroblasts to consider the effect of the sole environment.

      Unclear

      Response:

      • *

      we propose to use "APART from the fibroblast" to clarify the sentence and "to ONLY consider the environment effect".

      R1.45. We realised a downstream - performed

      Response:

      • *

      We fully agree with the reviewer's suggestion.

      R1.46. The profiles inferred by ReCoN were first very correlated in all three contexts. - unclear

      Response:

      • *

      The sentence was missing clarity and deserved being rephrased. We propose: "When looking at the absolute scores of ReCoN in all three contexts, results were initially highly correlated. To focus on context-specific differences, enrichments were performed using the log-ratio of each context profile over the mean of the other profiles."

      • *

      R1.47. Potentially the closest results are models that can predict the effect of perturbations on cell line cultures. Several approaches in the literature employ either transformers or optimal transport to predict the effect of perturbations in single cell datasets. One of the main issues is an underlying necessary assumption that the perturbation effect will be larger than the heterogeneity (in cell lines for example), which becomes increasingly difficult when considering in-vivo experiments. ReCoN obviously goes beyond this by considering explicitly the presence of different cell types but distinctions of cell types are sometimes quite arbitrary and potentially application of ReCoN to some of the in-vitro culture datasets, even on cell lines, could be a way to test its performance and benchmark it against other methods.

      The main bottleneck in the application of this framework to 'personalisation' of therapies, mentioned even in the abstract as a potential future goal for such an approach, will be the lack of data. This approach requires single cell level descriptions of the system at hand, plus additional datasets to build the model structure. To a certain extent, public data of related tissues/contexts can be used, but it will be necessary to test the dependence of performance on coherence of the input data to develop sufficient trust to use it for new predictions, especially in a medical field.

      • *

      We thank the reviewer for these reflections, which raise several distinct points that we would like to add in the discussion.

      Cell line perturbation is indeed a close and active field of research, with notably numerous models based on optimal transport and VAE and relevant benchmarks(Radig et al. 2025)*. In our view, ReCoN tries to take a complementary angle, by both focusing on the environment effect and using a network-driven approach providing explainability. *

      These perturbation methods are typically benchmarked on single cell line screenings, where cell-cell communication is highly limited or absent by design, while ReCoN is specifically designed to exploit multiple cell types interactions. Furthermore, ReCoN relies on a network that aims to provide only explainable hypotheses and molecular cascades. They also typically learn from different data, as ReCoN only uses single-cell data and best perturbation prediction methods learn from a subset of perturbation experiments.

      Exploring the performance of ReCoN in perturbation predictions would require designing extensive comparisons with the state-of-the-art taking into account all these nuances which we believe goes outside of the scope of the present study. It however still raises a fundamental question for the development of the next methods and the need to assess whether the perturbation effect is actually larger than the heterogeneity, and we propose to extend the discussion to cover these aspects.

      Secondly, this comment raised a point about cell type definition, which can be a hard task and sometimes a wrong description of cells heterogeneity. We note that even if ReCoN relies on grouping cells in some way, it does not impose any particular cell type ontology: users can define their own cell types or cell states, since the CCC layer is typically inferred from single-cell RNA-seq alone and does not require canonical cell-type annotations. This flexibility allows ReCoN to accommodate finer or coarser groupings depending on the biological question. We do not propose a framework to take into account diversity in other ways than homogeneous clusters of cells, but we think that it constitutes an interesting future development of ReCoN or new multicellular modelling methods.

      Lastly, we fully agree that an important limitation for ReCoN's use is data availability and generation, which was also a limitation when identifying datasets for the manuscript's applications. We hope that the development of open source atlases will make it easier to leverage tissue-specific prior knowledge and increase potential application, prediction performances, and trust in ReCoN results.

      In conclusion, we propose to state in the discussion two new points:

      *1) extending multicellular perturbations (including gene knock-out) to conditions where cell types cannot be defined prior to the analysis, or are more to consider across a spectrum, will be an interesting future direction. *

      2) there is new a need for broad benchmarks covering both multicellular and single-cell line tasks to evaluate the trade-off between accounting for cell heterogeneity and overall prediction accuracy.

      Radig, J., Droit, R., Doncevic, D. et al. scArchon: a scalable benchmarking framework for assessing single-cell perturbation models. Genome Biol 27, 162 (2026). https://doi.org/10.1186/s13059-026-04104-z

      R1.48. The authors could comment on how their method compares to others that do not require single cell level information. Despite clear differences, it might be important to show the advantage of using this more complex approach that requires data that is less available. Given the ease with which bulk profiles can be constructed from single cell data, it might be possible to compare the approaches directly. For example, see

      1. Wang, S. Patkar, J.S. Lee, E.M. Gertz, W. Robinson, F. Schischlik, D.R. Crawford, A.A. Schäffer, E. Ruppin Deconvolving Clinically Relevant Cellular Immune Cross-talk from Bulk Gene Expression Using CODEFACS and LIRICS Stratifies Patients with Melanoma to Anti-PD-1 Therapy

      Mike van Santvoort, Óscar Lapuente-Santana, Maria Zopoglou, Constantin Zackl, Francesca Finotello, Pim van der Hoorn, Federica Eduati,

      Mathematically mapping the network of cells in the tumor microenvironment,

      Cell Reports Methods 2025

      We propose to extend the discussion with additional methods, notably from before single-cell technology developments. We did not plan to include this two specific methods, as to our knowledge, they don't provide output directly comparable to ReCoN's purpose.

      • The first work proposes to deconvolute the bulk RNA-seq profile into cell-type-specific expression profiles. It is an interesting reference, as it could allow applying ReCoN even to bulk RNA-seq, but they do not provide comparable results, as their final task corresponds to inferring the ligand-receptor interactions, without providing downstream molecular mechanisms.
      • The second method proposed in this paper, RaCInG builds cell-to-cell networks for individual patients. They do not explore the molecular interactions inside the cells themselves, which could be used to build personalised ReCoN's model but seem to be more a prior to recent CCC than ReCoN itself.
      • *

      • *

      Reviewer #2

      R2.1. It is not clear how well it performs in independent validations. Authors showed that it can predict the effect of cytokine perturbations in the immune dictionary by selecting an optimal alpha. Authors should validate that using the same alpha value of 0.8, it is possible to accurately predict the effect of cytokine perturbations in independent datasets. This is particularly concerning for cytokine-cell type pairs where the optimal alpha is not known. Therefore, the potential utility of Recon to estimate the effect of multicellular perturbations is not well established.

      • *

      Response:

      • *

      *The reviewers raised a very relevant point by pointing out that the alpha coefficient might vary between datasets. *

      • *

      The value of 0.8 was chosen because it produced the best results in two independent datasets, the immune dictionary and the heart failure showcases. We could here observe some cross-dictionary reproducibility. To complete these findings, we will also verify that 0.8 provides the best performance in a new showcase: the Human Cytokine Dictionary (Oesinghaus et al. 2025)

      • *

      We tried to contrast this choice by opening on the need to confirm the importance of the indirect effect. We propose to add a sentence explicitly commenting on the impact of these new findings on the alpha coefficient and its robustness value.

      • *

      It is also accurate to say that ReCoN cannot currently estimate the alpha parameter autonomously. We proposed this default value as it worked on both datasets, but it is possible that no default value could fit them all. The value of alpha is currently a default value, but users are completely free in the current implementation of ReCoN to modify its value depending on their needs

      If it was not the case, one option could be to fit its value using similar prior perturbations, when such data is available. For example, perturbing one or a few cytokines, a user could choose the value that explained the best the gene expression responses.

      • *

      R2.2. Authors claimed that optimal alpha value of 0.8 implies the dominance of indirect effect. But in contrast to this claim, the performance across cytokine-celltype pair only increased from 0.72 to 0.76, which seem to imply that indirect effects do not add much.

      *Response: *

      • *

      The range of performance improvement is an interesting point to discuss for us, as it roughly doubles the computational time and consequently a trade-off between resource usage and this improvement.

      • *

      While the average improvement from combining the direct and indirect effects observed on the first showcase was around 5%, it reached more than 10% in some cell types. We consider that it still corresponds to an interesting improvement for the current task. Indeed, it here "only" incorporates the coordination of immune cells to a cytokine stimulation, which should not necessarily change their profile drastically compared to isolated exposition.

      R2.3. How does the cell-type specific effects prediction perform by just considering the intracellular layers? The authors constructed multiple variants of ReCoN to estimate unicellular and multicellular effects. How is the variant ReCoN-grn different from full ReCoN where gamma is set to zero.

      *Response: *

      • *

      We are thankful for this comment, which will help to restructure the section 2.2.

      • *

      As the ReCoN-GRN differs from the full ReCoN model, even with a gamma value of 0, as the latest include ligand-to-receptor weights. However, the ReCoN-GRN would correspond to the ReCoN-generic with an alpha of 0, which does not weight ligand-to-receptor links.

      • *

      We propose to clarify this detail in the section 2.2.2 by adding after the introduction of the ReCoN-generic model the sentence: "Note that ReCoN-grn corresponds to the ReCoN-generic model with alpha set to zero, where no indirect effects are considered. It differs from the full ReCoN model with alpha set to zero, which still includes ligand-to-receptor weights through the receptor-gene bipartite network."

      R2.4. In section 2.2, authors assert that if matching datasets are not available, GRN layer can be extracted from other datasets. How well does the GRN layer from one system generalizes to the other system in terms of perturbation prediction?

      *Response: *

      • *

      It is, of course, a complex question, as it probably strongly depends on the studied system. However, we believe while it is important to consider similar systems, using the same samples for the cell-communication and the GRN layer is not necessary.

      • *

      The first showcase that we propose explores exactly this case. We built the GRN from two unpaired datasets, and the cell communication from a third one. It provided convincing performances, justifying our earlier claim. It is additionally something done in most methods contextualising prior knowledge, which usually comes from other samples and sometimes even other organs (Browaeys, Saelens, and Saeys 2020, Jin et al. 2021, Badia-i-Mompel et al. 2023).

      • *

      To provide additional insights, we will run the new Human Cytokine Dictionary showcase using both 1) multiomics methods on external PBMC datasets, and 2) a single-cell RNA-seq only method on the Human Dictionary directly. We will then be able to show performances using both data and corresponding methods.

      • *

      To justify more clearly our claim according to reviewer's comment, we propose highlighting in the showcase itself this justification: ".... this showcase highlights the possibility to combine networks obtained from distinct datasets...".

      Related to combining datasets, we propose to clarify the reasons behind our choices for the Immune Dictionary showcase with the additional supplementary text proposed in response to the comment R1.4.

      • *

      Badia-i-Mompel P, Wessels L, Müller-Dott S et al. Gene regulatory network inference in the era of single-cell multi-omics. Nat Rev Genet 2023;24(11):739-54. https://doi.org/10.1038/s41576-023-00618-5.

      Browaeys R, Saelens W, Saeys Y. NicheNet: modeling intercellular communication by linking ligands to target genes. Nat Methods 2020;17(2):159-62. https://doi.org/10.1038/s41592-019-0667-5.

      Jin S, Guerrero-Juarez CF, Zhang L et al. Inference and analysis of cell-cell communication using CellChat. Nat Commun 2021;12(1):1088. https://doi.org/10.1038/s41467-021-21246-9.

      R2.5. In the abstract, authors claimed that ReCoN can predict the effect of gene knockouts. But authors did not show any application or validation to support this claim.

      Response:

      • *

      We indeed had no showcase that could explicitly measure the performance of ReCoN directly for gene knockout, while the possible application was introduced in the abstract.

      * We believe that ReCoN could be used in the future to infer such perturbations, but we fully agree that this claim cannot be presented without justification.

      We propose to remove the introduction of gene-knockout there, and to introduce it in the discussion opening instead, specifying that it will require specific experience and constitutes a possible future extension of the work.*

      R2.6. The communication between cells might be dependent on their spatial proximity. Is it possible to construct the CCC layer by incorporating the context-matched spatial data? How would that affect the performance of multicellular response prediction?

      Response:

      • *

      *This is a very interesting comment as numerous methods using spatial transcriptomic data have been published recently. *

      • *

      In the current formulation, the beta coefficient Bi_j modulates the impact of the cell type i on the cell type j. If the spatial transcriptomic data can inform on the proximity between cell types, and its overall impact on their communication, users could enforce more communication between some.

      • *

      However, as ReCoN is a cell-type centric model, adding spatial information can only be done at a general scale, or by modelling independently spatial regions such as presented in the Microenvironments heart infarction showcase. It means that ReCoN cannot beneficiate from the potential of spatial transcriptomic as much as models representing the tissue structure.

      R2.7. In the fibroblast application in Fig 4d, based on the cardiac cell types expression in region type, they are predicting fibroblast gene expression. Wouldn't the most direct benchmarking be comparison with observed fibroblast expression from the ST (after deconvolution perhaps)?

      Response:

      • *

      This was a helpful comment to guide the restructuration of the microenvironment heart infarction showcase, as we believe the whole showcase objective was not formulated clearly enough.

      • *

      We aim at modelling the impact of the environment on the transcriptome. As the complete transcriptome of a cell results from numerous interacting variables, we believe that comparing the correlation between ReCoN's scores and the transcriptome would not evaluate the prediction of the environment impact.

      • *

      For this reason, we wanted to compare the results to the specific differences from the microenvironment. We focused on gene set enrichment that seemed less noisy for such a comparative experiment, in particular from Visium10X data that has a particularly high dropout rate.

      • *

      We propose to strengthen the validation by providing molecular insights into the three groups of cells studied.

      The spatial data themselves are bulk, adding a layer of noise over the small number of genes captured by Visium. Instead of a correlation with the deconvoluted spots, we have equivalent single-cell RNA-seq fibroblast data annotated in the same study, which matches the three modelled niches. We propose to conduct a differential expression here and try to compute a correlation between these groups and ReCoN scores, providing a quantitative analysis.

      If the correlation was low because of the noise in the data (notably leading to the permutation of individual gene orders even if overall biological signals and gene set orders are conserved), we will additionally do a pathway enrichment over this data, enriching also the qualitative validation.

      R2.8. Section 2.6 Besides the cytokine section, it is difficult to assess the added value of this approach. Likely there is a lot of valuable findings here but difficult to say because the assessment is very qualitative.

      Response:

      • *

      One of the challenges around this work was to find relevant dataset to evaluate ReCoN. We tried to complete the direct quantitative evaluation from the Immune Dictionary with another quantitive evaluation from the heart atlas multicellular programs, despite a much less direct validation.

      • *

      We hope that the production of new perturbation experiments over multicellular datasets, especially cell-type targeted perturbations, will provide more opportunities to validate the different findings and claim from our current manuscript.

      • *

      On a similar note, no method seemed proposing similar predictions to be compared to. It led to the use of Nichenet score and the current decomposition of the ReCoN model in the section 2.2.1 to evaluate the contribution of the model.

      R2.9. The article is dense and writing should be reorganized for better readability.

      Minor issues -

      No p-values in figures.

      *Response: *

      • *

      We agree that integrating values directly in the panels would make the reading of the figure easier. We would like to introduce the p-values in the panels 2d, 2e, 2f, 2g. We had forgot to indicate in the legend of the panel 4.d that all bold scores were associated with a p-value *

      R2.10. Typo - ReCoN-genetic should be - ReCoN-generic.

      • *

      Response:

      • *

      We are thankful for noticing the typo and corrected it in the new version.

      • *

      R2.11. Authors may consider adding figures to describe their results on balance between direct and indirect effects in section 2.2.2.

      • *

      Response:

      • *

      Depending on the new findings on the indirect effect iterations, we propose adding an additional panel on their combination or a supplementary figure.

      • *

      R2.12. Redundancy in the following two lines -

      o While these approaches effectively describe what tissue-wide programs are coordinated, they generally offer limited insight into the molecular mechanisms that establish or regulate these programs.

      o Despite their ability to identify coordinated tissue-wide programs, multicellular program analyses typically offer limited insight into the underlying molecular mechanisms that orchestrate these programs.

      • *

      Response:

      • *

      We propose in the version of the manuscript to remove the first sentence. In our opinion, starting the next paragraph by this clarification seems more helpful to guide the reader than having it at the end of the previous one.

      3. Description of the revisions that have already been incorporated in the transferred manuscript

      Please insert a point-by-point reply describing the revisions that were already carried out and included in the transferred manuscript. If no revisions have been carried out yet, please leave this section empty.

      • *

      4. Description of analyses that authors prefer not to carry out

      Please include a point-by-point response explaining why some of the requested data or additional analyses might not be necessary or cannot be provided within the scope of a revision. This can be due to time or resource limitations or in case of disagreement about the necessity of such additional data given the scope of the study. Please leave empty if not applicable.

      R2.13. The direct and indirect effects are treated in two separate steps. In reality of course these effects are operating simultaneously. I wonder if this could be better modelled by iterating through the two steps. It might be worthwhile

      trying to see if that improves the performance.

      We thank the reviewer for this interesting idea, and propose to add a supplementary text to present the result of this discussion to the readers.

      • *

      The direct effect is supposed to be measurable from the first iteration only, as we try to represent the effect of direct receptor binding. Regarding the indirect effect, iterations could be done to model the indirect effect, which could represent more distant effect in time.

      • *

      On an algorithmic note, the indirect effect already allow several "iterations" of this effect, as each random walk can loop between all cell types until restart. However, it does not allow to control the weight of the different successive transition. In practice, with a high restart probability, an extreme weight is given to the first "iteration" over the second, as there is three layers to cross to explore the next cell.

      • *

      First, we propose clarifying this section of the manuscript, to explain the depth of the indirect effect explorations.

      • *

      Biologically, it is highly possible that these iterations have an important role to explain the complete reaction of the cells. However, we believe that it hits a major limitation of our modelling, and RWR based exploration in general, as it goes against the enforcement of restarts.

      • *

      We aim to represent pairwise measurements, representing the impact of one node on another. But random walks without restart are not naturally well fitted to this problem, as they naturally converge to a stationary distribution ((László, Lov, and Erdos 1996)). In the case of ReCoN, it means that each gene and receptor, if we pushed the exploration indefinitely, would have the same probability to end up on each node of the system.

      • *

      The restart mitigates this impact and enforces the impacts of the seeds by ensuring that the walkers stay close to the seed. (Tong, Faloutsos, and Pan 2006). By iterating successively from the new distribution obtained from the RWR, we would go against this important probability and progressively converge toward the stationary distribution from classical random walks.

      • *

      So we completely share the opinion of the reviewer that the iterative nature of the indirect effect should be explored too, but we don't believe that ReCoN can model them accurately. We hope that new exploration methods will be able to decipher the importance of these iterations, once additional arguments have been gathered to justify the global interest of considering the indirect effect.

      • *

      Bibliography:

      • *

      László L, Lov L, Erdos O. Random Walks on Graphs: A Survey. 1 Jan. 1996:1-46.

      • *

      Tong H, Faloutsos C, Pan J yu. Fast Random Walk with Restart and Its Applications. Sixth Int Conf Data Min ICDM06 Dec. 2006:613-22. https://doi.org/10.1109/ICDM.2006.70.

    1. Culture and Society – Diversity and Multi-Cultural Education in the 21st Century Some travelers pride themselves on their willingness to try unfamiliar foods, like the late celebrated food writer Anthony Bourdain (1956-2017). Often, however, people express disgust at another culture’s cuisine. They might think that it’s gross to eat raw meat from a donkey or parts of a rodent, while they don’t question their own habit of eating cows or pigs. Such attitudes are examples of ethnocentrism, which means to evaluate and judge another culture based on one’s own cultural norms. Ethnocentrism is believing your group is the correct measuring standard and if other cultures do not measure up to it, they are wrong. As sociologist William Graham Sumner (1906) described the term, it is a belief or attitude that one’s own culture is better than all others. Almost everyone is a little bit ethnocentric. A high level of appreciation for one’s own culture can be healthy. A shared sense of community pride, for example, connects people in a society. But ethnocentrism can lead to disdain or dislike of other cultures and could cause misunderstanding, stereotyping, and conflict. Individuals, government, non-government, private, and religious institutions with the best intentions sometimes travel to a society to “help” its people, because they see them as uneducated, backward, or even inferior. Cultural imperialism is the deliberate imposition of one’s own cultural values on another culture. When people find themselves in a new culture, they may experience disorientation and frustration. In sociology, we call this culture shock. In addition to the traveler’s biological clock being ‘off’, a traveler from Chicago might find the nightly silence of rural Montana unsettling, not peaceful. Now, imagine that the ‘difference’ is cultural. An exchange student from China to the U.S. might be annoyed by the constant interruptions in class as other students ask questions—a practice that is considered rude in China. Perhaps the Chicago traveler was initially captivated with Montana’s quiet beauty and the Chinese student was originally excited to see a U.S.- style classroom firsthand. But as they experience unanticipated differences from their own culture, they may experience ethnocentrism as their excitement gives way to discomfort and doubts about how to behave appropriately in the new situation. According to many authors, international students studying in the U.S. report that there are personality traits and behaviors expected of them. Black African students report having to learn to ‘be Black in the U.S.’ and Chinese students report that they are naturally expected to be good at math. In African countries, people are identified by country or kin, not color. Eventually, as people learn more about a culture, they adapt to the new culture for a variety of reasons. Cultural relativism is the practice of assessing a culture by its own standards rather than viewing it through the lens of one’s own culture. Practicing cultural relativism requires an open mind and a willingness to consider, and even adapt to, new values, norms, and practices. Perhaps the greatest challenge for sociologists studying different cultures is the matter of keeping a perspective. It is impossible for anyone to overcome all cultural biases. The best we can do is strive to be aware of them. Pride in one’s own culture doesn’t have to lead to imposing its values or ideas on others. And an appreciation for another culture shouldn’t preclude individuals from studying it with a critical eye. This practice is perhaps the most difficult for all social scientists.

      Delete this entire section it is a repeat from begining of 1.4.

    1. Author response:

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

      eLife Assessment

      The nematode C. elegans is an ideal model in which to achieve the ambitious goal of a genome-wide atlas of protein expression and localization. In this paper, the authors explore the utility of a new and efficient method for labeling proteins with fluorescent tags, evaluating its potential to be the basis for a larger, genome-wide effort that is likely to be very useful for the community. While the evidence for the method itself is solid, carrying out this project at a large scale will require significant additional feasibility studies.

      We appreciate the editor’s recognition that the evidence for our method is solid and that a genome-wide protein atlas in C. elegans would be highly valuable to the community. However, we respectfully disagree that “significant additional feasibility studies” are required. Take the yeast proteome-wide GFP tagging project (Huh et al., Nature 2003). It achieved ~75% coverage of ~6,000 proteins directly from an established protocol without any prior significant feasibility studies, at least to our knowledge. While the C. elegans genome is 3 times in size, we would argue that our tagging protocol may even be less labor intensive as it does not involve any cloning and the screening is visual, requiring no molecular biology skills. Reviewer 3 notes: ‘They also provide convincing evidence that labelling the whole proteome is an achievable goal with relatively limited resources and time.’

      Our pilot study validates all key parameters for genome-wide scaling: editing efficiency at novel loci with untested reagents, viability of tagged worms, and detectability of multiple spectrally separated fluorophores across expression ranges. These address the core technical, biological, and practical challenges of large-scale endogenous tagging in a multicellular organism, leaving no fundamental barriers in our view.

      The proposed cost and timeline align quite favorably with established large-scale consortium projects: e.g., ENCODE pilot analyzed 1% of the human genome at ~$55 million over 4 years; Mouse Knockout Consortium scaled to ~20,000 genes over 20 years (ongoing) with ~$100 million; Human Protein Atlas mapped ~87% of proteins with antibodies in fixed cells (through much more labor intensive methods) over 20+ years at >$100 million. With ~8% of C. elegans genes already tagged (WormTagDB) and labs already tagging entire gene classes (PMID: 40463100), scaling our protocol to the proteome is feasible, potentially covering the genome in 5-6 years by a single lab or faster with distributed effort at a reagent cost of merely $2.2 million. The main barriers now are funding commitment and assembling collaborators, not further feasibility testing.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Eroglu and Hobert demonstrate that injecting CRISPR guides and repair constructs to target three genes at a time, tagging each with a different fluorescent protein, and selecting which gene to tag with which fluorophore based on genes' expression levels, can improve the efficiency of gene tagging.

      Strengths:

      This manuscript demonstrates that three genes can be targeted efficiently with three different fluorophores. It also presents some practical considerations, like using the fluorophore least complicated by agar/worm autofluorescence for genes with low expression levels, and cost calculations if the same methods were used on all genes.

      Weaknesses:

      Eroglu has demonstrated in a previous publication that single-stranded DNA injection can increase the efficiency of CRISPR in C. elegans while inserting two fluorescent proteins and a co-CRISPR marker into three loci. The current work is, therefore, an incremental advance. In general, I applaud the authors' willingness to think ahead to how whole proteome tagging might be accomplished, but I predict that the advance here will be one of many small advances that will get the field to that goal.

      Our manuscript indeed builds on prior multiplex editing (including our own co-CRISPR work), but the manuscript's primary contribution is not a novel technical breakthrough per se. Instead, our main goal was to pilot and strategize a feasible path to whole-proteome tagging in C. elegans and, most critically, test the following key parameters: (1) success rate of triple pools with prior untested reagents at novel targets; (2) utility of fluorophores across expression levels; (3) major effects on tagged protein function. In prior multiplexing, we used two targets which we already knew could be edited quite efficiently, with the 3rd target a point mutation with nearly 100% efficiency. Thus, it was not at all clear that picking 3 random genes and replacing the 3rd highly efficient locus with another less efficient large insertion would work or be sufficiently scalable for thousands of novel genes with unvalidated reagents at first pass.

      The title vastly oversells the advance in my view, and the first sentence of the Discussion seems a more apt summary of the key advance here.

      Some injections target genes on the same chromosome together, which will create unnecessary issues when doing necessary backcrossing, especially if the mutation rate is increased by CRISPR.

      We disagree with the reviewer’s assessment of the need for backcrossing, for two reasons: (1) Prior studies have shown that off-target mutations are not a serious concern in C. elegans (reviewed in PMID: 26336798). For instance, WGS of strains after CRISPR/Cas9 found negligible off-target effects (PMID: 25249454, PMID: 30420468 – using similar RNP/ssDNA method and multiple guides; PMID: 23979577, PMID: 27650892 using other methods). Targeted sequencing studies have reported similar findings, using various CRISPR/Cas9 methods, with essentially no mutations at sites other than the intended target (PMID: 23995389; PMID: 23817069). (2) If the goal is to tag the entire genome, the introduction of backcrossing should not reasonably be a routine part of the initial tagging.

      Lastly, if one really does want to backcross, the existence of tags on the same chromosome is actually an advantage because it permits selection for recombinants with wild-type chromosomes.

      Also, the need for backcrossing and perhaps sequencing made me wonder if injecting 3 together really is helpful vs targeting each gene separately, since only 5 worms need to be injected.

      Apart from our disagreement regarding backcrossing, we are puzzled by the reviewer’s comment. Why would one do single tagging at a time, rather than triple tagging if the whole point is to scale up tagging? It is important to keep in mind that the rate limiting step for tagging the whole genome is the number of injections that can be done per day. Since there is no cloning to generate the repair templates/guides and all other reagents are commercially available and not sample specific, these can be prepared quite rapidly. Being able to isolate multiple lines (together or independently) from the same injection increases throughput 3-fold and in our view does not provide any disadvantages as individual tags can be isolated independently if desired.

      Beyond the numerous technical advantages pooling provides (also lower cost and throughput for making injection mixes as well as imaging), our results show that it yields epistemic benefits as well: we would never have noted the subcellular pattern in Fig. 6B, C with different sets of mitochondria being marked by different mitochondrial proteins had we imaged them separately or even aligned to a pan-mitochondrial landmark. As we mentioned in the discussion, grouping proteins predicted to localize to the same compartment together can simultaneously test how uniform or differentiated such compartments are during the screen.

      The limited utility of current blue fluorescent proteins makes me wonder if it's worth using at all at this stage, before there are better blue (or far red) fluorescent proteins.

      We do not think that the utility of current BFPs is that limiting. At least the theoretical brightness of mTagBFP2 is comparable to that of EGFP (PMID: 30886412), which was useful for the bulk of currently tagged proteins. Due to modestly higher autofluorescence in the blue spectrum, the practical brightness is somewhat less ideal, but we have shown that many proteins are expressed high enough to be detected quite well with mTagBFP2 by eye at low magnification. We also note that many tags that are not visible by eye under a dissection scope become visible with long exposure cameras of widefield microscopes or modern confocal (GaAsP) detectors, so the list of genes detectable with mTagBFP2 is likely to be much higher. We routinely use mTagBFP2 to super-resolve subnuclear structures with endogenous tags (e.g., in the nucleolus), with some tags having lower annotated FPKMs than the genes tested here.

      Some literature reviews, particularly in the Introduction and Abstract, rely too much on recent examples from the authors' laboratory instead of presenting the state of the field. I'd like to have known what exactly has been done with simultaneous injection targeting multiple loci more thoroughly, comparing what has been accomplished to date by various laboratories' advances to date.

      We are not sure what the reviewer is referring to. In the Abstract, we do not refer to any literature. In the Introduction, we cite 28 papers, 6 of those from our lab (4 of which providing examples of protein tags). We do not believe that this can be fairly called an unbalanced presentation of the state of the field.

      This being said, we have gladly expanded our Introduction to provide more background on co-CRISPRing. Labs have routinely used co-conversion (“coCRISPR”) markers for picking out their intended edits (e.g., point mutations or insertions), as it has been shown by multiple groups that a CRISPR/Cas9 edit at one locus correlates with efficiency at other simultaneous targets (PMID: 25161212). Generally, making point mutations with the Cas9/RNP protocol is highly efficient, especially at specific loci such as dpy-10. However, multiple FP-sized insertions have not been routinely attempted. We and only one other group have successfully attempted it using previously working targets and reagents (e.g., 28% in PMID: 26187122). Importantly, the efficiency of such multiple insertions has never been assessed at scale and using entirely untested reagents at novel sites – critical parameters to determine for a whole genome approach. So, we test here (1) the efficiency of triple insertions and (2) the chance of getting them with new and untested guides and reagents.

      In our view, since we have to use some injection/coCRISPR marker anyway for those genes which are not expressed at dissecting-scope visible levels (likely most genes), using highly expressed intended targets as improvised markers in a pooled approach makes our approach much more efficient. It allows us to find the worms with the highest chance of yielding CRISPR insertions, which we can screen with higher power methods for the dimmer targets, while enabling us to co-isolate other intended targets. Insertions, being often heterozygous in F1, can be segregated independently if desired, or homozygosed together to facilitate maintenance then outcrossed individually by those interested in studying specific genes in more detail.

      In the revised version of this manuscript, we now discuss some of these points in the introduction section:

      “Currently, around 1554 proteins representing 8% of the proteome are estimated to have been endogenously tagged (Leyhr et al., 2025). However, at current rates, tagging the proteome is projected to take around 100 years and likely involve numerous duplicate attempts on a small number of commonly studied proteins (Leyhr et al., 2025). It will thus be crucial for the field to coordinate tagging efforts and scale up tagging protocols to enable coverage of the entire genome at a reasonable timescale and cost. Given the number of injections is a major time-limiting factor, pooling multiple injections into one would at minimum cut tagging time by a factor of 3. In C. elegans, screening for novel CRISPR/Cas9-induced genomic edits is already facilitated either by use of co-injection markers (i.e., plasmids that form extrachromosomal arrays) that yield phenotypes or fluorescence in progeny of successfully injected worms, or co-editing well characterized loci using established and highly efficient reagents which likewise yield visible phenotypes. In the latter approach, termed “co-CRISPR”, worms edited at the marker locus are most likely to also carry the intended edit (Arribere et al., 2014). Recent methods for CRISPR/Cas9 mediated genomic insertions have pushed efficiencies to sufficient levels to simultaneously insert multiple fluorophores (e.g., mNeonGreen and mScarlet) as well as a co-CRISPR marker (dpy-10) at three independent loci in a single injection (Eroglu et al., 2023; Paix et al., 2015). These attempts pooled reagents previously established to work efficiently and targeted genes that were known to yield functional fusion proteins when tagged. Thus, while in principle current methods could allow tagging of at least 3 independent loci in one injection if a co-CRISPR marker is omitted, it is not known to what extent such an approach could be generalized across the genome with previously unvalidated reagents (i.e., guides and repair template homology arms) at novel loci to yield functional tags”

      Reviewer #2 (Public review):

      The manuscript by Eroglu and Hobert presents a set of strains each harboring up to three fluorescently tagged endogenous proteins. While there is technically nothing wrong with the method and the images are beautiful, we struggled to appreciate the advance of this work - who is this paper for?

      We consider this paper to have two purposes: (1) motivate the community to come together to consider such genome-wide tagging approach; (2) provide a reference point for funding agencies that such an aim is not unreasonable and will provide novel interesting insights.

      As a technical method, the advance is minimal since the first author had already demonstrated that three mutations (fluorophore insertion and co-CRISPR marker) could be introduced simultaneously.

      We agree that the basic principle is similar. However, it was not clear that triple pooling three novel large edits would work, given the numbers in our original paper or that it would be scalable.

      The dpy-10 coCRISPR marker previously used is a highly efficient single site, with close to 100% hit rate. We also knew in the earlier study that the two pooled insertions already worked quite efficiently and did not disrupt the function of targeted proteins. Exchanging these plus dpy-10 for three novel tags was not guaranteed to succeed for many potential reasons, including both biological and technical. For instance, such a “marker free” approach necessitates that a significant number of targets in the genome should be expressed highly enough to be visible by fluorescence stereomicroscopy when tagged with current best fluorophores. The chance of disrupting gene function by tagging was also not explored in detail in C. elegans, nor whether one untested guide is generally sufficient. We think that establishing these parameters was meaningful and necessary for the goal of whole genome tagging. We have clarified some of these points in the text.

      As a pilot for creating genome-scale resources, it is not clear whether three different fluorophores in one animal, while elegantly designed and implemented, will be desired by the broader community. 

      The usage of three different fluorophores is largely driven by the ability to co-inject and therefore cut injection effort by a factor of three. Moreover, having all three fluorophores together facilitates imaging and maintenance. Lastly, co-labeling has the potential to reveal unexpected patterns of co-localization or lack thereof (example: two mitochondrial proteins that we found to not have overlapping distribution). We clarified this point in the revised text in both the results and discussion.

      Finally, the interpretation of the patterns observed in the created lines is somewhat lacking. A Table with all the observations must be included. This can replace the descriptions of the observations with the different lines, which could be somewhat laborious for the reader, and are often wrong. There are numerous mistaken expectations of protein expression here, but two examples include:

      We are not convinced that our expectations are mistaken. Below we respond to the reviewer’s specific examples, and we are open to hear from the reviewer about additional cases.

      (1) The expectation that ACDH-10 is enriched in the intestine and epidermal tissues (hypodermis).

      There are multiple paralogs of this protein (see WormPaths or WormFlux) that may share functions in different tissues. There is also no reason to assume that fatty acid metabolism does not occur in other tissues (including the germline). Finally, there are no published studies about this enzyme, so we really don't know for sure what it's doing.

      The expression of acdh-10 is annotated in multiple scRNA datasets as intestine and epidermal enriched (CeNGEN/Taylor et al. 2021, highest in epidermis; Ghaddar et al 2023 highest in intestine). We did not mean to imply that fatty acid metabolism does not occur in the gonad, nor that a paralog of acdh-10 could not be performing the same function in tissues where acdh-10 is not expressed.

      However, this raises an important question: why have different paralogs doing the same thing? Duplicate genes with the same function are generally not evolutionarily stable (PMID: 11073452, PMID: 24659815). That there are such striking tissue specific expression patterns of an essential or widely expressed protein class suggests that paralogs of the gene likely differ in some meaningful parameter that might align with tissue-specific functional needs or regulation. The reviewer’s statement that ‘there are no published studies about this enzyme, so we really don't know for sure what it's doing’ is in fact an excellent demonstration of our point; finding out where the duplicates are expressed can provide a starting point to uncover potential differences between the paralogs. At the very least it can delineate to what degree paralogs diverge in their expression across the proteome and identify which such cases merit further study. In a more ideal scenario, prior information of protein function could indicate that the involved pathway requires tissue specific regulation.

      (2) The expectation that HXK-1 is ubiquitously expressed.

      Three paralogous enzymes are all associated with the same reaction, and we have shown that these three function redundantly in vivo, perhaps in different tissues (PMID: 40011787).

      The cited paper (PMID: 40011787) does not show where they are expressed. We discussed redundancy/paralogs above in point 1, and in our view the same applies here. They may perform the same reaction but are likely to differ in some meaningful way, be it regulation or rate of activity, for them to be stably maintained as functional genes over evolution.

      Moreover, single-cell RNA-seq data (PMID: 38816550) also show enrichment of hxk-1 in gonadal sheath cells.

      The Ghaddar et al. and CeNGEN/Taylor et al. datasets do not show this. The scRNA paper cited (PMID: 38816550) also shows enrichment in neurons, pharynx, coelomocyte and germ cells which we did not note. In our view, these in fact further support our goals: often, transcript datasets alone (frequently used to infer tissue function) do not sufficiently predict protein expression. One can post hoc find an scRNA-seq dataset that aligns somewhat with our protein observations, but how does one know which to trust a priori? Disagreements between transcript datasets will ultimately require resolution at the protein level, in our view.

      To clarify these points, we added the following to the discussion section:

      “We also noted unexpected cell type dependent distributions of proteins involved in broadly important metabolic processes such as ACDH-10, which was depleted from the germline compared to other tissues, and HXK-1, which was highly enriched in the gonadal sheath. Notably, for these as well as other cases, scRNA-seq datasets were not sufficient to deduce a priori the observed cell type specific differences at the protein level. Importantly, many genes encoding metabolic enzymes including acdh-10 and hxk-1 have paralogs that likely perform similar catalytic functions. Yet, duplicate genes with identical functions are generally not evolutionarily stable (Adler et al., 2014; Lynch and Conery, 2000); thus such genes are likely to differ in some meaningful parameter (e.g., regulation or activity) that might align with tissue-specific functional needs. Fully annotating the expression patterns of paralogs at the protein level could indicate which tissues require unique metabolic needs and indicate which paralogous genes have undergone sub- versus neo-functionalization. For those proteins that are less functionally understood, unexpected distributions might indicate which merit further study.”

      The table should have at least the following information: gene/protein name - Wormbase ID - TPM levels of single cell data assigned to tissues for L2, L4, and adult (all published) - tissues in which expression is observed in the lines presented by the authors.

      We added some of this information such as annotated expression levels in young adults from various scRNA datasets (but not larval datasets as we did not image these). We note that each of these studies use different pipelines and report different metrics (scaled TPM/Z-score versus Seurat average expression versus TPM), so comparisons between them are not informative unless they are integrated and analyzed together.

      Reviewer #3 (Public review):

      Summary:

      The authors argue that establishing the expression pattern and subcellular localisation of an animal's proteome will highlight many hypotheses for further study. To make this point and show feasibility, they developed a pipeline to knock in DNA encoding fluorescent tags into C. elegans genes.

      Strengths:

      The authors effectively make the points above. For example, they provide evidence of two populations of mitochondria in the C. elegans germline that differ qualitatively in the proteins they express. They also provide convincing evidence that labelling the whole proteome is an achievable goal with relatively limited resources and time.

      We appreciate the referee’s recognition that whole proteome tagging is feasible.

      Weaknesses:

      Cell biology in C. elegans is challenging because of the small size of many of its cells, notably neurons. This can make establishing the sub-cellular localisation of a fluorescently tagged protein, or co-localizing it with another protein, tricky. The authors point out in their introduction that advances in light microscopy, such as diSPIM, STED, and ISM (a close relative of SIM), have increased the resolution of light microscopy. They also point out that recent advances in expansion microscopy can similarly help overcome the resolution limit.

      (1) Have the authors investigated if the three fluorescent tags they use are appropriate for super-resolution microscopy of C. elegans, e.g., STED or SIM? Would Elektra be better than mTAGBFP2? How does mScarlet3-S2 compare to mScarlet 3?

      All three tags work for ISM (i.e., Airyscan). We previously tried Electra (not for the genes tested here) but could not isolate positive tags. Given Electra is not that much brighter on paper than mTagBFP2 we did not pursue it further, though we recognize that these may simply have been unlucky injections. mScarlet3-S2 is quite a bit dimmer than mScarlet3 on paper – the advantage is that it has higher photostability. In our view, the limiting factor will be having FPs that are bright enough to screen, image and scale to the whole genome, so brightness will likely provide an advantage over photostability at this stage.

      (2) Have the authors investigated what tags could be used in expansion microscopy - that is, which retain antigenicity or even fluorescence after the protocol is applied? It may be useful to add different epitope tags to the knock-in cassettes for this purpose.

      mSG and mSc3 retain fluorescence after fixing with formaldehyde. We have not tested mTagBFP2 fluorescence in fixed worms. We agree that adding different epitope tags would be useful.

      The paper is fine as it stands. The experiments above could add value to it and future-proof it, but are not essential. If the experiments are not attempted, the authors could refer to the points above in the discussion.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Merged figures appear saturated, and use colors that won't work for red-green colorblind viewers. 

      For all figures, we also show individual channels separately, which is common practice for making fluorescence images accessible to colorblind readers (PMID: 33788834). Figures highlighting non-overlap like 6B and C are already in accessible colors when merged (blue/green) and include a numerical quantification. 3-color RGB images preserve the greatest information for the highest number of individuals.

      (2) Targeting ubiquitously expressed genes as a proof of concept gives me some concern that this might underestimate the challenges that may be experienced with less widely expressed genes.

      While the genes were predicted to be ubiquitously expressed, many were not in practice, like HXK-1 and F54C8.1, which were also among the lower expressed genes on our list and highly cell type restricted. As discussed, the more tissue restricted a gene, the likelier that bulk RNA levels underestimate expression. Such genes are therefore more likely to be detected in a specific tissue. We routinely isolate tissue restricted endogenous tags, including those expressed in only a few neurons, with bulk FPKMs lower than the ranges tested in this manuscript.

      (3) Some results are not shown or referenced (autofluorescence, for example, is shown using a schematic in Figure 1C).

      We now provide representative images alongside what would be expected to be observed by eye during screening.

      (4) It would be useful to describe how to recover worms from what is shown in Figure 1A. 

      In the revised version, we added the following in the caption for Fig. 1A:

      “Selected worms expressing the brighter tag can be screened for dimmer tags by higher magnification and long exposure imaging. Worms can be recovered directly from slides if immobilized by levamisole as described (Ghanta et al., 2021). Alternatively, single hermaphrodite worms can be isolated, allowed to lay eggs, then screened.”

      (5) A blue bar of data must be missing from Figure 3B injection pool 5.

      As stated in the text, “All but one tag (cox-6B::mTagBFP2) was visible in the F1 generation of injected P0 animals, and these were subsequently isolated among F2 worms positive for the other tags in the pool.”

      To clarify that data points are not unintentionally omitted, we added the following text to the caption of Fig. 3B:

      “For group 5 including cox-6B::mTagBFP2, worms with detectable levels of mTagBFP2 fluorescence were not recovered in the F1 generation but were isolated among progeny of F1s positive for mStayGold and mScarlet3; we were thus unable to quantify efficiency for this locus at F1.”

      (6) Some expression or localization patterns were unexpected, but complications like germline silencing and protein mislocalization, with a small fraction localizing normally and rescuing function, were not presented as possibilities. Viability is used to confirm function, but without presenting whether this means 100% viability, less, or just the ability to maintain a strain.

      We already do discuss mislocalization and functionality issues in the Discussion, as well as tradeoffs of alternate methods. Any existing method to observe biological molecules, be it protein, RNA or DNA, has multiple drawbacks and sources of artifacts, which are unlikely to be fully eliminated in the foreseeable future.

      In regard to germline silencing of endogenously tagged genes in C. elegans, there is actually very little evidence for this. Collectively, various labs have now generated over 200 reporter alleles of germline-expressed genes (WormTagDB), with robust expression throughout the germline and retention of function. Likewise, numerous of our tags across fluorophores showed robust germline expressions including EEF-1A.1::mTagBFP2, Y22D7AL.10::mStayGold, and HAT-1::mScarlet3. In fact, overall transcript levels generally tended to underestimate germline enrichment at the protein level. We note that single-copy transgenes driven by eef-1A.1/eft-3 promoter by itself are frequently not expressed in the germline (PMID: 31064766); that we could detect EEF-1A.1 robustly in the germline when tagged endogenously is evidence that silencing is unlikely to be a widespread concern, and at the least less of a concern than single copy transgenes. We appreciate that for a transgene, presence/absence of specific sequence elements and genomic loci play a role in expression, but an endogenous tag captures all such information at a given locus.

      Indeed, we found only two reports of endogenous tags being silenced in the germline, the first being a novel tag (not fluorophore) which initially prevented expression at the tagged locus (PMID: 30109984), but after making changes to the sequence to avoid silencing signals the authors could rescue expression and thereafter saw robust expression in various novel contexts with this tag. The second example (PMID: 34547227) leaves open the possibility that germline repression of that particular gene might be a part of its endogenous regulation.

      Nevertheless, given it is probably rare if occurs at all, it will likely take a large scale tagging effort to uncover such cases at sufficient numbers to study. In our view, this further justifies tagging at large, ideally genomic, scales. If we do discover that there are numerous annotated germline proteins which we don’t observe by tagging, that would be interesting to study on its own.

      (7) Halotag is presented in the Discussion as a small tag, but it is bigger than GFP.

      Thank you for catching this. We have removed the discussion of Halotag. Given the comparable size to FPs, it would be unlikely to alleviate issues of tag functionality.

      (8) It would be useful to include FPKMs and viability percentages in Table 1.

      FPKM is included in column 6, but the title for this column is cut off. In the revised table FPKM values are now shown more clearly across stages.

      We did not quantify viability percentage. In our view it does not yield an informative metric when there is little information about the protein’s required dosage for function, which was the case for most proteins here. A haplosufficient gene might yield a full brood size even if 50% of protein function is lost; conversely, a highly dose sensitive protein could yield penetrant and severe inviability with mild perturbation of function. It also is not actionable information at this stage if there is no alternate tagging strategy as a baseline of comparison. The worms we picked to image all have viable embryos as adults, so in those individuals the genes were likely to be sufficiently expressed and functional.

      (9) Because establishing that a guide works well is a limiting step for many CRISPR experiments (once a guide works well, it's easy to inject 5 worms and get lines), I wondered if testing that for many genes is what is really needed in the field at this stage. 

      Guide quality is rarely an issue in C. elegans, as for all the genes here we tried only one guide, all of which were previously untested. We now clarified this in the discussion section:

      “Notably, we find that previously untested guide RNAs and homology arms perform exceptionally well at novel loci, as we only tested one set of reagents for each locus which yielded satisfactory tagging rates.”

      (10) For a manuscript where the injection is so central to what was done, I was surprised to read in the Acknowledgments that all of the injections were done by someone who is not included as an author.

      We are likewise surprised by such a comment but gladly clarify: Chi Chen has been with us as an expert microinjection specialist for more than 25 years and her very important technical contributions have been acknowledged in many dozen papers. Multiple authorship guidelines, including COPE’s and ICMJE’s, state that technical contributions alone do not qualify for authorship.

      Reviewer #2 (Recommendations for the authors):

      (1) We would encourage the authors to provide systematic validation of the reported insertions. The manuscript reports that 24 of 30 tags were isolated and visible, but does not clearly state whether each isolated line was confirmed by sequence‑level validation to be correctly in‑frame and free of unintended mutations at the target locus.

      We appreciate the reviewer’s concerns on fidelity. These parameters have been assessed in prior published work (e.g., PMID: 30504364, PMID: 34748534) and in our hands are in the range of 80% whenever we sequence non-fluorescent tags of similar sizes. The efficiencies we observed are high enough that one can expect to recover numerous worms with the exact intended sequence for each target, though we would argue mutations within the FP reporter are less likely to matter if it retains high fluorescence.

      (2) The manuscript presents aggregated success counts (e.g., 8/10 mTagBFP2 tags, 9/10 mStayGold, 7/10 mScarlet3) and useful narrative descriptions of injection outcomes. We also suggest including per‑locus success rates.

      Figure 3B shows per locus success rate and source data is provided for this figure. Each dot is an individual injection and the Y axis is per locus rate. We now worded this more clearly in the figure’s caption.

      “Total insertion efficiencies per locus for the indicated targets across injection pools.”

      (3) For pools that required re‑injection after initial failures, we would like to see a description of the specific changes that were made to the injection mixes or procedures (e.g., new repair template prep, different Cas9 reagent lot, guide redesign). This will be useful troubleshooting information for others.

      We re-made the exact same injection mix but with nanodrop to ensure the purity of the repair templates as assessed by absorbance ratios (A260/230 and A260/280) were sufficient after each purification step. No other changes were made. This is now specified in the methods section in the following way:

      “For re-runs of pools 4, 6 and 10 which failed initially, we regenerated the repair templates and ensured that after each column purification, the A260/230 ratio of the purified DNA was ≥2.2 and A260/280 was 1.8 ± 0.05 when measured with a Nanodrop spectrophotometer.”

      (4) The authors state that the fluorophore sequences are codon-optimized for C. elegans. We suggest they provide the exact donor/tag sequences, specifically state whether the fluorophore sequences contain any synthetic/artificial introns, or whether other sequence modifications (e.g., silent PAM‑disrupting mutations) were included in the donor templates. 

      This information is provided in Supplementary Table 1.

      (5) Page 3: Include a reference for "The C. elegans genome encodes around 20,000 genes" 

      We added a reference to the most recent release of the genome (WS237, May 2013). Spieth et al., 2014.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors aimed to uncover novel therapeutic vulnerabilities in APC-mutant colorectal cancer (CRC), which constitutes the majority of CRC cases. They hypothesized that modulating oxygen-sensing pathways (via PHD inhibition) could disrupt adaptive stress responses in these tumours.

      Strengths:

      The study employs a powerful, two-pronged approach to identify Molidustat's targets. By using both Thermal Proteome Profiling (TPP) and an orthogonal chemical proteomic competition assay, the authors provide compelling evidence that GSTP1 is a genuine, direct off-target, effectively addressing the common limitation of indirect effects in proteomic screens.

      Weaknesses:

      (1) In Figure 1, the current data rely on a single guide RNA (sgRNA). To make the data solid, at least two independent sgRNAs targeting different regions of PHD2 should be used.

      We thank the reviewer for raising this. Clarity on the CRISPR strategy was missing from the original submission and we have now added the following to the Methods (Page 4). We did not use a single sgRNA. PHD2 was targeted with a pool of three chemically modified crRNAs:

      (IDT Alt-R; target sequences: 5'-TACAACCAGCATATGCTACA, 5'GTGGCTGCCGAAGCCGAGCC, 5'-GATAAGATCACCTGGATCGA)

      Delivered as in vitro assembled ribonucleoprotein complexes with high-fidelity Cas9. This format has been reported to achieve high on-target efficiency while minimising off-target cutting [1,2] such that any residual stochastic off-target events are distributed across the population and are not expected to manifest as a coherent phenotype at the population level. Working with pooled, unselected knockouts rather than single-cell clones also avoids the confounds of clonal heterogeneity that normally motivate the use of multiple independent guides and rescue experiments in single-clone workflows. We have previously validated this approach for GSTP1 knockout in a separate single-cell proteomics study [3], where loss of GSTP1 protein was observed in over 90% of single cells and GSTP1 was the most significantly altered protein between sgControl and sgGSTP1 populations.

      (2) Figure 3E: Asn205 site should be mutated to prove that whether Molidustat inhibits GSTP1 activity via Asn205 or not.

      This is a good suggestion, and we explored it in silico before concluding it was not tractable. We used PyMol mutagenesis to model Molidustat binding to GSTP1 variants at the predicted contact residues: Asn205 was mutated to Ala, Gly and Ser; Trp39 (predicted to hydrogen-bond Molidustat) was mutated to Ala, Phe and Thr; and a Tyr8Phe/Asn205Ser double mutant was also modelled. In every case, Molidustat reoriented within the active site and adopted an alternative hydrogen-bonding configuration (most commonly with Tyr8), yielding a docking score equal to or better than binding to native GSTP1 (Author response image 1– Author response image 4). The model therefore does not predict any single or double point mutant that would ablate Molidustat binding in a clean, interpretable way, and we could not design a rational loss-of-interaction mutant on this basis. Given this limitation, and that definitive mapping of the binding interface would require co-crystallography, which is beyond the scope of the present study, we have moved the docking model to the supplement and flagged it as predictive rather than definitive.

      Author response image 1.

      Molidustat in native GSTP1

      Author response image 2.

      Molidustat docking with mutated GSTP1, Asn205 mutated to Gln205

      Author response image 3.

      Molidustat docking with mutated GSTP1, Tyr39 mutated to Phe39

      Author response image 4.

      Molidustat docking with mutated GSTP1, Asn205 mutated to Ser205 and Tyr8 mutated to Phe8

      (3) Figure 5B and 5C: The metabolic imbalance phenotype observed upon dual knockout of PHD2 and GSTP1 requires rescue experiments to confirm on-target specificity.

      We thank the reviewer for this important point and agree that rescue experiments could represent the most direct demonstration of on-target specificity for the metabolic phenotype observed in Figures 5B and 5C. These rescue experiments are necessary when working with single clones, as they allow for comparing a knock-out clone with a reconstituted pool and sidestep the issue of clonal heterogeneity.

      In our case, we think that there is no advantage to doing so, as we work with pooled knockouts, so any clonal heterogeneity is diluted in the pool.

      One could even make the case that such a rescue experiment would introduce additional artefacts. Combined loss of PHD2 and GSTP1 leads to reduced cellular viability, with decreased proliferation and increased apoptosis, consistent with a synthetic lethal interaction. To devise a rescue experiment, we would have to isolate a single-cell clone (the pool is not a complete 100% knock out, WT cells would outgrow the knock out cells). The isolation of such a clone that has overcome the anti-proliferative insult of the double knockout is likely to have a phenotype distinct from the original, pooled population, as would the rescued have from the WT cells. For these reasons, we have not performed rescue experiments in the current study. We have added the absence of a rescue as a limitation to the study in the discussion

      “While genetic rescue experiments would provide definitive confirmation of on-target specificity, the pronounced loss-of-fitness and apoptotic phenotype observed upon combined PHD2 and GSTP1 loss limited the feasibility of establishing stable rescued double-knockout populations, and therefore represents a limitation of the current study.”

      Reviewer #2 (Public review):

      Summary:

      The authors aimed to determine Molidustat targets and the potential utility of these findings. They clearly demonstrate that Molidustat interferes with GSTP1 and some other proteins on top of PHD2. They also demonstrate that PHD2 deletion is not sufficient to recapitulate Molidustat effects in cells and proteomes. Finally, they demonstrate synthetic lethality in organoids for Molidustat and APC deletion.

      Strengths:

      The data on Molidustat proteomes, GSTP1 binding, inhibition and metabolic health of organoids is really clear. All biochemical, docking and omic data are really strong. The potential impact of these findings could be the use of Molidustat in APC null tumours and awareness of potential off-target effects.

      Weaknesses:

      A main but minor weakness is that Molidustat also inhibits other PHDs, although these are less expressed. PHD1 has been shown to control the cell cycle and be expressed in the colon, where it is needed for viability. Although this does not explain the lack of effect of other PHD inhibitors, it does warrant some discussion. The use of MTT is not very good to detect viability when it measures metabolism; this also needs to be discussed and perhaps supplemented with colony or cell number measurements.

      Great point, for this reason, we have assayed apoptosis throughout. In addition, we have added a clonogenicity assay with APC organoids. Organoid cells were treated with an acute dose of Molidustat. We subsequently measured the level of Lgr5 (a stem cell marker) and of the ability of the cells to generate organoids (these data have been added as Figure 5 F-G.)

      Reviewer #3 (Public review):

      In this paper, the authors revealed that Molidustat can induce a dose-dependent increase in Caspase-3/7 activity in the HT29 cell line, which is an APC-mutant colorectal cancer cell line. More importantly, they found that targeting PHD2 alone cannot cause cell death. By using thermal proteome profiling (TPP) and orthogonal chemical proteomic competition assays, they determined GTSP1 as a previously undiscovered off-target of Molidustat. They also revealed that combined PHD2 and GSTP1 loss leads to an increase in intracellular ROS and apoptosis. Moreover, they evaluated the effects of Molidustat in colonic organoids and showed that

      Molidustat has a high selectivity for colonic organoids with activated WNT signaling and/or KRAS pathway alterations, and this effect is not reproduced by hydroxylase inhibition alone, providing a new potential approach to targeting both PHD2 and GTSP1 for the treatment of APC-mutant CRC.

      Specific comments:

      (1) What is the possible molecular mechanism of dual GSTP1/PHD2 loss, inducing cell death?

      This is an important question. Our data support a model in which combined loss of GSTP1 and PHD2 disrupts cellular redox homeostasis, leading to accumulation of reactive oxygen species, increased GSSG/GSH ratios, and depletion of antioxidant buffering capacity. This redox imbalance is accompanied by downregulation of pro-survival pathways. In this context, activation of apoptotic signalling, as evidenced by increased caspase-3/7 activity and proteomic enrichment of apoptosis-associated pathways, contributes to the observed cell death phenotype.

      While apoptosis is supported by our data, the magnitude of oxidative stress suggests that additional oxidative stress-associated cell death mechanisms may also contribute. We have clarified this point in the Discussion (Page 11).

      (2) Can the authors mutate the binding site of Molidustat on GTSP1 to verify the in silico docking results?

      This is a very important question. Currently, the model is of limited value. Reviewer 1 had a similar question. Can we refer you to Reviewer 1, question 2.

      (3) Evidence for Molidustat inhibiting PHD2 activity or stabilising HIF-1α should be provided.

      We thank the reviewer for this suggestion. Data showing HIF-1α stabilisation and evidence of downstream signalling is now added to Supplementary Figure 1.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      I only have minor suggestions:

      Molidustat also inhibits other PHDs, although these are less expressed. PHD1 has been shown to control the cell cycle and be expressed in the colon, where it is needed for viability. Although this does not explain the lack of effect of other PHD inhibitors, it does warrant some discussion. The use of MTT is not very good to detect viability when it measures metabolism; this also needs to be discussed and perhaps supplemented with colony or cell number measurements.

      This is correct, PHD1 is of particular interest, given the effects inhibition/knock-out has on the inflamed colon. We have added a new paragraph to the Discussion (Page 13) that addresses the isoform selectivity of Molidustat. We note that, although developed as a PHD2 inhibitor, Molidustat retains appreciable activity against PHD1 and PHD3 [4], and we discuss the non-redundant and in some contexts opposing roles of PHD1 and PHD2 in the colon, PHD1 loss is protective in DSS colitis [5] and restrains colitis-associated tumour growth, whereas PHD2 loss in the tumour and stroma is reported to inhibit metastasis and treatment response [6]. We further note that this pattern of isoform engagement is shared with other pan-PHD inhibitors that did not phenocopy Molidustat in our screens, indicating that PHD isoform profile alone is insufficient to explain Molidustat’s distinctive activity and pointing to GSTP1 off-target engagement as the key distinguishing feature. We argue that localised colonic delivery (as discussed earlier in the Discussion) would concentrate drug at the APC-mutant epithelium while limiting systemic exposure.

      We fully agree with the reviewer, MTT measures metabolic activity/NADH levels rather than viability in the strict sense, and that this is particularly relevant for a compound that perturbs redox metabolism. We have added a clonogenicity assay in APC organoids (Fig. 5 F-G) to supplement the MTT and Cleaved Caspase 3 assays already present in the manuscript.

      (1) Lee, J. K. et al. Directed evolution of CRISPR-Cas9 to increase its specificity. Nat. Commun. 9, (2018).

      (2) Sakovina, L., Vokhtantsev, I., Vorobyeva, M., Vorobyev, P. & Novopashina, D. Improving Stability and Specificity of CRISPR/Cas9 System by Selective Modification of Guide RNAs with 2′-fluoro and Locked Nucleic Acid Nucleotides. Int. J. Mol. Sci. 23, (2022).

      (3) Makar, A. N., Holkham, J., Lilla, S., Wilkinson, S. & von Kriegsheim, A. Overcoming preservation challenges to enable single-cell proteomics of fixed cell and tissue samples with retained proteome integrity. Preprint at https://doi.org/10.1101/2025.03.10.642380 (2025).

      (4) Flamme, I. et al. Mimicking hypoxia to treat anemia: HIF-stabilizer BAY 85-3934 (molidustat) stimulates erythropoietin production without hypertensive effects. PLoS One 9, (2014).

      (5) Tambuwala, M. M. et al. Loss of prolyl hydroxylase-1 protects against colitis through reduced epithelial cell apoptosis and increased barrier function. Gastroenterology 139, (2010).

      (6) Leite de Oliveira, R. et al. Gene-Targeting of Phd2 Improves Tumor Response to Chemotherapy and Prevents Side-Toxicity. Cancer Cell 22, (2012).

    1. Author response:

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

      eLife Assessment

      This study used pupillometry to provide an objective assessment of a form of synesthesia in which people see additional color when reading numbers. It provides convincing evidence that subjective color ratings are matched by changes in pupil size that recapitulate brightnessmediated changes when exposed to the real color. The work provides a valuable contribution to the literature on both synesthetic perception and the use of pupillometry to probe perception and related psychological processes.

      We were pleased to learn that our manuscript was of interest to the reviewers and the editor. We thank the reviewers for their useful feedback and have addressed all their comments in the revised version. We here give the most prominent changes as quotes.

      We thank all reviewers and for their very helpful input.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Knowing that small pupil-size variations accompany brightness variations (even when these are illusory), the authors asked whether pupil constrictions would accompany the synesthetic perception of a brighter color (compared with a darker one), induced by the presentation of a blackwhite character. This grapheme-colour synesthesia is only experienced by a few participants, sixteen of whom were enrolled in this study. The results reliably showed that a relative pupil constriction would "betray" the perception of a brighter color in these participants, while no such effect would be observed in control participants who were asked to report a color in association with each grapheme, even though they did not perceive any.

      Strengths:

      The main strength of the study lies in its combination of psychophysics (brightness ratings) and pupillometry, which allowed for showing clear-cut results.

      Weaknesses:

      Some relatively minor weaknesses concern the ancillary analyses, which tackle secondary questions and are not entirely convincing.

      (1) The linear mixed model approach is a powerful way to identify important variables, but it does not clarify whether the key factors are between-subject or between-trial variations. Some variables are inherently defined at a subject level (e.g., PA scores), others are not. I would strongly recommend an alternative visualisation of the results to examine inter-individual variability.

      Visualizing the highly idiosyncratic effects is indeed challenging. Addressing R1’s point 4 and a point brought up by R2, we updated all figures to now visualize pupil size in millimeters instead of arbitrary units. Furthermore, we added a supplementary figure (supplementary figure 4) that visualizes pupil size change without demeaning (please see reply to point 4).

      To get a better grasp of the interaction between lightness and coupling strength, we further included the supplementary figure 5 that splits by lightness and coupling strength in synesthetes.

      Furthermore, as this review and response will be publicly available, Author response image 1 provides participant-mean traces per lightness bin in addition to the overall means and hopefully makes the stability/variability of effects visually clearer (in addition to the strip plots that attempt this for the average response).

      Author response image 1.

      We hope that these additional visualizations make the effects of interest more transparent. Ultimately, however, the LME figure likely provides the information best, albeit at the cost of complexity.

      (2) It is not clear why taking the first derivative of pupil size in Figure 5 would isolate the effect of arousal, eliminating those of luminance and contrast changes (in fact, one could argue for the opposite, since arousal effects are generally constant for extended periods of time while contrast effects are typically more local and transient).

      First, please note that the results in 2.3.1 cannot be explained by task or context effects such as luminance and contrast: the exact same active color reporting task (same task and context) was presented to synesthetes and non-synesthetes.

      Indeed, the reviewer is correct that the first derivative does not eliminate other concurrent pupil-driving effects, that was expressed wrongly in our original text. Indeed, any stimulus-locked effect, such as the luminance and contrast effects, but also the effort effect will reflect similarly in the derivative measure.

      We did take the derivative because pupil responses driven by other non-trial related activity, such as increasing tiredness or excitement over the course of trials differ almost by necessity between participants, thus creating variability. However, these effects are most likely happening at a slower timescale and thus show less in the derivative measure. Accordingly in past research, we previously found clearer response-locked effects in the past when using a derivative measure (Douze et al., 2025; Ten Brink et al., 2024). This way, we also hoped to get rid of such variability that happens between participants for this between participant analysis.

      Even if we were to use the same baseline corrected analysis, we would arrive at the same conclusion: we here directly compared baseline-corrected pupil sizes by taking individual differences into account (using a LME). In other words, we tested for the same question, but not relying on the derivative. We thus compared baseline-corrected pupil sizes using over-time LMEs. Group (active control vs. synesthete) gained significance between ~1.7s and 3s, aligning with the derivative-based result.

      Author response image 2.

      t-values of a per-time point LME predicting pupil response from group (synesthete/active control) Group reached significance.

      In sum, we deem the derivative more powerful/more appropriate in this context, but the interpretation of findings does not hinge on that analysis choice (as can be seen in the Author response image 2).

      We corrected the claims on the derivative as a measure cleaning out other effects that indeed was oversimplified as it stood. We now write:

      “Mental effort presents in task-evoked pupil dilations, yet other factors simultaneously affect the pupil, such as luminance and contrast changes at trial onset, as well as slower trends across the session (e.g., fatigue). To reduce the influence of these slower, non-trial-locked fluctuations while retaining the trial-evoked dynamics, we calculated the first derivative of the pupil time course to assess the velocity of pupillary changes (Butterworth filter, 18 Hz, order 3, 2.5 Hz lowpass, following our previous works [60, 61]).”

      Douze, B. T., Ten Brink, A. F., Dijkerman, H. C., & Strauch, C. (2025). Pupil responses objectively index pharmacologically altered tactile sensitivity. Cortex, 193, 90-104.

      Ten Brink, A. F., Heiner, I., Dijkerman, H. C., & Strauch, C. (2024). Pupil dilation reveals the intensity of touch. Psychophysiology, 61(6), e14538.

      (3) It is a pity that responses to physical brightness modulations were only measured in the synesthete group, not in controls, as this would have allowed for ruling out differences in pupil reactivity across the two populations.

      The reviewer is correct that this would allow additional comparisons, but argue that light responses in healthy control samples are very well documented and stereotypical. For instance, Bergamin & Kardon (2003) provide very systematic latency estimations, for low-luminance change stimuli in the realm of about 320ms that can accelerate to about 250ms for very strong luminance changes. Our relatively small luminance increments should thus be expected in this range. Indeed, this also well describes the response latencies we observed in synesthetes when exposed to the colored disks. While there is no detailed information about participants in Bergamin & Kardon (2003), data from previous studies shows very similar pupil light response profiles in a healthy student control population that matches our synesthetes well demographically (Strauch, Romein et al., 2022 Figure 2a, exact same lab as for the present study; Koevoet et al., 2025 Figure 3a). See also the further responses, baseline pupil size in millimeters across groups did not differ.

      Together, we can safely conclude that pupil light responses in synesthetes are not different from pupil light responses in controls. We agree with the reviewer that this is a sensible point to also make in the manuscript:

      “Specifically, pupil size first responded significantly to physical luminance after 330 ms (see Supplementary Figure 7 for per-timepoint LME; in line with response latencies of similar control populations, see Bergamin & Kardon [52], Koevoet et al. [40], and Strauch et al. [53]), but only responded significantly to synesthetic lightness at about 870 ms (see also Figure 3c vs e and Figure 4 for per-timepoint LME)”.

      Bergamin, O., & Kardon, R. H. (2003). Latency of the pupil light reflex: sample rate, stimulus intensity, and variation in normal subjects. Investigative Ophthalmology & Visual Science, 44(4), 1546-1554.

      Koevoet, D., Naber, M., Strauch, C. & Van der Stigchel, S. Presaccadic Attention Shifts Up-and Downwards: Evidence From the Pupil Light Response. Psychophysiology 62, e70047 (2025).

      Strauch, C., Romein, C., Naber, M., Van der Stigchel, S., & Ten Brink, A. F. (2022). The orienting response drives pseudoneglect—Evidence from an objective pupillometric method. Cortex, 151, 259-271.

      (4) Another concern is with the visualisation of the pupil traces in Figure 3 (main results); these were heavily pre-processed (per-participant demeaned), losing any feature besides the effect of interest and generating the unrealistic expectation that perception of dark/bright colors generate a net dilation/constriction of the pupil - whereas perception-related modulations of pupil size are always relative and generally small compared to the numerous other effects registered in pupil size. It would be far better to see the actual profiles, preserving the unfolding of dilations and constrictions over time, especially since these are further analysed in Figures 4 and 5.

      Indeed, the expectation that any dark synesthetic experience would lead to pupil dilation whereas any bright synesthetic experience would lead to constriction is not warranted – it would only do that relative to the counterfactual of not having that experience.

      Many factors affect the pupillary signal at the same time, and often differently across individuals (think of tiredness etc.), making merely baseline corrected traces seemingly noisy. Our visualization highlights that there is a systematic part to that variation that lies in the synesthetic brightness experience.

      Visualizing the effects of idiosyncratic experiences, varying within and between participants is challenging. For the theoretical insight brought about through our paper in Figure 4 (synesthesia being sensory in nature), demeaning is favorable in our opinion as it isolates the effect of interest in visualization. However, for methodological reasons and to better show effect sizes etc., there is certainly use in additional transparency. We now thus provide non-demeaned traces in the supplementary material as the reviewer suggested and also refer to these in the main manuscript. Furthermore, all figures are now provided in millimeters, with all pupil related analysis being rerun and updated to this end (without qualitative changes to the results). This should further rectify possibly inflated expectations about the absolute size of effects and allows to put effects into perspective across studies. We now added:

      “Pupillary data were transformed from arbitrary eyelink units to millimeters using a conversion factor obtained with an artificial eye (see Hayes & Petrov, 2016).”

      Hayes, T. R., & Petrov, A. A. (2016). Mapping and correcting the influence of gaze position on pupil size measurements. Behavior research methods, 48(2), 510-527.

      Impact:

      Despite these weaknesses, and especially if they are adequately addressed in the review, this work is likely to improve our understanding of synesthesia, providing a new tool to quantify the subjective sensations; an interesting potential extension would be using pupillometry for tracking changes over time of the synesthetic experiences, opening up the possibility to evaluate the importance of learning for this peculiar experience.

      We were happy to read our manuscript was evaluated this positively and hope that our replies can address the remaining smaller concerns and make findings more transparent to the readers.

      Reviewer #2 (Public review):

      Synesthesia is a neurological condition where stimulation of one sensory channel leads to involuntary, automatic, and consistent experience of another, unrelated percept. For example, Sir Francis Galton (1880, Nature) famously described the robust tendency of some individuals (synesthetes) to associate numerals with a distinct color. Ever since, synesthesia has continued to attract a broad interest in the cognitive neurosciences in light of its implications for the study of domains such as perception, consciousness, and brain connectivity, among others.

      Strauch, Leenaars, and Rouw measured pupil size in a group of 16 grapheme-color synesthetes and two matched control groups. The participants were presented with gray digits - that is, visual stimuli having identical physical properties in terms of brightness. Each participant subsequently rated the corresponding evoked color and brightness: unlike controls, synesthetes did so in a very consistent and reliable fashion. Accordingly, this was also shown in their pupils: despite the same objective luminance, digits associated with brighter percepts caused their pupils to constrict, and digits associated with darker percepts caused their pupils to dilate more than controls. These results highlight how crossmodal correspondences are deeply rooted in synesthetes, and put forward pupillometry as a particularly appealing biomarker for some phenomenological experience (at least those grounded in "brightness").

      Further strengths of the technique are its temporal resolution and its responsiveness to several constructs. Across several tasks, the authors show, for example, that responses to synesthetic light are somewhat slower than responses to real light (i.e., they are likely mediated), but at the same time faster than responses to mental imagery. The role of mental imagery can also be reasonably dismissed when considering the second feature of pupil size: its responsiveness to mental effort and cognitive load. The pupils tend to dilate with demanding, challenging tasks, and this was the case when control participants were asked to report the color of a digit for which they did not consistently experience a synesthetic association. The same task was, instead, seemingly effortless for synesthetes, again speaking in favor of the automaticity of number-color correspondences in their case.

      Overall, the findings by Strauch, Leenaars, and Rouw are highly significant for the field and likely to be impactful. The strength of their evidence, when accounting for the relatively small sample size and the inherent variability of both phenomenology (color perception and subjective reporting) and physiology (pupil size), is adequate and sufficiently convincing.

      We were glad to read this overall very positive assessment of our work and thank the reviewer for the additional non-public suggestions for improvements.

      Reviewer #3 (Public review):

      Summary:

      In the present study, the authors examined pupillary responses to uncolored stimuli (number graphemes) among number-color synesthetes and non-synesthetes. After seeing a digit, the synesthetes and active control participants were asked to indicate which color they perceived using three dimensions of hue, saturation, and lightness. The lightness values were the primary independent variable for follow-up analyses. To see how the pupil responded to psychologically "bright" and "dark" digits, the authors split the reported lightness values at the median and plotted them. The synesthetes showed a pupillary constriction to digits they perceived as bright and dilation to digits they perceived as dark. Active control participants did not show that effect. In a subsequent block, only the synesthetes were shown the colors they reported perceiving as colored discs. Their pupillary responses were similar. The authors also found that the differences in pupillary responses between light and dark perceptions (with digits) were only slightly delayed in their onset to the perception of a colored disc, and therefore, the color perception accompanying a digit is unlikely to be effortful or a retrieved association, but occurs rather automatically.

      Strengths:

      The authors employed a well-controlled and designed quasi-experiment comparing colorgrapheme synesthetes to non-synesthetes and showed convincingly that the color perceptions accompanying graphemes alter the physical perception of brightness. They also made a reasoned attempt to rule out the possibility that color associations are occurring effortfully via retrieved associations.

      We appreciate the positive assessment and useful suggestions for revision.

      Weaknesses:

      There are some areas in which the implications of these findings could be elaborated upon. I had the following questions:

      (1) Are the pupillary responses among synesthetes, which objectively do not seem to match the degree of physical stimulation entering the retina, in any way maladaptive for eye functioning? I understand the constriction/dilation of the pupil to not only benefit visual acuity but also to protect the retina from damage. Are synesthetes at any risk of retinal damage due to over-dilation of the pupil to brighter stimuli? Or are these effects of a magnitude that is too small to matter? As reported in arbitrary units, it was hard to know how large these effects were in terms of measurable changes in dilation (e.g., millimeters).

      This is an interesting point. Some argue that pupil size changes in a mid-range mildly affect optics thus affecting detection performance, contrast perception, and depth of field (Eberhardt et al., 2022, Mathôt & Ivanov 2019, Ruuskanen, Boehler, & Mathôt, 2025), rather than serving a protective role for the retina (Mathôt, 2018). Indeed, any effects reported here were quite small. We agree with the reviewer that this can be made more accessible by reporting effects in millimeters. We thus now adjusted all figures accordingly and write in the methods section:

      “Pupillary data were transformed from arbitrary eyelink units to millimeters using a conversion factor obtained with an artificial eye (see Hayes & Petrov, 2016).”

      Note that even the largest effects here (those elicited by physical luminance change in block 2 for the synesthetes) only caused differences in pupil size of about 0.3mm. This lies below the maximal pupil dilations observable in response maximal effort (about 0.5mm), for instance, and substantially below the full range of pupil size changes elicited through strong luminance stimulation (several millimeters). We therefore deem the changes in pupil size as obtained in our study too minor to be practically maladaptive for optics/perception.

      Eberhardt, L. V., Strauch, C., Hartmann, T. S., & Huckauf, A. (2022). Increasing pupil size is associated with improved detection performance in the periphery. Attention, perception, & psychophysics, 84(1), 138-149.

      Hayes, T. R., & Petrov, A. A. (2016). Mapping and correcting the influence of gaze position on pupil size measurements. Behavior research methods, 48(2), 510-527.

      Mathôt, S., & Ivanov, Y. (2019). The effect of pupil size and peripheral brightness on detection and discrimination performance. PeerJ, 7, e8220.

      Mathôt, S. (2018). Pupillometry: Psychology, physiology, and function. Journal of cognition, 1(1), 16.

      Ruuskanen, V., Boehler, C. N., & Mathôt, S. (2025). The Interplay of Spontaneous Pupil-Size Fluctuations and EEG Power in Near-Threshold Detection. Psychophysiology, 62(3), e70035.

      (2) Likewise, is the automatic synesthetic merging of two percepts something that could be learned such that natural synesthetes and "artificial" synesthetes would look similar? For example, if a group of non-synesthetic participants were to learn a color-grapheme association to automaticity, would you expect their pupillary responses to the graphemes look similar to the synesthetes'? If so (or if not), what would this tell us anything about the phenomenology of synesthesia?

      We find this question most interesting. Likely, different synesthesia researchers wouldn’t even fully agree on the most plausible answers to these questions. Training studies have shown that nonsynesthetes can be trained to associate particular colors to particular graphemes, as revealed in the synesthetic Stroop effect: interference effects of the learned color onto reporting the typeface color of the grapheme. The degree to which non-synesthetes can be trained to become similar to synesthetes is however still topic of debate.

      We now discuss as follows:

      “Future studies could examine to what degree training a non-synesthete to associate specific colors to particular inducers (e.g., digits), can provide similar patterns of results as genuine synesthesia (Bor et al., 2014, Colizoli et al., 2012, Rothen & Meier, 2014). Could learning produce similar brightness-related pupil effects in non-synesthetes? Similarly, would effort-linked responses diminish with increased training duration? The perhaps most interesting question relates to response latencies: Would a trained participant ever be able to produce brightnessrelated pupil effects as fast as a synesthete?”

      Bor, D., Rothen, N., Schwartzman, D. J., Clayton, S., & Seth, A. K. (2014). Adults can be trained to acquire synesthetic experiences. Scientific reports, 4(1), 7089.

      Colizoli, O., Murre, J. M., & Rouw, R. (2012). Pseudo-synesthesia through reading books with colored letters. PloS one, 7(6), e39799.

      Rothen, N., & Meier, B. (2014). Acquiring synaesthesia: insights from training studies. Frontiers in human neuroscience, 8, 109.

      (3) Do the synesthetic perceptions of digit graphemes merge in a sensible way? For example, if a synesthete sees a particular color with the digit 1, and a different color with the digit 9, what do they perceive when they see 19? or 1-9, or 1 9? Is there color blending, or an altogether different color perception?

      This is a very interesting question indeed. While each synesthete will have their own specific expression of synesthesia, there are regularities in how a combination of digits evokes synesthetic color. First, if asked about the color of a specific digit, each digit keeps its own color, as the color of a digit is linked to the identity of the digit (Dixon et al., 2006). Context effects are however possible, in particular when context alters the interpretation of the digit (Myles et al., 2003). A particularly common context in a multi-digit number is a dominant first digit, spreading its color to the subsequent digits in the number. However, as the digit color is linked to digit identity, what does ‘not’ happen is a mixing of colors into a qualitatively new color; for example, a yellow "1" and blue "9" do not merge into a green "19".

      Dixon, M. J., Smilek, D., Duffy, P. L., Zanna, M. P., & Merikle, P. M. (2006). The role of meaning in grapheme-colour synaesthesia. Cortex, 42(2), 243-252.

      Myles, K. M., Dixon, M. J., Smilek, D., & Merikle, P. M. (2003). Seeing double: The role of meaning in alphanumeric-colour synaesthesia. Brain and Cognition, 53(2), 342-345.

      Many thanks for the constructive assessment of our work.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) I am not sure I'd use the term 'cross-modal' given that the case considered here (graphemecolor) is purely visual.

      The reviewer is absolutely right: the term 'cross-modal' has a historical background rather than reflecting an exact factual accuracy. The term is still commonly used however, as it readily reflects how the induced additional experience is always of a different (sub)type than the inducing experience. There is a cross-over between experiences that might occur within the same sensory modality, or even induce awareness of a particular concept. But key to synesthesia is the crossover experience as the inducer and concurrent are different (sub)types of experiences. For example, seeing a letter can evoke a synesthetic experience of seeing a color, or evoke awareness of a particular gender or personality of that letter, but does not evoke another letter. To remain consistent with literature, we refer to 'cross-modality' when explaining the link to previous literature, but generally switched to using 'cross-over experience':

      “Therefore, synesthesia might provide a unique window into how the brain’s constructive processes can generate additional, conscious content, in cross-over experiences, often across modalities, going all the way down to the level of sensory phenomenology.”

      We adjusted throughout the manuscript accordingly.

      (2) I would not recommend focusing the introduction on the problem of qualia; this is a much more general and complex question than the one addressed in the study; the space of the introduction may be better used to present the actual object of study, giving a better picture of the synesthetic phenomenon and of previous work aimed at characterising it (behavioural, including PA scores and consistency measures, and neuroimaging). It is important to discuss how the pupillometric approach differs from the previously adopted neuroimaging techniques and what it can add to those.

      We agree that qualia is a very general and complex question. However, we respectfully disagree that this complex question is not the object of the study. What is remarkable about synesthesia is not the presence of an additional perceptual association per se, but the presence of a specific perceptual experience. As illustration, think of a test where an unconscious color association to the word 'banana' was tested. While a generic 'yellow' could semantically be linked and would likely be obtained in the (e.g. priming) experimental results, a follow-up question of picking on a color wheel the exact shade of yellow to this association, or describing the perceptual sensation of the color, would be non-sensical to the participants.

      This sharply contrasts with the current study: synesthetes, but not non-synesthetes, indicate a perceptual sensation of additional colors, and subsequently indeed the sensory properties of this percept (experienced brightness) affects the objective reflection of this sensation (pupil size) in synesthetes but not in non-synesthetes. In our view, the presence of additional qualia is key in understanding what sets synesthetic apart from non-synesthete associations, including so-called cross-modal correspondences (unconscious consistent associations across modalities, common to us all). We even believe that the reported qualia is what makes synesthesia so interesting in the first place. We now more clearly explain this link to qualia better in the introduction.

      "The most remarkable aspect of synesthesia is the subjective perceptual phenomenology of the induced colors, setting these sensations apart from color memory, thought, or amodal association. The contrast between synesthetes and non-synesthetes can thus offer an interesting doorway into examining qualia, the subjective perceptual phenomenology or first person (what's-it-like) perspective."

      We also improved the explanation of the synesthetic phenomenon, including a more detailed characterisation of behavioural measures (including consistency scores) and added neuroimaging studies. These changes have been incorporated into the text in response to previous comments (point 1- reviewer 1).

      Please note that we have chosen not to include more detailed discussion of PA scores. Our results show a trend but do not allow for a conclusive interpretation on PA scores, and we feel that placing greater emphasis on this topic might therefore be confusing or even misleading. Still, it would be a very interesting topic for follow-up research to examine how alterations in characteristics of the synesthetic experience influence pupil responses.

      The different synesthesia types all share the defining characteristics of an additional conscious and consistent experience. Synesthetes can verbally report their additional experience, and synesthetic sensations can be measured in behavioral paradigms such as the ’synesthetic Stroop’ effect, or brain activation patterns in sensory cortex [15]. Furthermore, test-retest paradigms show how synesthetic, but not non-synesthetic associations are highly specific and consistent [16-18]. Thus, over the past decades, research has established synesthesia as a ’real’ condition that can reliably be identified using behavior, neurophysiology, and neuroimaging [11, 13, 15–21]. The most remarkable aspect of synesthesia is the subjective perceptual phenomenology of the induced additional sensation, i.e., color in grapheme-color synesthesia. This sets synesthetic sensations apart from (color) memory, thought, or amodal association. Synesthesia can thus offer an interesting doorway into examining qualia, the subjective perceptual phenomenology or first person (what’s-it-like) perspective.

      We now discuss the pupillometric approach as it differs from the previously adopted neuroimaging techniques as follows:

      “Compared to neuroimaging studies [12,15,51], pupillometry may offer a more direct window into synesthetic phenomenology, as the directionality between pupil light reflex and perceived brightness is straightforward. Finally, improved understanding of the underlying processes can be obtained by contrasting responses to perceived versus actual (physical) brightness, given that the pupil light reflex is a well-characterised reflex arc involving few inferential steps.

      This adds to the explanation that was already present on how the current approach differs from previous techniques, and what it can add to those techniques:

      "Instead, current paradigms capturing synesthesia employ objective measures, but fail to capture its phenomenology [16, 17, 21, 23]."

      (3) There are a few typos and word repetitions.

      Many thanks – we identified typos and repetitions after another set of careful reads and hope to have eradicated them completely now.

      Reviewer #2 (Recommendations for the authors):

      I am overall very supportive of this work, but addressing the following points may enrich it further:

      (1) Paragraph 2.2.1. Here, models do not seem to compare synesthetes versus controls but rather assess the effects of interest separately in the two groups. The fact that experimental effects are significant in synesthetes, but not in controls, does not tell us much about differences between groups. Controls (e.g., Figure 3) do show a similar trend, albeit clearly smaller. There is one passage in which this issue appears to be tackled (page 10): "Critically, in an LME ran on synesthetes and controls and using only graphemes and the interaction of group and lightness as predictors, we found lightness to predict pupil size in synesthetes (t = -2.754, p = 0.006), but not controls (t = -1.134, p = 0.257)." But I am not sure that the reported statistics belong to the interaction - they seem to refer to the lightness effect within each group, not the difference.

      This is an important point, power for between-group comparisons is inherently limited for n = 16 per group (while still feasible for overall responses, things become trickier when less trials remain). A simple model of pupil ~ grapheme + group * lightness_scaled + (1 | participant) shows no significant interaction (despite one group showing the effect and the other not showing the effect significantly). The additional negative effect for group is in line with the effort-related effect reported later in the manuscript. Where does this leave us? Based on the lightness responses alone, the group difference can be characterized as a quantitative distinction, but the degree in which it is also a qualitative distinction cannot clearly be determined from current data. We revised the manuscript to make sure that such an interaction is not implied/ point to the absence of the significance of that interaction.

      The sensory nature of synesthetic color is supported by within-synesthete analyses, where coupling strength parametrically modulates the lightness-pupil relationship in a theoretically predicted manner. Importantly, the effort-related findings provide a complementary and statistically robust group comparison: synesthetes and controls performing the identical colorreporting task showed significantly different pupil dilation rates, directly demonstrating that the two groups differ in how they access color information. Together, these two independent pupillometric signatures, one tracking perceptual quality, one tracking effort, converge on the same conclusion and mutually reinforce the interpretation that synesthetic color constitutes genuine sensory phenomenology.

      Author response image 3.

      We now make this more explicit in the manuscript as follows:

      “We found significant modulations of pupil size by the lightness of the grapheme's synesthetic color - sustained and in the to-be-expected time window. Specifically, the pupil constricted more for brighter reported colors, and dilated more for darker reported colors, as predicted (Average pupil size 800-4000ms, t = -3.601, p < 0.001). In an LME ran for synesthetes and controls and using only graphemes and lightness as predictors, we found lightness to predict pupil size in synesthetes (t = 2.844, p = 0.004), but not controls (t = 0.606, p = 0.544). However, when taking group as interacting factor in a joint LME, there was no interaction of lightness and group (t = -0.949 p = 0.342).”

      and

      “For controls a separate model was run, now without the PA score as predictor (not assessed for controls). Neither lightness (t = -0.815, p = 0.415), coupling strength (t = 0.438, p = 0.661), nor their interaction gained significance (t = -1.058, p = 0.290; all for average pupil size between 800 ms and 4000 ms). Critically, we also ran a LME with the three-way interaction of coupling strength, group, and lightness (Wilkinson notation: pupil = grapheme + group + lightness * group + coupling strength * lightness * group + (1 | participant)). This analysis revealed a significant three-way interaction between lightness, coupling strength, and group (F = 3.86, p = .021), indicating that the lightness × coupling strength effect on pupil size was not equivalent across groups. Decomposing this interaction by group, the lightness × coupling strength slope was significant in synesthetes (t = 2.59, p = .010) but not in controls (t=-1.01, p=.311), suggesting that reported lightness and its coupling strength were more consistently related to pupil size in synesthetes than in controls. Note however, that this decomposition does not directly test whether the two slopes significantly differ from each other, however. Lastly, pupil size was marginally larger in controls than in synesthetes (t = 1.94, p = .062; see later sections for more in-depth analyses)”

      (2) The authors choose to analyze pupil size in arbitrary eye tracker units. This is fine, although I would recommend assessing and reporting whether the average pupil size (e.g., during the baseline) is roughly comparable between groups. The size of the effects may be difficult to compare between groups in the presence of very different baseline pupil size.

      Please see Author response image 4 for Baseline pupil sizes per group in millimeters. There were no differences between groups.

      Author response image 4.

      F2, 45) = 0.707, p = 0.499 (One-way Anova).

      We now write:

      “Baseline pupil sizes did not differ between groups (F(2, 45) = 0.707, p = 0.499).”

      We agree with the reviewer that millimeters are a more intuitive measure and updated all figures throughout manuscript and supplementary materials accordingly. We also briefly added to signal processing that this conversion was applied.

      “Pupillary data were transformed from arbitrary eyelink units to millimeters using a conversion factor obtained with an artificial eye (see Hayes & Petrov, 2016).”

      Hayes, T. R., & Petrov, A. A. (2016). Mapping and correcting the influence of gaze position on pupil size measurements. Behavior research methods, 48(2), 510-527.

      (3) If I understand correctly, the main task counted 120 trials overall (12 per digit). It seems, however, that only 3 and 4 participants remained with at least 50 trials (or 25 per median split by lightness) after preprocessing. This appears to be quite a massive data loss: is there a reason behind it? Please also clarify: the overall percentage of discarded trials; whether the median split by lightness was computed on all responses or only on those of the remaining, valid trials.

      This is an important point for clarification indeed. The exclusion of participants in Figure 3 applies only to that particular visualization, not to the statistical analyses. The linear mixed effects models (LMEs) used all available valid trials from all participants, with no participant-level exclusions. The figure-specific threshold (≥25 trials per median-split bin) was applied purely for display clarity, as plotting participants with very few trials per bin would produce unreliable/noisy and thus visually misleading traces (as we note in the figure caption and point readers to Supplementary Figure 1, which shows the same visualization without any exclusions).

      Since the paradigm required participants to repeat discarded trials until 120 valid trials were collected, all participants thus contributed exactly 120 valid trials to the analyses. There was therefore no data loss at the analysis level for the LME that is central to the claims of the manuscript (albeit more complex to grasp than the t-tests between bins).

      Why were there sometimes so little trials per brightness bin?

      First, participants differed in how dark or bright (synesthetic or forced-report) colors were overall, meaning that differing proportions thereof would fall above or below the 0.5 cutoff that overall, well represented the sample (but not necessarily every single participant). Note that this median split was not performed per individual but across all color reports to allow an apples-to-apples comparison.

      Second, participants often reported colors that differed in Hue and Saturation, but not Lightness. This is in line with synesthetes picking certain colors more often than others, as compared with non-synesthetes (Rouw & Root, 2019; Ward et al., 2025).

      We now include a new Supplementary Figure that visualizes responses on the Hue and Saturation dimensions of HSL space for both synesthetes and controls; fully saturated reports appear on the outer edge. We refer to the supplementary figure in the caption of Figure 2 as follows:

      "See Supplementary Figure 1 for color reports on the hue and saturation axes.”

      Rouw, R., & Root, N. B. (2019). Distinct colours in the ‘synaesthetic colour palette’. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1787).

      Ward, J., Maciel, S., Rouw, R., Simner, J., & Root, N. (2025). Synaesthesia is linked to differences in music preference and musical sophistication and a distinctive pattern of sound-color associations. Psychology of Music, 53(3), 453-473.

      Minor points:

      (1) "Building on this evidence, we hypothesized that the cross modal color phenomenology in synesthesia can, if truly sensory in nature, could likewise be (...)" -> may need rephrasing (can/could).

      Many thanks, fixed.

      (2) Caption of Figure 1: "Block 2 (synesthetes only): a colored disk and gray central patch, matching the average indicated color per digit, and the number and luminance of pixels of said digit were presented to assess externally triggered light responses." -> I find this sentence a bit hard to follow; perhaps consider rephrasing it.

      Agreed, we rephrased to:

      Block 2 (synesthetes only): a colored disk was presented, colored according to the synesthete's average indicated color for that digit. At its center sat a gray patch matching the luminance and pixel area of the original digit from Block 1, together allowing assessment of externally triggered light responses.

      (3) Figure 2 b: Consider truncating the y-axis to 1 if that improves the visualization.

      We adjusted the axis accordingly and added a bit more detail in the caption for the interpretation of the measure.

      (4) Caption of Figure 3 points to "see Supplementary Figure 1", but it should probably be SF2.

      Many thanks for spotting, all references to supplementary figures have been checked and are corrected now.

      Elvio Blini

      Reviewer #3 (Recommendations for the authors):

      (1) As a minor comment, there are some terms that felt overused in the manuscript. For example, the words "extraordinary" and "exceptional" were used multiple times throughout. I believe I understand the authors to mean them in their descriptive sense (i.e., outside the realm of typical experience), but in context, those words make it seem like they are touting their own experiment as "exceptional" or "extraordinary," which I don't believe was their intention.

      We agree. We removed words such as exceptional and extraordinary when they do not directly refer to the sensation throughout the manuscript (which is indeed how we intended to use it). We hope that this removes unnecessary and convoluting hyperbole.

      (2) It seemed counterintuitive to me that the color consistency score would be reverse-coded. In this case, the scores actually seem to indicate inconsistency, rather than consistency. Perhaps the raw scores can be inverted for a more intuitive interpretation that aligns with the terminology. I understand that they were following a previous publication in their method (Rothen et al., 2013).

      This manner of coding is counter-intuitive indeed. However, there are both logical and practical reasons to this approach. Importantly, this is indeed the standard way of reporting color consistency in synesthesia research (Carmichael et al., 2015; Eagleman et al., 2007; Root et al., 2025; Rothen et al., 2013). The calculation is based on a simple logic; a higher number reflects a larger distance in color space. An additional advantage is the clear and intuitive zero- reference: a score of zero implies choosing the exact same color. Finally, it intuitively reflects the distinction between synesthetes and non-synesthetes; there is by definition little variation across synesthetes (visualized at the bottom of the graph), then a 'cut-off line' (if consistency is used as diagnostic tool), and then the height of the range shows how large the range in consistency is, in that particular sample of non-synesthetes. In a way we therefore inherit a confusing definition/standard, but changing it would lead to new confusion instead. We now specifically clarify this in the caption as follows:

      “Note that higher consistency is reflected in lower color distance, hence lower values [17].”

      Carmichael, D.A., Down, M.P., Shillcock, R.C., Eagleman, D.M., Simner, J., 2015. Validating a standardised test battery for synesthesia: does the synesthesia battery reliably detect synesthesia? Conscious. Cogn. 33, 375–385

      Eagleman, D.M., Kagan, A.D., Nelson, S.S., Sagaram, D., Sarma, A.K., 2007. A standardized test battery for the study of synesthesia. J. Neurosci. Methods 159 (1), 139–145.

      Root, N., Chkhaidze, A., Melero, H., Sidoro -Dorso, A., Volberg, G., Zhang, Y., & Rouw, R. (2025). How “diagnostic” criteria interact to shape synesthetic behavior: The role of self-report and test–retest consistency in synesthesia research. Consciousness and Cognition, 129, 103819.

      Rothen, N., Seth, A.K., Witzel, C., Ward, J., 2013. Diagnosing synaesthesia with online colour pickers: maximising sensitivity and specificity. J. Neurosci. Methods 215 (1), 156–160.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      (1) All outcomes are attributed specifically to L6b neurons, but the genetic manipulation is not specific to L6b neurons. The authors acknowledge this as a limitation, but in my view, this global manipulation is more than a limitation - it affects the overall interpretations of the data. The Hoerder-Suabedissen et al., 2018 paper shows sparse, but also dense, expression of Drd1a+ neurons in brain regions outside of the L6b. Given this issue, the results are largely overstated throughout the paper.

      We appreciate the reviewer’s careful reading and concern that some of our statements may have overstated the implications of our data. The Drd1a Cre mouse model used (FK164) has a relatively selective expression of Drd1a Cre in cortex, but indeed some expression is seen subcortically. This is an acknowledged limitation which is now explicitly addressed in the revised manuscript.

      (2) It is not clear to me that the "silencing" of Drd1a+ neurons was verified.

      In our previous publications, we showed confirmation of the loss of regulated synaptic vesicle release from the Cre-positive neuronal population (Marques-Smith et al., 2016; Hoerder-Suabedissen et al., 2018; Messore et al., 2024). This has now been described in the revised manuscript.

      (3) There were various discrepancies (and potentially misattributions) between the stated significant differences in Supplementary Table T1 data and Figure 3a & S2 spectral plots. This issue makes it difficult to effectively evaluate the main text and stated outcomes.

      We thank the reviewer for their careful attention to the statistical analyses and for noting the inconsistencies in how the results of the spectral analysis were presented: in the text we described two-way ANOVAs with according posthoc tests but in the figures significance markers were positioned based on multiple t tests. We have now carefully revised the spectral results and implemented a consistent approach in statistical reporting and spectral plots. We have updated Supplementary Table T1, Figure 3a and S2 to ensure that all statistics are presented consistently throughout the manuscript, i.e. with two-way ANOVAs and accompanying posthoc tests. Please note that we performed all spectral analyses in the range between 0.5 and 128 Hz (excluding the range between 49-51.5 Hz due to electrical noise from the power grid) but only plot the range between 0.5-30 Hz as the spectral bands most relevant for sleep neurophysiology are contained in this range.

      Related, the authors stated that post hoc comparisons of EEG spectral frequency bins were not corrected for multiple testing. Instead, significance was only denoted if changes in at least two consecutive frequency bins were significant. However, there are multiple plots in which a single significance marker is placed over an isolated bin (i.e., 4c, 6, S5, S6). Unless each marker is equivalent to 2 consecutive frequency bins, these markers should be removed from the plots. Otherwise, please define the frequency and size of these markers in the main text.

      In line with the previous comment, we have adjusted markers to reflect the results from posthoc tests after two-way ANOVAs.Please note that Figure 6 and the related supplementary figures S5 and S6 have now been removed from the manuscript, as careful re-analysis indicated that the sample size was too low to support a strong conclusion regarding the comparison of orexin effects between genotypes. We stated in the text that we would only include posthoc significance when at least two consecutive bins were significant, but this was indeed not supported in our figure, where each marker reflects one 0.25 Hz bin. We have now adjusted our code to ensure that only markers are plotted when at least two consecutive bins are significant in bin-wise posthoc comparisons.

      (4) A rainbow color scale, as in Figure 3, we've now learned, can be misleading and difficult to interpret. The viridis color scale or a different diverging color scale are good alternatives.

      Thank you for pointing this out, we have adjusted the colour scale.

      (5) How much time elapsed between vehicle/orexin A & B infusions?

      There were 2-4 non-infusions days between infusions. We have added this information to methods.

      (6) For Figure 6, there are statistical discrepancies between the main text and the plots (pg. 10):

      (a) The text claims post hoc differences for relative ORXA frontal EEG, but there are no significance markers on the plot.

      (b) The text states that there were no post hoc differences for the relative ORXA occipital EEG, but significance markers are on the plot.

      (c) The main test for the relative ORXB frontal EEG was not significant, but there are post hoc significance markers on the plot.

      (d) For relative ORXB occipital EEG, there are significant markers on the plot outside of the stated range in the text.

      We agree with the reviewer, and we decided to exclude this figure from the manuscript as the sample size for some key comparisons was too low to support any strong conclusions and therefore presenting this analysis is potentially misleading. We explain the rationale for excluding this analyses in the revised manuscript.

      (7) Some important details are only available in figure captions, making it difficult to understand the main text. For example, when describing Figure 3c in the main text on page 7, it is not clear what type of transitions are being discussed without reading the figure caption. Likewise, a "decrease," "shift," and "change" are mentioned, but relative to what? Similar comment for the EEG theta activity description on pages 7 - 8. Please add relevant details to the main text.

      We have adjusted the wording in the main text to reflect more precisely which comparisons are shown in the figures.

      (8) Statistical comparisons for data in Figure 3e, post hoc analyses for data in Figure S7a-b REM data, and post hoc analyses for Figure S7c (not b) occipital EEG should be included to support differences claims. Please denote these differences on the respective plots.

      Please note that the previously named Supplementary Figures S5 and S6 have been removed from the manuscript, and that the Supplementary Figure S7 in this comment refers to the figure currently named Supplementary Figure S5.

      We have added the statistical comparisons for Figure 3e, Supplementary Figure S5A and Figure S5b to the results section. In Figure S5c, there was an overall genotype difference, but there was no significant time x genotype interaction, so we have not performed posthoc tests and did not plot posthoc significance markers for this figure. We have adjusted the wording in the results section to make this clearer. We have adjusted the reference to the figure S5c which was incorrect, thank you for your careful attention.

      (9) In the subsection titled "Layer 6b mediates effects of orexin on vigilance states (pg. 8)," there does not seem to be any stated differences between control and L6b silenced mice. A more accurate subtitle is needed.

      We agree with the reviewer and the title of this sub-section has now been changed accordingly.

      Reviewer #2 (Public review):

      Weaknesses:

      (1) Although the authors used a highly selective approach to silence layer 6b neurons, the observed changes in EEG oscillations cannot be solely attributed to layer 6b neurons because of the ICV route for orexin administration.

      We thank the reviewer for this important comment. The ICV route of orexin administration cannot guarantee that only cortical Drd1a-Cre–expressing neurons are reached by orexin, and the Drd1a-Cre driver line is highly selective but not entirely specific for layer 6b neurons (see also response to reviewer #1, comment 1). We have therefore changed the wording of the stated effects and addressed this consideration in the Limitations section of the manuscript. Please note that, as mentioned above, Figure 6 has now been excluded from the manuscript.

      (2) The rationale for using only male rats is not provided.

      We thank the reviewer for highlighting this omission. We now provide the rationale for using only male mice in the methods section as follows: “In the current study, only male mice were used, because our experimental protocol precluded the possibility of accurately monitoring the oestrous cycle, which has marked effects on brain activity, arousal and vigilance states. We therefore decided to use male mice only for the current study but are planning to use both sexes in future work.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Better descriptions of L6b connectivity will improve clarity in the second paragraph of the Introduction (pg. 3). For example, it is not explicitly stated that L6b projects to L5 before the authors describe L5. Therefore, the L5 description seems irrelevant.

      We thank the reviewer for this request for clarification. We mention the connectivity between L6b and L5 because L5 pyramidal neurons have recently been found to play a key role in sleep-wake regulation (Krone et al., Nat. Neurosci. 2021; Honjo et al., 2025; Wasilczuk et al, 2025; Krone et al., 2025). We have now amended the corresponding section of the introduction to emphasise the potential functional relevance of this connection as follows:

      “L5, the major output layer of the cortex, is also bidirectionally communicative with higher order thalamic nuclei (Hoerder-Suabedissen et al., 2018) as well as layer 5 pyramidal neurons (Zolnik et al., 2024). Since several subtypes of L5 pyramidal neurons have recently been shown to play important roles in distinct aspects of sleep-wake regulation (Krone et al., 2021, 2025; Hong et al. 2023; Wasilczuk et al. 2025; Honjo et al., 2025; Chouafeev et al., 2025); depth of anaesthesia (Wasilczuk et al. 2025), and the influence of stress on sleep (Chouafeev et al. 2025) the projections of orexin-sensitive L6b to L5 pyramidal neurons may be a key circuitry in the top-down regulation of brain states.”

      (2) There are plots where the y-axis tick label appears to be offset from the tick mark (4a, S5b, S6a).

      Thank you for spotting this graphical issue. We have removed the y-axis tick labels from Figure 4a to avoid confusion. Please note that we decided to remove Figure S5 and Figure S6, because after careful re-analysis we concluded that the group size was too small to draw conclusions on orexin spectra and that any results could be potentially misleading.

      (3) The 2-h time constant, I believe, is depicted in Figure 4H (not 4G).

      Thank you for spotting this. We have corrected the figure legends accordingly and double-checked that Figure 4G depicts the 2-h time constant and Figure 4H the 6-h time constant.

      (4) "...although there was an indication of a higher absolute theta-peak power in layer 6b silenced mice (Figure S6)," pg. 10. It is not clear to me how the data lead to this conclusion.

      Thank you for identifying this inconsistency, which resulted from a preliminary statistical analysis subsequently corrected. We have now improved the statistical analysis of spectral data (for more details see comments to both reviewers in public response) and removed this statement, which in fact is no longer supported by the data.

      (5) Exclusion of female mice is not listed as a limitation.

      We now discuss this limitation as follows:

      “In the current study, only male mice were used, because our experimental protocol precluded the possibility of accurately monitoring the oestrous cycle, which has marked effects on brain activity, arousal and vigilance states. We therefore decided to use male mice only for the current study but are planning to use both sexes in future work.”

      (6) A brief description of why Cplx3 and Tbr1 antibodies are being used will be helpful to include in the Methods (pg. 21) in addition to what is in the figure caption.

      We have added the following information to the methods section to clarify why we used these two antibodies: “rabbit α-Cplx3 to distinguish between L6a and L6b” “mouse α-Tbr1 to identify the L5-6 boundary”

      (7) Including a label/title for the Figure 2c spectral plots will be helpful. It is not immediately clear if these are light period & dark period data or frontal & occipital data.

      Thank you for pointing this out, we have updated the figure legend to clarify what is shown on this Figure

      Similar comments for S2 and S3a plots. Including a state label on the plots will be helpful in addition to the caption description.

      We have now added the state labels for Figure panels S2 and S3a for improved clarity.

      Reviewer #2 (Recommendations for the authors):

      This is a soundly conducted and well-written study that enhances our understanding of the cortical control of states of consciousness. I do not have any major concerns, but would like the authors to consider some alternate possibilities as suggested in my comments below:

      We thank the reviewer for this positive assessment of our manuscript and the helpful suggestions.

      (1) Given that the inactivation of layer6b neurons did not affect the time spent in sleep-wake states, to me it appears that these neurons likely have a role in creating the background neural conditions/oscillations supportive of an activated state rather than a direct role in behavioral state control.

      We completely agree with the reviewer and have made the wording more consistent throughout the manuscript, now using “brain state control” rather than “behavioural state control” to clarify that the main effect observed in the L6b-silenced mouse model is a change in spectral characteristics reflecting brain oscillations, rather than effects on vigilance states, which were modest.

      (2) Does the observed shift in REM sleep-related theta-peak frequency in the occipital derivation suggest changes in local neural processes, or could it be just a matter of better signal detection because theta is most prominent at or around the hippocampal region, which is approximately the location of occipital electrodes in this study.

      The source of the shift in REM sleep–related theta peak frequency in the occipital derivation cannot be established with EEG recordings alone. Additional intracortical or intrahippocampal recordings would be necessary to distinguish between the two possible explanations proposed by the reviewer. We have discussed this further in the revised manuscript.

      (3) Orexinergic system innervates multiple subcortical sites and widely covers the cortex too, because of which the effect of ICV orexins cannot be attributed to just layer6b neurons as described in the manuscript ("Layer 6b mediates effects of orexin on brain activity.").

      We agree with the reviewer that this is a limitation. We have now adjusted the subtitle of the paragraph describing the results from the ICV administration of orexin and further mention this important consideration in the ‘limitations’ section of the discussion.

      (4) While the current study is focused on sleep-wake mechanisms, the findings reported here have much broader implications for behavioral and/or brain state arousal and provide a mechanistic bridge between different states of consciousness, including general anesthesia. Therefore, the authors may consider tying these findings with the recent work on the role of the prefrontal cortex in arousal from general anesthesia and slow-wave sleep (PMID: 35436248, PMID: 29937348, PMID: 33328847).

      We thank the reviewer for this excellent recommendation. We are now citing these papers in the revised manuscript.

      (5) It's up to the authors, but I do not see the need for the section on Clinical Implications. It's very speculative, and it makes the entire discussion section heavy.<br />

      We have considerably shortened the discussion of potential clinical implications to make the manuscript more concise.

      (6) Figure 1: It's difficult to compare the EEG power the way figures are set up right now. I think it would enhance clarity if the authors separate the plots based on state and show power from the control and silenced neuronal group in the same plot. Also, the colors are too similar (essentially a shade of green/blue) to provide effective visual resolution. This is especially true in panel d. Please consider changing the color scheme.

      This comment seems to refer to Figure 2 and subsequent figures with analysis of vigilance states and EEG spectra (Figure 1 contains histological images). We have selected the colour scheme for colour-blind individuals. Therefore, the main difference is in the saturation, not the colour of the plots. We have tested the visibility of the colour scheme on a high-resolution screen with the original image files and can reassure the reviewer that the genotype differences, which are slightly blurred in the reduced-resolution figures provided within the combined text file for the review process, are easily distinguishable in the final figure quality.

      (7) I don't understand the y-axis scale in Figure 1. How can this be 500% and if it is, then 500% of what?

      This comment also seems to refer to the analysis of slow wave activity (SWA) in Figure 2 rather than to Figure 1 (histology figure). The percentage of SWA is normalised to the average SWA across the recording. Since NREM sleep is characterised by considerably higher SWA than wakefulness and REM sleep, the level of SWA during NREM sleep is in the range of 200-300%, and can be even higher after long wake episodes which are followed by a rebound of NREM sleep SWA. Hence, the upper limit of the y-axis in these (and subsequent) plots of SWA is 500% (of the average SWA). We have amended the figure legend to clarify that SWA is presented here as percentage of average SWA across the recording.

    1. Author Response:

      Reviewer #1 (Public review):

      Summary:

      The authors present a novel approach to subcellular spatial proteomics by combining laser microdissection with expansion microscopy and LC-MS/MS analysis (SPEx). They implement two different workflows for LMD and LC-MS/MS quantification:

      (1)The standard approach, where an area of interest is cut out by LMD, subjected to proteomics analysis, and compared to the rest of the cell without the dissected ROI.

      (2) The subtraction approach, where ROIs are removed, and the remaining cellular material is compared to samples containing both the surrounding material and the ROI.

      The authors assess the technique by applying it to subcellular targets of various sizes, volumes, and protein compositions such as the nucleus, nucleoli, and Golgi. They demonstrate that SPEx can identify proteins enriched or reduced in ROIs.

      Strengths:

      The broad, relatively easy, and inexpensive applicability of this approach to potentially many cell types and subcellular areas of interest provides an exciting alternative to subcellular fractionation, native immunoprecipitation, or genetically encoded proximity labeling constructs. Moreover, by visually selecting ROIs for subsequent analysis, subcellular context or organelle morphology can be taken into account, as discussed by the authors in the discussion section.

      Weaknesses:

      While strongly supporting the sharing of this approach, we have a number of comments and questions that will improve the impact of the manuscript:

      We thank the reviewer for the careful evaluation of our manuscript and the generally positive assessment. We plan on improving our manuscript based on the reviewers’ comments.

      (1) General:

      a) The manuscript would benefit from restructuring and language revision. In its current form, the writing is sometimes dense and verbose (in particular, the Results section). This makes it difficult to follow the authors' arguments.

      We will improve readability and clarity of the results section in the revised manuscript.

      b) The authors mention the possibility of selecting organelles based on morphology. This is left for the discussion, but it seems like a missed opportunity - the authors could compare individual organelles in different morphological states, e.g., connected vs. fragmented mitochondria.

      The authors agree with the reviewers’ assessment that investigating proteome of organelles based on morphology or cellular state is an exciting application of SPEx. While we plan experiments along this line in the future, we think that these experiments are beyond the scope of this manuscript, which is meant to describe the method and its general usefulness.

      (2) Technical:

      a) Why do the authors strive and optimize for a 10x expansion factor? Is SPEx compatible with a more standard 4x expansion, as e.g., used in the classic U-ExM approach (https://www.nature.com/articles/s41592-018-0238-1)? This could be added to the discussion.

      We aimed for 10x expansion solely because our ultimate goal is to cut out very small structures. Isolating structures as small as nucleoli would not be as reliable with a lower expansion factor (i.e. 4x) expansion. We did not assess the compatibility with U-ExM. We would assume that SPEx would also work with U-ExM as expansion method; omitting protease treatment, however. Still, we performed pilots with just 4x expansion (using TREx) in the early stages of optimization. We were able to isolate single cells and obtain similar protein coverage as with 10x expansion. We will further clarify our motivation to use 10x expansion in the discussion.

      We would also like to point out whether to U-ExM the standard method or not is rather subjective. Even though TREx was published three years later, it is also very widely used. The original expansion microscopy method was published three years prior to U-ExM.

      b) The U-ExM approach shows improved ultrastructural preservation when using 3%FA with 0.1% glutaraldehyde fixation (GA). Is SPEx compatible with the use of low amounts of GA for fixation?

      We tried different fixation methods in the early stages of this study (where expansion was not yet close to 10x). We saw a mild negative effect of GA on the expansion factor, so we avoided it in the later experiments since it also did not seem necessary to preserve the structure of our organelles of interest. However, the use of GA would generally be compatible with SPEx, potentially at the cost of a mild negative effect on expansion factor (see Author response image 1) and proteome coverage. We can add this information to the discussion.

      Author response image 1.

      Fixation methods mini-screen. Cells were fixed with the indicated reagents for 10 minutes at 37°C. After TREx expansion, the diameter of the nucleus was measured (A) and the resulting expansion factor compared to the non-expanded control was determined (B).

      Related to the above, was the anchoring efficiency reduced only to achieve a 10x expansion factor or does this additionally affect the proteome coverage?

      We solely lowered the anchoring in order to allow for higher expansion factors. In earlier pilots we performed proteomic analysis on samples that were just expanded 4x using standard TREx expansion (also using the original anchoring strategy from the TREx publication, consisting of 0.2 mg/ml AcX for overnight at RT). We presented the results of this pilot in Fig S1A. We still detected over 2,000 proteins from 10 cells, a coverage, which is highly similar to what we found in the final experiments (Figure 2F), in which the anchoring was lower yielding 10x expansion. Based on these data, we hypothesize that anchoring (and expansion factor!) has a negligible impact on protein coverage. We will clarify this in the manuscript.

      d) Have the authors considered using alternative anchoring approaches, such as GMA (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0291506#pone.0291506.s001), which potentially increase the amount of sample retained in the hydrogel, thus allowing for better proteome coverage? This could be added to the discussion.

      We did not use alternative anchoring approaches. We modified the TREx protocol to fit our purposes and since this was sufficient, we did not explore alternatives. However, using anchoring approaches, in which higher amounts of sample could be retained in the gel might be beneficial for the proteomics coverage. We will keep this suggestion in mind for future experiments. Thank you for the suggestion!

      e) The limitation of the approach to near-2D samples should be mentioned, and alternative approaches for more 3D samples could be discussed.

      The authors agree that SPEx is limited to near-2D samples at this point. We suggest that SPEx is applicable for 3D samples (e.g. in tissues) by performing cryosectioning. TREx has been shown to be compatible with sectioned tissue (Damstra et al., 2022). We will elaborate this in the discussion.

      f) How are peptides that are directly anchored to the hydrogel dealt with during LC-MS/MS analysis? Are they excluded, or can they be identified during the spectral search? The latter would allow us to get a deeper structural understanding of how proteins are actually anchored into hydrogels, which so far has not been assessed.

      The reviewer raises an interesting point. In general, peptides carrying the anchoring modification are analysed by LC-MS, but we did not include these specific modifications in the database search. Overall, we assumed that the labeling would be low and stochastic and hence should, if at all, only minimally affect the detection of peptides. Nevertheless, in response to the reviewers’ comment, we searched the MS data again for the crosslinking reagent linked to lysine residues. However, we could not get any confident hit for any peptide containing this modification. Since we cannot exclude that the modification precludes the identification of the corresponding peptides, we compared the number peptides generated by trypsin cleavage after arginine and lysine. As the human genome contains similar proportions of both amino acids, one would expect similar numbers of both peptide types being identified. Any modifications of lysine by the anchoring reagent used, would prevent tryptic cleavage and thus reduce the number of lysine peptides. As shown in Author response image 2, the number of lysine terminating is only slightly lower compared to arginine terminating peptides. Notably, the proteomics results of a different fixed human tissue sample directly extracted by laser capture micro dissection without expansion showed a very similar lysine to arginine peptide ratio. This indicates that the large majority of lysine residues is not modified and affected by the hydrogel anchoring.

      Author response image 2.

      Number of peptides identified either terminating with lysine (K) or arginine (R) across all samples shown in Figure 5F.

      An alternative approach to address this question would be to investigate if the peptide coverage of proteins detected by SPEx is enriched for peptides representing the folded core of proteins as opposed to the surface-exposed regions, which likely get more anchored into the hydrogel.

      Because of the negligible amounts of modified peptides, we did not investigate this potential bias of surface-exposed versus folded-core peptides.

      g) Same question regarding peptides with NHS labeling. Can they be identified, or do they just compete for ionization and thus negatively affect coverage and dynamic range of the LC-MS/MS approach?

      The reviewer raises a similar point as above for another lysine labeling used during the SPEx protocol. Again, we specifically looked for this modification by re-searching the raw MS data, but still could not identify any peptides, carrying this modification on a lysine residue. Even though we cannot exclude that this rather large modification prevents detection, considering the high number of lysine terminating peptides in our dataset (see Figure 2), we would expect that also this labeling step is stochastic and affects only a minor proportion of the proteins.

      h) How are the primary and secondary antibodies affecting the proteomics analysis identified as contaminants?

      We thank the reviewer for this comment. Since antibodies bind to proteins in a non-covalent manner, they will be released during the denaturing steps of the protocol. Of course, the antibodies will stay in the sample, be digested and analyzed and could, if very abundant, affect the analysis of the proteins from the samples. To check this possibility, we re-searched the MS data including the sequences of the antibodies used. To our surprise, we could not detect any peptides of these antibodies. This suggests that the concentrations of the antibodies used are much lower than those of the sample proteins and thus should not have any impact on the proteomics results.  We interpret this result also as a benefit of our method compared to organellar-IP.

      i) Have the authors observed differences in proteomics coverage of only antibody vs NHS-labeling? Depending on the questions above, could pure antibody-based labeling increase proteomic coverage?

      We did not perform this comparative analysis, since we always used NHS dyes. In the experiments presented in this manuscript, NHS dyes allowed easy visualization of the whole cell without the use of antibodies. This NHS staining was essential for this particular setup for sample acquisition. We cut out entire cells, cells lacking the nucleus and cells lacking the Golgi apparatus, which served as critical controls. However, other ways of detecting cell boundaries could be used to avoid NHS staining. As shown above, both, the anchor and NHS labeling are likewise sparse and stochastic. Moreover, we could not detect any impact of the antibody labeling to our results. Thus, we assume that both labeling procedures could be used.

      Reviewer #2 (Public review):

      Summary:

      This study introduces a method that combines physical expansion of cells, imaging-guided isolation of defined regions, and protein identification to enable compartment-resolved analysis of protein composition at the subcellular scale. The authors aim to address a central limitation in existing approaches, namely the loss of spatial information during sample preparation or the indirect nature of proximity-based labeling methods. Using several cellular compartments as examples, they demonstrate that their approach can recover compartment-enriched protein sets and identify candidate proteins with previously unassigned localization.

      Strengths:

      A major strength of this work is the conceptual simplicity and accessibility of the approach. By combining established techniques in a modular way, the method avoids the need for genetic manipulation or specialized labeling strategies, making it broadly adaptable across experimental systems. The ability to directly select regions of interest based on imaging represents a clear advantage over indirect enrichment strategies and allows flexible targeting of both membrane-bound and non-membrane-bound compartments.

      The experimental design is also a strong aspect of the study. The use of complementary comparison strategies-analyzing isolated compartments alongside matched "subtracted" controls-provides an internal framework for assessing enrichment and depletion, increasing confidence in spatial assignment. The application of the method across multiple organelles of different sizes and properties demonstrates versatility, and the reported specificity for several compartments is encouraging. In particular, the ability to profile small and biochemically challenging structures highlights a potentially important niche for the approach.

      Weaknesses:

      Despite these strengths, several methodological limitations constrain the interpretation of the results. The most important relates to spatial accuracy in three dimensions. While lateral resolution is improved through physical expansion, the lack of depth resolution introduces uncertainty regarding contributions from structures above and below the selected region. Although the authors argue that this does not substantially affect specificity, the current evidence is largely indirect, and a more rigorous quantification of potential contamination would strengthen this conclusion.

      Quantitative interpretation also remains challenging. Because the measurements reflect total protein abundance rather than local concentration, differences in compartment size and protein density can influence enrichment values, particularly for small structures embedded within larger volumes. This issue is evident in the analysis of smaller compartments and complicates direct comparison across conditions. Additional normalization or modeling would help clarify how to interpret these measurements.

      Another limitation concerns variability in the expansion process and its downstream consequences. Differences in expansion factor across samples may affect the definition of regions of interest and introduce variability in sampling, yet the impact of this variability is not fully explored. Similarly, the use of a modified chemical treatment to preserve proteins for downstream analysis is central to the workflow but is not extensively validated with respect to preservation of spatial organization.

      While the identification of previously unannotated proteins is an appealing aspect of the study, validation is limited to a small number of examples, and broader support from independent datasets or literature context is lacking. In addition, the study primarily focuses on steady-state measurements in a single cell type, and therefore does not yet demonstrate the ability of the method to capture dynamic or condition-dependent changes in protein localization.

      Finally, the positioning of the method relative to existing approaches could be more clearly articulated. Although qualitative comparisons are provided, a more systematic and quantitative benchmarking against alternative strategies would help readers better understand the specific advantages and trade-offs.

      We thank the reviewer for the careful evaluation of the manuscript and for the constructive feedback. We think the reviewer raises valid points and will address them in the revised manuscript.

      Reviewer #3 (Public review):

      Franziscus et al. describe an elegant approach for spatially specific proteome analysis. To achieve this, they expand fixed cells and subsequently use a laser to micro-dissect a region of interest, which is then analyzed by mass spectrometry.

      They demonstrate the effectiveness of their approach by analyzing the nucleus, nucleolus, and the Golgi, and benchmark their hits against previous datasets for these organelles.

      The manuscript is very well written and nicely guides the reader through the applied methods. The presented data is convincing, and I do not see the need for additional experimental verification of the protocol. The only minor concern is the novelty of the method and the presentation. A combination of expansion, laser microdissection, and proteomics has been applied in the past (PMID: 36450705, PMID: 39477916). In the manuscript, one of these studies is cited, though it does not become clear that this approach is already described. However, Franziscus et al. describe the approach better and make it more accessible to the reader, especially since the other studies described this methodology in combination with tissue expansion and not in combination with single cell expansion as it is done here. I would ask the authors to be clearer in the introduction about what others have already done and what their contribution is here. In general, I am convinced that the community will benefit from the presented protocol to analyze organelle proteomics in detail.

      We thank the reviewer for the careful evaluation of our manuscript and overwhelmingly positive assessment. We apologize for the omission of the mentioned citations, and will adjust the introduction to make it clearer what has already been done and what the advance our method provides.

      References

      Damstra HG, Mohar B, Eddison M, Akhmanova A, Kapitein LC, Tillberg PW. 2022. Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). eLife 11:e73775. DOI: https://doi.org/10.7554/eLife.73775

      Gambarotto D, Hamel V, Guichard P. 2021. Ultrastructure expansion microscopy (U-ExM). Methods in Cell Biology 161:57–81. DOI: https://doi.org/10.1016/bs.mcb.2020.05.006, PMID: 33478697

      Liffner B, Silva TLA e., Vega-Rodriguez J, Absalon S. 2024. Mosquito Tissue Ultrastructure-Expansion Microscopy (MoTissU-ExM) enables ultrastructural and anatomical analysis of malaria parasites and their mosquito. BMC Methods 1:13. DOI: https://doi.org/10.1186/s44330-024-00013-4

    1. Author response:

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

      We thank the editor and reviewers for their constructive questions, valuable feedback, and for approving our manuscript. We truly appreciate the opportunity to improve our work based on their insightful comments. Before addressing the editor’s and each referee’s remarks individually, we provide below a point-by-point response summarizing the revisions made.

      Duplication of control groups across experiments

      We appreciate the reviewers’ concern regarding the potential duplication of control groups. In the revised manuscript, we have explicitly clarified that independent groups of control mice were used for each experiment. These details are now clearly indicated in the Materials and Methods section to avoid any ambiguity and to reinforce the rigor of our experimental design (Page 15, Line 453-455): “Furthermore, knockout animals and those treated with pharmacological inhibitors or neutralizing antibodies shared the same control groups (chow and HFCD), as required by the animal ethics committee.”

      Validation of the MASLD model

      To strengthen the metabolic characterization of our MASLD model, we have now included additional parameters, including liver weight, Picrosirius staining and blood glucose measurements. These data are presented as new graphs in the revised manuscript and support the metabolic relevance of the HFCD diet model (Figure Suplementary S1). The corresponding description has been added to the Results section (Page 5, Lines 116-117) as follows: “Mice fed HFCD showed no increase in liver weight and collagen deposition as evidenced by Picrosirius staining (Fig. S1A and Fig. S1C)”

      Assessment of liver injury in RagKO and anti-NK1.1 mice

      We fully agree that assessment of liver injury is essential for these models. For mice treated with antiNK1.1, ALT levels are shown in Figure 4G, confirming increased liver injury after treatment. Regarding Rag⁻/⁻ mice, the animals exhibit exacerbation of liver injury when fed a HFCD diet and challenged with LPS (Page 7, Lines 183–184). The corresponding description has been added to the Results section (Page 7, Lines 175-176) as follows: “Interestingly, Rag1-deficient animals under the HFCD remained susceptible to the LPS challenge (Fig. 4C) with exacerbation of liver injury (Fig. 4D) ”

      Discussion of limitations

      We have expanded the Discussion section to provide a more comprehensive and balanced perspective on the limitations of our model and experimental approach (Page 13-14, Lines 401–414) “Our study presents several limitations that should be acknowledged and discussed. First, we cannot entirely rule out the possibility that our mice deficient in pro-inflammatory components exhibit reduced responsiveness to LPS. However, our ex vivo analyses using splenocytes from these animals revealed a preserved cytokine production following LPS stimulation. These results suggest that the in vivo differences observed are primarily driven by the MAFLD condition rather than by intrinsic defects in LPS sensitivity. Second, the absence of publicly available single-cell RNA-seq datasets from MAFLD subjects under endotoxemic or septic conditions limited our ability to perform direct translational comparisons. To overcome this, we analyzed existing MAFLD patients and experimental MAFLD datasets, which consistently demonstrated upregulation of IFN-y and TNF-α inflammatory pathways in MALFD. In line with these findings, our murine model revealed TNF-α⁺ myeloid and IFN-y⁺ NK cell populations, thereby reinforcing the validity and translational relevance of our results.”. This revision highlights the constraints of the MASLD model, the inherent variability among in vivo experiments, and the interpretative limitations related to immunodeficient mouse strains.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In Figure 4 the authors are showing the number of IFN+ positive CD4, CD8, and NK 1.1+ cells. Could they show from total IFNg production, how much it goes specifically on NK cells and how much on other cell populations since NK1.1 is NK but also NKT and gamma delta T cell marker? Also, in Figure 2E the authors see a substantial increase in IFNg signal in T cells.

      While we did not specifically assess IFNγ production in NKT cells or other minor populations, our data indicate that the NK1.1+CD3+ cells (NKT cells) cited in Page 7, Lines  188-192 were essentially absent in the liver tissue of LPS-challenged animals, as shown in Supplementary Figures 3C and S10. The corresponding description has been added to the Results section (Page 7, Lines 188-192) as follows: “We observed that the number of NK cells increased in the liver tissue of PBS-treated MAFLD mice compared with mice fed a control diet (Fig. 4E). LPS challenge increased the accumulation of NK1.1+CD3− NK cells in the liver tissue of MAFLD mice and the absence of NK1.1+CD3+ NKT cells (Fig. S3C and 4E)”.

      This absence was consistent across all experimental conditions, corroborating our focus on NK1.1+CD3− cells as the primary source of NK1.1-associated IFNγ production. Furthermore, data demonstrated in Figure 2E illustrate the presence of IFNγ primarily in NK cells. Therefore, the observed IFNγ signal, attributed to NK1.1+ cells, predominantly reflects conventional NK cells, with minimal contribution from NKT or γδ T cells.

      (2) In Figure 4C, the authors state that the results suggest that T and B cells do not contribute to susceptibility to LPS challenge. However, they observe a drop in survival compared to chow+LPS. Are the authors certain there is no statistical significance there?

      The observed decrease in survival is consistent with our expectations, as T and B cells are not the primary source of interferon-gamma (IFNγ) in this context. Even in their absence, animals remain susceptible to LPS challenge due to the presence of other IFNγ-producing cells that drive the observed lethality. We have carefully re-examined the statistical analysis and confirm that it was correctly performed.  

      (3) Since the survival curve and rate are exactly the same (60%) in Figures 3F, 3G, 4C, 4F, 5G, and 5H I would just like to double-check that the authors used different controls for each experiment.

      The number of mice used in each experiment was carefully determined to ensure sufficient statistical power while fully complying with the limits established by our institutional Animal Ethics Committee. To minimize animal use, the same control group was shared across multiple survival experiments. Despite using shared controls, the total number of animals per experimental group was adequate to produce robust and reproducible survival outcomes. All groups were properly randomized, and the shared control data were rigorously incorporated into statistical analyses. This strategy allowed us to maintain both ethical standards and the scientific rigor of our findings.

      (4) In Figure 5 the authors are saying that it is neutrophils but not monocytes mediate susceptibility of animals with NAFLD to endotoxemia. However, CXCR2i depletion and CCR2 knock out mice affect both monocytes/macrophages and neutrophils. And in Figures 5E, 5G, and 5H they see that a) LPS+CXCR2i decreases liver damage more than LPS+anti Ly6G, b) HFCD mice challenged with LPS and treated with anti-LY6G do not rescue survival to levels of CHOW LPS and c) anti Ly6G treatment helps less than CXCR2i. Therefore, from both knock out mice and depletion experiments the authors can conclude that most likely monocytes (but potentially also other cells) together with neutrophils are substantial for the development of endotoxemic shock in choline-deficient high-fat diet model.

      While neutrophils express CCR2, our data clearly show that CCR2 deficiency does not impair neutrophil migration, as demonstrated in Supplemental Figures 5A and 5B (added to the manuscript, page 8, lines 213–217). The corresponding description has been added to the Results section (Page 8, Lines 213217) as follows: ``Interestingly, animals deficient in monocyte migration (CCR2-/-) showed a high mortality rate compared to wild type after LPS challenge and neutrophil migration is not altered (Fig. 5SA and Fig. 5SB)``, In contrast, CCR2 deficiency primarily affects monocyte recruitment, yet in our experimental conditions, monocyte depletion or CCR2 knockout did not significantly alter the severity of endotoxemic shock, indicating that monocytes play a minimal role in mediating susceptibility in HFCD-fed mice.

      To specifically investigate neutrophils, we used pharmacological blockade of CXCR2 to inhibit migration and antibody-mediated neutrophil depletion. Both approaches have consistently demonstrated that neutrophils are critical factors in endotoxemic shock.

      These findings support our conclusion that neutrophils are the primary cellular contributors to susceptibility in HFCD-fed mice during endotoxemia, with monocytes making a negligible contribution under the tested conditions.

      (6) In Figure 6A (but also others with PD-L1) did the authors do isotype control? And can they show how much of PD1+ population goes on neutrophils, and how much on all the other populations?

      To address this issue, we performed additional analyses to assess the distribution of PD-L1 expression on CD45+CD11B+ leukocytes. These new results, detailed on Page 9, lines 245-250, and now presented in Supplemental Figure 6, demonstrate that PD-L1 expression is predominantly enriched in neutrophils compared to other immune subsets. This observation further reinforces our conclusion that neutrophils represent a major source of PD-L1 in our experimental model.

      To ensure the robustness of these findings, we also included FMO controls for PD-L1 staining in the newly added Supplemental Figure S6. These controls validate the specificity of our gating strategy and confirm the reliability of the detected PD-L1 signal. The corresponding description has been added to the Results section (Page 9, Lines 245-250) as follows: ``First, we observed that only the MAFLD diet caused a significant increase in PD-L1 expression in CD45+CD11b+ leukocytes after LPS challenge (Fig. S6C). We observed that within this population, neutrophils predominate in their expression when compared to monocytes (Fig. 6SA, Fig. 6SB, and Fig. 6SD). Furthermore, PD-L+1 neutrophils showed an exacerbated migration of PD-L1+ neutrophils towards the liver (Fig. 6A and 6B)”

      (7) In Figure 6D it is interesting that there is not an increase in PD-L1+ neutrophils in LPS HFCD IFNg+/+ mice in comparison to LPS chow IFNg+/+ mice, since those should be like WT mice (Figure 6A going from 50% to 97%) and so an increase should be seen?

      The apparent difference between Figures 6A and 6D likely reflects inter-experimental variability rather than a biological discrepancy. Although the absolute percentages of PD-L1⁺ neutrophils varied slightly among independent experiments, the overall phenotype and trend were consistently maintained namely, that PD-L1 expression on neutrophils is enhanced in response to LPS stimulation and modulated by IFNγ signaling. Thus, the data shown in Figure 6D are representative of this consistent phenotype despite minor quantitative variation.

      (8) In Figure 7 do the authors have isotype control for TNFa because gating seems a bit random so an isotype control graph would help a lot as supplementary information, in order to make the figure more persuasive

      To address the concern regarding gating in Figure 7, we have included the FMO showing TNFα as a histogram Supplementary Figure 8gG. These control reaffirm the accuracy and reliability of our gating strategy for TNFα, further supporting the robustness of our data. The corresponding description has been added to the Results section (Page 9, Lines 272-274) as follows:`` We observed an exacerbated TNF-α expression by PD-L1+ neutrophils from MAFLD when compared to control chow animals (Fig. 7A, Fig. 7B, Fig. 7D, and Fig8SG).

      (9) Figure 6C IFNg+/+ mice on CHOW +LPS is same as Figure 8E mice chow +LPS but just with different numbers. Can the authors explain this?

      Although the data points in Figures 6C and 8E may appear similar, we confirm that they originate from entirely independent experiments and represent distinct datasets. To enhance clarity and avoid any potential confusion, we have adjusted the figure presentation and sizing in the revised manuscript. These changes make it clear that the datasets, while comparable, are derived from separate experimental replicates.

      (10) Figure 1E chow B6+LPS is the same as Figure 5D B6+LPS but should they be different since those should be two different experiments?

      We confirm that Figures 1E and 5D correspond to data obtained from independent experiments. Although the experimental conditions were similar, each dataset was generated and analyzed separately to ensure the reproducibility and robustness of our results.

      Reviewer #2 (Recommendations for the authors):

      (1) Why did you look at kidney injury in Figure 1D? I think this should be explained a little.

      We assessed kidney injury alongside ALT, a marker of liver damage, because both the liver and kidneys are among the primary organs affected during sepsis and endotoxemia. This rationale has been added to the manuscript (page 5, lines 129–131): “Remarkably, compared to the Chow group, HFCD mice exposed to LPS did not show greater changes in other organs commonly affected by endotoxemia, such as the kidneys (Figure 1D).” By evaluating markers of injury in both organs, we aimed to determine whether our physiopathological condition was liver-specific or indicative of broader systemic injury.

      (2) I know Figure 2C isn't your data, but why are there so few NK cells, considering NK cells are a resident liver cell type? Doesn't that also bring into question some of your data if there are so few NK cells? And the IFNG expression (2E) looks to mostly come from T-cells (CD8?).

      The data shown in Figure 2C were reanalyzed from a separate NAFLD model based on a 60% high-fat diet. Although this model differs from ours, the observed low number of NK cells is consistent with expectations for animals subjected solely to a hyperlipidic diet, which primarily provides an inflammatory stimulus that promotes recruitment rather than maintaining high baseline NK cell numbers.

      In our experimental model, these observations align with published data. Specifically, liver tissue from NAFLD animals typically exhibits low baseline NK cell numbers, but upon LPS challenge, there is a marked increase in NK cell recruitment to the liver. This dynamic illustrates the interplay between dietinduced inflammation and immune cell recruitment in our experimental context and supports the interpretation of our IFNγ data.

      (3) In your methods, I think you didn't explain something. You said LPS was administered to 56 week old mice, but that HFCD diet was started in 5-6 week old mice and lasted 2 weeks, then LPS was administered. So LPS administration happened when the mice were 7-8 weeks old, right?

      We thank the reviewer for pointing out this inconsistency in our Methods section. The reviewer is correct: the HFCD diet was initiated in 5–6-week-old mice, and LPS was administered after 2 weeks on the diet, such that LPS challenge occurred when the mice were 7–8 weeks old.

      We have revised the Methods section (add page 15-16, lines 474–480).  to clarify this timeline and ensure it is accurately described in the manuscript. The corresponding description has been added to the Materials and Methods section (Page 14, Lines 436-442) as follows: “Lipopolysaccharide (LPS; Escherichia coli (O111:B4), L2630, Sigma-Aldrich, St. Louis, MO, USA) was administered intraperitoneally (i.p.; 10 mg/kg) in C57BL/6, CCR2 -/-, IFN-/-, and TNFR1R2 -/- mice. The HFCD was initiated in 5–6 week-old mice, and LPS was administered after 2 weeks on the diet, meaning that LPS administration occurred when the mice were 7–8 weeks old, with body weights ranging from 22 to 26 g. LPS was previously solubilized in sterile saline and frozen at -70°C. The animals were euthanized 6 hours after LPS administration”.

      (4) Throughout the manuscript, I would consider changing the term NAFLD to something else. I think HFCD diet is a closer model to NASH, so there needs to be some discussion on that. And the field is changing these terms, so NAFLD is now MASLD and NASH is now MASH.

      We appreciate the reviewer’s comment regarding the terminology and disease classification. In our experimental conditions, the animals were subjected to a high-fat, choline-deficient (HFCD) diet for only two weeks, a period considered very early in the progression of diet-induced liver disease. At this stage, histological analysis revealed lipid accumulation in hepatocytes without evidence of hepatocellular injury, inflammation, or fibrosis. Therefore, our model more closely resembles the metabolic-associated fatty liver disease (MAFLD, formerly NAFLD) stage rather than the more advanced metabolic-associated steatohepatitis (MASH, formerly NASH).

      Indeed, prolonged exposure to HFCD diets, typically 8 to 16 weeks, is required to induce the inflammatory and fibrotic features characteristic of MASH. Since our objective was to study the initial metabolic and immune alterations preceding overt liver injury, we believe that using the term MAFLD more accurately reflects the pathological stage represented in our model. Accordingly, we have revised the text to align with the updated nomenclature and disease context.

      (6) I am concerned about over interpretation of the publicly available RNA-seq data in Figure 2. This data comes from human NAFLD patients with unknown endotoxemia and mouse models using a traditional high-fat diet model. So it is hard to compare these very disparate datasets to yours. Also, if these datasets have elevated IFNG, why does your model require LPS injection?

      We thank the reviewer for their thoughtful comments regarding the interpretation of the RNA-seq data presented in Figure 2. We would like to clarify that the human NAFLD datasets referenced in our study do not specifically include patients with endotoxemia; rather, they focus on individuals with NAFLD alone.

      Comparing data from human and murine MAFLD models, we observed that NK cells, T cells, and neutrophils are present and contribute to the hepatic inflammatory environment. Our reanalysis indicates that the elevations of IFNγ and TNF in NAFLD are primarily derived from NK cells, T cells, and myeloid cells, respectively.

      In our experimental model, LPS administration was used to evaluate whether these immune populations particularly NK cells are further potentiated under a hyperinflammatory state, leading to exacerbated IFNγ production. This approach allows us to determine whether increased IFNγ contributes to worsening outcomes in NAFLD, providing mechanistic insights that cannot be obtained from static human or traditional mouse datasets alone.

      (7) The zoom-ins for the histology (for example, Figure 1E) don't look right compared to the dotted square. The shape and area expanded don't match. And the cells in the zoom-in don't look exactly the same either.

      We have thoroughly re-examined the histological sections and the corresponding zoom-ins, including the example in Figure 1E. Upon verification, we confirm that the zoom-ins accurately represent the highlighted areas indicated by the dotted squares. The apparent discrepancies in shape or cellular appearance are likely due to minor differences in orientation or cropping during figure preparation. Nevertheless, the content and regions depicted are consistent with the original sections.  

      (8) Did the authors measure myeloid infiltration in the CCR2-/- mice? Did you measure Neutrophil infiltration in the TNF-Receptor KO mice?

      Analysis of CD45+ cell migration in CCR2 knockout mice, as shown in Supplemental Figure 5C and 5D, demonstrates that the absence of CCR2 does not impair overall leukocyte migration. Similarly, assessment of neutrophil migration in TNF receptor (TNFR1/2) knockout mice, presented in Supplemental Figure 8A, shows that neutrophil trafficking is not affected in these animals. These results indicate that the respective knockouts do not compromise the migration of the analyzed immune populations, supporting the interpretations presented in our study.

      (9) Regarding Methods for RNA-seq Analysis. Was the Mitochondrial percentage cutoff 0.8%, because that seems low. And was there not a Padj or FDR cutoff for the differential expression?

      The mitochondrial percentage in our scRNA-seq analysis reflects the proportion of mitochondrial gene expression per cell, which serves as a quality control metric. A low mitochondrial gene expression percentage, such as the 0.8% cutoff used here, is indicative of highly viable cells.

      For differential gene expression analysis, we employed the FindMarkers function in Seurat with standard parameters: adjusted p-value (Padj) < 0.05 and log2 fold change > 0.25 for upregulated genes, and adjusted p-value < 0.05 with log2 fold change < -0.25 for downregulated genes. These thresholds ensure robust identification of differentially expressed genes while balancing sensitivity and specificity.

      (10) Regarding Methods for Flow Cytometry. How were IFNG and TNF staining performed? Was this an intracellular stain? Did you need to block secretion? TNF and IFNG antibodies have the same fluorophore (PE), so were these stainings and analyses performed separately?

      Six hours after LPS challenge, non-parenchymal liver cells were isolated using Percoll gradient centrifugation. Because the animals were in a hyperinflammatory state induced by LPS, no in vitro stimulation was performed; all staining was carried out immediately after cell isolation. Detection of IFNγ and TNF was performed via intracellular staining using the Foxp3 staining kit (eBioscience). Due to both antibodies being conjugated to PE, IFN-γ and TNF-α staining and analyses were conducted in separate experiments. These distinct staining protocols and analyses are detailed in Supplemental Figures 10 and 11. The corresponding description has been added to the Materials and Methods section (Page 16, Lines 490-493) as follows: ``As animals were already in a hyperinflammatory state, no additional in vitro stimulation was required. Intracellular detection of IFN-γ and TNF-α was conducted using the Foxp3 staining kit (eBioscience). Since both antibodies were conjugated to PE, staining and analyses were performed in separate experiments``

      Reviewer #3 (Recommendations for the authors):

      (1) Achieving an NAFLD model/disease is the starting point of this study. I understand that a two-week HFCD diet period was applied due to the decrease in lymphocyte numbers. Was it enough to initiate NAFLD then? Or is it a milder metabolic disease? Which parameters have been evaluated to accept this model as a NAFLD model?

      Indeed, the two-week HFCD diet induces an early-stage form of NAFLD, characterized by initial fat accumulation in the liver without significant hepatic injury. While this represents a milder metabolic phenotype, it is sufficient to study the inflammatory and immune responses associated with NAFLD. To validate this model, we assessed multiple parameters: liver weight, blood glucose levels, and collagen deposition. These measurements confirmed the presence of early-stage NAFLD features in the animals, providing a relevant and reliable context for investigating susceptibility to endotoxemia and immune cell dynamics. They are shown in Figure Suplementary 1 and the text was included in the manuscript (Page 5, Lines 116-117): “Mice fed HFCD showed no increase in liver weight and collagen deposition as evidenced by Picrosirius staining (Fig. S1A and Fig. S1C) ”.

      (2) It is true that the CD274 gene (encoding PD-L1) and the IFNGR2 gene, corresponding to the IFNγ receptor, are among the upregulated genes when authors analyzed the publicly available RNAseq data but they are not the most significantly elevated genes. What is the reasoning behind this cherrypicking? Why are other high DEGs not analyzed but these two are analyzed?

      We highlighted the expression of the IFN-γ receptor (IFNGR2) and CD274 (encoding PD-L1) in the publicly available RNA-seq data to align and corroborate these findings with the key results observed later in our study. To avoid redundancy, we chose to present these genes in the initial figures as they are directly relevant to the subsequent analyses. Regarding the broader analysis of human RNA-seq data, our primary objective was to identify enriched biological processes and pathways, which served as a foundation for the focus and direction of this study.

      (3) Figures 3C-3G: I understand that IFNg-/- and NFR1R2a-/- mice are not showing elevated liver damage but it may simply be because of the non-responsiveness to the LPS challenge. I suggest using a different challenge or recovery experiments with the cytokines to show that the challenge is successful and results are caused by NAFLD, truly. The same goes for Figure 6: Looking at Figure 6D one may think that IFNg deficiency alters the LPS response independent of the diet condition (or NAFLD condition).

      We appreciate the reviewer’s insightful comment and fully understand the concern regarding the potential non-responsiveness of IFN-γ⁻/⁻ and TNFR1R2a⁻/⁻ mice to the LPS challenge. To address this point and confirm that these knockout animals are indeed responsive to LPS stimulation, we conducted an additional set of ex vivo experiments.

      Specifically, WT and cytokine-deficient (IFN-γ⁻/⁻) mice were fed either Chow or HFCD for two weeks, after which spleens were collected, and splenocytes were challenged in vitro with LPS. We then quantified TNF, IFN, and IL-6 production to confirm that these mice are capable of mounting cytokine responses upon LPS stimulation.

      Due to current breeding limitations and a temporary issue in colony maintenance of TNF-deficient mice, we were unable to include TNFR1R2a⁻/⁻ animals in this additional experiment. Nevertheless, we prioritized performing the analysis with the available knockout line to avoid leaving this important point unaddressed.

      These additional data demonstrate that IFN-γ-deficient mice remain responsive to LPS, reinforcing that the differences observed in vivo are related to the NAFLD condition rather than a lack of LPS responsiveness.

      (4) Figure 1 vs Figure 4: Rag-/- mice seem more susceptible to LPS-derived death even after normal conditions. But If I compare the survival data between Figure 1 and Figure 4, Rag-/- HFCD diet mice seem to be doing better than wt mice after LPS treatment. (1 day survival vs 2 days survival). How do you explain these different outcomes?

      We thank the reviewer for this insightful question regarding the survival data in Figures 1 and 4. Although there is a one-day difference in survival outcomes, Rag-/- mice consistently exhibit increased susceptibility to LPS-induced mortality can influence the exact survival timing. Nonetheless, across all experiments, Rag-/- mice display a reproducible phenotype of heightened sensitivity to LPS challenge, which is supported by multiple independent observations in our study.

      (5) How do you explain Figure 4J in connection to the observation presented with Figure 7: TNFa tissue levels, even though significant, seem very similar between the conditions?

      We would like to clarify that the animals in this study are in a metabolic syndrome state, with early-stage NAFLD characterized by hepatic fat accumulation without significant tissue injury, as shown in Figure 1C.

      Under these conditions, the LPS challenge triggers an exacerbated inflammatory response, leading to increased secretion of IFN-γ and TNF-α, primarily from NK cells and neutrophils. While TNFα levels may appear visually similar across conditions, the HFCD mice exhibit a heightened predisposition for an amplified immune response compared to chow-fed mice. This difference is consistent with the functional outcomes observed in our study and highlights the diet-specific sensitization of the immune system.

    1. Author response:

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

      We thank the editors and reviewers for their assessment of this manuscript, and for the positive words highlighting the value of undertaking evaluation of small molecule drugs for snakebite in the neotropics, inclusive of the quality of this work and the value of the validated screening pipeline. We completely agree that the next steps for this work will be to evaluate the preclinical efficacy of the identified drugs in mouse models, though this considerable undertaking will form the basis of future work. Critically, the pipeline that we describe herein facilitates the selection of the most appropriate candidates to progress into such mouse studies, aligning with the 3Rs principles for minimising the need for animal research. The comment around insufficient venom characterisation seems somewhat misplaced – the objective of this project was not to characterise the venoms used, but to evaluate the in vitro inhibition of venom toxin family activities and identify the potential utility of specific repurposed drugs as therapeutics for snakebite in the neotropics. Venom characterisation of the diverse samples used in this project would represent an entire project and manuscript in its own right. We are pleased that the reviewers highlight the gap in research on serine protease inhibitors and the value this paper has in highlighting that more research is required in this area to identify a candidate that is more suitable for future clinical use than nafamostat.


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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Small molecule therapeutics for snakebite have received a lot of attention for their potential to close the gap between bite and treatment, where antivenom is not immediately available.

      Strengths:

      There has been a lot of focus on Africa, Asia, and India, but very little work related to neotropical regions. The authors seek to begin filling this gap in the preclinical literature. The authors use well-developed methods for preclinical assessment.

      Weaknesses:

      A clearer and more focused discussion of the limitations of the overall present work would be desirable (e.g. protection vs. rescue, why marimastat over prinomastat for in vivo assays when both have been through clinical trials for other indications; real-world feasibility of nafamostat, which has a half-life of 1-2 minutes compared to camostat, which has a half-life of hours). All of this could be improved in a revision.

      We thank the reviewer for their shared opinion of the potential value of small molecules as snakebite envenoming therapeutics and their insight on the gap in focus in the neotropics, which this manuscript aims to address.

      Our work in this manuscript included standard practice of pre-incubation between drug and venom for all in vitro studies, and sequential (i.e. not co-incubation) administration in the egg model. In our revised manuscript we will make these distinctions clearer. Use of a ‘rescue’ approach in the in vitro assays is not feasible due to the rapid destruction of the substrates used for assay readouts. The clearest rationale for the use of rescue models relates to their power within in vivo preclinical models (i.e. murine envenoming models) which, following the in vitro characterisations presented in this paper, are the logical next step for evaluating small molecule drugs for inhibiting neotropical snake venoms.

      Although both marimastat and prinomastat are repurposed drugs that have undergone clinical evaluation for other indications, marimastat has been more extensively characterised preclinically than prinomastat for snakebite, and will soon enter Phase II clinical trial evaluation for this indication (https://www.ddw-online.com/ophirex-to-produce-snake-venom-inhibitor-for-lstm-study-40669-202602/). Marimastat also has a longer half-life in humans of 8-10 hours (Millar et al. 1998), compared to prinomastat (2-5h, Hande et al. 2004). We will more clearly highlight the rationale for selecting marimastat in the revised manuscript.

      Although we appreciate the reviewer’s point regarding the short half-life of nafamostat (which is typically given by continuous iv infusion due to its short half-life), in the manuscript we have already stated that we do not recommend the progression of nafamostat as a snake venom serine protease (SVSP) inhibitor candidate due its low efficacy and off target effects. We highlight the need for the community to identify other serine protease inhibitors that might have utility for snakebite.

      Reviewer #2 (Public review):

      Summary:

      The authors set out to test whether a defined set of small molecules can lessen damaging effects caused by venoms from several Bothrops species, and whether these effects are consistent enough to suggest a broadly applicable approach. They present a cross-venom dataset spanning in-vitro activity readouts and blood-based functional outcomes, and include a chicken embryo model to explore whether venom inhibition can translate into improved survival. The central message is that certain small molecules can reduce specific venom-driven effects across multiple samples, providing a comparative resource for the field and a basis for prioritizing future validation.

      Strengths:

      The main value of this work is the breadth and structure of the dataset, which places multiple venoms and multiple readouts into a single, comparable framework that should be useful for readers evaluating patterns across samples. The experimental flow is generally coherent, moving from activity measurements to functional outcomes and then to an in-vivo test, which helps the reader understand how the authors link mechanism-oriented assays to more integrated endpoints. The manuscript also provides practical information for the community by highlighting which readouts appear most consistently affected across venoms, which can help guide hypothesis generation and study design in follow-up work.

      Weaknesses:

      Several aspects of the study design and framing reduce the confidence with which readers can translate the findings beyond the specific experimental context presented. The evidence base is strongest in controlled in-vitro settings, while the bridge to real-world effectiveness remains limited, particularly for understanding performance under conditions that better reflect delayed treatment and systemic exposure. As a result, the manuscript is best interpreted as a well-organized comparative screening study with promising signals, rather than a definitive demonstration of a broadly effective, deployable intervention.

      We appreciate the reviewer’s opinion on the thorough and logical workflow we present in this manuscript and the value this pipeline providers the field for future and parallel work. We agree with the reviewer that this provides a well-organized comparative screening study applicable to different snake species or therapeutics. In relation to the comment on this manuscript being a definitive demonstration of a broadly effective, deployable intervention we agree with their opinion and are happy to clarify that while the evidence presented in this manuscript is promising, there is much work still to do before such molecules are ready for deployment for treating snakebite. Ultimately, this manuscript supports the growing evidence of the promising utility of marimastat and varespladib, and extends this evidence to neotropical snake venoms in a comparative manner. The next step will be to evaluate the efficacy of these molecules within in vivo murine preclinical models, which will be crucial for further supporting the evidence base for onward translation.

      Reviewer #3 (Public review):

      In this work, the authors wanted to evaluate repurposed small molecule inhibitors for the treatment of envenomation by snakes of the Bothrops genus; one of the most medically relevant in the Americas. I believe the objectives of the research were clearly achieved, and compelling evidence for the ability of these molecules to neutralize enzymatic and toxic activities of metalloproteinases and phospholipases in all the tested venoms is provided. Furthermore, the work highlights the limited efficacy of the tested serine protease inhibitor, suggesting a need for drug discovery campaigns to address toxicity caused by this protein family. The methods are well designed and performed, and the use of both in vitro and in vivo methodologies makes this a thorough and robust work.

      These results are extremely relevant, since they take us one step further to a potential orally administered snakebite treatment. The existence of such a treatment could improve the outcomes for thousands of snakebite victims worldwide. I have a few comments and questions that I hope will be useful to the authors:

      We thank the author for their high regard for the purpose and execution of this work. Their insight in relation to questions are supportive for an improved manuscript and discussion points for the field.

      During the introduction, the authors mention that small-molecule inhibitors can neutralize the localized tissue damage via cytotoxicity of some venoms, and cite PLA2s, SVMPs and/or cytotoxic 3FTxs as the main causing agents of this pathology. I am not aware of any direct effect described by small molecule inhibitors on cytotoxic 3FTxs alone. Has this been observed at all? Or is it more likely that the small molecule inhibitors act on the enzymatic toxins only, preventing synergistic effects with 3FTxs?

      We apologise for this error on our behalf. While inhibitory molecules have been described for cytotoxic 3FTxs, these are not small molecules as alluded to in the previous version of the manuscript. We have amended this text in our revised manuscript.

      I think it would be relevant to address the effects of non-enzymatic PLA2s, such as myotoxin II, which have been described in detail within Bothrops venoms. I believe there is some evidence of Varespladib also having a neutralizing effect on the myotoxicity caused by these non-enzymatic PLA2s. I suggest adding a comment about the contribution of these toxins in the discussion or in the section where PLA2 activity of the venoms is compared. In my opinion, right now it seems like these were overlooked.

      We thank the reviewer for highlighting this point. We agree that this is highly relevant and would benefit from discussion in the revised manuscript given the nature of our assays and the non-enzymatic mechanism of action of certain Bothrops PLA<sub>2</sub>s. We have added this to the discussion.

      Regarding Marimastat and the other MP inhibitors, are there any studies showing that they don't have an effect on endogenous MPs? I understand they have been approved for human use before, but is there any indication that they would not have an effect at the doses that would be required to treat envenomation?

      Most matrix metalloproteinases inhibitors will act on endogenous MPs to at least some extent (variable potency on different MMPs). Marimastat has demonstrated activity against endogenous metalloproteinases, including MMP1, which was hypothesised to cause severe joint pain when used chronically (i.e. frequent dosing over many weeks) for indications such as cancer, though this effect was reversible within 8 weeks of cessation of drug administration (Wojtowicz-Praga, 1998). Thus long-term use of matrix metalloproteinases inhibitors can cause safety concerns. However, the anticipated duration of dosing for snakebite, which is an acute life-threatening condition, is a few days. It is therefore unlikely that prior safety concerns observed following chronic dosing in cancer studies would apply to its potential use as a snakebite field therapy.

      Regarding the quenched fluorescence substrate used for enzymatic activity. Is there a possibility that some of the SVMPs would not act on this substrate, and therefore their activity or neutralization is not observed? Would it be relevant to test other substrates, such as gelatin, collagen, or even specific clotting factors?

      It has been observed that certain SVMPs (specifically several PI SVMPs) are not active against this ES010 substrate in vitro. The substrate used in the in vitro SVMP assay is reported by the manufacturer as a substrate for a wide range of MMPs which target the extracellular matrix components mentioned by the reviewer, i.e. collagenases and gelatinases as well as matrilysins, stromelysins and elastate. This in vitro assay combined with the coagulation assays are complementary in covering the main targets of SVMPs (ECM and clotting cascade), prior to haemorrhagic assessment in the egg model. Thus, we are confident that activity for the broad range of SVMP isoforms will be captured through the screening pipeline we have developed.

      Finally, could the authors comment or provide some bibliography regarding the translatability of the chicken embryo model in the context of envenomation?

      Our current model is based on an earlier egg embryo model (Sells et al. 1997, Sells et al. 1998 and Sells et al. 2000) which described good correlations (p<0.01) with the standard WHO murine preclinical envenoming model. These studies have assessed correlations for minimal haemorrhagic doses (MHDs), LD50s and ED50s in both models for a selection of viper venoms. As chicken embryos at day 6 of development have incomplete neural arcs, the model is not well suited for assessing neurotoxic effects, but can be effectively used for addressing venom-induced haemorrhage and lethality and for testing therapeutics. In addition, a more recent study (Yusuf et al. 2023) reported almost identical LD50s for the venom of Bitis arietans between the two in vivo approaches. The model is also being pursued as a preclinical testing model by an antivenom manufacturer with the focus of reducing the use of rodents in batch release testing (Verity et al. 2021). We will provide further clarification on the rationale for using the egg model, including the supportive references outlined above, in the revised manuscript.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      The manuscript provides a useful comparative dataset across multiple Bothrops venoms and supports SVMP inhibition as a broadly effective lever in the authors in-vitro work. However, the strength of the 'pan-Bothrops' and translational claims is currently limited by insufficient characterization of the exact venom samples tested and by experimental designs that fall in clinically realistic rescue.

      Major comments:

      (1) The venoms used in this study are historical batches and are not formally characterized beyond SDS-PAGE and literature summaries, despite well-known intra- and inter-population venom variability; this weakens the generalization of the conclusions.

      To address this comment, we have increased clarity on our venom sources being historic, Due to the historic source locality is not available beyond country of origin, with the exception of B. lanceolatus which is endemic to Martinique. Figure 1 also makes clear that we agree with the reviewer that the variation is high within Bothrops species. We discuss this variation on the limitations in our sampling for making broad conclusions throughout the first paragraph of the discussion, with the final sentence stating Future proteomic characterisations of the specific venom samples used in this study, which were all sourced from a historical collection (except for B. lanceolatus), would be informative in this regard. Although venom composition of our samples has not been characterised, the focus of the manuscript is the characterisation of the whole venom functional activity through a wide ranging screening pipeline, and the generalisation of our findings is supported by the diversity of the venom samples (i.e. several species) despite them not being characterised (which is not critical for the focus of the study).

      (2) On a technical comment, the venom inhibition assays appear to rely on drug-first or preincubation conditions, which can easily overestimate efficacy compared with real snakebite envenomation, where toxins distribute and engage targets rapidly. Here, a translational gap is the clinical feasibility of the 'repurposed' inhibitors, as it is unclear whether the drugs central to the conclusions (especially marimastat, prinomastat and varespladib) are realistically available or stocked in hospitals or could be deployed in regions where Bothrops envenoming occurs. I think that the manuscript should clearly distinguish this from candidates with a plausible access and delivery pathway.

      Our work in this manuscript includes standard practice of pre-incubation between drug and venom for all in vitro studies, and sequential (i.e. not co-incubation) administration in the egg model. None of our methods administer drug-first. Throughout the methods and figure legends we have made these distinctions clearer. Use of a ‘rescue’ approach in the in vitro assays is not feasible due to the rapid destruction of the substrates used for assay readouts. The clearest rationale for the use of rescue models relates to their power within in vivo preclinical models (i.e. murine envenoming models), which would be the next step for this research programme.

      While the evidence presented in this manuscript is promising, there is much work still to do before such molecules are ready for deployment for treating snakebite, inclusive of the requirement to complete clinical trials, cost-benefit analysis and policy change and manufacturing/distribution feasibility assessments. Ultimately, this manuscript supports the growing evidence of the promising utility of marimastat and varespladib, and extends this evidence to neotropical snake venoms in a comparative manner. The next step will be to evaluate the efficacy of these molecules within rescue in vivo murine preclinical models, which will be crucial for further supporting the evidence base for onward translation. To further support this point we have included an additional section to the manuscript discussing the current preclinical and clinical progression of prinomastat and marimastat, which also incorporates the public comment on selection of marimastat over prinomastat.

      (3) In my opinion, the Nafamostat results and discussion need reframing, given weak SVSP inhibition and intrinsic anticoagulant behavior at 5 µM. Excluding it from certain analyses undermines interpretability, and it may be more appropriate to include it throughout as an explicit negative control condition (showing its baseline anticoagulant effect) rather than omitting it.

      Although we understand the reviewers opinion here, we disagree and believe that including nafomastat as a ‘negative control’ may present a negative reflection on the benefit that an efficacious serine protease inhibitor could provide. Furthermore, as the intrinsic anticoagulant effect of nafamostat cannot be de-coupled from direct SVSP toxin inhibition we were unable to interpret the activity which undermines the results. This can be seen in Figure 3b, which demonstrates that a false positive result would occur. For the serine protease assay, we do clearly discuss the lack of efficacy and justification of why EC<sub>50</sub> testing wasn’t appropriate within the guidance of our screening protocols.

      In the manuscript we have now further justified our approach in relation to the limitations of nafamostat as a snake venom serine protease (SVSP) inhibitor candidate due its low efficacy and off target effects. We highlight the need for the community to identify other serine protease inhibitors that might have utility for snakebite.

      (4) The data presentation needs consistent statistical analyses (currently absent for multiple key figures, including Figures 2, 3, 4, 6 and 7) and a clearer explanation for the dose of venom and drugs you choose. For example, Figure 3 relies on a fixed 5 µM drug concentration and very different venom amounts (50-100-250 ng), but it is not discussed whether such exposures are achievable in vivo, or how these concentrations map onto expected pharmacokinetics in patients. Likewise, Bothrops venoms can contain both pro- and anticoagulant activities, so the authors should justify how their framework accounts for anticoagulant components and why the observed plasma phenotypes are interpreted as they are

      In relation to the reviewers comment on the need for consistent analysis we thank the reviewer for flagging this and have now included these in figures 3, 4, 6 and 7. However, Figure 2 is presented to display the variation between all the venoms and ultimately used to select the most relevant doses for the latter inhibition experiments, therefore statistical analysis is not relevant for this figure. The updated statistical analysis now includes the following, which has been included in the relevant figure legends and results sections;

      Figure 3 - Bars indicate significant results (p = <0.05) identified through one-way ANOVA with Dunnett’s multiple comparisons test to the DMSO control

      Figure 4 - two-way ANOVA with Šídák's multiple comparisons test of each venom control compared to the matched venom treated with inhibitor

      Figure 6 – the CT and MCF data were analysed independently using one-way ANOVA with Tukey’s multiple comparisons test

      Figure 7 - Log-rank test (Mantel-Cox) with Holm- Šídák's multiple comparisons test against treatment vs venom-only control

      We have ensured that all figure legends clearly indicate the venom and drug dose to aid the clarity which the reviewer requested.

      The comment Figure 3 relies on a fixed 5 µM drug concentration and very different venom amounts (50-100-250 ng), but it is not discussed whether such exposures are achievable in vivo, or how these concentrations map onto expected pharmacokinetics in patients. is an understandable query however, in vitro assessment such as those carried out in this manuscript are not designed to directly inform pharmacokinetic/pharmacodynmanic interpretations, largely because they do not replicate real world envenoming (i.e. preincubation would not occur between a venom and treatment). This is why, as stated, follow on preclinical and clinical assessments are needed for onward progression of these inhibitors to inform dosing regimens that might achieve the necessary exposures required for in vivo venom neutralisation. That being said, PK/PD work has been initiated within Phase I trials, for example with DMPS Abouyannis et al. 2025 demonstrated a plasma exposure of >10 µg/mL for single doses of 1,200 mg and higher. This is equivalent to 80 µM, which although is lower than the EC<sub>50</sub> for some venoms in the clotting assay (Figure 3J), the venom dose (50 to 250 ng/ 50 µL, i.e. 1,000 to 5,000 ng/µL) is estimated to be >1000 times higher than a natural envenoming by Bothrops atrox at less than 1 ng/mL in serum (https://doi.org/10.1016/j.toxicon.2022.09.010). These extrapolations therefore indicate that the doses selected in our studies would have human clinical relevance.

      Finally, in terms of anticoagulant venom effects - these would be observed in our experimental approach either as reduced kinetic responses in the plasma clotting assay (as observed with nafamostat in Figure 3B) or as a prolonged clotting time in the thromboelastography assay (Figure 6). As stated in the results section Comparison of coagulation profiles, all of the venoms tested presented with a procoagulant effect. If underlying anticoagulant activity from PLA<sub>2</sub> toxins was to arise after inhibition of the procoagulant toxins (i.e. SVMPs by marimastat), as has been seen for certain other snake venoms previously, this would result in a percentage inhibition far greater than 100% in the plasma assay (Figure 3C to I) or as a prolonged clotting time in the thromboelastography assay. These described anticoagulant profiles were not observed with any venom tested in this study.

      (5) Finally, the in vivo evidence is limited to a chicken embryo model. To support your hypothesis, a conventional mouse model with delayed post-envenomation dosing (24-36 h monitoring) is needed to address both safety/toxicity and post-exposure efficacy, and to define a realistic therapeutic window, especially because venom toxins act very quickly and the timing of administration is central to the clinical utility of any small-molecule approach.

      We agree with the reviewer that the next important step for this research activity is utilising murine preclinical models to validate the in vitro and preliminary in vivo findings described in this manuscript. However, as stated above, this study provides the initial evidence base that the promising utility of marimastat, DMPS and varespladib as repurposed snakebite drugs extends to a range of neotropical viper venoms. Evaluating the safety, efficacy (both precincubation and rescue approaches) and PK/PD relationships to inform optimal dosing strategies of these molecules will be crucial next steps for the field. However, these activities are far from trivial and will take several years of additional research, and therefore fall outside the scope of this initial manuscript.

      To address the concern related to the evidence is limited to a chicken embryo model, we have included additional sentences to discuss the wider use of the egg model within snakebite research and related translation to murine studies.

      Minor comments:

      (1) Figure 2D: How do you discuss the fact that "no venom" has SVSP activity?

      The data for all in vitro assays in Figure 2 is presented as AUC from the raw data (absorbance or fluorescence), for consistency across assay. Therefore, all assays (B to D) have background signal in the absence of venom. The SVSP assay has a greater background signal.

      (2) For better understanding, I would suggest adding a dedicated column in Figure 4A with Nafamostat SVSP data reported as "N/D" where applicable.

      As stated in the results, due to the weak inhibitory activity EC<sub>50</sub> assessment was not justified, therefore adding this column would be redundant.

      (3) The introduction is too long relative to the experimental content and would benefit from tightening to sharpen the motivation and unmet need.

      We thank the reviewer for their opinion and we have reviewed the introductory section again. While we made minor edits throughout, we decided not to make substantial modifications to it.

      Reviewer #3 (Recommendations for the authors):

      I only have some minor comments:

      (1) In line 100, the word "that" is repeated.

      We thank the reviewer for spotting this error, which we have corrected.

      (2) Line 433. I believe the word "compromising" should be substituted by "comprising" here.

      We thank the reviewer for spotting this.

      (3) Figure 1 and supplementary: Bothrops asper venom has been very thoroughly studied, and using only one study from Costa Rica might underestimate the venom variation within the species. I suggest looking at the following study: https://doi.org/10.1016/j.toxicon.2022.106983. Maybe it is not necessary to change anything, but worth looking into.

      We appreciate the reviewer flagging this paper, it has been added to the manuscript (reference 48) and has provided additional data for Figure 1 and Supplementary table 1.

      (4) Methods: Given the intraspecies variation described for some of these species, I believe it is relevant to add the locality of origin of the venoms, and not only the country. I, of course, understand this is often unknown for historical samples.

      We have included the following sentence in the methods. Due to the historic nature of the venom samples, the source locality is not available beyond country of origin, with the exception of B. lanceolatus which is endemic to Martinique.

      (5) Figure 3: It is not very accurate to show an SD when the sample number is 2. I suggest, when possible, showing the mean and the two data points in the plots. This also applies to other figures where n=2. Also, in Figure 3D, does Marimastat seem to have an anticoagulant effect, or is this just within normal variation?

      We have removed the statement in the statistics paragraph of the methods Standard deviation (SD) for all kinetic reads and standard error for AUC is reported based on Prism v10 but kept the sentence. The sample sizes for HTS assays including the SVMP, PLA<sub>2</sub> and coagulation experiment are the average of the means from independent assays (n >2 within each independent assay). We understand the reviewer’s opinion on limited meaning of SD as well as SE for Fig 3 A to I, therefore we have changed the error bars to range, as we think that displaying the individual points would result in a lack of visual and analytic clarity.

      In relation to the query about marimastat anticoagulant effect in Fig 4D, as shown in 4B marimastat has no direct anticoagulant effect. The >100% inhibition for marimastat is likely to be normal variation as this is a biological assay which has high variability. However, it could also be that the strong inhibition of the SVMPs in B. asper along with limited SVSP activity has unmasked an anticoagulant effect of the remaining PLA<sub>2</sub> toxin which has high activity in this venom. That being said, as B. asper has a similar profile, we would have expected to see a similar profile in B. atrox in both the plasma and TEG assays. Therefore, assay variation seems the most likely reason for this observation.

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary

      In this review paper, the authors describe the concept of neural correlates of consciousness (NCC) and explain how noninvasive neuroimaging methods fall short of being able to properly characterise an unconfounded NCC. They argue that intracranial research is a means to address this gap and provide a review of many intracranial neuroimaging studies that have sought to answer questions regarding the neural basis of perceptual consciousness.

      Strengths

      The authors have provided an in-depth, timely, and scholarly contribution to the study of NCCs. First and foremost, the review surveys a vast array of literature. The authors synthesise findings such that a coherent narrative of what invasive electrophysiology studies have revealed about the neural basis of consciousness can be easily grasped by the reader. The review is also, to the best of my knowledge, the first review to specifically target intracranial approaches to consciousness and to describe their results in a single article. This is a credit to the authors, as it becomes ever harder to apply strict tests to theories of consciousness using methods such as fMRI and M/EEG it is important to have informative resources describing the results of human intracranial research so that theorists will have to constrain their theories further in accordance with such data. As far as the authors were aiming to provide a complete and coherent overview of intracranial approaches to the study of NCCs, I believe they have achieved their aim.

      We appreciate the reviewer's positive feedback on our work.

      Weaknesses

      Overall, I feel positive about this paper. However, there are a couple of aspects to the manuscript that I think could be improved.

      (1) Distinguishing NCCs from their prerequisites or consequences

      This section in the introduction was particularly confusing to me. Namely, in this section, the authors' aim is to explain how intracranial recordings can help distinguish 'pure' NCCs from their antecedents and consequences. However, the authors almost exclusively describe different tasks (e.g., no-report tasks) that have been used to help solve this problem, rather than elaborating on how intracranial recordings may resolve this issue. The authors claim that no-report designs rely on null findings, and invasive recordings can be more sensitive to smaller effects, which can help in such cases. However, this motivation pertains to the previous sub-section (limits of noninvasive methods), since it is primarily concerned with the lack of temporal and spatial resolution of fMRI and M/EEG. It is not, in and of itself, a means to distinguish NCCs from their confounds.

      As such, in its current formulation, I do not find the argument that intracranial recordings are better suited to identifying pure NCCs (i.e. separating them from pre- or post-processing) convincing. To me, this is a problem solved through novel paradigms and better-developed theories. As it stands, the paper justifies my position by highlighting task developments that help to distinguish NCCs from prerequisites and consequences, rather than giving a novel argument as to why intracranial recordings outperform noninvasive methods beyond the reasons they explained in the previous section. Again, this position is justified when, from lines 505-506, the authors describe how none of the reported single-cell studies were able to dissociate NCCs from post-perceptual processing. As such, it seems as if, even with intracranial recording, NCCs and their confounds cannot be disentangled without appropriate tasks.

      The section 'Towards Better Behavioural Paradigms' is a clear attempt to address these issues and, as such, I am sure the authors share the same concerns as I am raising. Still, I remain unconvinced that the distinguishing of NCCs from pre-/post- processing is a fair motivation for using intracranial over noninvasive measures.

      We agree that distinguishing proper NCCs from their prerequisites or consequences is primarily a matter of experimental design and theoretical framework, not merely of recording modality. We did not mean to imply that intracranial recordings inherently solve this dissociation.This is now explicitly stated that at the beginning of this section. Instead, we argued that the high signal-to-noise ratio and spatiotemporal accuracy of sEEG offer a stronger "testing ground" for the null findings often relied on by no-report paradigms. This is now also further clarified in the revised section “Limits of noninvasive measures”.

      We also explicitly acknowledge, as the reviewer noted, that even the most precise recordings require careful task dissociations to distinguish NCCs from their prerequisites and consequences.

      (2) Drawing misleading conclusions from certain studies

      There are passages of the manuscript where the authors draw conclusions from studies that are not necessarily warranted by the studies they cite. For instance:

      Lines 265 - 271: "The results of these two studies revealed a complex pattern: on the one hand, HGA in the lateral occipitotemporal cortex and the ventral visual cortex correlated with stimulus strength. On the other hand, it also correlated with another factor that does not appear to play a role in visibility (repetition suppression), and did not correlate with a non-sensory factor that affects visibility reports (prior exposure). These results suggest that activity in occipitotemporal cortex regions reflecting higher-order visual processing may be a precursor to the NCC but not an NCC proper."

      It's possible to imagine a theory that would predict HGA could correlate with stimulus strength and repetition suppression, or that it would not correlate with prior exposure (e.g. prior exposure could impact response bias without affecting subjective visibility itself). The authors describe this exact ambiguity in interpretation later in the article (line 664), but in its current form, at least in line 270 (when the study is most extensively discussed), the manuscript heavily implies that HGA is not an NCC proper. This generates a false impression that intracranial recordings have conclusively determined that occipitotemporal HGA is not a pure NCC, which is certainly a premature conclusion.

      We agree that our interpretation of these studies (lines 265–271 of the previous version of the manuscript) was presented too definitively. We have modified the text (now lines 314-317) to soften this conclusion and align it with the more nuanced discussion later in the manuscript. Specifically, we now frame this as a "suggested dissociation" rather than a conclusive finding (line 730), and we explicitly acknowledge that alternative interpretations remain viable.

      Line 243: "Altogether, these early human intracranial studies indicate that early-latency visual processing steps, reflected in broadband and low gamma activity, occur irrespective of whether a stimulus is consciously perceived or not. They also identified a candidate NCC: later (>200 ms) activity in the occipitotemporal region responsible for higher-order visual processing."

      The authors claim in this section that later (>200ms) activity in occipitotemporal regions may be a candidate for an NCC. However, the Fisch et al. (2009) study they describe in support of this conclusion found that early (~150ms) activity could dissociate conscious and unconscious processing. This would suggest that it is early processing that lays claim to perceptual consciousness. The authors explicitly describe the Fisch et al results as showing evidence for early markers of consciousness (line 240: '...exhibited an early...response following recognized vs unrecognised stimuli.) Yet only a few lines later they use this to support the conclusion that a candidate NCC is 'later (>200ms) activity in the occipitotemporal region' (line 245). As such, I am not sure what conclusion the authors want me to make from these studies.

      This problem is repeated in lines 386-387: "Altogether, studies that investigated the cortical correlates of visual consciousness point to a role of neural responses starting ~250 ms after stimulus onset in the non-primary visual cortex and prefrontal cortex."

      This seems to be directly in conflict with the Fisch et al results, which show that correlates of consciousness can begin ~100ms earlier than the authors state in this passage.

      We thank the reviewer for pointing out this inconsistency. We agree that stating ">200 ms" conflicts with the findings of Fisch et al. (2009), who observed dissociations as early as ~150 ms. Our goal was to contrast the very early, stimulus-driven responses with the later responses that reflect consciousness. However, as the reviewer correctly notes, the exact "onset" of these signals varies across studies and paradigms. To address this, we have removed the specific ">200 ms" mentioned in line 245 of the previous version of the manuscript and updated the timing in line 284 to "starting 150 ms" to better reflect the results of Fisch et al. We also clarify that while the exact latency depends on the paradigm, a consistent finding is that activity representing conscious contents in higher-order visual cortex follows an initial wave of unconscious processes (lines 809-810).

      (3) Justifying single-neuron cortical correlates of consciousness

      The purpose of the present manuscript is to highlight why and how intracortical measures of neural activity can help reveal the neural correlates of perceptual consciousness. As such, in the section 'Single-neuron cortical correlates of perceptual consciousness', I think the paper is lacking an argument as to why single-neuron research is useful when searching for the NCC. Most theories of consciousness are based around circuit or system-level analyses (e.g., global ignition, recurrent feedback, prefrontal indexing, etc.) and usually do not make predictions about single cells. Without any elaboration or argument as to why single-cell research is necessary for a science of consciousness, the research described in this section, although excellent and valuable in its own right, seems out of place in the broader discussion of NCCs. A particularly strong interpretation here could be that intracranial recordings mislead researchers into studying single cells simply because it is the finest level of analysis, rather than because it offers helpful insight into the NCCs.

      It is true that many prominent theories of consciousness were developed based on macroscopic observations, largely due to the prevalence of non-invasive recordings in humans. However, we argue that recording single-unit activity is important for several reasons, and we made this clearer in the revised version. First, signals like fMRI, EEG (or even LFP) often conflate multiple distinct neural populations. SUA allows us to dissociate neurons representing the percept from neighboring neurons involved in task-related confounds (e.g., motor preparation or arousal) that would otherwise be blurred together. Therefore, some percepts might be represented by sparse coding involving a small, specific population of "concept" or "percept" cells. Electrophysiological studies in animal models reveal that various cognitive processes are encoded within neuronal subspaces that only emerge when single-unit activity is analyzed as lower-dimensional projections of the broader neural activity manifold (Mante et al., 2013; Ebitz & Hayden, 2021; Jayazeri & Afraz, 2017). Importantly, many neural computations are only discernible through the lens of population dynamics (i.e. with single neuron activity) (Vyas et al., 2021). We believe that providing high granularity through SUA recordings prevents over-aggregation of data, ensuring that even system-level theories can build on biologically accurate foundations.

      Moreover, some theories are defined at the cellular level. For instance, the Dendritic Integration Theory (Bachmann et al., 2020) posits that the integration of feedforward and feedback signals occurs at the level of individual pyramidal neurons. Without SUA, these cellular mechanisms remain untestable. Beyond spatial granularity, SUA also provides excellent temporal granularity, which is crucial for testing theories that rely on the precise timing of spikes (e.g., neural synchrony). As LFPs reflect average activity across populations, only SUA can confirm whether individual neurons lock their spikes to a specific phase, a mechanism hypothesized to bind features into a conscious whole.

      We added these points to a new section in the revised manuscript. References:

      Bachmann, T., Suzuki, M., & Aru, J. (2020). Dendritic integration theory: A thalamo-cortical theory of state and content of consciousness. Philosophy and the Mind Sciences, 1(II).

      Ebitz, R. B., & Hayden, B. Y. (2021). The population doctrine in cognitive neuroscience. Neuron, 109(19), 3055-3068.

      Jazayeri, M., & Afraz, A. (2017). Navigating the neural space in search of the neural code. Neuron, 93(5), 1003-1014.

      Mante, V., Sussillo, D., Shenoy, K. V., & Newsome, W. T. (2013). Context-dependent computation by recurrent dynamics in prefrontal cortex. nature, 503(7474), 78-84.

      Vyas, S., Golub, M. D., Sussillo, D., & Shenoy, K. V. (2020). Computation Through Neural Population Dynamics. Annual Review of Neuroscience, 43(1), 249-275.

      (4) No mention of combined fMRI-EEG research

      A minor point, but I was surprised that the authors did not mention any combined fMRI-EEG research when they were discussing the limits of noninvasive recordings. Intracortical recordings are one way to surpass the spatial and temporal resolution limits of M/EEG and fMRI respectively, but studies that combine fMRI and EEG are also an alternative means to solve this problem: by combining the spatial resolution of fMRI with the temporal resolution of EEG, researchers can - in theory - compare when and where certain activity patterns (be they univariate ERPs or multivariate patterns) arise. The authors do cite one paper (Dellert et al., 2021 JNeuro) that used this kind of setup, but they discuss it only with respect to the task and ignore the recording method. The argument for using intracranial recordings is weaker for not mentioning a viable, noninvasive alternative that resolves the same issues.

      We thank the reviewer for this point. We have added a discussion of fMRI-EEG to the "Limits of noninvasive measures" section (lines 167-171). While we acknowledge that fMRI-EEG is a powerful non-invasive tool for bridging spatial and temporal scales, we note that it relies on merging an indirect metabolic signal with a weak electrophysiological one filtered by the skull, which is computationally complex and often noisy. In contrast, intracranial recordings provide direct measures of both local field potentials and spiking activity within the same neural population, offering interpretability and signal-to-noise ratio that non-invasive combinations cannot match. In our view, this is not just an alternative to these methods, but a unique means of accessing the underlying neuronal ground truth.

      Reviewer #2 (Public review):

      Summary:

      In this work, the authors review the study of the neural correlates of consciousness (NCCs). They discuss several of the difficulties that researchers must face when studying NCCs, and argue that several of these difficulties can be alleviated by using intracranial recordings in humans.

      They describe what constitutes an NCC, and the difficulties to distinguish between an NCC proper from the prerequisites and consequences of conscious processing.

      They also describe the two main types of experimental designs used to study NCCs. These are the contrastive approach (with its report and non-report variants), and the supraliminal approach, each with its own merits and pitfalls.

      They discuss the limitations of non-invasive methods, such as fMRI, EEG and MEG, as well as the limitations of the use of invasive recordings in non-human animals.

      After setting the stage in this way, the authors provide an extensive review of the knowledge acquired by using invasive recordings in humans. This included population-level measurements in vision and in other sensory modalities, as well as single-neuron level studies. The authors also discuss studies of subcortical NCCs.

      The second half of this work discusses the theoretical insights gained through the use of intracranial recordings, as well as their limitations, and a perspective for future work.

      Strengths:

      This work offers an impressive review, which will serve as a useful reference document, both for newcomers to the study of NCC and for experienced researchers. The inclusion of non-visual and subcortical NCCs is of particular merit, as these have been understudied.

      Besides serving as a review, this work includes a perspective, exploring several directions to pursue for the progress of the field.

      We thank the reviewer for acknowledging the strength of our work.

      Weaknesses:

      The intention of the authors is to argue how some of the problems faced when studying NCCs are alleviated by the use of intracranial recordings in humans. But in some cases, the link between the problems related to the study of NCCs and the advantages of intracranial recordings over non-invasive methods is not clear.

      For example, the authors explain the difficulties in distinguishing between true NCCs from their prerequisites and consequences. This constitutes a difficult conceptual problems that plague all recording techniques. The authors don't provide a convincing explanation of how intracranial recordings offer advantages over EEG or MEG when dealing with these problems.

      We agree that the distinction between proper NCCs and their prerequisites or consequences is a fundamental challenge that affects all recording modalities. We did not intend to imply that intracranial recordings are a "silver bullet" for solving this conceptual problem in isolation, and we now explicitly state that at the beginning of this section (line 101).

      We have revised the section on "Distinguishing NCCs from their prerequisites or consequences" to clarify that intracranial recordings are a powerful tool when used in conjunction with appropriate experimental designs, rather than a standalone solution to these conceptual difficulties.

      For example, the authors explain how the use of non-report designs to rule out post-perceptual processing relies on null results, which, according to them, are harder to interpret given the low resolution of non-invasive methods. But the interpretation of null results is actually more complicated in the case of intracranial recordings. As the coverage achieved by the electrodes is sparse, if a null result is attested, it remains possible that a true effect was present in a nearby patch of cortex out of coverage.

      It is true that a null result in an intracranial study may simply reflect that the relevant neural population was not sampled by the specific electrode implantation scheme. However, we argue that interpreting null results is equally, if not more, complicated in non-invasive methods, albeit for different reasons. While M/EEG offers broader coverage, it is blind to many cortical sources because of their orientation (radial sources in MEG) or their location in deep sulci and subcortical structures. The signal-to-noise ratio of M/EEG is also much lower than that of intracranial EEG, making it more likely that null results obscure the existence of subtle effects (Parvizi & Kastner, 2018).

      To address this, we revised the manuscript to clarify that intracranial recordings provide high local certainty within the sampled regions (lines 224-227), whereas non-invasive methods provide broader coverage (lines 247-249). We now explicitly emphasize that drawing conclusions from null results based on intracranial recordings requires caution regarding electrode placement. We also point out that these approaches are complementary: M/EEG can identify large regions of interest, while sEEG can then provide high-resolution "ground truth" to confirm whether those regions are part of the NCC.

      Reference: Parvizi, J., & Kastner, S. (2018). Promises and limitations of human intracranial electroencephalography. Nature Neuroscience, 21(4), 474-483. https://doi.org/10.1038/s41593-018-0108-2

      The authors argue that the spatial resolution of intracranial recordings is better than that of EEG and MEG. While this is technically true (especially compared to EEG), the true spatial scale of the NCCs is unknown. If NCCs' span is in the mm range, then the additional spatial resolution of intracranial recordings might not be an advantage.

      We agree with the reviewer that the exact spatial scale of the NCC remains a topic of ongoing debate. However, we believe that the advantage of intracranial recordings holds true whether the NCC spans millimeters or centimeters. The main spatial limitation of non-invasive electrophysiology (M/EEG) is not just its spatial resolution but also the inverse problem. Since scalp sensors detect a mixture of signals from across the brain, different cortical configurations can produce identical scalp patterns. This makes it challenging to precisely locate the NCC or distinguish it from nearby activity (e.g., motor or attentional signals). When recording intracortically, a widespread NCC could be captured across multiple adjacent channels with high accuracy. Conversely, if the NCC is focal, it can be isolated with high spatial resolution. In either case, intracranial recordings eliminate the spatial ambiguity inherent in scalp recordings. We have revised the Introduction (lines 158-164) to clarify that the "spatial advantage" of intracranial recordings also pertains to the inverse problem, not merely to the ability to record from smaller cortical areas.

      Another factor that should be taken into consideration when assessing the spatial resolution of intracranial recordings is that while the listening zone of individual intracranial contacts is small, coverage is sparse and defined by clinical criteria (something that the authors discuss). In practice, the activity recorded by contacts is usually attributed to anatomically defined ROIs with a scale in the cm range. Given the sparse and uneven (across regions and patients) coverage afforded by intracranial recordings, the advantage of intracranial recordings in terms of spatial resolution is overstated.

      We thank the reviewer for raising this point regarding how intracranial data is often aggregated into regions of interest. We agree that if researchers generalize findings to large anatomical regions without accounting for single-channel recordings, some of the spatial benefits of intracranial recordings are indeed mitigated. We toned down some of the original claims accordingly, and acknowledged more clearly that clinical constraints of sEEG lead to sparse coverage (245-249).

      However, we maintain that even when using an ROI-based approach, intracranial recordings offer a clear advantage over non-invasive methods, in that they represent a direct measure from a specific patch of tissue, rather than a statistical estimate that may be contaminated by "leakage" from distant sources. To address the reviewer’s concern, we have updated the manuscript (lines 244-245) to emphasize the importance of relying on MNI coordinates and individual anatomy rather than solely on broad ROI labels.

      Appraisal of whether the authors achieved their aims:

      In this work, the authors have gathered an impressive review and have discussed several important problems in the field of study of NCCs, as well as provided a perspective on how the field could move forward.

      What is less clear is how the use of intracranial recordings per se holds potential to overcome problems such as the distinction between true NCCs and the prerequisites and consequences of conscious processing.

      Discussion of the likely impact of the work on the field:

      This work has the potential of becoming a must-read for anyone working in the field of consciousness research.

      Reviewer #3 (Public review):

      Summary:

      This narrative review provides a clear, well-structured, and comprehensive synthesis of intracerebral recording work on the neural correlates of consciousness. It is written in an accessible manner that will be useful to a broad community of researchers, from those new to iEEG to specialists in the field.

      Strengths:

      The manuscript successfully integrates methodological and theoretical perspectives and offers a balanced overview of current, sometimes contradicting evidence. As such, the manuscript is important as it calls for a concerted and better exploration of NCCs using iEEG in the future.

      We thank the reviewer for stating the importance of our work and its potential contribution to the field.

      Weaknesses:

      The manuscript extensively discusses the use of "report" as a criterion for identifying conscious perception and its limitations for separating between correlates of consciousness and post-consciousness processes, yet the term is not defined at the outset. The authors should specify what they mean by "report" (e.g., verbal report, nonverbal self-report, or any meta-cognitive indication of experience). Importantly, this definition should be explicitly linked to the theoretical landscape: whether the authors adopt an access-consciousness perspective in which (self) reportability is central, or whether the review also aims to address phenomenal consciousness. Making this conceptual grounding explicit at the beginning will help readers interpret the empirical work surveyed throughout the review.

      We agree that a clear definition of report is essential for the reader to interpret the empirical findings presented. We have added a definition to the Introduction (lines 108-111), specifying that we use "report" to refer to any explicit behavioral response (whether verbal, manual, or otherwise) that communicates a subject’s subjective state.

      Regarding the conceptual distinction between Phenomenal and Access consciousness, we refer to recent work from some of the co-authors (Mudrik et al., 2025), which suggests that P and A should not be seen as two types of consciousness, but rather as two necessary conditions for conscious experience. While a full discussion of this distinction is beyond the scope of this review, we now clearly state that our focus is on identifying neural activity that reflects the subjective experience itself, regardless of the downstream requirements of report.

      Reference: Mudrik, L., Faivre, N., Pitts, M., & Schurger, A. (2025). On a confusion about there being two types of consciousness. Trends in Cognitive Sciences. https://doi.org/10.1016/j.tics.2025.11.012

      In addition, the review would benefit from an earlier introduction of the distinction between states and contents of consciousness. This distinction becomes important in the later section on anaesthesia, sleep, and epileptic seizures, where the focus shifts from content-specific NCCs to alterations in global states. Presenting these definitions upfront and briefly explaining how states and contents interact would strengthen the coherence of the manuscript.

      We agree that clarifying the distinction between contents and levels of consciousness early on provides a stronger framework for the paper.

      We have added a brief clarification in the Introduction (lines 63-76): "It is also helpful to distinguish between levels of consciousness, defined as a global level of arousal or wakefulness (e.g., being awake vs. under anesthesia), and the contents of consciousness, defined as the specific subjective experiences one has while conscious (e.g., perceiving a visual stimulus; Bayne et al., 2016; Laureys, 2005). While the majority of this review focuses on 'content-specific' NCCs, the two dimensions are intrinsically linked, as global states typically set the conditions for the occurrence of specific conscious contents."

      Overall, this is an excellent and timely review. With clearer initial theoretical definitions of consciousness, the manuscript will offer an even stronger conceptual framework for interpreting intracerebral studies of consciousness.

      We thank the reviewer again for this highly positive assessment of the manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I would like to reiterate that I believe this is a very scholarly piece of writing, and I congratulate the authors on producing such a useful and timely manuscript. Below, I suggest just a few ways the authors may resolve some of the issues I raised in the public review. However, I would like to emphasise that these are merely suggestions - the authors may think of different and better ways to address these comments that are more in line with either their thinking or writing style, and I would certainly encourage the authors to follow their own preferences if they feel they are at odds with my suggestions.

      For the longer comment questioning whether intracranial recordings are really a way to isolate NCCs from their pre- and post-processing, there are two ways the authors could resolve this. One is that they collapse the section distinguishing NCCs from their prerequisites and consequences into the previous section regarding limits of noninvasive measures. For instance, they could make the point that null results are easier to interpret with intracranial recordings in this previous section. Then they could discuss how specific intracranial studies have been able to resolve questions of pre-/post- processing confounds when they introduce studies later in the manuscript. At the moment, the Distinguishing NCCs from their prerequisites and consequences section, at least to me, undermines the argument of why intracranial recordings are important because it spends too much time describing how tasks are the core component of isolating pure NCCs, and not the recording method.

      Alternatively, the authors could keep the structure as it is. In this case, I would urge the authors to emphasise the role of intracortical recordings here and to make the argument that this is a problem that intracortical recordings (rather than novel tasks) can solve more convincingly. Citing specific studies that combined intracortical recordings with no-report paradigms and emphasising how the invasive recording allowed the researchers to reach a conclusion that would not have been possible with noninvasive measures would also be helpful.

      We thank the reviewer for these useful suggestions and agree that we would not want readers to take from this paper that design issues can be fixed by using invasive recordings. Because confounding issues are crucial in research on the NCC, we believe it is important to include a section on this topic in the Introduction. However, as we explained in our response to the public review, we revised the section introducing Human intracranial electrophysiology to reflect that intracranial recordings are a complementary tool that improves the interpretability of no-report paradigms, rather than a “silver bullet” solution for confound issues. We also explicitly say now that this problem is relevant to all techniques in the study of consciousness, including intracranial recordings (line 101). Additionally, based on the reviewer’s suggestion, we have added a more detailed explanation of how studies that pair intracranial recordings with no-report paradigms provide a unique insight in the Temporal Insights section (lines 822-823).

      For my comment: Drawing misleading conclusions from certain studies, I think the public review speaks for itself. I would recommend that the authors make sure they are drawing correct conclusions from the studies they cite, and make clear from the outset where there is ambiguity in interpretation.

      We thank the reviewer for bringing these ambiguities to our attention. As explained in the response to the public review, we have modified the text accordingly.

      Finally, with regard to the single-cell analyses, I would imagine that most readers will share at least some scepticism around single neurons being the appropriate level of analysis for revealing the basis of perceptual experience. As such, I think it would strengthen the manuscript greatly if the authors could provide a brief argument as to how such work can either inform theories of consciousness or contribute more generally to the study of NCCs, given that the field and its theories are mostly biased towards studying system-level neural processes. I think single-cell analyses are extremely valuable to NCC research, and the authors have a good opportunity to frame these studies accordingly.

      We agree. As detailed in the response to the public review, we now specify (1) how a higher level of granularity in electrophysiological measurements can distinguish between awareness-related signals and confounds, (2) that these measurements provide an opportunity to study neuronal population dynamics where various cognitive processes have been shown to emerge in animals and (3) that single-neuron measurements are necessary to test predictions of theories that are defined at the cellular level

      Reviewer #2 (Recommendations for the authors):

      Recommendations for improving the writing and presentation:

      My compliments for having written an impressive review. Overall, I think that this is a beautiful piece of work that will be of great use to the community. My only concern is that the advantages of intracranial recordings over non-invasive methods in solving the difficulties faced in the study of NCCs are overstated.

      Here I provide more precise comments for your consideration.

      (1) On page 5, lines 100 to 102, you argue that "Scalp EEG and MEG have limitedanatomical resolution due to the overlap of deep and superficial brain signals at the scalp level and, in the case of EEG, the scattering of the adjacent electrical signals through the scalp". It would be good to provide precise estimates of the spatial resolutions of EEG, MEG and intracranial recordings, with accompanying references. Consider also that MEG is relatively insensitive to deep sources. I recommend this paper: Piastra et al. 2020 https://onlinelibrary.wiley.com/doi/10.1002/hbm.25272

      We thank the reviewer once again for their positive evaluation of our work. As detailed in the response to the public reviews, we now clarify that intracranial recordings provide high local certainty within the sampled regions (lines 224-227), whereas non-invasive methods provide broader coverage (lines 247-249). We thank the reviewer for their additional suggestions and have clarified our concern about the anatomical conclusions that can be drawn from scalp EEG and MEG data (lines 158-164).

      (2) On page 11, you describe work showing that activity in the occipitotemporal cortex mightreflect a precursor to consciousness, but not an NCC proper, except for the case of faces, in which the fusiform seems to behave like a true NCC. Could you discuss how these seemingly contradictory results could be reconciled?

      One possibility is that activity in some parts of the occipitotemporal cortex instantiates content-specific NCCs, i.e., correlates that are only specific to certain stimulus types (in this case: faces), while activity in other parts instantiates precursors of the NCCs. Because faces have been extensively studied, we might have uncovered the content-specific NCCs for these stimuli but not for others. This is now discussed in the text on lines 342-344. Based on reviewer 1’s suggestion, we have also toned down our claim about occipitotemporal activity being a precursor to the NCC.

      (3) From line 322, you start to discuss connectivity analyses. Adding a subheading mightimprove readability.

      We appreciate the suggestion; however, adding a subheading to a single paragraph would require restructuring the entire section, which could disrupt the flow. We believe the current format maintains clarity and cohesion.

      (4) In line 329, you write "It remains unclear to what extent these connectivity patterns reflectpost-perceptual processing and how the signals associated with perceptual consciousness in the occipitotemporal cortex interact with frontoparietal regions." But it's not clear why this is the case.

      We meant to make two separate points: (1) these studies did not control for report-related activity using no-report paradigms and (2) there has been no investigation so far of the interaction between occipitotemporal and frontoparietal signals associated with perceptual consciousness. These two points have been clarified in the text (lines 378-381).

      (5) In line 692, it would be good to clarify that Pereira 2021 is a single-neuron study.

      This has been clarified in the text.

      (6) The phrase "more research/work is needed" is repeated several times.

      Thank you for pointing this out. To avoid redundancy, we have deleted the second mention of this phrase.

    1. Quality at parity hasn't unlocked majority adoption. Plant-based nuggets — the format that has reached sensory parity in blinded testing — still hold only 2 to 3% of the conventional nugget category. If matching taste isn't sufficient, then taste investments alone may have lower returns than the parity-headroom argument suggests.

      Think about this more and state in a a more reasoned logical way. Note that we're largely thinking about price here (as well as taste, nutrition and availability). We're largely focused on the the impact of cost and price on consumption and substitution. In fact, skeptics were saying that "we don't care too much about substitution and price impacts because 1. it has such a low market share and 2. it's not taste or nutrition comparable."

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      1. General Statements

      We thank the reviewers for their constructive evaluation of our manuscript. We are pleased by the overwhelmingly positive consensus regarding the quality and significance of our data. In particular, the reviewers highlighted that this is a "nice, clean study with interesting data" and noted that our in vivo functional genetic findings in the Drosophila wing are "clearly a strength" that "moves the paper beyond cell-culture correlations" to provide a "simple, straightforward take-home message".

      The principal critique across the reports concerns the extent of direct mechanistic evidence linking Groucho (Gro) to regulation of the early elongation checkpoint. Several reviewers suggested additional genomic experiments, including RNA-seq, PRO-seq, or Pol II ChIP approaches, to further examine transcription and pausing behaviour. However, we would like to flag up that genomic datasets addressing these questions across multiple Drosophila cell lines have already been published previously, including work from our own group and others.

      The primary objective of the current study is therefore not to replicate these existing genomic analyses, but rather to build directly upon them. We identify a consistent genomic association between Gro and pausing/elongation factors across cell types. Importantly, we extend these findings beyond genomic correlations through in vivo genetic analysis in the developing Drosophila wing.

      1. Description of the planned revisions

      • *

      • *

      Reviewer 1

      The figures and text could lay out the logic of the genetic interactions for non-Drosophila readers. For example, the comparison of single and double copies of Gro-RNAi to combinatorial knockdowns, when it is additive, and when it is interpreted as synergistic.

      The statistical analyses presented in Figure 5C, including Fisher’s exact tests comparing phenotype distributions between genotypes, were intended to address the distinction between additive and synergistic genetic interactions. However, we agree that the presentation of these comparisons could potentially be made clearer for readers less familiar with Drosophila genetic interaction assays. We would therefore be open to revising the presentation of Figure 5 and the accompanying explanatory text following editorial guidance and with consideration of the intended readership of the eventual journal.

      The statistical analysis of the phenotype distributions should be shown more clearly (Fig. 5B).

      Figure 5B is intended to present the distribution of observed phenotypic classes and does not include statistical comparisons. A similar analysis has been published for experiments looking at the phenotypes of moderate Groucho overexpression in the wing in the presence of HDAC inhibitors (Winkler et al., 2010 doi.10.1371/journal.pone.0010166). Statistical analyses of the genetic interaction experiments are presented separately in 5C. We therefore believe the current presentation of Figure 5B is appropriate for illustrating phenotype frequencies rather than statistical inference, but we will consider moving this panel to the Supplementary material.

      Minor comments

      -Figure 5 would gain clarity if the phenotype classes/panel letters were shown more clearly on the images. -The legends of the wing figures should be expanded, especially for readers outside the Drosophila field. -"in vivo" should be italicised consistently.

      We agree that clearer labelling of phenotype classes, panel annotations and expanded figure legends could improve the accessibility of Figure 5, particularly for readers less familiar with Drosophila wing phenotypes and genetic interaction assays. We would therefore be open to revising the presentation of this figure and its accompanying legends in a future revised version.

      We thank the reviewer for noting the typographical inconsistency of italics for in vivo. This will be corrected during manuscript revision and proofing.

      __Reviewer #2 __

      Reviewer #2 (Significance (Required)):

      I think this is nice little paper providing a simple, straightforward take-home message. It does not conceptually shake the world, and the evidence consists of (nice) correlations, with no direct proof put forward for the conclusions. I am not a Drosophila geneticist but probably rather an 'expert' on basic transcription mechanisms. I think the data in the paper are of high quality, if limited in scope, and that the conclusions are supported by the results, but I do not think the results or conclusions will have a big audience. Having said that, I found it interesting to learn about this group of repressors and their likely mode of action.

      On the other hand, it is worth emphasizing that proteins such as NELF and CDK9 would arguably be expected to be found at very many genes, as promoter-proximal pausing does exist at a plethora of genes, also genes that are house-keeping genes, ie not regulated by cell type or stimuli. So, lots of genes with pausing are not regulated by modulation of pausing. So, basically, the fact that knockdown of the repressor Groucho and loss of pausing is additive does not in my opinion necessarily mean that Groucho works by stabilizing pausing. Although it is admittedly a reasonably assumption, Groucho could also work by repressing transcription initiation; the genetic outcomes of 'double relief' would be the same, ie higher transcription levels. I think a brief comment to this effect might be appropriate, especially in the absence of (difficult to obtain) direct evidence that the transcription initiation step is not affected by Groucho.

      While we agree that the current study does not directly exclude possible effects of Groucho on transcription initiation, previously published work has already provided evidence arguing against repression by Groucho occurring primarily through inhibition of transcription initiation or prevention of pre-initiation complex assembly. Groucho-bound transcriptional start sites were previously shown to retain RNAP II occupancy, active chromatin features, and detectable basal transcriptional activity despite repression (Kaul et al., 2014).

      To acknowledge this possibility and explain why it is unlikely, we will add the sentence “While effects on transcription initiation cannot be completely excluded, previous work argues against Gro repressing transcription primarily through inhibition of transcription initiation. Gro-bound promoters remain accessible, overlap RNAP II occupancy, and retain active chromatin features and basal transcriptional activity” to the start of the third paragraph of the Discussion.

      Reviewer #3

      The methods section is lacking details on how ChIP-seq was performed in the BG3 cell line. The methods section does a good job of indicating how the data were processed. Information on the antibodies and conditions used is critical, as is whether spike-in controls were used.

      The generation of the ChIP-seq data from BG3 cells has already been published. __We will add the line “The production of ChIP-seq datasets for Gro binding in Kc167, S2R+ and BG3 cells has been described elsewhere (Kaul, Schuster and Jennings, 2014; Bar-Cohen et al., 2023)” in the Analysis of ChIP-seq data subsection of the Methods. __

      1. Description of analyses that authors prefer not to carry out

      • *

      __Reviewer #1 __ Major comments 1. The main weakness is the lack of a mechanistic link between Gro and the early elongation checkpoint. This is really the main point for this reviewer. The manuscript builds an interesting model, and the data support a functional connection between Gro and pausing-related factors, but the mechanistic link is absent. At present, the paper relies on co-localisation of ChIP peaks and genetic interaction in vivo. This is interesting and supportive, but with several possible interpretations. The title and some parts of the text are thus a bit stronger than what is directly demonstrated. Two possibilities could be proposed: either tone down the mechanistic claim or strengthen it experimentally. A more direct assay of pause release or productive elongation after Gro depletion at endogenous targets would be highly valuable. For example, Gro-KD followed by Pol II Ser2-P ChIP, or promoter vs. gene body analysis on Gro-bound genes, ideally comparing genes with Gro at TSS vs. not-TSS, would greatly support the proposed model. If the assay is established, this seems feasible in about 4 months.

      We thank the reviewer for this thoughtful comment. We agree that the current study does not directly measure genome-wide RNAP II pause release following Gro depletion. However, several key observations linking Gro with promoter-proximal pausing have already been published and are summarised in the Introduction. Previous work demonstrated that Gro occupancy correlates with paused genes and that depletion of Gro reduces RNAP II pausing and increases elongating RNAP II at the endogenous E(spl)mbeta-HLH locus, an established target gene of Groucho-mediated repression (Kaul et al., 2014; doi.10.1371/journal.pgen.1004595). We also note that several of the experiments proposed by the reviewer have already been addressed in previous work. Specifically, Kaul et al. (2014) demonstrated that Gro depletion increases elongating RNAP II (Ser2-P) at the endogenous E(spl)mbeta-HLH locus while total promoter-associated RNAP II occupancy remains largely unchanged. Promoter versus gene body analyses in that study further supported a role for Gro in regulating progression through the early elongation checkpoint rather than transcription initiation.

      The aim of the current manuscript was therefore to build upon these earlier mechanistic and genomic observations by asking whether the relationship between Gro and pausing-associated factors extends across multiple cell types and whether it has functional significance in vivo. By integrating comparative genomic analyses with sensitised developmental genetic assays in the wing, we provide evidence that Gro functionally interacts with multiple regulators of the early elongation checkpoint during development.

      The bioinformatic part could be strengthened on "distinct TF repertoires" between cell types.The authors interpret the cell type-specific Gro recruitment as reflecting distinct transcription factor repertoires in BG3, Kc167 and S2R+ cells. This is interesting, but not really shown. To make this point more strongly, the author could provide a map of TF expression across different cell types, especially for the TFs corresponding to the enriched motifs they discuss. Otherwise, this remains speculative.In line, the manuscript discusses enriched motifs in BG3 and compares them to Kc167 and S2R+ cells, but this remains a bit descriptive. A clearer side-by-side comparison would strengthen the paper. This is particularly relevant to the motifs used in interpreting cell type-specific recruitment.


      The interpretation that cell type-specific Gro recruitment reflects differences in transcription factor repertoires is based on several previously established observations already described in the manuscript. BG3 cells are derived from the larval CNS, whereas Kc167 and S2R+ cells are embryonic haemocyte-like lines (Cherbas et al., 2011; doi.10.1101/gr.112961.110). Transcriptomic analyses have further shown that these Drosophila cell lines maintain stable and distinct lineage-associated transcriptional identities, including differences in transcription factor expression (Cherbas et al., 2011). Given the diversity of transcription factors known to recruit Gro, the observed cell-type-specific binding patterns and motif enrichments are consistent with the distinct lineage-associated transcriptional programmes previously described for these cell lines.

      1. Several overlap analyses could be discussed more in depth. A few statements feel too strong for the actual percentages. For example, the GAF overlap in BG3 is around 51% genome-wide and 56% at TSS, which is meaningful, but not especially high. The text already states that it is not universal, and this point could be discussed more clearly.

      We note that the manuscript already explicitly states that overlap between Gro and GAF is not universal. Given the diversity of factors known to recruit Gro and the broad genomic distribution of GAF, we consider overlap frequencies of approximately 50% to represent a substantial association, particularly at transcription start sites. Importantly, the interpretation does not rely on complete co-occupancy between these factors, but rather on the observation that Gro-bound regions show significant enrichment for multiple factors associated with promoter-proximal pausing across different cell types.

      Similarly, for the UpSet plot, the wording around the "most frequent" combination could be toned down, because this is not a dominant pattern.

      The statement that the overlap between Gro, Nelf-E, GAF, Cdk9 and RNAP II represents the “most frequent” combination refers specifically to the relative frequency of the intersection categories within the UpSet analysis. In this context, the overlap between all five factors represents the largest intersection category identified (306 of 649 Gro peaks), with the next most frequent category containing substantially fewer peaks (90 of 649). We therefore feel that the current wording accurately describes the distribution observed in the analysis.

      More generally, I think the manuscript needs a clearer quantitative breakdown of TSS versus non-TSS peaks for the overlap analyses with NELF, GAF, Cdk9 and CycT. Several interpretations depend on this distinction, and right now, this is not always clear enough.

      The overlap analyses presented in Figure 3 explicitly distinguish between TSS and non-TSS peaks, and the corresponding quantitative overlap frequencies are described in the Results section. We do not consider that additional breakdowns are required for interpretation of the current data as this distinction is already incorporated into both the analyses and figure presentation.


      The "enhancer chromatin" interpretation is interesting, but not fully integrated with the genomic distribution. The observation that Gro is enriched in open enhancer-type chromatin is interesting and supports the idea that Gro does not act mainly through classical repressed chromatin. However, Gro peaks are also enriched at promoters and introns, and this reviewer feels that the manuscript does not fully connect these observations. Where are these enhancer-type peaks located exactly? Are they often intronic? Can this be correlated with the distribution of Gro peaks? This would help the reader and also strengthen the discussion because intronic Gro peaks are present in the data, but are not well integrated into the model.

      In the current manuscript, “enhancer chromatin” refers to chromatin states defined by combinations of enhancer-associated histone modifications, including H3K4me1, H3K27ac and H3K56ac as defined by Skalska et al.,2015 (doi.10.15252/embj.201489923), rather than exclusively to distal intergenic regulatory regions. As described in the chromatin-state analysis, these enhancer-associated chromatin signatures do occur at intronic regulatory regions, including regions classified as active intron chromatin. We therefore do not consider the enrichment of Gro peaks at promoters, enhancers and intronic regions to be mutually exclusive observations within this framework.

      Intronic enhancer localisation is common in Drosophila, where the compact organisation of the genome results in many developmental regulatory elements residing within introns (Arnold et al., 2013; doi.10.1126/science.1232542). We therefore consider the presence of Gro peaks within intronic regions to be fully consistent with the observed enrichment of Gro binding within enhancer-associated chromatin states.

      The in vivo part is a strength, but some important points need clarification.The in vivo section is a clear highlight of the manuscript. It gives functional relevance to the model and moves the paper beyond cell-culture correlations. That said, a few points need to be clearer:-RNAi efficiency is not clear for the tested genes, especially the pausing factors. This is important because the differential effects between NELF subunits could simply reflect differences in knockdown efficiency.

      While differences in RNAi efficiency could potentially contribute to variation in phenotype strength between individual knockdowns, multiple biological explanations could also account for the differing effects observed between NELF subunits, including differences in protein stability, residual complex activity, or subunit-specific functions. Importantly, the central conclusion of the manuscript does not depend on quantitative comparison of phenotype strength between individual NELF components, but rather on the observation that perturbation of multiple pausing-associated factors genetically interacts with Gro in vivo.

      If RNAi validation is possible with existing reagents, this seems realistic within 3 months.

      The manuscript focuses on the genetic interactions observed between Gro and pausing-associated factors in vivo rather than on quantitative comparison between individual RNAi lines. As no specific validation experiments were proposed, we are not currently planning additional RNAi validation analyses for the present study.

      The discussion could be expanded, especially because the mechanism is not fully shown.Since the direct mechanism is still missing, the discussion could compensate. Right now, the proposed model is interesting, but it still leaves many open questions. For example:-Is Gro affecting the recruitment or activity of elongation factors?-Could looping or enhancer-promoter communication contribute?-How should the intronic Gro peaks be interpreted in the model?-In the wing, could the phenotype be discussed more mechanistically, in light of what is already known about Gro and derepression of vein-promoting genes?For example, a model figure could help here.


      We thank the reviewer for these thoughtful suggestions.

      Several of the points raised by the reviewer are discussed in the manuscript already. For example, we discuss the possibility that Gro influences the activity or recruitment of elongation-associated factors. We agree that enhancer-promoter communication and chromatin looping are a plausible component of this mechanism. As the Drosophila genome is compact and intronic enhancers are highly prevalent, topological looping provides a clear physical framework for how Gro molecules distributed at non-TSS sites regulate promoter-proximal machinery. Indeed, we have previously published this model (Kaul, Schuster, and Jennings, 2015; see Figure 1C; doi.10.1080/21541264.2014.1000709). Our current in vivo and genomic findings build directly upon this model, suggesting that within these established looped configurations, Gro acts locally to interface with and stabilize the pausing machinery.

      With respect to the wing phenotypes, the Discussion focuses primarily on the interpretation of the observed genetic interactions between Gro and pausing-associated factors rather than on defining the precise downstream target genes contributing to vein phenotypes. We agree that additional mechanistic dissection of these developmental phenotypes would be interesting. However, this would require a substantial expansion of the study into the detailed developmental and signalling mechanisms underlying vein specification, which lies beyond the primary focus of the current manuscript.

      OPTIONAL: It would be interesting to know whether the same peak distribution / functional logic is observed in mammalian TLE orthologs. This is not essential for the current conclusions, but it would broaden the impact.

      Determining whether similar genomic distributions and functional relationships are conserved for mammalian TLE orthologues will be an important future project. However, relatively little comparable genome-wide TLE occupancy data are currently available, meaning that such analyses would require a substantial independent undertaking beyond the scope of the present study.

      Minor comments -Please explain why promoters were defined as {plus minus}250 bp from the TSS. This seems rather narrow.

      Promoters were defined as ±250 bp from annotated transcription start sites. This window size is commonly used in Drosophila genomic studies, where the compact organisation of the genome means that broader windows frequently overlap adjacent genes.

      -Please clarify why S2R+ cells are included in the comparative part but are not followed in the same way in some downstream analyses.

      S2R+ cells were included in the comparative analyses to determine which aspects of Gro recruitment were shared across multiple cell types and which were cell-type specific. Some downstream analyses focused on BG3 and Kc167 cells because these lines had the most extensive corresponding datasets available for the chromatin and pausing-factor analyses performed in the current study.

      __Reviewer #3 __ Here Martínez Quiles and Jennings investigate the role of the Groucho repressor in BG3 cells. This extends a previous study that used S2R+ cells, published previously by one of the authors, as well as Kc167 cells. They find that Gro is recruited to gene promoters in a cell-type-specific manner. Gro associates with open chromatin, is mostly associated with enhancer regions, and is primarily excluded from regions of the genome that are repressed by Polycomb. After studying its function in cell culture, the authors investigate the role of Gro in a wing-specific background. The findings here are mostly correlative, showing that loss of Gro results in stronger phenotypic defects when combined with loss of factors including NELF-B or NELF-D, LARP7, and bin3. They propose that Gro acts to attenuate gene expression during early gene expression. This claim would be greatly strengthened if the authors provided RNA-seq data in addition to the ChIP-seq data shown in this manuscript, especially to examine gene expression patterns among the different cell lines studied here. At present, this is a correlative study that does not illuminate the mechanism of Gro in directly regulating promoter-proximal pausing or RNA polymerase behavior.

      We thank the reviewer for this suggestion. However, extensive transcriptomic analyses of Drosophila cell lines, including Kc167, S2R+ and BG3-derived lines, have already been published (Cherbas et al., 2011), together with RNA-seq analyses following Gro depletion (Kaul et al., 2014). In addition, the association between Gro occupancy and paused genes has also been reported previously (Kaul et al., 2014; Chambers et al., 2017; doi. 10.1186/s12864-017-3589-6).

      While additional RNA-seq analyses could further characterise transcriptional differences between cell lines, RNA-seq alone would not directly determine whether altered transcript levels arise specifically through changes in promoter-proximal pausing, as opposed to effects on transcription initiation, transcript stability, or indirect downstream regulatory effects. We therefore do not consider additional RNA-seq analyses necessary to support the central conclusions of the present study.

      Figure 2-3: For the ChIP-seq data, scale the y-axis in the same manner to better understand enrichment between the samples.

      These ChIP-seq datasets were generated independently using different antibodies and experimental conditions, direct comparison of enrichment magnitudes across datasets would not be biologically meaningful. Accordingly, our analyses focus on significant peak calls and overlap relationships rather than relative signal intensity. Applying identical y-axis scaling across all tracks would obscure significant enrichment in several datasets and could therefore be misleading.

      RNA-seq data between different cell lines would greatly enhance the authors findings or Pro-Seq to really show a relationship with Gro binding and promoter proximal pausing.

      We note that RNA-seq datasets for Gro depletion in Kc167 and S2R+ cells have already been published previously (Kaul et al., 2014), together with evidence linking Gro occupancy to paused genes (Kaul et al., 2014; Chambers et al., 2017). We therefore do not consider that additional RNA-seq analysis would substantially strengthen the central conclusions of the current manuscript.

      Moreover, RNA-seq alone cannot distinguish if altered transcript abundance reflects changes in promoter-proximal pausing from other mechanisms influencing transcript abundance. While PRO-seq approaches could provide further mechanistic information regarding RNAPII dynamics, such experiments are beyond the scope of the present study.

      This study helps to further clarify how Gro binds DNA in different cell types and indicates that may intersect with factors involved in promoter proximal pausing. The study is highly correlative and would require additional work to show a mechanistic link between Gro and transcription attenuation due to promoter proximal pausing.

      While we agree that PRO-seq approaches could provide additional mechanistic information regarding RNAPII dynamics, establishing an appropriate experimental and analytical framework for these analyses would require a substantial extension beyond the scope of the present study. In addition, several aspects of the relationship between Gro occupancy, transcriptional repression, and promoter-proximal pausing that underpin these suggestions have already been addressed in previously published work, including RNA-seq analyses following Gro depletion (Kaul et al., 2014), evidence linking Gro occupancy with paused genes (Kaul et al., 2014; Chambers et al., 2017), and studies demonstrating that Gro-mediated repression does not occur through inhibition of pre-initiation complex assembly. The current manuscript is therefore intended to build upon these existing findings by integrating comparative genomic analyses with new in vivo genetic interaction data.

      • *
    1. Author response:

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

      eLife Assessment

      This important study sought to investigate the role that early childhood malaria exposure plays in the development of antibody responses to unrelated pathogens and vaccine-derived antigens in Kenyan children. In this natural experiment, the authors compare antibody levels among children who have been exposed to different levels of malaria transmission by using protein microarray technology. Although the findings are of importance, the evidence remains incomplete, and the analysis would benefit from a more in-depth evaluation of potential confounders. With the appropriate analysis, the findings will be of great interest for global health, immunology, and vaccine development.

      We thank the editors for highlighting the need for a more comprehensive evaluation of potential confounding. We agree that this is a critical aspect of the study and have now undertaken additional analyses to address this directly.

      The original longitudinal cohort was designed to investigate the acquisition of naturally acquired immunity to malaria and did not include systematic collection of anthropometric/nutritional, environmental or socioeconomic data, precluding direct adjustment for these factors within the primary dataset. However, to assess whether there were population-level differences in these factors, we leveraged contemporaneous hospital-based surveillance data from the same geographic regions, which includes measurements of anthropometry and nutritional status (muac, weight-for-age, and height-for-age) and detailed infection diagnostics.

      Using this independent dataset, we fitted mixed-effects regression models adjusting for age, calendar year, and concurrent infections (RSV, parainfluenza, influenza A, human metapneumovirus, OC43). For all three anthropometric indices, we found no evidence of systematic differences between children from Junju and Ngerenya. Adjusted differences were small and centred around zero (muac: −0.12, 95% CI −0.38 to 0.15, weight-for-age: −0.05, −0.28 to 0.19, height-for-age: 0.08, −0.17 to 0.33), with no consistent directional effect.

      As the longitudinal cohort was randomly selected from these underlying populations, these findings suggest that the groups were broadly comparable with respect to nutritional status and there were no differences in their exposure to the infections that were included in the analysis. We have incorporated these analyses into the revised manuscript, added a new figure focussed on this analysis -fig. 6, updated the statistical analysis and discussion sections), and believe they substantially strengthen the evidence by addressing a key source of potential confounding.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The study shows that childhood malaria can weaken the antibody response to other vaccines and infections. This suggests that early exposure to P. falciparum may have a long-lasting effect on immunity, with implications for vaccine efficacy in endemic areas.

      Strengths:

      This study stands out for its longitudinal design, the use of robust immunological techniques, and the comparison between areas with different levels of malaria exposure. Its findings reveal that early malaria can weaken the response to childhood vaccines, with important implications for public health in endemic regions.

      We thank the reviewer for this comment

      Weaknesses:

      One of the study's main limitations is the lack of functional data confirming the clinical impact of the low antibody levels. Furthermore, although multiple immune responses were measured, other important components, such as cellular immunity, were not assessed. Furthermore, the results may not be generalizable to other regions.

      We thank the reviewer for this important comment and agree that the absence of functional immunological assays is a limitation of the current study. Our analysis was designed to determine whether early-life malaria exposure is associated with durable alterations in antibody responses to unrelated pathogens and vaccine antigens, rather than to establish the downstream functional consequences of these differences. As such, the study is able to demonstrate a broad and persistent attenuation of humoral responses but cannot directly determine whether the lower antibody levels observed translate into reduced neutralising capacity or diminished protection at the individual level.

      We have revised the manuscript to make this distinction more explicit. In the revised discussion, we now state that although reduced antibody titres to vaccine-preventable pathogens may have implications for long-term protection, the clinical significance of these differences remains to be established in future studies incorporating functional assays and clinical outcome data.

      Reviewer #2 (Public review):

      Summary:

      The authors investigated whether early-life malaria exposure has long-term effects on immune responses to unrelated antigens. They leveraged a natural experiment in coastal Kenya where two adjacent communities (Junju and Ngerenya) experienced divergent malaria transmission patterns after 2004. Using 15 years of longitudinal data from 123 children with weekly malaria surveillance and annual serological sampling, they measured antibody responses to multiple pathogens using a protein microarray technology and ELISA.

      Strengths:

      (1) Extensive longitudinal data collection with weekly malaria surveillance, enabling precise exposure classification.

      (2) Use of a natural experiment design that allows for causal inference about malaria's immunological effects.

      (3) Broad panel of antigens tested, demonstrating generalized rather than antigen-specific effects.

      (4) Within-cohort analysis in Ngerenya controls for geographic and environmental factors.

      (5) Validation of key findings using both serologic microarray and ELISA.

      (6) Important public health implications for vaccine strategies in malaria-endemic regions.

      We thank the reviewer for these comments

      Weaknesses:

      (1) Lack of participants' characteristics (socio-economic, nutritional, physical).

      We thank the reviewer for this important comment. We have now included a detailed summary of participant characteristics in Table 1to provide context for the study population. This includes key demographic and longitudinal variables stratified by cohort (Junju and Ngerenya), including sex distribution, age at study entry and exit, duration of follow-up, number of visits per participant, and total serum samples analysed. Detailed data on socio-economic status, nutritional status, and other environmental or physical characteristics were not consistently available across all participants and time points, and therefore could not be included. This has now been explicitly stated as a limitation in the discussion.

      (2) Somewhat limited sample size (longitudinal analysis of 123 children total), with further subdivision reducing statistical power for some analyses.

      We thank the reviewer for this important observation. The study is based on an intensively followed cohort with weekly malaria surveillance and repeated serological measurements throughout childhood, allowing detailed characterisation of early-life exposure and subsequent immune trajectories. This depth of longitudinal sampling provides resolution that is not achievable in larger cross-sectional studies. We acknowledge that subdivision of the cohort reduces statistical power for some analyses. Nevertheless, the key findings were consistent in several independent comparisons, including a reduction in antibody levels for broad panel of antigens in the malaria endemic setting, within-cohort analyses in Ngerenya that replicated this observation, and the confirmation of results generated on the protein microarray on the ELISA platform. The consistency of these findings across analytical approaches and measurement platforms reduces the likelihood that the observed effects are driven by small-sample variability. We have clarified this point in the revised discussion to emphasise that the strength of the study lies in the depth and longitudinal resolution of the data rather than the absolute sample size.

      (3) Potential confounding by unmeasured socioeconomic, nutritional, or environmental factors between communities.

      We thank the reviewer for this important point and agree that residual confounding between communities must be considered. As outlined in reponse to the editorial assesment, we have undertaken additional analyses using contemporaneous population-level data from the same regions and found no evidence of systematic differences in anthropometric indices between children from Junju and Ngerenya after accounting for age, calendar year, and concurrent infections, with effect estimates small and crossing zer. In addition, the within-Ngerenya analysis provides an internal comparison within a shared geographic and environmental setting, reducing the likelihood that unmeasured socioeconomic or environmental differences between communities account for the observed associations. The new analyses suggest that major population-level differences in nutritional status or infection burden are unlikely to explain the observed patterns. We have clarified this point in the revised discussion and explicitly acknowledge the possibility of residual confounding.

      (4) Lack of ability to determine the direction of the associations found between malaria exposure and other IgG levels to unrelated pathogens.

      We agree that, as an observational study, our analysis cannot definitively establish the direction of the association between malaria exposure and antibody responses to unrelated antigens. However, several features of the study design strengthen the inference that early-life malaria exposure contributes to the observed differences. First, malaria exposure was characterised prospectively through intensive weekly surveillance, allowing precise temporal definition of exposure in early childhood. Second, within the Ngerenya cohort, where children were exposed to different levels of malaria due to a rapid decline in transmission, those with even limited early-life exposure exhibited lower antibody responses at 10 years of age than malaria-naïve peers, despite residing in the same geographic and environmental context. In addition, we now show that these differences are not confined to a single timepoint but are evident across the full longitudinal follow-up after adjustment for age and repeated measurements. While we cannot exclude the possibility of residual confounding or bidirectional relationships, the convergence of evidence from the natural experiment design, within-cohort contrasts, and age-adjusted longitudinal analyses supports early-life malaria exposure as a key contributor to long-term differences in antibody responses. We have clarified this in the discussion.

      (5) Despite good longitudinal data, the main analysis was conducted as a cross-sectional analysis at age 10 for many comparisons, which limits the understanding of temporal dynamics.

      We thank the reviewer for highlighting this point. While age 10 was initially used as a standardised reference point for cross-sectional comparisons, the underlying dataset is longitudinal, with repeated antibody measurements across childhood. To address this more directly, we have now complemented these analyses with antigen-specific mixed-effects regression models incorporating all available longitudinal data, with adjustment for age and a random intercept for repeated measurements within individuals. These models demonstrate that the differences between cohorts are not confined to the age-10 cross-section but are evident in an age-adjusted longitudinal framework for multiple antigens. We have retained the age-10 comparisons for reference, but the primary inference is now based on the longitudinal mixed-effects analyses. These changes are reflected in the revised results and statistical analysis sections. We thank the reviewer for this astute point, which we think has substantially improved the manuscript.

      (6) Statistical analysis is limited to univariable comparisons without consideration for confounders or adjusting for multiple comparisons.

      We agree that the original analyses relied primarily on univariable comparisons. In the revised manuscript, we have extended the analytical framework to include mixed-effects regression models that account for age effects and repeated measurements within individuals. These models estimate the average age-adjusted difference in antibody responses between cohorts across the full follow-up period. We have also applied false discovery rate (FDR) correction to account for multiple antigen testing. For multiple antigens, the direction and magnitude of cohort differences remain consistent under this approach, strengthening the robustness of the findings beyond the original univariable comparisons. These analyses have been incorporated into the revised results and statistical analysis sections.

      (7) No mechanistic understanding of how early malaria exposure creates lasting immunosuppression.

      We agree that this study does not directly resolve the mechanistic basis underlying the observed long-term differences in antibody responses. The primary aim of this work was to identify and characterise durable alterations in humoral immune profiles associated with early-life malaria exposure, rather than to define the cellular or molecular pathways involved. However, our findings are consistent with a growing body of experimental and clinical literature suggesting that malaria infection can induce sustained perturbations in B cell and T cell compartments, including the expansion of atypical memory B cells, altered germinal centre responses, and increased regulatory immune activity. These mechanisms have been proposed to impair the generation and maintenance of effective humoral immunity. In the revised discussion, we have clarified that the mechanistic basis of this phenomenon remains to be fully defined and have expanded the discussion of plausible pathways in light of existing literature. We now explicitly position our findings as providing population-level evidence of a durable immunological phenotype that warrants further mechanistic investigation.

      (8) No understanding of the clinical Implications of the reduced IgG levels observed in the area with high malaria exposure.

      We agree that this study does not directly establish the clinical consequences of the reduced antibody levels observed in malaria-exposed children. The primary objective of this study was to characterise long-term differences in humoral immune profiles associated with early-life malaria exposure, rather than to assess downstream clinical outcomes or functional antibody activity. We have clarified this limitation in the revised discussion. Nevertheless, the breadth and consistency of the observed differences for multiple vaccine-preventable and infectious antigens raise the possibility that early-life malaria exposure may have implications for long-term immune protection. We now emphasise in the revised discussion that future studies incorporating functional assays and clinical outcome data will be required to determine whether these serological differences translate into altered susceptibility to infection or reduced vaccine effectiveness.

      Assessment of Claims:

      The data appear to support the authors' primary claims, but the strength of the evidence is limited, and the results should be interpreted with caution. Together with the currently available evidence of P. falciparum's impact on the host's immune function, this natural experiment design provides further evidence for a relationship between early malaria exposure and reduced antibody responses. The within-Ngerenya analysis controls for geographic factors and thus enhances the quality of the evidence, however, it still fails to account for the physical, nutritional, and socio-economic factors that may have driven the observed changes. Additionally, the mechanism underlying this effect remains unclear, and the clinical significance of reduced antibody levels is not established.

      We thank the reviewer for this assessment and for recognising the strengths of the natural experiment design and within-cohort analyses. We agree that, as an observational study, our findings should be interpreted appropriately. In the revised manuscript, we have undertaken additional analyses and clarifications to strengthen the evidential basis of our conclusions and to address the points raised. To address potential confounding by nutritional and related factors, we analysed contemporaneous hospital-based surveillance data from the same geographic populations since nutritional and socioeconomic variables were not consistently collected during the course of longitudinal follow up. For three independent anthropometric indices of nutrition status (muac, weight-for-age, and height-for-age), we found no evidence of systematic differences between children from Junju and Ngerenya after adjustment for age, calendar year, and concurrent infections. As the longitudinal cohort subjects were randomly drawn from these populations, these findings suggest that the two groups were broadly comparable with respect to early-life growth and nutritional status.

      We agree that the mechanistic basis of the observed differences is not resolved in this observational study. We have clarified this point in the revised discussion and expanded our consideration of plausible biological pathways based on existing literature, including perturbations in B cell and T cell compartments. Similarly, we now explicitly state that the clinical implications of reduced antibody levels remain to be determined and will require studies incorporating functional assays and clinical outcomes. We believe these revisions strengthen the manuscript by providing a more comprehensive interpretation of the data.

      Impact and Utility:

      This work has fundamental implications for understanding vaccine effectiveness in malaria-endemic regions and may contribute to informing vaccination strategies. The findings, if strengthened, would suggest that children in areas of high malaria transmission may require modified immunization approaches. The dataset provides a valuable resource for future studies of malaria's immunological legacy.

      We thank the reviewer for this comment

      Context:

      This study builds on prior work showing acute immunosuppressive effects of malaria but uniquely attempts to demonstrate the durability of these effects years after exposure. The natural experiment design addresses limitations of previous observational studies by providing a more controlled comparison.

      We thank the reviewer for this comment

      Recommendations for the authors:

      Reviewing Editor Comments:

      We suggest that further analyses of potential confounders such as anthropometric indices, socioeconomic status, and comorbidities would render the evidence more robust.

      We thank the Reviewing Editor for this important suggestion. We agree that careful consideration of potential confounding factors is critical to the interpretation of these findings, and have undertaken additional analyses to address this.

      Because anthropometric and related socioeconomic measurements were not collected systematically within the original longitudinal malaria cohort, we assessed potential population-level differences using hospital-based surveillance data from the same geographic regions. This dataset includes measurements of anthropometry (mid-upper arm circumference, weight-for-age, and height-for-age) as well as detailed infection diagnostics in childhood. Using these data, we fitted regression models adjusting for age, calendar year, and concurrent, clinically diagnosed infections. For all three anthropometric indices, we found no evidence of systematic differences between children from Junju and Ngerenya, with effect estimates small and crossing zero (fig. 6). As the longitudinal cohorts were randomly selected from these populations, these findings suggest that the groups were broadly comparable with respect to nutritional status and infection exposure. With respect to socioeconomic status and comorbidities, detailed individual-level data were not available within the longitudinal cohort. However, the within-Ngerenya analysis, where children with differing early-life malaria exposure were compared within the same geographic and environmental setting, provides a complementary control for these factors. We have incorporated these additional analyses and clarifications into the revised manuscript statistical analysis, discussion lines and believe they strengthen the robustness of the findings by addressing key sources of potential confounding.

      Reviewer #1 (Recommendations for the authors):

      The manuscript is well written, with clear and informative figures that effectively support the findings.

      We thank the reviewer for this comment

      Suggestions:

      (1) Although the study well controlled for malaria exposure, other environmental or infectious factors that influence immunity could be considered:

      Nutritional status in childhood (malnutrition impacts immune response), co-infections (helminths, respiratory viruses), socioeconomic differences, or differences in access to health services, even minimal, between Junju and Ngerenya.

      We thank the reviewer for highlighting the potential influence of environmental, infectious, and socioeconomic factors on immune responses. We agree that these are important considerations in the interpretation of observational data. To address nutritional status and concurrent infectious exposures, we analysed contemporaneous hospital-based surveillance data from the same geographic populations. This dataset includes measurements of anthropometric indices (mid-upper arm circumference, weight-for-age, and height-for-age) alongside detailed clinical diagnostics for common childhood infections. Using regression models adjusting for age, calendar year, and concurrent infections, we found no evidence of systematic differences in anthropometric profiles between children from Junju and Ngerenya (fig. 6). These findings suggest that the populations from which the longitudinal cohorts were randomly selected were comparable with regard to early-life growth and nutritional status. We agree that we cannot fully exclude the influence of unmeasured factors such as helminth infections, socioeconomic variation, or subtle differences in healthcare access. However, the within-Ngerenya analysis, where children with differing early-life malaria exposure were compared within the same geographic, environmental, and healthcare setting, provides an internal control for many of these factors. The persistence of similar patterns within this setting supports malaria exposure as a key contributor of the observed differences. We have clarified these considerations in the revised discussion and believe that, the additional analyses and within-cohort comparisons strengthen the robustness of our conclusions while acknowledging the limitations inherent to observational studies.

      (2) Measurement of other immunological markers:

      In addition to IgG, include: B cell subpopulations (naive, memory, atypical), cytokine levels (IL-10, IFN-γ) to characterize the immunological microenvironment.

      You could include these recommendations in the text for future studies.

      We thank the reviewer for this thoughtful suggestion. We agree that detailed immunophenotyping, including characterisation of B cell subpopulations and cytokine profiles, would provide important insight into the mechanisms underlying the observed differences in antibody responses. In the revised manuscript, we have expanded the discussion to highlight these important avenues for future work, including the potential role of altered B cell subsets (and regulatory or inflammatory cytokine environments in shaping long-term humoral responses).

      Reviewer #2 (Recommendations for the authors):

      The manuscript is well-written.

      We thank the reviewer for this comment

      (1) Methodological Clarifications:

      Do the authors have any information regarding the characteristics of these children that could be of use in understanding their immune responses better? (e.g., weight, height, BMI, socioeconomic status, HB level, access to health care, etc.).

      We thank the reviewer for highlighting the importance of participant characteristics in interpreting immune responses. Anthropometric and related clinical measures were not collected systematically within the original longitudinal malaria cohort, as the study was designed to investigate the acquisition of naturally acquired immunity to malaria.

      To address this, we analysed contemporaneous hospital-based surveillance data from the same geographic populations, which include measurements of anthropometric indices (mid-upper arm circumference, weight-for-age, and height-for-age) alongside detailed infection diagnostics. Using regression models adjusting for age, calendar year, and concurrent infections, we found no evidence of systematic differences in anthropometric profiles between children from Junju and Ngerenya (fig. 6) Detailed individual-level data on socioeconomic status, haemoglobin levels, and healthcare access were not available within the longitudinal cohort impeding direct adjustment in the longitudinal cohorts. However, the within-Ngerenya analysis, where children with differing early-life malaria exposure were compared within the same geographic and healthcare setting, provides an internal control for many of these factors. These considerations are now clarified in the revised discussion.

      Could the authors provide more detailed statistical analysis, including power calculations and multiple comparison corrections?

      In the revised manuscript, we have extended the statistical analysis and now include antigen-specific mixed-effects regression models incorporating all available longitudinal measurements, which is comprehensively described in the statistical analysis section. We have also applied false discovery rate (FDR) correction to account for multiple testing across antigens, and report both unadjusted and FDR-adjusted significance in the revised results. With respect to power, the sample size was determined by the number of children meeting inclusion criteria within the long-term surveillance cohorts in terms of availability of a sufficient number of longitudinal samples. We have clarified this in the revised manuscript.

      Clarify the criteria for selecting the 123-child subset from the larger surveillance cohorts.

      We thank the reviewer for this comment. The 123 children included in this analysis were selected from the larger surveillance cohorts based on the availability of sufficiently dense longitudinal serum sampling as described above. Specifically, children were required to have at least eight longitudinal samples available in the archive, enabling robust assessment of within-individual antibody trends over time. This criterion was applied to ensure adequate temporal resolution to examine the long-term stability of malaria-associated effects on antibody responses. Children with fewer available samples were therefore excluded, as limited sampling would not allow reliable characterisation of longitudinal patterns. We have clarified these inclusion criteria in the revised manuscript.

      (2) Additional Analyses and Data Presentation:

      The authors could consider dose-response analyses relating malaria episode frequency/timing to degree of immunosuppression or even AMA-1 IgG levels and degree of immunosuppression. How do they associate over time?

      We thank the reviewer for this suggestion. To address this, we examined the relationship between malaria exposure (using cumulative febrile malaria episode count derived from longitudinal surveillance data) and the magnitude of heterologous antibody responses. In mixed-effects models adjusting for age and repeated antibody measurements, higher malaria episode burden was associated with lower antibody responses against multiple antigens (fig 7).

      Analyze whether the effects vary by specific age at malaria exposure.

      We agree that age at exposure is an important consideration. We have now assessed how the relationship between malaria burden and antibody responses varies with age by including age as a non-linear term and modelling interactions between malaria exposure and age as described above. These analyses did not suggest substantial heterogeneity in the association over age, and therefore we have retained the simpler presentation for clarity.

      Provide correlation analyses between different antibody responses to assess whether suppression is generalized.

      We have addressed this by modelling responses jointly across a panel of heterologous antigens and by examining antigen-specific associations. The direction of effect was consistent for the majority of antigens, with no evidence of opposing trends, supporting a broad rather than antigen-specific effect.

      The authors could consider moving Figures 2a and b to the supplementary material.

      We thank the reviewer for this suggestion. We carefully considered whether panels 2a and 2b could be moved to the supplementary material. However, we have retained them in the main text because they provide a simple, intuitive illustration of how AMA1 antibody responses track with malaria exposure at the individual level, complementing the population-level analysis shown in fig. 2c. We feel that this helps establish the biological validity of the microarray platform in a way that is immediately interpretable to the reader, and therefore supports the interpretation of subsequent analyses.

      The authors could consider replacing Figures 3a and b with IgG levels from ALL vaccinated children and ALL non-vaccinated children.

      We thank the reviewer for this suggestion. We would like to retain these figures for the same reasons that have been articulated above for figures 2a and b.

      (3) Discussion Enhancements:

      The authors should consider expanding the discussion to address the limitations of the data more thoroughly, particularly regarding the potential differences between cohorts that could have contributed to the results.

      We have expanded the discussion to more explicitly address potential differences between cohorts that could contribute to the observed findings, including nutritional, socioeconomic, and environmental factors.

      The discussion needs to acknowledge the lack of directionality for the associations observed. As stated above, although I agree in general terms with the observations that the authors have made, it is not possible to distinguish between a suppressive effect of malaria on immune responses to infection-derived pathogens or a protective effect of malaria that leads to less exposure to infection-derived pathogens (and consequently lower IgG levels). The mechanisms behind these could include things like different health-seeking behaviors or social interactions from kids who have malaria versus those who don't, for example.

      We agree that, as an observational study, we cannot definitively establish the direction of the association between malaria exposure and antibody responses to unrelated antigens. We have now clarified this limitation explicitly in the discussion. We acknowledge the alternative interpretations raised by the reviewer, including the possibility that differences in exposure to other pathogens, potentially driven by behavioural, environmental or healthcare-related factors, could contribute to the observed patterns. At the same time, we note that the natural experiment design, prospective malaria exposure classification, and within-Ngerenya comparisons support early-life malaria exposure as a key contributing factor. We have revised the discussion to reflect this balance.

      Extend the discussion of potential biological mechanisms underlying durable immunosuppression.

      We thank the reviewer for this suggestion. We have expanded the discussion to more fully consider potential biological mechanisms that could underlie the observed long-term differences in antibody responses. Specifically, we now discuss evidence from prior studies indicating that malaria infection can induce sustained alterations in B cell and T cell compartments, including expansion of atypical memory B cells, disruption of germinal centre responses, and increased regulatory immune activity. We position our findings as providing population-level evidence of a durable immunological phenotype, while noting that targeted mechanistic studies will be required to define the underlying pathways.

      Extend the discussion around the clinical implications of the observed antibody level differences.

      In the revised discussion, we highlight that studies incorporating functional assays and clinical outcome data will be required to determine whether these serological differences translate into altered susceptibility to infection or reduced vaccine effectiveness.

      (4) Technical Issues:

      Could the authors please:

      (1) Clarify microarray data processing and quality control procedures.

      We thank the reviewer for this request. We have expanded the methods section to provide additional detail on microarray data processing and quality control procedures.

      (2) Provide information on inter-assay variability and batch effects.

      We have expanded the methods section to clarify how these were evaluated and addressed. Inter-assay variability was monitored using pooled adult serum included on every slide as a consistent positive control. This allowed us to assess slide-to-slide consistency in signal detection across the full antigen panel. In addition, fluorophore-conjugated IgG and IgA controls were printed directly onto each miniarray to confirm scanner performance independently of antigen–antibody interactions. At the sample level, each specimen was assayed on two independent miniarrays per slide, generating four spatially separated replicate measurements per antigen. Technical variability was quantified using the coefficient of variation (CV), and measurements with CV >20% were excluded from downstream analyses.

      (3) Include details on how missing data were handled in longitudinal analyses.

      We thank the reviewer for highlighting this point. We have added clarification in the statistical analysis section describing how missing data were handled. Specifically, mixed-effects models were used, which accommodate unbalanced longitudinal data without requiring imputation, allowing all available observations to contribute to the analysis.

      (4) Include details of the parameters of the LOWESS analysis shown in Figure 1.

      We have expanded the figure 1 legend to include the parameters used for the loess smoothing shown, including the smoothing span.

      (5) Include details of the samples used for Figure 3d (Negative and Pooled Adult Serum).

      We have clarified in the methods the nature and purpose of the samples used in Figure 3d. The negative control consisted of phosphate-buffered saline applied to a full miniarray in place of serum, allowing assessment of background and non-specific signal in the absence of antibody binding. The pooled adult serum comprised a composite of sera from multiple healthy adults from the same setting and was included as a positive reference sample, expected to contain a broad repertoire of antigen-specific antibodies. These controls were included on each slide to enable interpretation of assay performance, with the negative control defining baseline signal and the pooled adult serum providing a consistent reference for antigen recognition across the microarray.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Strengths:

      This work sets a benchmark for integrative 3D genomics in oncology. Its methodological sophistication and conceptual advances establish a new paradigm for studying nuclear architecture in disease.

      We appreciate the very kind words.

      Weaknesses:

      Major Issues

      (1) Functional tests would strengthen the observed links between structure and gene changes. For example, the COL12A1 gene loop formation correlates with its increased expression. Disrupting this loop using CRISPR-dCas9 at chr6 position 75280 kb could prove whether the loop causes COL12A1 activation. Such experiments would turn strong correlations into clear mechanisms.

      We agree that targeted disruption of specific loops such as COL12A1 will be important for functional validation of the causal relationships between enhancer-promoter loop formation/dissipation and changes in gene expression. However, the intent of our current study was to profile changes in genome organization at a global scale to deduce general features of cancer progression-associated changes in genome organization, rather than to explore specific loop interactions. The current findings are a foundation for more targeted functional follow-up studies.

      (2) The H3K27ac looping idea needs deeper validation. Data suggests H3K27ac loss weakens loops without affecting CTCF. Testing how cohesin proteins interact with H3K27acmodified sites would clarify this process. Degron systems could rapidly remove H3K27ac to observe real-time effects. Also, the AP-1 motifs found at dynamic loop sites deserve functional tests. Knocking down AP-1 factors might show if they control loop formation.

      We agree that modulating histone modifications or transcription factors would provide insights into the underlying mechanisms driving the changes we observed. However, such studies utilizing degrons or small molecule inhibitors that globally knock down either H3K27ac or specific transcription factors are often difficult to interpret. For example, assessing the role of AP-1 factors, as suggested, would be complicated by the variety of AP-1 proteins. In addition, H3K27ac reduction could inhibit loop strength either directly (i.e. by reducing cohesin recruitment) or indirectly (i.e. by reducing gene expression which could in turn affect loop strength). Parsing out the exact relationships between these features will require extensive follow-up work and falls outside of the scope of the current study.

      (3) Connecting findings to patient data would boost clinical relevance. The MCF10 model is excellent for controlled studies. Checking if TAD boundary weakening occurs in actual patient metastases would show real-world importance. Comparing primary and metastatic tumor samples from the same patients could reveal new structural biomarkers. If tissue is scarce, testing cancer cells with added stroma cells might mimic tumor environment effects.

      We have leveraged publicly available datasets to link the observations from the progression model to clinical samples. Specifically, we have compared our datasets to chromatin organization data in non-cancerous mammary epithelial cells (HMEC), five cell lines representing distinct cancer subtypes ranging from less (luminal) to more aggressive (triple negative, TNBC), as well as tissue samples from TNBC patients with contralateral normal controls. We explored the conservation of both loops and TADs identified in the MCF10 progression system in each of these maps, paying particular attention to how features that are differential between MCF10 cells differ across other cancer cell types. We observe a high degree of conservation of static loops and TAD boundaries among the cancer samples, as well as some degree of cell-specific changes among loops and boundaries that change during MCF10 progression. These findings are included in Supplemental Figures 3 and 4 and are discussed on page 7.

      Minor Issues

      (1) Adding a clear definition for static loops would help readers. For example, state that static loops show less than 10 percent contact change across replicates.

      Static loops are defined as loops with a fold-change of 1.5 or more between any two MCF10 cell lines and an adjusted p-value of less than 0.025 considering change across biological and technical replicates. This definition is stated on page 6).

      (2) In the ABC model analysis, removing promoter regions from the enhancer list would focus results on true long-range interactions.

      The ABC model already excludes the promoter of each gene. Only self-promoters are excluded, whereas the model allows promoters of other genes to act as potential long-range enhancers of the target gene. We have added text to make this clear (see page 11).

      (3) Briefly noting why this study sees TAD weakening while other cancer types show different patterns would provide useful context.

      The biological reason for TAD weakening in the MCF10 model is not known, but neither the mechanism for boundary weakening nor the reason for apparently different behavior amongst cancers is known. We expanded the text on this discussion slightly, but we refrain from making any definitive claims. We do note that differences in the types of cancer studied or the methods used for detecting changes in TADs (i.e. different sensitivities and thresholds for detecting change) could be responsible (see page 15). We also mention that the loss of insulation at many TAD boundaries detected in our study are subtle changes in intensity that could be potentially missed if using methods tailored to find more drastic changes in TAD architecture.

      Reviewer #2 (Public review):

      While the conclusions are broadly supported, methodological and analytical refinements are required.

      We appreciate these comments.

      (1) Model representativeness. The long-term culture-adapted MCF10 genome harbours extensive aneuploidies and translocations. Validation of key COL12A1/WNT5A loop dynamics in an independent breast-cancer line (e.g., MDA-MB-231, T47D) or in patientderived organoids/PDX models would strengthen generalizability.

      Although the generation of Micro-C datasets in additional cell lines is outside of the scope of this study, we used publicly available Hi-C data from triple negative breast cancer (TNBC) progression and patient samples (Kim, Han & Chun et al. 2022) to assess generalizability of the MCF10 model findings. While these maps are lower resolution than the Micro-C maps used in our study, they are of sufficient depth to detect loops at a similar resolution (10 kb). We report these findings in Supplemental Figures 3 and 4 and discuss them on page 7.

      We find that chromatin loops and TAD boundaries detected across the MCF10 system are highly conserved across all other mammary epithelial lines studied. Chromatin loops that were more prominent in MCF10AT1 and MCF10CA1a lines were also significantly stronger in TNBC cells. Insulation score boundaries that were weakened in MCF10CA1a showed strong insulation across all cell lines in TNBC. These findings highlight that different model systems indeed have distinct profiles of structural change, just as they have distinct gene expression profiles.

      It is worth noting that direct comparison at individual loci is complicated by variations in gene expression profiles between the MCF10 model and the TNBC progression model; for example, COL12A1 is not significantly upregulated between normal and TNBC tissues in this study (unlike in the TCGA-BRCA data) and is downregulated between HMEC and TNBC cell lines. Regardless, our analysis provides some indication of conserved and divergent features in the various model systems.

      (2) The study remains purely correlative; no perturbation experiments are conducted to demonstrate causal roles of chromatin loops on gene expression. CRISPR interference (CRISPR-Cas9-KRAB/HDAC) or enhancer deletion/inversion should be applied to 3-5 pivotal loops (e.g., COL12A1, WNT5A) to test their impact on target-gene expression and cellular phenotypes (e.g., proliferation, migration).

      We agree that targeted disruption of specific loops such as COL12A1 will be important for understanding the causal relationships between enhancer-promoter loop formation/dissipation and changes in gene expression. However, the intent of our current study was to profile changes in genome organization at a global scale to deduce general features of cancer progression-associated changes in genome organization, rather than exploring specific loop interactions. The current findings are a foundation for more targeted follow-up functional studies.

      (3) The manuscript lacks integration with clinical datasets. Integrate TCGA-BRCA data to assess whether elevated COL12A1/WNT5A expression associates with overall survival (OS) or distant metastasis-free survival (DMFS)

      To assess clinical significance of specific loci, we have queried expression of all differentially expressed genes in the MCF10 progression system among TCGA-BRCA expression data. We summarize our findings in Supp. Fig. 5E and discuss them on page 8.

      We found that roughly 25% of genes that change in our model also change significantly in breast cancer, but only roughly half of those genes change in the same direction (i.e. up-regulated in MCF10CA1a vs MCF10A, and up-regulated in tumor vs normal samples). Interestingly, there was a higher degree of directional agreement between latechanging genes (i.e. genes that change in MCF10CA1a compared to MCF10A and MCF10AT1) than early-changing genes (i.e. genes that change in MCF10AT1 and MCF10CA1a compared to MCF10A).

      We have also explored the impact of select highlighted genes on overall survival (OS). We present these data in Supp. Fig. 6 and discuss it on page 8. While not all genes showcased in this study have a significant impact on overall survival, most trend in the same direction as their differential expression would suggest (i.e. genes more highly expressed in cancer vs tumor also have a hazard ratio above 1).

      Reviewer #3 (Public review):

      The differential topology analysis and its integration with transcription is very well done- one of the best versions of this I have read in the 3D genome field!

      We appreciate the reviewers’ endorsement.

      However, the paper is framed largely as a cancer biology study, and it teaches us much less about this. I am worried that some of the trends for each topologic feature are not going to be consistent across the pre-malignant-malignant-metastatic spectrum and would like the authors to soften some of their claims a bit regarding how this clarifies our understanding of cancer evolution.

      We agree that the strength of the study lies in its deep mapping of chromatin architecture and the landscape of enhancers and differentially expressed genes, which we hope to use to better understand the relationship between chromatin structure and gene expression, regardless of their cancer relevance. To better relate the findings in the progression system to cancer, we have added new data from direct comparisons of the MCF10 progression system with multiple patient-derived cancer cell lines and cancer tissues. These data are shown in Supp. Fig. 3 and 4 and discussed on p. 7. Regardless, we have softened the claims regarding cancer progression throughout the manuscript.

      Weaknesses:

      Major Concerns:

      (1) The integration of gene expression and chromatin loops is intriguing. The authors' differential analysis, however, omits consideration of genes that are on and simply further upregulated versus genes that transition on/off or off/on. It would be nice to see the authors break out looping patterns for these two different patterns of regulation, as it may be instructive regarding the rules for how EP loops govern transcription.

      To address different types of gene expression patterns, we analyzed 108 genes that went from an unexpressed or “off” state (2 or fewer read counts) in one cell line to an expressed “on” state (100 or more read counts) in another, and 111 genes that go from “on” to “high” (1000 or more read counts). We present these data in Supp. Fig. 8 and discuss the findings on page 9. While neither of these genes were enriched for differential loops, a large number overlap with loop anchors. We found a relationship between loop strength and gene expression levels; genes that are more strongly expressed are more likely to overlap with the anchor of a chromatin loop. All gene sets show similar strong trends at distal regulatory regions.

      (2) Given the paucity of differential loops at the majority of genes whose expression changes, the authors should examine chromatin subcompartments, as these may associate more with differential transcription.

      We present subcompartment analysis in Supp. Fig. 9. Our CALDER compartment calls are qualitative rather than quantitative, so to explore this we examined how compartments change genome-wide and at specific promoters. We show these data in Supp. Fig. 9 and discuss the findings on page 10-11. We see that between any two cell types, a majority of changes occur between closely related subcompartments, i.e. from A.2.2 to A.2.1 (1 step more A-like) or B.1.1 (1 step more B-like). The promoters of differentially expressed genes have minimal subcompartment changes, but genes that shift from on to off have larger changes. Differentially expressed genes with promoters that shift by multiple subcompartments have significant impacts on fold-change, but smaller shifts have minimal impacts on gene expression. In summary, small changes in subcompartments are very common and have little impact on gene expression, while larger changes are infrequent and correlate more strongly with changes in gene expression.

      (3) The authors could push their TAD analysis further by integrating it with transcription. Can they look at genes and their enhancers that span these altered boundaries to see if these shifts impact transcription?

      We provide this analysis in Supp. Fig. 9. We started, as suggested, by looking at genes with distal enhancers (as determined by the ABC model) that span a single TAD boundary. However, the number of genes that fit this definition was relatively small, so we expanded to look at any genes with promoters in the proximity (50kb) of differential insulation score boundaries, for which we saw the same trends with more robust signal. Our findings are shown in Supp. Fig. 9 and discussed on page 10. We found that genes near weakened boundaries are not enriched for differentially expressed genes, while those near strengthened boundaries are. Comparing the fold-change of genes near strengthened, weakened, and static boundaries showed a significant inverse correlation between boundary strength and gene expression, although effect sizes were small. These results show that changes in TAD boundary insulation have small but noticeable impacts on gene expression.

      (4) The progression of cancer critically goes from a benign -> pre-malignant -> malignant -> metastatic series of steps. The AT1 line is described as 'premalignant' and thus the authors' series omits a malignant line. While I think adding such a sample is an unreasonable request at this point (as it would have had to have been studied in 'batch' with these other samples), the authors should acknowledge that they omit this step and spend some time discussing the genetic, morphologic, and phenotypic features for their 3 conditions. The images in Figure 1S aren't particularly useful- they don't tell the reader that these cells are malignant/benign. The karyotypic data are intriguing but not fully analyzed, so it is hard to know what true phenotype these cells represent. For example, malignant means DCIS/invasive carcinoma - so then what does this pre-malignant cell model represent? The described alteration in the AT1 line is a Ras oncogene, so in some sense, the transition to this line really is just +/- Ras. The authors could spend some time thinking about the effects of Ras specifically on the 3D genome.

      We have expanded our discussion of the relevance of the MCF10 model on page 4, and the limitations of the model on page 17. The MCF10 progression model has been extensively used by many laboratories, and its properties have been discussed in detail (i.e. Polizzotti et al. 2012). Critically, the MCF10AT1 cell line is the product not only of Ras oncogene expression but then derived from a 100-day-old precancerous lesion that formed a squamous carcinoma in a mouse, and over this time it accumulated additional changes. The MCF10AT1 line is considered pre-malignant as it has accrued critical changes that prepare it for the metastatic transition, but it does not immediately form tumors when injected back into mice. Unlike the MCF10DCIS cell line which is malignant but not metastatic, the more aggressive MCF10CA1a is classified as both malignant and highly metastatic, forming tumors that quickly metastasize to the lungs in mouse xenografts. While both MCF10AT1 and MCF10CA1a are tumorigenic, we acknowledge the lack of a nonmetastatic malignant cell line in the discussion on page 17. We have also provided updated karyotype characterization of the cell lines used in this study in Supp. Fig. 1B and now include full composite karyotypes in the Methods section (page 18).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The reviewer’s recommendations are the same as their public review comments. See our response to the review comments above.

      Reviewer #2 (Recommendations for the authors):

      (1) If conditions permit, it is recommended that inclusion of primary human mammary epithelial cells (HMECs) to distinguish immortalisation-specific from malignancy-specific 3D changes.

      Micro-C data of equal resolution is not available for HMECs. We have, however, incorporated analysis of publicly available deeply sequenced Hi-C data of HMECs into several figures that explore the conservation of loops and TADs in these cells (Supp. Fig. 3 and 4).

      We find that chromatin loops and TAD boundaries detected across the MCF10 system are highly conserved across all other mammary epithelial lines studied. Chromatin loops that were more prominent in MCF10AT1 and MCF10CA1a lines were also significantly stronger in TNBC cells. Insulation score boundaries that were weakened in MCF10CA1a showed strong insulation across all cell lines in the TNBC system. These findings highlight that different model systems indeed have distinct profiles of structural change, just as they have distinct gene expression profiles.

      (2) The relationship between loop alterations and copy-number variations (CNVs) is not explored. If conditions permit, it is recommended that overlay differential loops with SNP/Indel/CNV data to exclude spurious differences arising from structural alterations.

      While we have not conducted an in-depth SNP analysis, we have clarified our discussion of the karyotype analysis on pages 21 and 23 and how we mitigated these effects when identifying differential loops between cell lines.

      (3) The horizontal and vertical coordinates of the diagram are difficult to view; it is recommended that the size of the text on the picture be adjusted to ensure that it is clear to read. Some of the text coordinates of the figure are labeled in gray; it is recommended that they be in black.

      The clarity of the figures has been improved.

      Reviewer #3 (Recommendations for the authors):

      I really like this paper. I think if the cancer focus can be down-emphasized (because I'm not fully clear what we've really learned about cancer), then it represents a nice dataset and a thoughtful, comprehensive analysis.

      We greatly appreciate the kind words and helpful feedback. The cancer focus has been toned down throughout the manuscript, as suggested.

      Minor Concerns:

      (1) The authors present a nice summary of the topological changes across samples. However, summary statistics can mask noise/bias and also don't fully convey the effect size of the reported changes. Highlighting individual loci and visualizing these would strengthen the paper and participate in maintaining a high standard for our genomic studies of topology, in which we summarize, but also provide representative examples. I would appreciate seeing more example plots at distinct loci (even if in the supplemental information).

      We have included several more example regions in Supp. Fig. 7 and 12, including four looped genes that change similarly between the MCF10 series and TCGA-BRCA data (2 stably looped genes and 2 differentially looped genes, 2 up-regulated and 2 downregulated), and six differentially looped and differentially expressed genes (3 which change in the same direction as the loops, and 3 which change in the opposite direction).

      (2) "To identify loops that changed significantly during cancer progression, we assessed changes in contact frequency among every loop in each cell type, correcting for karyotypic differences that result in differences in coverage between cell lines (see Methods)." The Methods section is not adequately explained. Also, could you go a bit deeper to define if these large-scale changes shift the 3D genome specifically? This is hard, but there may be some low-hanging fruit given the otherwise fairly isogenic features in your model.

      We have added more detail to the Methods section on pages 21 and 23 on how karyotypic abnormalities were included in our analysis and differential loop calling. A deeper analysis of how large-scale karyotypic changes affect chromatin organization (i.e. through the formation of neoloops and TADs through translocations) is indeed an attractive subject, but due to its complexity requires a separate dedicated study.

      (3) "Approximately half of chromatin loops featured some combination of active gene promoters and enhancers within 10kb of loop anchors". The authors have high-resolution topology data and should be more stringent; these features should have to overlap loop anchors or at least use a distance less than 10kb, which, in some sense, forfeits the advantages of high-resolution topology data.

      The threshold of 10kb was chosen for several specific reasons: First, the loop sizes detected here are large enough that this relatively large region still represents a small fraction of the loop span, and these regions are reasonably considered anchor-proximal. Second, the loops we detect are non-punctate, both in aggregate analysis (Figure 1H, bottom) and at individual loci (see example regions), showing increased contact frequency among several 5kb or 10kb bins. Therefore, adding 10kb to either side (2 pixels on 5kb maps and 1 pixel on 10kb maps) ensures that the full region of increased contact frequency is included. Finally, ultra-resolution Hi-C data has also shown that loops remain diffuse even with 1kb resolution maps (albeit they do get smaller than the 30kb used here) (Harris & Gu 2023). We have added a brief justification of this overlap size to the text on page 24.

      (4) "These results show that not only changes in either contact frequency and enhancer activity correlate with increased gene expression, but they also correlate with each other, suggesting a potentially linked functional role during enhancer-promoter communication." The authors could use this opportunity to disentangle the contributions of loops and chromatin modifications a bit more. The exceptions are of interest - e.g., loop is stable, gene expression changes or loop changes, gene expression does not. Highlighting exemplar cases for these exceptions (rather than just a genomics summary) would be nice to see.

      The additional example regions we have included in Supp. Fig. 7 and 12 now showcase a wider variety of scenarios; in addition to more examples of static loops with gene expression changes (Fig. 2, Supp. Fig. 7E-F) and differential loops with matching gene expression changes (Fig. 4, Supp. Fig. 7C-D, Supp. Fig. 12A-C), we now also feature examples of differential loops where gene expression changes in the opposite direction (i.e. a strengthened loop at a down-regulated gene, Supp. Fig. 12D-F).

    1. I started undoing the 'participatory' design plans I unilaterally made to reconceive acollective methodology with more uncertain, voluntary, and relational dynamics. Surprisingly, this'ineffective' ongoing turn became a strength rather than a limitation—

      No plan is unilateral, we are a conduit of past relationships, of people who have influenced us, and we acknowledge this so much that we allow the transference of autonomy through "differently abled" people guardians, stewards of nature, animal caretakers, and political representatives.

      What Volpi is looking for without stating is a sustainable equalised economy where there are no power monopolies and notable hierarchies that may lead to oppression. But to say that "inefficiency" is a "strength" unkowingly perpetuates those oppressive structures, because this "inefficiency" is almost exclusive of wealthy people. Volpi's language is colonised, as they probably don't realise this.

      Say they get involved in an actually slow process, one where they don't propose, but wait for others to ask, one, like an ethnography, where they learn and listen and don't try to impose themselves and their ideas because that is the productivist system that academia perpetuates... then the group they end up in will either be a marginally small group of outcast people, or privileged (or both), with minimal potential impact for change; or they will end up in a bigger already existing association where they in a way "inflitrate" and only over multiple years start to achieve trust capital to push their ideas (having also taken some others' in order to claim epistemic humility and a certain representativeness).

      Let's see... how do I spell this? We must not condone infinite growth, but when it comes to things like ending poverty, I think our stance should be unambiguously clear that this is progress, that this is positive.

    Annotators

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This manuscript addresses an important methodological issue-the fragility of meta-analytic findings-by extending fragility concepts beyond trial-level analysis. The proposed EOIMETA framework provides a generalizable and analytically tractable approach that complements existing methods such as the traditional Fragility Index and Atal et al.'s algorithm. The findings are significant in showing that even large meta-analyses can be highly fragile, with results overturned by very small numbers of event recodings or additions. The evidence is clearly presented, supported by applications to vitamin D supplementation trials, and contributes meaningfully to ongoing debates about the robustness of meta-analytic evidence. Overall, the strength of evidence is moderate to strong.

      Strengths:

      (1) The manuscript tackles a highly relevant methodological question on the robustness of meta-analytic evidence.

      (2) EOIMETA represents an innovative extension of fragility concepts from single trials to meta-analyses.

      (3) The applications are clearly presented and highlight the potential importance of fragility considerations for evidence synthesis.

      Reviewer #3 (Public review):

      (1) The manuscript would benefit from a clearer explanation of in what sense EOIMETA is generalizable. The author mentions this several times, but without a clear explanation of what they mean here.

      This is a point I was remiss not to better elucidate. With regards to generalisation, the text has been modified to explicitly state that generalisability in this context means no specific study dependence, just a net number of subjects required to flip a result. The text reads:

      “Atal's method is highly useful, but one possible objection is that it has the downside of non-generalisability, as it finds very specific combinations of trials and patients that would have to be re-coded (events classified as non-events and vice-versa) for results to become insignificant. For example, an Atal meta-analytic fragility of 4 pertains to a specific and often unique circumstance when 4 patients could be recoded from a specific study or combinations thereof to change outputs, but this does not generalise to any 4 patients in that meta-analysis. This makes this definition of meta-analytic fragility useful but not general, and perhaps less intuitive to interpret than a typical RCT fragility metric. In this work, we establish a generalizable meta-analytic fragility metric, based upon Ellipse of Insignificance (EOI) analysis for dichotomous outcome trials. This method creates a pool of events and non-events in both arms, adjusted for weighing, and answers the general question of how many patients would have to be effectively recoded in a meta-analysis for results to flip, without requiring specific study identification.”

      (2) The authors mentioned the proposed tools assume low between-study heterogeneity. Could the author illustrate mathematically in the paper how the between-study heterogeneity would influence the proposed measures? Moreover, the between-study heterogeneity is high in Zhang et al's 2022 study. It would be a good place to comment on the influence of such high heterogeneity on the results, and specifying a practical heterogeneity cutoff would better guide future users.

      This is a very fair observation, and I need to better explain myself here! So there are effectively two measures of heterogeneity considered in this work; the typical value from a meta-analysis and the measure of divergence between the crude and the inverse-variance weighed adjusted – when these differ my small amounts, one could conceivably use either measure. I’ve changed the text to better reflect this, including:

      “This modification in akin to pooled in a meta-analysis, and adjusts for study level heterogeneity. After this modification, a standard EOI analysis can then be applied to the vector . In addition, we can also employ ROAR analysis to the same vector, yielding the raw number of patients in either or both arm who could be added a given direction to change the result, and exact combination of control and experimental group redactions required to change the result from a significant finding to a null one. Caveats for implementation and interpretation are outlined in the discussion section.”

      (3) I think clarifying the concepts of "small effect", "fragile result", and "unreliable result" would be helpful for preventing misinterpretation by future users. I am concerned that the audience may be confusing these concepts. A small effect may be related to a fragile meta-analysis result. A fragile meta-analysis doesn't necessarily mean wrong/untrustworthy results. A fragile but precise estimate can still reflect a true effect, but whether that size of true effect is clinically meaningful is another question. Clarifying the effect magnitude, fragility, and reliability in the discussion would be helpful.

      This is an excellent suggestion – I’ve tried to do it with percentages, as in table 2, but these are minute in the case of the vitamin D trials, partially I suspect because they are extraordinarily weak. The Cohen’s H for these meta-analyses yields tiny values, which I think might be tied to the virtually negligible percentages we obtain for number needed to flip. With stronger data, it might be worth expanding this into a useful heuristic measure for robustness, though I don’t think vitamin D data as in this work is going to help us much. In light of the reviewer’s excellent comment, I added the following:

      In light of the reviewer’s excellent comment, I added lines 230-240 in the revised manuscript.

      (4) Comments on revisions:

      I am unable to find the author's responses to my previous round comments (Reviewer #3) in the revision package, though replies to the other reviewers are present. I will provide my updated feedback once these responses are available for review.

      My sincere apologies, I neglected the specific comments in error – this document should address them now, thank you again for giving this your time and consideration!

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Fogel & Ujfalussy report an extension of a visualization tool that was originally designed to enable an understanding of detailed biophysical neuron models. Named "extended currentscape", this new iteration enables visual assessment of individual currents across a neuron's spatially extended dendritic arbor with simultaneous readout of somatic currents and voltage. The overall aim was to permit a visually intuitive understanding for how a model neuron's inputs determine its output. This goal was worthwhile and the authors achieved it. Their manuscript makes two additional contributions of note: (1) a clever algorithmic approach to model the axial propagation of ionic currents (recursively traversing acyclic graph subsections) and (2) interesting, albeit not easily testable, insights into important neurophysiological phenomena such as complex spike generation and place field dynamics. Overall, this study provides a valuable and well-characterized biophysical modeling resource to the neuroscience community.

      Strengths:

      The authors significantly extended a previously published open-source biophysical modeling tool. Beyond providing important new capabilities, the potential impact of "extended currentscape" is boosted by its integration with preexisting resources in the field.

      The code is well-documented and freely available via GitHub.

      The author's clever portioning algorithm to relate dendritic/synaptic currents to somatic yielded multiple intriguing observations regarding when and why CA1 pyramidal neurons fire complex spikes versus single action potentials. This topic carries major implications for how the hippocampus represents and stores information about an animal's environment.

      Weaknesses:

      While extended currentscape is clearly a valuable contribution to the neuroscience community, this reviewer would argue that it is framed in a way that oversells its capabilities. The Abstract, Introduction, Results, and Methods all contain phrases implying that extended currentscape infers dendritic/synaptic currents contributing to somatic output., i.e. backwards inference of unknown inputs from a known output. This is not the case; inputs are simulated and then propagated through the model neuron using a clever partitioning algorithm that essentially traverses a biologically undirected graph structure by treating it like a time series of tiny directed graphs. This is an impressive solution, but it does not infer a neuron's input structure.

      We are sorry if our text could be interpreted as if we were inferring unobserved inputs from the known outputs. This was not intentional and we were unaware of the possibility of such interpretation.

      In fact, at the beginning of the Results, we started the description of the extended currentscape method by explicitly stating that we need to measure the input currents: “Our method … requires measuring the membrane and axial currents throughout the dendritic tree of a neuron (in every node of the circuit)”.

      To further clarify that our method starts with measuring the input currents, we made this information explicit already in the abstract (“Our approach relies on the iterative decomposition of the axial current flowing between neighbouring compartments in proportion to the underlying membrane currents measured in the model.”), and in the Introduction (“Even if the membrane currents are known, studying the impact of particular ion channels on the neuronal response in such a dynamical system under in vivo conditions is hindered by two major obstacles”). We also rewrote several parts of the text to remove any phrases that could imply the inference of the inputs (line 568). We believe that after clarifying this at the beginning of the paper, the readers will not misinterpret our descriptions later in the text.

      Because a directed acyclic graph architecture is shown in Figure 2, it is unintuitive that the authors can infer bidirectional current flow, e.g. Figure 3 showing current flowing from basal dendrites and axon to soma, and further towards the apical dendrites. This is explained in Methods, but difficult to parse from Results amidst lots of rather abstract jargon (target, reference, collision, compartment). Figure 2 would have presented an opportunity to clearly illustrate the author's portioning algorithm by (1) rooting it in the exact morphology of one of their multicompartmental model neurons and (2) illustrating that "target" and "reference" have arbitrary morphological meanings; they describe the direction of current flow which is reevaluated at each time step.

      We thank for this comment. We agree that the concepts introduced here to explain our method are rather abstract and could be difficult to understand. To help the reader we followed the instructions of Reviewer and redesigned Fig. 2 to provide a step by step explanation of the extended currentscape method. In particular,

      We used a simpler model where the structure of the graph can be directly related to the morphology of the model.

      We show that the target node can connect multiple subtrees with axial currents flowing in different directions. We explain that in this case the inward and the outward subtrees are pruned and partitioned separately.

      We provide a glossary in Table 1 to ensure that the readers can follow our description and do not get lost amidst lots of rather abstract jargon.

      We also clarified that although the target compartment is chosen arbitrarily by the user, it remains the same for all time points throughout the analysis.

      Analyses in Figure 7, C and D, are insightfully devised and illuminating. However, they could use some reconciliation with Figure 5 regarding initiation of individual APs versus CSBs within place fields.

      We thank the reviewer for the positive comments and also for pointing out the potential source of misunderstanding. We slightly changed the text at Fig 5 to emphasize that this is a single example trial, and we added the following sentence to the paragraph describing Fig 7CD: “Consequently, the somatic current dynamics before the iAP and the CSB presented in Fig 5Cc-Dd can be regarded as illustrative samples from a broad distribution, but the differences observed between them are not representative.}”

      The intriguing observations generated by extended currentscape also point to its main weakness, which the authors openly acknowledge: as of now, no experimental methods exist to conclusively tests its predictions.

      We agree with the Reviewer that not being able to apply our extended currentscape method to reveal the current types driving real neurons recorded in vivo is currently a weakness of our approach. However, we would like to emphasize that it may be feasible to use it to estimate the spatial distribution of the membrane currents driving the cell based on in vivo voltage imaging data, as we briefly outline in the discussion.

      Reviewer #2 (Public review):

      Summary

      The electrical activity of neurons and neuronal circuits is dictated by the concerted activity of multiple ionic currents. Because directly investigating these currents experimentally isn't possible with current methods, researchers rely on biophysical models to develop hypotheses and intuitions about their dynamics. Models of neural activity produce large amounts of data that is hard to visualize and interpret. The currentscape technique helps visualize the contributions of currents to membrane potential activity, but it's limited to model neurons without spatial properties. The extended currentscape technique overcomes this limitation by tracking the contributions of the different currents from distant locations. This extension allows tracking not only the types of currents that contribute to the activity in a given location, but also visualizing the spatial region where the currents originate. The method is applied to study the initiation of complex spike bursts in a model hippocampal place cell.

      Strengths.
>

      The visualization method introduced in this work represents a significant improvement over the original currentscape technique. The extended currentscape method enables investigation of the contributions of currents in spatially extended models of neurons and circuits. 
>

      Weaknesses.

      The case study is interesting and highlights the usefulness of the visualization method. A simpler case study may have been sufficient to exemplify the method, while also allowing readers to compare the visualizations against their own intuitions of how currents should flow in a simpler setting. 
>

      We thank the reviewer for this comment. In fact we had been also considering to include a simpler case study to illustrate the extended currentscape method in the original submission. In accordance with the comments from Reviewer 1, we now use a simple model to introduce the concepts in Figure 2 and provide a few examples where the reader can compare the results with their own intuition in simpler cases.

      Recommendations for the authors:

      Reviewing Editor Comments:

      (1) Model complexity vs. intuition/validation. The case study relies on a very complex CA1 model, making it difficult to build intuition about current flow and to validate the visualization. Inclusion of a simpler benchmark (e.g., soma plus a dendrite with two branches, fewer compartments) is recommended to demonstrate how the extended currentscape behaves in a more tractable setting.

      Inspired by the suggestions of the Reviewers, we modified Figure 2 and now first use a simple model with a soma and a dendrite with two branches to introduce the concepts of our analysis. We start with a few examples where the reader can compare the results with their own intuition in simpler cases.

      (2) Rationale and citations for input structure. The in vivo-like input design (untuned inhibition; 12 co-tuned excitatory clusters with large conductances; the goal of generating place fields) would benefit from a more explicit rationale and substantially more literature support. Alternative plausible scenarios (e.g., distributed co-tuned inputs and homosynaptic plasticity) should be articulated, and choices situated within the experimental literature on CA1 excitation/inhibition, including tuning and anti-tuning results.

      We extended the paragraph in the Results describing the input structure and added the most important references there. We added further references to the Methods section where we argue that “Reliable place cell tuning can be achieved by functional synaptic clustering without increased excitatory drive in the place field (Ujfalussy and Makara 2020) or via strong excitatory drive without input clustering (Grienberger et al., 2017, Ujfalussy and Makara, 2020). However, experimental data indicates that both of these mechanisms are present and contribute to the activity of place cells (Adoff et al., 2021,Tasciotti et al., 2025)” and “although interneurons can display spatial tuning, they typically have a broad tuning with low selectivity (Ego-Stengel et al., 2007, Dupret et al., 2013, Geiller et al., 2020). A weak disinhibition within the place field can also contribute to the selective firing of place cells (Geiller et al., 2022, Valero et al., 2022), this was not necessary for place cell activity in novel environments (Geiller et al., 2022) and the overall inhibitory input to place cells is largely untuned (Grienberger et al., 2017).”

      (3) Scope of PCA-based claims. The interpretations derived from the PCA analysis appear broader than warranted, given subcellular heterogeneity and the dominance of somatic action potential variance. These claims should be tempered with more explicit statements about what PCA can and cannot resolve in this context.

      We thank the Reviewer for the opportunity and encouragement to clarify this part of the text. We agree with the Editor and the Reviewers that the results of the PCA analysis can not be used to support claims regarding the presence or the absence of independent dendritic events. In fact, we aimed to use it as an illustration that global activity tends to dominate PCA analysis even when the “neuron is mainly driven by strong, functionally clustered synaptic inputs to a few dendritic branches”. We acknowledge that we did not formulate this point clearly in the original submission. Therefore we substantially rewrote this part of the Results and performed additional analysis to clarify that there is a substantial amount of soma-independent dendritic activity in our model that remains invisible for a PCA based analysis.

      Reviewer #1 (Recommendations for the authors):

      Major concerns:

      (1) Depolarization-inactivated K+ may be an important consideration to model burst-firing.

      Our current model includes 2 kinds of transient K+ channels that show inactivation after depolarization: a proximal and a distal type, as the original model in Jarsky et al., 2005. We now made this explicit in the main text (line 178).

      (2) Description of the in vivo-like model's excitatory and inhibitory input structure needs many more citations of biological studies to communicate rationale for the author's decisions, e.g. untuned inhibitory neurons, organization of a subset of excitatory inputs into 12 function synaptic clusters with co-tuned presynaptic neurons and outsized synaptic conductances. The goal is clearly to create CA1 pyramidal neurons with place fields, which would be helpful to state upfront. But additionally, (a) place fields could arise from homosynaptic potentiation of distributed co-tuned excitatory inputs (e.g., Bittner, et al. 2017 study describing BTSP made no assumptions) and (b) CA1 inhibitory interneurons can be spatially tuned (Ego-Stengel & Wilson, 2006; Wilent & Nitz, 2007; Geiller, et al. 2020) and even anti-tuned (Geiller, et al. 2021).

      We thank the Reviewer for pointing out the lack of appropriate references in this section. We made the following changes in the manuscript:

      (1) Stated explicitly that the goal was to create place cell activity.

      (2) Added references to the main text to justify our choices of the inputs (lines 234-241).

      (3) We included a longer rationale for the choice of synaptic clusters and the lack of inhibitory (anti-)tuning in the Methods section, describing the neuron model. In brief, Adoff et al., 2021 reported more clustering of excitatory inputs within the place field. In our model, the degree of clustering is somewhat larger than the clusters reported. Although inhibitory neurons can be tuned, their tuning is much weaker than that of place cells and seems to play only a minor role in the generation of place fields (Grienberger et al., 2017). The presence of inhibitory anti-tuning is controversial: although Geiller et al., 2021 reported weak (~10%) anti-tuning, they did not find it in novel environments, indicating that it is not needed for spatially selective activity (lines 628-646).

      (3) Interpretation of principal component-based analyses shown in Figure 4 could be toned down. As written in section "CSBs in the CA1 pyramidal neuron", it sounds like CA1 pyramidal neuron dendrites display minimal autonomous activity. However, PCA does not seem well-suited to address the heterogeneity of subcellular voltage dynamics over physiologically relevant timescales. Somatic action potentials, and their backpropagation/modulation of dendritic voltage, would of course explain a very large fraction of variance. However, if local dendritic events summate over fine timescales to initiate somatic firing, it is hard to imagine this important nuance being detected. On the other hand, it is hard to imagine single dendritic branches driving robust somatic firing except in the relatively extreme situation in which large numbers of synapses synchronously drive the same branch to initiate a local Ca2+ spike (Figure 3, A-C).

      We agree with the reviewer that PCA can not reveal the potential dendritic origin of somatic APs, and thus is not suitable to assess the role of local dendritic spikes in shaping the output of the cell. We wanted to highlight here that even in cells with excitable dendrites driven by strong, local input clusters, exhibiting frequent local dendritic spikes, the dendritic membrane potential dynamics will be dominated by global fluctuations with surprisingly little sign of local dynamics in the PCA components. As the reviewer also pointed out, this may not be surprising as local events either remain spatially restricted and thus contribute little to the overall variability of the dendritic Vm or they initiate somatic APs and will thus be counted as global events.

      To demonstrate the high propensity of local dendritic events, we analysed local Vm peaks in dendritic branches and found that ~7.6% of the peaks were not coupled to somatic APs.

      Although this number could seem low, we emphasize that most of the 92.4% of the dendritic peaks coupled to APs potentially reflect the backpropagation of the same somatic events to multiple dendritic sites. To confirm this, we performed an additional analysis measuring the spatial extent (number of branches involved) of the individual dendritic events. We found that 90% of the events remained local, restricted to a few dendritic branches, while 10% of the events were global, associated with BAPs and involving the majority of the dendritic tree. Interestingly, these global events dominate the PCA analysis and are responsible for >90% of the dendritic Vm peaks. These results are included in a new panel in Figure 4H.

      We conclude that, “this way, although only 10% of the dendritic Vm events were associated with bAPs, they were ~60-times larger than local events and they dominated the PCA analysis even in the presence of local regenerative dendritic events driven by strong, functionally clustered synaptic inputs.” We believe that this model and analysis could serve as an important benchmark for future experimental studies investigating the structure of membrane potential correlations in in vivo voltage imaging data (Lee et al., 2026).

      (4) One suggestion would be to display more data as shown in Figure 4F, with a longer X axis to clarify the temporal relationship between local dendritic spikes and the first somatic action potential.

      We added a few more examples including the CSBs presented in Fig8G-I as a new supplementary Figure S4. We also slightly extended the x-axis on this supplementary figure as the reviewer requested.

      If the models indicate that passively filtered EPSPs drive most somatic action potentials, as seems to be the case in Figure 5, then this would also be helpful to show as in Figure 4F.

      In Fig 5 we showed two examples of isolated APs. The first AP was indeed driven by passively filtered EPSPs. The second one was preceded and possibly caused by a dendritic spike, as highlighted by the black arrowhead labelled c in Fig. 5Cc. We further analysed the currents driving iAPs in Fig 7B and C, and found that there is considerable heterogeneity in the magnitude of the dendritic Na currents driving the soma before action potentials. Figure 8 and Figure S3 (now Fig. S5) show further examples for iAPs driven either by passively filtered EPSPs or dendritic spikes. We also included these examples in the new supplementary Figure S4.

      (5) Another suggestion would be to use one-hot vectors containing onset times of different event types, since this would divorce the amplitude/duration of events from their influence over total variance.

      In this paper our goal was to illustrate the ability of the extended currentscape method to reveal the origin of the axial currents driving neuronal activity. In Fig. 4, our primary intention was to characterize the membrane potential response of the model in a way that is easily comparable with experimental data. To further quantify the frequency of local events, we added a new panel showing the spatial extent of dendritic events (Fig. 4H). To make our model more comparable with recent publications, we also calculated two additional metrics used to evaluate the relationship between somatic and dendritic activity (Fig 4I-J). We hope that these additional analyses help the reader to characterize the prevalence and impact of local dendritic events on somatic activity.

      (6) From section "Input conditions for complex spike burst generation", paragraph 2: "Note that synapse density, the ion channel mechanisms and the input statistics are identical for tuft and oblique branches,...". The authors should justify this parameterization given the numerous known differences between tuft and oblique branches in both of these regards and acknowledge accompanying interpretational caveats.

      We agree with the reviewer that experimental data demonstrated several significant differences between the tuft and oblique branches regarding both the inputs they receive and the way they process it. However, in the present paper we chose not to include these differences for several reasons:

      Here we aimed to focus on the abilities of the dendritic currentscape methods and use CSBs as a case study to illustrate how dendritic currentscape can reveal the membrane currents underlying complex neuronal responses.

      Currently there is no CA1PN model that would be able to reproduce all data regarding tuft and oblique integration and would be able to fire calcium spikes. We only wanted to make minimal modifications to the existing CA1PN model to make it capable of generating Ca-spikes and CSBs. We are currently working towards developing and extensively testing a new model, examining the role of these regional differences in CSB generation.

      Although there is information regarding input statistics and dendritic physiology in the literature, many of the relevant parameters are underconstrained. We wanted to avoid overfitting by keeping the model simple.

      By maintaining identical inputs and ion channel distribution we can distinctly highlight the special role of tuft morphology in CSB generation. Altering the inputs or the ion channel density for the tuft would make the interpretation more ambiguous, and elucidating the specific role of the different factors in CSB generation is the subject of future investigations.

      In sum, although we acknowledge that our model does not reflect the full complexity of CA1 PNs and its inputs, we regard this simplicity as a useful feature of the model. We added a section discussing potential future extensions of the model and highlighting interpretational caveats in the discussion (lines 482-490).

      (7) Given the debate in the field regarding the level of functional autonomy present in dendrites, the authors' finding that dendritic voltage largely tracks that of the soma (though see concern above re: PCA), and their access to specific currents, the authors have an important opportunity investigate the divergence between Ca2+ and voltage sensors as reporters of dendritic activity.

      For instance, why have some studies reported relatively common isolated dendritic Ca2+ transients in CA1 pyramidal neurons while other studies, including voltage imaging studies, have reported the opposite?

      We thank the Reviewer for the opportunity to highlight a few important points regarding functional autonomy of dendrites based on the analysis of our model. We would like to first note that only parallel calcium and voltage imaging studies will be able to ultimately resolve this debate. Nevertheless, below we briefly summarize our take on this issue.

      (1) In general, most Ca2+ imaging studies found that soma-independent dendritic events are rare. "Isolated dendritic transients (no coincident somatic event; see fig. S6, C and D, for example) were overall rare. Isolated apical dendritic Ca2+ transients, which have not previously been reported in CA1PNs, were larger and more frequent than those observed in basal dendrites." (O’Hare et al., 2022). "Activity in the ... basal dendrites ... along the track but outside of the place field was rarely observed” (Sheffield and Dombeck, 2014) and “overall, isolated dendritic transients were similar in size but occurred far less frequently than coincident dendrite-soma transients”, or “data indicate that spatially reliable dendritic firing was almost exclusively yoked to somatic tuning, likely reflecting strong backpropagation of burst firing during traversals of the somatic PF” (Rolotti et al., 2022). Consistent with this observation, a dendritic Vm peak chosen randomly from any branch has ~93% probability to be related to a bAP in our model. However, it is also true that ~90% of events in the model are local events, simply because isolated events involve ~60-times fewer branches (1.8 on average) than events associated with bAPs (114 branches) in the model. If the spatial extent of typical local events are also similarly small in real neurons as in the model, then even rare occurrences of dendritic events may reveal substantial dendritic independence. We added a section quantifying the functional autonomy of dendrites in the model in the main text, around Fig 4H.

      (2) Ca2+ indicators are slower and nonlinear and thus they are somewhat unreliable reporters of dendritic voltage events, especially in distal dendrites (Wu et al., 2026; Gonzalez et al., 2026). To illustrate this, we calculated three metrics in our model that were also reported in recent dendritic Ca2+ imaging studies (Rolotti et al., 2022, Sheffield et al., 2014, 2017). First, we calculated the fraction of bAPs detected in a branch (called dendrite-soma coupling in Rolotti et al., 2022, see their Fig. 2C) as a function of the distance of the branch from the soma (our new Fig. 4I). In the Ca2+ imaging data, this was essentially constant ~30% between distances 5-100 µm from the soma. In contrast, the fraction of bAPs detected in the model was 100% in this range as bAPs propagation failures did not occur before µ100 µm. This is also consistent with a recent voltage imaging study showing that even low-transmission bAPs reliably propagate to the proximal dendrites (Lee et al., 2026, Fig 3G). The low and distance independent dendrite-soma coupling reported by Rolotti et al. can only be reconciled with the known biophysics of neurons if the recorded calcium signal is unreliable reporter of the underlying voltage. Indeed, it has been reported that Ca signals associated with bAPs can be absent in some dendritic branches (Landau et al., 2022) or that local, nonlinear Ca signals can appear in the absence of local regenerative voltage response (Weber et al., 2016, Tran-Van-Minh et al., 2016) and that the Ca signals are highly variable across cells (Eltes et al., 2019).

      Second, we calculated the fraction of local events as a function of the distance from the soma (our Fig 4J; see also Fig. 2F in Rolotti et al.). When averaged across all branches, this was somewhat lower in the model (18%) than in the data (38%) which, again, could be explained by the low reliability of detecting global voltage events in all compartments based on the calcium signal.

      Third, the range of branch-spike-prevalence (BSP) values in our model (0.5-0.9; Fig. 4H) seem consistent with that reported (0.4-0.8) at first (Fig 4C of Sheffield et al., 2014; Fig 2 of Sheffield et al., 2017). However, we note that there are several important differences: for technical reasons, Sheffield et al. reported BSP for place field traversals and not for individual events, and they measured Ca2+ dynamics in the basal dendrites. Since bAPs are almost always present in all basal dendrites in the model (basal BSP > 0.9 for all events with somatic spikes) and place field traversals were always accompanied by somatic APs, BSP for basal dendrites would be nearly 1 in the model. Thus, the lower BSP values reported by Sheffield et al. could be explained by the limited reliability of the Ca2+ indicators in reporting regenerative voltage events in neuronal processes.

      We briefly discussed these differences in the Discussion (lines 474-478).

      (3) Finally, to our knowledge, there are 3 relevant in vivo voltage imaging studies in CA1 PNs. Liao et al., 2024 found that in induced place cells the tuning of dendritic events (presumably local or back-propagating Na-spike) was similar to the somatic tuning, which is consistent with our model where dendritic activity and tuning is dominated by bAPs. However, they did not acquire simultaneous signals from the dendrites and the soma so they could not study the independence of the dendritic events. Lee et al. (2026) found that only 10% of the dendritic events are not associated with a somatic spike, which is lower than the number of independent events in the model. However, the events they found were generated in the distal apical trunk (their Fig 3D) and they could not record from the most distal branches where most of the isolated events were generated in our model. Gonzalez et al., 2026 measured voltage and calcium in selected locations within the dendritic tree, and could not reliably estimate the fraction of isolated events throughout the cell. (Gonzalez et al, 2024 measured voltage only in single spines and soma, but did not quantify independent dendritic events; Wong-Campos et al., 2023 measured dendritic integration and bAPs in L23 branches; Wu et al. 2026 recorded in CA2 neurons.)

      We added a paragraph in the discussion comparing the level of functional autonomy present in the model dendrites to recent Ca- and voltage-imaging studies (lines 467-474).

      Minor concerns:

      (1) Abstract:

      There is a need to explain what currentscape is - even at the cost of not invoking its name. To a reader not familiar with currentscape, the abstract is extremely difficult to understand.

      We reworded the title and the abstract to make them more accessible to readers not familiar with the term currentscape.

      (2) "Currentscape analysis of place field dynamics" section:

      It would be helpful to emphasize upfront that dendritic determinants of individual somatic APs versus CSBs will be discussed separately. Since somatic action potentials are discussed before CSBs, I found this section initially confusing as I attributed those findings to CSBs until reading the next paragraph.

      We added a sentence to clarify that we analysed subthreshold responses, APs and CSBs separately.

      (3) Bottom of p2 discussing mixed literature on what drives CSBs in CA1 PCs:

      Overall accurate and useful point, but an important nuance is glossed over which misportrays state of field. References ex vivo studies that fail to drive CSBs with somatic current injection and in vivo study successfully doing so. These aren't really conflicting results. In vivo current injection co-occurs with spontaneous synaptic input, which is high in CA1 and results in PCs that are significantly depolarized at rest relative to those in acute slices. Bittner 2017 ex vivo results are consistent with this: CSBs driven by Cs+-based internal solution to block K+ channels (partially, using strategy of purposefully high series resistance). Similar situation in vivo given that A-type K+ channels are inactivated by depol. Resulting increase in input resistance lowers input threshold to CSB. This is clarified in Results, p.5: "Under in vivo-like synaptic input conditions (see below and Methods), dendritic Ca2+-spikes could also be evoked by somatic current injection (Fig. S1E), as in Bittner et al. (2015).", which makes p. 2 feel especially awkward.

      We agree with the Reviewer that these are not necessarily conflicting results. We rephrased this section, emphasizing that the role of the different input pathways in the initiation of CSBs are not clear.

      (4) Abbreviating "pyramidal neuron" with PC is confusing:

      PC often means place cell. The authors could change this, such that PC refers to "pyramidal cell", or else use PN as an abbreviation. It is important to avoid confusion, especially because place cell dynamics feature prominently in the manuscript.

      Thanks for the suggestion. We replaced PC with PN throughout the manuscript.

      (5) Only apical dendritic parameters are described in section 2 of Results, but the full morphology is shown in Figure 3B with basal currents shown in panels C and F. Some clarification is needed - either what currents were considered for basal dendrites and why, or else why basal dendritic current parameters were not considered for this simulation using apical dendritic current injection but nonetheless examining basal dendritic currents.

      We clarified in the text that the original model contained a standard set of Na and K channels (line 178).

      (6) Clarify "i" and "s" in the Figure 3C legend - "intrinsic" and "synaptic" white letterings are small/hard to see in the bottom subpanels.

      We now spell out intrinsic and synaptic in the Figure and increased the contrast of the letterings.

      (7) Regarding the computational benefit of recursively decomposing axial currents along an adaptively truncated acyclic graph, it would be useful to (a) include a supplemental figure benchmarking this approach to standard approaches to quantify the described gain in computational efficiency and (b) describe computing hardware in the Methods.

      We included an estimated benefit of the pruning process (line 758) as well as the utilised computing hardware and the simulation times in the Methods (line 776).

      Reviewer #2 (Recommendations for the authors):

      The manuscript is in great shape, it is well organized, and the figures are gorgeous. I believe that the extended currentscape is a great extension of the original currentscape method. In particular, the possibility of partitioning currents by the spatial location of their sources is a great addition. 
>

      Recommendations:

      (1) The method is applied in the context of an interesting case study that highlights its usefulness. However, the model in the study is so complex that it is difficult to develop an intuition of how currents should be flowing, and this makes it hard to intuitively validate the visualization method. I think that applying the extended currentscape in a simpler model - maybe a soma with a dendrite with two branches, fewer compartments - would be instrumental in developing this intuition. 
>

      We now first use a simple model with a soma and a dendrite with two branches to introduce the concepts in Figure 2 and provide a few examples where the reader can compare the results with their own intuition in simpler cases. We also added the currentscape analysis of a standard, two-compartmental model from Pinsky and Rinzel, 1994 as Supplementary Figure 1.

      (2) I found a number of typos and minor stylistic details you may want to fix in a revised version of the manuscript.

      (a) Abstractine, line 12. I believe the word "recursive" is a bit technical at this point. It's meaning in this context becomes clear after ones goes through the details of the algorithm (Figure 2). 
>

      We replaced the word “recursive” with “iterative”. We hope that this will make the abstract clearer for the readers. In fact, we realized that the word iterative is a better description of the algorithm, so we replaced the “recursive” with “iterative” consistently throughout the manuscript.

      (b) Figure 1, caption."Since we included the capacitive current, the magnitude of the inward and the outward currents is identical (Kirchhoff's law)."This sentence can be confusing. If the inward and outward currents are the same, the membrane potential doesn't change. I believe that you are including the capacitive current in the inward (or outward) currents.

      Indeed, we included the capacitive current in the inward or outward currents. We changed the text to clarify this.

      (c) Lines 92-93. I do not fully understand this sentence. Are you making an assumption? What does 'continuos flow of axial current' mean?
>

      By ‘continuous flow of axial current’ we meant a spatially continuous stream of axial currents flowing from the reference to the target. To clarify this, we added the explanatory sentence: “i.e., if the axial current is not blocked or reversed between the reference and the target.”

      (d) Equation (1.) Why summing axial currents over j? Is this for the case of a branching point?

      The compartment could be 1) part of a continuous segment of dendritic branch, where axial currents can flow from the distal and the proximal direction (sum over 2); 2) It can be a branch point with 3 axial currents; 3) or it can be a leaf compartment with only one axial current, in which case the summation is not relevant. We clarified this in the text.

      (e) Figure 2, caption. Typo. "When the axial currents flows…" Should it be 'current'? - Figure 3, caption. Typo in (C) "Extended currentscape" 
>

      Corrected.

      (f) Figure 4. I cannot see the grey lines or the dotted lines mentioned in the caption. 
>

      We added an arrow highlighting the gray and the dotted lines in the figure.

      (g) Figure 5, caption. "Red boxes highlight regions analyzed in panels B-D."Because this is a spatially extended model, region may be confused with spatial location, but you are highlighting a temporal interval.
>

      We rephrased the caption referring to temporal intervals now.

      (h) Line 341. This is a numerical experiment, correct? 
>

      We clarified in the text and added that it was indeed a simulation experiment.

      (i) Line 349. Should it be 'distributions'? 
>

      Corrected

      (j) Line 422. Typo. Missing space 'in vivousing'
>

      Corrected

      (k) Line 537. "Preprocessing membrane…" I found this entire subsection a bit confusing and hard to read.

      We rephrased this subsection to clarify it and facilitate reading.

    1. Author response:

      eLife Assessment

      This study provides fundamental insights by demonstrating that the Nanog mRNA coding sequence (CDS) and 3′UTR domains are spatially segregated and functionally distinct in pluripotent stem cells and blastocysts, with 3′UTR-enriched border cells primarily influencing morphogenesis and CDS-enriched inner cells largely regulating transcription and epigenetic programs. The work opens a novel conceptual avenue for understanding how separable mRNA domains can differentially control cell behavior and differentiation. However, the evidence is incomplete, as key aspects of the molecular nature, biogenesis, and precise characterization of the separated 3′UTR and CDS RNA species, as well as causal links between their perturbation and the observed phenotypes (e.g., via rescue and deeper characterization of 3′UTR elements), remain to be fully established.

      We thank the editors and the three reviewers for their careful and constructive engagement with our manuscript. We greatly appreciate the reviewers’ recognition of the conceptual significance of the study and their thoughtful suggestions for strengthening the mechanistic and molecular characterization of the work. We have carefully considered all points raised and outline below the revisions planned for the revised manuscript.

      The phenomenon of differential CDS and 3’UTR expression is not unique to Nanog. Independent 3’UTR and CDS expression and differential CDS/3’UTR usage has been observed across multiple genes, tissues, and developmental contexts, including genome-wide (Mercer et al., 2011) and transcriptome scale studies (Kocabas et al., 2025, Ji et al., 2021). Prior studies have proposed that isolated 3’UTRs may arise through regulated RNA processing pathways coupled to exonucleolytic degradation and, in some cases, recapping mechanisms (Malka et al, 2017, Haberman et al., 2024). While the precise molecular mechanisms underlying isolated Nanog CDS and 3’UTR generation remain unresolved, our observations (contained here) support regulated RNA processing models. Our original submission included a brief discussion of this topic; however the revised manuscript will include substantially expanded analyses and discussion of the generation of isolated Nanog CDS and 3’UTR species.

      The revised manuscript will address the major concerns regarding:

      (1) The molecular nature, biogenesis, and precise characterization of the separated 3′UTR and CDS mRNA species

      (2) The causal relationship between perturbation of these RNA species and the observed phenotypes, including additional rescue experiments and deeper computational characterization of putative, functional 3′UTR elements.

      Specifically:

      (A) New supplementary analyses and schematics designed to further clarify the conceptual and mechanistic framework of the study, including:

      (i) Computational examination of the Nanog 3’UTR across all reading frames for open reading frames (ORFs).

      (ii) As suggested by Reviewers 1 and 3, single cell traces of Nanog mRNA expression from the full-length mESC dataset used in this study, illustrating distinct transcript isoforms and CDS/3’UTR expression patterns across individual cells, complementing the color-coded tSNE analyses currently presented in Fig. 2.

      (iii) Expanded schematic model and analyses addressing possible mechanisms underlying the generation of isolated Nanog CDS and 3’UTR enriched RNA species, including transcript architecture, predicted RNA structural barriers, and exonucleolytic processing models.

      (iv) Expanded discussion of the predominantly nuclear localization of the Nanog 3’UTR signal and its implications for transcript biogenesis, processing, and potential noncoding functions.

      (B) Correction of all minor labeling errors.

      (C) Additional experimental analyses, including:

      - Expansion of Nanog 3’UTR overexpression and rescue experiments to include cell spreading assays.

      - Expanded analysis of the effects of ROCK pathway inhibitors on colony morphology and cytoskeletal organization.

      - Examination of the ability of ROCK inhibition to restore normal embryoid body formation.

      Collectively, these planned revisions are intended to strengthen the mechanistic framing, molecular characterization, and broader significance of the study while clarifying the interpretation and scope of the conclusions.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      There is evidence that some genes encode mRNAs from which separate processed transcripts may arise, separating the coding sequence (CDS) from the 3'-UTR, and with both mRNA elements remaining stable in the cell. However, the functional consequences of these mRNA fragments have not been firmly established. In the manuscript by Yang et al., the authors probe the mRNA domain architecture of Nanog in the context of embryonic stem cell colonies and blastocysts. The authors detect spatial separation of Nanog CDS-containing mRNA from abundant Nanog 3'-UTR RNAs depending on the cell position in 2D embryonic stem cell colonies or in blastocysts.

      Strengths:

      The phenotypic analyses of the Nanog mRNA hold promise for revealing distinct roles for the Nanog encoded protein and a separate RNA encompassing the Nanog 3'-UTR.

      Weaknesses:

      There are a number of questions about the molecular nature of the mRNA species that the authors should address in order for the results to be firmly established, as noted below.

      (1) It is not clear how the authors verified that their probes are specific for Nanog CDS or 3'-UTR regions. Especially for the 3'-UTR probe, it is confusing why colonies show green only regions, suggesting only the CDS is present. I would expect the CDS and 3'-UTR probes to colocalize in the interior cells. Is it possible that the 3'-UTR probe is targeting another RNA?

      We thank the reviewer for raising the important question of probe specificity. We realize that the data that underlying this concern is the absence of colocalizing between CDS and 3’UTR probes in colony border cells.

      The absence of CDS/3’UTR colocalization in colony border cells is not due to probe failure but instead reflects the principal observation underlying the study. If Nanog CDS and 3’UTR sequences were present exclusively as intact full-length transcripts in a strict stoichiometric ratio, Nanog positive cells would be expected to be positive for both probes (appearing yellow). Instead, border cells exhibit strong 3’UTR signal with minimal or absent CDS signal, while adjacent interior cells show the opposite pattern.

      The fact that both probes robustly detect signal within the same sample but in spatially distinct cell populations, argues that both probes are functional and that the observed differential localization reflects genuine biological differences in levels of transcript components.

      The CDS probe targets ~300 bp within the coding region, while the 3’UTR probe targets ~300 bp within the proximal region of the Nanog 3’UTR. Hybridization specificity was validated as described in the Methods and in our previous studies (Kocabas et al 2015; Ji et al 2021), including negative controls. We additionally now provide a supplemental figure (New Figure 1-figure supplement 2A), highlighting that the Nanog 3’UTR and CDS probes label cell populations distinct from each other, further indicating their specificity.

      In addition, full-length scRNA seq datasets from both mouse and human ESCs demonstrate differential CDS/3’UTR expression patterns for Nanog and many other genes. To further clarify this point, the revised manuscript will include single cell transcript traces from mESCs illustrating the distinct Nanog isoforms detected across individual cells (New Figure 2-figure supplement 1A)

      (2) It would help for the authors to include a graphic similar to Figure 3, Figure Supplement 1A, that diagrams the location of the CDS and 3'-UTR probes (this should also be done for Oct4 and Sox2). This graphic could also show all potential polyadenylation signals.

      We agree that additional schematic clarification would improve readability. The revised manuscript will include schematics showing the locations of the CDS and 3’UTR probes for Nanog, Sox2 and Oct4 (New Fig. 1- figure supplement 1A).

      (3) I think, based on the fluorescence patterns, there is evidence that the signal for the Nanog 3'-UTR probe is nuclear (images with DAPI staining), but this is not commented on that I could find. This should be discussed, as nuclear retention has implications for the noncoding function of the 3'-UTR fragment.

      The reviewer is correct that the Nanog 3’UTR signal mostly nuclear. Whie this was noted in (the original) Figure 1-figure supplement 2A, we agree that it is possible that mechanistic and functional implications were not sufficiently discussed in the original manuscript. The revised manuscript will include expanded discussion of the relationship between nuclear localization transcript processing, and potential noncoding functions of isolated Nanog 3’UTR species

      (4) Figure 2, Figure Supplement 1A needs a better explanation. It's not clear how the reads map to the different regions of the Nanog mature mRNA. The authors should show examples at different ratios of CDS to 3'-UTR. Do the reads have a sharp boundary at the junction of where the isolated 3'-UTR is thought to occur?

      We thank the reviewer for this suggestion. The revised manuscript will include new single cell read maps across the Nanog locus from full length mESC scRNA-seq datasets (New Figure 2-figure supplement 1A), illustrating distinct CDS enriched and 3’UTR enriched transcript isoforms across individual cells.

      These analyses indicate that some CDS dominant transcripts contain 3’UTR sequence, while many appear to contain little or no detectable 3’UTR sequence. Conversely, many 3’UTR enriched transcripts contain only minimal or truncated CDS sequence. Importantly full CDS and 3’UTR mRNA components are frequently not present in a strict 1:1 ratio, either within individual cells, or across cell populations.

      The revised manuscript will also include expanded supplementary analyses integrating transcript architecture, predicted RNA structural barriers, polyadenylation analysis, and single cell coverage patterns to further examine possible mechanisms underlying the generation of isolated Nanog CDS and 3’UTR species (New Figure 2-figure supplement 1B,C).

      (5) I looked in the Zenbu browser at human NANOG CAGE mapping in the FANTOM5 dataset. I could not see evidence for substantial capping of a 3'-UTR fragment when filtering for embryonic cell types. Given the strong signal for the 3'-UTR in border cells, I would expect to see evidence for capping if the RNA were indeed capped. This suggests that if it exists, it is likely uncapped and (as noted in point 3) is likely nuclear retained.

      Prior studies have reported isolated uncapped and recapped 3’UTR species in multiple systems (Malka et al, 2017; Haberman et al, 2024). We agree that the predominantly nuclear localization and lack of a strong CAGE signal for Nanog are important observations and will expand discussion of these points in the revised manuscript.

      (6) Are there predicted polyadenylation signals near the end of the CDS that would generate a short 3'-UTR, and are these signals conserved across mammals?

      Computational analysis of the mouse Nanog 3'UTR identifies a single canonical PAS (AATAAA) at position 1074, located at the 3’ end of the annotated 3’UTR and this terminal PAS is conserved across mammals. These analyses will be included as a supplementary figure and discussed further in the revised manuscript section addressing Nanog transcript biogenesis.

      (7) It would help to see a zoomed-in view of the region targeted by one of the guide RNAs in the 3'-UTR, and where that site is relative to the polyadenylation signal. Is the polyadenylation signal upstream, i.e., CDS proximal?

      This will be provided in the revised manuscript (New Figure 2-figure supplement 1C,i) Two guide RNAs were used to generate the Nanog 3’UTR deletions. The downstream guide is upstream of the terminal polyadenylation signal at nt 1074 to preserve polyadenylation of the remaining Nanog CDS containing transcript.

      Consistent with this, all Nanog 3’UTR knockout lines retain normal Nanog protein levels. The revised manuscript will include supplementary schematics showing guide RNA positions relative to the CDS, 3’UTR probes, and terminal PAS.

      (8) A final note, the use of green and red together will be challenging for those who are colorblind. Providing a different false color palette would be helpful. 

      We appreciate this attention to accessibly. The red/green color combination was chosen to provide the highest contrast between CDS and 3’UTR signals in the in situ hybridization experiments, which is important for visualizing their differential spatial localization. We will ensure that figure legends clearly indicate channel assignments throughout the manuscript.

      I am refraining from comments on the cell biology and morphological insights, as they are remote from my core expertise.

      Reviewer #2 (Public review):

      Summary:

      This manuscript shows that the coding sequence (CDS) and 3' untranslated region (3'UTR) of mRNA transcripts from the Nanog gene have distinct expression patterns and functions. In both human and mouse embryonic stem cells colonies and blastocysts, these domains are spatially segregated, with 3'UTR-enriched cells occupying the borders and CDS-enriched cells residing in the interior. CDS mRNA expression is correlated with the expected regulation of transcription and epigenetics associated with the Nanog protein. Interestingly, expression of the 3'UTR appears to play an independent role in cell behavior and colony morphogenesis. Indeed, deletion of the 3'UTR causes specific defects in cell spreading and protrusive activity, with alteration in the localization of adhesion and cytoskeleton-associated proteins. Remarkably, a large proportion of those defects are rescued upon ROCK inhibition. Deletion of either Nanog CDS or 3'UTR leads to distinct modifications in the differentiation competence.

      Strengths:

      The independent role of 3'UTR mRNA domains, although identified in neurosciences a couple of years ago, is a novel and exciting field relatively unexplored in early development.

      The manuscript offers a multilayer series of experiments, in ES cells colony, blastocysts, and embryoid bodies, including imaging, -omics, genetic and pharmacological challenges, and differentiation experiments, thereby unveiling very convincingly the role of Nanog 3'UTR in morphogenesis.

      Weaknesses:

      The pathways leading to the generation of those distinct transcript domains are unknown. Although the functional differential roles are well demonstrated whether the expression patterns are a cause or a consequence of the cells' localization in the embryo remains to be explored.

      We thank the reviewer for these thoughtful comments and for recognizing the potential significance of independent 3’UTR functions in early developmental systems.

      Regarding the mechanisms underlying generation of distinct CDS and 3’UTR transcript domains, the revised manuscript will include new supplementary analyses and schematic models addressing possible Nanog transcript processing pathways, as outlined above.

      We agree that the relation between spatial location and Nanog 3’UTR expression is an important question. Specifically, it remains unclear whether cells first acquire high Nanog 3’UTR expression and subsequently localize to the colony border or whether border position itself promotes high Nanog 3’UTR expression.

      Our current data suggest that both processes may contribute. Deletion of the Nanog 3’UTR does not prevent colonies from establishing border/interior pattern, indicating that high Nanog 3’UTR is not strictly required for border pattern itself. At the same time, Nanog 3’UTR overexpression and rescue experiments increased the likelihood of border localization, suggesting that elevated Nanog 3’UTR expression promotes behaviors associated with border occupancy.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript, Yang et al reported distinct functions of the protein-coding sequence (CDS) and the 3' untranslated region (UTR) in the Nanog mRNA in pluripotent stem cells. They first observed different localization patterns for the CDS and 3' UTR in embryonic stem cells and in blastocyst embryos, and this pattern correlates with cell populations in different pluripotent states based on single-cell sequencing data. To characterize the potentially distinct functions of these regions, the authors generated knockout (KO) cell lines in which either the CDS or the 3' UTR was genetically ablated. These deletions led to different phenotypes in multiple assays. These results provided evidence that the CDS and 3' UTR of an mRNA could have distinct functions. Although these results are potentially interesting, several questions need to be addressed before the validity of their conclusion can be confirmed.

      Strengths:

      This study provides evidence for distinct functions of the protein-coding sequence and 3' untranslated region of an mRNA in pluripotent stem cells. The concept could be more broadly applied.

      Weaknesses:

      The initial observation (distinct localization of CDS and 3' UTRs) and the causal relationship between the KO and phenotype need further validation.

      Major points:

      (1) The authors showed distinct localization patterns of the CDS and 3' UTRs in human and mouse ESCs and blastocysts, and the overlap between their signals was minimal (Figure 1). Does this mean that the CDS and 3' UTR RNAs exist separately? For example, in cells that only showed signals for 3' UTRs, do these RNAs only contain 3' UTRs and lack CDS? Was this confirmed by RNA-seq experiments? If so, how are they generated (i.e., by transcription from a novel promoter or partial degradation of the full-length mRNAs)? This is a key question. Without a clear characterization of these RNAs, the rest of the study cannot be substantiated.

      We thank the reviewer for raising this important question, which overlaps substantially with several key points raised by Reviewer #1 concerning the molecular nature and characterization of the Nanog CDS and 3’UTR species.

      Colony border cells exhibit strong Nanog 3’UTR signal with minimal detectable CDS signal, while adjacent interior cells show the reciprocal pattern. These observations strongly suggest the existence of distinct Nanog transcript species rather than exclusively full-length transcripts containing stoichiometric amounts of both CDS and 3’UTR sequence.

      This conclusion is independently supported by full-length Smart-seq2 scRNA seq datasets from both mouse and human ESCs, which provide transcript coverage across both CDS and 3’UTR regions.

      (2) To confirm that the phenotypes of CDS or 3' UTR KO cells were caused by the deleted regions instead of other artifacts, rescue experiments should be performed.

      Rescue experiments were included in the original submission (Fig. 4). The revised manuscript will expand these analyses to include cell spreading. We will also include additional ROCK pathway modulation experiments.

      (3) As over-expression of the 3' UTR showed a phenotype, important regions within it should be identified, and also the possibility that the 3' UTR contains open reading frame(s) and is translated should be tested.

      The revised manuscript will also include supplementary computational analyses of the Nanog 3’UTR, including open reading frame prediction, Kozak scoring, and evolutionary conservation analysis. (New Figure 2-figure supplement 1B). These analyses identify no evidence for strongly supported coding potential within the 3’UTR. Further, isolated Nanog 3’UTR transcripts are largely confined to the nucleus, making active translation unlikely.

      The revised manuscript will include new supplementary analyses addressing Nanog transcript structure and possible biogenesis mechanisms (New Figure 2-figure supplement 1C).

      References:

      ViennaRNA/RNA fold – Lorenz et al 2011 Algorithms Mol Biol 6:26- RNA Secondary Structure stem loop, minimum free energy (MFE) prediction

      NCBI BLASTP- Altschul et al (1990) J Mol Biol 215:403- ORF conservation, protein sequence similarity search

      NCBI Entrez/Biohthon- Cock et al (2009) Bioinformatics 25:1422- sequence retrieval

      PhastCons/UCSC multiz alignments- Siepel et al (2005) Genome Res 15:1034- evolutionary conservation scoring

      UCSC Genome Browser- Kent et al. (2002) Genome Res 12:996-1006- conservation track access

      Eaton et al (2020) Mol Cell 78:439- Stall model

      Brannan et al (2012) Genes Dev 26:2621-Stall model

      Addition to Methods.

      ORFs (≥10 amino acids) were identified in all three forward frames according to Kozak (1987). Evolutionary conservation was assessed by BLASTP (Altschul et al., 1990) against RefSeq proteins. Poly(A) signals were identified by pattern matching for canonical and non-canonical hexamers. Conserved sequence blocks were obtained from UCSC PhastCons tracks (Siepel et al., 2005). RNA secondary structures were predicted using ViennaRNA RNAfold (Lorenz et al., 2011) with a sliding 80-nt window. The stall model for isolated transcript generation follows Eaton et al. (2020).

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      We thank the reviewers and we are glad that they acknowledge this work to be a timely contribution to a quickly moving field and a valuable tool to generate testable hypothesis. We are pleased that reviewer #2 highlights that “a major strength is the combination of orthogonal evidence types” and that the tool serves to generate novel hypothesis. The revised manuscript will sharpen the positioning of the study within this context. Additional experimental evidence will be provided to address the points raised by reviewers #1 and #3.

      Reviewer #1* 1.The authors do not co-IP ARF1. This does not surprise me as small GTPases often hydrolyse their GTP during lysis. *

      We agree that this is likely due to transient association and GTP hydrolysis during lysis and will add a section to the manuscript.

      There have been a number of ARF1 bioID screens done- have the authors checked if their complex has turned up here?

      We will include this in the revised manuscript.

      1. I am a bit confused by some of the interpretation about KO and loss of JTB staining. They interpret: "The SYS1 acts as a Golgi recruitment factor for both ARFRP1 and JTB". The ARFRP1 has been published and is a cytosolic protein, so that makes sense. However, the JTB is not cytosolic by a membrane protein, so cannot be "recruited". Now maybe it is retained in the Golgi by this interaction, but if that is the case you would still expect signal on another organelle or the plasma membrane (and we see it isnt degraded in the lysosome due to the western blot). I am confused by the authors model here.

      We will clarify the phrasing and will provide a clearer interpretation, also considering the other improved imaging experiments that will be included in the revised manuscript.

      4.The authors validate their JTB antibody and confirm the fact that there are not reduced SYS1 levels in the JTBKO- this is very clear (albeit unquantified). What I do not see validated is the SYS1KO. I think this is quite important.

      We will validate SYS1 KO using TIDE and/or western blotting.

      5.The colocalisation in panel 3D is weak and unclear to me. It is not quantified. It is not clear if there have been 3 repeats.

      The revised manuscript will include improved imaging data. We will repeat relevant experiments, include appropriate controls and quantify where necessary.

      6.The imaging in figure 3 is not clear in places, and it stands out in a very clear manuscript. I cannot see the JTB in panel F. There are no scale bars. The dynamic range of the image is not utalised. I do not see the stain in the JTB in either of the sys1 KO, i do not see the SYS1-FLAG staining in the complement, and it is not quantified at all. It may all seem trivial, but (to me) this is an absolutely critical bit of biology data to support the informatics.

      The revised manuscript will include improved imaging data. We will repeat relevant experiments, include appropriate controls and quantify where necessary.

      7.I am a bit unconvinced by the interpretation of it being a retrograde trafficking complex. This is for 2 key reasons- 1) the VSV-G is antrograde (despite unusually they interpret a "severe defect in retrograde transport"). 2) Even if it was only having an effect in the retrograde direction I would still remain a little open minded about it as you can easily mistake trafficking of a protein in one direction for another if an unknown protein (SNARE for example) has defective trafficking.

      We used VSVG-KDEL in this assay. This setup specifically measures retrograde trafficking. We will clarify this in the revised manuscript. We will clarify in the Discussion that we confirmed a role in retrograde trafficking but cannot exclude a role in anterograde trafficking

      Reviewer #2

      Major comment: scope and interpretation of DepMap-derived functional evidence The manuscript could benefit from more clearly defining the scope of the functional evidence used to nominate complexes. The central co-dependency signal is derived from DepMap 24Q2 CRISPR gene-effect profiles, which are primarily cancer cell-line fitness/proliferation data. This is an important limitation because the resulting correlations may preferentially capture complexes or pathways that influence viability in proliferating cancer cells, while missing complexes active in differentiated, tissue-specific, stimulus-dependent, or non-proliferative contexts. Conversely, some correlations may reflect shared cancer-lineage or fitness dependencies rather than direct participation in a stable complex. The authors are appropriately cautious in stating that DepCom is not a complete inventory of human protein complexes, but the title, framing, and resource description could still be read as implying a more general catalogue of functional protein complexes. The authors might consider adding a clearer introduction to DepMap and explicitly discuss how the cancer-cell-line origin of the data affects interpretation of the 518 predicted complexes. This could be addressed without new experiments, for example by adding text early in the Results section explaining what the CRISPR gene-effect scores measure, and by expanding the Discussion to clarify that DepCom represents structurally plausible complexes prioritized by co-dependency across cancer cell lines, rather than an unbiased or context-independent map of human protein complexes. The selection of highlighted examples would also benefit from clearer justification. The peroxisome, actin, WNK/TSC22D2, and Golgi/JASS examples are biologically interesting, but the rationale for choosing them is not always explicit. Were they selected because they were novel, high-confidence, disease-associated, experimentally tractable, or representative of different resource categories? Briefly stating the selection criteria would help readers understand whether these examples are illustrative case studies or representative outcomes of the pipeline.

      We agree with the reviewers' assessment that this resource should be viewed as hypothesis-generating and that the overall framing should be improved. We will revise the manuscript at the appropriate sections, according to the more detailed comments of all reviewers.

      Minor comments

      1. Clarify post-clustering removal of large/problematic protein families and complexes. In the Methods, the authors state that "clusters of histones and keratin clusters, as well as the mito-ribosome, complexes of the electron transport chain and the mediator complex" were removed because of their large sizes. This filtering step would benefit from additional detail. Please specify the criteria used to define these removed clusters, how many clusters/proteins were removed at this stage, and whether removal was based only on size or also on biological/manual curation. It would also be helpful to explain why these proteins or clusters were removed after clustering rather than excluded before graph construction and clustering, since highly connected or compositionally biased protein families could potentially influence neighboring cluster assignments. If available, a brief robustness check showing that pre-removal of these proteins gives similar candidate complexes would strengthen confidence in the clustering procedure.

      We will add the requested information to the relevant section. Alongside the manuscript we will also provide lists of the complexes before and after every filtering step

      1. Clarify the rationale for excluding complexes larger than 5000 residues. The 5000-residue cutoff is understandable for AF3 computational cost, but the manuscript should briefly state how many candidate complexes were excluded by this cutoff and whether this preferentially removes known large assemblies. This would help readers understand the scope of complexes that DepCom is expected to miss.

      Alongside the manuscript we will now also provide lists of the complexes before and after every filtering step.

      1. Improve wording in the CAP1/CFL1/WDR1/ACTB example. The sentence "Additionally, CAP1 works in concert with CFL1 to accelerate depolymerisation, though if a four-protein complex consisting of actin, WDR1, CAP1 and CFL1 is relevant is not clear" is difficult to parse. Possible revision might be something like: "Additionally, CAP1 works in concert with CFL1 to accelerate depolymerisation, although it remains unclear whether actin, WDR1, CAP1 and CFL1 form a stable four-protein complex in cells." This more clearly separates known biology from the speculative interpretation of the DepCom prediction.

      Wording will be improved.

      1. Improve reproducibility details for AF3 predictions. The Methods state that predictions were run using a local AF3 installation, but reproducibility would be improved by reporting relevant AF3 settings, number of seeds/models per complex, whether templates were used, how disordered regions were handled, and whether predictions were repeated for all complexes or only selected examples. This is especially important because the manuscript notes that multiple predictions can yield different subunit arrangements.

      We will provide detailed settings in the methods section. Regarding disordered parts: All predictions used full length sequences (canonical UNIPROT ID) for each protein, so disordered residues are included. If disordered regions have low PLDDT and poor PAE, these regions will simply not score as interfaces in AlphaBridge. The one exception where we did crop structures is Figure 2D, but purely for visualization purposes, the full length complex did score in the pipeline (uncropped).

      Reviewer #3

      Co-essentiality is not the same as physical complex membership. This is the biggest conceptual concern. Genes in the same pathway are co-essential whether or not their products bind. The authors lean on the structural prediction step to filter this out, but that means the entire pipeline rests on AF3+AlphaBridge being correct about who interacts with whom. There is no independent benchmarking shown of how often AlphaBridge calls a true positive vs a false positive at the chosen 0.5 cutoff. Why 0.5? Where does that number come from? A short benchmarking section using known complexes (CORUM 5.0, hu.MAP 2.0, the PDB) would make the choice defensible. Right now it reads as arbitrary.

      We thank the reviewer for bringing up the need for such an important clarification. We fully agree that co-essentiality does not equal physical interaction and structure predictions are imperfect. This is precisely the logic underlying our pipeline design, not a limitation we overlooked. The two data sources are used sequentially and serve distinct roles: first, we construct protein sets that are connected through networks of predicted binary physical interactions; then we cluster these based on DepMap correlations, selecting likely physical complexes that display co-essentiality between their components.

      In other words, clustering on DepMap data alone would certainly return many spurious correlations: as the referee points out “Co-essentiality is not the same as physical complex membership”. Anchoring the search space with structural predictions substantially reduces this noise. Neither data source alone is sufficient, nor do we claim either is definitively "correct": the value lies in their combination. We hope improved phrasing in the revised manuscript will highlight this better.

      Regarding benchmarking AlphaBridge score: we have benchmarked AlphaBridge, in response to reviewer feedback on the original AlphaBridge paper (Structure, Cell Press). In the figure here it is clear that in our benchmark of PDB structures (with

      Comparison to existing resources is incomplete. I can't help but wonder what was found here that would not have been possible by analysing existing resources. CORUM 5.0 (7,193 mammalian complexes, ~71% human-derived; Tsitsiridis et al. 2024 NAR), hu.MAP 2.0 (Drew et al. 2021, ~6,965 complexes from >15,000 MS experiments), BioPlex 3.0 (Huttlin et al. 2021, 118,162 interactions in HEK293T), ad the Complex Portal already cover a large fraction of the human complexome. The authors compare to PDB, the original interactome paper, and Complex Portal, but they explicitly skip CORUM and hu.MAP, both of which are central reference resources in this space. Without including these, the "60 complexes unique to DepCom" number is not really meaningful. This needs to be redone properly.

      We will add the comparison with Corum and hu-MAP in the revision.

      Validation rate is one out of 518. The JASS work is solid, but a single experimentally validated complex out of 518 gives the reader essentially no estimate of how often the rest of the predictions are correct. Even a smaller systematic effort, say IP-MS on five to ten predicted novel complexes in the same cell line, would do an enormous amount to establish how trustworthy the resource is. The authors already have the V5/IP-MS pipeline running. Right now the manuscript implicitly asks the reader to trust 517 predictions on the strength of one validation.

      In this paper we validated one out of the 60 complexes we claim are new. Notably we provide new biological data and demonstrate how consulting our resource, or following the same logic of combining functional and structural information, can lead to new exciting discoveries. We note that out of the 518 complexes we list, 69 complexes are exactly mirrored in the PDB and/or Complex Portal, while for another 389 there is partial evidence. Thus, our dataset is amply validated, and at the same time contains data to enable new discoveries. We also note, that following the release of our resource eight months ago, a new high-impact publication “validated” a complex we have independently picked in DepMap (Oosterheert et al, Choreography of rapid actin filament by coronin, cofilin and AIP1, Cell, 2025). We will rephrase relevant sections (also in response to reviewer 2) to increase clarity about validation.

      The functional and disease clustering is potentially circular. GO terms and STRING associations are themselves derived in large part from the published literature on protein function, including text mining channels in STRING, much of which is downstream of complex membership. Of course complexes cluster into "DNA repair" and "vesicle trafficking" if you cluster on GO and STRING. The same applies to Open Targets, which integrates GWAS Catalog, ClinVar, literature mining, and other sources. The clustering is fine as a navigation aid for the website, but it is not, as currently presented, an independent validation of anything. I would tone the discussion down accordingly.

      We did not mean to present the clustering as an independent validation. We will tone down the discussion accordingly.

      AF3 limitations on this class of problem. AF3 itself acknowledges limitations (Abramson et al. 2024, including the December 2024 addendum), and subsequent benchmarking has flagged disordered regions, dynamic/large assemblies, and certain transmembrane systems as known weak points. The JASS complex is largely transmembrane, the WNK1-TSC22D2 example involves disorder-to-order transitions, and several flagship examples involve large multi-domain proteins. The authors acknowledge some of this in passing but should state explicitly which complexes were trimmed, how the trimming choices were made, and whether predictions were repeated with different seeds to check stability. Figure S4 is a good start, but for a resource paper a more systematic seed-stability analysis is warranted.

      No complexes were trimmed for the initial AF3 predictions. The WNK1-TSC22D2 example was trimmed and re-predicted only for visualization purposes. We apologize for the misunderstanding and will state this more clearly.

      AF3 certainly has limitations. Regarding disordered regions, these will almost always be assigned a poor pLDDT (also if AF3 wrongly folds them into helices). AlphaBridge will not pickup these low pLDDT regions as interfaces. Regarding dynamic assemblies, these might again lead to poor confidence scores and consequently these will not be picked up as interfaces by AlphaBridge. If AF3 confidence metrics are analyzed properly, the main concern for both disordered regions and dynamic assemblies is to miss true positive interactions, rather than finding false positive. As we did not aim to identify all possible human complexes, we consider focusing on the most confidently predicted interactions to be a fair trade off.

      While the JASS complex is indeed a membrane protein complex, the predictions are exceptionally confident across multiple seeds (we can provide predictions from multiple seeds for revision), and validates experimentally. Of course, structure predictions are no substitute for experimental structures, as cautioned multiple times throughout the manuscript.

      Figure S4 shows that despite the complex overall geometry being flexible, the interaction sites are predicted with high confidence across different poses. Since the aim of this study was to identify proteins interacting with each other, not accurate structures (which need to be solved experimentally), we argue that recomputing all structures with multiple seeds is disproportionately expensive computationally and would delay publication of a timely study while adding little.

      Statistics are thin in several places. On the Fisher exact test for Golgi/ER enrichment in V5-JTB IP-MS (Supplemental Table 1), an odds ratio of 2.77 is modest, and there is no comparison to a matched control IP. Is this more than expected by chance against an appropriate background? The IP-MS volcano plots show many significant proteins, but how was the background controlled? On the LLM section, no quantitative evaluation is presented at all and the assessment is admitted to be subjective.

      We will qualify the conclusions drawn from the IP-MS experiments. We maintain that together with the additional cell biology data, we build a compelling and convincing picture for this JASS complex.

      Experimentally, the background is controlled by measuring enrichment over WT cell lines that have undergone the same IP procedure as the V5-SYS1/JTB expressing cells (lysis, incubation with the anti-V5 conjugated beads, same wash procedure and sample processing), as is the standard in the field. We will clarify in the Methods section. Regarding identification, FDR rate was set to 1% at protein and peptide level and peptide spectrum matches (PSMs) were additionally filtered for SequestHT Xcorr score >1.

      We agree with the referee that the LLM interpretation is subjective and cannot be benchmarked. We suggest revising the resource and the paper, only providing structured LLM prompts to facilitate users asking the right questions, but we will not provide the LLM answers as part of the resource.

      The 4�ACTB speculation. The authors themselves note the AlphaBridge score declines from 0.9 (1�ACTB) to 0.78 (4�ACTB), yet they speculate about functional implications. This is exactly the kind of post-hoc rationalisation around weak evidence that should either be supported with experiment or removed. Either remove or qualify as speculative.

      We will qualify this as speculative

      The LLM-assisted analysis. I am genuinely uncomfortable with releasing 76 LLM-generated complex annotations as part of a published resource when the authors openly state these have "not been systematically validated". Putting these summaries on a website with the imprimatur of a peer-reviewed paper will lead to them being cited and reused. At minimum, the website needs prominent warnings on every page where an LLM summary appears, the prompts must be fully reproducible (not just downloadable as JSON), and a small validation table, say 10 complexes scored by a domain expert for accuracy of each claim, should be included as a supplemental figure. As it stands this section reads like an enthusiastic add-on that has not been thought through with the same care as the rest of the work.

      We thank the referee for bringing forward this consideration. We agree to remove the LLM answers for the 78 complexes from the manuscript and from the website, to ensure that the outputs cannot be cited. We will provide two different objective structure prompts for download to encourage variety in responses for curious users who want to explore. We will add a prominent disclaimer noting that responses resulting from these prompts cannot be interpreted as facts without validation.

      We cannot guarantee reproducibility with modern LLM inference architecture. Even if seeds are kept the same and temperature=0, floating-point non-determinism in GPU operations, distributed inference, and batch effects may lead to different results. Furthermore, models go through many different iterations rapidly. As a consequence, it is impossible for us to guarantee reproducibility

      Cutoffs and cluster numbers need stability analysis. The cutoff for the 75th-percentile DepMap correlation (mean of random + 3 SD = 0.147) is reasonable but should be accompanied by an FDR or precision/recall estimate against a labelled reference set. The choice of 20 final clusters in functional clustering (because that gave a peak in silhouette score) and 14 for disease clustering should also be supported by stability analysis, e.g. resampling.

      The 75th percentile cutoff is, in our opinion, well justified and sufficient for our purposes. FDR and precision recall need a set of true and false positives. The DepMap correlation clusters are an intermediate step in our pipeline and do not necessarily hold the final complexes. How can intermediate reference DepMap clusters be constructed and defined as true or false positives? Even if we would score clusters that contain a known complex as true positives, how to define false positives? If clusters do not contain a known complex, that does not necessarily mean that these proteins don’t interact, just that they have not been shown to interact yet.

      We will run resampling to improve confidence in the choice of cluster number.

      Internal numerical consistency. The bioRxiv preprint abstract refers to 354 high-confidence multi-protein complexes, while the body of the manuscript discusses 518 (224 dimers + 294 multimers). The relationship between these numbers should be stated explicitly. Likewise, the breakdown of "60 unique to DepCom" into 41 heterodimers + 19 multimeric should be reconcilable in the figures and tables. The number "9,764 unique seed proteins" should also be clarified to confirm it is the DepCom-internal seed set and not inherited from the Zhang et al. coverage or hu.MAP 2.0 (9,963 proteins). These are easy fixes but matter for a resource paper.

      BioRxiv preprint: The preprint that the reviewer read is an older version, which will be updated. .

      The 9,764 unique seed proteins is from the Zhang et al paper, and are the human proteins identified to confidently interact with at least one other human protein. We will make this more clear.

      Mander's overlap coefficient. The VSV-G(ts045)-KDELR retrograde-transport assay is well established and the experiment is clean, but MOC has been increasingly criticised in the colocalisation literature (Adler & Parmryd 2010, 2021). Best practice is to also report Manders' M1/M2 coefficients or Pearson's correlation alongside MOC. Adding these would be straightforward and would strengthen Fig 4B.

      We will improve co-localization measures where appropriate.

      Minor comments 1. Page 4: "candidate sets of potential multi-protein complex members". Pick one, they are either candidates or potential, not both.

      Will be addressed.

      Page 7: "Complex 294... mechanistic basis for CFL1 and WDR1 cooperation has only recently been described". Please update the reference list and language given how recent this is.

      Will be addressed.

      Page 7: JTB is described as "poorly characterised". This is a bit too strong. JTB has been studied in the context of TGF-β-induced mitochondrial regulation (Kanome et al. 2007), cytokinesis and chromosomal passenger complex association (Platica et al. 2011), the structural characterisation of its extracellular domain (Rousseau et al. 2012), and breast cancer biomarker work (Jayathirtha et al. 2022). A more accurate framing would be "incompletely characterised, with previously reported but functionally unresolved roles". The novelty here is the Golgi connection, which is genuine.

      We will rephrase.

      Page 8: the citation of Blomen et al. 2015 Science for "Golgi-related synthetic lethality" should be checked against the actual supplementary data of that paper to confirm the JTB attribution is correct.

      Will be check.

      Figure 1: as in many omics papers, please think of us colourblind readers. The pink-green DepMap correlation scale will be hard for some of us.

      The color scheme in use, alongside others, was tested with two colleagues that have different variants of colour blindness and was judged to be the best compromise.

      Figure 5A and 5B: 21 and 14 colour-coded clusters respectively in a single UMAP is too much. Consider splitting into separate panels by broad theme or providing an interactive version only.

      We will focus on a subsection, and provide the full interactive version on the homepage

      Page 11: "manually evaluated the quality of outputs". By whom, blinded to which model produced which output? Methods are silent on this.

      As stated above, we will remove the LLM part

      Some figures show "hairballs" with very limited informative content. Fig. 1B left panel and the AlphaBridge wheel plots in particular convey relatively little at the size shown.

      We will try and find a way to draw the AlphaBridge circular plots in better resolution; we do not however that the reviewer’s observation might be an artefact of the PDF file distributed to reviewers.

      The reference list looks a bit thin on prior systematic complexome efforts. BioPlex 3.0 (Huttlin et al. 2021 Cell), hu.MAP 2.0 (Drew et al. 2021 MSB) and CORUM 5.0 (Tsitsiridis et al. 2024 NAR) should all be cited and discussed.

      We will include the additional references where appropriate

      The discussion section drifts into general comments about AI in science that don't add much. I would cut about a third of it and use the space for a more careful framing of the actual contribution.

      We will shorten the discussion section and phrase more carefully.

      General assessment Reviewer #3: The strongest aspect of this study is the JASS complex story. The IP-MS, the SYS1-KO rescue experiment, the VSV-G(ts045)-KDELR transport assay, and the orthogonal CRISPR screens with diphtheria and Pseudomonas exotoxins together build a convincing case for JTB as a regulator of Golgi-to-ER retrograde trafficking. This part of the paper is genuinely nice work and would stand on its own. The pipeline itself, combining structural predictions with functional dependency data and filtering with AlphaBridge, is sensible and timely. It is a reasonable demonstration of how confidence filtering should be done at this kind of scale. The main limitations concern the resource framing. After reading the manuscript several times I am still trying to identify the central novel contribution beyond the JASS validation. The interactome predictions are taken from Zhang et al., DepMap is public, AF3 is public, AlphaBridge is the authors' own previously published tool, and GO/STRING/Open Targets/dbPTM are all public. The manuscript is essentially an integrative pipeline plus a website plus one experimentally followed-up complex. The framing oversells what is genuinely new. The authors' own comparison (Fig. S3) shows 60 complexes "unique to DepCom" out of 518, of which 41 are heterodimers and only 19 are multimeric. Nineteen genuinely novel multi-protein complexes is still a contribution but it is a long way from the 354/518 that the abstract and discussion implicitly emphasise. The validation rate (one of 518) and the missing comparisons to CORUM 5.0 and hu.MAP 2.0 are the two issues that most need addressing.

      We will rephrase these issue to adjust the framing. We would put forward that the main contribution of this manuscript is to present an integrative framework that combines data from orthogonal sources to highlight the possibility of structure prediction models to serve as a discovery tool. The reviewer identifies correctly (albeit derogatorily) that this is “essentially” an integrative pipeline. But it is an integrative pipeline that combines genetics and computational structure predictions in a novel (to the best of our knowledge) way and surfaces interesting new biology. The biology of the JASS complex goes well-beyond simple validation experiments, and we believe its discovery (based on our data) carries more value that the reviewer attributes to it.

    2. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #1

      Evidence, reproducibility and clarity

      Characterising protein complexes is a fundamental goal in modern molecular cell biology. Here, Uckelmann and colleagues have presented a solution to part of this problem. By combining functional clustering with alphafold modelling, they present a high throughput bioinformatic solution. The paper and figures are exceptionally clear and well presented. The conclusions are reasonable, and the data interesting. I am a cell biologist with expertise in molecular machinery of trafficking, so the focus of my review will be on the identification of a new complex, that is proposed to have a role in retrograde trafficking. On the whole I find this a interesting and convincing finding. However I have some comments and questions that I hope may help the authors. I will naturally focus my comments on the cell biology.

      1.The authors do not co-IP ARF1. This does not surprise me as small GTPases often hydrolyse their GTP during lysis. 2.There have been a number of ARF1 bioID screens done- have the authors checked if their complex has turned up here? 3.I am a bit confused by some of the interpretation about KO and loss of JTB staining. They interpret: "The SYS1 acts as a Golgi recruitment factor for both ARFRP1 and JTB". The ARFRP1 has been published and is a cytosolic protein, so that makes sense. However, the JTB is not cytosolic by a membrane protein, so cannot be "recruited". Now maybe it is retained in the Golgi by this interaction, but if that is the case you would still expect signal on another organelle or the plasma membrane (and we see it isnt degraded in the lysosome due to the western blot). I am confused by the authors model here. 4.The authors validate their JTB antibody and confirm the fact that there are not reduced SYS1 levels in the JTBKO- this is very clear (albeit unquantified). What I do not see validated is the SYS1KO. I think this is quite important. 5.The colocalisation in panel 3D is weak and unclear to me. It is not quantified. It is not clear if there have been 3 repeats. 6.The imaging in figure 3 is not clear in places, and it stands out in a very clear manuscript. I cannot see the JTB in panel F. There are no scale bars. The dynamic range of the image is not utalised. I do not see the stain in the JTB in either of the sys1 KO, i do not see the SYS1-FLAG staining in the complement, and it is not quantified at all. It may all seem trivial, but (to me) this is an absolutely critical bit of biology data to support the informatics. 7.I am a bit unconvinced by the interpretation of it being a retrograde trafficking complex. This is for 2 key reasons- 1) the VSV-G is antrograde (despite unusually they interpret a "severe defect in retrograde transport"). 2) Even if it was only having an effect in the retrograde direction I would still remain a little open minded about it as you can easily mistake trafficking of a protein in one direction for another if an unknown protein (SNARE for example) has defective trafficking.

      Significance

      Characterising protein complexes is a fundamental goal in modern molecular cell biology. Here, Uckelmann and colleagues have presented a solution to part of this problem. By combining functional clustering with alphafold modelling, they present a high throughput bioinformatic solution. The paper and figures are exceptionally clear and well presented. The conclusions are reasonable, and the data interesting. I am a cell biologist with expertise in molecular machinery of trafficking, so the focus of my review will be on the identification of a new complex, that is proposed to have a role in retrograde trafficking. On the whole I find this a interesting and convincing finding.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary

      The strength of this manuscript lies in the behavior: mice use a continuous auditory background (pink vs brown noise) to set a rule for interpreting an identical single-whisker deflection (lick in W+ and withhold in W− contexts) while always licking to a brief 10 kHz tone. Behaviorally, animals acquire the rule and switch rapidly at block transitions and take a few trials to fully integrate the context cue. What's nice about this behavior is the separate auditory cue, which shows the animals remain engaged in the task, so it's not just that the mice check out (i.e., become disengaged in the W- context). The authors then use optical tools, combining cortexwide optogenetic inactivation (using localized inhibition in a grid-like fashion) with widefield calcium imaging to map what regions are necessary for the task and what the local and global dynamics are. Classic whisker sensorimotor nodes (wS1/wS2/wM/ALM) behave as expected with silencing reducing whisker-evoked licking. Retrosplenial cortex (RSC) emerges as a somewhat unexpected, context-specific node: silencing RSC (and tjS1) increases licking selectively in W−, arguing that these regions contribute to applying the "don't lick" policy in that context. I say somewhat because work from the Delamater group points to this possibility, albeit in a Pavlovian conditioning task and without neural data. I would still recommend the authors of the current manuscript review that work to see whether there is a relevant framework or concept (Castiello, Zhang, Delamater, 'The retrosplenial cortex as a possible 'sensory integration' area: a neural network modeling approach of the differential outcomes effect of negative patterning', 2021, Neurobiology of Learning and Memory).

      The widefield imaging shows that RSC is the earliest dorsal cortical area to show W+ vs W− divergence after the whisker stimulus, preceding whisker motor cortex, consistent with RSC injecting context into the sensorimotor flow. A "Context Off" control (continuous white noise; same block structure) impairs context discrimination, indicating the continuous background is actually used to set the rule (an important addition!) Pre-stimulus functional-connectivity analyses suggest that there is some activity correlation that maps to the context presumably due to the continuous background auditory context. Simultaneous opto+imaging projects perturbations into a low-dimensional subspace that separates lick vs no-lick trajectories in an interpretable way.

      In my view, this is a clear, rigorous systems-level study that identifies an important role for RSC in context-dependent sensorimotor transformation, thereby expanding RSC's involvement beyond navigation/memory into active sensing and action selection. The behavioral paradigm is thoughtfully designed, the claims related to the imaging are well defended, and the causal mapping is strong. I have a few suggestions for clarity that may require a bit of data analysis. I also outline one key limitation that should be discussed, but is likely beyond the scope of this manuscript.

      Major strengths

      (1) The task is a major strength. It asks the animal to generate differential motor output to the same sensory stimulus, does so in a block-based manner, and the Context-Off condition convincingly shows that the continuous contextual cue is necessary. The auditory tone control ensures this is more than a 'motivational' context but is decision-related. In fact, the slightly higher bias to lick on the catch trials in the W+ context is further evidence for this.

      (2) The dorsal-cortex optogenetic grid avoids a 'look-where-we-expect' approach and lets RSC fall out as a key node. The authors then follow this up with pharmacology and latency analyses to rule out simple motor confounds. Overall, this is rigorous and thoughtfully done.

      (3) While the mesoscale imaging doesn't allow for cellular resolution, it allows for mapping of the flow of information. It places RSC early in the context-specific divergence after whisker onset, a valuable piece that complements prior work.

      (4) The baseline (pre-stim) functional connectivity and the opto-perturbation projections into a task subspace increase the significance of the work by moving beyond local correlates.

      Key limitation

      The current optogenetic window begins ~10 ms before the sensory cue and extends 1s after, which is ideal for perturbing within-trial dynamics but cannot isolate whether RSC is required to maintain the context-specific rule during the baseline. Because context is continuously available, it makes me wonder whether RSC is the locus maintaining or, instead, gating the context signal. The paper's results are fully consistent with that possibility, but causality in the pre-stimulus window remains an open question. (As a pointer for future work, pre-stimulusonly inactivation, silencing around block switches, or context-omission probe trials (e.g., removing the background noise unexpectedly within a W+ or W- context block), could help separate 'holding' from 'gating' of the rule. But I'm not suggesting these are needed for this manuscript, but would be interesting for future studies.)

      We thank the reviewer for the comprehensive summary of our work.

      We also thank the reviewer for highlighting the work from the Delamater group (Castiello et al., 2021), and we now briefly discuss this paper on P. 14 Lines 434-437 writing: “RSC was shown to contribute to negative patterning in behavioral tasks requiring rats to learn that the simultaneous presentation of two stimuli lead to an opposite outcome than each individual stimulus (Castiello et al., 2021).”

      We also agree with the reviewer’s noted ‘Key limitation’ regarding the role of RSC as either maintaining context representation or serving a gating function. The reviewer proposes an exciting set of further experiments inactivating RSC at different time points to investigate when RSC activity is needed. We hope to carry out such experiments in the future. We now include a brief discussion of this interesting point on P. 14-15 Lines 455-459 writing: “First, further inactivation experiments would shed light on the timing at which RSC activity is necessary for the integration of contextual information. Specifically, it would be of great interest to inactivate RSC at different time points such as during the intertrial interval or at the transition between contexts.”

      We have of course also addressed each of the more detailed comments from the “Recommendations for the authors” section, please see below.

      Reviewer #2 (Public review):

      Summary:

      The authors aim to understand the neural basis of context-dependent sensory processing and decision-making.

      Strengths:

      They used an innovative behavioral paradigm where the action-outcome association changes independent of the sensory stimulus. This theoretically allows the authors to disentangle the effect of behavioral context on sensory processing. Using this approach combined with optogenetic silencing, they discover that RSC activity is necessary for suppressing a lick response when the stimulus switches to the unrewarded context.

      Weaknesses:

      Sensory processing appears to be entangled with jaw/tongue movement initiation. Activity in M1 and RSC during auditory-evoked lick responses appears to be identical to activity during whisker-evoked lick responses, indicating that movement initiation is the main driver of M1/RSC activity, rather than changes in the flow of sensory information. If sensory information were the main driver of the initial M1/RSC response, then auditory evoked responses should have a longer latency. Perhaps this is beyond the resolution of the calcium indicator or imaging frame rate. It is not clear from the data shown if differences in S1 activity when comparing W+ and W- stimulation are caused by context-sensitive sensory processing or whisker movement following whisker deflection.

      We thank the reviewer for the comments on our work and we agree that separating sensory processing and movement initiation is very important. In the revised manuscript, we have carried out several new analyses to specifically address the points of the reviewer. The most important point is that context-dependent activity in RSC emerges at ~50 ms after the whisker stimulus, which precedes any differences in movements of the jaw or whisker. Although sensory and motor representations become increasingly entangled after stimulus delivery, we think that the first ~100 ms after the whisker stimulus is a relatively safe period for analysing sensory processing and decision making before overt context-dependent differences in movements.

      Addressing the specific point “Activity in M1 and RSC during auditory-evoked lick responses appears to be identical to activity during whisker-evoked lick responses, indicating that movement initiation is the main driver of M1/RSC activity, rather than changes in the flow of sensory information.” - We have now directly compared the pattern of cortical activity evoked by whisker and auditory stimuli in correct trials in the W+ context (new Figure 3 – figure supplement 2). As expected, activity in wS1/wS2 and A1 is stronger in whisker and auditory trials respectively, following their sensory modalities. However, we also evidence a stronger response of wM1/wM2 in whisker trials as early as 40 to 60 ms following the stimulus, showing the specificity to the whisker system. We also observe a stronger response of RSC to whisker than to auditory stimulus. The auditory and whisker evoked responses are therefore different.

      Addressing the specific point “If sensory information were the main driver of the initial M1/RSC response, then auditory evoked responses should have a longer latency. Perhaps this is beyond the resolution of the calcium indicator or imaging frame rate.” – As stated above, the responses to auditory and whisker stimuli are different.

      Addressing the specific point “It is not clear from the data shown if differences in S1 activity when comparing W+ and W- stimulation are caused by context-sensitive sensory processing or whisker movement following whisker deflection.” - We think that the data shown in Figure 3F-H indicate that differences in S1 activity when comparing W+ and W- stimulation are not directly caused by context-sensitive sensory processing. On P. 9 Lines 270273 we write: “Early after stimulus onset, whisker deflection evoked similar activation of primary and secondary whisker somatosensory cortices (wS1 and wS2) in both W+ and W− contexts.” Indeed, context separation in wS1/wS2 only emerged later than 100 ms, which is indeed confounded by the difference in movement evoked by the sensory stimulus (now quantified in new Figure 3 – figure supplement 4). On the contrary RSC and wM1/2 responses to the whisker stimulus were different in W+ and W- at early time points (~50 ms for RSC and ~80 ms for wM1/2) which is consistent with context dependent sensory processing. At least 2 hypotheses could explain the absence of early difference in whisker evoked activity in wS1/wS2 between W+ and W-. The first one is that sensory activity in wS1/wS2 is not modulated by contextual information at all, while the alternative option would imply that sensory activity is mediated by different neuronal populations depending on context with an overall similar average response. We think this is an interesting question which we hope to address in future experiments using Neuropixels recordings and multiphoton cellular imaging to address the single neuron representation of whisker stimulus in wS1/wS2 according to context in the task presented here.

      We have of course also addressed each of the more detailed comments from the“Recommendations for the authors” section, please see below.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Suggestions to strengthen the manuscript (no new data collection)

      (1) The block-switch dynamics were clearly demonstrated behaviorally. It would be very powerful to mirror this with an analysis of neural data around the block-switch: how do the various areas adjust immediately after a shift in the continuous contextual sound? Does the RSC show any evidence of changing activity patterns? How does the within-trial activity dynamic look as a function of the number of trials from the context switch? This could be done with the data collected for Figure 3 (for within-trial dynamics), but also for the pre-stimulus baseline activity data (Figure 4A-B).

      We thank the reviewer for raising this interesting point. We have now investigated the change of cortical activity at the transition between contexts (new Figure 3 – figure supplement 5). At the context transition, both to W+ and to W- contexts, we observed a rapid activation of the auditory cortex (new Figure 3 – figure supplement 5A). In addition, there appeared to be a slightly higher activation of RSC when transitioning to W- rather than to W+ (new Figure 3 – figure supplement 5A). In the future, it will be of great interest to further investigate this phenomenon.

      We also evaluated the whisker deflection-evoked responses of the different cortical regions according to the number of whisker trials from context switch (new Figure 3 – figure supplement 5B&C). This analysis revealed that while the sensory response in wS1 and wS2 were constant over the time course of a context block, the response of wM1/2 and especially RSC became progressively lower in the W- context, consistent with the behavioral results in Figure 1 supporting time-dependent contextual integration.

      Overall, these results strengthen the role of RSC and wM1/2 in integrating contextual information to guide the response to the whisker stimulus, and we thank the reviewer for raising this important point.

      (2) It might be useful to state 'earliest among the imaged dorsal cortical areas,' and briefly acknowledge potential subcortical contributors (since those were not explored and could be earlier than cortical areas).

      We agree with the reviewer. In the Summary, on P. 2 Line 39-40 we now write: “Widefield calcium imaging revealed that retrosplenial cortex was the first dorsal cortical area to show context discrimination in response to whisker stimulation”. On P. 8 Lines 257-258, we now write: “To investigate the spatiotemporal neural dynamics underlying task execution, we recorded calcium activity across the dorsal cortex in transgenic mice”. On P. 13 Lines 416-420 we now write: “Functional imaging of cortical activity with two different genetically-encoded calcium indicators each showed similar spatiotemporal dynamics of whisker sensory processing with the earliest contextdependent divergence in signalling being detected in RSC, out of the imaged dorsal cortical areas (Figure 3).” On P. 15 Lines 470-473, we now write: “Finally, it is of course important to note that many subcortical regions (as well as non-dorsal cortical regions, which were not imaged) are likely to contribute importantly to context-dependent task performance.”

      (3) Fit a simple exponential/logistic to lick probability vs time-since-switch (your Figure 1Hstyle analysis) to report a time constant with CIs; it will help quantify the integration of the continuous cue.

      We thank the reviewer for this suggestion. We have fitted an exponential to the grand average data to quantify the time constants for integration of contextual information before the presentation of the first whisker stimulus of the block (see new Figure 1H). On P. 6 Lines 170-173 we now write: “To assess whether this temporal integration would differ between contexts we fitted an exponential to the time evolution of the lick probability. This suggested a faster transition to the W+ context than to the W- context (W+ time constant: 9.4 s, W- time constant: 15.5 s) (Figure 1H).”

      (4) Because catch-trial false alarms are higher in W+ than W−, report per-context d′ and criterion for whisker trials (using signal detection theory); this separates sensitivity from bias and makes the behavioral shift more interpretable. It is also further proof that the behavior is contextual (versus a compound stimulus, for example).

      We have computed the d’ and criterion for the whisker trials in the W- and W+ contexts. (see new Figure 1 - figure supplementary 1D). As suggested by the reviewer, this further supports that the behavior is driven by contextual information.

      (5) For the pre-stimulus seed-correlation analysis, can you regress out the pupil/jaw/whisker activity to confirm whether the context modulation is (or is not) movement-driven? It would be helpful to better understand whether the baseline correlation is driven by differences in lowlevel factors between the contexts, versus the higher-level decision rule/context.

      The reviewer raises an interesting point. However, we did not find a straightforward way to regress out movements, and thus we leave this point for future in-depth analysis. On P. 11 Lines 354-357 we now write: “It is important to note that these context-dependent changes in resting-state functional connectivity could relate to the overt context-dependent movements in the prestimulus baseline (Figure 1I&J) and/or a manifestation of higher-level internal rule representations.”

      (6) For the earliest divergence analysis, is this consistent across animals and across sessions within animals? Can you show per-mouse distributions of first-crossing times (d′>2) for RSC vs wM1/2/wS2? This would help provide confidence in this key finding.

      The d’ presented in Figure 3H is computed as the discriminability between contexts at the population level, meaning that at each timepoint (from Figure 3F) we compared the 2 distributions built on N=6 mice. As such if the divergence between context was not consistent across animals this d’ would be low. That said, as suggested by the reviewer, we further investigated this context divergence at single mouse level and single session level. Our analysis supporting the main finding (Figure 3F-H) is shown in new Figure 3 – figure supplement 3.

      First, we show the results for a single mouse across sessions in Figure 3 – figure supplement 3A. We show the stimulus aligned activity in correct whisker trials in both contexts for the 3 recording sessions. For each session we quantified the main effect size defined as the difference of the trial average between contexts. Plotting the difference of mean response, we consistently observed that RSC ramps-up before wM1/2 for the 3 sessions.

      Second, across all individual mice: we further aggregated the session average responses to show discriminability between context for each region at the single mouse level (Figure 3 – figure supplement 3B). We show that RSC is the first region to exhibit context separation in 4 out of the 6 mice that we recorded. In 2 other mice all regions seemed to show context separation but without clear temporal ordering.

      Finally, when averaging across mice, we observed a clear separation and first discrimination in RSC (Figure 3F-H and Figure 3 – figure supplement 3C).

      Overall, these further analyses suggest that the early divergence of RSC activity appears to be robust with a consistent mean difference in single sessions and single mice, as well as across the population of mice. We think this analysis has strengthened our manuscript and we thank the reviewer for the valuable suggestion.

      (7) For the opto mapping data, could you provide P(lick) effect sizes with CIs per grid site? It would also be nice to summarize the qualitative dichotomy: RSC/tjS1 increases licking in W−; canonical wS1/wS2/wM/ALM decreases licking across contexts (to my understanding).

      We now provide the P(lick) effect sizes for the main cortical areas studied in the paper in Figure 2 – figure supplement 1C. This shows the relative change in lick probability in optogenetic trials compare to control trials for each mouse.

      Reviewer #2 (Recommendations for the authors):

      (1) Do mice move their whiskers after stimulus onset? If so, are these movements dependent on behavioral context? What causes the increase in S1 activity during auditory-evoked response trials?

      To answer the reviewer’s questions we have further investigated whisker movements following the sensory stimuli (whisker and auditory correct trials) in both contexts. The results of this analysis are presented in new Figure 3 – figure supplement 4.

      We find that mice move their whiskers shortly after the whisker stimulus in both contexts. The time course of whisker angle in correct whisker trials is similar in both contexts with a discriminability index (d’) consistently below 1. The whisker speed in response to stimulus is slightly higher in the W+ context compared to W- with a d’ slightly above 1 after ~100 ms. We also observed evoked whisker movements in auditory trials independent of context. Thus, whisker movements are indeed evoked by the sensory stimuli, but the overall context-dependent modulation of whisker movements is weak. The early differences in whisker-evoked cortical activity in W+ compared to W- contexts are therefore more likely related to the integration of contextual information than to differences in evoked movements.

      The reviewer is correct to point out that wS1 activity increases in auditory trials (Figure 3E). The response is initially very weak, but becomes more prominent after ~100 ms following the auditory tone. We do not know the underlying mechanisms, but there are several likely explanations. First, as discussed above, there are indeed some whisker movements evoked in response to the auditory stimulus (Figure 3 – figure supplement 4), which could result in sensory input to wS1. Equally, the increase could relate to licking, given the broad representation of movements in cortex and an appropriate reaction time in auditory trials (Figure 3C). Alternatively, wS1 activity in auditory trials could also be related to input connectivity from auditory cortex, top-down input from frontal cortex or subcortical regions such as high-order POm.

      (2) What do the authors think is causing the W+ vs W- difference in S1/S2 activity approximately 100ms after whisker deflection?

      The late W+ vs W- difference in wS1/wS2 activity could be explained by several factors. First this could be due to the difference in whisker movements after ~100 ms as shown in Figure 3 – figure supplement 4. Second this could be driven by the lick vs no lick activity (see reaction time in Figure 3C for whisker trials ~110 ms). Finally, this could be partly due to some movement independent top-down contextual information reaching wS1/wS2 at late time points. Overall, our claim in the paper is that there was no contextual difference in whisker primary and secondary cortices at early time points (before movement). On P. 9 Lines 270-273 we explicitly write: “Early after stimulus onset, whisker deflection evoked similar activation of primary and secondary whisker somatosensory cortices (wS1 and wS2) in both W+ and W− contexts.” In contrast, our main findings are grounded in the divergence of cortical activity in RSC and wM1/2 at early time points (<100 ms).

      (3) The choice of PC3 seems arbitrary. Is there no task-relevant information in PC1 and PC2?

      We appreciate the point raised by the reviewer and have clarified the reasoning leading to PC3 selection in the main text, where on P. 12-13 Lines 384-391 we now write: “The loadings of the first principal components were uniformly distributed and could reflect a late movement driven activation distributed across all cortical areas (Figure 4 – figure supplement 2C&D). PC2 loadings show variation along the anteroposterior axis that could reflect differences between sensory and motor regions but its time course does not separate between lick and no lick in control conditions (Figure 4 – figure supplement 2C&D). The loadings of PC3 highlighted task-related cortical regions and its time course exhibited clear differences comparing lick and no-lick trials.” In addition, we now also show the time courses for PC1 and PC2 in Figure 4 – figure supplementary 2D.

      Overall, the reasoning is the following:

      PC1 has spatially-homogeneous positive loadings (Figure 4 – figure supplementary 2C) and activity along PC1 gradually ramps up following sensory stimulation (Figure 4 – figure supplementary 2D). It is likely driven by widespread activation of the cortex following the whisker stimulus and the lick response. As such we believe that the taskrelated information captured by PC1 is movement related and not necessarily informative about processing of whisker and context.

      PC 2 has loadings varying along the antero-posterior axis (Figure 4 – figure supplementary 2C), which could be relevant for the task, but its time-course does not discriminate between lick and no lick neither in W+ nor W- (Figure 4 – figure supplementary 2D).

      PC3 has both loadings that vary between several cortical regions involved in the task (Figure 4 – figure supplementary 2C) and a time course that separates between lick and no lick in both contexts (Figure 4 – figure supplementary 2D). We thus focus on PC3 to investigate the effect of optogenetic inactivation on whisker stimulus evoked activity.

      The remaining components beyond PC3 contain a very small fraction of variance and were thus not considered.

      (4) Figure 3 - Supplement 1: What explains the change in fluorescence in GFP/tdT mice during W+ stimulation? Is it brain movement on the z-dimension? Could this explain differences in calcium imaging results?

      We thank the reviewer for this question. The nature of intrinsic signals is a complex topic, but brain movement is unlikely to contribute importantly, because under similar behavioral conditions we (and others) typically find brain movements to be on the scale of a few microns. The three most widely-reported contributions to intrinsic optical changes in cortex relate to:

      (i) Light scattering – as neurons integrate synaptic inputs and fire action potentials, the neuronal elements swell slightly due to the ionic and water fluxes (see for example Vincis et al. Cell Reports 2015, doi: 10.1016/j.celrep.2015.06.016). This reduces the refractive index mismatch between the intracellular and extracellular space. This in turn reduces light scattering, which could result in fluorescence increases.

      (ii) Hemodynamics – changes in blood volume and changes in oxygenation/deoxygenation will change the absorption of light at different wavelengths, in an activity-dependent manner (also forming the basis of BOLD fMRI signals).

      (iii) Flavoproteins – endogenous fluorescent proteins, such as flavoproteins present at high levels in mitochondria, have been reported to change their fluorescence depending upon neuronal activity, presumably in relationship to increased mitochondrial activity.

      We therefore think it is very important to image GFP/tdTomato-expressing mice as controls, and we would suggest that this should be carried out more commonly in the field. Indeed, similar to our results, another study (Yogesh et al., eLife 2025, doi: 10.7554/eLife.104914) recently reported upon the importance of carefully examining intrinsic fluorescence changes, which were found to be present in both wide-field and two-photon imaging of GFP expressing mice.

      Our results reported in Figure 3 – figure supplement 1, show that GFP/tdTomato signals over the first ~120 ms following whisker stimulation were much smaller that the equivalent changes in GCaMP6f/jRGECO1a-expressing mice, and therefore would only have a minor contribution to our analyses. However, we refrained from analysing fluorescence changes at later post-stimulus times, because the intrinsic signals indeed become increasingly prominent as the mice initiate licking.

    1. Author response:

      The following is the authors’ response to the original reviews

      General note

      We have issued a new release of the general Peekbank database, 2026.1, which includes more data integrity checks and several more datasets. As a result of this release, the underlying dataset we use in our paper has shifted slightly. The shifts represent a relatively small proportion of the total data and thus these changes have caused only relatively minor changes to our numerical results. We also highlight that we now include a small amount of data regarding children younger than 12 months, increasing the developmental range of our analysis (see Figure 1).

      Reviewer 1 (Public review):

      The limitations of the study are acknowledged to some extent, but need to be improved and ensured that they run throughout the manuscript. Thus, in the discussion, the authors note that the approach is observational and exploratory, and highlight for me a key alternative explanation of the findings, namely that faster children could be faster due to their larger vocabulary, rather than faster children learning more words. Indeed, the latter explanation for the relationship is called into question, given that growth in speed was not related to growth in vocabulary. Here, the authors note that the null result may be related to the fact that they do not sufficiently precise estimates of growth slopes, rather than taking the alternative explanation seriously that there may not be as causal a link between being a faster word learner and a better word learner (learn more words).

      Thank you very much for your challenging and thoughtful comments. In hindsight we did not realize that the way we were writing about our results was ambiguous between several interpretations (one of which we endorse and one of which we do not).

      We respond below to the specific suggestions about causal directionality in the longitudinal analysis, but we certainly believe that we cannot draw strong conclusions about causality from our dataset and have attempted throughout the paper to remove causal language that might have crept into our interpretation.

      In response to your comments, we have made a number of key revisions aimed at qualifying and clarifying our points:

      • The abstract now prominently notes that our design is observational: “In an observational study…”

      • The abstract notes a positive and a negative result in the relationship between word recognition and vocabulary: “Further, across a range of longitudinal models, speed, accuracy, and vocabulary were coupled. Children with overall faster word recognition tended to show faster vocabulary growth, though developmental growth in word recognition skill was not specifically associated with growth in vocabulary.”

      • The abstract removes potential casual language in the final sentence: “... these findings support the view that word recognition is a skill that develops gradually across early childhood and that this skill is deeply intertwined with early language learning.”

      • A new paragraph in the Results introduces the potential hypotheses investigated via the longitudinal models.

      • The final paragraph of the Results section sharpens the contrast between two possible growth hypotheses: “However, we did not find evidence for the stronger version of this claim: in neither the non-linear growth model nor the linear SEM did we find evidence that increases in speed were related to increases in vocabulary size. Thus, our findings do not support a ‘virtuous cycle’ model in which increases in recognition specifically lead to increases in vocabulary size.”

      We hope these changes lead to a manuscript that better aligns with the limitations of the study.

      This is especially since, but correct me if I’m wrong here, the current vocabulary size is not taken into consideration in the model examining vocabulary growth. Given the increasing number of studies showing that current vocabulary knowledge predicts vocabulary growth (Laing, Kalinowski et al, Siew & Vitevitch), one simple alternative explanation is that current vocabulary knowledge predicts both current word recognition skill and later vocabulary knowledge. Is there anything in the data speaking against this hypothesis?

      We think the reviewer’s overall point is generally correct, as we described above, but we want to clarify a specific statistical point. The non-linear longitudinal model of vocabulary growth does in fact take into account a child’s average vocabulary size. (This point feels tricky in a non-linear model but it’s actually quite similar to a linear model for the purposes of this discussion). Basically, vocabulary (at all timepoints) is modeled as a function of age, with both main effects and interactions with age. Critically, each participant is also modeled as having a random intercept capturing their deviation from the average growth pattern across ages (as expressed by the fixed effects). In this model, the “main effect” (here captured by the intercept for the logistic curve in the model) that we observe for speed indicates that vocabulary growth for individuals is predicted to be faster (their curve is shifted left) if their RTs are fast. The presence of the random effects in this model thus “controls” for the fact that some participants have overall higher vocabularies (and are shifted up relative to the average growth curve).

      But, we note that this model does not show an “interaction effect” (here captured by the null effect of RT on the slope parameter in the logistic model). That’s one of the null effects that we now call out much more prominently in the abstract and end of the results (per our response above).

      Equally, while the SEM examines vocabulary growth controlling for age, I wonder about the other way around. What would happen to the effect of age on word recognition skill (in the LME model, S8) if one were to add concurrent vocabulary size? So does chronological age explain word recognition skill or vocabulary knowledge? Right now, the manuscript describes this effect purely related to chronological age, but is it age per se or other cognitive abilities, including a key change across development, namely, vocabulary size? Thus, the presentation of the skill learning hypothesis suggests that age is a proxy for experience, while you actually have here a very nice proxy for experience in terms of children’s vocabulary size.

      Again, thank you for engaging with this tricky set of issues. Overall, our goal is to adjust the manuscript to reflect points of agreement; in particular, we agree that age is a proxy for language experience, vocabulary, and other cognitive changes, and we have stated this explicitly now in the intro to the factor analyses: “In our prior analyses, chronological age acts as a proxy for greater language experience and larger vocabulary as well as a host of other correlated developmental changes in cognition. Now we explicitly explore relations to vocabulary growth and the triadic relationship between age, word recognition, and vocabulary.”

      On the statistical side, we do think that the NLME (non-linear mixed effects; the logistic growth mode) effectively controls for average vocabulary size, as described above. The longitudinal SEM also relates vocabulary growth to growth in word recognition skill. In both models, we find no evidence for coupled growth; instead the evidence points to children with higher baseline word recognition skill showing faster growth in vocabulary (speed intercept significantly related to vocabulary slope, -.14, p < .01) but not the reverse (vocabulary intercept not strongly related to speed slope; -.01, ns).

      More generally, we hope our edits to the paper, detailed above, both clarify this tricky set of issues and also remove inappropriate casual language throughout.

      Critically, while the discussion is more nuanced, the way the abstract is concluded and the way the Introduction is phrased suggest that the study is able to answer a causal question, which, as the authors themselves note, is not possible. The abstract, for instance, states that word recognition becomes faster, more accurate and less variable...consistent with a process of skill learning. And also that this skill plays a role in supporting early language learning, which is very causal language. I don’t think you can really claim that you are testing the two hypotheses you suggest here. The work is definitely embedded in the context of these hypotheses, but are you really able to test them? My worry is that while the discussion is more nuanced, the extent to which this study will then be cited down the line as showing that children learn more words down the line because they are faster at recognizing words, and anything that you can do to tamper with such interpretations would be good for the literature. For me, this should not just be relegated to the discussion but should be touched upon in the abstract and Introduction.

      Thanks for pushing us to be more precise with how we frame and describe our findings. We agree with the reviewer that our findings do not warrant strong conclusions about the causal role of word recognition skill in vocabulary growth. Per our response above, we have now tried to carefully revise our language throughout the paper (in particular, in the abstract and introduction, as noted by the reviewer).

      Finally, it would help to talk more about the mechanisms at work in any relationship between word recognition and language learning. It seems to me that this would rely on some predictive processing framework, given the description on page 4, and it would be good to make this clear (faster and more accurately you can recognize a ball, better use this evidence to infer the speaker’s intended meaning).

      Thanks, this is a great point. We’ve revised this text and added references to predictive processing, unpacking a problematic paragraph into two:

      “Familiar word recognition -- as measured by LWL -- is hypothesized to play a key role in language learning (19). The idea, in a nutshell, is that the faster and more accurately a child can process incoming words, the more opportunities they have for learning. Consider a child hearing the utterance "Can you put the ball in the crate?" The better the child can recognize the word "ball", the better they can use this evidence to help infer the speaker's intended meaning, allowing possible inferences about the meaning of the less familiar word, "crate" (20).

      “Real time language processing, including word recognition, relies heavily on predictive processing, in which comprehenders integrate expectations from prior linguistic context with noisy and ephemeral incoming signals (21, 22). The more input a child receives, the better their predictions are likely to be, and hence the more they can learn (19, 23). Indeed, measurements of children's language input at home are consistently associated with their vocabulary size (24, 25). And, in line with this predictive processing framework, one important study found that children's word recognition speed mediated the longitudinal relationship between home language input and vocabulary growth (26). Thus, word recognition is thought to be a key support for ongoing word learning.”

      Equally, when referring to word recognition, it would be good to clarify what this refers to - how well a child knows what a word refers to (and in the context of LWL, what it does not refer to) or how quickly it directs attention to what is referred to.

      Thanks, we’ve added a capsule definition in the second paragraph, and added the sentence “This procedure [LWL] measures the general construct of word recognition by operationalizing knowledge of a meaning as visual attention to a specific named referent.” We hope this clarifies the relationship between LWL and word recognition.

      With regards to the data, I wonder if there is a clustering of kids past 24 months that is happening here, looking at Figures 1 and 2, where it seems like there is less change past the 24-month point. Is there any way to look at whether the effect of age or vocabulary on word recognition is not linear but asymptotic?

      Thanks for pointing this out; we do see what you are talking about but think it’s being handled appropriately in the analysis. In Figure 1 it clearly looks like changes to RT are asymptotic – this is why we analyze the logarithm of RT throughout the paper. In Supplement S6 we show that reaction time is indeed best fit by a log-log function. Your question about Figure 2 asks whether there is further structure beyond the log-log fit; in Supplement S7 we show some analyses that suggest a polynomial fit is not better than the log-log fit; there is some small additional linear effect of age over and above the log-log fit, but it’s minor and pretty hard to interpret in our view.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Page 3. Word production may manifest in overt behaviour but need not reflect complete knowledge. A child can say the word dog and use it to refer to a cat.

      This is a good point. Since we are not able to speak to the precision of meaning representations (an important issue in its own right), we have omitted the phrase “with incomplete knowledge.”

      Page 4. The first two sentences of the paragraph beginning with word recognition ability... don’t go together. The second sentence does not support the claim that word recognition plays a role in language learning.

      Thanks, we’ve tried to smooth out this transition as part of unpacking the role of predictive processes.

      Page 4. “predicts children’s standardized test scores years later” - make clear what test scores are here.

      We added some additional details. The specific tests were the CELF (expressive language) and the KABC (IQ), but we thought too much detail might be distracting.

      Page 5. I love Table 1, but would like for the data to be weighted somehow. So, given that some studies had a lot more trials and more children, what percentage of the data did this study contribute? That allows a clearer view of how biased the sample is in certain studies. The x in CDIS and longitudinal could be aligned to the right. I kept wondering why there was an x near some trials.

      Thanks, we’ve adjusted the table to add the percentage of the total dataset (in trials) due to each study and fixed the alignment issue.

      Page 6. 12 million individual samples: what samples are these? Individual data points per trial per time point. Making this clear would be great.

      Clarified, thanks.

      Page 9. Your accuracy measures only seem to consider the target. From what I remember of my preferential looking days, this measure usually also includes the distractor. Why do you not do this? This is especially since you have such a wide age range, so if a 12-month-old only looks for about 50 per cent of the trial and spends that time looking at the target, that is very different from a child who looks at the screen all of the trial and spends less time looking at the target here.

      Sorry for any lack of clarity: we do in fact compute accuracy as the ratio of looking to target over looking to target plus looking to distractor. We have added this information to the parenthetical referenced above: “... accuracy (more target looking; computed as the ratio of target to target plus distractor looking)”.

      Page 12. I only found out that age was in this model by looking at S9.

      Thanks for mentioning this omission, we’ve clarified in the text: “We initially add age as an additional variable to our models to explore whether this factor structure relates to age; later we treat age as a predictor of latent factors.”

      Page 12. Isn’t it trivial that speed and accuracy show negative covariance, especially given how you measure accuracy? Thus, if I take longer to fixate the target, I have less time to look at the target during the trial. If, however, I included the distractor in my accuracy measure, then I could still take longer to look at the target, but still look more at the target than the distractor.

      Thanks for mentioning that this covariance is not the key result of interest; that observation didn’t come out in the text. Now we note that this covariation is “... as expected since they [speed and accuracy] are derived from the same data.” Note per above that accuracy is computed as target / target + distractor looking; even so, your observation is correct: slower looking at the target means lower accuracy at least to some degree.

      Page 19. If you excluded data from trials with less than 50% of timepoints, how did this vary across age? Arguably, your study has to worry less about this, given your sample size, but it would be nice to know, which you could include in the percentage of data that each study contributed to the final sample.

      Thanks, we’ve added this information to a new table in S1.

      Reviewer #2 (Public review):

      First, I wasn’t entirely clear about what the authors meant by “word recognition ability”. For much of the manuscript (including the use of the term “word recognition ability” itself), this comes across as an intrinsic ability or skill that improves with development. Alternatively, the speed and accuracy metrics taken from studies in Peekbank might capture children’s increasing knowledge of the common, concrete words typically used in these studies. To me, this is a somewhat different construct from a general skill at recognizing words. It would be helpful if the authors could clarify which construct they intend to capture, or if it is not possible to distinguish between these constructs from the Peekbank data.

      In response to this comment and related comments above, we’ve added text to the first two paragraphs trying to clarify the general construct that we’re talking about – recognizing the meaning of a word in real-time language comprehension. We’ve also clarified several times throughout the introduction that we’re talking about familiar word recognition, that is, the ability to recognize specific known words. Further, we directly acknowledge the issue above in the introduction:

      “Critically, most word recognition paradigms use words that children at the target age are reported to understand and produce. They are thus not indices of vocabulary size but rather measures of how quickly and accurately the child can recognize a familiar spoken word and use it to guide their visual attention to a referent. However, it is unknown the extent to which specific responses reflect an individual child's general speed of language processing versus their familiarity of specific words.”

      Second, and relatedly, if the source of the age-related improvements is increasing experience with the common concrete words used in the Peekbank studies, then one might expect word recognition and improvements with age to be related to word frequency, given that more frequent words are experienced more often. Word frequency predicts word knowledge when assessed using CDI data. Can effects of frequency be detected in Peekbank word recognition metrics? If not, why? Similarly, is the speed and accuracy of word recognition in Peekbank data related to CDI-derived word age of acquisition, and again, if not, why?

      This is a fascinating set of ideas, and one that we’ve pursued extensively using the Peekbank data. Unfortunately, we think it is out of scope for the current paper, which focuses on child-level metrics (including vocabulary and processing measures). Right now the current paper doesn’t include any analysis of individual words.

      Just to expand a bit on the problem here: unfortunately, modeling word recognition as a simple linear function of (log) word frequency is only possible in the case that distractors are held constant (e.g., “ball” always has “book” as its distractor), because distractor frequency plays an important role in the recognition process. However, in our dataset, words are paired with many different distractors across studies. This property means a fairly complex model of the LWL decision process would be necessary for a model to successfully predict effects for individual words. While such a model is an exciting research goal, it’s not something we can include in the current manuscript.

      Finally, there is a bit of a risk of the main findings of this paper coming across as a foregone conclusion. I.e., how could it be otherwise that word recognition improves with development?

      Reviewer #2 (Recommendations for the authors):

      Regarding the feedback about the risk of the findings coming across as a foregone conclusion - perhaps a primary place in the paper where it would be useful to clarify this point is on page 6, in the paragraph beginning, “We investigate two specific hypotheses here. First, one influential theory...”. Here, it might be worth clarifying whether there are alternative ideas about the emergence of word recognition in childhood that predict different patterns, so that the findings of the current paper can be framed as shedding new light on word recognition in development, rather than a confirmation of the common-sense idea that word recognition must improve over development.

      Thanks, we appreciate this feedback and it’s something we’ve struggled with in this project. Our conclusion is that this paper does not constitute a binary hypothesis test of e.g., whether word recognition is linked to vocabulary development. Instead, we lean into the idea that there are empirical issues (rather than hypotheses) that have not been quantified sufficiently. Thus, we end the revised introduction with the following paragraph:

      “Across both of these issues, the contribution of our work here lies in the detailed quantitative description of development. Nearly every theory of language learning assumes some role for continuous developmental change in word recognition, but these assumptions have not previously been anchored to specific measurements. Hence neither the functional form of the assumed changes nor their concurrent and predictive relationships to vocabulary have been quantified. We leverage the Peekbank dataset to accomplish these goals.”

    1. Author response:

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

      We would like to express our deep appreciation to the editor and reviewers for their constructive comments and suggestions, which have significantly improved the quality of our manuscript. In response, we have carefully revised the manuscript, addressed all comments, and performed additional experiments and analyses to strengthen our findings.

      (1) We repeated retrograde tracing using CTB-647 to verify precise targeting of SPN and DGC neurons, as shown in the new Figure 7.

      (2) We performed dual retrograde tracing combined with fiber photometry or optogenetic activation to investigate the role of PMC dual-projecting neurons in the control of urination, as shown in Figure supplements 11 and 12.

      (3) We conducted new experiments activating PMC<sup>ESR1+</sup> neurons after PDNx to assess their role in urination, as shown in new Figure 6.

      (4) We added a more detailed analysis of the dynamics of neural responses in PMC<sup>ESR1+</sup> neurons in Figure supplements 3F-3G.

      (5) We analyzed peak Ca<sup>2+</sup> signals in the PMC during and after the onset of EMG bursting, as shown in Figure supplement 4F.

      (6) We added a comparison of spontaneous and light-induced spikes in PMC<sup>ESR1+</sup> neurons, as shown in Figure supplements 3B–3C.

      (7) We expanded the Discussion to address how PMC<sup>ESR1+</sup> neurons coordinate bladder contraction and sphincter relaxation to control both the initiation and suspension of urination.

      We hope these revisions meet the reviewers' expectations and contribute to the improvement of our manuscript.

      Reviewer #1 (Public review):

      Summary:

      Urination requires precise coordination between the bladder and external urethral sphincter (EUS), while the neural substrates controlling this coordination remain poorly understood. In this study, Li et al. identify estrogen receptor 1-expressing neurons (ESR1+) in Barrington's nucleus as key regulators that faithfully initiate or suspend urination. Results from peripheral nerve lesions suggest that BarEsr1 neurons play independent roles in controlling bladder contraction and relaxation of the EUS. Finally, the authors performed region-specific retrograde tracing, claiming that distinct populations of BarEsr1 neurons target specific spinal nuclei involved in regulating the bladder and EUS, respectively.

      Strengths:

      Overall, the work is of high quality. The authors integrate several cutting-edge technologies and sophisticated, thorough analyses, including opto-tagged single unit recordings, combined optogenetics, and urodynamics, particularly those following distinct peripheral nerve lesions.

      We are grateful for your insightful and constructive comments, which affirmed the importance and technical depth of our work. Thank you for dedicating your expertise and time to reviewing our manuscript. Guided by your suggestions, we have revised the paper as detailed below.

      Weaknesses:

      (1) My major concern is the novelty of this study. Keller et al. 2018 have shown that BarEsr1 neurons are active during urination and play an essential role in relaxing the external urethral sphincter (EUS). Minimally, substantial content that merely confirms previous findings (e.g. Figures 1A-E; Figures 3A-E) should be move to the supplementary datasets.

      Thank you for this valuable and constructive comment. We fully agree that the novelty of our study relative to Keller et al., 2018 must be made explicit. Keller et al. established that PMC<sup>ESR1+</sup> neurons are active during socially evoked urine-marking behavior (voluntary urination) and demonstrated their essential role in relaxing the EUS. Their study mainly focused on behavioral context and EUS relaxation. In contrast, our work addresses a distinct, mechanistic question: how these same neurons participate in reflexive, physiological urination and coordinate both bladder detrusor contraction and EUS relaxation.

      Novel aspects of the present study:

      (1) Temporal dynamics of PMC<sup>ESR1+</sup> neurons during reflexive micturition.

      Using opto-tagging and single-unit recordings, we reveal the precise firing pattern of PMC<sup>ESR1+</sup> neurons during reflexive voiding. Simultaneous fiber photometry, cystometry, and EUS-EMG recordings demonstrate that population-level activity of PMC<sup>ESR1+</sup> neurons precedes and tightly correlates with both bladder contraction and EUS relaxation a coordination not previously demonstrated.

      (2) Causal role in reflexive urination.

      Manual closed-loop optogenetic inhibition at the onset of reflexive voiding acutely terminates EUS bursting and bladder contraction, immediately halting urine release.

      (3) Dual control of bladder and EUS.

      Optogenetic activation combined with selective pelvic or pudendal nerve transection shows that PMC<sup>ESR1+</sup> neurons drive both bladder contraction and EUS relaxation, revealing a coordinating role beyond EUS relaxation alone.

      (4) Anatomical substrate for coordinated control of bladder contraction and EUS relaxation in reflexive urination.

      Retrograde tracing identifies three spinal-projecting sub-populations: SPN-only, DGC-only, and dual-targeting neurons, providing a circuit-level explanation for the simultaneous control of bladder and EUS.

      Following your suggestion, panels that merely replicate Keller et al. (former Figures 1A–1E and Figures 3A–3E) have been moved to new Figure Supplements 1 and 7, respectively, so that the main figures now emphasize the new mechanistic findings.

      (2) I also have concerns regarding the results showing that the inactivation of BarEsr1 neurons led to the cessation of EUS muscle firing (Figures 2G and S5C). As shown in the cartoon illustration of Figure 8, spinal projections of BarEsr1 neurons contact interneurons (presumably inhibitory) that innervate motor neurons, which in turn excite the EUS. I would therefore expect that the inactivation of BarEsr1 should shift the EUS firing pattern from phasic (as relaxation) to tonic (removal of relaxation), rather than stopping their firing entirely. Could the authors comment on this and provide potential reasons or mechanisms for this finding?

      Thank you for this crucial comment. We apologize that the representative EUS-EMG traces in Figures 2G and S5C were too small to be clearly seen and that the corresponding results description was not sufficiently accurate. We have now replaced these EMG traces with enlarged versions (revised Figures 2G and S5C) and revised the corresponding Results section (lines 184, 197, 340-341). Based on the enlarged traces, we found that acute photoinhibition of PMC<sup>ESR1+</sup> neurons at the onset of phasic EUS-EMG bursting shifted the EUS firing pattern from large-amplitude phasic bursts to low-amplitude tonic firing. This suggests that ongoing activity of PMC<sup>ESR1+</sup> neurons is required to maintain phasic EUS bursting. A similar shift from phasic to tonic EUS-EMG activity during optogenetic silencing of PMC<sup>ESR1+</sup> neurons was reported by Keller et al., 2018 (Figure supplement 8C), confirming the reproducibility of the phenotype. We propose that the potential mechanism of this low-amplitude tonic activity may be mediated in part by a spinal reflex pathway (the guarding reflex) for preventing urination, whereby the loss of PMC<sup>ESR1+</sup> neurons-mediated supraspinal facilitation reduces inhibition of spinal interneurons, leading to enhanced baseline excitability of EUS motor neurons in response to bladder afferent input during bladder distension (William C. de Groat et al., Comprehensive Physiology. 2015, PMID: 25589273).

      (3) Current evidence is insufficient to support the claim that the majority of BarEsr1 neurons innervate the SPN but not DGC. The current spinal images are uninformative, as the fluorescence reflects the distribution of Esr1- or Crh-expressing neurons in the spinal cord, along with descending BarEsr1 or BarCrh axons. Given the close anatomical proximity of these two nuclei, a more thorough histological analysis is required to demonstrate that the spinal injections were accurately confined to either the SPN or the DGC.

      Thank you for raising this important concern. To rigorously verify that our spinal injections were confined to either the SPN or the DGC, we performed new retrograde-tracing experiments in ESR1-Cre and CRH-Cre mice. We injected a mixture of AAV-Retro-DIO-mCherry or AAV-Retro-DIO-EGFP with the retrograde tracer CTB-647 specifically into the SPN or DGC (Methods, lines 465-466). Only animals in which CTB-647 fluorescence was strictly limited to the target nucleus, without detectable spread to the adjacent region, were included in the analysis (new Figures 7A and 7E). These results confirm our original observation that PMC<sup>ESR1+</sup> neurons comprise three distinct spinal-projection subpopulations: one (19.0%) targeting the SPN, one (52.2%) innervating the DGC, and a third (28.8%) projecting to both regions (Results, lines 304–306; new Figures 7F–7H). In addition, the majority of PMC<sup>CRH+</sup> neurons project to the SPN but not the DGC (new Figures 7B–7D; Results, lines 297–301). We have assembled new Figure 7 using the newly acquired spinal images and the validated data.

      Reviewer #1 (Recommendations for the authors):

      From the abstract: "Anatomically, PMCESR1+ cells possess two subpopulations projecting to either the pelvic or pudendal nerve". I don't think these neurons directly project to either nerve.

      Thank you for this precise comment. We apologize for incorrectly stating that PMC<sup>ESR1+</sup> cells project directly to the pelvic or pudendal nerves. In the revised Abstract (lines 32–36) we have rephrased the sentence to clarify the actual anatomy: “Anatomically, PMC<sup>ESR1+</sup> neurons consist of three distinct spinal-projection-based subpopulations: one targeting the sacral parasympathetic nucleus (SPN), one innervating the dorsal gray commissure (DGC), and a third that projects to both regions, thereby enforcing the coordination of bladder contraction and sphincter relaxation in a rigid temporal sequence.”. We trust this revision now accurately reflects the anatomical findings.

      Reviewer #2 (Public review):

      Summary:

      The authors have performed a rigorous study to assess the role of ESR1+ neurons in the PMC to control the coordination of bladder and sphincter muscles during urination. This is an important extension of previous work defining the role of these brainstem neurons, and convincingly adds to the understanding of their role as master regulators of urination. This is a thorough, well-done study that clarifies how the Pontine micturition center coordinates different muscle groups for efficient urination, but there are some questions and considerations that remain.

      Strengths:

      These data are thorough and convincing in showing that ESR1+PMC neurons exert coordinated control over both the bladder and sphincter activity, which is essential for efficient urination. The anatomical distinctions in pelvic versus pudendal control are clear, and it's an advance to understand how this coordination occurs. This work offers a clearer picture of how micturition is driven.

      We sincerely thank you for highlighting the rigor of our study and for recognizing the advance in understanding how PMC<sup>ESR1+</sup> neurons exert coordinated, anatomically segregated control over bladder and sphincter. We also appreciate the constructive suggestions that helped us further improve clarity, which we address point-by-point below.

      Weaknesses:

      The dynamics of how this population of ESR1+ neurons is engaged in natural urination events remains unclear. Not all ESR1+ neurons are always engaged, and it is not measured whether this is simply variation in population activity, or if more neurons are engaged during more intense starting bladder pressures, for instance. In particular, the response dynamics of single and doubly-projecting neurons are not defined. Additionally, the model for how these neurons coordinate with CRH+ neuron activity in the PMC is not addressed, although these cell types seem to be engaged at the same time. Lastly, it would be interesting to know how sensory input can likely modulate the activity of these neurons, but this is perhaps a future direction.

      Thank you for this insightful comment. First, we agree that not all ESR1+ neurons are consistently engaged during urination (Figure 1B). Because bladder pressure was not measured during the opto-tagging experiments, we cannot determine whether this reflects trial-to-trial variability in population activity or pressure-dependent recruitment of additional neurons. We speculate that stronger starting bladder pressures may recruit a larger subset of ESR1+ neurons, analogous to graded, pressure-dependent recruitment observed in peripheral sensory neurons (Bruns et al., J Neural Eng. 2011, PMID: 21878706; Marshall et al., Nature. 2020, PMID: 33057202).

      Second, using fiber photometry recording and optogenetic activation, we examined the dynamics of dual-projecting neurons in the PMC that were retrogradely labeled from the SPN and DGC. Their activity correlated with bladder contraction and sphincter relaxation, and optogenetic activation sequentially induced these events to trigger urination (see Recommendation #8). Although retrograde labeling captured only a subset of dual-projecting neurons, the results indicate that they coordinate bladder and sphincter activity.

      Third, previous studies suggest that PMC<sup>CRH+</sup> cells are associated with bladder contraction and likely serve as an integration center for context-dependent micturition behavior (Hou et al., Cell. 2016, PMID: 27662084; Ito et al., Elife. 2020, PMID: 32347794). We therefore propose that PMC<sup>CRH+</sup> cells establish the baseline conditions and contextual readiness for voiding, whereas PMC<sup>ESR1+</sup> cells act as the executive command to reliably initiate and execute the event.

      Finally, we agree that sensory inputs likely modulate PMC<sup>ESR1+</sup> neuron activity. Although this falls beyond the scope of the present study, it represents an important avenue for future investigation.

      Reviewer #2 (Recommendations for the authors):

      (1) In the introduction, the authors write that Keller 2018 only showed this ESR1 population to induce EUS relaxation, but those results also do show bladder contraction with photostimulation of this population. While the authors' work extends this finding in important ways, this should be acknowledged (line 60).

      Thank you for this important correction. We have now revised the Introduction to explicitly acknowledge that stimulation of neurons expressing estrogen receptor 1 (ESR1) in the PMC (PMC<sup>ESR1+</sup>) contributes to sphincter relaxation and increased bladder pressure (Introduction, lines 60-62), as originally reported by Keller et al., 2018.

      (2) I think a more detailed analysis of the dynamics of neural responses in the PMC ESR1 neurons would be valuable. For example: are the same cells always engaged before micturition, or do different populations activate on different trials? Can the authors comment on the half of the opto-tagged ESR1 population that is not firing during urination? Do they ever fire? A cell-by-cell analysis of which neurons are engaged over multiple trials would be very valuable to understand the dynamics of population activity. Figure 1H shows cumulative sessions, but what do single sessions look like?

      Thank you for these valuable comments. In response, we have performed refined single-trial analyses of neuronal activity, as detailed in the point-by-point replies below.

      For example: are the same cells always engaged before micturition, or do different populations activate on different trials?

      Among 11 PMC<sup>ESR1+</sup> units that showed urination-related excitation, 8 units exhibited a consistent firing increase in every voiding trial, whereas the remaining 3 increased their discharge in >78 % of trials (Figure 1B; new Figure supplement 3F). Thus, the same PMC<sup>ESR1+</sup> cells are recruited repeatedly, rather than distinct populations being activated on different trials. We have added this clarification to Results (lines 106–108).

      Can the authors comment on the half of the opto-tagged ESR1 population that is not firing during urination? Do they ever fire? A cell-by-cell analysis of which neurons are engaged over multiple trials would be very valuable to understand the dynamics of population activity.

      Approximately half of the opto-tagged PMC<sup>ESR1+</sup> cells showed no increase in firing rate during urination, yet exhibited spontaneous spikes at other times (new Figure supplement 3G), confirming their electrical competence. Because the PMC also participates in defecation, uterine activity, and other pelvic functions (Rouzade-Dominguez et al., Eur J Neurosci. 2003, PMID: 14686905; Schellino et al., Frontiers in Neuroanatomy. 2020, PMID: 33013330; Quaghebeur et al., Auton Neurosci. 2021, PMID: 34391125), these ESR1+ neurons may serve functions other than urination. We have now added this cell-by-cell analysis and discussion to the manuscript (Results, lines 108-112).

      Figure 1 H shows cumulative sessions, but what do single sessions look like?

      As shown in new Figure supplements 3F–3G, single-session raster plots reveal that PMC<sup>ESR1+</sup> neurons display consistent firing patterns across individual trials. Neurons whose firing rate increased during urination did so in most trials (Figure supplement 3F), whereas neurons unrelated to voiding remained silent or showed no discernible rate change during voiding across trials (Figure supplement 3G). These single-session observations are consistent with the cumulative population analysis shown in Figure 1H (new Figure 1B).

      (3) Supplemental Figure 4: It seems clear from this figure that NVCs are only occurring when the sphincter fails to engage. Can the authors quantify how often this is the case?

      Thank you for this important point. We have now quantified the occurrence of non-voiding contractions (NVCs) across all 229 bladder contraction events from 3 mice shown in Supplemental Figure 4. NVCs were observed exclusively when the external urethral sphincter failed to relax, accounting for 62/229 events (27.1 %), whereas coordinated voiding contractions (VCs) occurred in the remaining 167 events (72.9 %). These new data are presented in Figure supplement 4C.

      (4) Continuing from the above point: the authors say that the insufficient top-down drive or strength of activity from PMC ESR1 neurons is why NVCs occur. In looking closely, it also seems there is a small hump and subsequent increase in the calcium signal when the EUS bursting begins (particularly clear in Supplementary Figure 4). Could this instead mean that the bursting/urethral activity itself is feeding back onto the PMC to continue/enhance its activity, and it is instead the lack of sphincter bursting that results in the NVC? Could the authors analyze the signal during and after bursting starts? This model is consistent with one of the classic reflexes defined by Barrington, in which urethral fluid flow/activation enhances bladder contraction. The Figure 4 transection experiments do not fully answer this, as the authors are driving activity in the PMC at this time, but they could test this using PDN transection with fiber photometry recording.

      Thank you for this important point. We fully agree that EUS bursting may provide excitatory feedback to the PMC that sustains or even amplifies its activity, and that the absence of such feedback could underlie NVCs. To test this possibility, we re-analyzed the fiber-photometry traces aligned to the onset and offset of each EUS bursting (new Figure supplement 4). A small but consistent hump in the Ca<sup>2+</sup> signal appeared before bursting onset and the Ca<sup>2+</sup> signal continued to rise throughout the bursting (Figure supplement 4B, yellow arrow). The amplitude at bursting offset was significantly higher than both the NVC peak and the level recorded at bursting onset. These observations support the interpretation that urethral fluid flow/activation supplies excitatory feedback that reinforces PMC activity and bladder contraction, consistent with Barrington’s classic reflex. We have incorporated these new analyses into the revised manuscript (lines 145–155 and Figure supplement 4F).

      We agree that the positive-feedback loop described by Barrington’s classic urethra-to-bladder reflex is an intriguing mechanism. However, the PDN-transection experiment in Figure 4 was designed to determine if bladder contractions triggered by PMC<sup>ESR1+</sup> cells can proceed in the absence of sphincter bursting, not to evaluate this reflex. Incorporating simultaneous fiber-photometry recording into the PDN-transection experiment would therefore go beyond the scope of the present study. In future work we are keen to combine PDN transection with fiber photometry to further determine whether the urethra-to-bladder reflex contributes to the sustained PMC activity observed in our paradigm.

      (5) In Figure 4, is the timing of sphincter engagement different with ChR2 stimulation from what normally occurs? It appears that the bursting happens immediately upon activation whereas bladder contraction is a bit delayed.

      Thank you for this important observation. We have carefully re-examined the EMG traces from all animals shown in Figure 4. We confirm that the onset of sphincter bursting activity during ChR2 stimulation is indeed more rapid than during natural reflex voiding; nevertheless, the onset of phasic sphincter bursting during ChR2 stimulation remained delayed relative to the intravesical pressure rise (see Figure 8B).

      The immediate sphincter discharge visible in some trials was tonic EUS discharge or rare irregular bursting, not the typical EUS bursting. This tonic pattern corresponds to the spinal guarding reflex that suppresses urine leakage (Fowler et al., Nature Reviews Neuroscience. 2008, PMID: 18490916; Keller et al., Nature Neuroscience. 2018, PMID: 30104734). These segments were identified by their amplitude and spectral content and excluded from burst-onset analysis. Our analysis protocol therefore distinguishes tonic guarding activity from true phasic bursting, ensuring that only the latter was used to determine burst timing.

      (6) The explanation on line 299 about how spinal reflexes are impinging on this circuit is confusing. I agree that the bladder contraction stopping later than the EUS signal likely has something to do with spinal reflexes, but it seems this could instead be feedback from the urethral fluid flow, which continues bladder contractions (urethra-destrusor facilitative reflex). Could the authors clarify their thoughts here?

      Thank you for highlighting this ambiguity. We agree that the delayed cessation of bladder contraction could equally reflect either (1) the urethra-to-bladder facilitative reflex driven by ongoing urethral fluid flow or (2) spinal reflexes that we described. In the revised manuscript (Results, lines 343–349), we have re-worded the paragraph to make this dual possibility explicit, thereby avoiding an overly strong emphasis on spinal mechanisms alone.

      (7) A note on phrasing: the authors frequently say PMCESR1 cells drive sphincter relaxation, but then show an effect on sphincter bursting. Experienced readers might realize that relaxation and bursting are connected, but this might be confusing for readers and should be clarified in the text.

      Thank you for highlighting the potential ambiguity. We agree that the sentence “PMC<sup>ESR1</sup> cells drive sphincter relaxation” can seem paradoxical when our data show increased EUS bursting. In adult mice, the EUS does not remain continuously relaxed during voiding; instead, it generates rhythmic bursting composed of high-frequency spike clusters (active periods) alternating with low tonic activity (silent periods), resulting in rhythmic contractions and relaxations of EUS. This phasic activity acts as a pump that facilitates urine flow through the narrow rodent urethra (Kadekawa et al., Am J Physiol Regul Integr Comp Physiol, 2016, PMID: 26818058). The EUS bursting activity we recorded is consistent with the results reported in previous studies (Keller et al., Nat Neurosci, 2018, PMID:30104734; Ito et al., Elife, 2020, PMID:32347794).

      Consequently, when PMC<sup>ESR1</sup> neurons initiate bursting, they simultaneously generate the relaxation phases that separate the spikes. To make this explicit we have replaced the phrase “PMC<sup>ESR1+</sup> cells drive sphincter relaxation” with “PMC<sup>ESR1</sup> neurons trigger EUS bursting, which generates rhythmic sphincter contractions and relaxations.” (Results, page 7, lines 219-221). We have applied similar clarifications throughout the revised manuscript (Results, lines 125-129). We hope this revision eliminates any apparent contradiction.

      (8) The question remains as to which neurons (dual projecting, single projecting, or all?) are active in natural urination. This is possible to do through dual injection of retrograde virus in SPN and DGC that could coordinately turn on Gcamp, but this challenging experiment is perhaps beyond the scope of this paper. Even still, the authors could discuss their model for whether the dual- and single-projecting neurons are all engaged at once in a natural urination event. Do the authors have any data that could provide insight as to when these sub-populations are active? Results from the opto-tagging in Figure 1 (and comment #2 about single neuron firing properties) might provide a foundation for hypotheses or insights.

      Thank you for this valuable suggestion. We have now performed the experiment you proposed: dual injection of retrograde virus (AAV-Retro-Cre and AAV-Retro-DIO-GCaMP6s) in SPN and DGC were used to selectively label PMC dual-projecting neurons, and a 200-µm optic fiber was implanted above the PMC to record their Ca<sup>2+</sup> dynamics during natural urination (Figure supplement 11A and Methods, lines 470–474, 652-655). Dual-projecting neurons exhibited robust activation throughout the entire voiding phase that was tightly correlated with intravesical pressure rise and EUS bursting (Figure supplements 11A–11H). However, technical limits of current retrograde tools preclude selective isolation of single-projecting (SPN-only or DGC-only) subsets for independent fiber-photometry recordings and injection restricted to one target unavoidably labels both single- and dual-projecting cells. We now state this technical limitation explicitly (Discussion, lines 426-430).

      Accordingly, in the revised Discussion (lines 389-406), we integrate fiber-photometry Ca<sup>2+</sup> signals with single-unit data from opto-tagged recordings to propose several testable, non-mutually-exclusive models for how dual- and single-projecting PMC<sup>ESR1+</sup> neurons are engaged during natural urination: “Based on population dynamics obtained by fiber photometry (Figures 1D-1H, Figure supplements 1A-1F, and Figure supplements 11A-11H) and single-neuron firing properties recorded via optrode (Figures 1A-1C), we propose several mechanistic models for the engagement of dual- and single-projecting PMC<sup>ESR1+</sup> neurons during natural micturition. One possibility is that all three populations (dual-projecting, SPN-projecting and DGC-projecting neurons) are co-activated, with the dual-projecting subset acting as a “bridging amplifier” that sustains rising bladder pressure while coordinating EUS relaxation. Alternatively, SPN-projecting neurons may be recruited first to initiate bladder contraction, followed by DGC-projecting neurons that evoke EUS bursting and facilitate urine entry into the urethra; once flow begins, the urethro-detrusor facilitative reflex could recruit dual-projecting neurons to further enhance voiding efficiency. In addition, contextual or state-dependent urination—such as scent-marking behavior characterized by multiple voiding events with smaller volumes than reflexive urination—may predominantly rely on sequential and cooperative activation of single-projecting neurons. Other recruitment sequences remain conceivable. Future studies combining diverse urination-related behavioral paradigms with simultaneous recordings from projection-specifically labeled PMC neurons will be required to validate and refine these models.”

      Reviewer #3 (Public review):

      Summary:

      The paper by Li et al explored the role of Estrogen receptor 1 (Esr1) expressing neurons in the pontine micturition center (PMC), a brainstem region also known as Barrington's nucleus (Hou et al 2016, Keller et al 2018). First, the author conducted bulk Ca2+ imaging/unit recording from PMCESR1 to investigate the correlations of PMCESR1 neural activity to voiding behavior in conscious mice and bladder pressure/external urethral muscle activity in urethane anesthetized mice. Next, the authors conducted optogenetics inactivation/activation of PMCESR1 to confirm the contribution to the voiding behavior also conducted peripheral nerve transection together with optogenetics activation to confirm the independent control of bladder pressure and urethral sphincter muscle.

      We sincerely thank you for providing a thoughtful summary and insightful comments on our study.

      Weaknesses:

      (1) The study demonstrates that pelvic nerve transection reduces urinary volume triggered by PMC ESR1+ cell photoactivation in freely moving mice. Could the role of pudendal nerve transection also be examined in awake mice to provide a more comprehensive understanding of neural involvement?

      Thank you for this valuable suggestion. We conducted an additional experiment to determine the contribution of the pudendal nerve to PMC<sup>ESR1+</sup> neuron-driven voiding in awake mice. Bilateral pudendal nerve transection (PDNx) reduced the optogenetically evoked urine volume compared with sham-operated controls, yet photoactivation of PMC<sup>ESR1+</sup> neurons still reliably induced urination after PDNx (new Figure 6). Thus, bilateral integrity of the pudendal nerve is required for efficient PMC<sup>ESR1+</sup> neuron-driven voiding, most likely by transmitting the signals that entrain rhythmic EUS bursting. These data and experimental details have been incorporated into Figure 6, Results (lines 272–276), and Methods (lines 542–545).

      (2) While the paper primarily focuses on PMCESR1+ cells in bladder-sphincter coordination, the analysis of PMCESR1+-DGC/SPN neural circuits - given their distinct anatomical projections in the sacral spinal cord - feels underexplored. How do these circuits influence bladder and sphincter function when activated or inhibited? Also, do you have any tracing data to confirm whether bladder-sphincter innervation comes from distinct spinal nuclei?

      Thank you for this critical comment. To determine how PMC<sup>ESR1+</sup> neurons that target distinct sacral nuclei influence bladder–sphincter coordination, we first focused on the dual-projecting subset in a new experiment (Figures supplement 11 and Methods, lines 470–477, 652-655, 669-673). Dual retrograde virus injections into SPN and DGC selectively labelled PMC dual-projecting neurons, a subset of which are ESR1+. Fiber-photometry recordings showed that these cells were active during bladder contraction and sphincter relaxation (Figure supplements 11E-11H), whereas optogenetic activation reliably initiated urination: bladder pressure rose immediately and was followed by rhythmic EUS bursting (Figure supplements 11I-11N and 12B; Results, lines 309-313, 332-335). Thus, the dual-projecting sub-population is sufficient to coordinate bladder contraction with sphincter relaxation. Current retrograde tools do not allow selective isolation of single-projecting (SPN-only or DGC-only) subsets; injecting only one target unavoidably labels both single- and dual-projecting cells. Consequently, we cannot yet compare the functional impact of pure SPN-only versus DGC-only PMC populations. This limitation is now stated explicitly in the revised Discussion (lines 426–430).

      In our 2025 paper (Yan et al., Commun Biol, 2025, PMID: 40259086), we used PRV-based retrograde tracing to show that SPN and DGC constitute two separate spinal nuclei controlling the bladder and the EUS, respectively. Classic studies have reached the same conclusion (Yao et al., Nat Neurosci, 2018, PMID: 30361547; Karnup & De Groat, IBRO Reports, 2020, PMID: 32775758; Karnup, Auton Neurosci, 2021, PMID: 34391124). These citations and a concise summary have been added to the Results (lines 289–294).

      (3) Although the paper successfully identifies the physiological role of PMCESR1+ cells in bladder-sphincter coordination, the study falls short in examining the electrophysiological properties of PMC ESR1+-DGC/SPN cells. A deeper investigation here would strengthen the findings.

      Thank you for this thoughtful suggestion. While a detailed electrophysiological characterization of PMC<sup>ESR1+-DGC/SPN</sup> neurons would provide complementary information, the primary goal of the present study was to define the in vivo functional dynamics and behavioral role of these neurons during natural urination. As you suggested, further electrophysiological analysis of PMC<sup>ESR1+-DGC/SPN</sup> neurons will be an important direction for our future work.

      (4) The parameters for photoactivation (blue light pulses delivered at 25 Hz for 15 ms, every 30 s) and photoinhibition (pulses at 50 Hz for 20 ms) vary. What drove the selection of these specific parameters? Moreover, for photoactivation experiments, the change in pressure (ΔP = P5 sec - P0 sec) is calculated differently from photoinhibition (Δpressure = Ppeak - Pmin). Can you clarify the reasoning behind these differing approaches?

      Thank you for this opportunity to clarify our experimental design. The photoactivation protocol (25 Hz, 15 ms pulses) was chosen because PMC<sup>ESR1+</sup> neurons faithfully follow this frequency without depolarisation block and it reliably triggers voiding (Keller et al., Nat Neurosci, 2018, PMID:30104734). For photoinhibition we originally stated “50 Hz, 20 ms pulses”, but this was an error. Consistent with the same study (Keller et al., Nat Neurosci, 2018, PMID:30104734), we used continuous light (constant illumination) to maintain sustained suppression. The Methods section has been corrected (lines 659-661, 690-691).

      The ΔP formula was tailored to the temporal profile of each manipulation. For activation, ΔP (P<sub>5 sec</sub> - P<sub>0 sec</sub>) captures the rapid pressure rise after light onset; the same window was used in (Hou et al., Cell. 2016, PMID: 27662084). For inhibition, because saline infusion produces rhythmic reflex voiding, we delivered light at the onset of EUS bursting (i.e. when pressure was already at ~peak). Inhibition abruptly stops the bladder contraction, so the bladder cannot return to its pre-void baseline. The Δpressure (P<sub>peak</sub> – P<sub>min</sub>) was therefore used to quantify the extent to which the ongoing pressure wave was aborted by photoinhibition. P<sub>min</sub> is the lowest value reached before the next infusion-driven upswing, making the metric insensitive to the slow baseline drift produced by continuous infusion. These clarifications have been added to the Methods (Methods, lines 676-677, 679-680, 692-693).

      (5) The discussion could further emphasize how PMCESR1+ cells coordinate bladder contraction and sphincter relaxation to control urination, highlighting their central role in the initiation and suspension of this process.

      Thank you for this valuable comment. We have revised the Discussion to emphasize that PMC<sup>ESR1+</sup> neurons coordinate urination by sequentially driving bladder contraction followed by sphincter relaxation through their dual projections to the SPN and DGC. We also emphasized that this coordination is essential for the initiation and effective execution of voiding (Discussion, lines 369-388). In addition, in the revised Discussion (Discussion, lines 389-406), we integrate fiber-photometry Ca<sup>2+</sup> signals with single-unit data from opto-tagged recordings to propose several testable, non-mutually-exclusive models for how PMC<sup>ESR1+</sup> cells are engaged during natural urination.

      (6) In Figure 8, The authors analyze the temporal sequence of bladder pressure and EUS bursting during natural voiding and PMC activation-induced voiding. It would be acceptable to consider the existence of a lower spinal reflex circuit, however, the interpretation of the data contains speculation. Bladder pressure measurement is hard to say reflecting efferent pelvic nerve activity in real time. (As a biological system, bladder contraction is mediated by smooth muscle, and does not reflect real-time efferent pelvic nerve activity. As an experimental set-up, bladder pressure measurement has some delays to reflect bladder pressure because of tubing, but EUS bursting has no delay.) Especially for the inactivation experiment, these factors would contribute to the interpretation of data. This reviewer recommends a rewrite of the section considering these limitations. Most of the section is suitable for the results.

      We agree with the reviewer that bladder pressure, mediated by smooth muscle contraction, provides an indirect measure of efferent pelvic nerve activity and is subject to both physiological and experimental delays. Regarding potential delay from the tubing system, pressure propagates in fluid at approximately 1000 m/s (Kela & Pekka, Proceedings of World Academy of Science Engineering & Technology, 2009, DOI: 10.5281/zenodo.1080526). Given that the total tubing length in our setup is 0.5-1 meter, this gives an estimated transmission delay of only 0.5-1 ms. However, this delay is negligible compared with the observed time difference (~700 ms) between the cessation of EUS bursting and the termination of bladder contraction. Theoretically, pressure transmission is not expected to introduce a temporal delay. However, we cannot exclude the possibility that the pressure measurement itself may impose such a delay, because bladder pressure does not necessarily reflect efferent pelvic nerve activity in real time. Future studies using simultaneous recordings of bladder pressure and pelvic nerve discharges will help clarify whether a true temporal delay exists. Nevertheless, we agree that additional physiological or peripheral factors may also contribute to this difference in timing. As suggested by the reviewer, we have revised the discussion to consider the potential influence of other factors, such as urethra-detrusor facilitative reflex (Results, lines 343-349).

      Reviewer #3 (Recommendations for the authors):

      (1) In opto-tag experiments, a comparison of average AP waveform during behavior and during light stimulation should be included as criteria. It should be mostly the same waveform.

      Thank you for bringing this to our attention. We have now added this comparison as an inclusion criterion in the revised manuscript. Figure supplement 3B shows representative examples of the average waveforms, and Figure supplement 3C displays the distribution of correlation coefficients between spontaneous and light-evoked spikes for all recorded PMC<sup>ESR1+</sup> units, all of which exhibited r > 0.8.

      (2) Optical fiber implantation seems to be done in two different methods. In Figure 1 and Figure 2, the fiber tip is positioned just above PMC but in Figure 3 it seems to be angled. The information should be included in the Methods section.

      Thank you for this important comment. We have now clarified in the Methods that for Figures 1 and 2, the optical fibers were implanted vertically above the PMC, whereas for Figure 3, the left optical fiber was implanted at a 33° lateral angle targeting the PMC (Methods, lines 499-503).

      (3) In the closed-loop inhibition experiments of Figure 2, the parameters to start closed-loop photo-inactivation were not described in the method. If it is a manual closed loop, it should be described clearly.

      Thank you for raising this important point. We apologize for omitting these details in the original Methods. We have now added a complete description of the manual closed-loop photo-inhibition protocol, including the triggering criteria and operator-controlled timing, in the revised Methods section (lines 602–605).

      (4) In Figure 7A/E the authors provide a spinal cord image to show the injection site, but the image is misleading. The figure only shows AAV-infected CRH/ESR1 neurons in the spinal cord section. It does not indicate the AAV injection site or the terminal distribution.

      Thank you for your important comment. We apologize for providing a spinal cord image that did not accurately depict the injection site. To rigorously verify that our spinal injections were confined to SPN or DGC, we performed new retrograde-tracing experiments in ESR1-Cre and CRH-Cre mice. A mixture of AAV-Retro-DIO-mCherry or AAV-Retro-DIO-EGFP with the retrograde tracer CTB-647 was injected specifically into SPN or DGC. Only animals in which CTB-647 fluorescence was strictly limited to the target nucleus, without spread to the adjacent region, were included (new Figures 7A and 7E). These data confirmed our original observations and have been pooled in Figure 7. The manuscript and figure have been updated accordingly (Results, lines 297-301, 304-306; Methods, lines 465–466).

    1. Author response:

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

      We thank both editors and the three reviewers for their constructive criticism of our work. As a result of these comments, we have made several significant revisions to the paper that we believe strengthen and clarify our major results:

      (1) Following suggestions from Reviewers #1 and #3, we have have improved our introduction to the different fitness concepts (lines 105–148) and streamlined the discussion of the logit encoding (lines 175–190). In particular, we have moved the most technical points to the SI (Sec. S3).

      (2) Based on criticisms of our usage of the population dynamics model from Reviewers #1 and #3, we significantly revised our explanation of the motivation and interpretation of this model (lines 284–310 and 323–336) and our discussion of the generalizability of these results (lines 678–728), including the possible effects of interactions besides resource competition.

      (3) Following a request from Reviewer #3, we have expanded our analysis of epistasis to systematically test all possible double mutants between qualitative types of trait perturbations in the model. We have added a new main text figure (Fig. 3), new SI figures (Figs. S9–S15), a new subsection in the Results (lines 344–395), and corresponding new sections in the Methods (lines 864–892) and SI (Sec. S8).

      (4) Following concerns from Reviewers #2 and #3 about the limited empirical data, we have expanded our analysis of the LTEE data (new main text Fig. 4, revised text on lines 416–439, and revised SI Figs. S16–S18) and have analyzed two new benchmarking datasets for bulk fitness to test our predictions (new main text Fig. 6, new Results subsection on lines 561–590, and new SI Figs. S24 and S25).

      (5) Following the criticism of Reviewer #3 about the lack of a clear recommendation on fitness quantification that provides the greatest value for a given scientific question, we have better explained what we think the scientific consequences of fitness are as a motivation for our analysis (lines 82–88, 319–322, and 615–630) and replaced the final flowchart figure with a step-by-step guide in the Methods to implement our recommendations in practice (lines 964–982).

      Reviewer #1 (Public review):

      The authors point out that the fitness estimates obtained from different experimental assays (monoculture, pairwise competition, or bulk competition) are not generally equivalent, not even with regard to the fitness ranking of different genotypes. Using a computational model based on experimentally measured growth phenotypes for knockout strains in yeast, as well as data from Lenski’s Long Term Evolution Experiment (LTEE), they derive a set of best practice rules aimed at extracting the optimal amount of information from such experiments.

      The study is very complete on a technical level and I have no suggestions for further analyses. However, I feel the readability and the conceptual focus of the manuscript could be significantly improved by rearranging the material with regard to the contents of the main text vs. the Methods and the Supplement. Detailed recommendations:

      (1) Regarding readability, the large number of references to material in the Methods and Supplement fragment the main text and make it difficult to follow.

      We understand the challenges these references pose to the flow of the main text; we have attempted to keep those references to a minimum, while ensuring that technical details of the work are fully documented and referenced for completeness.

      (2) Conceptually, it seems to me that the current presentation obscures the reasons why we should care about fitness in the first place. In the first paragraph of Results, the authors define fitness “as any number that is sufficient to predict the genotype’s relative abundance x(t) over a short-time horizon”. To me, this seems like an extremely narrow and not very interesting definition. Instead, I view fitness as an intrinsic property of a genotype that allows us to predict its performance under a range of conditions, including in particular conditions that are different from the experimental setup that was used to obtain the fitness estimates. The latter viewpoint is well expressed in Supplementary Section S1, where the authors discuss the notion of fitness potential. I would recommend to move at least part of this discussion to the main text.

      We appreciate the reviewer’s viewpoint and have moved that conceptual discussion from the SI to the beginning of the Results section to give readers a broader perspective on fitness (lines 105–148). We use “potential” in analogy with potential energy in physics and have clarified this on lines 126–135.

      What we call fitness potential, like the other notions of fitness we discuss in this paper (relative and absolute fitness), is still specific to an environmental condition. Fitness as a property intrinsic to a genotype and independent of any environment, as the reviewer mentions, is an interesting concept but beyond the scope of this paper, which is focused on analyzing fitness measurements that are inevitably environment-specific and we have clarified this on lines 142–148. While it is true that this definition of fitness is narrow, it is what can be empirically measured directly, and thus we believe it is crucial to understand how to best interpret that data.

      By comparison, the arguments in favor of the logit encoding that currently opens the Results session are rather straightforward and could be shortened significantly.

      We agree and have condensed this section (lines 175–192).

      (3) Similarly, the modeling strategy used in this work is quite subtle and needs to be explained more fully in the main text. The authors use growth traits (lag time, growth rate, and yield) extracted from monoculture experiments on a yeast knockout collection and feed them into a specific mathematical model to simulate pairwise and bulk competition scenarios. Since a key claim of the work is that monoculture experiments are generally poor predictors of competitive fitness, the basis for this conclusion and the assumptions on which it is based need to be described clearly in the main text. In the current version of the manuscript, this information has been largely relegated to the Methods section.

      We agree that our motivation for the population dynamics model and growth curve data was not clearly explained. We have significantly revised this section of the Results in the main text (lines 284–310).

      In particular, we recognize the potential for misunderstanding this material we do not intend the relative fitness values calculated from this model to be interpreted as predictions of the true relative fitness between yeast deletion strains. Rather, we use the population dynamics model for our proof of principle: that the most basic features of microbial population dynamics in laboratory experiments, as captured by this model (resource competition, lag phase, growth phase, saturation), are sufficient to create discrepancies between common fitness statistics used in these experiments (different encodings, time scales, choices of reference subpopulations). We have added a statement to highlight existing work on monoculture predictors for competition outcomes [32, 34, 36, 37] on lines 453–459.

      Reviewer #1 (Recommendations for the authors):

      In the discussion of the LTEE in Section S8, the authors write on page 8 that “we couldn’t fit the fitted values a,b in ref. 29 so we were unable to check it”. I don’t understand this sentence - is the claim that the fit in ref. 29 was incorrect?

      We have clarified this point in the SI (now Sec. S9). Our point was not that the fit in Wiser et al. 2013 is incorrect, but merely that we could not find the exact values of the fitted parameters they obtained documented in their paper, so we could not compare our own fitted parameters directly to theirs.

      Also, at the end of the section, the authors refer to theory work on the long-term fitness trend in the LTEE. Here, two early references arguing for a logarithmic increase in fitness could be mentioned as well:

      International Journal of Modern Physics B 12,:361-391 (1998) Evolution and Extinction Dynamics in Rugged Fitness Landscapes Paolo Sibani, Michael Brandt, and Preben Alstrøm

      J. Stat. Mech. (2008) P04014 Evolution in random fitness landscapes: the infinite sites model Su-Chan Park and Joachim Krug

      We thank the reviewer for providing these two references and have added them to the list of previous works on long-term fitness trends at the end of the section (now Sec. S9).

      Reviewer #2 (Public review):

      Summary:

      The manuscript “Quantifying microbial fitness in high-throughput experiments” provides a comprehensive analysis of the various approaches to quantifying fitness in microbial evolution, focusing on three primary factors: encoding of relative abundance, time scale of measurement, and the choice of reference subpopulation. The authors systematically explore how these choices impact fitness statistics and provide recommendations aimed at standardizing practices in the field. This manuscript aims to highlight the impact of differing fitness definitions and the methodologies utilized for analysis and how that can significantly alter interpretations of mutant fitness, affecting evolutionary predictions and the overall understanding of genetic interactions in the experiments. Although this manuscript focuses on a critical issue in the quantification of fitness in high throughput experiments, it heavily relies on only one experimental dataset (Warringer et al 2003) and one organism i.e, Yeast (Saccharomyces cerevisiae) grown in a defined medium, the environmental influence is not completely captured. While the theoretical framework is strong, more experimental examples with more organisms (i.e., more datasets) in their analysis and comparison would enhance the manuscript, especially its conclusion.

      We have expanded our analysis of competition data from the Long-Term Evolution Experiment in E. coli (lines 416– 439), including adding a main text figure (Fig. 4) along with the three SI figures (Figs. S16–S18). We have also added two completely different data sets that directly test our predicted discrepancies in fitness estimates from bulk competition experiments. From this data we have added a new main text figure (Fig. 6), two new SI figures (Figs. S24 and S25), and a new section at the end of the Results (lines 563–590).

      We wish to clarify, though, that the aim of this study is to develop theory on fitness quantification choices and minimal examples to demonstrate the potential for discrepancies between these choices. While we appreciate the reviewer’s interest in understanding how discrepancies in fitness statistics vary across organisms and environments, that is an empirical question beyond the scope of this paper.

      Strengths:

      The choices for quantifying fitness in evolution experiments are critical and highly relevant given the increasing prevalence of high-throughput experiments in evolutionary biology. The authors methodically categorize fitness statistics and their implications, providing clarity on a complex subject. This structured approach aids in understanding the nuances of fitness measurement. The manuscript effectively highlights how different choices in fitness measurement can influence fitness rankings and the understanding of epistasis, which is important for modeling evolutionary dynamics.

      Weaknesses:

      The theoretical framework is robust, but the manuscript could benefit from more empirical examples to illustrate how different fitness quantification methods lead to varied conclusions in experiments.

      Please see our response to the previous comment on this point.

      The discussion on the choice of reference subpopulation could be expanded with the influence of the environment or the condition. Different types of reference groups might yield different implications for fitness calculations, and further elaboration would enhance this section.

      While we agree that studying how environmental conditions affect fitness is an important and interesting problem, it goes beyond the scope of this paper, which focuses on the basic theory of quantifying microbial fitness from highthroughput experiments. Applications of this theory to empirical questions about environmental variation would be best served by their own studies. We have added a statement clarifying this goal (lines 144–148).

      We are unsure how the choice of reference subpopulation is related to this issue. In our view, if the goal of a mutant fitness measurement is to predict how that mutant would behave when arising spontaneously and competing against its immediate ancestor, the gold-standard reference subpopulation must always be the mutant’s immmediate ancestor, or another mutant that is known to be phenotypically equivalent to the ancestor (e.g., neutral mutants in the case of a large mutant library). Other choices of reference subpopulations would not provide directly meaningful information in this regard.

      The authors overgeneralize some findings; for instance, the implications of fitness measurement choices could vary significantly across different microbes or experimental conditions. A more detailed discussion would strengthen the conclusion.

      We certainly agree that the consequences of fitness quantification choices could vary significantly across organisms and environments; our goal for this paper is to demonstrate what discrepancies are possible in principle and in particular how they depend on basic features of microbial population dynamics (e.g., variation in yield). We have added two separate paragraphs in the Discussion section to address the generalizability of our results in the context of pairwise (lines 678–710) and bulk fitness measurements (lines 711–728).

      Overall, this manuscript is a significant contribution to the field of evolutionary biology, addressing a critical issue in the quantification of fitness but lacks more experimental support to make it a wider claim. By systematically exploring the factors that influence fitness measurements, the authors provide valuable insights that can guide future research - the framework is computationally thorough but needs a more detailed explanation of concepts instead of generalizing.

      We have improved our explanation of several of the important concepts. In particular, we have significantly revised our explanation of the population dynamics model (lines 284–310) to emphasize its role as a null model to demonstrate how fundamental aspects of microbial growth are sufficient to cause discrepancies between fitness statistics. We have also revised two paragraphs on the generalizability of our results in the Discussion section (lines 678–728).

      Further work is needed, particularly to incorporate empirical examples and expand certain discussions to include environmental variation and their impact, which would improve clarity and applicability.

      We have added a sentence at the beginning of the Results section to acknowledge the environmental dependence of fitness (lines 142–148). We believe further discussion of that issue is beyond the scope of this paper, as it would require a significant amount of additional data and/or environmental modeling.

      Reviewer #2 (Recommendations for the authors):

      In addition to the comments from the previous sections, other specific comments:

      (1) Figure 5 needs to be populated with additional parameter details. For example, include brief descriptions of each parameter involved in the encoding, time scale, and reference choices. This will help users understand the implications of each choice. Adding these details will make the flow diagram more comprehensive, aiding researchers in implementing these steps more clearly.

      Following this comment and another comment about this figure from Reviewer #3, we decided to replace this figure with a new Methods section with step-by-step instructions (lines 964–982).

      (2) Duplication in Line 620: “Nevertheless, the fact that we see the fact that we see...” This redundancy needs to be corrected.

      We thank the reviewer for pointing this out; we have rewritten this paragraph.

      (3) More experimental data comparisons and their assessment concerning various microbial systems and multiple environmental conditions are recommended to support the claim.

      Please see our responses to the related public comments.

      Reviewer #3 (Public review):

      Summary:

      The authors present analyses of different fitness measures derived from empirical data from yeast knockout mutants and the long-term evolution experiment (LTEE) with Escherichia coli to explore discrepancies and identify preferred methods to estimate relative fitness in high-throughput experiments. Their work has three components. They first discuss the different “encodings” of relative abundance data and conclude that logit transformations are preferred because they transform nonlinear abundance trajectories into linear trajectories with greater predictive power. Next, they compare per-generation with per-growth cycle relative fitness estimates inferred from simulations of pairwise competitions based on published growth traits for the yeast strains and on published pairwise competition measurements for the LTEE data. Both data sets show quantitative and qualitative (i.e. rank order) discrepancies of estimates across different time scales, which are highlighted by considering possible underlying causes (i.e. trade-offs between growth traits) and consequences (i.e. epistasis among mutations affecting different growth traits). Finally, the authors compare simulated pairwise and bulk (i.e. where many mutants compete during a growth cycle in a single environment) competition assays based on the yeast knock-out mutants and demonstrate an optimal ratio of collective mutants to wild-type strains that minimizes both sampling error and overestimation of fitness estimates when compared with pairwise competitions.

      Strengths:

      The study deals with a highly relevant topic. Fitness is central to general evolutionary theory, but also poorly defined and implies different traits for different organisms and conditions. For microbes, which are often used in evolution experiments, high-throughput experiments may yield different measures to quantify abundance over time, from individual growth traits to bulk competition experiments. Hence, it is relevant to consider discrepancies among those measures and identify preferred measures with respect to predicting population dynamics and evolutionary processes. The present study contributes to this aim by (i) making readers aware of differences among commonly used fitness estimates, (ii) showing that simulated (yeast) and calculated (E. coli) competitive fitness may differ across time scales, and (iii) showing that bulk competitions may yield relative fitness estimates that are systematically higher than pairwise competitions. The study is rather thorough on the theory side, with extensive derivations and analyses of various fitness measures using their resource competition model in the Supplementary Information. The study ends with a few practical recommendations for preferred methods to infer relative fitness estimates, that may be useful for experimentalists and stimulate further investigations.

      Weaknesses:

      The study has several limitations. Perhaps the most apparent limitation is the lack of a clear answer to the question of which fitness measure is best “in the light of first principles”. The authors show clear discrepancies between fitness estimates across different time scales or using different reference genotypes in bulk competition and provide useful recommendations based on practical considerations (e.g. using pairwise competitions as the “golden standard”), but it remains unclear whether these measures provide the greatest value for the questions researchers may want to answer with them (e.g. predict shifts in genotype frequencies).

      We agree on the importance of considering the scientific questions researchers want to answer in determining the best way to quantify fitness. We have revised both the Introduction (lines 82–88) and the Discussion (lines 615–630) to more clearly explain possible downstream questions researchers may wish to answer with fitness data, and thus why discrepancies in that data based on analysis choices may be important.

      We believe that the text does provide a specific recommendation (second subsection of the Discussion, lines 635– 658) for how to quantify relative fitness: using the logit encoding (rather than other encodings), measuring fitness per-cycle (rather than per-generation), and using the wild-type or a phenotypically-equivalent proxy as reference subpopulation to calculate pairwise fitness in a bulk competition (rather than using the mutant library as a whole). This recommendation is based on first principles: the logit encoding is based on the principle of the logistic equation as the null model of relative abundance dynamics (lines 635–637), the choice of the per-cycle timescale is based on the principle that in non-steady state environments the time scale for measuring selection should not depend on the wild-type growth (lines 640–645), and the choice of reference population is based on the principle that a mutant’s fitness should serve as a predictor of its dynamics when arising de novo at low frequency and competing against its wild-type (lines 648–653).

      A second limitation is that the authors analyse fitness differences arising solely from resource competition, whereas microbes often interact via other mechanisms, e.g. the production of anticompetitor toxins, cross-feeding of metabolites, or lack of growth to enhance their persistence in stress conditions. Without simulations of these processes, understanding discrepancies among fitness measures is necessarily limited.

      We agree that other interactions are important in many microbial ecosystems and could affect measurements of fitness. We discuss the possibility of these other interactions and their potential consequences for fitness on lines 697– 710.

      We focus on resource competition in this paper, however, for two reasons. One is that we are using it as a null model: resource competition is always present, and thus it provides an important baseline for discrepancies in fitness statistics in the absence of any other assumptions. Indeed, our results are that this minimal assumption alone is sufficient to produce a wide range of significant discrepancies, which provides the proof of principle that choices of fitness quantification matter. We have clarified this in a revised explanation of the population dynamics model on lines 294–304.

      The second reason is that fitness measurements of the type discussed in this paper are typically performed on mutants that have only small genetic differences with their ancestor (e.g., a point mutation or gene deletion). While more complex interactions between such similar genotypes are not impossible, we expect them to be rare, in which case resource competition is the only interaction. Explicit modeling of other interactions is an important question for future work, but would require more detailed models and data of those phenomena, and thus would go beyond the scope of the present study. We have added a sentence to explain our emphasis on resource competition on lines 298–301 and 690–697.

      In addition, the analysis of trade-offs between growth traits causing these discrepancies during resource competition seems confounded by biases in measurement error or parameter estimation, at least for growth rate and lag time (Figure 2B), where the replicate estimates for the wildtype show a similar negative correlation.

      The tradeoff between growth traits was only an incidental observation and is not necessary for the fitness statistic discrepancies we analyze in this paper; the only important pattern in the growth traits is the existence of mutants with reduced yields (so as to reduce the wild-type log fold-change in a competition) as well as variation in one other trait under selection (lag time or growth rate in this model). We have clarified this mechanism on lines 328–336, which is demonstrated by Fig. S7. Since these tradeoffs are not relevant to the results and we agree that their significance may be unreliable due to the noisiness of the data, we have removed mention of them.

      Third, the study does not validate relative fitness predictions from growth traits (as is done for the yeast mutants) with measured relative fitness estimates using competition assays, while such data are available, e.g. for the LTEE. This would strengthen their inferences about preferred fitness measures.

      The goal of our modeling with the yeast growth trait data is not to test the ability to predict competition experiments from monoculture data; that has been the focus of previous studies [32, 34, 36, 37]. Rather, we use the population dynamics model for a proof of principle: that the most basic features of microbial population dynamics in laboratory experiments, as captured by this model (resource competition, lag phase, growth phase, saturation), are sufficient to create discrepancies between common fitness statistics used in these experiments (different encodings, time scales, choices of reference subpopulations). The yeast growth curve data merely provides realistic parameters for this model, to ensure we are studying a biologically relevant regime of the dynamics. To avoid this misconception, we have revised our explanation of this model and the data on lines 284–310.

      Fourth, the analysis of epistasis between mutations affecting different growth traits (shown in Figure 3) based on the LTEE data could be better introduced and analysed more comprehensively. Now, the examples given in panels C-F seem rather idiosyncratic and readers may wonder how general these consequences of using fitness estimates based on different time scales are.

      We agree that this analysis was incomplete and missed an opportunity to emphasize this important consequence of fitness quantification. We have thus expanded this analysis into a systematic test of all possible double mutants between qualitative types of trait perturbations in the model. We have added a new main text figure (Fig. 3), new SI figures (Figs. S9–S15), a new subsection in the Results (lines 346–395), and corresponding new sections in the Methods (lines 864–892) and SI (Sec. S8).

      Finally, the study is generally less accessible to experimentalists due to the extensive and principled treatment of specific population dynamic models and fitness inferences. This may distract from the overarching aim to identify fitness measures that are most accurate and useful for predictions of population dynamics and evolutionary processes.

      We appreciate this concern as we do hope to make the paper as broadly accessible as possible, especially to experimentalists who measure microbial fitness. To this end, we have reduced the technical discussion of encodings in the first section of the Results (lines 164–187); revised explanations of the population dynamics model (lines 284–310), importance of growth trait variation (lines 328–336), and epistasis (lines 346–395) to better emphasize the conceptual intuition of these parts; and added a step-by-step guide for our recommended best practices of quantifying fitness in bulk competition experiments (lines 964–982).

      In this light, the motivation for the initial discussion of the importance of how to best encode relative abundance (Figure 1) is unclear. Also, the conclusion, that logit encoding is preferred, because it linearizes logistic growth dynamics and “improves the quality of predictions”, is not further motivated. Experimentalists using non-linear models to infer fitness from growth curves or competition assays may miss the relevance of this discussion.

      The motivation for the discussion of encodings is that it is one of the choices made differently by researchers, mainly using either the logit (more common in experimental evolution and population genetics studies) or log encoding (more common in TnSeq analyses). As such we believe it is important to explain where this choice comes from (a transformation of relative abundance data to make it approximately linear in time, and thus amenable to characterization by a single slope parameter) and why we believe the logit encoding is more logical in most cases. We have streamlined and revised this subsection to make it clearer (lines 164–187).

      Our argument for favoring the logit encoding in most cases is based on the logistic model being a null model for relative abundance dynamics (Sec. S3). In light of the reviewer’s comments, we have realized this may be confusing because there are two common usages of logistic dynamics that are biologically distinct. What we mean by logistic model is the dynamics of relative abundance x of a mutant in competition with other genotypes:

      Here s turns out to be the relative fitness under the logit encoding. On the other hand, researchers also use a logistic ODE to describe the dynamics of absolute abundance N of a single strain in monoculture (e.g., as in a growth curve):

      We believe the reviewer’s last point refers to Eq. (2), whereas our argument about the logit encoding is based on Eq. (1). We have added a note to clarify this distinction for the reader (lines 192–196).

      Reviewer #3 (Recommendations for the authors):

      In addition to my general comments in the public review, I have several more specific recommendations:

      (1) Line 183-189: unclear why logit-based relative fitness is preferred. Abundance data are not typically binomial.

      We agree this claim about abundance data was incorrect and have removed it. We have revised the section to focus on motivating the logit encoding from logistic dynamics of relative abundance as a null model for most systems (main text lines 175–187 and Sec. S3).

      (2) Line 205: it may be mentioned that s(logit) is the same as the “selection rate constant” often used in microbial studies.

      We have added a sentence clarifying the equivalence of the logit-encoded relative fitness to the selection coefficient in population genetics (lines 188–190).

      (3) Line 368: why do mutations that increase biomass yield also increase WT LFC? Is this, because they grow slower and hence allow the WT more time to grow?

      Mutants with higher yield allow the wild-type to achieve higher log fold-change because those mutants consume fewer resources per cell, which frees up more resources for the wild-type to consume and increase its overall growth. It’s not about growth rate or time, as this would occur even for mutants whose growth rates are identical to the wild-type’s. We have revised our explanation of how variation in growth traits differentially affects fitness statistics (lines 323–340) and epistasis (lines 361–378).

      (4) Line 382-386: you may want to cite Ram et al. (2019, 10.1073/pnas.1902217116), who also did such analyses for experimental data from E. coli.

      We have cited this work as Ref. [34].

      (5) Line 415: perhaps use “bulk relative fitness” instead of “total relative fitness”, to contrast with “pairwise relative fitness”.

      We acknowledge the language in this section can be subtle. However, “bulk” is not a sufficient identifier for the concept of total relative fitness as bulk competition experiments (with many genotypes competing simultaneously) can be used to measure either total relative fitness or pairwise relative fitness. (In pairwise competition experiments with only two genotypes, these two types of fitness are identical.) As such we adhere to our original language but have added words to clarify which type of experiment (bulk or pairwise) we are talking about in a given context (e.g., on lines 495–504).

      (6) Line 451-453: why does a population in bulk competition consume resources more slowly than in pairwise competitions?

      Mutant libraries used in bulk competition experiments usually include a large number of deleterious mutants, which grow more slowly than the wild-type. Thus these populations typically consume resources more slowly than a population in a pairwise competition would, where a large part of the population is the wild-type.

      (7) Line 565: I don’t understand how one can compare relative fitness to other timescales.

      Relative fitness, as we’ve defined it, has units of rate, since it describes the rate of change of relative abundance (or an encoding of it) over some time scale (e.g., a batch growth cycle or a generation). Therefore it can be compared to other times scales of the system, such the rate of new mutations arising or the rate of genetic drift fluctuations, as long as they are measured in the same units. This comparison is important to population genetics analyses, such as determining whether the population is in the strong selection-weak mutation limit or the clonal interference regime.

      (8) Line 620 repeats text.

      Thank you, we have revised this paragraph and removed the typo.

      (9) Figure 1C+D: the link between the scenarios on the left and the graphs on the right may be better explained. For example, it may help to make explicit that the 4 scenarios in panel C show the same relative fitness per cycle and that mutant and wildtype have the same growth rate, but different growth periods in both scenarios in panel D. It is also unclear whether the grey dot links to the upper scenario in D.

      We have clarified this issue in the caption and changed the colors to avoid this confusion.

      (10) Figure 2E: it is unclear why “mutants with equal fitness are assigned the lowest rank”.

      This was a technical comment about how to handle ties in our analysis of mutant rankings, but it is moot since no exact ties actually occur in our simulations. We have removed this remark to avoid confusion.

      (11) Figure 2F: the axis labels are confusing, as for the WT estimates no LFC mutant exists. It would also help to make explicit in the legend against which WT replicate/reference strain each strain has competed.

      We agree the inclusion of wild-type replicates in this plot was confusing and unnecessary, so we have removed them. The mutants compete against a wild-type with traits defined by their median values across all wild-type replicates; this is noted in Fig. 2A and the Methods section on our analysis of this data (lines 809–813).

      (12) Figure 5: I am not sure this is needed, as its information is rather limited.

      We agree and have removed this figure.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Reviewer #1

      Summary: This manuscript has presented a high-throughput fluorescence recovery after photobleaching (HiT-FRAP) platform to screen genes affecting the dynamics of the nucleolar scaffold nucleophosmin (NPM1). The platform included the siRNA-based screening of 65 RNA helicases, 9 phylogenetically related helicase pairs, and 290 ribosomal proteins along with selected assembly factors. These factors were classified as those accelerating or decelerating NPM1 dynamics based on the t1/2 measurements. Combined with nucleolar morphological changes, the authors identified that depletion of early-stage (A-F) and later-stage (G-H) LSU assembly factors resulted in different nucleolar phenotypes, suggesting the pre-ribosome assembly can impact nucleolar morphology. Further exploring the potential mechanis m suggested that the NPM1's intrinsically disordered region (IDR) contributed to the nucleolar organization and dynamics.

      Together, this well-designed study uncovered that the ribosome assembly, both the early and late ribosomal precursors can influence biophysical properties of the nucleolus. Below please find our concerns for the authors to consider to strengthen the major conclusions.

      Major comments:

      The main conclusion that NPM1's biophysical states directly impact its interaction strength with ribosome intermediates (and thereby nucleolar dynamics) should be further strengthened as listed below:

      1). Given the nucleolus's complexity, an additional GC factor, or/and one more marker of other nucleolar regions, should be examined to substantiate the proposed impact of LSU-associated factors on nucleolar morphology (Figures 3, 4).

      We thank the reviewer for this very important point. We have now included representative images for representative hits in major phenotypic clusters co-stained for SURF6, another GC marker, which shows similar localization patterns as NPM1 (Fig. S4B). For other nucleolar subcompartments, we have included images obtained from a cell line harboring endogenously tagged FBL-mNeonGreen (a marker for the DFC) for representative hits (Fig. S4A). We see a similar overall distribution of the DFC within the GC (i.e. DFCs distribute to fill the area of the disrupted GC), confirming our screen results. We look forward to further examining the changes in nucleolar subcompartment architecture in future work.

      As additional support, we note that we probed NOG2, NOP53, and NOP2 in our IF results, all of which are GC-localized factors. We see a very similar distribution for these factors in our hits as for NPM1 (see Fig. S8D). In addition, FISH data for pre-rRNA precursors show similar morphological patterns as NPM1, further confirming our results (Fig. S7). We have noted this in text and have also included representative images in supplement.

      2). Additional experiments are needed to support the proposed model that ribosomal intermediates, especially the pre-LSU complexes could determine nucleolar biophysical properties through the interaction with NPM1. Their direct interaction by biochemical assays should be provided. Also, when analyzing the interaction with other nucleolar factors, the authors should provide data that show NPM1 mutant expression levels were comparable to endogenous levels (Figures 4, 6).

      We agree that directly probing NPM1's interactions with LSU precursors is critical to supporting our model, and we have addressed this through several complementary biochemical approaches. First, we performed immunoprecipitation of tagged NPM1 (NPM1-mScarlet, IP-ed using RFP-trap agarose) and assessed interaction with pre-LSU rRNA transcripts via Northern blot (Fig. 5D). We find that NPM1 interacts strongly with the 32S pre-rRNA. Second, we performed sucrose gradient sedimentation and find that NPM1 preferentially co-migrates with pre-60S complexes (Fig. 5B). Together with previous reports of NPM1-pre-LSU interactions, these data provide direct biochemical support for the proposed interaction.

      To test whether interaction strength with pre-LSUs could regulate NPM1 dynamics, we next asked whether our NPM1 mutants that differ in their dynamics in turn interact differentially with pre-LSU complexes. Using co-IP Northern blot for ITS2 and sucrose co-sedimentation, we find that NPM1 mA3 pulls down more 32S and co-sediments more robustly with pre-60S complexes, while NPM1 mB2 shows reduced association (Fig. 5D, E; Fig. S10F, G). These data support that the strength of the NPM1-pre-LSU interaction is a determinant of NPM1 exchange dynamics, and, by extension, of nucleolar biophysical properties.

      Exogenous mutant NPM1 is expressed at approximately 10% of endogenous levels (Fig. S10A). We address this in two ways. First, all interaction comparisons are made between WT and mutant exogenous constructs, not against endogenous NPM1, controlling for expression level differences. Second, we observe similar effects on interactions both in the presence of endogenous NPM1 and in null backgrounds, indicating that the differences we detect reflect NPM1 mutation, not expression level.

      3). Northern Blotting should be done to dissect which pre-rRNA intermediates interact with NPM1 and contribute to the nucleolar dynamics (Figures 4B, D, F). These additional experiments should be feasible within a reasonable timeframe.

      We agree with the reviewer and have performed northern blots for major hits in our different nucleolar phenotypes, and results reinforce what we see by FISH and qPCR (Fig. S6B). Briefly, depletion of the “RNA Exosome” hit SKIV2L2 results in smearing of pre-rRNA precursors that harbor both ITS1 and ITS2 and an accumulation of the 12S, in keeping with its role in end-processing of these transcripts. For “Other” hit PHF5A, we see an enrichment for 47S/45S/41S species, consistent with an early precursor stall. Notably, we do not see this phenotype for depletion of “Other” hit CNOT1, which suggests multiple processing defects may lead to a similar nucleolar phenotype. Treatment with PolI inhibitor CX5461 shows a depletion in ITS1 containing transcripts, and minimal impact on ITS2-containing transcripts, similar to FISH results. Lastly, depletion of “LSU” hits NOP53 and RPF2 leads to accumulation of the 32S and 12S species, in keeping with accumulation of abortive pre-LSUs.

      In addition, the authors should provide the code and the hardware control procedures for HiT-FRAP to ensure reproducibility.

      We thank the reviewer for this thoughtful suggestion. We have made our software available on GitHub (https://github.com/jess-sheu/colony_blob_bleacher) and archived on Zenodo

      (https://doi.org/10.5281/zenodo.20275447).

      According to the authors' statement, all the experiments are adequately replicated, and the statistical analysis is adequate.

      Minor comments:

      To enhance clarity and focus, consider the following:

      1). Simplifying the HiT-FRAP screening section (Fig. 1-3) would emphasize the significant findings.

      We have simplified text throughout to better highlight significant findings.

      2). Expanding analysis and experimental validation could help to solidify the interdependency between rRNA / ribosome precursors and the NPM1- driven nucleolar dynamics (Fig. 4-5). Indeed, additional experiments suggested above in the major concerns should be supplemented here.

      We have performed additional experiments to demonstrate the interdependency between ribosomal precursors and their interaction with NPM1 in shaping nucleolar dynamics, as described above.

      Reviewer #1 (Significance (Required)):

      This work has established a powerful toolkit, named HiT-FRAP, to identify factors involved in the organization and regulation of the membrane-less nucleolus, which will be useful for understanding the complexity not only the nucleolus, but likely other condensates in cells in the future. Using this platform and with the Granular Component (GC)-localized NPM1 as an indicator of nucleolar morphology, the authors found that the biophysical properties of the nucleolus are sensitive to the ordered assembly of ribosomes, in particular the LSU maturation steps at the GC. This finding is important as it suggests the interdependency between the dynamic rRNA processing and the functional assembly and morphology of the nucleolus. Further studies are warranted to analyze the dynamics of other nucleolar constituents, particularly those localized at other sub-nucleolar regions, to fully depict how exactly the nucleolar function is coordinated with its biophysical properties.

      Reviewer #2

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      Summary: The nucleolus is a multiphase biomolecular condensate whose primary function is ribosome biogenesis. There are mounting evidences that the material state of condensates is important for their function. Here the authors have probed how the material property of the nucleolus responds to inhibitions of ribosome biogenesis.

      They have assessed nucleolar dynamics (molecular diffusivity) of a nucleolar protein, NPM1, by fluorescence recovery after photobleaching (FRAP). NPM1 is a protein that labels the periphery of the nucleolus (the so-called granular component, GC). (The nucleolus has 3 main subcompartments: the internal fibrillar centers, the middle dense fibrillar components, and the GC).

      One of the main findings of the work is that inhibition of late steps of ribosome biogenesis increases fluidity (faster recovery of NPM1), while inhibition of earlier (and inhibition of mRNA processing -but see below) rather increases rigidification (slower recovery). They then attempt to correlate what is interpreted as biophysical changes to pre-ribosomal intermediates and interaction with NPM1.

      Practically, the authors have produced reporter cell lines (HeLa) expressing stably (CRISPR engineering) mono or bi-allelic fluorescent version of NPM1; they have developed a powerful platform to conduct high throughout FRAP (this is really good); they have calibrated their system, initially with basic perturbations (ATP depletion, proteasome inhibition, etc), and then they focused on a family of trans-acting factors: the helicases, investigating systematically their effect on NPM1 recovery. They then extended their initial candidate-based screen to additional factors (using STRING interactions). This is nice and useful. Later in the work, they include in their analysis additional (morphological) features of nucleoli to cluster functionally their hits, as was done earlier by others in similar works. Finally, using recently published structural data (CryoEM), they attempt to correlate groups in the cluster with particular pre-ribosomal species. This part is less advanced and weaker than the initial part of the paper (screens and FRAP measurements).

      Major comments:

      -A major comment is with the compositional analysis of precursor intermediates that should be better defined. The stage assignment of particles is not quite as good as the screening part of the paper. At the RNA level, the authors provided FISH, as histograms of quantifications (see e.g. Fig 4D, and Fig SS6E). It would be necessary to show images, and to perform biochemistry. At the protein level, the authors provide immunostaining, but it does not really prove the detected protein is part of a particle,..

      We thank the reviewer for this important critique. We have taken several steps to address both the stage assignment and biochemical characterization concerns.

      Regarding stage assignment: We have consolidated our LSU phenotypic clusters (previously LSU1 and LSU2) into a single "late pre-LSU" group based on their shared features and proximity in PCA space. We want to be clear that this consolidation is intended to more accurately represent what our data can support: the screen reliably identifies factors whose perturbation produces a coherent late LSU assembly phenotype, and we do not wish to overstate the resolution of state assignment from imaging data alone. Sub-cluster distinctions are retained in supplementary materials for transparency. We have revised language throughout to reflect this framing.

      Regarding biochemical characterization of intermediates: We have now performed Northern blots on strong hits within our phenotypic groups (Fig. S6B). For LSU cluster hits, we observe accumulation of the 32S and 12S species, indicating a stall in ITS2 processing, which is directly consistent with our ITS2 FISH results and confirms that the RNA-level phenotypes reflect genuine pre-rRNA processing defects rather than indirect effects. For "Other" group factor PHF5A, we observe 47/45/41S accumulation consistent with an early processing stall. We have also added representative FISH images to Fig. S7 to allow direct visual assessment of RNA-level phenotypes.

      Regarding protein-level particle assignment: We agree that IF alone cannot establish that assembly factors are incorporated into discrete pre-ribosomal particles rather than existing as free factors. To more directly test whether the LSU cluster phenotypes reflect accumulation of genuine pre-ribosomal particles rather than mislocalized free factors we used NOP53 knockdown as a representative LSU cluster perturbation and, similar to RPF2 knockdown, see an accumulation of ITS2 and NOG2 in the nucleolus by FISH and IF (Fig. 4E). We then performed nuclear sucrose gradient fractionation and found that NOG2 co-migrates with the LSU peak and does not enrich in soluble fractions (Fig. 4F-H), supporting the interpretation that late pre-LSU particles accumulate in the nucleolus upon disruption of LSU cluster genes. Importantly, we also observe a strong decrease in co-sedimentation of NPM1 with the LSU peak upon depletion of NOP53 (Fig. 4G,H). This result, together with the Northern blot and FISH data, provides biochemical and cell biological evidence that the nucleolar phenotypes we identified by HiT-FRAP are associated with accumulation of late LSU assembly intermediates.

      -Another concern is to know if NPM: a GC component located periphery of the condensate and a late assembly factor is an appropriate marker for assessing the effects on nucleolar material state of all (including early and late) inhibitions.

      Would factors involved in earlier ribosomal assembly steps, and localized more internally would not be better tools to evaluate change in material states caused by alterations in early steps?

      We appreciate this important point and agree that NPM1 reports primarily on GC dynamics. However, we would argue this is a feature rather than a limitation for two reasons.

      First, the GC is the terminal assembly compartment through which pre-ribosomal particles must transit before nuclear export. Perturbations to earlier assembly steps, including FC/DFC-localized processes, likely propagate into GC dynamics, because stalled or aberrant particles accumulate in or are excluded from the GC. NPM1 FRAP thus functions as a downstream integrator of upstream assembly status, not only a reporter of GC-proximal events. This interpretation is consistent with our observation that depletion of early factors (and, therefore, depletion of downstream intermediates) do produce detectable NPM1 phenotypes in our screen. Second, the pattern of our screen results supports rather than undermines this logic: the striking enrichment of late LSU factors and near-complete absence of SSU hits is precisely what one would predict if NPM1 reports selectively on pre-LSU flux through the GC. A sensor that reported indiscriminately on all condensate perturbations would not produce this specificity.

      We do acknowledge, however, that NPM1 cannot report on material state changes that are compartmentally confined to the FC or DFC and do not propagate outward. Extending this approach to internal markers remains an important future direction. To clarify the scope of our readout, we have revised the text to specify that we are monitoring GC dynamics, and we have added representative images of fibrillarin localization in Supplemental Figure S4A to illustrate the relationship between DFC and GC compartments in our experimental system.

      -About the engineered cell lines used for screening by FRAP (Fig 1S): NPM1-mNeonGreen (biallelic with reduced expression of NPM1) and mScarlet (heterozygous): There is a need to characterize pre-rRNA processing in both cell lines to show they are not affected for ribosome biogenesis. This is important information since the entire work is based on these cells.

      We have performed a Northern blot across the cell lines used in this paper as compared to their parent cell line and see no substantial difference in rRNA processing. We have included this data as Supplemental Figure 1D.

      The screening cells are HeLa cells implying they are not physiologically regulated for p53. Nucleolar surveillance is a key regulatory surveillance loop triggered by ribosome biogenesis inhibitions leading to p53 stabilisation. How could this affect this work? Should key findings be confirmed in diploid p53 positive cells?

      We acknowledge that our choice of HeLa cells limits our ability to distinguish cell-type-specific responses from more universal mechanisms and have added an explicit discussion of cell choice in the main text. To begin exploring the impact of p53, we performed gene depletions for representative hits across phenotypic clusters in untransformed, diploid hTERT-RPE cells that were lentivirally-transduced with NPM1-mScarlet and assessed nucleolar morphological phenotypes at smaller scale (Figure S6C, Supplementary Text). At baseline, RPE cells show more and smaller nucleoli than HeLa cells, which may reflect a difference in basal nucleolar assembly and, potentially, ribosome biogenesis, in keeping with previous observations that transformed cells rely more heavily on ribosome biogenesis than non-transformed.

      Upon gene depletion, we found that hits from the "RNA exosome" cluster shows a different phenotype than seen in HeLa cells, where we observe less size difference and a marked decrease in eccentricity, which may reflect a p53 or cell type specific response. Depletion of the “Other” cluster gene PHF5A results in a milder though qualitatively similar phenotype as seen in HeLa cells, with nucleolar rounding and an increase in NPM1 intensity. Depletion of “LSU”-associated hits in RPE cells very robustly replicated most of the nucleolar features we observed in HeLa, which suggest that these are likely generalizable responses to LSU disruption. We have included this data in Supplementary Figure 5C. We note that we did not directly test whether p53 is stabilized upon depletion of our hits in RPE cells, and whether p53 activation feeds back on condensate dynamics remains an open area for future work. However, the concordance of LSU-associated phenotypes across HeLa and RPE cells, which differ substantially in p53 status, transformation state, and baseline nucleolar architecture, supports the generalizability of our core findings.

      -About factor depletion, e.g. helicases, it's important to consider direct versus indirect effects on ribosome biogenesis, the timeline of depletion should be well described in the paper. Apparently, most factors, including the helicases were depleted for 72 hours, this is very long considering most of them play important roles in essential processes for cell homeostasis implying severely reduced growth at the time of capture (and the possibility of indirect effects).

      We thank the reviewer for this important point. To directly address depletion timeline, we performed time courses for strong hits and monitored nucleolar morphology at 24 and 48 hour intervals (now included in Fig. S3D). Morphological changes begin to emerge by 48 hours across phenotypic classes; for the RPF2 LSU phenotype specifically, nucleolar expansion and decreased NPM1 intensity are detectable as early as 24 hours, inconsistent with a general stress response and more consistent with a direct downstream consequence of LSU assembly disruption. Moreover, despite all targeted genes being essential for homeostasis, phenotypic profiles are cluster-specific and associated with multiple genes of coherent function, which suggests that observed impacts are downstream of specific pathway inhibition rather than a general cellular stress response.

      -Another cause of concern is that some perturbations (factor depletion) affect very deeply nucleolar structure/morphology (eg uL2 depletion shown in Fig 2C); how easy/difficult was it to control/make sure that a correct area was obliterated in the FRAP experiment using the (remarkable) data-adaptive approach. For cases where the nucleolus was deeply affected how did you check that a significant nucleolar area had been selected for analysis? It would be good to describe this in the text.

      We manually ensured our segmentation protocol accurately captured nucleoli, defined by higher intensity regions of NPM1, for all depletion cases during screen development. As this is the key factor in ensuring where the bleach point is, most bleaches, even in disrupted cases, bleached the nucleolar interior. To address this point, we have included figures in the supplement (Fig. S4D) that show bleaching time courses for select highly disrupted hits uL2 and eL39.

      • Fig 6C, interaction of NPM1 constructs with pre-ribosomes: the authors have tested interaction with select nucleolar proteins (NOP53, NOP2, NOG2, and uL2), which is not the same as preribosomes.

      It would be important to see the interactions with precursors (Fig S9C, now histograms) please show the actual data, this was tested by qPCR, please show classical northern blots as RTqPCR have shown their limits in such applications.

      Indeed, we cannot distinguish between assembly factors/ribosomal proteins that are associated with NPM1 in their latent, non-pre-LSU bound state versus those that are part of a developing ribosome. We have addressed this gap in several ways. Firstly, we have performed IP-northern blots for tagged NPM1-mutants, as suggested, and find that the mA3 mutant co-IPs more 32S than WT, while the mB2 binds less (Fig. 5D). We also performed sucrose gradient analysis of pre-ribosomal complexes and find that the mA3 mutant co-sediments more with the pre-60S peak, while mB2 co-sediments less (Fig. 5E). These findings are consistent with in vitro findings in the field that B2 mediates interactions with rRNA, while A3 occludes B2 through intramolecular interactions. Collectively with our co-IP western data, we believe the evidence strongly suggests that NPM1 mutants interact differentially with pre-LSU complexes.

      -Minor comments:

      -The effects of mRNA processing disruption on nucleolar dynamics could be (is most likely) very indirect (the so-called "slow hits"). The respective time course of inhibitions is important to describe.

      We direct the reviewer to our response above for other phenotypes. For our "slow hit" / "Other" cluster, we also used the splicing inhibitor PladB as an orthogonal approach. Strikingly, nucleolar rounding was detectable within less than one hour of treatment, well before any general cell health effects would be expected, while dynamics changes required approximately 24 hours — suggesting that morphological and biophysical responses are kinetically separable and that the early morphological response is directly downstream of splicing inhibition. We have included a representative rounding timecourse in Fig. S8E.

      Reviewer #2 (Significance (Required)):

      -General assessment: strengths and limitations

      Strengths: -The automated platform for high throughput FRAP\

      -The authors develop a potentially interesting model where they attempt to connect rigidification/fluidity of a condensate to its function in assembly of large ribonucleoprotein complexes. -The manuscript reads very well; it has been prepared with great care (figures). Some complicated concepts are explained very well (Introduction/Discussion). Limitations: -particle stage assignment based on FISH and immunostaining only. The authors have not demonstrated that the LSU1 cluster = state F and LSU2 cluster = states G/H

      -Advance: -Technological advance, high throughput FRAP, a powerful platform to interrogate macromolecular diffusivity.

      -Several nucleolar screens have been conducted in the past (but at steady-state, not using FRAP), in these works textural and morphological features were used together with dimensionality reduction techniques to define functional clusters of genes that impact the homeostasis of the nucleolus. Often these references are cited but it could be useful to expand a bit on some of the earlier findings to bring the new ones in perspective. Some clusters (typically, the transcriptional cluster that disrupts the nucleolus; and the late binder ribosomal proteins) have been well identified before.

      -Audience: Cell biologists, scientists involved in ribosome biogenesis research, scientists with an interest in helicases. The growing condensate community.

      -Describe your expertise: ribosome biogenesis, structure-function relationships in the nucleolus, technological development in microscopy.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      Summary: The authors use high throughput FRAP (HiT-FRAP) in arrayed genetic screens of HeLa cells expressing nucleophosmin (NPM1)-fluorescent protein variants to monitor the biophysical properties of the nucleolus in response to genetic perturbations. HiT-FRAP uses a data adaptive imaging strategy to automatically identify and photobleach fluorescently labeled organelles in living cells and acquire movies for FRAP. Quantitative analysis of FRAP curves include t1/2 and mobile fraction. NPM1 was monitored since it is an important nucleolar scaffolding protein that is thought to interact with many pre-ribosome intermediates.

      The authors depleted 65 RNA helicases (+ 9 pairs) with siRNA and found that 15 of them either increased or decreased t1/2. Knockdowns were confirmed with western blotting. RNA helicase knockdowns with faster NPM1 diffusion were associated with large subunit (LSU) assembly. Most RNA helicase knockdowns with slower NPM1 diffusion were associated with early rRNA processing via the small subunit (SSU) intermediate. The authors screened an additional 290 gene depletions of many ribosomal proteins and assembly factors. With this expanded set of perturbations, they categorized nucleoli based on four morphological features in addition to t1/2 and mobile fraction. Using principal component analysis (PCA), the authors identified clusters of genes with similar effects on NPM1 dynamics and nucleolar morphology. From this secondary screen, the majority exhibited slower NPM1 dynamics. The knockdowns associated with faster NPM1 dynamics were associated with LSU assembly, similar to the helicase experiments. The authors further analyzed several mutants of NPM1 to elucidate the likely interactions between the scaffolding protein and ribosome biogenesis factors. The accumulation of early ribosomal intermediates were associated with decreases in NPM1 dynamics, and accumulation of late intermediates led to increased NPM1 dynamics. The findings established a link between the biophysical properties of the nucleolus and the stages of ribosome biogenesis.

      Major comments:

      • The claims are supported by experimentation.
      • No additional experiments requested.
      • The experiments are adequately replicated, and statistical analysis is sufficient. • Methods are very detailed, which should facilitate reproducibility. Minor comments:
      • Prior studies are referenced appropriately.

      • A bit more coverage of background on the nucleolar scaffolding protein, nucleophosmin (NPM1) would be helpful in the introduction, perhaps in favor of the details on ribosome biogenesis o Paragraph 2 could be shorter or placed elsewhere

      We thank the reviewer for this suggestion and have now included some background on NPM1 in the introduction and have shortened paragraph 2.

      • Figures

      o In Figures 2 - 5: explicitly state in the figure caption what dotted lines are encircling (entire cell?)

      We have now included this in the figure captions (they encircle the nucleus).

      o In Figures 2 - 5: explicitly state what the mp-inferno LUT intensity in the images is quantitating (amount of NPM1?)

      We have now included this in the figure captions (NPM1/mScarlet intensity).

      o Figure 7: more detail in the figure caption

      We have now expanded our model figure caption.

      • The paper is quite dense with a lot of nice work, discussing many different genetic perturbations. It feels a bit overwhelming, and I think the biological significance gets somewhat lost in the presentation of all the data. Perhaps some of the presentation of results can be moved to the supplement in favor of a "leaner" main text. Currently, there are only figures in the supplement, but I feel that some of the text that is not central to the key conclusions can be moved to the supplement. I found myself getting a bit bogged down and having to re-read several times to catch the takeaway messages. Some of the clarifying statements that are found in the discussion section can be moved to the results section. In short, some reorganization would help with readability. One suggestion is to move the Inhibition of rRNA transcription or the RNA exosome leads to nucleolar fragmentation and/or the Perturbation of mRNA processing pathways results in slowed NPM1 dynamics and accumulation of rRNA precursors in the nucleolus to the supplement.

      We thank the reviewer for this helpful suggestion. Due to this and other reviewers, we have now simplified discussion of phenotypic groups, including combining the “LSU” phenotypes into a single group and discussing LSU1/2 in the supplementary text. In addition, while we have chosen to keep the “rRNA transcription/exosome” and “Other” descriptions in the main text, they have been condensed and included in one main section with the other ribosome biogenesis phenotypes to highlight this key takeaway. Remaining discussion of phenotypes is now in supplemental text, as suggested.

      Reviewer #3 (Significance (Required)):

      • General Assessment: The main claim of the paper is that nucleolar phenotype (measured by morphology and NPM1 diffusivity) is correlated with stages in ribosome assembly - i.e. the stage of ribosome assembly determines the biophysical properties of the nucleolus. A strength of the study is the wide range of genetic perturbations tested enabled by the high throughput FRAP. With FRAP, I do worry a bit about using t1/2 as the sole dynamic measurement, but it is not a deal breaker. The authors introduce morphology as another way to characterize the nucleoli. • The claims are well supported by extensive experiments and data. The experiments are well designed, and proper controls were conducted. To validate the method, the authors used perturbations of NPM1 dynamics from the literature including ATP depletion, blocking glycolysis and oxidative phosphorylation, inhibition with MG132, and treatment with sodium arsenite. They observed slower NPM1 diffusivity under all validation conditions. • Advance: The authors have introduced a high-throughput technique for extracting diffusivity with FRAP, yielding a lot of data, but I think the paper suffers a bit in trying to present so much data in the main text. The mechanistic biological insights are compelling but get a bit overshadowed. Improved organization can help the messages come across more clearly. • To my knowledge, there is not a similar study in the literature as the detailed mechanisms of ribosome biogenesis are not well studied. • Audience: The audience for this manuscript seems to be biophysical researchers, thought there may be broader interest due to the wide screening of genetic perturbations. • Expertise: I have evaluated this manuscript from the perspective of a single-molecule biophysicist that studies protein-protein interactions between ribosome biogenesis factors. I am not an expert in FRAP, but I use FCS.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #2 (Public review):

      Summary:

      This study uses dental traits of a large sample of Chinese mammals to tract evolutionary patterns through the Paleocene. It presents and argues for a 'brawn before bite' hypothesis -- mammals increased in body size disparity before evolving more specialized or adapted dentitions. The study makes use of an impressive array of analyses, including dental topographic, finite element, and integration analyses, which help to provide a unique insight into mammalian evolutionary patterns.

      Strengths:

      This paper helps to fill in a major gap in our knowledge of Paleocene mammal patterns in Asia, which is especially important because of the diversification of placentals at that time. The total sample of teeth is impressive and required considerable effort for scanning and analyzing. And there is a wealth of results for DTA, FEA, and integration analyses. Further, some of the results are especially interesting, such as the novel 'brawn before bite' hypothesis and the possible link between shifts in dental traits and arid environments in the Late Paleocene. Overall, I enjoyed reading the paper and I think the results will be of interest to a broad audience.

      Weaknesses:

      For the original draft of the manuscript, I had four major concerns with the study, especially related to the sampling, diet, and evidence for the 'brawn before bite' hypothesis. I still believe that the original issues that I raised may be weaknesses of the study. For example, there is still limited discussion on diets (even though the dental topographic analyses used in the study are designed for inferring diets). And I find the results a little challenging to interpret because teeth of multiple positions are included in the same samples, which seems problematic. That said, the authors have addressed each of my previous concerns and have made major revisions, including running new analyses, and thus I support the paper.

      This revised submission includes only minor changes aimed at clarifying the main text.

      Reviewer #2 (Recommendations for the authors):

      I appreciate that the authors made many improvements to their study based on reviewers' comments. I don't have any remaining major issues with the paper, but I do have several minor comments.

      Thank you for taking the time to provide additional helpful feedback on our study. We have made minor revisions to the manuscript based on your suggestions. Please see our point-by-point response below.

      Lines 48-50. I reiterate my suggestion in my previous review to explicitly state which clade is being discussed, which is important because several major mammal groups beyond placentals (metatherians, multituberculates, dryolestoids, gondwanatherians) survived the K-Pg and had very different diversification patterns. You mention "mammal taxonomic diversity" but in the next sentence say "This initial placental mammals diversification ..." and later mention "stem placental/eutherian lineages." To stay consistent, you might replace "mammal" (L48) and "placental mammals" (L50) with "eutherian(s)" (usually defined as stem + crown placentals). If you follow this suggestion, then elsewhere in the paper I recommend replacing "mammals" with "eutherians" for consistency.

      Thank you for this suggestion. We modified the use of “mammals” throughout the text to general reference to the group only; specific mentions of the dataset analyzed are revised to “eutherians.”

      Lines 75-83. I respect the authors' hesitancy to reconstruct specific diets for the fossil taxa (L75-83), especially considering that dental topographic analyses (DTAs) often struggle to differentiate diets in extant taxa (e.g., Pineda-Munoz et al. 2016 Methods Ecol Evol). I still think that the authors might be able to interpret dietary trends from their results (e.g., an increase in average OPCR values indicating a shift toward more herbivorous diets) - I think discussing dietary trends would be an interesting discussion topic later in the paper. That said, I also recognize that different DTA results seem to show conflicting dietary trends (based on my limited knowledge of those metrics) so maybe that complicates things too much.

      We concur with Reviewer 2 that dietary inferences of DTA data are premature, especially given the ongoing controversies of its use in studies of extant mammal teeth. We kept our current scope of discussion unchanged.

      Lines 75-77. "early mammals ... are beyond the reach of conventional phylogenetic bracketing approaches to dietary reconstruction." But your fossils (eutherians) are certainly within 'phylogenetic brackets' of modern clades (therians, i.e. Eutheria + Metatheria). Maybe you're alluding to the fossils being stem lineages of extant subgroups like Ungulata, which means we can't bracket them specifically within those eutherian subgroups? So, I recommend revising or expanding your statement for clarity. Also, the considerable phylogenetic uncertainty for Paleocene groups (e.g., Halliday et al. 2015) complicates this issue, which you could mention.

      We modified the sentence to now say “Additional complications with ecomorphological analysis of these stem eutherians include the uncertainty in their dietary ecology, having diverged prior to the crown radiation, and uncertainty in phylogenetic positions of Paleocene taxa [7]; thus, they are beyond the reach of conventional phylogenetic bracketing approaches to dietary reconstruction.”

      Line 84. "We investigated dental topography-performance shifts ...". You haven't introduced dental topography or even mentioned teeth yet, and "performance shifts" is vague. So, this phrase might confuse readers. Maybe you can just erase it and start the sentence with "We investigated the timing of ecomorphological ..."?

      We made the recommended revision.

      Lines 104-105 (and elsewhere). "Dental traits paralleled Paleocene global and regional environmental conditions" and "We found that dental topographic trait variability in Paleocene mammals in south China tracked global and regional climatic changes". These conclusions seem a little too assertive to me. Your sample is grouped into 3 rough time bins (of somewhat uncertain ages) and is from a relatively small geographic range - that seems like very limited information for inferring links between dental patterns and climatic changes, especially global patterns. I think it's worth HYPOTHESIZING that dental traits are linked to environmental/climatic changes (with results like those in Figure 2A & B as evidence to support that hypothesis), but I wouldn't make that claim with any confidence. So, I recommend that you temper your relevant conclusion statements. For example, for Line 105, you could replace "We found ..." with "We posit ..." (L105). I would make similar changes to similar statements throughout the paper (e.g., L243).

      Thank you for this suggestion to temper our phrasing. We edited throughout the text to make our interpretations less assertive.

      Figure 1 (and your response to reviewers). Why was the timescale changed to 65.5 Ma for the K-Pg boundary? The K-Pg is 66 Ma (not 65.5), which is the age you mention in the text (e.g. Pg 3 L39) and is well established in the literature - see recent papers from the Paul Renne lab for a more exact age.

      We revised the figure to have the K-Pg at 66 Ma.

    1. Author response:

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

      We thank you for the time you took to review our work and for your feedback! The main changes to the manuscript are:

      (1) We have performed additional experiments to increase the number of recordings from frontal and occipital electrodes (previously 51 (occipital: O1+O2) and 26 (frontal: Fp1+Fp2), now 133 and 102). The additional data have strengthened many of our results, including for example the trend for a latency difference between occipital and frontal electrodes that was likely underpowered and is now significant (Figure 3E). We have updated all relevant figures to include the additional data (Figures 2–6, Figure S4, Figure S5). None of the main conclusions have changed.

      (2) As suggested by reviewer 1, we have conducted additional experiments to rule out the possibility that the observed effects were driven by the temporal order of open and closed loop sessions (new Figure S6). We also found another 9 participants who were willing to go on the ‘vomit comet’ of six degrees of freedom (6DOF) playback (previously 5, now 14). These data have further strengthened our conclusion that playback halt responses in 4DOF and 6DOF playback are not substantially different (Figure S4).

      (3) To address the point of reviewers 2 and 3, that mismatch negativity (MMN) responses would be larger on temporal electrodes, we conducted additional experiments in which we also recorded from temporal electrodes T3–T6. We have now added a comparison of visuomotor mismatch and MMN responses on T3–T6 electrodes as Figures S8–S9. On all electrodes, visuomotor mismatch responses were larger than MMN responses.

      (4) As suggested by reviewer 1, we have added an analysis of the experience-dependent changes in mismatch responses comparing frontal and occipital responses early and late in the session (new Figure 4).

      (5) As suggested by reviewer 2, we conducted additional experiments in an independent cohort of participants (note, without concurrent EEG) to measure eye movements triggered by visuomotor mismatches. We found eye-movement speed and blink/eye-closure changes, but these had longer latency than visuomotor mismatch responses (Figure S7).

      (6) Finally, as suggested by reviewers 2 and 3, we applied independent component (ICA) and time–frequency analyses to the EEG data. We show these results and explain why they are not applicable or useful in our case in the responses below.

      Please note, during the revision, we found that a part of our analysis used a bandpass of 0.2-100 Hz while a 1-100 Hz bandpass filter was used elsewhere. This has now been standardized to a 1-100 Hz bandpass filter, and the corresponding methods were updated. This resulted in no relevant changes to the figures. Additionally, the 50 Hz band-stop filter was erroneously described in the methods as 49-51 Hz. The filter used was 40-60 Hz, and the methods have been updated to reflect this.

      Reviewer #1 (Public review):

      In this paper, the authors wished to determine human visuomotor mismatch responses in EEG in a VR setting. Participants were required to walk around a virtual corridor, where a mismatch was created by halting the display for 0.5s. This occurred every 10-15 seconds. They observe an occipital mismatch signal at 180 ms. They determine the specificity of this signal to visuomotor mismatch by subsequently playing back the same recording passively. They also show qualitatively that the mismatch response is larger than one generated in a standard auditory oddball paradigm. They conclude that humans therefore exhibit visuomotor mismatch responses like mice, and that this may provide an especially powerful paradigm for studying prediction error more generally.

      Asking about the role of visuomotor prediction in sensory processing is of fundamental importance to understanding perception and action control, but I wasn't entirely sure what to conclude from the present paradigm or findings. Visuomotor prediction did not appear to have been functionally isolated. I hope the comments below are helpful.

      (1) First, isolating visuomotor prediction by contrasting against a condition where the same video stream is played back subsequently does not seem to isolate visuomotor prediction. This condition always comes second, and therefore, predictability (rather than specifically visuomotor predictability) differs. Participants can learn to expect these screen freezes every 10-15 s, even precisely where they are in the session, and this will reduce the prediction error across time. Therefore, the smaller response in the passive condition may be partly explained by such learning. It's impossible to fully remove this confound, because the authors currently play back the visual specifics from the visuomotor condition, but given that the visuomotor correspondences are otherwise pretty stable, they could have an additional control condition where someone else's visual trace is played back instead of their own, and order counterbalanced. Learning that the freezes occur every 10-15 s, or even precisely where they occur, therefore, could not explain condition differences. At a minimum, it would be nice to see the traces for the first and second half of each session to see the extent to which the mismatch response gets smaller. This won't control for learning about the specific separations of the freezes, but it's a step up from the current information.

      In theory, it is correct that the open loop (playback) session is predictable. However, this is relatively unrealistic. The open loop session is a 5-minute sequence that participants have only experienced once before, when they were generating it in the closed loop session a couple of minutes earlier. It is unlikely that participants would remember the entire sequence to a precision of less than a second, which is what they would need to predict the mismatch event. However, the reviewer is correct that it is possible that the mismatch events lose salience with time, for example as a consequence of participants losing interest in the task with time, or by undergoing some form of adaptation. To address this, we repeated the experiments with the sequence of closed and open loop sessions reversed (Figures S6A-S6C), and we analyzed the responses as a function of time within the session (Figures S6D and S6E), as suggested.

      The reversed-order design consisted of (1) open loop session: a playback, in which participants viewed the recorded closed loop session of a previous participant. This was followed by (2) a closed loop session, in which participants actively walked through the tunnel and experienced visuomotor mismatch events. Using this design, we again found that responses in the closed loop session were significantly larger than in the open loop session (Figures S6A-S6C).

      In addition, we analyzed both new and previously collected data as a function of time in the session. We computed moving average responses across 10 mismatch or playback halt trials at different percentages of progress through the paradigm (Figures S6D and S6E). This analysis revealed no consistent experience-dependent changes that could account for the observed differences between closed and open loop session. While there was indeed some form of experience dependent attenuation of visuomotor mismatch responses (see new Figure 4), the difference at the transition from mismatch to playback halt (and vice versa) far exceeded these adaptation effects (Figures S6D and S6E). This analysis was performed only on data from participants for whom we had both closed and open loop sessions and met our inclusion criteria.

      We used a similar analysis to test whether early and late responses within a session systematically differed (new Figure 4). Here, to maximize the chance of finding a difference, we compared early (first five) and late (last five) trials. Behaviorally, participants reduced their walking speed following mismatch events, with a significantly larger reduction during early trials (14.3%) than during late trials (5.7%) (Figure 4A). Neural responses mirrored this pattern primarily on frontal electrodes: frontal activity showed a clear attenuation from early to late trials (Figure 4B), consistent with the reduction in behavioral responses. In contrast, changes on occipital electrodes were much smaller between early and late trials (Figure 4C-4D). Thus, experience-related modulation is substantially stronger in frontal compared to occipital regions.

      In sum, we do not believe that the difference between visuomotor mismatch responses and playback halt responses can be explained by differences in the predictability of mismatch and playback halt events.

      (2) Second, the authors admirably modified their visual-only condition to remove nausea from 6 df of movement (3D position, pitch, yaw, and roll). However, despite the fact it's far from ideal to have nauseous participants, it would appear from the figures that these modifications may have changed the responses (despite some pairwise lack of significance with small N). Specifically, the trace in S3 (6DOF) and 2E look similar - i.e., comparing the visuomotor condition to the visual condition that matches. Mismatch at 4/5 microvolts in both. Do these significantly differ from each other?

      Yes, the 6DOF playback halt response shown in the previous Figure S3 and the mismatch response shown in previous Figure 2E are significantly different (Author response image 1).

      Author response image 1.

      Comparison of visuomotor mismatch response (A) and 6DOF playback halt response (B) from the original submission with statistics of the comparison (C).

      Nevertheless, to strengthen this conclusion, we collected additional data in the 6DOF condition. We show the comparison for participants for whom both closed loop (active) and open loop sessions (6DOF) were recorded within the same recording session (14 participants) in Figure S4. Consistent with our previous findings, visuomotor mismatch responses were significantly larger than 6DOF playback halt responses (Figures S4A-S4C). And we found no evidence of a difference between 6DOF and 4DOF playback halt responses (Figures S4D and S4E).

      (3) It generally seems that if the authors wish to suggest that this paradigm can be used to study prediction error responses, they need to have controlled for the actions performed and the visual events. This logic is outlined in Press, Thomas, and Yon (2023), Neurosci Biobehav Rev, and Press, Kok, and Yon (2020) Trends Cogn Sci ('learning to perceive and perceiving to learn'). For example, always requiring Ps to walk and always concurrently playing similar visual events, but modifying the extent to which the visual events can be anticipated based on action. Otherwise, it seems more accurately described as a paradigm to study the influence of action on perception, which will be generated by a number of intertwined underlying mechanisms.

      We are not entirely sure we understand the point here correctly. If the reviewer is suggesting that visuomotor coupling is not describable by the ideas of predictive processing, we disagree. However, given that the papers the reviewer is pointing to are premised on what seems to be a somewhat unorthodox interpretation of predictive processing when it comes to cortical circuits, we suspect this is contributing to the misunderstanding here. Let us briefly explain. In the two papers, Press and colleagues argue that most experiments cannot distinguish between “predictive cancellation” and “gated suppression”. This is indeed relatively tricky, even when one has single neuron data. The question is, does movement simply suppress sensory feedback (as is likely the case e.g. in the famous example of the cricket), or does movement result in a precise removal of only the self-generated sensory reafference? The first good evidence of the latter happening in any system is quite recent (Keller and Hahnloser, 2009). The premise the authors build their argument on is that the theory posits that “the brain predictively ‘cancels’ expected action outcomes from perception” (from the abstract of one of the papers). This is incomplete. The minimum circuit for predictive processing is composed of 3 neuron types: positive prediction error neurons, negative prediction error neurons, and internal representation neurons. Only the positive prediction error neurons have the predictive cancellation property the authors discuss. This is not the case for either negative prediction error neurons, or for the internal representation neurons. Negative prediction error neurons are excited by predictions and suppressed by sensory input (i.e. if anything, they are “predictively amplified”). This circuit is relatively well characterized in mouse cortex – for a brief summary see (Keller and Mrsic-Flogel, 2018). Note, this is not our idea of course – the original formulation of predictive processing (Rao and Ballard, 1999) was built to explain end-stopping. These are responses to the absence of an expected line that were stronger than would be expected from classical theories (i.e. negative prediction error responses). In mouse visual cortex, we know that a sudden break in the coupling between locomotion and visual flow selectively activates layer 2/3 negative prediction error neurons. Thus, if human cortex also implements a predictive processing like circuit with positive and negative prediction error neurons, we would expect a break in visuomotor coupling to drive a measurable response in visual cortex (by exciting the population of negative prediction error neurons – this is also why we are quite excited by the phase reversal of visual and mismatch responses as this could indicate that mismatch activates negative prediction error neurons first and positive prediction error neurons later, and vice versa for visual stimulation – negative prediction error neurons are more superficial in cortex (O’Toole et al., 2023)). We do indeed find a response over occipital cortex consistent with the negative prediction error response we observe in mouse cortex. The difficulty in distinguishing “predictive cancellation” and “movement driven suppression” comes only when looking at positive prediction error type responses (that are suppressed by predictive inputs) but does not apply to negative prediction error responses. The predictive processing circuit we are testing is the one described by (Keller and Mrsic-Flogel, 2018; Rao and Ballard, 1999), and here the break in visuomotor coupling is a stimulus that drives negative prediction error responses. Note, other authors who have thought about cortical implementations of predictive processing (e.g. (Bastos et al., 2012)) have glossed over the problem that individual neurons cannot trivially encode both positive and negative errors. Prediction errors are a signed quantity. If neurons signal prediction errors in firing rates and are close to zero firing rate at baseline (as is the case in layer 2/3 of cortex), they cannot (short of rather exotic ideas) encode a signed prediction error. Hence such proposals are not very useful for thinking about prediction error responses in cortex. For these reasons, we see no problem with referring to the response as a prediction error response. This is in line with a large body of mouse research (using a nearly identical paradigm) on the topic.

      One could of course argue that gated suppression could also mean that movement relieves suppression. Thus, one could assume that some neurons are suppressed by movement while others are enhanced. If one allows for enough neuron and stimulus specificity in the precision of the movement related suppression and enhancement of responses, the two models (predictive processing and gated suppression) become equivalent, and the discussion becomes semantic. See (Vasilevskaya et al., 2023) for an extended discussion on this point, and the reasons why we think predictive processing is a more useful model than gated suppression (keep in mind, gated suppression only explains the data if we allow for stimulus/neuron specific gain factors of the suppression, in which case the two models are equivalent).

      More minor points:

      (1) I was also wondering whether the authors may consider the findings in frontal electrodes more closely. Within the statistical tests of the frontal electrodes against 0, as displayed in Figure 3c, the insignificance of the effect of Fp2 seems attributable to the small included sample size of just 13 participants for this electrode, as listed in Table S1, in combination with a single outlier skewing the result. The small sample size stands out especially in comparison to the sample size at occipital electrodes, which is double and therefore enjoys far more statistical power. It looks like the selected time window is not perfectly aligned for determining a frontal effect, and also the distribution in 3B looks like responses are absent in more central electrodes but present in occipital and frontal ones. I realise the focus of analysis is on visual processing, but there are likely to be researchers who find the frontal effect just as interesting.

      That is correct; our data in frontal electrodes was likely underpowered. The reason we have fewer data in frontal electrodes is that eye-blink artifacts are particularly strong in frontal channels, resulting in a larger proportion of trials failing to meet our data inclusion criteria. We have now added more data from frontal and occipital electrodes by including additional experimental sessions. In addition, we applied less stringent trial-exclusion criteria, requiring that no artifacts occur within the time window −0.5 to 1 s relative to the event trigger (instead of −0.5 to 2 s). This adjustment allowed us to retain a larger number of trials. As anticipated by the reviewer, this increase in data was sufficient to confirm a significant response to the visuomotor mismatch event at both frontal electrodes (Figure 3C). The expanded dataset also revealed a significant difference in response onset times between occipital and frontal electrodes (Figure 3E), an effect that was not significant previously. In addition, we have included analysis comparing early and late mismatch responses in frontal and occipital electrodes (Figure 4).

      (2) It is claimed throughout the manuscript that the 'strongest predictor (of sensory input) - by consistency of coupling - is self-generated movement'. This claim is going to be hard to validate, and I wonder whether it might be received better by the community to be framed as an especially strong predictor rather than necessarily the strongest. If I hear an ambulance siren, this is an especially strong predictor of subsequent visual events. If I see a traffic light turn red, then yellow, I can be pretty certain what will happen next. Etc.

      This is a statistical argument. Every movement – throughout life – is directly and immediately coupled to sensory feedback and has been throughout evolutionary history. The vast majority of visual input you receive (we estimate, well above 99%) is the consequence of your own movements (e.g. every few 100 ms your eye movements cause a full field change in your visual input). The same is likely true of proprioceptive and somatosensory input – the vast majority is the direct consequence of your own movements (not other people poking you). This is likely different in the auditory system where a much larger fraction of the input is externally driven (depending a bit on how much one likes to talk). But even here the best predictor is self-motion (most non-self-generated sounds one experiences in life are very difficult to predict with millisecond precision). The example the reviewer gives is a good illustration of this. Take the siren that hails the appearance of an ambulance. The siren tells us that an ambulance will appear, but not how it will look, not when exactly it will appear, and with only very low resolution as to where it will appear. Incidentally, if you ask people to draw an ambulance they tend to draw a WWII style white square vehicle with a red cross on the side – a style of ambulance they likely have not ever seen in life. Their visual predictions of what they are about to see are very low resolution. We catastrophically fail at making pixel perfect predictions from learned stimulus associations of this nature. The traffic light example is difficult to compare to visual feedback control of movement as it is a much simpler prediction of a single bit in the form of a change in color of an existing object.

      In addition, consider how often (in life) you have seen an ambulance after hearing it? 100 times maybe? Maybe less. How often have you seen traffic lights change - 10 000 times? 100 000 times? Now consider, how often you have experienced the visual consequences of moving your head or eyes to the left (keep in mind this includes micro saccades) – at a conservative, once per second, that is somewhere on the order of 1 000 000 000. This is not even in the same ballpark. Our brains can certainly learn to make the ambulance and traffic light type predictions - to some extent - but by far the best predictor of sensory feedback (simply by virtue of the physics of how our body interacts with the world) is self-motion.

      We think this is an argument we can make based on first principles, and one that is frequently overlooked in the field, as experiments often focus on training people or animals to learn novel associations that, especially in the case of mice, we often have no idea whether cortical circuits can even learn. We should focus experiments on the predictive systems our brains have evolved since long before the evolutionary appearance of ambulances and traffic lights. We understand that the reviewer may disagree with this, but unless the reviewer has a concrete example of an even stronger predictor (as measured by frequency of experience, consistency in coupling, and precision in timing – we can’t think of one), it is a point we will make.

      (3) The checkerboard inversion response at 48 ms is incredibly rapid. Can the authors comment more on what may drive this exceptionally fast response? It was my understanding that responses in this time window can only be isolated with human EEG by presenting spatially polarized events (cf. c1, e.g., Alilovic, Timmermans, Reteig, van Gaal, Slagter, 2019, Cerebral Cortex).

      We don’t know, but it is not inconsistent with previous reports. For example, compare the “standing” and “fast walking” target ERP responses in Figure 5 of (Gramann et al., 2010). Both here and in our data, the fast response peak is only really apparent in the direct comparison of visual responses recorded while participants were walking to those when they were stationary.

      While we have taken great care to calibrate the timing of the visual display with the EEG recording, one could be worried that the alignment is off by as much as tens of milliseconds. However, even if this were so, one could use P1 as a reference and determine that the fast peak roughly precedes P1 by about 40 ms. Which again would result in a latency of about 50 ms of the fast walking peak (assuming P1 peaks at about 90 ms). In sum, we have added a reference to the previous work (that we found thanks to the reviewer’s comment) but fear we have nothing intelligent to say beyond that.

      Reviewer #2 (Public review):

      Summary:

      This study investigates whether visuomotor mismatch responses can be detected in humans. By adapting paradigms from rodent studies, the authors report EEG evidence of mismatch responses during visuomotor conditions and compare them to visual-only stimulation and mismatch responses in other modalities.

      Strengths:

      (1) The authors use a creative experimental design to elicit visuomotor mismatch responses in humans.

      (2) The study provides an initial dataset and analytical framework that could support future research on human visuomotor prediction errors.

      Weaknesses:

      (1) Methodological issues (e.g., volume conduction, channel selection, lack of control for eye movements) make it difficult to confidently attribute the observed mismatch responses to activity in visual cortical regions.

      (2) A very large portion of the data was excluded due to motion artefacts, raising concerns about statistical power and representativeness. The criteria for trial inclusion and the number of accepted trials per participant appear arbitrary and not justified with reference to EEG reliability standards.

      (3) The comparison across sensory modalities (e.g., auditory vs. visual mismatch responses) is conceptually interesting, but due to the choice of analyzing auditory mismatch responses over occipital channels, it has limited interpretability.

      We have responded to these points in the more detailed itemization below.

      The authors successfully demonstrate that visuomotor mismatch paradigms can, in principle, be applied in human EEG. However, due to the issues outlined above, the current findings are relatively preliminary. If validated with improved methodology, this approach could significantly advance our understanding of predictive processing in the human visual system and provide a translational bridge between rodent and human work.

      Reviewer #2 (Recommendations for the authors):

      Overall, the study addresses an interesting and underexplored question (translation of the visuomotor mismatch responses observed in rodents to humans). Below, please find a list of specific suggestions for improvement

      Introduction:

      (1) "updating internal representations and internal models" - what is the difference between the two, and why is it relevant to this study?

      In a nutshell, an internal model is the synaptic weight matrix that transforms between coding spaces. An internal representation is the activity pattern coding for the current representation. See (Aizenbud et al., 2025; Keller and Mrsic-Flogel, 2018) for more lengthy elaborations. The fact that the mechanism used for representation update can also be used to update internal models (i.e. solve the credit assignment problem) is likely the prime advantage of predictive processing (see work from the Bogacz lab). The relevance to the current study is justifying why predictive processing is a reasonable hypothesis for the function of cortex.

      (2) "Certain stimuli can be predicted from the preceding sensory input" vs. "Predictions can also be based on memory" - how are these two different? Do you mean specific (e.g., long-term associative or episodic) memory types in the latter?

      Correct, this is an arbitrary distinction that primarily makes sense in the light of experimental approaches. In this particular case, we were talking about spatial memory. We made this explicit to increase clarity.

      (3) "the strongest predictor - by consistency of coupling - is self-generated movement"

      (a) Externally induced movement, while not self-generated and therefore not predicted, will also generate sensory coupling, so is it really only about consistency?

      Externally induced movement (as in somebody else moving one’s arm we are not sure this is what the reviewer means) will induce sensory-sensory coupling but not sensorimotor coupling. We might be misunderstanding the point. In case the reviewer means stimuli that trigger movement as in us asking participants to walk, or a sudden startle stimulus that makes them jump in all such cases there are of course sensorimotor predictions. Sensorimotor predictions are driven by efference copies of the motor command thus all movements whether ‘voluntarily’ executed or triggered by an external stimulus will drive sensorimotor predictions. (All of this of course assumes that the predictive processing theory is correct.)

      (b) Do you mean temporal consistency (minimal lags), statistical contingencies (same movements linked to the same sensory inputs), or both? How does it differentiate sensorimotor/visuomotor mismatch responses from responses to incongruent stimuli in sensory modalities (e.g. audiovisual)?

      Both. We have rephrased the sentence to try to make this clearer. See also response to reviewer 1 minor point 2 above.

      How does it differentiate sensorimotor/visuomotor mismatch responses from responses to incongruent stimuli in sensory modalities (e.g. audiovisual)?

      Most cross-modal associations are much less consistent (the exact sound of a glass shattering is always slightly different and impossible for us to predict), and orders of magnitude less frequently experienced, than sensorimotor associations. Again, see also response to reviewer 1 minor point 2 above.

      (4) "Every movement is directly coupled to sensory feedback throughout life"

      This may be the case for proprioceptive and/or somatosensory feedback, but not necessarily for visual feedback (e.g., a mouse moving its tail), which is the topic of the study.

      Correct, there are movements that can be disconnected from visual feedback. Most of the time, most movements however are not, and we are studying one of the more prominent ones that is clearly not decoupled locomotion. The contrast we aim to highlight here very prominently is that there is still this vague idea in the field that you can take a participant, or a mouse, and expose them/it to a few tens or hundreds of trials of some sensory stimulus contingency and then probe for prediction error responses to a pattern only recently if at all learned. Given the life-long experience of subjects and mice, is it really surprising that oddball responses are less strong than a sensorimotor mismatch?

      (5) "However, the overall level of this motor-related activity is much higher than one would expect simply from predictions of visual feedback that are compared against visual input."

      Could you please clarify what one would expect in this case, and/or back it up with citations?

      This is in reference to the fact that there are very strong movement related signals in the mouse visual cortex that persist even when the mouse is in complete darkness. In darkness, movements should not trigger any visual feedback change hence the activity is difficult to explain as a movement related prediction of visual flow. We have rephrased this section of the introduction to make this clearer.

      (6) "The more precise the prediction and comparison, the less motor-related activity should be detectable in visual cortex."

      I think this conflates two issues. A good match between prediction and input would indeed result in sensory attenuation. However, sensory precision, at least in active inference, can upregulate prediction error responses. Since predictions cannot be assumed to be perfect (due to external or internal noise), increased precision may therefore augment activity. See e.g. https://doi.org/10.1007/s10339-013-0571-3

      We agree with the reviewer – the phrasing here was misleading. We do not mean precision in the predictive processing sense, but the precision of sensorimotor control necessary for the behavior. We have rephrased the corresponding section of the manuscript.

      (7) Neither the introduction nor the discussion refers to previous human EEG studies on sensorimotor mismatch responses, where sensory feedback doesn't match motor actions (e.g. https://doi.org/10.3758/s13423-021-01992-z ; https://www.sciencedirect.com/science/article/pii/S0028393214003777 ; https://www.sciencedirect.com/science/article/pii/S0028393219301265).

      The studies cited by the reviewer primarily test how discrete violations of learned action–outcome associations are represented in the brain, whereas our visuomotor mismatch paradigm probes violations of continuous sensorimotor coupling during ongoing action. The paradigms are conceptually different both in how strong the coupling is (lifelong vs. learned in the experiment), and in how prediction errors are likely used (visuomotor control vs. stimulus detection). We have added a brief part to our introduction discussing this.

      Results:

      (1) A very large proportion of the dataset was excluded due to movement artefacts. This is rather problematic as

      (a) the rationale behind finding mismatch responses is that motion-related (neural) signals should affect visual cortical activity, so it's essential to disentangle these neural signals from artefacts;

      Correct, we excluded 21.7% of the total data for visuomotor mismatch paradigm. Note, this percentage compares to other similar studies of EEG recordings during movement (Oliveira et al., 2016). By “problematic”, we assume the reviewer means the fact that we have artefacts, not that we exclude trials with artefacts. The movement artefacts are typically caused by the acceleration during stepping in participants with a heavy gait. None of these movement artefacts are time locked to any of the responses we investigate. Thus, they should just appear as increased levels of noise if not excluded. We don’t understand why the reviewer thinks this is particularly problematic for our analysis/conclusions (beyond the trivial consequence of increasing noise levels that would only cause us to underestimate the strength of the mismatch signals we report).

      (b) the criterion for the number of trials of 15 triggers (per condition?) is arbitrary and lower than widely used in the literature, so authors should demonstrate that this is a sufficient number to observe a measurable ERP even for those participants with 15 triggers;

      We have between 16 and 25 visuomotor mismatch events per participant. Author response image 2 is a selection of single participant examples with different number of trials. The number of mismatch events is limited by the fact that we introduce them approximately every 10 - 15 s and have a total duration of the closed loop session of 5 minutes. Thus, on average, we expect to have 24 mismatch events. But we are not sure we understand the logic of the comment, if we set exclusion too low, we just risk losing a response in the noise. And we clearly have stronger and higher signal to noise mismatch responses with an average of 20 trials compared to visual responses during movement with an average of 40 trials or MMN responses with an average of 28 trials.

      Author response image 2.

      Reliable ERPs can be observed with as few as 16 trials across EEG channels. (A) Histograms showing the distribution of the number of valid mismatch trials per participant for each electrode pair (Fp1–2, C3–4, P3–4, O1–2). (B) Representative EEG responses to visuomotor mismatch events from a single participant, recorded at electrode pairs Fp1–2, C3–4, P3–4, and O1–2. Waveforms were computed using the indicated number of trials (shown above each trace). Dashed vertical red lines are onset and offset of the visuomotor mismatch.

      (c) it seems that the seemingly static "visual" condition resulted in a larger proportion of data rejected due to movement (or, as later mentioned, nausea) than the "visuomotor" condition, which is counterintuitive and needs further explanation;

      This is a misunderstanding the ‘visual paradigm’ the reviewer is referring to are the experiments shown in Figure 1. Here we record visual responses in both sitting and walking participants. In this experiment, as in others, exclusion was primarily driven by part of the paradigm where the subjects were moving. To make this clearer we have added Table S2 to the manuscript that provides an overview of trials excluded by paradigm and session.

      (d) authors mention eye movements as a potential issue, which should be possible to detect from frontal channels. Additionally, it's not entirely clear how many datasets were discarded (the results section mentions 19/48 in the visual condition, then 4+11 in the playback condition - isn't this the same condition?)

      The visual paradigm corresponds to the data shown in Figure 1, in which participants viewed a flipping checkerboard in both a walking and a stationary session. The open loop session is part of the visuomotor paradigm shown in Figure 2, where participants were exposed to a replay of the visual flow that had been self-generated during the preceding closed loop session, including the visual flow halts that constituted visuomotor mismatches in the closed loop session. Please note, to avoid such confusion, we have attempted to standardize the usage of paradigm (visual vs. visuomotor) and session (sitting vs. walking, and closed loop vs. open loop) throughout. In addition, we have added a table to summarize the number of excluded trials by paradigm and session as Table S2 to the manuscript.

      In comments 1 and 2 of the public review, the reviewer also points out that we did not control for eye movements and we presume relatedly claims that we did not use common EEG reliability standards. Regarding the first point, we performed additional experiments in an independent cohort of participants to test whether eye movements could account for the visuomotor mismatch responses. We recorded eye movements during closed loop sessions and found that changes in eye speed (Figure S7A) or blink rate (Figure S7B) following the mismatch stimulus had a longer latency than visuomotor mismatch responses in EEG. This suggests that the visuomotor mismatch response cannot be explained by eye blinks or changes in eye movement speed. Regarding the second point, we are not sure we understand. Trial exclusion based on a fixed voltage threshold of 100 µV is relatively common, and our rejection rates are on par, and particularly on occipital electrodes even lower, with other work in EEG recordings during locomotion or movement (see e.g. (Oliveira et al., 2016)).

      Nevertheless, we did attempt to apply independent component analysis (ICA) based filtering to the EEG data (Delorme and Makeig, 2004). However, these methods were designed for high channel density recordings. With only 8 channels, ICA is unable to reliably isolate eye movement or motion artefact components of the EEG. To illustrate this, we tested two artifact-rejection strategies. In the first approach, components associated with non-neural artifacts (e.g., muscle activity, line noise, eye movements) were removed only if at least 90% of the component’s variance was assigned to a single artifact class (Author response image 3A). In the second, more permissive approach aimed specifically at reducing eye movement artifacts, components were removed if artifact-related activity exceeded 90% for non-eye artifacts, while the threshold for eye-related components was lowered to 60% (Author response image 3C). We lowered the threshold for excluding eye-related components to ensure that EEG signals influenced by eye movements were effectively removed. In both cases - whether the eye-component threshold was set to 90% or 60% - the averaged responses to visuomotor mismatch trials remained largely similar to the previously reported data, despite higher noise in some traces. Interestingly, when we then followed the ICA filtering by our voltage threshold based exclusion with a threshold of 100 µV, the resulting traces closely resembled the patterns described in the paper (Author response image 3B and 3D). Thus, we conclude the nonICA filtered responses are easier to interpret, free of any potential ICA filtering artifacts, and far less parameter choice (of the ICA filtering) dependent.

      Author response image 3.

      Removal of artifacts identified with ICA does not change the visuomotor mismatch responses. (A) Visuomotor mismatch responses recorded from occipital electrodes after artifact correction. Components associated with non-neural artifacts (e.g., muscle activity, line noise, eye movements) were removed only if ≥90% of the component’s variance was attributed to a single artifact class. Solid black line represents the mean, and shading indicates the SEM across participants. Dashed vertical red lines are onset and offset of the visuomotor mismatch. (B) As in A, but excluding trials with amplitudes exceeding 100 µV. (C) As in A, but components were removed if artifact-related activity exceeded 90% for non-ocular artifacts, while the threshold for eye-related components was lowered to 60%. (D) As in C, but excluding trials with amplitudes exceeding 100 µV.

      (2) The finding that mismatch responses are observed at all channels, with differences in amplitudes but not latencies, indicates that volume conduction may affect the results. I would strongly suggest accounting for this using a method appropriate for the very small number of channels, e.g., phase lag index.

      We are not sure we understand. The phase lag index is a method to estimate functional connectivity in a way that corrects for volume conduction (using phase lag). We make no claims about functional connectivity; thus, we are not sure what the reviewer is suggesting we do. The fact that the visual and visuomotor mismatch responses were measurable on all electrodes could indeed be in part explained by volume conduction, but we see no way to estimate the volume conduction contribution. From mouse calcium imaging data, we know that both visual and visuomotor mismatch responses spread across large parts of dorsal cortex (including frontal regions like the ACC).

      With the addition of new data, the latency difference between occipital and frontal electrodes - previously observed only as a trend - is now statistically significant (Figure 3E). Occipital responses emerge earlier than frontal responses, suggesting that mismatch-related activity likely originates in sensory visual regions and subsequently propagates to more frontal areas, as similar to what had been reported in mouse cortex (Heindorf and Keller, 2024).

      (3) The authors compare different types of mismatch responses (including auditory oddballs) in the same set of (occipital) channels, but doesn't this undermine the spatial specificity of the results? Classical auditory mismatch negativity is typically observed over central channels, so weaker amplitudes of auditory mismatch responses in occipital channels are likely trivially explained by modality differences. As such, I'm not convinced that this comparison is informative even in a qualitative manner.

      To address this point, we conducted additional auditory oddball experiments with recordings over the auditory cortex (channels T3, T4, T5, and T6). Given our central reference, these channels should capture the strongest mismatch negativity. The amplitude of the visuomotor mismatch response exceeded that of mismatch negativity on all tested channels (new Figures S8 and S9).

      (4) On a similar note, is the polarity reversal found for visual vs. mismatch responses specific to occipital channels?

      Thank you for this interesting question. In fact, polarity reversal was consistently observed across all recorded channels; this has now been added as a main figure to the manuscript (Figure 5).

      (5) Figure S4C seems to cut off one outlier, and I don't see this outlier included in the boxplot.

      Correct, that is why we describe the boxplots in the figure legend as: “Boxes mark median, quartiles, and range of data not considered outliers.” The axes were now adjusted to include all data points.

      Discussion:

      "A central tenet of the cortical circuit for predictive processing is the split into separate populations of neurons that compute positive and negative prediction errors (Keller and Mrsic-Flogel, 2018; Rao and Ballard, 1999)" - this may be the case for visuomotor mismatch signals or reward prediction errors, but signed PEs do not play a central role in other proposed microcircuits for predictive processing in the perceptual domain (e.g. Bastos)

      Signed prediction errors do not play a central role in proposed cortical microcircuits for predictive processing that do not burden themselves with making a concrete proposal for the implementation of the prediction error computation. The (Bastos et al., 2012) work is a good example of this. The equation for the error term provided in that paper is clearly signed (nothing stops the error from going negative), but no proposal is made for how layer 2/3 excitatory neurons are supposed to signal this quantity. With baseline activity levels close to zero in layer 2/3, there really is only one way to do this, and that is separate populations of negative and positive prediction error neurons. With non-zero baseline firing rate, one could do this bidirectionally around a mean firing rate (as is typically thought of dopaminergic RPE neurons). There are more abstract Bayesian implementations that assume logarithmic transformations that could also implement a prediction error-like system without negative firing rates. But given the absence of any physiological evidence, we will refrain from discussing these. However, most importantly, there is now considerable evidence for the existence of both negative and positive prediction error neurons in layer 2/3 of mouse visual cortex. Thus, by “cortical circuit for predictive processing” we here mean those that make biologically plausible proposals for prediction error computations. Also note, the (Rao and Ballard, 1999) model is probably the prime example for what the reviewer calls a proposed microcircuit for predictive processing in the “perceptual domain”.

      Reviewer #3 (Public review):

      Summary:

      Solyga, Zelechowski, and Keller present a concise report of an innovative study demonstrating clear visuomotor mismatch responses in ambulating humans, using a mobile EEG setup and virtual reality. Human subjects walked around a virtual corridor while EEGs were recorded. Occasionally, motion and visual flow were uncoupled, and this evoked a mismatch response that was strongest in occipitally placed electrodes and had a considerable signal-to-noise ratio. It was robust across participants and could not be explained by the visual stimulus alone.

      Strengths:

      This is an important extension of their prior work in mice, and represents an elegant translation of those previous findings to humans, where future work can inform theories of e.g., psychiatric diseases that are believed to involve disordered predictive processing. For the most part, the authors are appropriately circumspect in their interpretations and discussions of the implications. I found the discussion of the polarity differences they found in light of separate positive and negative prediction errors, intriguing.

      Weaknesses:

      The primary weaknesses rest in how the results are sold and interpreted.

      Most notably, the interpretation of the results of the comparison of visuomotor mismatches to the passive auditory oddball induced mismatch responses is inappropriate, as suboptimal electrode choices, unclear matching of trial numbers, and other factors. To clarify, regarding the auditory oddball portion in Figure 5, the data quality is a concern for the auditory ERPs, and the choice of Occipital electrodes is a likely culprit. Typically, auditory evoked responses are maximal at Cz or FCz, although these contacts don't seem to be available with this setup. In general, caution is warranted in comparing ERP peaks between two different sensory modalities - especially if attention is directed elsewhere (to a silent movie) during one recording and not during the other. The authors discuss this as a purely "qualitative" comparison in the text, which is appreciated, and do acknowledge the limitations within the results section, but the figure title and, importantly, the abstract set a different tone. At least, for comparisons between auditory mismatch and visuomotor mismatch, trial numbers need to be equated, as ERP magnitude can be augmented by noise (which reduces with increased numbers of trials in the average).

      To address this point, we conducted additional auditory oddball experiments with recordings over the auditory cortex (channels T3, T4, T5, and T6). Given our central reference, these channels should capture the strongest mismatch negativity. Nevertheless, the amplitude of the visuomotor mismatch response exceeded that of mismatch negativity on all tested channels (these results are now shown in the new Figures S8 and S9), and the response power was significantly greater for the visuomotor mismatch than for mismatch negativity. Independent of electrode we test, the visuomotor mismatch response has a power 5 to 10 times higher than that of the MMN response. And the number of trials per participant that met quality criteria was comparable between the visuomotor mismatch paradigm (mean = 23 trials) and the auditory mismatch paradigm (mean = 28 trials) (Author response image 4).

      Author response image 4.

      Number of trials included for analysis is comparable between visuomotor and oddball paradigm. (A) Histogram showing the distribution of the number of valid trials per participant for O1-2 electrode pair in visuomotor mismatch paradigm. (B) Same as in A but for deviant stimulus presentations in the oddball paradigm.

      And more generally, the size of the mismatch event at the scalp does not scale one-to-one with the size at the level of the neural tissue. One can imagine a number of variables that impact scalp level magnitudes, which are orthogonal to actual cortex-level activation - the size, spread, and polarity variance of the activated source (which all would diminish amplitude at the scalp due to polyphasic summation/cancelation). The variance of phase to a stimulus across trials (cross trial phase locking) vs magnitude of underlying power - the former, in theory, relates to bottom-up activity and the latter can reflect feedback (which has more variability in time across trials; the distance of the scalp electrode from the activated tissue (which, for the auditory system, would be larger (FCz to superior temporal gyrus) than for the visual system (O1 to V1/2)). None of this precludes the inclusion of the auditory mismatch, which is a strength of the study, but interpretations about this supporting a supremacy of sensory-motor mismatch - regardless of validity - are not warranted. I would recommend changing the way this is presented in the abstract.

      We agree with the point that the EEG response does not need to reflect the total cortical activation. However, the discussion in the abstract (and elsewhere) is in the context of clinical experiments where the underlying cortical activity pattern is irrelevant if it does not trigger a clinically measurable (by EEG in this case) response. The abstract only makes a comparison to MMN implicitly in this sentence “Second, a paradigm that can trigger strong prediction error responses and consequently requires shorter recording times could simplify experiments in a clinical setting.” We are not sure how to phrase this even more carefully – the statement at face value is a truism. The reviewer, we assume, takes exception to the unstated implication that visuomotor prediction errors trigger stronger responses than MMN. Given the data we have, we assume most authors would not consider it an overstatement to make that claim outright.

      Otherwise, the data are of adequate quality to derive most of their conclusions.

      The authors claim that the mismatch responses emanate from within the occipital cortex, but I would require denser scalp coverage or a demonstration of consistent impedances across electrodes and across subjects to make conclusions about the underlying cortical sources (especially given the latencies of their peaks). In EEG, the distribution of voltage on the scalp is, of course, related to but not directly reflective of the distribution of the underlying sources. The authors are mostly careful in their discussion of this, but I would strongly recommend changing the work choice of "in occipital cortex" to "over occipital cortex" or even "posteriorly distributed". Even with very dense electrode coverage and co-registration to MRIs for the generation of forward models that constrain solutions, source localization of EEG signals is very challenging and not a simple problem. Given the convoluted and interior nature of human V1, the ability to reliably detect early evoked responses (which show the mismatch in mouse models) at the scalp in ERP peaks is challenging - especially if one is collapsing ERPs across subjects. And - given the latency of the mismatch responses, I'd imagine that many distributed cortical regions contribute to the responses seen at the scalp.

      This is an excellent point we have rephrased throughout to “over occipital cortex” instead of “in occipital cortex”.

      I think that Figure 3C, but as a difference of visual mismatch vs halting flow alone (in the open loop) might be additionally informative, as it clarifies exactly where the pure "mismatch" or prediction error is represented.

      We performed the analysis as suggested (Author response image 5). Visuomotor mismatch responses are stronger on all electrodes compared to playback halt responses. This difference is also larger in data recorded on occipital electrodes.

      Author response image 5.

      Comparison of the difference between visuomotor mismatch and playback halt on all electrodes. Average response strength was calculated within a 100 ms window centered on the peak of the average visuomotor mismatch response across all electrodes. Boxes mark median, quartiles, and range of data not considered outliers. Each circle represents data from one participant. **: p<0.01, *: p<0.05, Fp1-2: 20 participants, C3-4: 31 participants, P3-4: 35 participants, O1-2: 32 participants.

      As a suggestion, the authors are encouraged to analyse time-frequency power and phase locking for these mismatch responses, as is common in much of the literature (see Roach et al 2008, Schizophrenia Bulletin). This is not to say that doing so will yield insights into oscillations per se, but converting the data to the time-frequency domain provides another perspective that has some advantages. It fosters translations to rodent models, as ERP peaks do not map well between species, but e.g., delta-theta power does (see Lee et al 2018, Neuropsychopharmacology; Javitt et al 2018, Schizophrenia research; Gallimore et al 2023, Cereb Ctx). Further, ERP peaks can be influenced by the actual neuroanatomy of an individual (especially for quantifying V1 responses). Time frequency analyses may aid in interpreting the "early negative deflection with a peak latency of 48 ms " finding as well.

      We have performed time–frequency power and phase-locking analyses for both visual responses (Author response image 6 and Author response image 7) and visuomotor mismatch and playback halt responses (Author response image 8 and Author response image 9), as suggested. We have added the results of these analyses here, as these are not fully developed yet. We may add these to a future publication, for which we would properly want to quantify stability of these effects.

      In brief, time–frequency representations of power did identify potentially interesting differences between walking and sitting sessions in the visual paradigm. Inter-trial phase coherence (ITPC) revealed an early increase in alpha-band synchronization suggesting that phase alignment of alpha oscillations may contribute to the early differences in visual responses between walking and sitting. The same analyses were applied to visuomotor mismatch and playback halt responses. Time–frequency power analysis revealed an increase in delta-band power during visuomotor mismatch, consistent with previous reports linking delta activity to prediction error processing, including reward prediction errors (Cavanagh, 2015), unexpected final words (Webb and Sohoglu, 2025), and visual deviance detection (West et al., 2024). Notably, it appears as if the increase in delta power emerged first over occipital electrodes and appeared later over more frontal electrodes, forming a spatiotemporal gradient of onset across the scalp.

      Delta power changes were markedly reduced in the playback halt responses at the time of visual flow cessation. While some power changes were observed, they occurred primarily at visual flow onset rather than at flow offset. Inter-trial phase coherence analysis further revealed delta-band synchronization over occipital electrodes following visuomotor mismatch, whereas the playback halt response showed strong phase synchronization in both delta and theta bands following visual flow onset.

      Author response image 6.

      Time–frequency representations of EEG power changes during the visual paradigm. (A) Time–frequency maps showing changes in spectral power relative to baseline for electrodes Fp1–2, C3–4, P3–4, and O1–2 following checkerboard reversal in the sitting session. The dashed red vertical line indicates the time of the checkerboard reversal (0 s). (B) As in A, but recorded while participants were walking.

      Author response image 7.

      Inter-trial phase coherence (ITPC) for visual trials during sitting and walking. (A) ITPC across trials for electrode pairs Fp1–2, C3–4, P3–4, and O1–2 following checkerboard reversal in the sitting session. The dashed red vertical line marks the time of the checkerboard reversal (0 s). (B) As in A, but recorded during walking.

      Author response image 8.

      Time–frequency representations of EEG power changes during visuomotor mismatch and playback halt responses. (A) Time–frequency maps showing changes in spectral power relative to baseline for electrodes Fp1–2, C3–4, P3–4, and O1–2 following visuomotor mismatch presentation. Dashed vertical red lines are onset and offset of the visuomotor mismatch. (B) As in A, but for playback halts.

      Author response image 9.

      Inter-trial phase coherence (ITPC) for the visuomotor mismatch and playback halt responses. (A) ITPC across trials for electrode pairs Fp1–2, C3–4, P3–4, and O1–2 following visuomotor mismatch presentation. Dashed vertical red lines are onset and offset of the visuomotor mismatch. (B) As in A, but for playback halts.

      Finally, the sentence in the abstract that this paradigm " can trigger strong prediction error responses and consequently requires shorter recording times would simplify experiments in a clinical setting" is a nice setup to the paper, but the very fact that one third of recordings had to be removed due to movement artifact, and that hairstyle modulates the recording SnR, is reason that this paradigm, using the reported equipment, may have limited clinical utility in its current form. Further, auditory oddball paradigms are of great clinical utility because they do not require explicit attention and can be recorded very quickly with no behavioral involvement of a hospitalized patient. This should be discussed, although it does not detract from the overall scientific importance of the study. The authors should reconsider putting this statement in the abstract.

      We have added a paragraph to the discussion to address these points. Note, we get robust and strong responses with very few trials (Author response image 2). The fact that we need to discard up to 21.7 % of trials due to movement/eye blink artefacts, does little to change the fact that we need much fewer trials and have larger and more robust responses compared to other EEG paradigms. Finally, we understand that sometimes not needing participants to pay attention to the task is useful. However, having a paradigm that is engaging and fun for participants and takes 5 minutes of recording time is probably equally often of advantage.

      Reviewer #3 (Recommendations for the authors):

      Minor points:

      (1) In the Introduction, I'm not sure that the logic comes through as to what the authors aim to illustrate by comparing mice to humans, in terms of precision and "movement modulation". In some cases, the precision of the comparison is referred to, and in others, the precision of the prediction (I think?). I'm not sure if they mean for this to be different or not. Simlarly, on line 81, "If indeed the precision of visuomotor coupling determines the amount of motor modulation of visual responses" - here I'm a little confused, as "amount of motor modulation" to me, the term "modulation" refers to a conditional modifier (if moving, than suppress visual movement resposnes. if not moving, then amplify visual movement repssones) rather than movement driven activity. The way I'm reading it, the authors mean the latter, but I could be misunderstanding.

      We have rephrased this section of the introduction.

      (2) I think it could be helpful, in the sentence starting on line 65, to reiterate that this observation of higher-than-expected motor activity in V1 is in mice (if I'm understanding it correctly). I also found myself tangled up in the difference between motor-related activity in V1 and motor-modulation in V1 in this paragraph.

      We have rephrased this section of the introduction.

      (3) For signal power, was the amplitude squared on individual trials prior to averaging, or after averaging? If prior, it would help with separating amplitude modulations from phase variance.

      In our previous analysis, power was computed by squaring the amplitude after trial averaging (Author response image 10A). We repeated the analysis using the alternative approach in which power was calculated for individual trials and then averaged (Author response image 10B). Although this method yields substantially higher absolute power values, the overall pattern of results remains unchanged: visuomotor mismatch responses continue to show significantly higher power than visual responses. To look at the phase variance we additionally analyze inter-trial phase coherence (Author response image 7 and Author response image 9).

      Author response image 10.

      Visuomotor mismatch responses have more power compared to visual responses. (A) Comparison of power between visuomotor mismatch and visual responses, calculated within a 0 - 0.5 s time window following stimulus onset. Power was computed by squaring the amplitude after trial averaging. Boxes indicate the median and interquartile range, with whiskers showing the range excluding outliers; circles represent data from individual participants. ***p < 0.001. (B) Same comparison as in (A), but with power calculated by squaring the amplitude of individual trials prior to averaging.

      (4) The "the world suddenly flew forward!" response from the participant, I understand, and I believe that it is useful to illustrate a point. I do not understand the "Are you printing this? - Hi Mom! " part of the participant response, and I'm not sure it adds to the paper, beyond amusement, which seems inappropriate.

      One of the authors (the one who did none of the experiments) finds this endlessly hilarious and as the reviewer notes, it might add amusement more generally. “Inappropriate” might be a bit harsh – according to our favorite AI chatbot: “Amusement provides significant mental, physical, and social value by offering a necessary escape from routine, reducing stress, and fostering a connection. It enhances well-being through endorphin-releasing experiences and encourages social bonding, learning, and joy.” Nevertheless, we have censored the offending passage.

      Aizenbud, I., Audette, N., Auksztulewicz, R., Basiński, K., Bastos, A.M., Berry, M., Canales-Johnson, A., Choi, H., Clopath, C., Cohen, U., Costa, R.P., Filippo, R.D., Doronin, R., Errington, S.P., Gavornik, J.P., Gillon, C.J., Granier, A., Hamm, J.P., Hertäg, L., Kennedy, H., Kumar, S., Ladd, A., Ladret, H., Lecoq, J.A., Maier, A., McCarthy, P., Mei, J., Mejias, J., Mikulasch, F., Mudrik, N., Najafi, F., Nejad, K., Nejat, H., Oweiss, K., Petrovici, M.A., Priesemann, V., Rudelt, L., Ruediger, S., Russo, S., Salatiello, A., Senn, W., Sennesh, E., Sima, S., Uran, C., Vasilevskaya, A., Vezoli, J., Vinck, M., Westerberg, J.A., Wilmes, K., Xiong, Y.S., 2025. Neural mechanisms of predictive processing: a collaborative community experiment through the OpenScope program. https://doi.org/10.48550/arXiv.2504.09614

      Bastos, A.M., Usrey, W.M., Adams, R.A., Mangun, G.R., Fries, P., Friston, K.J., 2012. Canonical microcircuits for predictive coding. Neuron 76, 695–711. https://doi.org/10.1016/j.neuron.2012.10.038

      Cavanagh, J.F., 2015. Cortical delta activity reflects reward prediction error and related behavioral adjustments, but at different times. NeuroImage 110, 205–216. https://doi.org/10.1016/j.neuroimage.2015.02.007

      Delorme, A., Makeig, S., 2004. EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis. J. Neurosci. Methods 134, 9–21. https://doi.org/10.1016/j.jneumeth.2003.10.009

      Gramann, K., Gwin, J.T., Bigdely-Shamlo, N., Ferris, D.P., Makeig, S., 2010. Visual evoked responses during standing and walking. Front. Hum. Neurosci. 4, 202. https://doi.org/10.3389/fnhum.2010.00202

      Heindorf, M., Keller, G.B., 2024. Antipsychotic drugs selectively decorrelate long-range interactions in deep cortical layers. eLife 12, RP86805. https://doi.org/10.7554/eLife.86805

      Keller, G.B., Hahnloser, R.H.R., 2009. Neural processing of auditory feedback during vocal practice in a songbird. Nature 457, 187–90. https://doi.org/10.1038/nature07467

      Keller, G.B., Mrsic-Flogel, T.D., 2018. Predictive Processing: A Canonical Cortical Computation. Neuron 100, 424–435. https://doi.org/10.1016/j.neuron.2018.10.003

      Oliveira, A.S., Schlink, B.R., Hairston, W.D., König, P., Ferris, D.P., 2016. Proposing Metrics for Benchmarking Novel EEG Technologies Towards Real-World Measurements. Front. Hum. Neurosci. 10, 188. https://doi.org/10.3389/fnhum.2016.00188

      O’Toole, S.M., Oyibo, H.K., Keller, G.B., 2023. Molecularly targetable cell types in mouse visual cortex have distinguishable prediction error responses. Neuron 111, 2918-2928.e8. https://doi.org/10.1016/j.neuron.2023.08.015

      Rao, R.P.N., Ballard, D.H., 1999. Predictive coding in the visual cortex: a functional interpretation of some extra-classical receptive-field effects. Nat. Neurosci. 2, 79–87. https://doi.org/10.1038/4580

      Vasilevskaya, A., Widmer, F.C., Keller, G.B., Jordan, R., 2023. Locomotion-induced gain of visual responses cannot explain visuomotor mismatch responses in layer 2/3 of primary visual cortex. Cell Rep. 42, 112096. https://doi.org/10.1016/j.celrep.2023.112096

      Webb, J.M., Sohoglu, E., 2025. Cortical tracking of prediction error during perception of connected speech. https://doi.org/10.1101/2025.07.18.665498

      West, C.L., Bastos, G., Duran, A., Nadeem, S., Ricci, D., Groves, A.M.R., Wargo, J.A., Peterka, D.S., Leeuwen, N.V., Hamm, J.P., 2024. A lasting impact of serotonergic psychedelics on visual processing and behavior. https://doi.org/10.1101/2024.07.03.601959

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Rolland and colleagues investigated the interaction between Vibrio bacteria and Alexandrium algae. The authors found a correlation between the abundance of the two in the Thau Lagoon and observed in the laboratory that Vibrio grows to higher numbers in the presence of the algae than in monoculture. Timelapse imaging of Alexandrium in coculture with Vibrio enabled the authors to observe Vibrio bacteria in proximity to the algae and subsequent algae death. The authors further determine the mechanism of the interaction between the two and point out similarities between the observed phenotypes and predator prey behaviours across organisms.

      Strengths:

      The study combines field work with mechanistic studies in the laboratory and uses a wide array of techniques ranging from co-cultivation experiments to genetic engineering, microscopy and proteomics. Further, the authors test multiple Vibrio and Alexandria species and claim a wide spread of the observed phenotypes.

      Comments on revisions:

      I thank the authors for their additional work on the manuscript. My comments were addressed to my satisfaction.

      Dear Reviewer #1, we thank you for your careful evaluation of our manuscript and for the time and effort you dedicated to this review. We are pleased that the revised version has addressed your concerns to your satisfaction.

      Reviewer #2 (Public review):

      Goal summary

      The authors sought to (i) demonstrate correlations between the dynamics of the dinoflagellate Alexandrium pacificum and the bacterim Vibrio atlanticus in natural populations, ii) demonstrate the occurrence of predation in laboratory experiments, iii) demonstrate that predation is induced by predator starvation, and iv) test for effects of quorum sensing and iron-uptake genes on the predation process.

      Strengths include

      - Data indicating correlated dynamics in a natural environment that increase the motivation for study of in vitro interactions

      - Experimental design allowing clear inference of predation based on population counts of both prey and predators in addition to microscopy-based evidence

      - Supplementation of population-level data with molecular approaches to test hypotheses regarding possible involvement of quorum sensing and iron update in predation

      Weaknesses include

      - A quantitative analysis of effects of manipulating V. atlanticus density on rates of predation would have been valuable

      - Lack of clarity in some of the methodological descriptions

      Appraisal

      The authors convincingly demonstrate that V. atlanticus can prey on A. pacificum, provide strongly suggestive evidence that such predation is induced by starvation and clearly demonstrate that both iron availability and correspondingly the presence of genes involved in iron uptake strongly influence the efficacy of predation.

      Discussion of impact

      This paper will interest those interested in the diversity of forms of microbial predation and how microbial predatory behavior responds to environmental fluctuations. It will also interest those investigating bacteria-algae interactions and potential ecological controls of algal blooms. It may also interest researchers of microbial cooperation in light of the suggestion of communication between predator cells.

      Dear Reviewer #2, we sincerely thank you for the time you devoted to this second review of our manuscript. We greatly appreciate your thoughtful comments, which helped us further improve the clarity and precision of the manuscript. All your additional recommendations have been carefully considered and addressed in the revised version and in our responses below.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (2) The authors' reference to Fig. 4a did not address our concern about density potentially affecting the outcomes shown in Fig. 3. Fig. 4a does not provide any quantitative effects of manipulating Vibrio density. But the new density numbers the authors added in response to point (33) do seem to address our concern, because Vibrio densities become lower in the older cultures, excluding the possibility that the increased predation in older cultures might have been due higher Vibrio densities. We think this should be stated explicitly.

      (33) See point (2) above. We think the authors should explicitly state in the text that the increased predation in older cultures was not due higher Vibrio densities in those older cultures, referring to their data.

      As recommended by Reviewer#2, we added the sentence “Importantly, Vibrio densities decreased with culture age, ruling out the possibility that the stronger predation observed in older cultures was driven by higher bacterial densities” in the results section “Attack of A. pacificum ACT03 is activated by V. atlanticus LGP32 starvation.”

      (45) Is it known that bacterial predators collectively feed more on other bacteria than on microbial eukaryotes in natural habitats? While this certainly seems most likely, it's stated as fact and so should either the statement should be supported with relevant citations or phrased as a likely hypothesis.

      As suggested, we rephrased this sentence “Predatory bacteria are found in a wide variety of environments and are commonly described as feeding on other bacteria, although some cases of predation on microbial eukaryotes have also been hypothesized” in the discussion section.

      (46) Perhaps "Conceiving predators as free-living organisms that kill other organisms and feed on them, this study suggest that Vibrios engage in a novel form of predation in which they kill and feed on algae."

      The reference to 'developing' a predator behavior is not clear. What is meant by 'develop'? It seems unnecessary.

      The use of italics when writing Vibrio is inconsistent.

      We agree that the reference to “developing” a predatory behavior was unclear and unnecessary. We therefore revised the sentence as follows: “Conceiving predators as free-living organisms that kill other organisms and feed on them, this study suggests that Vibrio engages in a novel form of predation in which it kills and feeds on algae.” We also corrected the inconsistent use of italics for Vibrio throughout the manuscript.

      (48) The authors might wish to revise this sentence, as although M. xanxthus does have contact-dependent killing mechanism, it is our understanding that both Lysobacter and myxobacteria can kill some prey at a distance with diffusible secretions.

      The sentence “These bacteria must be in close proximity to their prey in order to cause lysis and utilize their biomass, regardless of the prey's species” was replaced by “These bacteria may require close proximity to their prey to cause lysis and utilize their biomass, although some can also kill prey at a distance through diffusible secretions”.

      (50) Why not directly say 'predatory behavior?

      We totally agree and have reworded the sentence.

      Line by line feedback:

      28 '...the phycosphere, an interface ...'

      We agree and have revised the wording.

      24 'In the attack stage, Vibrios...'

      This sentence has been rephrased as recommended.

      35 surrounds -> surround

      The correction has been done.

      36 The lysis is induced by the cells not by the 'stage'. We would rephrase to 'in which the lysis and consumption of the dinoflagellates occurs'

      This sentence has been rephrased as recommended.

      41 'a new mechanism that could to be involved' -> 'a new mechanism that could be involved ...'

      The correction has been done.

      61 forms

      The correction has been done.

      98 'the role...in'

      The suggested correction has been performed.

      103 'Qpcr' -> 'qPCR'

      Thank you for spotting this typo. “Qpcr” was corrected to “qPCR” in the manuscript.

      125 Misplaced punctuation

      The punctuation was corrected.

      152 The use of '.' vs 'x' to indicate multiplication when writing numbers is inconsistent. In some cases both are missing.

      Numbers have been corrected throughout the manuscript.

      231 I would rephrase 'poor nutrient stress' to 'little nutrient stress' or 'no nutrient stress'

      The rephrasing was carried out as suggested.

      310 R and used packages are not cited

      We added the citation (R Core Team, 2024). Linear models, QQ plots (which are part of linear models), tests, and AICs are included in R by default and are credited to the R Core Team.

      The sentence “Statistical analyses were performed using R 3.6.3 software” was replaced by “Statistical analyses were performed using R 3.6.3 software (R Core Team, 2024) using Rstudio”.

      358 'are capable of simultaneously attacking'

      The expression “are capable of simultaneously attacking” was revised in the manuscript to improve clarity and readability.

      366 'exponential growth phase'

      We have corrected the wording to “exponential growth phase” in the revised manuscript.

      430 The large difference in incubation time between the sea-water vs nutrient-rich treatments and use of different media are unfortunate. These additional variables compromise the ability to directly ascribe observed differences to starvation.

      We agree, the sentence “The comparative analysis of the proteome of V. atlanticus LGP32 incubated 60 h in artificial seawater (ENSW) versus V. atlanticus LGP32 grown 12 h in Zobell nutrient-rich medium revealed 10 proteins modulated by nutrient stress (Fig. S2)” was replaced by “The comparative analysis of the proteome of V. atlanticus LGP32 incubated 60 h in artificial seawater (ENSW) versus V. atlanticus LGP32 grown 12 h in Zobell nutrient-rich medium revealed 10 proteins that were differentially abundant under these two contrasting conditions (Fig. S2)”

      443 Somewhat unclear sentence. I would rephrase this to "Remarkably, of the 10 proteins identified by proteomic analysis and eliminated by mutation, only elimination of PvuB prevented V. atlanticus from attacking A. pacificum ACT03."

      To clarify this point, the sentence “Remarkably, among the 10 proteins identified by proteomic analysis only V. atlanticus LGP32 mutant lacking pvuB failed to attack A. pacificum ACT03 (Fig. 4C; ANOVA p <0.001)” was replaced by “Remarkably, of the 10 proteins identified by proteomic analysis and eliminated by mutation, only elimination of PvuB prevented V. atlanticus from attacking A. pacificum ACT03 (Fig. 4C; ANOVA p <0.001).”

      445 'attack simultaneously' -> 'simultaneously attack'

      The suggested modification has been done.

      450 H3BO4 is written as Boron later, it would be good to call it boron here as well so that it is easier to make the connection for the reader.

      We agree, we modified the manuscript and called it boron.

      459 'no linked' -> 'no link'

      The text was modified accordingly.

      483 'which induces' -> 'which induce'

      The correction has been made.

      519 The use of Vibrio atlanticus and V. atlanticus is inconsistent within the text.

      We have checked and modified the manuscript in accordance with the recommendations.

      807-808 The use of the phrase 'Akaike information criterion (AICc) models' is confusing. Aren't these models just generalized linear models? It should be rephrased to make clear that the AICc is just a test that is used to select which model to use.

      We clarified this point by revising Figure 1 legend. The sentences “(C) Result of Akaike information criterion (AICc) models tested to explain the mean value of degraded Alexandrium cells (dead cells) in spring. (D) Wald test of the AICc model attributing the mean value of degraded cells of Alexandrium in spring to free Vibrio “were replaced by “(C) Results of the Akaike Information Criterion (AICc) test conducted to select a model for explaining the mean value of dead Alexandrium (degraded cells) in spring. (D) Wald test of the AICc model explaining the mean value of dead Alexandrium in spring by free Vibrio”

      827 The chronological sequence of snapshots is not very clear. Perhaps it would be clearer if pictures over a shorter timeframe were used to clearly show the gathering of the V. atlanticus cells near the algal cells.

      To address this point, we removed the first and the last 14 seconds of the snapshots to clearly show the gathering of the V. atlanticus cells near the algal cells, and we added an arrow on Fig. 2D to indicate the chronological order.

    1. Author response:

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

      We would like to thank the editors and the reviewers for the thorough and insightful comments and suggestions. Addressing them has strengthened our manuscript. We have carefully addressed all reviewer comments, as described in detail below, as well as additional comments we received from others. In addition, we made two substantive updates to the manuscript:

      (1) We improved the estimation of uncertainty in the model predictions by computing 95% confidence intervals using 120 bootstrapped datasets (instead of the 100% of 10 bootstrapped datasets in the original submission) to match the number of bootstrap for the validation dataset.

      (2) We selected a slightly different hyperparameter value based on follow-up analyses suggested by Reviewer 1, which provided very useful information.

      Importantly, none of these changes alter the main results or conclusions of the paper.

      Beyond these changes and those outlined below, we also worked to improve the clarity of the prose throughout as well as added various additional citations to the literature.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This paper presents an ambitious and technically impressive attempt to map how well humans can discriminate between colours across the entire isoluminant plane. The authors introduce a novel Wishart Process Psychophysical Model (WPPM) - a Bayesian method that estimates how visual noise varies across colour space. Using an adaptive sampling procedure, they then obtain a dense set of discrimination thresholds from relatively few trials, producing a smooth, continuous map of perceptual sensitivity. They validate their procedure by comparing actual and predicted thresholds at an independent set of sample points. The work is a valuable contribution to computational psychophysics and offers a promising framework for modelling other perceptual stimulus fields more generally.

      Strengths:

      The approach is elegant and well-described (I learned a lot!), and the data are of high quality. The writing throughout is clear, and the figures are clean (elegant in fact) and do a good job of explaining how the analysis was performed. The whole paper is tremendously thorough, and the technical appendices and attention to detail are impressive (for example, a huge amount of data about calibration, variability of the stim system over time, etc). This should be a touchstone for other papers that use calibrated colour stimuli.

      Weaknesses:

      Overall, the paper works as a general validation of the WPPM approach. Importantly, the authors validate the model for the particular stimuli that they use by testing model predictions against novel sample locations that were not part of the fitting procedure (Figure 2). The agreement is pretty good, and there is no overall bias (perhaps local bias?), but they do note a statistically-significant deviation in the shape of the threshold ellipses. The data also deviate significantly from historical measurements, and I think the paper would be considerably stronger with additional analyses to test the generality of its conclusions and to make clearer how they connect with classical colour vision research. In particular, three points could use some extra work:

      (1) Smoothness prior.

      The WPPM assumes that perceptual noise changes smoothly across colour space, but the degree of smoothness (the eta parameter) must affect the results. I did not see an analysis of its effects - it seems to be fixed at 0.5 (line 650). The authors claim that because the confidence intervals of the MOCS and the model thresholds overlap (line 223), the smoothing is not a problem, but this might just be because the thresholds are noisy. A systematic analysis varying this parameter (or at least testing a few other values), and reporting both predictive accuracy and anisotropy magnitude, would clarify whether the model's smoothness assumption is permitting or suppressing genuine structure in the data. Is the gamma parameter also similarly important? In particular, does changing the underlying smoothness constraint alter the systematic deviation between the model and the MOCS thresholds? The authors have thought about this (of course! - line 224), but also note a discrepancy (line 238). I also wonder if it would be possible to do some analysis on the posterior, which might also show if there are some regions of color space where this matters more than others? The reason for doing this is, in part, motivated by the third point below - it's not clear how well the fits here agree with historical data.

      Thank you for raising this important point. We have now added analyses of the effects of the two smoothness-related hyperparameters, ε and γ (see Appendix 10).

      First, we swept a range of values for each hyperparameter (ε: 0.1 – 1; γ: 0.000001 – 0.003) and evaluated model performance using 5-fold cross-validation of the dataset used to fit the WPPM, quantifying predictive accuracy on held-out test data. We used the mean negative log likelihood averaged across the held-out data in the cross validation as our measure of predictive accuracy (Figs. S27-31).

      The two hyperparameters affect cross-validation accuracy in a similar manner. With γ fixed at 0.0003, predictive accuracy is highest for ε in the range of approximately 0.3–0.5 and drops quite rapidly for ε < 0.3. We attribute this drop to oversmoothing. Cross-validation accuracy also decreases, albeit more gradually, for ε > 0.5. We attribute this to increased variance due to undersmoothing relative to the power of our datasets. Similarly, with ε fixed at 0.4, predictive accuracy is highest for γ values between approximately 0.0001 and 0.001, declines rapidly for smaller γ (oversmoothing), and more slowly for larger γ (undersmoothing).

      Second, we examined how the hyperparameter ε affected the agreement between the WPPM fit and the MOCS validation data. Specifically, at each ε, for each participant, we computed the linear regression between WPPM thresholds and validation thresholds at 25 reference locations. Then, we examined the slope and correlation coefficient of all participants as a function of ε. We found a classic bias–variance tradeoff. Excessive smoothness introduces bias by failing to capture structure in the data, whereas insufficient smoothness increases variance in model predictions. These results further support a choice of ε = 0.4 as lying near the optimal balance between bias and variance (Fig. S32).

      Based on these analyses, we selected for the final analysis ε = 0.4, slightly smaller than the preregistered value used in the original submission (0.5), while retaining the original value of γ (0.0003).

      We now discuss these reasons for changing this value in the revision, as well as provide a more general discussion of the importance and practicalities of hyperparameter choice in Bayesian approaches to analyzing data (Discussion / Prior specification).

      (2) Comparison with simpler models. It would help to see whether the full WPPM is genuinely required. Clearly, the data (both here and from historical papers) require some sort of anisotropy in the fitting - the sensitivities decrease as the stimuli move away from the adaptation point. But it's >not< clear how much the fits benefit from the full parameterisation used here. Perhaps fits for a small hierarchy of simpler models - starting with isotropic Gaussian noise (as a sort of 'null baseline') and progressing to a few low-dimensional variants - would reveal how much predictive power is gained by adding spatially varying anisotropy. This would demonstrate that the model's complexity is justified by the data.

      In the 5-fold cross-validation analysis described above (and now presented in Appendix 10), we found that when ε or γ is small, the stronger smoothness constraint leads to threshold ellipses that are nearly identical to each other across color space. Under these conditions, model predictions show poor accuracy on held-out test data and lead to poor predictions of the validation data. This observation addresses the underlying point raised by the reviewer, albeit in a different way than suggested: it shows that a degree of spatially varying anisotropy is necessary to capture the structure of the data. We now make this point in the paper (Discussion / Prior specification).

      More broadly, we employed the WPPM as a prior that imposed smoothness but not much other obvious structure, and used this to learn about the psychometric field. We are currently working to understand how we can best use our current data to improve the prior we would apply to future measurements. There are a number of approaches to this. One would be to seek a parametric mechanistic model that can describe the current data, and to the extent this is possible formulate prior distributions over the parameters of the model. The results reported here thus provide a foundation for deriving and evaluating more structured priors that would even more efficiently leverage future datasets, but with the feature that they impose more structure. We have added this perspective to the Discussion / Extensions of the WPPM framework.

      (3) Quantitative comparison to historical data. The paper currently compares its results to MacAdam, Krauskopf & Karl, and Danilova & Mollon only by visual inspection. It is hard to extract and scale actual data from historical papers, but from the quality of the plotting here, it looks like the authors have achieved this, and so quantitative comparisons are possible. The MacAdam data comparisons are pretty interesting - in particular, the orientations of the long axes of the threshold ellipses do not really seem to line up between the two datasets - and I thought that the orientation of those ellipses was a critical feature of the MacAdam data. Quantitative comparisons (perhaps overall correlations, which should be immune to scaling issues, axis-ratio, orientation, or RMS differences) would give concrete measures of the quality of the model. I know the authors spend a lot of time comparing to the CIE data, and this is great.... But re-expressing the fitted thresholds in CIE or DKL coordinates, and comparing them directly with classical datasets, would make the paper's claims of "agreement" much more convincing.

      Although we are sympathetic to this request, we have chosen not to implement the sort of quantitative comparison requested by the reviewer. The reason is that an important feature of color thresholds is that they depend on the spatial (e.g. Kelly, 1974; Poirson & Wandell, 1996; Danilova & Mollon, 2025) and temporal (e.g. Kelly, 1974) properties of the stimuli, and on the observer’s state of adaptation (e.g. Loomis & Berger, 1979; Krauskopf & Gegenfurtner, 1992). Because (as the reviewer notes below) the spatial and temporal properties of our stimuli were not matched to those of the comparison datasets, our purpose in making these comparisons was to examine qualitative agreement, as well as to situate our results in the literature and to demonstrate that our approach allows us to read out thresholds around the references and in the color spaces used in other studies. We would not expect detailed quantitative agreement with the current dataset because of differences in stimuli.

      As a consequence of this, we think we would be overreaching to quantify the differences between our data and classic datasets. This consideration is particularly important for the MacAdam measurements, where because of the matching adjustment procedure used, the observer’s state of adaptation is likely to have varied (by amounts that are difficult to estimate) from one reference to the next (e.g. Danilova & Mollon, 2025). We have clarified the manuscript with respect to these points (Results / Comparison with previous measurements).

      A point to make on this topic is that an important and interesting future direction that emerges from our work is to develop efficient methods to characterize the dependence of the full discrimination field on ancillary variables, such as those that describe spatial and temporal properties and/or the state of adaptation, which we now also mention in the paper (Discussion / Implications for the mechanisms of color perception). Although not the primary motivation, doing so would enable comparison of data with a wider range of studies.

      We do agree that the comparisons to CIELAB predictions work better when we express them in CIELAB, and have now done so (Fig. 3D; Fig. S24-S26).

      Kelly, D. H. (1974). "Spatio-temporal frequency characteristics of color-vision mechanisms." Journal of the Optical Society of America 64(7): 983–990.

      Poirson, A. B. and B. A. Wandell (1996). "Pattern-color separable pathways predict sensitivity to simple colored patterns " Vision Research 36(4): 515–526.

      Danilova, M. V. and J. D. Mollon (2025). "Effect of stimulus size on chromatic discrimination." Journal of the Optical Society of America A 42(5).

      Loomis, J. M. and T. Berger (1979). "Effects of chromatic adaptation on color discrimination and color appearance." Vision Research 19(8): 891–901.

      Krauskopf, J., Gegenfurtner, K. (1992). "Color discrimination and adaptation." Vision Research 32(11): 2165–2175.

      Overall, this is a creative and technically sophisticated paper that will be of broad interest to vision scientists. It is probably already a definitive method paper showing how we can sample sensitivity accurately across colour space (and other visual stimulus spaces). But I think that until the comparison with historical datasets is made clear (and, for example, how the optimal smoothness parameters are estimated), it has slightly less to tell us about human colour vision. This might actually be fine - perhaps we just need the methods?

      Related to this, I'd also note that the authors chose a very non-standard stimulus to perform these measurements with (a rendered 3D 'Greebley' blob). This does have the advantage of some sort of ecological validity. But it has the significant disadvantage that it is unlike all the other (much simpler) stimuli that have been used in the past - and this is likely to be one of the reasons why the current (fitted) data do not seem to sit in very good agreement with historical measurements.

      As the reviewer notes, our stimuli head in the direction of ecological validity (see also Hedjar et al., 2025) and indeed this was a consideration when we chose them, at the cost of limiting the degree of comparison we can make with prior studies (as discussed above). Another reason we chose our stimuli is that they enable the current data to be used as a basis of comparison with stimuli where we add specularity, change object shape, and vary object pose in the future. These manipulations are not possible with flat matte patches. Such experiments are of interest to us, as they will tell us about how effectively color may be used to differentiate stimuli in cases where other ecologically important variables co-vary. We now mention this motivation in the paper (Results / Task and Stimuli).

      Hedjar, L., M. Toscani and K. R. Gegenfurtner (2025). "Importance of hue: color discrimination of three-dimensional objects and two-dimensional discs." Journal of the Optical Society of America A 42(5).

      Reviewer #2 (Public review):

      Summary:

      Hong et al. present a new method that uses a Wishart process to dramatically increase the efficiency of measuring visual sensitivity as a function of stimulus parameters for stimuli that vary in a multidimensional space. Importantly, they have validated their model against their own hold-out data and against 3 published datasets, as well as against colour spaces aimed at 'perceptual uniformity' by equating JNDs. Their model achieves high predictive success and could be usefully applied in colour vision science and psychophysics more generally, and to tackle analogous problems in neuroscience featuring smooth variation over coordinate spaces.

      Strengths:

      (1) This research makes a substantial contribution by providing a new method to very significantly increase the efficiency with which inferences about visual sensitivity can be drawn, so much so that it will open up new research avenues that were previously not feasible. Secondly, the methods are well thought out and unusually robust. The authors made a lot of effort to validate their model, but also to put their results in the context of existing results on colour discrimination, transforming their results to present them in the same colour spaces as used by previous authors to allow direct comparisons. Hold-out validation is a great way to test the model, and this has been done for an unusually large number of observers (by the standards of colour discrimination research). Thirdly, they make their code and materials freely available with the intention of supporting progress and innovation. These tools are likely to be widely used in vision science, and could of course be used to address analogous problems for other sensory modalities and beyond.

      Weaknesses:

      It would be nice to better understand what constraints the choice of basis functions puts on the space of possible solutions. More generally, could there be particular features of colour discrimination (e.g., rapid changes near the white point) that the model captures less well.

      This comment bears conceptual similarity to Reviewer 1’s question about the hyperparameters of our prior, as it is basically asking whether we might be oversmoothing through the choice of form and number of basis functions. The hyperparameter sweeps we now present suggest that within the choice of basis functions we used, we are operating at a reasonable point on the bias-variance tradeoff curve - we can see bias emerging with a smoother prior, and variance increasing with a less smooth prior. Our expectation is that varying the smoothness of the prior in other ways, such as by varying the form and number of the basis functions, would lead to similar tradeoffs.

      We did perform one additional check that shows, within our current framework, that adding more basis functions is unlikely to change things much. This was to plot the fit weights as a function of Chebyshev basis order (Figure S4 in Appendix 2). These decline to near zero at the highest order we used, suggesting that adding more would not alter the inferred psychometric field, given our hyperparameter choices. Although we could explore this question further by explicitly fitting the data using more basis functions along with different hyperparameter choices, or different functional forms for the basis functions, we decided not to pursue this in favor of performing the other additional analyses we now present.

      We resonate with the reviewer’s concern that assuming smoothness, both by assuming that isoperformance contours are elliptical and by assuming that these vary smoothly with reference, might cause us to miss features of the true underlying field in cases where that field varies rapidly or the isoperformance contours are asymmetric or non-elliptical. Our approach to this was to measure the validation thresholds and demonstrate that any bias in our WPPM-inferred field is small for these measurements. Because we shared the reviewer’s intuition that the adapting point is a candidate location where there might be less smooth variation, we measured a validation threshold at this reference for every subject. Nonetheless, we only measured in one direction around the adapting reference for each subject. We considered validation approaches where we measured full ellipses at a set of validation references, but we were worried about effects of uncertainty reduction and perceptual learning which might distort thresholds at highly sampled locations.

      It is the case that if one wanted to study the discrimination field in more detail around a particular reference, one could concentrate trials in a smaller model space around that reference, and for the same number of trials use a prior with less smoothness relative to the underlying stimulus space. Indeed, simply halving the size of the stimulus space that maps onto the [-1,1] model space and keeping the same prior over the model space effectively halves the degree of smoothness expressed with respect to the stimulus space. Thus our methods could prove useful in studying more rapid variations in the discrimination field if one hypothesized that they might occur around particular reference choices, but this would still rest upon the elliptical assumption. To relax that assumption, one could use the threshold field estimation methods implemented in AEPsych, which incorporate a smoothness assumption but do not assume elliptical isoperformance contours. Weakening the prior in this way would, however, increase trial demand to obtain similar measurement precision.

      As a general matter, we don’t think it is possible to leverage smoothness for trial efficiency on the one hand and at the same time be completely sure that there isn’t some aspect to the underlying ground truth that has been smoothed over. Carefully choosing the degree of prior smoothness together with the number of experimental trials in the context of a particular content problem is an important part of bringing the WPPM and related methods to bear, and one where simulation and held-out data both play an important role.

      We now bring these points out more fully in the paper (Discussion / Extensions of the WPPM framework; Discussion / Prior specification).

      Chen, C.-C., J. M. Foley and D. H. Brainard (2000). "Detection of chromoluminance patterns on chromoluminance pedestals I: threshold measurements." Vision Research 40(7): 773–788.

      The substantial individual differences evident in Figure S20 (comparison with Krauskopf and Gegenfurtner, 1992) are interesting in this context. Some observers show radial biases for the discrimination ellipses away from the white point, some show biases along the negative diagonal (with major axes oriented parallel to the blue-yellow axis), and others show a mixture of the two biases. Are these genuine individual differences, or could the model be performing less accurately in this desaturated region of colour space?

      We agree that these differences are interesting. We have now added more complete bootstrapped confidence regions in these (Appendix 8) and the other comparison figures (Appendix 6, 7, 9), so that an estimate of measurement precision is directly available in these figures. These confidence regions suggest that the individual differences in this region of color space are real. A longer-term goal is to develop more mechanistic models that can account for individual subject data through parameter choice. This might lead to insight into what differs in the visual system across individuals.

      Reviewer #3 (Public review):

      Summary:

      This study presents a powerful and rigorous approach for characterizing stimulus discriminability throughout a sensory manifold, and is applied to the specific context of predicting color discrimination thresholds across the chromatic plane.

      Strengths:

      Color discrimination has played a fundamental role in studies of human color vision and for color applications, but as the authors note, it remains poorly characterized. The study leverages the assumption that thresholds should vary smoothly and systematically within the space, and validates this with their own tests and comparisons with previous studies.

      Weaknesses:

      The paper assumes that threshold variations are due to changes in the level of intrinsic noise at different stimulus levels. However, it's not clear to me why they could not also be explained by nonlinearities in the responses, with fixed noise. Indeed, most accounts of contrast coding (which the study is at least in part measuring because the presentation kept the adapt point close to the gray background chromaticity, and thus measured increment thresholds), assume a nonlinear contrast response function, which can at least as easily explain why the thresholds were higher for colors farther from the gray point. It would be very helpful if a section could be added that explains why noise differences rather than signal differences are assumed and how these could be distinguished. If they cannot, then it would be better to allow for both and refer to the variation in terms of S/N rather than N alone.

      We agree with the reviewer. We are measuring SNR and attributing it to noise, but cannot identify from the data whether changes in SNR across color spaces are due to changes in noise, to a nonlinear relationship between stimulus space and the observer’s response space with noise in the response space held fixed, or both. We now make this point where we introduce the Results / Wishart Process Psychophysical Model and reiterate it in the Discussion / Extensions of the

      WPPM framework.

      Related to this point, the authors note that the thresholds should depend on a number of additional factors, including the spatial and temporal properties and the state of adaptation. However, many of these again seem to be more likely to affect the signal than the noise.

      We don’t disagree. Indeed, as we noted in our response to a comment by Reviewer 1 and above in the context of individual differences, we are very interested in developing a mechanistically plausible model that accounts for the data. If we or others are able to do so, that would provide a basis for parsing performance into separate signal and noise effects. And if such a model has natural ways in which additional variables affect its predictions, measuring the effects of these variables would be a way to provide evidence in favor of the model (Discussion / Implication for the mechanisms of color perception - Extensions of the WPPM framework).

      An advantage of the approach is that it makes no assumptions about the underlying mechanisms. However, the choice to sample only within the equiluminant plane is itself a mechanistic assumption, and these could potentially be leveraged for deciding how to sample to improve the characterization and efficiency. For example, given what we know about early color coding, would it be more (or less) efficient to select samples based on a DKL space, etc?

      The more we are willing to assume about the structure of the psychometric field, the more efficiently we can measure it. As the reviewer correctly notes, this principle applies to trial placement as well. We are currently using an adaptive method (AEPsych) that starts with a fairly weak smoothness prior and attempts to place trials using heuristics that aim to minimize the expected uncertainty in the posterior. As we learn more about the discrimination field, we should be able to leverage stronger priors to increase trial efficiency. This point is closely related to one we made above about developing stronger priors that capture what we have learned in this study. Such priors could also help improve trial placement. For a prior that has a relatively small number of parameters, for example, perhaps a mechanistic prior, methods such as Quest+ (Watson, 2017) may be used for trial placement.

      Watson, A. B. (2017). "QUEST+: A general multidimensional Bayesian adaptive psychometric method." J Vis 17(3): 10.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I do not think that the authors need to perform additional experiments. However, I would like to see some additional analyses regarding the assumptions made in the fitting procedure and how they affect the final maps.

      I also think some more quantitative comparisons with historical data would be valuable - at the moment, a lot of the comparisons are simply 'by eye'.

      It would have been nice to have the code and data available during the review procedure - I'm sure these will be released with excellent documentation?

      We addressed the first two points in the public review section. The code is now available online as is the data. These links are now provided in the paper (Methods and Materials / Data and code availability).

      Reviewer #2 (Recommendations for the authors):

      Minor points

      I have a few suggestions for additions and small changes.

      (1) Several examples of covariance matrix fields are shown in Figure 1, 4, but these are for simulated examples. It would be nice to see the fields actually fit the data! I would be interested in seeing this for all participants in an Appendix, and maybe for participant CH in the main paper?

      We have made the changes (see Figure 4 and Figure S3).

      (2) I have not worked through all the math in the appendices line by line, but it seems to be complete, and the model validation results speak for themselves. I think the authors have done a pretty good job of explaining the model conceptually (not easy), but I struggled with the 'weighted sum' step in Figure 4 and the main text. I would appreciate a bit more hand-holding here, e.g, why is an 'overcomplete' representation needed as an intermediate, and providing an intuition of why there are 12 matrices in the overcomplete representation and what each matrix in this representation represents.

      We have now added more explanations in the figure legend and text (Fig. 4 and Methods and Materials / The Wishart Process Psychometric Model).

      (3) Individual differences: There is a section on this in the manuscript, and it's concluded that there are only "modest" individual differences. However, in Figure S20, the individual differences, I think, are huge and place observers almost in qualitatively different categories! Some observers show a radial bias in discrimination ellipses, others seem to show basically a bias along the negative diagonal, and others a mixture of both biases. These ellipses are at a desaturated part of colour space - is it possible that there are some rapid changes in the underlying noise in this region that the Wishart fit has not captured due to relatively sparse sampling or the fact that the basis functions are all fairly low spatial frequency? I wondered whether the results are constrained by the choice of Cartesian rather than polar basis functions, e.g, polar basis functions may have better allowed fine-grained changes near the white point but slower changes at higher saturations away from the white point.

      We agree that the individual differences are meaningful and, in some cases, quite pronounced. Our intent in describing the differences as “modest” was to emphasize that the overall structure of the psychometric fields remains broadly consistent across observers. We have revised the Results to note and more fully describe these differences.

      Regarding the possibility that sharp changes in the underlying noise near the achromatic point might not be fully captured by the current model, we agree that this is an important consideration. The current implementation uses relatively low-order Chebyshev basis functions that primarily capture smooth global variations in the psychometric field. While validation analyses indicate that these basis functions capture the dominant structure in the data, they may be less sensitive to sharp local variations such as those that could occur near the white point. Future work could address this by mapping the model space to a smaller region around the achromatic reference or by exploring alternative basis sets (e.g., polar or Zernike functions) that may better capture such localized structure. This is discussed above in this response and now addressed in Discussion / Extensions of the WPPM framework.

      On sampling, I wondered if the results might have been biased by the strongly biased ellipse that occurs at the grey point. If not, and the model is accurate in this region of colour space, I think this figure does show some large individual differences, and it would be good to comment on these in the individual differences section of the manuscript.

      Based on our analysis of trial placement (Fig. S1), the adaptive algorithm does not appear to have disproportionately concentrated trials near the gray point. In fact, more trials were allocated to the edges of the stimulus space than to the center. This suggests that the WPPM estimates are unlikely to be driven primarily by performance in the gray region. In addition, we examined the threshold ellipses around the gray reference in DKL space and found that they are broadly consistent across participants (Figs. S22–S23). Together, these analyses suggest that the anisotropy observed near the gray point reflects a genuine property of the psychometric field rather than an artifact of the sampling procedure.

      As noted just above, we have added additional text about individual differences in the Results and referenced it in the Discussion.

      (4) The manuscript seems unusually free of typographical errors, but I noticed that in many places "Krauskopf and Karl 1992" is cited! Also, I think something has gone wrong with the legend to Figure 2 - perhaps the order of panels was swapped around, but the legend was not fully updated. There is a repeated reference to the "summary of regression slopes" which seems to be in 2 positions, after C and G. It would make more sense to label panel G as D and progress from there, or switch the order of the panels so that G is on the bottom row.

      Thank you for catching those errors. They are now fixed.

      Reviewer #3 (Recommendations for the authors):

      A minor point (or perhaps major if your last name is Gegenfurtner) is that the reference to Krauskopf and Karl is incorrect.

      They are now fixed.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      In the paper, the authors compare the performance of their new version to two previous approaches. Figure 2b shows that the new toolbox performs similarly to the previous deep-learning-based toolbox, but requires only an anatomical scan, which is a significant improvement. They also compare it to an older method that uses an atlas without requiring deep learning. For eccentricity and pRF size predictions, both deep-learning methods perform better than the older approach. For polar angle, a critical parameter for delineating visual field maps, the gain is substantially less. Moreover, the comparison to the atlas method (Benson2014) is not entirely fair, as, to our knowledge, there is also a more advanced atlas version that uses Bayesian fitting methods and already performs better than the old method. To better understand the gain of using deep learning, it would be beneficial if the authors also made the comparison to this more recent atlas-based approach. Moreover, it would be useful to know the correlations for the representative participant. Some examples of relatively "bad" maps would also be useful to have (and could be provided as supplementary information).

      We thank the reviewer for their constructive feedback. We plan to expand our benchmarking section to include the Bayesian model comparison. Note, however, that the additional accuracy gain afforded with the Bayesian model of retinotopy (Benson and Winawer, 2018) results from combining anatomical data with retinotopic maps estimated with a few minutes of functional data. The Bayesian model of retinotopy without such functional data is equivalent to Benson14. We plan to report the correlations (between predicted and empirical maps) for the representative participant shown in Figure 2 and include an additional supplementary figure showing retinotopic map predictions for a participant whose predictions deviate the most from empirical maps, as suggested by the reviewer.

      Figure 2b shows that the toolbox is quite good at estimating eccentricity and polar angle parameters, but less good at estimating the population receptive field (pRF) size. I will return to this latter point.

      An interesting feature is that while the toolbox is trained on a specific data set (HCP), it can, "out-of-the-box", be applied to different existing data sets, without the need to retrain the model. This is quite important for the general utility of the method. The results for this are shown in Figure 3. Again, in panel b, it can be seen that the toolbox does a good job at estimating eccentricity and polar angle values, but performs rather poorly for pRF size: the deepRetinotopy toolbox has a strong tendency to only estimate very small pRFs, particularly when applying it across different datasets. For this reason, at the moment, these estimates appear hardly useful. It would be very helpful for readers if the authors could clarify or elaborate on this point, particularly regarding the limitations of pRF size predictions. They explain that this could be due to the use of different types of stimuli, but even within the same (HCP) dataset, the predictions primarily suggest tiny pRFs, even though the training dataset also contains larger ones (which can be better seen in supplementary Figure 4). Showing the predictions for higher-order brain areas, which have larger pRFs on average, could serve a similar evaluation purpose. Presumably, the underlying reasons are complex and could relate to the use of different stimuli, different analysis toolboxes, and how the deep learning model is currently being trained. Possibly, the abundance of small pRFs at lower eccentricity in the training set (which is usually the case in any empirical analysis) has given the model a very strong bias toward predicting small pRFs.

      There would be various ways to verify which of these components is critical. For example, the model could be trained only on the bar stimuli of the HCP dataset, or the pRFs for all stimuli and datasets could be estimated using the same software tool. The latter seems important. For example, Supplementary Figure 4 indicates a high correlation between the Stanford and NYU cohorts that have used the same stimulus and analysis package, despite having different resolutions and scanners. Further investigation into the underlying reasons for these discrepancies would strengthen the paper. It would also provide valuable guidance for users of the toolbox on which toolbox predictions to trust and which not, as well as how well the model generalizes to other stimulus types, scanners, and image resolutions.

      We will expand our discussion of the limitations of pRF size prediction, highlighting that differences in visual stimuli, analysis toolboxes used to estimate pRF parameters from empirical data, and the current training of deepRetinotopy affect prediction accuracy. As the reviewer pointed out, the underlying reasons are complex, and it is difficult to isolate all the potential contributing factors. However, in addition to our expanded discussion, we also intend to present results from additional experiments that assess the impact of different loss functions on the range of predicted pRF sizes (to explain how training may partly account for the differences observed in the HCP dataset). We will also perform pRF fitting on at least one dataset using the same software/encoding model as in the HCP dataset (the training data) to illustrate that the lower performance in pRF size prediction in out-of-distribution datasets is also partly explained by differences in how the empirical maps were obtained.

      An aspect that is not directly apparent from the title, abstract, and introduction is that the deepRetinotopy toolbox does not by itself produce estimates of visual area labels or boundaries. It predicts only polar angle and eccentricity values. To predict labels and boundaries, the authors combine the toolbox with an atlas (the aforementioned Bayesian atlas). For visual areas V1 - V3, it does a very good job, in that the predictions are as good as the empirical ones. Notably, the authors indicate that the predictions for V2 and, in particular, V3 are worse than for V1, but Figure 4 clearly shows that predictions are as good as the empirical ones. More cannot be expected from a model that is trained on such empirical data.

      We will edit the introduction and abstract to make it clearer that the deepRetinotopy toolbox does not yet produce estimates of visual boundaries on its own.

      Irrespective of the limitations with respect to predicting pRF size, the toolbox opens up functionally oriented analyses of very large cohorts of healthy participants, of which only anatomical data is available. The authors present an example of this by confirming the existence of differences in horizontal and vertical asymmetries in the field maps of the visual cortex of children and adults. While Figure 5 confirms the existence of differences, the analysis could be expanded to provide deeper insights, such as normalized developmental trajectories for both asymmetries, given the size of the dataset. This would better highlight the true power of their approach.

      Although providing insights into developmental trajectories for horizontal and vertical asymmetries is beyond the scope of the current work, as it would require aggregating datasets such that individuals’ age span a larger range (ABCD dataset only contains individuals between 9-11 years old and the HCP Young Adult dataset between 22-36 years old), we plan to provide some complementary analyses (differences across ages and sex within the ABCD dataset).

      While the authors address limitations with respect to studying experience-dependent atypical functional organization, they do not address how the deepRetinotopy toolbox would handle (acquired) brain lesions. Addressing this, even if only speculative, would be welcome. Another welcome addition would be to see the predictions for additional brain areas, even if those would (presumably) be worse at present. Such information would nevertheless be essential for users considering applying this toolbox. Moreover, this could be a valuable resource serving as a benchmark for future iterations of either deepRetinotopy or other approaches.

      We plan to expand and report performance evaluation across other visual areas (using Wang atlas’ parcels) to serve as a benchmarking resource. Moreover, we will expand our discussion on how deepRetinotopy would handle brain lesions.

      Reviewer #2 (Public review):

      (1) The weak point of the contribution is the choice to limit anatomical quality assessments and error quantifications to just three early regions, V1-V3, even though the deepRetinotopy toolbox can delineate over 20 regions (including parietal, ventral, and lateral regions, such as IPS0-5, hV4, VO1-2, V3A, PHC1-2, LO1-2, and TO1-2).

      (2) The limit is fine for their large-scale application of the toolbox to age groups, as here, a clear hypothesis on early cortex variability was tested.

      (3) However, the introduction of the toolbox itself warrants quality assessments and comparisons to prior models and ground truth beyond V1-V3, just like the authors did in their prior publication of the predecessor model.

      (4) This is important as the vast majority of applications of this toolbox will likely go beyond V1-V3 to delineate dorsal, ventral, and lateral regions.

      (5) For the present paper, this will require only 1 or 2 additional figures, or extending their present figures 2 and 4 along the lines of their previous figure 7 (Ribeiro et al 2021), which included error measures for high-level regions. Ideally, you provide sub-graphs separately for early visual, dorsal, ventral, and lateral regions.

      (6) Going beyond V1-V3 is important for several reasons: first, future studies applying the software beyond V3 will need quantification for reassurance and justification. Second, for the sake of transparency, even if results are noisy or on par with prior models. Third, as a benchmark or reference point for future approaches.

      We thank the reviewer for their constructive feedback, and we agree that expanding our performance assessment beyond V1-3 would be a valuable benchmarking resource. Thus, we plan to evaluate retinotopic map prediction accuracy across visual areas defined by the Wang atlas’ parcels, expanding on the results reported in Figure 2, and provide it as a supplementary figure. However, performance estimation ultimately depends on the quality of the dataset used for evaluation. The empirical maps, although treated as ground truth, may themselves misrepresent the underlying retinotopic organization. As a matter of fact, the quality of the empirical data (HCP dataset and others) is indeed lowest in some of the higher-order visual areas.

      It may be unclear from the text that the deepRetinotopy toolbox does not yet produce estimates of visual boundaries on its own. Accordingly, we illustrate how deepRetinotopy toolbox’s predictions can be combined with another tool [the Ba yesian model of retinotopy from Benson and Winawer (2018)] to obtain visual area boundaries automatically. We will edit the introduction and abstract to make it clearer. Given the availability of empirical labels (currently only for V1-3) and the segmentation tool (which was only assessed for V1-3), we cannot expand Figure 4 to other visual areas as suggested.

      Reviewer #3 (Public review):

      Quantification of the Analysis: My main concern is that the analysis relies heavily on global summary measures such as correlation and Dice score. Those measures are useful, but the paper would be more informative if it also quantified boundary differences in millimeters, especially for comparisons such as the V1/V2 boundary in Figure 2. That kind of analysis would help readers understand how large the errors are in physically meaningful terms.

      We thank the reviewer for their constructive feedback. Following the reviewer’s suggestion, we plan to expand our segmentation evaluation to quantify the extent to which boundary predictions from deepRetinotopy’s maps deviate from those from empirical maps, in millimetres.

      Model fitting methods: I also think the discussion of prediction failures for pRF size should be more explicit. The mismatch is likely influenced by the fact that the training data and several evaluation datasets were fit with different models and different analysis software. In particular, the network was trained on non-linear size estimates from the HCP data, while the comparison datasets were derived using other packages and, in some cases, different model assumptions. That likely contributes to the spread in Figure 3b and should be discussed more directly. It is important to discuss that the pRF parameters were derived using different software tools.

      We will expand our discussion of the limitations of pRF size prediction, highlighting that differences in visual stimuli, different encoding models for estimating pRF parameters from empirical data, and the current training of deepRetinotopy affect prediction accuracy. In addition to our expanded discussion, we intend to also present results from additional experiments that assess the impact of those factors on pRF size prediction performance.

      Clarifying Model Accuracy: If deepRetinotopy generates a true "noise-removed" representation of functional mapping based on anatomy, then fitting it to one fMRI measurement should predict a second, independent fMRI run better than the noisy data from the first run does.

      The authors possess the exact data for this test. For the HCP dataset, the empirical fMRI data were explicitly separated into two halves: "fit 2" (the first half of the fMRI runs) and "fit 3" (the second half). They correlated these two halves to establish a "noise ceiling," the maximum possible reliability of the data. Looking at their results in Figure 2b, the correlation of the deepRetinotopy predictions falls below this noise ceiling. This means that the noisy functional Half 1 actually predicts functional Half 2 better than the anatomical model does.

      The authors should state this explicitly. A side-by-side plot of Half 1 predicting Half 2 versus deepRetinotopy predicting Half 2 would show that the anatomical model regularizes map location well, but misses reliable subject-specific variation that anatomy alone cannot capture.

      We will expand our benchmarking session to make these comparisons (“Half 1 predicting Half 2 versus deepRetinotopy predicting Half 2”) more explicit. It is important to highlight that there is more subject-specific variation that is currently not captured by our model, and it can also serve as a benchmarking resource for future model versions and newer approaches.

      The Hemodynamic Response Function: The assumptions used to generate the original empirical maps are permanently baked into the deep learning model. However, the authors explicitly mention the hemodynamic response function (HRF) only once, noting in the Methods that the modeled time series was "convolved with a canonical hemodynamic response function."

      Beyond this single mention, there is no direct discussion of how the assumption of a single canonical HRF across all 161 HCP training subjects might have systematically impacted or biased the network's predictions. The authors address cross-dataset differences broadly under the umbrella of "experimental design" and "fMRI preprocessing pipeline" biases, but the HRF is a core biological property that mediates the connection between the anatomy and the data. The authors should explicitly discuss how this canonical assumption limits or biases the resulting deepRetinotopy network.

      As Reviewers 3 and 1 have noted, the observed limitations in pRF size prediction stem from multiple underlying factors. One of those factors is indeed the HRF assumed in the encoding models. We will expand our discussion about factors that may introduce biases into deepRetinotopy predictions, including the HRF.

      Scoping the Input Data and Normative Use: The authors use FreeSurfer to generate a mean curvature map for the entire midthickness cortical surface. This full-hemisphere curvature map is resampled to a standard template surface space (32k_fs_LR), acting as the data frame that feeds input features into the neural network. However, while the network receives the full geometric structure of the hemisphere, it is explicitly trained to predict retinotopic parameters only within a restricted posterior ROI, based on the Wang et al. atlas and containing roughly 3,200 vertices per hemisphere.

      A useful experiment to try, and perhaps the authors have already considered this, would be to restrict the input features exclusively to the posterior vertices. Including all anterior vertices may make it harder for the network to fit the localized visual data. A brief commentary on why the full hemisphere was retained as input could be highly informative for researchers adapting this geometric deep learning pipeline.

      Thanks for this suggestion. We have not performed a systematic evaluation of using ROIs that span a larger portion of the cortex (including the full hemisphere). It is a great idea to do so and report it in our manuscript to inform other researchers interested in adapting our pipeline. We intend to also update our toolbox by retraining our models to take all posterior vertices as suggested, which would improve the coverage of current predictions.

    1. Author response:

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

      We thank the reviewers for their careful consideration of our work and constructive comments. We are glad that reviewers appreciated the rigor and value of our work. In response to the reviewer comments we have made the following changes:

      (1) Addition of new experiments on EndoA localization at the Drosophila NMJ (Fig. 2).

      (2) Addition of new experiments on Dap160 localization at the Drosophila NMJ (Fig. 2).

      (3) Addition of new experiments to validate Dynamin, Dap160 and EndoA antibodies (Fig. 2 – figure supplement 1).

      (4) Assessment of the activity-dependence of EndoA and Dap160 localization at the Drosophila NMJ (Fig. 3).

      (5) Assessment of the liprin-dependence of EndoA and Dap160 localization at the Drosophila NMJ (Fig. 8).

      (6) Addition of a limitations section to the discussion to directly address that spontaneous release was not fully ablated in our studies and might contribute to recruitment.

      (7) Addition of an outlook to the same section on what experimental avenues could address the limitations in the future.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Emperador-Melero et al. seek to determine whether recruitment of endocytic machinery to the periactive zone is activity-dependent or tethered to delivery of active zone machinery. They use genetic knockouts and pharmacological block in two model synapses - cultured mouse hippocampal neurons and Drosophila neuromuscular junctions - to determine how well endocytic machinery localizes after chronic inhibition or acute depolarization by super-resolution imaging. They find that acute depolarization in both models has minimal to no effect on the localization of endocytic machinery at the periactive zone, suggesting that these proteins are constitutively maintained rather than upregulated in response to transient activity. Interestingly, chronic inhibition slightly increases endocytic machinery levels, implying a potential homeostatic upregulation in preparation for rebound depolarization. Using genetic knockouts, the authors show that localization of endocytic machinery to periactive zones occurs independently of proper active zone assembly, even in the absence of upstream organizers like Liprin-α. Overall, they propose that the constitutive deployment of endocytic machinery reflects its critical role in facilitating rapid and reliable membrane internalization during synaptic functions beyond classical endocytosis, such as regulation of the exocytic fusion pore and dense-core vesicle fusion. Although many experiments reveal limited changes in the localization or abundance of endocytic machinery, the findings are thorough, and data substantially support a model in which endocytic components are organized through a pathway distinct from that of the active zone. This work advances our understanding of synaptic dynamics by supporting a model in which endocytic machinery is constitutively recruited and regulated by distinct upstream organizers compared to active zone proteins. It also highlights the utility of super-resolution imaging across diverse synapse types to uncover functionally conserved elements of synaptic biology.

      We thank the reviewer for the positive assessment of our study.

      Strengths:

      The study's technical strengths, particularly the use of super-resolution microscopy and rigorous image analyses developed by the group, bolster their findings.

      We thank the reviewer for highlighting the technical strength of our work.

      Weaknesses:

      One notable limitation, however, is the absence of interrogation of endocytic proteins previously suggested to be recruited in an activity-dependent manner, in particular, endophilin.

      We thank the reviewer for the suggestion. We have added experiments to assess the localization of two more proteins at Drosophila NMJs. These proteins are EndoA and Dap160, both of which have been reported to traffic between the synaptic vesicle cloud and the plasma membrane in response to stimulation [1-3]. In line with these studies, we observed that EndoA and Dap160 partially co-localize with a synaptic vesicle marker and with a periactive zone marker, indicating localization to both compartments (Fig. 2). However, neither high frequency stimulation nor expression of TeNT changed the levels or the distribution of these two proteins at the periactive zone (Fig. 3). Similarly, the deployment of these proteins at the periactive zone at the Drospophila NMJ was not dependent on the active zone scaffold Liprin-α (Fig. 8). Our data indicate that deployment of EndoA and Dap160 to the periactive zone does not require evoked synaptic activity.

      We believe that there are multiple plausible explanations for our findings compared to previous work on Endophilin, which we discuss on lines 407-410: “Increased synaptic enrichment was also observed for Endophilin at nematode NMJs in mutants with disrupted exocytosis (Bai et al., 2010). We do not see such large shifts in Endophilin following similar manipulations, which might reflect distinct synaptic architectures in the C. elegans dorsal cord versus Drosophila NMJ terminals.” Further, this study finds that a plasma membrane-tethered Endophilin strongly colocalizes with endocytic machinery and largely rescues function. This suggests that the plasma membrane is the primary functional compartment for Endophilin. Together with our work, we conclude that these data suggest that Endophilin constitutively, but not completely, localizes to the periactive zone.

      Reviewer #2 (Public review):

      Summary:

      This study examines whether the localization of endocytic proteins to presynaptic periactive zones depends on synaptic activity or active zone scaffolds. Using a combination of genetic and pharmacological perturbations in Drosophila and mouse neurons, the authors show that proteins such as Dynamin, Amphiphysin, AP-180, and others are still recruited to periactive zones even when evoked release or active zone architecture is disrupted. While the results are mostly negative, the study is methodologically solid and contributes to a more nuanced understanding of synaptic vesicle recycling machinery.

      We thank the reviewer for deeming our work solid and for highlighting its importance for the field.

      Strengths:

      (1) The experimental design is careful and systematic, covering both fly and mammalian systems.

      (2) The use of advanced genetic models (e.g., Liprin-α quadruple knockout mice) is a notable strength.

      (3) High-resolution imaging (STED, Airyscan) is well used to assess spatial localization.

      (4) The findings clarify that certain core assumptions - such as strict activity dependence of endocytic recruitment - may not hold universally.

      We thank the reviewer for pointing out these strengths.

      Weaknesses:

      (1) The study would benefit from a clearer positive control to demonstrate activity-dependent recruitment (e.g., Endophilin).

      We have added experiments to measure the localization of Endophilin, a protein previously reported to localize to the synaptic vesicle cloud [1], in Drosophila NMJs (Figs. 2 and 3). We observed that EndoA localized both to the synaptic vesicle cloud and to the periactive zone area. While stimulation did not enhance levels in either compartment, this outcome is not inconsistent with shuttling of protein between compartments during activity. Nevertheless, our data support a model in which EndoA, like the other tested endocytic proteins, is present at the periactive zone at rest.

      (2) The reliance on Tetanus toxin in the Drosophila NMJ experiments in my eyes is a limitation, as it does not block all presynaptic fusion events; this should be discussed more directly.

      We agree with the point of the reviewer. To more directly discuss it, we have included a “Limitations and Outlook” section in the revised version. We state that “conclusions that can be drawn on the roles of spontaneous release in periactive zone assembly remain limited” (lines 514-515). We further state that, while the manipulations that we included result in decreased spontaneous release, “it is possible that the remaining spontaneous release supports periactive zone assembly” (518-519) and that “Future studies might test manipulations with strong effects on miniature release including those affecting SNARE proteins and their regulators, with the caveat that these manipulations might have effects on upstream trafficking and in some cases on cell survival (Kaeser and Regehr, 2014; Santos et al., 2017).” (519-523).

      (3) The potential role of Dynamin in organizing other periactive zone proteins is not addressed and could be an important next step.

      We agree with the reviewer that this is an interesting possibility. On lines 454-455, we make the broad point that “interactions between endocytic proteins may further contribute to the anchoring of this apparatus”, and on lines 459-460, we specifically suggest a role for Dynamin by stating that “perturbing interactions between Dynamin-1 and Endophilin-A1 increases the distance between these proteins (Imoto et al., 2024), suggesting their binding has a scaffolding function.”

      (4) Some small changes in protein levels upon silencing are reported; their biological meaning (e.g., compensation vs. variability) is not fully clarified.

      These changes might include homeostatic adaptations. In the revised version of the manuscript, this is addressed on lines 135-137 and 405-407. We think it is overall difficult to assign biological meaning to small-magnitude changes, and chose to highlight the main point that there are no large-magnitude changes.

      (5) While alternative organizing mechanisms (actin, lipids, adhesion molecules) are mentioned, a more forward-looking discussion of how to test these models would be helpful.

      Following the reviewer’s suggestion, we have added an outlook section to the discussion where we provide suggestions for future studies (lines 510-543).

      (6) The authors should consider including, or at least discussing, a well-established activity-dependent endocytic protein (e.g., Endophilin) as a positive control to help contextualize the negative findings.

      We have included new experiments on EndoA at the fly neuromuscular junction (Fig. 2, Fig. 3, Fig. 8, Fig. 3 – figure supplement 1) and have added appropriate discussion of these findings as outlined above.

      Reviewer #3 (Public review):

      Summary:

      This study examines how synaptic endocytic zones are positioned using a combination of cultured neurons and the Drosophila neuromuscular junction. The authors test whether neuronal activity, active zone assembly, or liprin-α function is required to localize endocytic zone markers, including Dynamin, Amphiphysin, Nervous Wreck, PIPK1γ, and AP-180. None of the manipulations tested caused a coordinated disruption in the localization or abundance of these markers, leading to the conclusion that endocytic zones form independently of synaptic activity and active zone scaffolds.

      We thank the reviewer for reviewing our work.

      Strengths:

      The work is systematic and carefully executed, using multiple manipulations and two complementary model systems. The authors consistently examine multiple molecular markers, strengthening the interpretation that endocytic zone positioning is robust to changes in activity and structural assembly.

      We thank the reviewer for pointing out these strengths.

      Weaknesses:

      The main limitation is that the study does not test whether the methods used are sensitive enough to detect subtle functional disruption, and no condition tested produces clear disorganization of the endocytic zone. As a result, the conclusion that these zones assemble independently is supported by negative data, without a strong positive control for disassembly or mislocalization.

      We are confident that our methods are sensitive enough to detect changes within synaptic compartments. First, for mouse neurons assessed with STED microscopy, we have demonstrated that we can distinguish between the N- and the C-termini of the presynaptic protein Bassoon, which are positioned only a few tens of nanometers apart [4]. We have subsequently been consistently able to resolve the localization of pre- and postsynaptic proteins that also localize a few tens of nanometers apart and have established that genetic manipulations of active zone proteins induce detectable disruptions as assessed by STED microscopy [4-12]. Given that the periactive zone is larger than the distances that we can resolve, we are confident that we can detect changes in this area with enough sensitivity. Second, for Drosophila NMJs, we use a carefully validated workflow that allows assessing the distribution of periactive zone proteins and can detect subtle changes [13]. Unfortunately, there are no known manipulations that lead to periactive zone disassembly that could serve as a positive control, which reflects the little knowledge available in this field. We acknowledge that there may be subtle changes in protein localization that escape the resolution of our microscopy methods or experimental design, but this would not undermine the conclusion that the periactive zone remains assembled across the manipulations that we have tested. Overall, none of the manipulations we test induces a detectable disruption of the periactive zone. Naturally, we cannot exclude milder effects and have added a limitations section to discuss this possibility and some of the subtle changes we observe.

      This paper addresses a longstanding question in synaptic biology and provides a well-supported boundary on the types of mechanisms that are likely to govern endocytic zone localization. The conclusions are well justified by the data, though additional evidence would be needed to define the assembly mechanism itself.

      We thank the reviewer for the support of the conclusion of our study.

      Recommendations for the authors:

      Reviewing Editor Comments:

      This is a rigorous study that, while presenting largely negative data, delimitates the processes that control peri-active zone organization. In addition to the interpretive and technical comments below, we encourage the authors to consider extending this study in two areas. First, examining the activity-dependence of Endophilin, and perhaps other factors, being recruited to the PAZ, where previous research has indicated a positive role for activity. Second, further characterization of the role of miniature release events in potentially contributing to PAZ organization. Overall, this was a rigorous and well-executed study.

      We thank the reviewing editor for this positive assessment of our work.

      Reviewer #1 (Recommendations for the authors):

      (1) The rationale for comparing chronic inhibition to acute depolarization could be more clearly articulated. While this approach may be grounded in prior studies, the physiological consequences of chronic silencing differ markedly from those of transient activity, and these distinctions should be more explicitly addressed in the interpretation of results. For example, might lower intensity, chronic stimulation be a better comparison? Since fixation takes place immediately after stimulation, the time window to capture changes in protein recruitment may be curtailed.

      We thank the reviewer for this comment. The introduction of the manuscript now includes a rationale on lines 110-112. By inhibiting evoked synaptic vesicle fusion throughout the lifespan of neurons, we assessed whether this process is necessary for periactive zone assembly and concluded that it is not a requirement. By acutely depolarizing neurons with 50 mM KCl or with a 40 Hz train of action potentials, we were able to test whether synaptic vesicle fusion triggers the rapid recruitment of endocytic proteins to the periactive zone and concluded that this is not the case for most of the endocytic proteins that we studied. While these results indicate that a constitutive pathway must exist to assemble the periactive zone, we remain agnostic as to whether stimulation paradigms not tested in our study can enhance the deployment of endocytic proteins, especially over long periods of time. This may be the case for low, chronic stimulation, as suggested by the reviewer. We clarify these limitations on a “limitations and outlook” section of the discussion (lines 510-543).

      (2) Amphiphysin stood out as the only protein showing a notable change in opposite directions under either active zone protein knockout/blockers and Liprin-α knockout. Given the predominance of negative results, it would be valuable to devote more discussion to why Amphiphysin behaves differently. What functional role might it play in this context that sets it apart from other endocytic components?

      As suggested by the reviewer, we have extended the discussion on Amphiphysin. One possibility why Amphiphysin may respond differently to different genetic manipulations or changes in stimulation is that different endocytic proteins might belong to different endocytic submachineries. This is addressed on lines 421-424. On lines 444-449, we further discuss the subtle decrease in the levels of Amphiphysin and AP-180 in Liprin-α mutants. We suggest that the actin cytoskeleton may be the link between the active zone and the endocytic apparatus, and that this link may be partially disrupted in Liprin-α mutants. Overall, we note that Amphiphysin is still localized to the periactive zone at rest, and hence that it fits with the overall model of constitutive deployment that we propose.

      (3) The claim of activity-independence may need to be nuanced. Although the data suggest no recruitment in response to acute stimulation, the subtle changes following chronic inhibition complicate this interpretation, especially when considering redundancy. If activity-dependence is considered bidirectional, these findings might reflect a more complex regulatory mechanism. The interpretation in lines 188-190 more accurately captures this complexity than earlier generalizations.

      We agree with the reviewer that the dependence on activity should be discussed in a nuanced fashion. We have scrutinized the manuscript on this point and state throughout that recruitment is independent of evoked activity and not necessarily of any kind of activity. We believe that this interpretation is accurate because evoked release of neurotransmitter was ablated by the pharmacological and genetic manipulations that we used. Furthermore, we have included a “Limitations of the study” section in the discussion where we openly address that spontaneous fusion of synaptic vesicles cannot be ruled out as a potential mechanism to sustain periactive zone assembly (lines 514-523). Finally, we have expanded on the complexity of periactive zone assembly relative to activity. In particular, homeostasis may contribute to increased levels of endocytic proteins upon chronic blockade of evoked transmission (lines 404-406).

      (4) Given published work on endophilin's role in activity-dependent endocytic recruitment, adding endophilin (at least in the Drosophila NMJ experiments) would be highly informative.

      We thank the reviewer for the suggestion. We have added experiments to assess the localization of two more proteins at Drosophila NMJs. These proteins are EndoA and Dap160, both of which have been reported to traffic between the synaptic vesicle cloud and the plasma membrane in response to stimulation [1-3]. In line with these studies, we observed that EndoA and Dap160 partially co-localize with a synaptic vesicle marker and with a periactive zone marker, indicating localization to both compartments (Fig. 2). However, neither high frequency stimulation nor expression of TeNT changed the levels or the distribution of these two proteins at the periactive zone (Fig. 3). Similarly, the deployment of these proteins at the periactive zone at the Drosophila NMJ was not dependent on the active zone scaffold Liprin-α (Fig. 8). Our data indicate that deployment of EndoA and Dap160 to the periactive zone does not require evoked synaptic activity.

      We believe that there are multiple plausible explanations for these findings compared to previous work on Endophilin [3], which we discuss on lines 407-410:

      “Increased synaptic enrichment was also observed for Endophilin at nematode NMJs in mutants with disrupted exocytosis (Bai et al.,2010). We do not see such large shifts in Endophilin following similar manipulations, which might reflect distinct synaptic architectures in the C. elegans dorsal cord vs Drosophila NMJ terminals.” Further, this study finds that a plasma membrane-tethered Endophilin strongly colocalizes with endocytic machinery and largely rescues function. This suggests that the plasma membrane is the primary functional compartment for Endophilin. Together, all data are compatible with a model in which Endophilin constitutively, but not completely, localizes to the periactive zone.

      (5) Line 57 might have a typo in the citation.

      We thank the reviewer for pointing this out. The citations now include: Bai et al., 2010; Jiang et al., 2024; Koh et al., 2007; Winther et al., 2013 and Winther et al. 2015. Please note that these two last citations are grouped as Winther et al. 2013, 2015 following our formatting style.

      (6) Line 208 might be missing a citation that justifies parameters.

      In the revision, this information is discussed on lines 222-224, where we cite our prior work describing these data: “Each unit is divided into ‘mesh’ and ‘core’ regions, where the periactive zone mesh is a ~175 nm wide area localized at ~330 nm from the center, and the ‘core’ region is the interior to this mesh (Del Signore et al., 2023)”.

      Reviewer #2 (Recommendations for the authors):

      (1) Please consider including, or at least discussing, a well-established activity-dependent endocytic protein (e.g., Endophilin) as a positive control to help contextualize the negative findings.

      We thank the reviewer for the suggestion. We have added experiments to assess the localization of two more proteins at Drosophila NMJs. These proteins are EndoA and Dap160, both of which have been reported to traffic between the synaptic vesicle cloud and the plasma membrane in response to stimulation [1-3]. In line with these studies, we observed that EndoA and Dap160 partially co-localize with a synaptic vesicle marker and with a periactive zone marker, indicating localization to both compartments (Fig. 2). However, neither high frequency stimulation nor expression of TeNT changed the levels or the distribution of these two proteins at the periactive zone (Fig. 3). Similarly, the deployment of these proteins at the periactive zone at the Drosophila NMJ was not dependent on the active zone scaffold Liprin-α (Fig. 8). Our data indicate that deployment of EndoA and Dap160 to the periactive zone does not require evoked synaptic activity.

      We believe that there are multiple plausible explanations for our findings compared to previous work on Endophilin [3], which we discuss on lines 407-410: “Increased synaptic enrichment was also observed for Endophilin at nematode NMJs in mutants with disrupted exocytosis (Bai et al.,2010). We do not see such large shifts in Endophilin following similar manipulations, which might reflect distinct synaptic architectures in the C. elegans dorsal cord vs Drosophila NMJ terminals.” Further, this study finds that a plasma membrane-tethered Endophilin strongly colocalizes with endocytic machinery and largely rescues function. This suggests that the plasma membrane is the primary functional compartment for Endophilin. Together, all data are consistent with a model in which Endophilin constitutively, but not completely, localizes to the periactive zone.

      (2) Expand the discussion of TeNT's limitations-specifically that it does not block spontaneous fusion or alternative fusion pathways-and consider referencing more stringent tools (e.g., Botulinum toxins or SNARE mutants), even if they weren't used here.

      Following the reviewer’s suggestion, we have included a “Limitations and Outlook” section in the revised version. We state that “conclusions that can be drawn on the roles of spontaneous release in periactive zone assembly remain limited” (lines 514-515). We further state that, while the manipulations that we included result in decreased spontaneous release, “it is possible that the remaining spontaneous release supports periactive zone assembly” (518-519) and that “Future studies might test manipulations with strong effects on miniature release including those affecting SNARE proteins and their regulators, with the caveat that these manipulations might have effects on upstream trafficking and in some cases on cell survival (Kaeser and Regehr, 2014; Santos et al., 2017)” (520-523).

      (3) We encourage the authors to briefly discuss whether Dynamin might contribute to periactive zone structure beyond its role in membrane fission. Loss-of-function data could be particularly informative in future work.

      We agree with the reviewer that this is an interesting possibility. On lines 454-455, we make the broad point that “interactions between endocytic proteins may further contribute to the anchoring of this apparatus”, and on lines 459-460, we specifically suggest a role for Dynamin by stating that “perturbing interactions between Dynamin-1 and Endophilin-A1 increases the distance between these proteins (Imoto et al., 2024), suggesting their binding has a scaffolding function.”

      (4) Clarify the interpretation of increased endocytic protein levels upon chronic silencing - are these interpreted as homeostatic responses or experimental variability?

      We suggest that these changes might include homeostatic adaptations. We note that this increase is of the same magnitude as the increase in active zone proteins following a similar pharmacological manipulation on lines 405-406, where we state that “a mechanism for this effect might be a homeostatic response (Wen and Turrigiano, 2024) similar in magnitude to the increase in active zone protein levels following activity blockade (Held et al., 2020).”

      (5) The Discussion could be strengthened by sketching out more concrete experimental approaches to test candidate mechanisms (e.g., roles for actin, lipids, adhesion molecules) in organizing periactive zones.

      The potential roles of the cell adhesion molecules (lines 430-440), cytoskeleton and lipids (442-452) are addressed in the discussion. Furthermore, following the reviewer’s suggestion, we have added the following statement (lines 541-543): “This work builds a foundation to assess alternative mechanisms and models of periactive zone assembly, including roles of the cytoskeleton, lipids, adhesion molecules, and intrinsic endocytic protein interactions”. We hope that the reviewer agrees that the discussion of our paper is not the right format to provide a concrete experimental plan for future work. In our view, the discussion should put the findings of our experiments in the context of the field.

      Reviewer #3 (Recommendations for the authors):

      (1) At a spine synapse, the endocytic zone is estimated to be between 100-200nm from the active zone. The focus of the author's analysis is largely outside of this region (0-150nm), raising the question of whether the area studied may be outside of the area affected by the manipulations made. While STED systems claim ~80 nm resolution, this is rarely achieved in practice, and the authors do not report the effective resolution of their system. Reporting the resolution achieved would address this issue. In addition, super-resolution imaging does not appear to have been used at the Drosophila NMJ. The authors should clarify whether resolution limitations influenced the choice of analysis region and whether their imaging approach is sufficient to detect changes in the endocytic zone.

      We believe that it is unlikely that the relevant signals were missed. First, in mouse synapses, most signal corresponding to endocytic proteins was detected inside the selected region of interest. Our rationale to select the area was based on the fact that expanding the region analyzed would have reduced the sensitivity of our approach, as averaging over a larger area would dilute the signal. The resolution of our microscopy should not be a limitation either. In our previous work, we demonstrated that STED microscopy allows discriminating between the N- and the C-terminal termini of the presynaptic scaffold Bassoon, which are positioned only a few tens of nanometers apart [4]. This establishes that we can resolve differences at tens of nanometers in biological context, which is more relevant than the resolution measured with fluorescent beads (which we have repeatedly assessed to be ~80 nm laterally). Subsequently, we have also been consistently able to resolve the localization of pre- and postsynaptic proteins that also localize a few tens of nanometers apart [4-12]. Given that the periactive zone spans over a larger area than the distances that we can resolve experimentally in the examples above, we are confident that our measurements are sensitive enough to detect changes in this area.

      Second, for Drosophila NMJs, the choice for the region of interest and the overall analysis was done following a workflow validated in our previous work [13]. This method analyzes both immediately adjacent and more distant regions from the active zone, and does not exclude any region based on distance from the active zone as described on lines 222-224: “Each unit is divided into ‘mesh’ and ‘core’ regions, where the periactive zone mesh is a ~175 nm wide area localized at ~330 nm from the center, and the ‘core’ region is the interior to this mesh (Del Signore et al., 2023).” In our previous study, we analyzed the distribution of periactive zone proteins at rest with STED microscopy and with Airyscan confocal microscopy. The resolution provided by Airyscan is reported to be ~175 nm in XY and ~400 nm in Z, which is sufficient to assess localization to the periactive zone compartment imaging methods and is not inferior to imaging methods previously used to report changes in the distribution of endocytic proteins; for examples, see [1,2]. In the revised manuscript, we have added new data measuring the levels and distribution of EndoA and Dap160 using STED microscopy (Figure 3 – figure supplement 1). The results acquired with STED microscopy and with Airyscan confocal microscopy are consistent with one another.

      Overall, the accuracy of the imaging methods and analyses used in this study are sufficient to assess periactive zone structure given its size and organization.

      (2) Interestingly, in a number of cases, the authors observe significant differences in endocytic markers (Figure 1q, 4k, 6k, 6r). However, little is made of these differences. The authors should provide more discussion of these changes and how they make sense of them alongside their claims of a lack of effect from their manipulations.

      The reviewer raises a good point. We interpret these changes in two different ways. First, we suggest that changes observed in response to block of action potentials or disassembly of the active zone might be homeostatic. This is addressed on lines 135-137. Second, we discuss that the actin cytoskeleton may be the link between the active zone and the endocytic apparatus. Several active zone proteins interact with the actin cytoskeleton. One of them is Liprin-α. This interaction may explain the decrease in the level of Amphiphysin and AP-180 at the periactive zone in Liprin-α null neurons. This is addressed on lines 444-449. We hope that the reviewer agrees that overall, we should focus on the main conclusion that deployment of endocytic proteins persists over a number of manipulations and synapse types.

      (3) The graphs in Figure 1c and 1g, 3g, 4c, 4e, 6c, and 6g do not appear to be identical. If the solid line represents the mean and the lighter color represents the distribution of these data, these data appear to be different from one another. It is surprising that these differences are not significant. What statistical tests were used to determine whether the differences in these graphs are not significant? Is the issue that a relatively now number of synapses were examined (30-60)? Did the authors conduct a power analysis?

      We apologize if the display of our data and analyses was not clear. We do not perform statistical analyses on the line profiles. Instead, we perform it on two values that are extracted from line profiles. These values are (1) the distance between the peak intensity values of the protein of interest and the marker and (2) the peak intensity values. For example, in Figure 1, distances are quantified and statistically analyzed in panel j, and the peak levels are quantified and statistically analyzed in panel k. We have clarified this in the legend of current Figures 1, 4, 5, and 7.

      (4) The authors clearly state that their experiments address the role of evoked activity in endocytic zone positioning, but they do not examine whether spontaneous vesicle fusion might play a role. Given the availability of Drosophila mutants that decrease (Doc2, Dunc-13) or increase (syt1) spontaneous release, this is a notable omission. Ideally, these mutants should be examined. And at a minimum, the authors should discuss whether spontaneous release could contribute to endocytic zone organization.

      We agree with the reviewer that spontaneous fusion of synaptic vesicles may contribute to periactive zone organization. Many of the genetic manipulations that we used in mouse neurons result in a significant decrease in spontaneous release. This includes Ca<sub>V</sub>2 triple knockouts with a ~60% decrease in spontaneous fusion [10], RIM+ELKS quadruple knockouts with a ~70% decrease in spontaneous fusion [9] and Liprin-α quadruple knockouts with a ~50% decrease in spontaneous fusion [7]. We cannot rule out that the spontaneous release that is left is sufficient to mediate assembly functions. The conclusive way to address this possibility is using a manipulation that ablates spontaneous release without altering other pathways. However, to our knowledge, this is not available. The manipulations suggested by the reviewer might suffer from similar limitations, as they would change the frequency of spontaneous release without fully ablating it, and they would also affect evoked release. We have included a limitations section in the discussion where we address this (lines 514-523), specifically stating “conclusions that can be drawn on the roles of spontaneous release in periactive zone assembly remain limited. While many of the manipulations used here, including Ca<sub>V</sub>2 knockout (Held et al., 2020), RIM+ELKS knockout (Tan et al., 2022; Wang et al., 2016) and Liprin-α knockout (Emperador-Melero et al., 2024) in hippocampal neurons, and TeNT expression in fly NMJs (Sweeney et al.,1995) , result in 50% to 70% decreased spontaneous release rates, it is possible that the remaining spontaneous release supports periactive zone assembly. Future studies might test manipulations with strong effects on miniature release including those affecting SNARE proteins and their regulators, with the caveat that these manipulations might have effects on upstream trafficking and in some cases on cell survival (Kaeser and Regehr, 2014; Santos et al., 2017).” We hope that the reviewer agrees that assessing these mutants should be a topic of future studies, given that we already test many mutants in the paper.

      (5) In Figures 1 and 6, the authors assess presynaptic protein localization in cultured neurons, but it is unclear whether these are synaptic sites. Many presynaptic proteins traffic together and can accumulate at sites lacking postsynaptic specializations. The authors should validate that the observed spatial organization occurs at bona fide synapses, ideally by co-labeling with postsynaptic markers as done in Figure 4. If methods like these were used, providing more details on how synapses were identified and selected would be useful to the reader.

      While we understand the reviewer’s point, we are confident that the structures analyzed are bona fide synapses for three reasons, as we have established before across many papers [4-8,10-12,17].

      The diameter of the structures detected using the synaptic vesicle marker Synaptophysin aligns much more closely with the size of the large vesicle clusters found at presynaptic terminals than with that of a few transport vesicles.

      In side-view synapses, the bar-like distribution of the active zone marker (Bassoon or Munc13-1) at one edge of the vesicle cloud indicates that active zone proteins are organized at one edge of the vesicle cluster—consistent with the architecture of synapses.

      Synaptophysin is one of our key markers for detecting synapses. In our cultures, most of the Synaptophysin signal colocalizes with postsynaptic markers (either PSD-95 or Gephyrin), as we have established across many studies [4,7-12]. This indicates that the markers used here are sufficient to select synapses. Furthermore, the frequency at which synapses were identified using an active zone marker as the second marker was similar to that observed when using a postsynaptic marker, suggesting that we were not randomly including unrelated structures.

      (6) Many of the images, particularly of the Drosophila NMJ, are of low quality and are shown in very small images. In addition, the quality of the images throughout the paper makes it difficult to assess the author's analysis and results. The authors should provide larger, higher-quality images that show examples of the means for each of the examples shown. This is an issue for most of the figures, but is particularly prominent in the dNMJ. A minor additional point is that the authors should be clear whether the dNMJ images are collected at super-resolution or using a conventional microscope.

      We believe that the quality of our images is sufficient for the assessments made for the following reasons:

      These images were acquired with enough spatial resolution to assess levels at the PAZ as discussed in response to this reviewer’s first comment. In our previous work, we used images acquired at the same resolution and presented in the same manner for both mouse hippocampal synapses [6,7] and Drosophila NMJs [13,18]. In those previous studies, we drew conclusions at a similar level of detail as in the current study.

      In our view, our representative images are not inferior in quality to other papers in the field addressing similar questions [1,2,19,20].

      We have selected sample images based on the quantified mean values per condition. Hence, we strived to select panels that are objectively representative regarding the quantified parameters.

      We have specified microscopy methods in the figure legends. Specifically, for Drosophila NMJs, we used Airyscan confocal microscopy and STED microscopy. For each experiment, it is now stated which microscopy method was used in the corresponding legend.

      References:

      (1) Winther, Å. M. E. et al. An Endocytic Scaffolding Protein together with Synapsin Regulates Synaptic Vesicle Clustering in the Drosophila Neuromuscular Junction. J Neurosci 35, 14756–14770 (2015).

      (2) Winther, Å. M. E. et al. The dynamin-binding domains of Dap160/intersectin affect bulk membrane retrieval in synapses. J Cell Sci 126, 1021–1031 (2013).

      (3) Bai, J., Hu, Z., Dittman, J. S., Pym, E. C. G. & Kaplan, J. M. Endophilin functions as a membrane-bending molecule and is delivered to endocytic zones by exocytosis. Cell 143, 430–441 (2010).

      (4) Wong, M. Y. et al. Liprin-alpha3 controls vesicle docking and exocytosis at the active zone of hippocampal synapses. Proc Natl Acad Sci U S A 115, 2234–2239 (2018).

      (5) Emperador-Melero, J., de Nola, G. & Kaeser, P. S. Intact synapse structure and function after combined knockout of PTPδ, PTPσ, and LAR. Elife 10, (2021).

      (6) Emperador-Melero, J. et al. PKC-phosphorylation of Liprin-α3 triggers phase separation and controls presynaptic active zone structure. Nat Commun 12, 3057 (2021).

      (7) Emperador-Melero, J. et al. Distinct active zone protein machineries mediate Ca2+ channel clustering and vesicle priming at hippocampal synapses. Nature Neuroscience 2024 1–15 (2024) doi:10.1038/s41593-024-01720-5.

      (8) Tan, C., Wang, S. S. H., de Nola, G. & Kaeser, P. S. Rebuilding essential active zone functions within a synapse. Neuron 110, 1498-1515.e8 (2022).

      (9) Wang, S. S. H. et al. Fusion Competent Synaptic Vesicles Persist upon Active Zone Disruption and Loss of Vesicle Docking. Neuron 91, 777–791 (2016).

      (10) Held, R. G. et al. Synapse and Active Zone Assembly in the Absence of Presynaptic Ca(2+) Channels and Ca(2+) Entry. Neuron 107, 667-683.e9 (2020).

      (11) Chin, M. & Kaeser, P. S. The intracellular C-terminus confers compartment-specific targeting of voltage-gated calcium channels. Cell Rep 43, 114428 (2024).

      (12) Nyitrai, H., Wang, S. S. H. & Kaeser, P. S. ELKS1 Captures Rab6-Marked Vesicular Cargo in Presynaptic Nerve Terminals. Cell Rep 31, 107712 (2020).

      (13) Del Signore, S. J., Mitzner, M. G., Silveira, A. M., Fai, T. G. & Rodal, A. A. An approach for quantitative mapping of synaptic periactive zone architecture and organization. Mol Biol Cell 34, (2023).

      (14) Sweeney, S. T., Broadie, K., Keane, J., Niemann, H. & O’Kane, C. J. Targeted expression of tetanus toxin light chain in Drosophila specifically eliminates synaptic transmission and causes behavioral defects. Neuron 14, 341–351 (1995).

      (15) Kaeser, P. S. & Regehr, W. G. Molecular mechanisms for synchronous, asynchronous, and spontaneous neurotransmitter release. Annu Rev Physiol 76, 333–363 (2014).

      (16) Santos, T. C., Wierda, K., Broeke, J. H., Toonen, R. F. & Verhage, M. Early Golgi Abnormalities and Neurodegeneration upon Loss of Presynaptic Proteins Munc18-1, Syntaxin-1, or SNAP-25. Journal of Neuroscience 37, 4525–4539 (2017).

      (17) de Jong, A. P. H. et al. RIM C2B Domains Target Presynaptic Active Zone Functions to PIP2-Containing Membranes. Neuron 98, 335-349.e7 (2018).

      (18) Del Signore, S. J. et al. An autoinhibitory clamp of actin assembly constrains and directs synaptic endocytosis. Elife 10, (2021).

      (19) Imoto, Y. et al. Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis. EMBO Journal https://doi.org/10.1038/S44318-024-00145-X

      (20) Imoto, Y. et al. Dynamin is primed at endocytic sites for ultrafast endocytosis. Neuron 110, 2815-2835.e13 (2022).

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors investigate the relationship between 3D chromatin architecture and innate immune gene regulation in monocytes from patients with alcohol-associated hepatitis (AH). Using Hi-C technology, they attempt to identify structural changes in the genome that correlate with altered gene expression. Their central claim is that genome restructuring contributes to the hyper-inflammatory phenotype associated with AH.

      Strengths:

      (1) The manuscript employs Hi-C technology, which, in principle, is a powerful approach for studying genome organization.

      (2) The focus on disease-relevant genes, particularly innate immune loci, provides a contextually important angle for understanding AH.

      Weaknesses:

      (1) Sample Size: The study relies on an exceptionally small cohort (4 AH patients and 4 healthy controls), rendering the results statistically underpowered and highly susceptible to variability.

      (2) Hi-C Resolution unpaired to RNA seq: The data are presented at a resolution of 100kb, which is insufficient to uncover meaningful chromatin interactions at the level of individual genes. This data is unpaired.

      (3) Functional Validation: The manuscript lacks experiments to directly link changes in chromatin architecture with gene expression or monocyte function, leaving the claims speculative.

      (4) Data Integration: The lack of Hi-C with ATAC and RNA-seq data handicaps the analysis and really makes it superficial. In short, it does not convincingly demonstrate a functional relationship.

      (5) Confounding Factors: The manuscript neglects critical confounding variables such as comorbidities, medications, and lifestyle factors, which could influence chromatin structure and gene expression independently of AH.

      Appraisal of the Aims and Results:

      The manuscript sets out to establish a connection between chromatin architecture and AH pathology. However, the study fails to achieve its stated aims due to inadequate methods and insufficient data. The conclusions drawn from the Hi-C analyses alone are poorly supported, and the lack of functional validation undermines the credibility of the proposed mechanisms. Overall, the results do not provide compelling evidence to substantiate the authors' claims.

      Impact on the Field and Utility to the Community:

      The work, in its current form, is unlikely to have a meaningful impact on the field. The limited scope, methodological shortcomings, and lack of robust data significantly diminish its potential utility. Without addressing these critical gaps, the study does not offer new insights into the role of genome architecture in AH or provide useful methodologies or datasets for the community.

      Additional Context:

      The manuscript would benefit from a more comprehensive analysis of potential mechanisms underlying the observed changes, including the interplay between chromatin architecture and epigenetic modifications. Furthermore, longitudinal studies or therapeutic interventions could provide insights into the dynamic aspects of genome restructuring in AH. These considerations are entirely absent from the current study.

      Conclusion:

      The manuscript does not achieve its stated goals and does not present sufficient evidence to support its conclusions. The limitations in sample size, resolution, and experimental rigor severely hinder its contribution to the field. Addressing these fundamental flaws will be essential for the work to be considered a meaningful addition to the literature.

      Reviewer #2 (Public review):

      Summary:

      Dr. Adam Kim and collaborators study the changes in chromatin structure in monocytes obtained from alcohol-associated hepatitis (AH) when compared to healthy controls (HC). Through the usage of high throughput chromatin conformation capture technology (Hi-C), they collected data on contact frequencies between both contiguous and distal DNA windows (100 kB each); mainly within the same chromosome. From the analyses of those data in the two cohorts under analysis, authors describe frequent pairs of regions subject to significant changes in contact frequency across cohorts. Their accumulation onto specific regions of the genome -referred to as hotspots- motivated authors to narrow down their analyses to these disease-associated regions, in many of which, authors claim, a number of key innate immune genes can be found. Ultimately, the authors try to draw a link between the changes observed in chromatin architecture in some of these hotspots and the differential co-expression of the genes lying within those regions, as ascertained in previous single-cell transcriptomic analyses.

      Strengths:

      The main strength of this paper lies in the generation of Hi-C data from patients, a valuable asset that, as the authors emphasize, offers critical insights into the role of chromatin architecture dysregulation in the pathogenesis of alcohol-associated hepatitis (AH). If confirmed, the reported findings have the potential to highlight an important, yet overlooked, aspect of cellular dysregulation-chromatin conformation changes - not only in AH but potentially in other immune-related conditions with a component of pathological inflammation.

      Weaknesses:

      In what I regard as the two most important weaknesses of the work, I feel that they are more methodological than conceptual. The first of these issues concerns the perhaps insufficient level of description provided on the definition of some key types of genomic regions, such as topologically associated domains, DNA hotspots, or even DNA loci showing significant changes in contact frequency between AH and HC. In spite of the importance of these concepts in the paper, no operational, explicit description of how are they defined, from a statistical point of view, is provided in the current version of the manuscript.

      Without these definitions, some of the claims that authors make in their work become hard to sustain. Some examples are the claim that randomizing samples does not lead to significant differences between cohorts; the claim that most of the changes in contact frequency happen locally; or the claim that most changes do not alter the structure of TADs, but appear either within, or between TADs. In my viewpoint, specific descriptions and implementation of proper tests to check these hypotheses and back up the mentioned specific claims, along with the inclusion of explicit results on these matters, would contribute very significantly to strengthening the overall message of the paper.

      The second notable weakness of the study pertains to the characterization of the changes observed around immune genes in relation to genome-wide expectations. Although the authors suggest that certain hotspots contain a high number of immune-related genes, no enrichment analysis is provided to verify whether these regions indeed harbor a higher concentration of such genes compared to other genomic areas. It would be important for readers to be promptly informed if no such enrichment is observed, for in that case, the presence of some immune genes within these hotspots would carry more limited implications.

      Additionally, the criteria used to define a hotspot are not clearly outlined, making it difficult to assess whether the changes in contact frequencies around the immune genes highlighted in figures 5-8 are truly more pronounced than what would be expected genome-wide.

      Reviewer #3 (Public review):

      In this manuscript, the authors use HiC to study the 3D genome of CD14+ CD16+ monocytes from the blood of healthy and those from patients with Alcohol-associated Hepatitis.

      Overall, the authors perform a cursory analysis of the HiC data and conclude that there are a large number of changes in 3D genome architecture between healthy and AH patient monocytes. They highlight some specific examples that are linked to changes in gene expression. The analysis is of such a preliminary nature that I would usually expect to see the data from all figures in just one or two figures.

      In addition, I have a number of concerns regarding the experimental design and the depth of the analyses performed that I think must be addressed.

      (1) There is a myriad of literature that describes the existence of cell type-specific 3D genome architecture. In this manuscript, there is an assumption by the authors that the CD14+ CD16+ monocytes represent the same population from both healthy and diseased patients. Therefore, the authors conclude that the differences they see in the HiC data are due to disease-related changes in the equivalent cell types. However, I am concerned that the AH patient monocytes may have differentiated due to their environment so that they are in fact akin to a different cell type and the 3D genome changes they describe reflect this. This is supported by published articles for example: Dhanda et al., Intermediate Monocytes in Acute Alcoholic Hepatitis Are Functionally Activated and Induce IL-17 Expression in CD4+ T Cells. J Immunol (2019) 203 (12): 3190-3198, in which they show an increased frequency of CD14+ CD16+ intermediate monocytes in AH patients that are functionally distinct.

      I suggest that if the authors would like to study the specific effects of AH on 3D genome architecture then they should carefully FACsort the equivalent monocyte populations from the healthy and AH patients.

      (2) The analysis of the HiC data is quite preliminary. In the 3D genome field, it is usual to report the different scales of genome architecture, for example, compartments, topologically associated domains (TADs), and loops. I think that reporting this information and how it changes in AH patients in the appropriate cell types would be of great interest to the field.

      We thank the reviewers for their careful and thorough examination of our manuscript. We agree with all of their comments regarding the limitations of the study. Many of the criticisms focus on the small sample size of our study (n=4 for healthy controls and disease patients) in both Hi-C and single-cell RNA-seq experiments, and that these experiments are unpaired, or in other words, PBMCs came from different patients for each experiment.

      Unfortunately, these experiments are fairly complicated to perform, requiring patient cells and very expensive deep sequencing. We are not currently in a position to be able to easily or cost effectively increase sample size. In the case of Hi-C, we still believe our study to be of value as Hi-C is not a commonly used technique to study disease effects on chromatin, and very few studies have employed a large enough sample size to perform statistical comparisons. Additionally, to analyze the data at a higher resolution would require deeper sequencing, and unfortunately we do not have the resources to sequence these libraries deeper. Regarding the single-cell RNA-seq data, this dataset was generated for an earlier study [1] focusing on gene expression responses to LPS, and we were unable to get PBMCs from exactly the same patients to perform the Hi-C study.

      We disagree that our study has limited scientific value. Our study is the first to use Hi-C to show that the 3D genome architecture of primary monocytes is changed in a disease context. The only other study to follow a similar approach performed Hi-C in monocytes from 2 healthy and 2 Systemic lupus erythematosus (SLE) patients, and in their study the data from both patients were combined prior to comparison. No statistics were performed and their conclusion was no differences in genome architecture due to disease. They did find differences between primary monocytes and the THP1 monocytic cell line, but this lacked statistical analysis. Their conclusion was that inflammatory disease may not lead to genome wide changes in architecture. Our study, though a very different disease than SLE, shows statistically significant differences between AH and healthy controls. We believe our study lays the groundwork for how Hi-C can be used to study genome architecture in human disease, and the possible downstream effects.

      Confounding Factors: The manuscript neglects critical confounding variables such as comorbidities, medications, and lifestyle factors, which could influence chromatin structure and gene expression independently of AH.

      This is an interesting suggestion. This dataset only contains 4 AH patients, which we have included basic clinical data in Supplemental Table 1, including Age, HCA1c, Bilirubin, AST, ALT, Creatinine, Albumin, and MELD score. 3/4 of these patients are severe AH while 1 is moderate (AH2). Despite one patient being moderate, all four AH patients had similar correlations with each other, suggesting these disease specific differences we observed are not indicative of severity. More patient samples are needed to determine if genome architecture changes throughout disease progression. We have added this important discussion to the manuscript (page 12, lines 5-14).

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      The criteria used to determine which pairs of regions exhibit significant differences in contact frequency between alcohol-associated hepatitis (AH) and healthy controls (HC) are not disclosed. It would be beneficial for the authors to provide this information, including details such as the number of pairs tested, the nature of the statistical tests conducted, the method of multiple testing correction applied, as well as the significance thresholds used, and the number of loci-pairs below these thresholds for each chromosome. This information would greatly enhance the reader's understanding of the relevance of the reported findings.

      Thank you for this comment, though we are not sure we totally understand. All of our statistics were performed using multiHiCcompare [2], where we input all 8 datasets (.hic files from Juicer), then measured statistical differences between defined groups (HC vs AH). For our randomization studies, we randomized the group comparisons, so each group contained a mix of HC and AH.

      Second, a formal statistical definition of what constitutes a hotspot would be valuable for clarity.

      Thank you for this suggestion. Initially, hotspots were defined as just regions of the genome with a high frequency of very significant differential contacts. We have defined a more formal definition of “hotspot” based on similar criteria. A hotspot is defined by both adjusted p value and frequency of locations. First, we filtered all pair-wise chromosomal interactions by a very, very stringent padj < 0.0000001 to focus on only the most changed coordinates (Supplemental Table 4). Then we looked for regions of the genome with a high frequency of these differential locations. Borders for each hotspot were determined more liberally by looking at the full list of differential spots (padj < 0.05). Then we used code to list genes within each interacting region. We have added these important details to the Methods (page 14, lines 11-14).

      Third, a clear definition of the criteria used to identify different topologically associated domains (if these were indeed defined in the data and/or utilized in the analyses) would also be a helpful addition.

      Thank you for this suggestion, we did not identify TADs or really utilize TADs in any of these analyses.

      Likewise, several statements throughout the paper lack support from specific analyses, although it should be feasible to implement such analyses (or at least present them if they have already been conducted) to substantiate these claims:

      If randomizing samples does not result in significant differences between (randomized) cohorts, it would be beneficial to provide insights into the number of loci pairs that exhibit differences in frequency when using both the actual and randomized cohorts.

      Thank you for asking this question, as this is an important point. Using multiHiCcompare, if we compare WT (n=4) to AH (n=4), we get the results in the figures and supplementary data but if we randomize Group 1 (WT, WT, AH, AH) vs Group 2 (WT, WT, AH, AH), we get almost 0 significant changes in contact frequency. To show this more robustly, we performed 5 randomized comparisons and found far fewer changes in contact frequency between groups. This shows that these changes in contact frequency caused by disease are not random, but rather due to our real difference in AH. This point has been added to the Results (page 6, lines 15-17), and Methods (page 14, lines 16-21)

      If most changes in contact frequency occur locally, it would be useful to visualize the relationship between effect sizes and/or significance levels for the observed differences in frequency in relation to the distance between the involved loci. Additionally, comparing these results to the average baseline contact intensities as a function of distance would be informative. This comparison could help determine whether the distance decay in effect size/significance for the differences between AH and HC is faster or slower than the decay rates for baseline contact frequencies.

      This is a good suggestion. In our initial analysis, we made a number of figures relating chromosome positions, distance between loci, and statistics regarding the differential contact frequency. In the initial submission, we only showed Figure 3, which shows the logFC (log fold change) for the differential contact frequency by chromosomal position on both sides. To address this question, we have added a supplemental figure showing logFC as a function of the distance between two loci (new Supplemental Figure 3)

      Similarly, the assertion that most changes do not affect the structure of topologically associated domains (TADs) but occur either within or between TADs should be supported by specific testing; otherwise, or else, removed.

      Thank you, yes we have adjusted the language in the Discussion

      Furthermore, the authors should clarify whether differences in chromatin conformation are more pronounced around immune genes compared to genome-wide expectations. If this is not the case, it would be helpful to quantify the intensity of these differences around the highlighted genes in relation to the rest of the genome. To achieve this, I would suggest the following:

      Conduct enrichment analyses on the genes located within the most prominent hotspots to determine whether they are significantly enriched in immune genes (and, or, alternatively, in any other functional category).

      Estimate the average absolute fold change in contact frequency within all topologically associated domains (TADs) identified in the study. This would allow for the identification of immune gene-containing TADs highlighted in Figures 5-8, providing readers with a quantitative understanding of how anomalously different these genomic regions are with regards to the magnitude of its alterations in AH, compared to the rest of the genome.

      While some of the selected gene clusters appear to co-localize well with topologically associated domains (e.g., Figures 5A, 8A), others seemingly encompass either multiple TADs (Figure 6) or only portions of them (Figure 7). This should be clarified.

      Thank you, this is a great suggestion. In order to be as unbiased as possible, we took all genes present in the regions with the highest significant changes in genome (Supplemental Table 4) that we used to identify the hotspots. And you are correct, we do in fact see enrichment of genes involved in innate immune signaling. This has been added to Results (page 7, lines 19-25) and Figure 4.

      Finally, there are several minor issues concerning the figures that could be easily addressed to substantially enhance their readability:

      Font sizes in most figures should be increased, particularly for some axis labels and tick marks. This issue affects most figures; for instance, in Figure 4, it hinders the reader's ability to interpret the ranges of the data presented.

      Thank you, the figures have been adjusted

      Figures 5 to 8 (panels A and B) would benefit significantly from a more consistent format. Specifically, the gene cluster boxes should also be included in the right panels, and the gene locations should be displayed on the left in a uniform format across all figures (e.g., formatting Figures 7 and 8 to match the style of Figures 5 and 6).

      Figures 5 and 6 have a similar structure to each other because we were focusing on all of the genes in that chromosomal region. Figures 7 and 8 are different because we are focusing on how the region around a certain hotspot of interest changes.

      It is also important to note that the genes plotted in Figures 8C and 8D are not the same. Concerning these two panels, it would be valuable to clarify whether the data presented pertains exclusively to monocytes. If so, information regarding the number of cells analyzed and the number of donors from which they were drawn would also be beneficial.

      These figures are generated using scRNA-seq data. They represent all of the genes expressed in that region of the genome, in their chromosomal position. If a gene is not expressed in the scRNA-seq data, then it is not shown. I have debated with myself a lot on how to show gene expression in a region of the genome, but I think this is the clearest way to show this; including the genes that have no expression would make it more confusing. But yes, if you compare HC and AH, you see some differences in the list of genes. We have added more clarity to the figure legend for this figure.

      References

      (1) Kim, A., Bellar, A., McMullen, M. R., Li, X. & Nagy, L. E. Functionally Diverse Inflammatory Responses in Peripheral and Liver Monocytes in Alcohol-Associated Hepatitis. Hepatol Commun 4, 1459-1476 (2020). https://doi.org:10.1002/hep4.1563

      (2) Stansfield, J. C., Cresswell, K. G. & Dozmorov, M. G. multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments. Bioinformatics 35, 2916-2923 (2019). https://doi.org:10.1093/bioinformatics/btz048

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The study by Lemen et al. represents a comprehensive and unique analysis of gene networks in rat models of opioid use disorder, using multiple strains and both sexes. It provides a time-series analysis of Quantitative Trait Loci (QTLs) in response to morphine exposure.

      Strengths:

      A key finding is the identification of a previously unknown morphine-sensitive pathway involving Oprm1 and Fgf12, which activates a cascade through MAPK kinases in D1 medium spiny neurons (MSNs). Strengths include the large-scale, multi-strain, sex-inclusive design, the time-series QTL mapping provides dynamic insights, and the discovery of an Oprm1-Fgf12-MAPK signaling pathway in D1 MSNs, which is novel and relevant.

      Weaknesses:

      (1) The proposed involvement of Nav1.2 (SCN2A) as a downstream target of the Oprm1-Fgf12 pathway requires further analysis/evidence. Is Nav1.2 (SCN2A) expressed in D1 neurons?

      The authors mentioned that SCN8A (Nav1.6) was tested as a candidate mediator of Oprm1-Fgf12 loci and variation in locomotor activity. However, the proposed model supports SCN2A as a target rather than SCN8A. This is somewhat unexpected since SCN8A is highly abundant in MSN.

      Can the authors provide expression data for SCN2A, Oprm1, and Fgf12 in D1 vs. D2 MSNs?

      Author response image 1.

      We generated Author response image 1 to show both Scn2a and Scn8a are ubiquitously expressed in MSN and GABAergic neurons.

      (2) The authors should consider adding a reference to FGF12 in Schizophrenia (PMC8027596) in the Introduction.

      This is a relevant reference. We have cited it in the discussion section instead of introduction because we felt that is more relevant.

      (3) There is recent evidence supporting the druggability of other intracellular FGFs, such as FGF14 (PMC11696184) and FGF13 (PMC12259270), through their interactions with Nav channels. What are the implications of these findings for drug discovery in the context of the present study? Could FGF12 be considered a potential druggable therapeutic target for opioid use disorder (OUD)?

      The recent success in targeting FGF14 and FGF13 protein-protein interactions with sodium channels suggests that FGF12 could indeed be a druggable target for OUD. We have added a section to the Discussion exploring the potential for developing small-molecule modulators of the FGF12-Nav interface as a novel therapeutic strategy.

      Reviewer #2 (Public review):

      Summary:

      This highly novel and significant manuscript re-analyzes behavioral QTL data derived from morphine locomotor activity in the BXD recombinant inbred panel. The combination of interacting behavioral-pharmacology (morphine and naltrexone) time course data, high-resolution mouse genetic analyses, genetic analysis of gene expression (eQTLs), cross-species analysis with human gene expression and genetic data, and molecular modeling approaches with Bayesian network analysis produces new information on loci modulating morphine locomotor activity.

      Furthermore, the identification of time-wise epistatic interactions between the Oprm1 and Fgf12 loci is highly novel and points to methodological approaches for identifying other epistatic interactions using animal model genetic studies.

      Strengths:

      (1) Use of state-of-the art genetic tools for mapping behavioral phenotypes in mouse models.

      (2) Adequately powered analysis incorporating both sexes and time course analyses.

      (3) Detection of time and sex-dependent interactions of two QTL loci modulating morphine locomotor activity.

      (4) Identification of putative candidate genes by combined expression and behavioral genetic analyses.

      (5) Use of Bayesian analysis to model causal interactions between multiple genes and behavioral time points.

      Weaknesses:

      (1) There is a need for careful editing of the text and figures to eliminate multiple typographical and other compositional errors.

      We have performed a thorough review of the manuscript and corrected typographical errors, including "ddactivates" and other compositional issues.

      (2) There are multiple examples of overstating the possible significance of results that should be corrected or at least directly pointed out as weaknesses in the Discussion. These include:

      (a) Assumption that the Oprm1 gene is the causal candidate gene for the major morphine locomotor Chr10 QTL at the early time epochs. Oprm1 is 400,000 bp away from the support interval of the Mor10a QTL locus, and there is no mention as to whether the Oprm1 mRNA eQTL overlaps with Mor10a.

      We have clarified this in the text. While Oprm1 is located proximal to the peak, its massive size and the presence of a strong mRNA cis-eQTL in the NAc and hippocampus that precisely overlaps with the Mor10a QTL support interval provide robust evidence for its candidacy. We have added this detail to the Results section.

      (b) Although the Bayesian analysis of possible complex interactions between Oprm1, Fgf12, other interacting genes, and behaviors is very innovative and produces testable hypotheses, a more straightforward mediation analysis of causal relationships between genotype, gene expression, and phenotype would have added strength to the arguments for the causal role of these individual genes.

      We agree that mediation analysis would be a valuable addition. We revised the Results section to acknowledge that while the Bayesian network provides a comprehensive causal hypothesis, future studies employing formal mediation analysis could further strengthen these individual gene-to-behavior links.

      (c) The GWAS data analysis for Oprm1 and Fgf12 is incomplete in not mentioning actual significance levels for Oprm1 and perhaps overstating the nominal significance findings for Fgf12.

      We have updated the manuscript to include the specific significance levels for the human GWAS findings related to Oprm1 and Fgf12. We have clarified that the OPRM1 variant rs1799971 reached genome-wide significance (OR = 1.046, p = 4.92 × 10<sup>-9</sup>). Furthermore, we have ensured that the findings for FGF12 are described as nominally significant to avoid any overstatement of the results. For example, we now specify that the top FGF12 SNP rs1553460 achieved nominal significance (OR = 1.015, p = 0.021). The Results and Discussion sections have been revised to reflect these precise statistical values.

      Appraisal:

      The authors largely succeeded in reaching goals with novel findings and methodology.

      Significance of Findings:

      This study will likely spur future direct experimental studies to test hypotheses generated by this complex analysis. Additionally, the broad methodological approach incorporating time course genetic analyses may encourage other studies to identify epistatic interactions in mouse genetic studies.

      Reviewer #3 (Public review):

      Summary:

      This is a clearly written paper that describes the reanalysis of data from a BXD study of the locomotor response to morphine and naloxone. The authors detect significant loci and an epistatic interaction between two of those loci. Single-cell data from outbred rats is used to investigate the interaction. The authors also use network methods and incorporate human data into their analysis.

      Strengths:

      One major strength of this work is the use of granular time-series data, enabling the identification of time-point-specific QTL. This allowed for the identification of an additional, distinct QTL (the Fgf12 locus) in this work compared to previously published analysis of these data, as well as the identification of an epistatic effect between Oprm1 (driving early stages of locomotor activation) and Fgf12 (driving later stages).

      Weaknesses:

      (1) What criteria were used to determine whether the epistatic interaction was significant? How many possible interactions were explored?

      By design we only tested for epistasis between the Oprm1 and the Fgf12 loci—a single test of a non-linear interaction. As such there is no correction for multiple tests and no need for permutation. In other words the “nominal” P value in this case is the only relevant P value. We have added this clarification in the Results and Methods.

      (2) Results are presented for males and females separately, but the decision to examine the two sexes separately was never explained or justified. Since it is not standard to perform GWAS broken down by sex, some initial explanation of this decision is needed. Perhaps the discussion could also discuss what (if anything) was learned as a result of the sex-specific analysis. In the end, was it useful?

      We chose to analyze sexes separately AND jointly due to significant sex differences and sex by strain interactions in locomotion data. This rationale has been added to the results section. We also discussed sex-specific results in the revision.

      (3) The confidence intervals for the results were not well described, although I do see them in one of the tables. The authors used a 1.5 support interval, but didn't offer any justification for this decision. Is that a 95% confidence interval? If not, should more consideration have been given to genes outside that interval? For some of the QTLs that are not the focus of this paper, the confidence intervals were very large (>10 Mb). Is that typical for BXDs?

      The 1.5 LOD support interval is a standard metric for most QTL mapping studies, and does correspond approximately to a 95% confidence or support interval. Large intervals are common in BXD studies when effect sizes are moderate or recombination density is lower in specific regions. We have clarified the use of the 1.5 LOD interval in the Results section.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      In the vast majority of the figures, the text is too small to read.

      We have adjusted the font size in most of the figures.

      Reviewer #2 (Recommendations for the authors):

      (1) There is a need for careful editing of the text and figures to eliminate multiple typographical and other compositional errors. Examples of these include:

      (a) Figure 2E&F lacks identification of Oprm1 as the gene for cis-eQTL studies.

      (b) Figure 2H is fairly uninterpretable given the small font sizes. It should be excluded, put as a supplemental figure, or reconfigured to highlight the most important findings in a more legible manner.

      (c) Figure 4b: columns in the table need to be identified by a header row.

      We thank the reviewer for these comments and have addressed them in the revised version.

      Oprm1 is now labeled in Figure 2E and 2F, Figure 2G and 2H is now moved to the Supplementary material. And a header row is added to the table in Figure 4b.

      Reviewer #3 (Recommendations for the authors):

      Abstract

      (1) For the abstract, it might be simpler to name the alleles as "the C57BL/6J allele", etc., since B allele will confuse people unfamiliar with mouse nomenclature.

      It is critical to not confound the organism known as C57BL/6J with the genotype, allele, or haplotype that a mouse happens to inherit. Diverse types of mice inherit reference alleles but they may be only very distantly related the C57BL/6J strain. And even the C57BL/6J strain is a moving target that accumulates mutations that are not even consider reference. For example the mutation in Gabra2 of C57BL/6J is a de novo mutation that is not carried by many of the BXD strains since this mutation happened in JAX foundation stock after the BXDs were first established by Dr. Ben Taylor in the 1970s.

      The convention is to refer to mouse strains by one string and RRID, the abbreviation of that strain by a common code (often B6), and the abbreviation of the allele, genotype, or haplotype by the italic letter B. This has been the recommendation of the Mouse Nomenclature Committee (on which one of the authors has been a member) for well over 50 years.

      (2) I wondered if "also associated with a high B allele" could be reworded somehow; I had to re-read that sentence several times.

      This sentence has been reworded for clarity.

      (3) Parts of the abstract are written in the present tense, but then it switches to past ("we generated" but then "a Bayesian network analysis supports...").

      We have thoroughly revised the abstract. Following standard scientific writing conventions, we now utilize the past tense to describe the specific experimental actions and results of this study. We have maintained the present tense for established biological facts and the broader significance of the findings.

      (4) While the -log(p) values are all impressive, the abstract should indicate what threshold is used for genome-wide significance and how that threshold was obtained.

      We have added the significance threshold to the Abstract.

      (5) Do the details of the MAP kinase cascade need to be explained in the abstract? It feels like a lot of detail for an abstract and represents one of the most speculative aspects of the paper. Maybe just say you identified a possible network, but save the details for the main paper.

      This is a valid suggestion. We removed the specific MAP kinase from the abstract.

      Introduction

      (1) You could add a sentence explaining why using an LMM (GEMMA) was an improvement over the prior analysis.

      We have added a sentence explaining that GEMMA improves mapping power and better controls for population structure compared to previous methods.

      (2) When mentioning Philips 2010, you could indicate that it identified Oprm1. This might be easier than "In addition to Oprm1" which confused me at first because it had not been mentioned before, so 'in addition' was jarring.

      We have revised the text to state that Philip et al. (2010) originally identified the Oprm1 locus.

      Results

      (1) There are additional instances of the tense switching between past and present in the results section.

      We have standardized the tenses in the Results section.

      (2) "Ostn, Uts2d, Ccdc50, Gm10823, Fgf12, and Mb21d2" - before giving arguments for fgf12, can you clarify if there are coding variants or eQTLs for any of these genes?

      We have added a statement clarifying the coding variants for other genes in this interval and highlighting their eQTL status.

      (3) "a total number of 4,495 high-quality nuclei transcriptomes". Consider removing the word "number".

      Removed.

      (4) "approximately 6 males and 6 females" - could you point the reader to a supplementary table that has the exact number of individuals at the end of this sentence?

      The exact number of mice used in each of the BXD strains is not recorded in the original publication by Philip et al., with only mean and max was given. We have clarified that 6 is the average.

      (5) "computed using a subset" - please explain how you selected this subset (I assumed LD pruning, but why not be explicit. How many SNPs/markers were there originally, and how many are retained?

      We have specified that the subset of markers was selected via LD pruning to represent the genetic diversity of the BXDs.

      (6) A few words about how the significant threshold was obtained (permutation?) are needed.

      We have clarified that the significance threshold was obtained through 1,000 permutations.

      (7) Some of the GWAS results are presented for males and females separately (as well as combined). This is not typical, and so maybe a sentence explaining why the authors thought there might be sex specific GWAS results would be warranted.

      The rationale for sex-specific analysis is provided in the results section (significant sex difference and sex by strain interaction)

      (8) The correlation between the sexes of 0.68 could be evidence that there are sex-specific genetic effects, but could it also just be due to increased noise as you reduce sample size? What is the confidence interval for that number? Does it include 1? Or 0? If you randomly split the dataset, rather than splitting on the basis of sex, would you obtain higher correlations? The idea of sex differences is interesting, but a bit more work is needed to clarify these concerns.

      The correlation of 0.68 (95% CI: 0.52–0.79) significantly excludes both 0 and 1. The drop from r = ~0.86 at earlier intervals suggests a biological shift rather than noise due to sample size, as n remains constant (n = ~ 6 /sex/strain) across all time points. This divergence is driven by sex-specific genetic modifiers, such as the Fgf12 locus, which is more than twice as strong in females (LOD 10.6) as in males (LOD 4.3). We have addressed this in the revision.

      (9) Maybe I missed it, but how did you determine the threshold for significance for the epistatic interaction? Could you also clearly indicate how many possible cases of epistasis were examined/considered, since that dictates the correction for multiple testing.

      We only tested the interaction between the Fgf12 and the Oprm loci.

      (10) "To further examine whether Oprm1 and Fgf12 were co-expressed in the same cells of the NAc," can you first give an indication as to why you looked in NAc versus other brain areas you might have considered?

      We have added a sentence explaining that the NAc was chosen due to its central role in opioid reward and the observed strain differences in dopamine release in this region.

      (11) "...from every cell type conveyed a weak but significant positive correlation (r = 0.08, p = 1.8e-8) between the expression of Oprm1 and Fgf12 (Figure 7e). When we performed Pearson's correlation analysis within each individual cell cluster, only D1-MSN-3 had a significant positive correlation (r = 0.35, p = 6.1e-8, Figure 7f). In contrast, D1-MSN-2 had a significantly weak negative correlation (r = -0.12, p = 0.02, Figure 7g)." Can you explain why these correlations are relevant? What hypothesis are you testing?

      We have clarified that these correlations were used to test the hypothesis that Oprm1 and Fgf12 are co-expressed and potentially co-regulated within the same neuronal subtype to support their epistatic interaction.

      (12) "After the morphine locomotion tests were complete," can you give a specific timepoint? Like, was it exactly 180 minutes after the morphine injection?

      We have specified that naloxone was injected exactly 180 minutes after the morphine injection.

      (13) I appreciate the desire to relate the results of this paper to human GWAS results; however, I don't feel there is much worth discussing beyond the Oprm1 finding. Therefore, I would suggest removing this from the results section and instead just making it a discussion topic. The results presented are clearly the weakest part of this paper, and I personally think it is a shame to end the results section with something that is not very informative. But I suspect the authors may wish to retain this section, and I leave that decision to them and the editor.

      We have retained this section but moved some of the more speculative human data discussion to the Discussion section as suggested.

      Discussion

      (1) Typo "deactivates".

      Corrected to "activates".

      (2) The last sentence in the first paragraph again discusses the comparison to humans; I would remove this.

      That sentence is condensed.

      (3) "These data indicate that Oprm1 is a strong candidate gene for the Chr 10 locus associated with morphine-induced locomotion response." I would remind them of the eQTL for Oprm1 since this is a key piece of evidence supporting this gene as a candidate.

      We have added a reminder of the overlapping mRNA cis-eQTL for Oprm1.

      (4) "It is likely that differences in morphine-induced dopamine release are involved in the highly variable locomotor responses to morphine across the BXD family." I agree this might be true, but since you have no evidence to support this claim, is it worth mentioning at all?

      We have rephrased this as a hypothesis or cited relevant literature supporting this link in parental strains.

      (5) Could you include a sentence or two about why Philip 2010 didn't find Fgf12? Lack of markers? The difference between an LM and an LMM?

      We have added an explanation that the use of a high-density WGS-based marker set and the LMM (GEMMA) allowed for the detection of this novel locus that was previously missed.

      (6) Section titled "Cell-type specific gene expression in NAc". While this is interesting, you might also want to remind the reader that epistatic interactions do not necessarily require the genes to be expressed in the same cell or for their gene products to physically interact.

      We have added this caveat to the Discussion.

      (7) I think the Bayesian network section is not very strong. For example, they did not compare the results for their two chosen genes to the results they might have obtained if they had chosen other genes from their QTL intervals. My guess is that those other genes might have also produced results that were equally convincing. I'm not asking them to do that, but it reflects the risk of false positive results when taking an approach like this. Nevertheless, I am guessing the authors would prefer to include this section.

      We appreciate the reviewer pointing out this possibility and agree with this concern. We have added a statement acknowledging the risk of false positives in Bayesian modeling in this context and noting that these findings are intended as testable hypotheses

      Methods

      (1) How were the 2 HS rats selected? I had the impression that Dr. Telese's lab had access to snRNA-seq data from more than 2 HS rats.

      We have clarified that these rats were selected based on their addiction-like behavior phenotypes from a larger cohort.

      (2) I didn't look back, but did the main paper point out that the rats are treated with oxycodone rather than morphine?

      We have clarified this distinction in the Methods section.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      (1) I think this is an important paper, but I’m puzzled about a tension in the results. On the one hand, it looks like the behavioural gains post-TT happen rather smoothly over time (Figure 5). On the other hand, muscle synergy activations change abruptly at specific days (around day ~65 for Monkey A and around day ~45 for Monkey B; e.g., Figure 6). How do the authors reconcile this tension? In other words, how do they think that this drastic behavioural transition can arise from what appears to be step-by-step, continuous changes in muscle coordination? Is it “just” subtle changes in movements/posture exploiting the mechanical coupling between wrist and finger movements, combined with subtle changes in synergies, and they just happen to all kick in at the same time? This feels to me to be the core of the paper and should be addressed more directly.

      We thank the reviewer for this insightful comment, as it touches upon the central finding of our study. The apparent tension between the smooth behavioral recovery and the abrupt shift in neural strategy is indeed a key feature of the adaptation process. We propose that this reflects the interaction of two distinct, parallel processes operating on different timescales:

      A slow, gradual skill-learning process, where the monkeys incrementally developed and refined a compensatory motor strategy (i.e., the tenodesis effect). This slow refinement is responsible for the smooth improvement seen in the behavioral metrics over many weeks.

      A fast, switch-like adaptive process, which governs the activation of the primary muscle synergies. The initial ‘swap’ strategy, while simple, was biomechanically conflicting and inefficient. The CNS only abandoned this flawed strategy abruptly once the slow learning process had rendered the new compensatory strategy “good enough” to be a viable alternative.

      Therefore, the abrupt neural shift does not cause the behavioral improvement but is rather enabled by the gradual, underlying development of a better motor solution. To address this important point more directly within the manuscript, we added a new subheading to the Discussion section. This section is dedicated to explicitly framing our findings within this multi-timescale learning model, ensuring the link between the gradual behavioral recovery and the abrupt neural shift is clearly articulated.

      (2) The muscle synergy analyses, which are an important part of the paper, could be improved. In particular:

      (a) When measuring the cross-correlation between the activation of synergies, the authors should include error bars and should also look at the lag between the signals.

      We thank the reviewer for these excellent suggestions to improve our analysis.

      Error Bars: We agree that showing trial-to-trial variability is important. In our revision, we have added a shaded envelope (representing the SD across trials) to the cross-correlation plots in Figures 6, 9 and 10.

      Time Lag: We have performed the cross-correlation analysis allowing for variable time lags and extracted the lag yielding the maximum correlation coefficient (max CC) for each session, in addition to the zero-lag correlation presented in the main figures. As hypothesized, allowing variable lags often resulted in high max CC values throughout the adaptation period, potentially obscuring the clear swap-and-revert pattern visible in the zerolag analysis. This is likely because the primary adaptation involved changes in synergy timing rather than fundamental shape. However, the analysis of the lag itself proved informative. We observed significant fluctuations in the optimal lag during the early and mid-adaptation phases, particularly around the time of the ‘switch-back’, before the lag stabilized closer to zero in the late phase.

      We have added a description of this analysis to the Methods section. The results of the lag analysis are now presented in a new Supplementary Figure S6 and S7, and a sentence summarizing this finding has been added to the Results section.

      (b) Figure 7C and related figures, the authors state that the activation of muscle synergies reverts to pre-TT patterns toward the end of the experiments. However, there are noticeable differences for both monkeys (at the end of the “task range” for synergy B for monkey A, and around 50% task range for synergy B for monkey B). The authors should measure this, e.g., by quantifying the per-sample correlation between pre-TT and post-TT activation amplitudes. Same for Figures 8I, J, etc.

      We thank the reviewer for this detailed and insightful suggestion. We agree that our use of the term ‘reversion’ should be nuanced, as the recovery of the synergy activation patterns is substantial but not perfect.

      To formally quantify these remaining differences, we performed a rigorous quantitative comparison between the pre-surgery and final-day post-surgery activation profiles. We calculated the Cosine Similarity to assess the recovery of the temporal shape, and used a Permutation Test (n=10,000) to test for statistical distinctness between the pre- and post-surgery trajectories.

      Results: We found that while the temporal shapes were highly similar (Cosine Correlation > 0.90 for all synergies), the Permutation Test confirmed that the profiles remained statistically distinct (p < 0.0001) in both animals.

      We have added this quantification to the text (Results). This confirms our nuanced interpretation: while the primary temporal features of the synergies reverted, the recovered motor program represents a novel, ‘good enough’ solution that is robust and functional, rather than a mathematically perfect restoration of the original baseline.

      (c) In Figures 9 and 10, the authors show the cross-correlation of the activation coefficients of different synergies; the authors should also look at the correlation between activation profiles because it provides additional information.

      We thank the reviewer for this comment and the opportunity to clarify our terminology. We agree that analyzing the correlation between the full activation profiles is the most informative approach. In our manuscript, the terms ‘activation coefficients’ and ‘activation profiles’ both refer to the complete, time-varying activation patterns of the muscle synergies. Therefore, the crosscorrelation analysis presented in Figures 9 and 10 is indeed the correlation between these full activation profiles. To prevent any potential ambiguity for future readers, we have revised the manuscript to use the term ‘activation profiles’ exclusively and consistently when referring to these time-varying synergy activations.

      (d) The muscle synergy analysis for Monkey B is hindered by the fact that the authors lost the ability to record from the (very) functionally relevant FDS muscle. I’d repeat the synergy analyses without this muscle to understand to what extent the observed changes with respect to baseline are driven by the lack of this data.

      We thank the reviewer for raising this important methodological point. We agree that controlling for changes in the recorded muscle set is crucial for a valid comparison between pre- and post-surgical synergy structures. The reviewer’s concern is based on the premise that the FDS muscle was included in the pre-surgical analysis for Monkey B but absent from the postsurgical analysis.

      We would like to clarify that this is not the case. Due to the loss of the FDS signal post-surgery, we made the deliberate decision to exclude the FDS muscle from ALL synergy analyses for Monkey B, including the pre-surgical baseline period. This was done for the precise reason the reviewer identifies: to ensure a direct and unbiased “apples-to-apples” comparison and to avoid introducing the lack of this muscle as a confound. Therefore, the changes in synergy structure that we report for Monkey B can be confidently attributed to genuine physiological adaptation rather than an artifact of a changing input dataset.

      (e) Figure 11: The authors talk about a key difference in how Synergy B (the extensor finger) evolved between monkeys post-TT. However, to me this figure feels more like a difference in quantity - the time course than quality, since for both monkeys the aaEMG levels pretty much go back to close to baseline levels - even if there’s a statistically significant difference only for Monkey B. What am I missing?

      We thank the reviewer for this insightful question, as it has prompted us to refine our interpretation of this key finding. The reviewer correctly notes that the recovery trajectories of Synergy B appear different, and we agree that our original explanation can be improved.

      A more parsimonious interpretation, and one that we believe aligns better with the data, is that both monkeys likely underwent a similar ‘arms race’, but we captured different phases of this process. In Monkey A, our recordings (starting Day 29) captured the escalating phase of this neuromuscular conflict. In contrast, for Monkey B, recordings began on Day 20, by which time this rapid escalation had likely already occurred and peaked. This difference in the timing of the ‘arms race’ is consistent with our behavioral observations; Monkey A struggled for a longer period before performing the task proficiently, suggesting a more protracted overall adaptation process. Thus, the apparent difference in the figures is likely a reflection of the observational window and the individual adaptation rate of each animal, rather than a fundamental qualitative difference in their adaptive strategy. We have revised the text to present this more unified and coherent interpretation.

      (f) Lines 408-09 and above: The authors claim that “The development of a compensatory strategy, primarily involving the wrist flexor synergy (Synergy C), appears crucial for enabling the final phase of adaptation”, which feels true intuitively and also based on the analysis in Figure 8, but Figure 11 suggests this is only true for Monkey B. How can these statements be reconciled?

      We believe the reviewer may be referring to Monkey A in their comment, as the strong compensatory effect is indeed seen in this animal. The core of this issue, which we have clarified in our revision, is that both monkeys developed a compensatory tenodesis grasp but used different neural strategies to achieve it.

      For Monkey A, strong evidence for this strategy is provided by a clear temporal shift in the activation of its dedicated wrist flexor synergy (Synergy C). As we have now clarified in the manuscript, the peak of this synergy’s activation moved from occurring just after object contact to just before it, a re-timing well-suited to enable a tenodesis grasp.

      For Monkey B, the strategy was one of subtle re-timing rather than scaling. While the total aggregated activation of its primary flexor synergy (Synergy A) did not significantly increase, its temporal profile shifted. Specifically, activation prior to object contact increased, providing the necessary wrist flexion for its assistive tenodesis grasp, which was kinematically confirmed in Figure 12. This was achieved by reallocating activation from the post-contact phase, resulting in an earlier activation peak for the synergy overall. Crucially, a finer-grained analysis reveals a precise temporal sequence within this synergy’s activation: the wrist flexor component (PL) consistently peaked just before object contact to enable hand opening, while the finger flexor component (FDP) peaked just after contact to secure the grasp.

      This timing resolves the apparent biomechanical conflict. It also reveals that while both monkeys converged on the same biomechanical solution (a tenodesis grasp), the observable neural implementation appeared different. However, we must be cautious in directly comparing the computed synergy structures themselves, as the analysis for Monkey B was performed without the FDS muscle. The apparent “multi-functional synergy” in Monkey B is most likely a consequence of this missing data. What is clear and robust, however, is that both monkeys converged on a remarkably similar temporal solution: they both learned to re-time the activation of their key wrist flexor muscles to the pre-grasp phase.

      In Monkey A, this was observed in the temporal shift of its dedicated wrist flexor synergy (Synergy C). In Monkey B, this was observed in the temporal shift of the Palmaris Longus (PL) muscle itself (which, in our computed synergies, was grouped into Synergy A). This convergence on an identical temporal adaptation, regardless of the computed modular organization, is the key finding. We have revised the manuscript to articulate this more precise and defensible interpretation.

      (3) Experimental design: at least for the monkey who was trained on the “artificial task” (Monkey A), it would have been good if the authors had also tested him on naturalistic grasping, like the second monkey, to see to what extent the neural changes generalise across behaviours or are task-specific. Do the authors have some data that could be used to assess this even if less systematically?

      We thank the reviewer for raising this important point regarding the generalizability of our findings across different behaviors. We fully agree that a direct comparison of both tasks in the same animal would have been a valuable experiment. Unfortunately, we do not have systematic data on naturalistic grasping for Monkey A that would allow for such a direct comparison. We therefore view the two tasks as providing complementary evidence. Monkey A’s data shows the adaptation process during a highly stereotyped behavior, while Monkey B’s data demonstrates that a similar two-phase adaptive process occurs during a more naturalistic, unconstrained task. The convergence of these findings strengthens our overall conclusion that this multi-timescale adaptation is a robust principle of motor learning. Nonetheless, the reviewer raises a fascinating question about the task-specific tuning of motor synergies, which remains an excellent direction for future studies.

      (4) Monkey B’s behaviour pre-tendon transfer seems more variable than that of Monkey A (e.g., the larger error bars in Figure 5 compared to monkey A, the fluctuating crosscorrelation between FDS pre and EDC post in Figure 6Q). This should be quantified to better ground the results since it also shows more variability post-TT.

      We thank the reviewer for this excellent suggestion to formally quantify the presurgery behavioral variability. We have performed the suggested analysis on the "Grip Formation Time" metric (Fig. 5A), which was the comparable metric between the two tasks. Our calculation of the Coefficient of Variation (CV) confirms the reviewer’s observation. Monkey B’s pre-surgery performance was substantially more variable (CV = 81.93%) than Monkey A’s (CV = 46.62%). Furthermore, a non-parametric test for equal variances (Ansari-Bradley test) confirmed that this difference is highly statistically significant (p < 0.0001). We have added a description of this analysis to the Methods and reported this finding in the Results section to provide a clearer context for the baseline differences between the subjects.

      (5) Minor: Figure 12 is interesting and supports the idea that monkeys may exploit the biomechanical coupling between wrist and fingers as part of their functional recovery. It would be interesting to measure whether there is a change in such coupling (tenodesis) over time, e.g., by plotting the change in wrist angle vs change in MCP angle as a scatter plot (one dot per trial), and in the same plot show all the days, colour coded by day. Would the relationship remain largely constant or fluctuate slightly early on? I feel this analysis could also help address my point (1) above.

      We thank the reviewer for this excellent and insightful suggestion. We have performed the suggested analysis for Monkey B, plotting the trial-by-trial relationship between wrist and MCP angles for all recording days (New Figure 13).

      The results clearly show the gradual refinement of the tenodesis coupling. Pre-surgery, there was no correlation (R²=0.00). Immediately post-surgery (Day 22), the relationship was weak and variable (R²=0.16), reflecting an exploratory phase. Over the following weeks, the coupling became progressively stronger and more consistent, with the R² value peaking at 0.58 around Day 56, indicating a robust exploitation of the new strategy. The relationship then stabilized at a moderate level (R² ~0.2-0.3) in the final days. This analysis provides direct kinematic evidence for the slow, gradual skill-learning component of our two-state model. It beautifully complements our response to the reviewer’s first point by visualizing the underlying refinement process that occurred concurrently with the more abrupt neural shifts. We have added this new figure and a description of these results to the manuscript.

      Reviewer #2 (Public review):

      Weaknesses:

      The most notable weakness of the study is the incompleteness of the data. [...] As a result, it is difficult to make general conclusions from the study, and it awaits further analysis or the addition of another subject.

      We thank the reviewer for this critical and accurate assessment of the study’s limitations. The reviewer is correct that the datasets for the two monkeys are incomplete in different ways and that the tasks were not identical. We fully acknowledge these limitations throughout the manuscript. Rather than viewing these differences as a weakness that prevents generalization, we propose that they offer a unique strength in the form of complementary evidence. We consider the two animals not as a direct replication, but as two distinct case studies that test the same underlying hypothesis under different conditions.

      Monkey A, with its high-quality EMG and highly stereotyped task, provides a detailed, quantitative view of the neural adaptation process, allowing us to precisely characterize phenomena like the ‘neuromuscular arms race’.

      Monkey B, with its kinematic data and more naturalistic task, provides crucial evidence that the same fundamental principles, a two-phase adaptation and the eventual development of a compensatory strategy, generalize to a less constrained, more behaviorally relevant context. We believe the key finding is the convergence of the results. Despite the differences in individual strategy, task demands, and available data, both animals demonstrated the same core "swapand-revert" adaptive process. We propose that this convergence from heterogeneous sources lends support to the generalizability of our conclusions, suggesting that the multi-timescale adaptation we describe may be a general feature of motor learning following such perturbations. We agree that future studies with more subjects are needed to fully establish this principle. Nonetheless, we feel that the convergent evidence from these two complementary cases provides a valuable foundation for the model we present.

      A second weakness is the insufficient analysis of the movements themselves, particularly for Monkey A. [...] Since the authors have video data for both monkeys, it is surprising that it was not used to extract landmarks for kinematic analysis, or at least hand/endpoint trajectory, and how it is adjusted over time. Adding more behavior data and aligning it with the EMG data would be very helpful for characterizing motor recovery and is needed to support conclusions about underlying neural control strategies for functional improvement.

      We thank the reviewer for this important suggestion. The reviewer’s comment prompted us to re-examine our behavioral data, and we have now performed additional analyses that we agree provide a much clearer link between the neural changes and functional recovery.

      For Monkey A, we have quantified the ‘pull times’ on a day-by-day basis. This analysis reveals a clear, gradual learning curve: pull times were initially long and variable post-surgery but steadily decreased and stabilized over the recovery period. This provides a direct, quantitative measure of motor performance recovery for this animal.

      For Monkey B, we have performed a detailed analysis of the ‘grasp aperture’ prior to object contact. This kinematic analysis is particularly revealing, as it shows the development of the compensatory strategy in real-time. The grasp aperture was initially very small post-surgery, reflecting the monkey’s inability to open its hand. It then steadily increased over the next ~40 days as the monkey learned and refined the compensatory tenodesis grasp, before stabilizing at a new, functional baseline.

      We believe these new analyses directly address the reviewer’s concern by providing a more detailed picture of motor recovery. The grasp aperture data, in particular, offers a clear kinematic correlate for the slow, skill-learning process that we propose runs in parallel to the more abrupt neural reorganization. We have added these results as a new figure in the main text of our revised manuscript.

      Considering specific conclusions, the statement that the monkeys learned to use “tenodesis” over time by increasing activation of a wrist flexor muscle synergy does not seem to be fully supported by the data. [...] Given these issues, it is not clear how to align the EMG and kinematic data and interpret these findings.

      We thank the reviewer for this detailed and critical analysis. They raise an excellent point and have correctly observed that the adaptation is not a simple, uniform increase in wrist flexor synergy amplitude. Our interpretation, which we have clarified in the manuscript, is that the monkeys learned a more sophisticated strategy: a precise re-timing of the wrist flexor activation to occur earlier in the movement, specifically to pre-shape the hand for the grasp.

      For Monkey A: The reviewer correctly notes that the peak amplitude of Synergy C (the wrist flexor synergy) around the moment of grasp (0% task range) is lower in the final phase compared to baseline. However, the crucial change is temporal: the peak of this synergy’s activation shifts from occurring just after the grasp (~+1%) to occurring just before it (~-2%). This re-timing is perfectly suited to enable finger extension via the tenodesis effect immediately prior to object contact. The subsequent lower amplitude may reflect a more efficient, less forceful movement once this new skill was refined.

      For Monkey B: The reviewer is right that this monkey does not have a dedicated wrist flexor synergy and that the overall amplitude of the PL muscle does not increase dramatically. However, a closer look at its activity profile (Fig. S2-AN) reveals a clear and consistent increase in activation specifically in the pre-contact phase (~7% task range). This is the precise neural signature of the assistive tenodesis grasp that is kinematically confirmed in Figure 12. The monkey is not simply scaling up the synergy; it is strategically activating it earlier to prepare for the grasp.

      In summary, the key evidence linking the EMG to the tenodesis strategy is in the temporal domain. The learned re-timing of the wrist flexor activation to the pre-grasp phase is the crucial link that aligns the neural and kinematic data. We have revised the manuscript to make this distinction between amplitude scaling and temporal shifting clearer.

      A more minor point regarding conclusions: statements about poor task performance and high energy expenditure being the costs that drive exploration for a new strategy are speculative and should be presented as such. Although the monkeys did take longer to complete the tasks after the surgery, they were still able to perform it successfully and in less than a second and no measurements of energy expenditure were taken.

      We thank the reviewer for this important point regarding the precision of our language. We agree that statements regarding ‘high energy expenditure’ and the specific drivers for exploring a new strategy are interpretations of the data, not direct measurements, and should be framed as such.

      Our speculation about energetic cost is based on the significant increase in muscle co-activation we observed (e.g., Fig. 11), a phenomenon widely understood to be metabolically expensive. Similarly, while the monkeys were still successful, their prolonged movement times and inefficient motor patterns represent a clear performance deficit compared to their highly optimized presurgical baseline, which we propose acted as a driver for further adaptation. In our full revision, we have carefully revised the manuscript to soften these claims. We have used more speculative language, such as “we hypothesize that...”, “the likely cost of...”, or “may have provided the impetus for...” to ensure that our interpretations are clearly distinguished from our direct empirical findings.

      A small concern is whether the tendon transfer effect may fail over time, either due to scar tissue formation or tendon tearing, and it would be ideal if the integrity of the intervention were re-assessed at the end of the study.

      We thank the reviewer for raising this important point regarding the long-term integrity of the tendon transfer. We agree that a terminal anatomical re-assessment would be an ideal control. While a terminal assessment was not performed as part of this study’s protocol, we were able to monitor the transfer’s integrity throughout the study. We are confident the transfer remained functionally intact for two key reasons:

      (1) Physical Monitoring: We periodically used ultrasound imaging to non-invasively visualize the tendon repair, which allowed us to confirm its continued physical integrity.

      (2) Functional Evidence: This physical confirmation was corroborated by the functional data. Both animals achieved stable, proficient task performance that was maintained for months. Furthermore, the late-phase neuromuscular control strategies became highly consistent. A significant failure, such as a tendon tear or prohibitive mechanical scarring, would be incompatible with this sustained behavioral and neural stability.

      Nevertheless, we agree that a terminal assessment is an excellent methodological suggestion that should be incorporated into the design of future long-term studies of this nature.

      Reviewer #3 (Public review):

      (1) First, I find myself wondering about the physical healing process from the tendon transfer surgery and how it might contribute to the learning. Specifically, how long does it take for the tendons to heal and bear forces? If this itself takes a few months, it would be nice to see some discussion of this.

      We thank the reviewer for this insightful question about the potential contribution of the physical healing process to the adaptation timeline. Our surgical protocol was specifically designed to ensure the tendon transfer was biomechanically robust from the outset, minimizing the role of healing as a rate-limiting factor.

      We used a Pulvertaft weave technique, which is known to achieve mechanical strength equivalent to that of a native tendon shortly after the procedure (Graham et al., 2023). The repair involved more than two weaves and utilized high-strength suture material to maximize its initial forcebearing capacity. While full fibrous integration around the suture site typically occurs within approximately six weeks, the repair itself was strong enough to bear physiological forces immediately post-surgery. Therefore, the prolonged, complex, two-phase multi-month behavioral recovery and the neural reorganization we observed cannot be attributed to a slow physical healing process. Instead, this supports our conclusion that the observed timeline reflects the challenges and constraints of a purely neural adaptation and skill-learning process. To make this crucial point clear to all readers, we have added these details about the surgical method to the Methods section and included a brief discussion of its implications in the Discussion.

      (2) Second, I see that there are some changes in the muscle loadings for each synergy over the days, though they are relatively small. The authors mention that the cosine distances are very small for the conserved synergies compared to distances across synergies, but it would be good to get a sense for how variable this measure is within synergy. For example, what is the cosine similarity for a conserved synergy across different pre-surgery days? This might help inform whether the changes post-surgery are within a normal variation or whether they reflect important changes in how the muscles are being used over time.

      We thank the reviewer for this excellent and insightful suggestion. Establishing a baseline for normal day-to-day variability is an important control for our synergy analysis.

      We have performed this analysis in full. Specifically, to quantify baseline stability, we calculated the cosine similarity between the spatial synergy weights (W) of each individual recording day and the pre-surgery average. This provides a rigorous measure of day-to-day variability relative to the stable baseline structure. We have added these data to Figure 7 (Panel I), which plots the pre-surgery similarity (blue traces) alongside the post-surgery adaptation (red traces).

      We found that baseline stability was remarkably high, with cosine similarity consistently exceeding 0.99 (e.g., Monkey A: 0.99 ± 0.001). This quantification allows the reader to formally assess that the changes observed post-surgery (e.g., drops to ~0.80 or ~0.60 in Monkey B) are well outside the range of normal physiological fluctuation, representing subtle but genuine structural adaptation.

      (3) Last, and maybe most difficult (and possibly out of scope for this work): I would have ideally liked to see some theoretical modeling of the biomechanics so I could more easily understand what the tendon transfer did or how specific synergies affect hand kinematics before and after the surgery. Especially given that the synergies remained consistent, such an analysis could be highly instructive for a reader or to suggest future perturbations to further probe the effects of tendon transfer on long-term learning.

      We thank the reviewer for this excellent and forward-thinking suggestion. We completely agree that a detailed biomechanical model of the tendon transfer would be a powerful tool for understanding the mechanical consequences of the surgery and for interpreting the function of the recorded muscle synergies. However, creating a subject-specific musculoskeletal model with the fidelity required to accurately simulate synergy-to-kinematic transformations is a highly complex project that we feel is well beyond the scope of the current manuscript. Such an endeavor would constitute a major research project in its own right.

      Our study’s primary focus was to provide a detailed, longitudinal characterization of the in-vivo neural adaptation following this perturbation, a dataset that is itself rare and valuable. We aimed to document the physiological learning process as it unfolded over many months. Nonetheless, the reviewer’s point is exceptionally well-taken. Currently, we are constructing a monkey musculoskeletal model and performing tendon transfer on this model to investigate what kind of characteristics in the learning process reproduce the synergy changes observed in the experiments. Although this project is still in progress, to date, we have demonstrated that the robustness of synergies themselves is necessary for changes in muscle activity at the synergy level (Nakajima N, Wang S, Ogihara N, Oya T, Seki K, Funato T, Upper Limb Musculoskeletal Model of Macaque Monkey for Approaching Adaptation Mechanism to Tendon Transfer, Society for Neuroscience 2023, Washington DC, USA, 2023).

      The rich dataset we have collected in the present research could serve as an excellent foundation for developing and validating such a model in the future. We believe that combining these two approaches is a critical and exciting next step for the field, and we have highlighted this as a key future direction in our discussion.

      Recommendations for the authors:

      Reviewing Editor Comments:

      When revising the manuscript for resubmission, please try to improve the visual presentation of the data, which is a point highlighted by all three reviewers during the discussion, including making the presentation of monkey-specific results more consistent across subjects.

      We have comprehensively revised the figures to ensure a consistent and clear visual presentation, as requested. Specifically, we standardized the layout across all main and supplementary figures (placing Monkey A consistently in the top rows or left columns and Monkey B in the bottom rows or right columns) and applied unified color schemes throughout the manuscript. Furthermore, we harmonized the presentation of the analytical results, such as the specific cross-correlation pairings in Figures 9 and 10, to ensure that the data for both subjects are presented with identical logic, facilitating direct comparison.

      Reviewer #1 (Recommendations for the authors):

      (1) Please revise the writing; some words are missing (line 90), and some sentences could be clarified slightly, even if the paper is well written (lines 317-320). The paragraph including the idea of tenodesis could also be further clarified, I think.

      Thank you for pointing these out. We have corrected the missing word (osteoarthritis) on line 90. We have also revised lines 317-320 to remove ambiguity. Furthermore, the section describing the tenodesis effect (now section "Distinct neural implementations...") has been substantially rewritten for improved clarity, incorporating a more detailed explanation of the biomechanics.

      (2) In the Introduction, the authors cite Hunter and Eckstein 2009 and Mercuri and Muntoni 2013 without describing the pathological conditions; this will not be clear for not nonspecialists.

      Thank you. We have added brief descriptions ("osteoarthritis, a degenerative joint disease," and "muscular dystrophy, which involves progressive muscle weakness,") directly into the Introduction sentence where these references appear.

      (3) Data presentation: I often thought that the data could be presented more clearly:

      (a) For example, Figure 3D and 4D should show error bars around the mean to have a sense of the consistency of pre-lesion behaviour. Same for other figures like Figure 6.

      We appreciate the reviewer's suggestion to visualize data consistency. (a) Figures 3D, 4D, and 6 (EMG Profiles): For these figures, we opted to display mean traces and peak markers to clearly illustrate the temporal shifts and relationships between muscles. Overlaying multiple standard deviation envelopes in these comparative plots would significantly reduce legibility. However, to fully address the reviewer's request to see the consistency of pre-lesion behavior, we direct attention to Supplementary Figure S1, which presents the complete EMG profiles with full error tubes (Mean ± SD) for every recorded muscle. (b) Quantitative Analysis Figures: We ensured that variability is explicitly visualized in all statistical analyses. The crosscorrelation time-courses in Figures 6 (G-Q), 9, and 10 are plotted with shaded error tubes to show variance. Similarly, the aggregated EMG analysis in Figure 11 utilizes bar plots with explicit error bars to quantify the statistical consistency of the changes.

      (b) The autocorrelation analysis in Figure 6 should also include measures of lag if it’s not at zero lag. If it’s the latter, please specify it in the Methods.

      We thank the reviewer for this question regarding the cross-correlation analysis presented in Figure 6 (Panels G-J, P-Q). We confirm that this analysis was performed at zero time lag. To clarify this, we have added a sentence to the Methods section (Subsection "Crosscorrelation analysis") explicitly stating that the EMG cross-correlations shown in Figure 6 were calculated at zero lag. We have also added a clarifying note ("at zero time lag") to the description of these panels within the Figure 6 caption.

      (c) Seeing EMG patterns similar to those presented in Figures 3D and 4D at different times post-lesion (e.g., as a Supplementary figure) would also give readers a better intuition of the neural changes.

      We thank the reviewer for this suggestion to provide more intuitive examples of the neural changes. We realize we did not sufficiently highlight this in the main text, but this complete data is already available in the manuscript. Supplementary Figures S1 and S2 provide a comprehensive overview of the EMG patterns for all recorded muscles in Monkey A and Monkey B, respectively. These figures show the pre-surgery and post-surgery average profiles for all recording sessions as well as the average profiles from five different post-surgery landmark days, covering the entire adaptation period. We have added explicit cross-references to these figures in the main text.

      (d) I couldn’t fully understand the analysis in Figure 4E; clarify.

      We thank the reviewer for noticing this oversight. The reviewer is correct that Figure 4E was not referenced in the main text. This panel was intended to show the baseline kinematic profiles (MCP and wrist angles) for Monkey B's control session, corresponding to the average EMGs shown in panel 4D. Given that our more comprehensive kinematic analyses are now presented in Figure 12 and the new Figure 13, we believe panel 4E is largely redundant. To improve the clarity and focus of Figure 4, we have removed panel 4E and its description from the revised manuscript.

      (e) Some figures showing neural changes (e.g., Figures 6G-J, 6P,Q, Figures 9 and 10, and even Figure 11 for different reasons) would become more understandable if they were accompanied by the behavioural changes (e.g., something like Figure 5A on top of them).

      We agree that visualizing the temporal link between neural reorganization and behavioral recovery is essential for interpreting the data. We have implemented this suggestion by overlaying behavioral metrics onto the right y-axes of Figures 6 (G-Q), 9, 10, and 11. However, regarding the specific behavioral metric, we opted to overlay the maladaptive behavior/aberrant reaching metric (from Figure 5B) rather than the grip formation time (Figure 5A). We found that the maladaptive behavior profile provided a clearer and more direct correlate to the neural data, as its peak coincides precisely with the ‘swapped’ synergy phase, thereby effectively illustrating the functional cost of that specific neural state.

      (f) Some figure captions could be improved by adding more detail (e.g., for Figure 6).

      We agree. We have substantially expanded and improved the captions for Figure 6 and Figure 7 to make them more self-contained and guide the reader more effectively through the key findings presented in the panels. We have also reviewed other captions for clarity.

      (g) I’d show the cosine distance between synergies across days as a main figure, e.g., as part of Figure 7, because this is an important result.

      We agree that the longitudinal stability of the synergy structures is a crucial result that deserves prominence. We have implemented this suggestion by adding a new panel, Figure 7 (I, K) for primary synergies and Figure 8 (K, L) for secondary synergies, which plots the cosine similarity of the spatial synergy weights across the entire experimental timeline. This figure explicitly visualizes the high stability of the pre-surgery baseline (blue traces, similarity > 0.99) and contrasts it with the dynamic structural tuning observed during the post-surgery adaptation (red traces), providing a clear, day-by-day account of synergy evolution as requested.

      (h) In Figure 7C, D and G, H, it’d be interesting to also see in the background the EMG for the transferred muscle that belongs to each synergy, to appreciate their relationship.

      We thank the reviewer for this suggestion. To illustrate the close relationship between the primary synergies and their key constituent muscles, while avoiding visual clutter in the complex post-surgery plots, we have modified the pre-surgery panels of Figure 7 (C, D, G, H). In these panels, we have now overlaid the average pre-surgery EMG profile of the primary transferred muscle belonging to that synergy (e.g., FDS for Synergy A, EDC for Synergy B) as a thin, gray, dashed line. This visually confirms the tight correlation between the synergy profile and the muscle’s activity at baseline.

      (i) In page 10, the authors report as maladaptive behaviour the duration of the aberrant reaching component from day 29 (monkey A) and day 20 (monkey B). What was happening before those recording dates? Were the monkeys recovering?

      Thank you for this question. We have added two sentences to the start of the Results section (“Functional Recovery Follows...”) clarifying that the period between surgery and formal recordings included approximately one week of home cage recovery followed by several weeks of assisted task practice. Formal recordings began once the monkeys could perform the task consistently without assistance.

      (j) In the Methods (EMG Analysis), the authors state that they resumed their recordings post-TT “once they (the monkeys) were able to perform the task on their own”. It would be good if the authors made this more precise (e.g., based on success rate or another metric).

      We thank the reviewer for this suggestion to increase precision. We have revised the Methods section to include the specific criteria used for resuming post-surgical recordings. Recordings were restarted once the monkeys were able to perform the task independently (i.e., without assistance from the experimenter) and consistently achieved a successful trial count of at least 100 trials within a single experimental session.

      (k) Line 266- reads “Alternation of EMG activity in non-transferred muscle suggests one possibility: TT might alter the control strategy of coordinated muscle activity for hand movement by modifying the transferred muscles and their agonists as a cohesive unit”, however, some “muscles showed patterns that were incompatible with a simple swap” (Lines 255-256). Doesn’t this observation suggest that what happens is not a simple change in muscle synergies?

      We thank the reviewer for this insightful question regarding the interpretation of muscles with adaptive patterns incompatible with the primary ‘swap-and-revert’. We agree that these observations require careful consideration within the modular framework. Our interpretation is that these muscles do not represent evidence against modular control, but rather reflect the involvement of multiple modules adapting concurrently. Specifically, muscles like FCR and PL, which showed distinct patterns, are primary members of Synergy C (the wrist flexor synergy) in Monkey A. Their adaptive profile is therefore consistent with the task-specific recruitment and retiming of Synergy C as part of the compensatory tenodesis strategy, rather than being a deviation from the swap observed in Synergies A and B. Synergies represent the dominant, shared variance in muscle activity. While they capture the overall strategy, some degree of individual muscle variation or the influence of secondary synergies is expected. We have added a sentence to the Results section to clarify that these diverse patterns likely reflect the differential involvement of muscles in multiple adapting synergies. We believe the overall evidence still strongly supports the modulation of stable synergies as the primary mechanism of adaptation in this paradigm.

      (l) You may want to call synergy A and synergy B, synergy F and synergy E to make recall easier? (Same for synergy C and D, which could be F2 and E2).

      We thank the reviewer for this helpful suggestion aimed at improving clarity. We considered renaming the synergies based on function (e.g., F/E). However, given the number of figures and the complexity of a global change, and the fact that the functional roles of Synergies C and D differed between animals, we decided to retain the original A/B/C/D labels for consistency. To ensure clarity for the reader, we have carefully checked the manuscript to ensure that we consistently define the primary functional role of each synergy (e.g., "Synergy A, the primary finger flexor synergy") when it is discussed.

      (m) Lines 315-317 - “These pattens of changes in synergy 3 and 4, both contributed minimally to the EMG of transferred muscles” -> This statement puts the causality as synergies cause muscles to activate according to certain patterns, which is supported by work by several groups -including the authors- however, they could also reflect biomechanical and task constraints as other have argued; perhaps this tone would be better for the discussion?

      We thank the reviewer for this nuanced point regarding the interpretation of synergy contributions. We agree that the causal relationship between computed synergies and muscle activity is complex and can reflect both neural commands and task constraints. To address this, we have revised the sentence in question in the Results section. Instead of stating that the synergies "contributed minimally," we now state that the changes in these synergies "were associated with minimal EMG activity in the transferred muscles." This phrasing is more descriptive of the observation and less implicitly causal, while retaining the key point within the flow of the results. The subsequent sentences, which offer interpretation, are already framed speculatively ("This suggests...", "may have served...").

      (n) Line 403 How do the authors conclude from the synergy patterns in Figure 11 that the early post-TT is characterised by “an unstable and inefficient neural control strategy”? To me, this is shown clearly in the behaviour, not in these plots, unless I’m missing something?

      We thank the reviewer for this comment, which highlights the need to clearly connect our neural findings to the behavioral outcome. The reviewer is absolutely correct that the behavioral data (Fig. 5) provides the most direct evidence of instability and inefficiency during the early adaptation phase. Our intention was to argue that the neural patterns observed in Figure 11 provide a physiological correlate for this behavioral inefficiency. Specifically, the escalating aggregated EMG activity observed in the conflicted extensor synergy (Synergy B), which we term the ‘arms race’, represents significant muscle co-activation. Such co-activation is widely understood to be energetically costly and reflects a suboptimal control strategy where the CNS is essentially "fighting itself" against the altered mechanics. To make this link clearer, we have revised the concluding sentence of the relevant paragraph in the Discussion ("The early adaptation phase...") to explicitly state that this escalating co-activation is a known marker of inefficient recruitment and that it occurred concurrently with the period of poor behavioral performance shown in Figure 5.

      (o) Lines 469-471. The authors suggest that muscle synergies may be preserved post-TT because a modular approach (to motor control) may be computationally easy and metabolically cheap. To me, recent data suggest that the most parsimonious explanation is what they later say: that the nervous system may not be plastic enough to change this (e.g., see Makin and Krakauer, “Against reorganisation” also in eLife).

      We thank the reviewer for raising this important theoretical point and for referencing the relevant literature on constraints on cortical reorganization. We agree that the preservation of muscle synergies in the face of such a profound perturbation is a key finding that warrants careful interpretation. In our revised Discussion (section "The CNS Defaults to a Modular Strategy..."), we have now explicitly incorporated the perspective that synergy stability may reflect inherent constraints on neural plasticity, citing Makin and Krakauer (2023), alongside our original hypothesis regarding computational and metabolic efficiency. We present these ideas not as mutually exclusive, but as potentially complementary factors that both contribute to the CNS’s apparent preference for modulating existing modules rather than fundamentally restructuring them.

      (p) Lines 501-503. Also on interpretation. Would the metabolic cost indeed be much higher? Couldn’t the observed change in strategy be explained purely based on performance metrics?

      This is an important point. We agree that statements regarding high energy expenditure are interpretations, not direct measurements. We have carefully revised the manuscript (Abstract, Results, and Discussion) to soften these claims, using more speculative language (e.g., "likely costly," "what we propose was...") to clearly distinguish our interpretations from direct empirical findings.

      (q) Lines 538-. The authors link the initial adaptation phase to the fast process reported in adaptation studies and say that this leads to poor retention. However, it seems from their data that the behaviour is stable across (early) days, so doesn’t this rule out such an interpretation?

      We thank the reviewer for this insightful question regarding the interpretation of the early adaptive phase within the two-state model framework. The reviewer correctly notes that the early post-surgical behavior, while maladaptive, appeared relatively stable across days and did not show the rapid decay sometimes associated with the "poor retention" characteristic of the fast system. We agree that this apparent stability requires careful interpretation. In our revised Discussion (section "A Multi-Timescale Model..."), we now propose that the fast system is primarily responsible for the initial, rapid adoption of the ‘swap’ strategy in response to the large error signal. The subsequent persistence of this flawed but stable state for several weeks is likely not due to strong retention by the fast system itself, but rather reflects the time required for the parallel slow system to gradually develop a more effective compensatory strategy (i.e., the tenodesis grasp). Once this alternative strategy became viable, it enabled the abrupt "switchback," which we also attribute to the fast system recalibrating away from the highly costly swap strategy. Therefore, we believe our data is consistent with the involvement of a fast system driving rapid strategic shifts, even if the typical "poor retention" phenotype is masked by the lack of a viable alternative strategy during the early phase.

      Reviewer #2 (Recommendations for the authors):

      (1) The discussion would benefit greatly from a more careful comparison with prior work characterizing the response to experimental or clinical tendon or nerve transfer in different models.

      We thank the reviewer for suggesting these important references and for the recommendation to compare our findings more carefully with prior work. This is an excellent point, and we agree it will significantly strengthen the discussion. In our full revision, we have added a new paragraph to the Discussion section dedicated to this comparison. We discuss how our findings relate to classic work showing primate adaptive capacity beyond simple maladaptive responses (Sperry, 1947), EMG evidence for the persistence of original neural patterns alongside new ones in human patients (Illert et al., 1986), the critical role of altered peripheral biomechanics and myofascial force transmission in complicating adaptation (Maas & Huijing, 2012), and how our observation of synergy stability aligns with evidence for modular adaptation strategies (Berger et al., 2013). This comparison helps situate our unique findings of a multi-timescale process and synergy timing modulation within the broader context of motor relearning after musculoskeletal rearrangement.

      (2) Line 90 - Which disease or condition is studied in Hunter and Eckstein (2009)?

      Thank you. We have clarified this in the Introduction; the reference pertains to osteoarthritis.

      (3) Line 280 for clarity in text and as a reminder to the readers, please state which muscles are involved in each synergy grouping.

      We have updated the text (Results, 'Adaptation occurs through modulating...') to explicitly list the main contributing muscles for each synergy grouping (e.g., Synergy A: FDS and FCU for Monkey A). This provides the requested clarity regarding the functional identity of each synergy while maintaining readability. For the complete, quantitative muscle weight composition including minor contributors, we referred the reader to Figure 7 and Supplementary Table 1.

      (4) Line 180 There are differences in the time course for measurements between the behavioral metrics and EMGs. If not recorded at fixed time intervals, the differences in the time courses for the two monkeys should be explained.

      We thank the reviewer for this question regarding the time courses of our measurements. We interpret this comment in two ways, both of which we have addressed in the revised manuscript.

      First, if the reviewer is asking about the overall recording schedule, they are correct that sessions were not performed at fixed daily intervals, and the specific days sampled differed between monkeys. This non-uniform sampling was due to the practical constraints of longterm behavioral experiments (e.g., animal cooperation, scheduling, weekends) and the aim to capture data during key phases of adaptation. However, within any given session, behavioral (video) and EMG data were always collected concurrently.

      Second, if the reviewer is asking whether the set of days included differs between the behavioral plots (e.g., Fig 5) and the EMG/synergy plots (e.g., Figs 6, 9-11), this is a possibility depending on data quality criteria. Our criterion for including a session in the behavioral analysis was a minimum of 20 successful trials. However, for the more demanding synergy analysis, we required a higher minimum of 100 successful trials to ensure robust factorization. It is possible that a few sessions met the behavioral criterion but not the synergy criterion and were thus excluded from the latter analysis, leading to slight differences in the days presented across figures. To ensure full clarity, we have added text to the Methods section explicitly stating: (A) the rationale for the non-uniform daily sampling schedule, and (B) the specific minimum trial count criteria used for including data in the behavioral versus the synergy analyses, noting if this resulted in different sets of days being analyzed for different figures.

      (5) General figure comments - The figures are informative, but they could be better presented, designed, and formatted to explain the important results in the paper. The figures should be able to explain most of the key results without entirely referring to the text to find some of the details. I had a bit of trouble understanding Figure 9 & 10. I would also like to suggest that bringing raw data into some figures (e.g., EMG of different muscle groups), such as showing stability between the synergies, could improve the results and allow the story to flow with more clarity. Likewise, clearly showing the differences between baseline EMG measurements and post-surgery measurements could improve some of the result figures.

      We thank the reviewer for these important general comments on data presentation. We agree that the figures are the key to our story and are implementing several revisions based on this and other reviewer feedback to improve their clarity.

      General Presentation: We have conducted a thorough review of all figures to improve layout, consistency, and font legibility (addressing R3, 1 and the Reviewing Editor's comments). This includes adjusting the layouts of Figures 3, 4, and 6 for better alignment and clarity.

      Figures 9 & 10 (Cross-correlation): The reviewer mentioned having trouble understanding these figures. In our revision, we have substantially rewritten the captions for Figures 9 and 10 to be much more descriptive. We explicitly walk the reader through how to interpret the plots (e.g., "The ‘swap’ is evidenced by the drop in self-correlation... and a concurrent rise in antagonist-correlation...").

      Including "Raw Data" (EMG): We thank the reviewer for this suggestion to provide more intuitive examples of the neural changes. We realize we did not sufficiently highlight this in the main text, but this complete data is already available in the manuscript. Supplementary Figures S1 and S2 provide a comprehensive overview of the EMG patterns for all recorded muscles in Monkey A and Monkey B, respectively. These figures show the pre-surgery and post-surgery average profiles for all recording sessions as well as the average profiles from five different post-surgery landmark days, covering the entire adaptation period. These figures directly visualize the swap-and-revert pattern in the transferred muscles and their agonists (e.g., EDC, ED23), as well as the diverse and complex adaptations in other nontransferred muscles (e.g., FCR, PL), as requested. To make this clearer, we have added explicit cross-references to Supplementary Figures S1 and S2 within the main Results section to ensure readers are directed to this detailed data.

      Showing Differences (Pre vs. Post): To "clearly show the differences between baseline... and post-surgery measurements," we implemented the point-by-point statistical comparison of pre- vs. final-day synergy profiles (as suggested in R1, 2b). This has resulted in a new Supplementary Figure visually highlighting the precise periods in the task where the final profiles still differ significantly from baseline (Fig. S9).

      We believe these additions (new figures and improved captions) will make the results much clearer and more self-explanatory, as the reviewer suggested.

      (6) Figure 1 A table with all the acronyms would help with identifying all the muscles and their respective synergies (supplemental), especially when describing the muscles in the result of the discussion section.

      This is an excellent suggestion. We have created a comprehensive table (Supplementary Table 1) listing all muscle abbreviations, full names, primary functional groups, and assigned synergies for both monkeys. We have added a reference to this table in the Figure 1 caption and the Methods section.

      (7) Figure 2 - is this mainly from Monkey A? If so, it should be stated.

      We thank the reviewer for pointing out this omission. We have updated the caption for Figure 2 to clarify that the example data shown (ultrasound, trajectories, and quantitative plots) are from Monkey A.

      (8) Figure 3 & Figure 4 seems unbalanced because of the descriptive need to explain Monkey B’s tasks? The figure alignments could be better.

      We thank the reviewer for this comment on the visual presentation of Figures 3 and 4. The reviewer’s observation that the figures appeared ‘unbalanced’ was correct. This was a direct consequence of two issues: (1) the different tasks required slightly different schematics (the "descriptive need" the reviewer mentioned), and (2) the original Figure 4 contained an additional kinematic panel (formerly 4E) that was unique to Monkey B, which broke the parallel structure with Figure 3.

      To address this and significantly improve the alignment, we have now moved the unique kinematic panel (formerly 4E) to a new Supplementary Figure (Supplementary Figure S8). This change has allowed us to re-arrange the panels in Figures 3 and 4 so that they now follow the exact same order. We have also adjusted the layout to ensure that corresponding panels are of a consistent size. We agree that this creates a much better visual balance and makes the comparison between the two monkeys far more direct and clear, as the reviewer suggested.

      (9) Figure 5. It seems like the animals can still perform the task post-surgery, but with high variability. Maybe emphasize the differences in variability between baseline and postsurgery?

      We thank the reviewer for this suggestion to emphasize the changes in variability. We have now quantified this using the Coefficient of Variation (CV) for key behavioral metrics across different phases (Pre-surgery, Early, Mid, Late post-surgery). The results confirm the reviewer’s observation of high variability post-surgery, particularly in the early phase. For instance, Monkey A’s grip formation time CV spiked dramatically (Pre: 47% vs Early: 133%), while Monkey B’s remained high (Pre: 82% vs Early: 76%). Interestingly, while Monkey A’s variability returned close to baseline levels in the late phase (Late: 55%), Monkey B’s variability increased further (Late: 97%), suggesting persistent inconsistency despite functional recovery.

      We also observed metric-specific changes. Monkey A’s pull time became less variable than baseline later on (Pre: 65% vs Late: 43%), suggesting refinement of that action. Conversely, Monkey B’s grasp aperture remained consistently low throughout (Pre: 26% vs Late: 19%), indicating relatively precise kinematic control was maintained or quickly regained. We have added a summary of these findings to the Results section to provide a more complete picture of how behavioral variability evolved relative to baseline during the adaptation process.

      (10) Figure 6 quite a confusing figure. This figure needs to be better presented. The figure legends are hard to see for Monkey A vs Monkey B. At first, I thought Monkey B’s figure legend also represented Monkey A. I would suggest reorganizing the figures for clarity and coherence.

      We agree that the original presentation of Figure 6 was dense and potentially confusing. We have completely reorganized the figure to improve clarity and coherence.

      (1) Clear Separation: The figure is now structured with a strict separation between Monkey A (Left Panels, A-J) and Monkey B (Right Panels, K-Q), with prominent headers for each subject to prevent ambiguity.

      (2) Improved Legends: We have redesigned the legends to be larger and placed them explicitly within their respective subject’s section to ensure it is immediately clear which data they describe.

      (3) Visual Consistency: We have standardized the color schemes and axis layouts across this and all other figures to reduce cognitive load and facilitate easier comparison between subjects.

      (11) Figure 12 - This figure is incomplete without Monkey A’s results. The videos in the supplemental sections seem clear enough for some kinematic analysis. The story could be more supported with more thorough measurements of the kinematics from both animals to show how they differ over time and by highlighting the two phases. As a minor note, it would be helpful to present the kinematic data together with a schematic of when during the task the data are drawn from, using the % task range scale, since that is the standard throughout the paper.

      We thank the reviewer for their suggestions regarding the kinematic analysis. We agree that a parallel kinematic analysis for Monkey A, similar to that in Figure 12, would be ideal. We did attempt this. Unfortunately, while the supplemental videos for Monkey A are sufficient for observing the overall movement trajectory, they are not suitable for the detailed joint angle analysis the reviewer suggests. The videos for Monkey A were recorded at an insufficient frame rate that did not allow to reliably extract the rapid joint angle positions of the wrist and fingers during the grasping movement. This is the reason why this detailed kinematic analysis was limited to Monkey B, for which we had high-speed video recorded at 240 fps, allowing for a robust analysis of these fast movements.

      We have, however, expanded our kinematic analysis for Monkey B to show the refinement of the tenodesis strategy over the full time course (New Figure 13), which does help to highlight the different adaptive phases for that animal. We have also clarified in the manuscript (e.g., in the caption for Figure 12) that the lack of Monkey A data for this specific analysis was due to the lowresolution and low-frame-rate video available.

      We agree that defining the precise timing of the kinematic snapshot relative to our normalized task range is critical for accurate interpretation. In response, we have added a new panel (Figure 12C) that explicitly maps the kinematic snapshot to our standardized task timeline. This schematic clarifies that the joint angle analysis captures the hand configuration during the pre-shaping phase, specifically at 83 ms prior to object contact (which corresponds to -0.02% of the normalized task range). This ensures the kinematic data can be directly interpreted within the same temporal context as the EMG and synergy results presented throughout the paper.

      Reviewer #3 (Recommendations for the authors):

      First and most major: I found many of the figures much too small and incredibly difficult to read. Possibly the most difficult was Figure 7, where I had to zoom in a great deal to read what muscles corresponded to which bars. I don’t have specific suggestions here other than to make sure that figures are legible.

      We thank the reviewer for highlighting this important issue. We have comprehensively revised the figures to ensure they are legible at standard publication sizes. Specific improvements include:

      (1) Figure 7: We have significantly increased the font size of the x-axis muscle labels and optimized the bar chart spacing to ensure the muscle identities are readable without excessive zooming.

      (2) Global Updates: Across all figures, we have increased font sizes for axis labels and titles, removed unnecessary whitespace to maximize the data-to-ink ratio, and exported all final figures in high-resolution vector formats to ensure clarity.

      Second and more minor: I liked the setup of the manuscript, where the authors explained the unique benefits of their experimental methods and the question they were going after (“When confronted with structural changes to the musculoskeletal system, does the CNS adapt by modulating existing synergies, or by shifting toward more fractionated control strategies?”). However, the evolution of the paper made the answer to this question seem very confusing to me as I read it. The results show that monkeys initially modulated existing synergies in phase 1, but then reverted to the original modulation. This, in addition to the way the question was set up initially, made me think the conclusion was going to be that the synergies themselves changed in the second phase, but this paradoxically was not the case--synergies were stable throughout. I was left confused for the back half of the results section, until the discussion on tenodesis and developing compensatory movement strategies. So the answer is that the monkey learns by modulating existing synergies, but using different strategies in different learning phases. I’m not entirely sure how to avoid this confusion, but I wonder if there’s a way to foreshadow this finding earlier on.

      We thank the reviewer for this valuable feedback on the manuscript’s narrative structure. We understand how the initial framing (modulation vs. fractionation) followed by the reversion of the initial modulation could lead to confusion before the compensatory strategy is fully introduced. To address this, we have made two key adjustments in the revised manuscript:

      (1) In the Introduction, after posing the central question, we have added a sentence to subtly foreshadow that the adaptive process might be complex and multi-phasic, requiring analysis over extended timescales.

      (2) In the Results section, at the transition point between describing the reversion of the primary synergy timings and introducing the compensatory tenodesis strategy, we have added a short paragraph to explicitly signal that the reversion was not the complete solution and that a distinct compensatory strategy emerged concurrently.

      We believe these changes improve the narrative flow, provide better signposting for the reader, and mitigate the potential for confusion identified by the reviewer, making it clearer that the ultimate solution involved modulating existing synergies but via different strategies across distinct learning phases. We appreciate the reviewer’s help in identifying this area for improvement.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      The paper describes a biologically plausible version of JEPA using recurrent neural networks called RPL for recurrent predictive learning. Given an embedding z<sub>t</sub>, a recurrent neural network processes these inputs with the form: c<sub>t</sub>+1 = RNN(c<sub>t</sub>,z<sub>t</sub>). Then the predictive network f is predicting the future inputs with the format: min||f(c<sub>t</sub>) − stop grad(z<sub>t</sub>+∆<sub>t</sub>)||<sup>2</sup>. I understand that a prediction error is defined as: e = z<sub>t</sub>+∆<sub>t</sub> − f(c<sub>t</sub>) to model cortical measurements in the oddball task.

      The RPL model is also shown to build an internal world model, with ”real-world” data like the movement of moving animals or speech signals. The representation is then compared to V1 data and expected prediction error signals in an oddball setting. In a stacked hierarchy of RNN learning with RPL, the higher layers appear to learn high-level latent variables, although gradients are not propagated downward to the lower layers.

      The paper tackles an open question: Self-supervised learning is thought to be a fundamental principle to explain how computation is structured in the brain. Cortical data suggest qualitatively that prediction error is a core principle of representation learning in the brain, but the field is still looking for a simple yet expressive model that would explain how the cortex learns its representations. RPL contributes in that direction by making a useful link between cortical representation learning in RNN models and the JEPA learning algorithm that was demonstrated to scale to large world model learning from video data by Lecun’s group. It is very useful to connect this popular deep learning algorithm to cortical data.

      The model formalism is relatively elegant and simple: Simple next input prediction objectives are conceptually simple but not necessarily trivial to build at scale. There is a clear benefit in comparison with contrastive or IL methods because they are free from dataset-specific data augmentation and negative samples. Thereby moving the comp neuro field towards conceptually simpler models of representation in the cortex. Yet predictive only models (and in particular predictive models in latent space instead of pixel space) are not easy to build in a stable fashion. JEPA family is basically intended to solve this question; it is very nice and timely to bring this to comp neuro.

      The methodology combining comp neuro and deep learning makes sense: The conceptual and qualitative analogy with cortical prediction errors is relevant and consistent with what is expected as a model of self-supervised learning in cortical models. The methodology to compare RPL with IL and CL is methodologically meaningful and grounded: showing, for instance, how some of the models fail to represent some latent structure in some toy datasets is interesting.

      (1.1) h-RPL: The h-RPL is perhaps the most creative departure from the JEPA model family. It would be interesting to say more about what was particularly difficult to see in the latent variables emerging in the hierarchical model. I often find it magical that layer-wise learning rules of this type are not learning redundant representations. Any insights why this is not the case here would be potentially insightful.

      We thank the reviewer for this comment. Regarding representational collapse in h-RPL: each local circuit independently applies the same collapse-preventing strategy as the single-level RPL model: namely, the asymmetric prediction architecture combined with the stop-grad operator. Since this mechanism operates locally within each circuit, it is sufficient to prevent collapse at every level of the hierarchy independently (see also our response to Point P1.3).

      The more subtle question is why the circuits learn non-redundant rather than identical representations across the hierarchy. We believe two mechanisms are at play here: First, the hierarchical encoder is a stacked convolutional network, meaning that receptive field sizes grow with depth. This architectural inductive bias naturally encourages successive circuits to operate on increasingly spatially integrated features, creating a structural pressure toward learning complementary rather than redundant representations. Second, the growing expressivity of the network with depth means that higher circuits have access to richer, more abstract inputs from which they can extract higher-level latent structure that is not already captured by lower circuits. Together these factors: the local collapse-preventing mechanism and the depth-dependent growth in receptive field size and network expressivity presumably explain why h-RPL builds an increasingly refined and non-redundant representational hierarchy.

      What we will do: We will expand our discussion on this point in the revised manuscript. We plan to expand our quantification on how abstractions emerge in h-RPL in future work in which we will also study variations with top-down connections.

      (1.2) In general, I fully support the type of question and ideas that the paper is putting forward. It is, however, very hard in this research field to gain insight into specific conceptual contributions or specific bits of experimental data that the model puts forward. In pointing to the following weaknesses, I am encouraging the authors to lay out more clearly what the unique hypothesis is or the contribution of the RPL model that we should remember it for.

      Thanks for the positive feedback along with the constructive criticism, and we agree that articulating the core contributions more crisply would strengthen the paper.

      At its heart, we believe the paper makes two contributions we hope it will be remembered for. First, while prior work has established that invariant representations can be learned via local Hebbianlike learning rules, we show that learning equivariant representations alongside a latent dynamics model requires something qualitatively different: a local circuit; one with recurrent dynamics and an asymmetric predictive architecture. RPL provides a minimal concrete instantiation of this principle.

      Second, and perhaps more broadly, the model makes a structural prediction about (cortical) neuronal circuit organization: since the encoder, integrator, and predictor each perform functionally distinct computations, the framework implies the existence of corresponding cell types and connectivity patterns one should look for in experimental data.

      What we will do: We will sharpen these above messages in the revised manuscript to ensure these contributions are prominently highlighted throughout the paper.

      (1.3) Comparison with JEPA variants: JEPA variants are integrating different details into the learning algorithm. Integrating, for instance, “masking” of the latent encoder targets, or EMA in the style of BYOL or Siamese networks, for the predicted representations. It is great that RPL does not seem to need any of those (next input prediction is a natural implementation of masking, and EMA does not seem to be used). It is notoriously hard for the JEPA model to work without these features. Since some of these details are sometimes surprisingly crucial for a simulation to work, it would be good to report which of the other important details were key to live without EMA and masking. Is it the difference in learning rate, for instance? Or maybe the tasks considered are simply easy enough for any model to work; if so, it could be useful to acknowledge to what extent this is true.

      We thank the reviewer for raising this important point. There are two key mechanisms that ensure stable, non-trivial training in RPL. First, using a higher learning rate for the predictor relative to the encoder is crucial for stable training. This prevents the predictor from collapsing the encoder representations and was already noted empirically by Chen et al. (2021).

      Second, and more fundamentally, predicting at the level of the memoryless encoder output, rather than at the level of the recurrent integrator, is essential to prevent a degenerate solution in which the RNN simply learns to generate an internally predictable time series unrelated to the input. By anchoring the prediction target to the encoder, the model is forced to ground its representations in the sensory input. Intuitively, otherwise the RNN can simply “make up” a predictable time series, which satisfies the learning objective, but would not yield useful internal representations.

      Beyond these architectural points, previous work from our group (Srinath Halvagal et al., 2023) has shown mathematically that JEPAs without EMA avoid collapse via an implicit variance regularization mechanism, and we believe RPL benefits from the same principle. Indeed, we now have a more complete theoretical understanding of this, including identifiability proofs for the latent dynamical model under relatively mild assumptions (Mikulasch et al., 2026). This work has recently been accepted at ICML. Other than that, one has to ensure that representations are not already nearly collapsed at the beginning of training. In this paper, we used normalization layers (batchnorm) in the encoder to ensure this.

      Finally like all SSL paradigms the augmentation strength is an important hyperparameter that impacts the quality of learned representations. In the temporal predictive setting, the augmentation strength is fixed by the world itself. The only knob we have to play with is the prediction horizon ∆. While we typically focused on next-time-step (∆ = 1) prediction, we saw a clear effect in the case of the speech dataset where ∆ = 8, but not ∆ = 1, yielded useful representations for the tasks (Fig. 5b).

      What we will do: We will discuss the above points more prominently in the discussion to avoid them being overlooked in the methods. Additionally, we will include a plot on the empirical prediction horizon for the speech dataset in the supplementary material for reference.

      (1.4) Comparison with IL and CL: On a high level, the comparison with IL and CL algorithms is written as conclusive. I suspect that the failure modes of IL and CL that are described are not due to the algorithms themselves, but rather to the construction of invariance statistics or the choice of negative sample sets (the sets of samples among which variance 1 is requested by VICreg). For instance, if variance (or negative sample set) is taken only across time, the variance object identity is expected to collapse. Similarly, if the variance is taken across the object identity, the variance across time can collapse. So I wonder if the failure of IL and CL is induced by the construction of the variance definition.

      We thank the reviewer for this thoughtful point. Both RPL and CL implement an implicit variance regularizer by virtue of being JEPAs (Srinath Halvagal et al., 2023), whereas IL uses an explicit regularizer computed along both the batch and time dimensions to avoid representational and dimensional collapse. The failure modes of IL and CL therefore cannot be entirely attributed to the statistics of the input samples chosen for variance regularization, but are instead primarily determined by the choice of prediction and target representations.

      What we will do: We will clarify this in the Methods section of the revised manuscript.

      (1.5) Prediction error: When compared to the recording of cortical activity in Figure 7. It is not obvious from the figure which latent space we are talking about mathematically. Is the vector z, c or the prediction error e? This is rather important from a neuroscientific point of view, because the prediction error e is expected to explain the neuronal data. On the other hand, the prediction error e is only used in the learning algorithm to define the loss function, but it is not the communication medium between the RNN units c (or with the encoder z).

      In the brain, since the measurements are recorded as neural activity, they are communication channels between specific units (z or c). It is probably c or z that would already explain the oddball prediction error. I believe that other models, like Forward-forward of Nejad et al., have tried quite hard to address this apparent tension. Whether or not this is resolved by RPL, it thinks it would be beneficial to state the problem and clarify how the algorithm addresses or ignores the issue.

      Thanks for pointing out the issue with regards to clarity and for raising the important but subtle point about prediction error representation. To answer the immediate question asking which vector we use in Figure 7, it is the vector c corresponding to the integrator representations. We agree this should be stated explicitly and will update the manuscript accordingly.

      On the more general point, we agree that the tension between recordable neural activity and the computational role of prediction errors is an important issue. We do already briefly engage with it in the Discussion (subsection “Relation to previous modeling work”), where we note that under RPL “inter-areal communication is dominated by representations rather than error signals”. However, we agree that this point should be surfaced more directly.

      To elaborate, under classical predictive coding, prediction errors are the inter-areal communication channel and are therefore expected to be directly observable in neural recordings, e.g., as oddball responses. Under RPL, this is not the case: e is computed locally within a circuit and serves only as a learning signal for synaptic plasticity, not as a signal propagated between circuits or areas. What cortex primarily encodes and communicates in our framework are predictive representations, not reconstruction errors. Accordingly, what should map onto recorded population activity are the representations c (and z), while locally computed prediction errors could in principle remain observable as more circumscribed or transient mismatch-like signals within a circuit.

      We would like to push this point further. The reviewer frames this as a tension that RPL needs to resolve, but growing neurophysiological evidence suggests that classical residual-difference prediction errors may not be a dominant mode of cortical encoding in the first place. Furutachi, Franklin, et al. (2024) showed that V1 responses to unexpected visual stimuli do not encode how input deviates from predictions, but instead selectively amplify the representation of the unexpected stimulus itself. Very recently, Furutachi and Hofer (2026) generalize this into a revised framework in which feedforward pathways transmit sensory representations modulated by prediction-error magnitude, rather than residual differences. Vasilevskaya et al. (2026) constrain the space of plausible cortical algorithms via functionalinfluence experiments, also concluding that no variant of standard predictive processing is consistent with the full pattern of layer 2/3 ↔ layer 5 interactions; they propose a JEPA-based model, citing RPL as a promising candidate. The model by Nejad et al. (2025) similarly shares with RPL the property that representations, rather than residual errors, propagate between circuit elements.

      Taken together, the apparent tension may be less a problem RPL needs to resolve than one it is well positioned to explain, remaining consistent with the emerging picture of cortex as encoding amplified sensory features rather than transmitting residual errors across areas.

      What we will do: We will add missing information to the main text and sharpen the Discussion with these arguments.

      (1.6) Successor representation without value? I believe the term successor representation is historically relevant in a reinforcement learning (RL) setting and has a precise mathematical definition. Without RL, I feel that learning successor representation is conceptually identical to learning a transition matrix (aka, a primitive world model). I therefore wonder if the pitch for high-level framing of the successor representation is appropriately described or trivial.

      The reviewer makes a valid point on the concept of successor representations. To answer the immediate question, it is not entirely trivial, as we not only observe the emergence of the transition structure (Fig. 6c), but also the encoding of decaying future (but not past) state occupancy (Fig 6d,e). We largely adapted the terminology “successor-like representations” from the study by (Ekman et al., 2023), but we will elaborate a bit further for why we stuck to it. As nicely pointed out by the reviewer, the term “successor representations” was introduced in the RL literature (Dayan, 1993), but further adopted in neuroscience to describe the idea that a neuronal population encodes a predictive representation that reflects the expected future occupancy of future states under a given policy. Ekman et al. (2023) use the term “successor-like representations” to explain the phenomena where the neural activity in V1 (and hippocampus) represent both current and (discounted) future, but not past, state occupancies in a sequence learning task with no explicitly defined policy or value training. In other words, successor-like representations are simply predictive representations.

      What we will do: To deal with this dichotomy, we will replace “successor-like representations” with the term “predictive representations” in the abstract and clarify this distinction in the Results section of the revised manuscript.

      (1.7) Learning in RNN: Learning with recurrent networks appears to be a key in this model presented here (it is in the algorithm name). Yet, this aspect of the model and the literature on biologically plausible learning rules for RNN is not really discussed.

      We thank the reviewer for raising this concern. While h-RPL is one step toward more biologically plausible and spatially local learning rules, exploring it further in terms of temporal credit assignment is beyond the scope of the present study and would require a more systematic and in-depth analysis. However, moving toward more biologically plausible learning rules is an interesting research direction that we plan to explore, as we also mentioned in the Discussion (“Limitations and future research directions”).

      We think a viable strategy could be to combine a slim spatial credit assignment strategy such as feedback alignment (Nøkland, 2016; Lillicrap et al., 2016) with an online learning rule using eligibility traces for temporal credit assignment such as SuperSpike (Zenke et al., 2018) or e-prop (Bellec et al., 2020). Similar strategies have given promising results for CLAPP (Illing et al., 2021; Zihan et al., 2026).

      What we will do: Following the suggestion, we will discuss biologically plausible learning rules for RNNs in the Discussion.

      Reviewer #2 (Public review):

      This is a very interesting manuscript, which proposes a novel idea on how cortical networks may learn useful representations of sensory stimuli. The model implementing this idea is thoroughly tested in multiple experimental paradigms. The manuscript is very clearly written. I feel it may have a significant impact on our understanding of cortical circuitry.

      Reviewer #3 (Public review):

      This paper presents Recurrent Predictive Learning (RPL), a self-supervised model conceptually similar to Joint-Embedding Predictive Architecture (JEPA) models. RPL sequentially observes dynamic scenes to predict subsequent observations. A central claim of the work is that the model’s trained representations are simultaneously invariant and equivariant to transformations, such as movement properties that emerge without explicit supervision. These representational qualities are demonstrated through three experiments utilizing two simulated datasets and one naturalistic dataset. Furthermore, the latent embeddings are qualitatively compared with neural data, showing that the model reproduces the successor representation observed in human V1 and the local/global oddball effect in the monkey Prefrontal Cortex.

      The paper addresses a fundamental question relevant to both computational neuroscience and machine vision: how the brain learns representations that are simultaneously invariant and equivariant to transformations. The manuscript is well-written, easy to follow, and supported by clear visualizations.

      While JEPA-style models have recently gained significant traction in the artificial intelligence community, this paper nicely bridges the gap to neuroscience. By framing these architectures as a theory for visual learning in the brain, the authors provide valuable insights into how predictive frameworks can explain cortical processing.

      The qualitative alignment with V1 and PFC data is a particularly strong contribution, as it offers a potential mechanistic explanation for observed neural phenomena through the lens of selfsupervised learning.

      (3.1) The central claim, that both invariance and equivariance emerge spontaneously, requires further scrutiny (see Ghaemi et al., NeurIPS, 2025; Garrido et al., arXive, 2024). In particular, the synthetic ”moving animal” dataset used in this paper may be too simple to fully support this claim. In latent space prediction, a model must predict both the scene content and the dynamics of movement. Because movement (whether ego-motion or external) is often highly uncertain (or multi-modal), predictive models in naturalistic settings often ”collapse” toward learning purely invariant representations, ignoring the hard-to-predict dynamics. In the provided simulations, the movements are extremely predictable. In more complex scenarios, the model would likely prioritize content (invariance) over dynamics (equivariance) unless aided by action-conditioning or explicit factor estimation (Zhang et al., ICLR, 2026). The authors’ results in Figure 5 using naturalistic video seem to reflect this limitation, given the lower performance on the naturalistic videos compared to the synthetic datasets.

      We thank the reviewer for the feedback. We agree that further validation on more complex datasets would strengthen the claims, and we take this point seriously. If the reviewer has any suggestions for a specific alternative dataset, we would welcome any recommendations.

      Regarding the mouse video data specifically, we realized that this is a suboptimal benchmark rather than a shortcoming of our method. The culprit presumably is that the mice remain largely stationary, leading to a heavily imbalanced velocity distribution peaked near zero (Supplementary Fig. S9). This imbalance makes equivariance evaluation unreliable regardless of the learning algorithm. For example, end-to-end supervised training results in an R<sup>2</sup> of 0.19 compared to 0.08 ± 0.02 for RPL.

      Regarding the moving animal dataset, we note that the dynamics are not trivial from an SSL perspective: unlike moving MNIST (Srivastava et al., 2015), the dataset includes changes in scale and orientation, both features that invariance-focused SSL models can easily ignore, yet RPL recovers reliably. For example, this discrepancy can be seen in Supplementary Table S1 where we compare to InfoNCE and CPC. That said, we acknowledge the reviewer’s broader concern and will seek to validate RPL on more complex datasets.

      While it would be nice to compare to related work by Ghaemi et al. (2024), this study used 3DIEBench (Garrido et al., 2023). Unfortunately, 3DIEBench’s reliance on pair-based representations with annotated but random augmentations (such as rotations or color changes) precludes the possibility of smooth latent traversals that would be required for RPL to learn from the same dataset. We will look into whether it is computationally feasible to adapt or regenerate a similar dataset that meets the requirements for temporal prediction.

      Regarding stochasticity, we agree that predictive learning in latent space is most natural in approximately deterministic settings, whereas real world sensory information often comprises non-deterministic elements. While a deeper treatment of such stochastic environments is beyond the scope of the present manuscript, it will be the focus of ongoing and future work. Regarding ongoing work, it is worth mentioning that in recent work from our group (Hauri et al., 2026), we have demonstrated that RPL’s core objective can replace the reconstruction loss in Dreamer, achieving competitive performance in complex, stochastic environments. While we did not systematically evaluate equivariance in this study, the results suggests that representation-space predictive learning is viable beyond the deterministic regime.

      What we will do: We will make the point about the real-world mouse video dataset being a poor benchmark and include the additional R<sup>2</sup> values to show that. Further, we will try to identify or generate alternative datasets to back the equivariance claims and discuss our findings in the light of previous work, e.g., Ghaemi et al. (2024). Moreover, we will sharpen our discussion of our model’s limitations in stochastic settings and highlight notable connections to related work.

      (3.2) The framing of the RPL model as an entirely new theory of representation learning is slightly overstated. The focus on prediction in representation space rather than input space is the defining characteristic of JEPA and various other Self-Supervised Learning (SSL) models, even sequential prediction. While this paper clarifies the connection between these AI frameworks and cortical circuits, the work would be strengthened by more explicitly positioning RPL within the context of existing JEPA-style models and prior SSL theories of the visual system.

      Thanks for raising this point. We are unsure what the reviewer refers to. We did not frame our work as ”an entirely new theory of representation learning,” as the reviewer suggests. In fact, we highlight quite the opposite already in the title of our article, which reads: “Understanding neural circuit principles for representation learning through joint-embedding predictive architectures.” We do not claim novelty over JEPA as an ML paradigm, we adopt it precisely because it provides a principled, non-generative framework for predictive representation learning, and our goal is to develop a circuit level instantiation that accounts for neural circuit computation. We already discuss a body of previous work of self-supervised learning and JEPAs at length. Since the reviewer did not specify what they are missing, we will briefly reiterate what is already there.

      Our contribution is a theory of representation learning in the brain, built on JEPAs as the underlying ML framework. The Title and Introduction already position our work quite explicitly this way. Specifically, we mention prior work on JEPAs (CPC, BYOL, SimSiam, I-JEPA, seq-JEPA, V-JEPA, V-JEPA 2), while noting that “most JEPAs developed in machine learning are poor models of cortical computation” because of their reliance on negative sampling, transformers, masking, static images, and/or known parametrized transformations, and motivate RPL as the minimal candidate that “must instead rely on recurrent neural dynamics, learn from streaming sensory input without masking, support both invariant and equivariant representations, and reproduce key neurophysiological observations.”

      The Discussion (“Relation to previous modeling work”) further details the specific novelties of RPL relative to existing sequential JEPA-style and SSL models like CPC (Oord et al., 2018), V-JEPA (Bardes et al., 2024), V-JEPA 2 (Assran et al., 2025), seq-JEPA (Ghaemi et al., 2024). In brief:

      RPL is a recurrent JEPA based on RNN dynamics, not transformers, and learns from streaming sensory input without masking or random negative sampling;

      It explicitly compares three prediction-error topologies (RPL vs. invariance learning vs. contextprediction; Fig. 2, Suppl. Fig. S2, S6) and shows that asymmetric recurrent prediction is essential for jointly learning invariant and equivariant representations;

      Importantly, it does so via pure temporal prediction without access to underlying transformations, a property shared by very few JEPAs. The closest exception is VJ-VCR (Drozdov et al., 2024) which uses an explicit variance-covariance regularization (VCReg) in a JEPA, which we will cite in the revised manuscript;

      It provides the first hierarchical JEPA optimizing local prediction errors at multiple levels (h-RPL, Fig. 8), as envisioned by LeCun (2022) but not previously implemented;

      It connects directly to neurophysiological data: successor-like representations in human V1 and abstract sequence representations in macaque PFC, which provides qualitative correspondence between JEPA components and cortical activity that the existing JEPA literature, focused on ML benchmarks, does not address.

      Finally, our article already includes a discussion paragraph on recent self-supervised learning models in the context of the brain where we discuss work by Nejad et al. (2025) and Asabuki et al. (2025). Most other SSL theories of the visual system rely on static images and recognition tasks (Yerxa et al., 2024; Margalit et al., 2024). However, there are two studies that include temporal prediction objectives and are worth mentioning with more details: First, Bakhtiari et al. (2021) show that representations similar to ventral and dorsal pathways in the visual system can emerge in a two-pathway encoder architecture within the CPC model. Second, Niu et al. (2024) use a “straightening” objective together with VCReg as a practical model of the perceptual straightening hypothesis (H´enaff et al., 2019). Though not a JEPA (i.e., has no predictor network), it can decode equivariant factors in a sequential MNIST dataset where only single factors change throughout a video.

      What we will do: We will carefully review our discussion of previous work and further discuss Drozdov et al. (2024), Bakhtiari et al. (2021), and Niu et al. (2024) in the revised manuscript.

      (3.3) A significant challenge in latent-space SSL is avoiding “representational collapse” (where the model provides a trivial constant output). While the paper alludes to JEPAlike solutions, it lacks a detailed explanation (in both the text and the architectural schematics) of the specific technique used to prevent collapse. Consequently, it is difficult to evaluate the authors’ claim of “biological plausibility,” as the biological equivalents of common machine learning techniques (such as stop gradient) are not discussed.

      Thanks for pointing this out. Our model avoids collapse through the asymmetric stop-grad / predictor architecture. It does not require an EMA, when the predictor learns with a faster learning rate than the rest of the network (see also our response to Point P1.3).

      The use of stop-grad suggests that a circuit learning with RPL needs to compute a vector-based instructive learning signal. While we do not explicitly model the circuit level mechanisms of how this could be implemented in the brain, excitation-inhibition balance is one possibility (Rossbroich et al., 2025). Finally, differences in learning rate can be implemented both structurally or functionally in the brain (see Liu et al. (2025) for instance), or activity normalization is suggested as a canonical computation in biological neural circuits (Carandini et al., 2012).

      What we will do: We will make sure to discuss these putative biological mechanisms in the revised manuscript.

      (3.4) Recent work has shown that the capacity (size) of the predictor significantly influences the learned representations in a JEPA-type world model (Gorrido et al., 2024). In simpler scenarios, a large enough predictor can allow a model to ”memorize” dynamics rather than learning generalized equivariant features. It would be beneficial to see how the ratio of predictor size to encoder size affects the emergence of these features.

      Thanks for raising this concern. We don’t observe noticeable difference in position and velocity decoding when changing the width or depth of the MLP predictor in the moving animals data. However, performance on rotation speed and orientation decoding scales with the changes in width, but not depth of the predictor. This analysis excludes the effect of integrator’s capacity as it directly affects the dimensionality of the representations, even though it also effectively contributes to prediction computation in RPL.

      What we will do: We will include a figure how how task performance varies with the predictor’s width and depth.

      Methodological Clarifications

      (3.5) The authors mention a contrastive learning comparison but provide few details. Since contrastive learning is primarily a technique to avoid collapse, it would be a more rigorous baseline if implemented within the same architecture as RPL to isolate the effect of the predictive objective.

      Thanks for the question. We already use the same network model as in RPL for the contrastive predictive learning (InfoNCE) baseline in Supplementary Table S1 and mentioned in the main text (l.164).

      What we will do: We will mention the architecture of the non-linear predictor used for InfoNCE baseline in Methods more explicitly.

      (3.6) In the PFC data comparison (Figure 7f), there appears to be a discrepancy where the local and global conditions show nearly identical results in PFC, while different dynamics in the model. It is unclear if this is a visualization error or a genuine model deviation.

      Thanks for picking up on this subtlety in the experimental results. To clarify, it is a model deviation but an interesting one. The local and global responses do look quite similar in the original PFC data. They differ in that the global oddball (xY|xx and xx|xY) response has a secondary peak that encodes the presence of the global oddball, whereas the initial response is actually dominated by local oddball encoding (xY vs xx). Concretely, this results in the response to the xx|xY condition only showing up weakly in the data and at a time lag with respect to the initial local oddball response. Our model, however, does not show the transient initial response to local oddballs in the decoding direction for global oddballs. In a sense, the network model encodes the global oddball concept more robustly than is seen in the PFC data. That said, whether this indicates a genuine difference in representational strategies that needs to be further accounted for, or whether it is an issue stemming from limited sub-sampling of PFC neurons, remains unclear.

      (3.7) The criteria for selecting specific model variables for comparison with V1 versus PFC are not explicitly defined. Clarification is needed on whether the same latent variables were used for both brain regions or if different layers were selected.

      To clarify, the successor-like representations in human V1 and abstract representations in macaque PFC are two different experiments, so each has different latent variables requiring different RPL models. The architecture used for each experiment is detailed in Methods and the criteria for selecting each architecture was the simplest that should work given the task complexity. Throughout the paper, all representation analysis is done on the output of integrator (c) unless said otherwise. We hope this resolves the confusion.

      References

      Chen, Xinlei et al. (2021). “Exploring simple siamese representation learning”. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 15750–15758.

      Srinath Halvagal, Manu et al. (2023). “Implicit variance regularization in non-contrastive SSL”. In: Advances in Neural Information Processing Systems 36, pp. 63409–63436.

      Mikulasch, Fabian A et al. (2026). Understanding Self-Supervised Learning via Latent Distribution Matching. arXiv: 2605.03517[cs.LG].

      Furutachi, Shohei, Alexis D. Franklin, et al. (Sept. 2024). “Cooperative thalamocortical circuit mechanism for sensory prediction errors”. en. In: Nature 633.8029. Publisher: Nature Publishing Group, pp. 398–406. issn: 1476-4687. doi: 10.1038/s41586-024-07851-w.

      Furutachi, Shohei and Sonja B Hofer (2026). “Rethinking Predictive Processing”. In: Annual Review of Neuroscience 49.

      Vasilevskaya, Anna et al. (2026). “A functional influence based circuit motif that constrains the set of plausible algorithms of cortical function”. In: bioRxiv. doi: 10.64898/2026.01.29.702557. eprint: https://www.biorxiv.org/content/early/2026/01/29/2026.01.29.702557.full. pdf.

      Nejad, Kevin Kermani et al. (July 2025). “Self-supervised predictive learning accounts for cortical layer-specificity”. en. In: Nat Commun 16.1, p. 6178. issn: 2041-1723. doi: 10.1038/s41467-025-61399-5.

      Ekman, Matthias et al. (Feb. 2023). “Successor-like representation guides the prediction of future events in human visual cortex and hippocampus”. In: eLife 12. Ed. by Morgan Barense et al., e78904. issn: 2050-084X. doi: 10.7554/eLife.78904.

      Dayan, Peter (1993). “Improving generalization for temporal difference learning: The successor representation”. In: Neural computation 5.4, pp. 613–624.

      Nøkland, Arild (2016). “Direct feedback alignment provides learning in deep neural networks”. In: Advances in neural information processing systems 29.

      Lillicrap, Timothy P et al. (2016). “Random synaptic feedback weights support error backpropagation for deep learning”. In: Nature communications 7.1, p. 13276.

      Zenke, Friedemann et al. (2018). “Superspike: Supervised learning in multilayer spiking neural networks”. In: Neural computation 30.6, pp. 1514–1541.

      Bellec, Guillaume et al. (2020). “A solution to the learning dilemma for recurrent networks of spiking neurons”. In: Nature communications 11.1, p. 3625.

      Illing, Bernd et al. (2021). “Local plasticity rules can learn deep representations using self-supervised contrastive predictions”. In: Advances in Neural Information Processing Systems 34.

      Zihan, Wu S et al. (2026). “Can Local Learning Match Self-Supervised Backpropagation?” In: arXiv preprint arXiv:2601.21683.

      Srivastava, Nitish et al. (2015). “Unsupervised learning of video representations using lstms”. In: International conference on machine learning. PMLR, pp. 843–852.

      Ghaemi, Hafez et al. (2024). “Seq-JEPA: Autoregressive Predictive Learning of Invariant-Equivariant World Models”. In: NeurIPS 2024 Workshop: Self-Supervised Learning - Theory and Practice.

      Garrido, Quentin et al. (2023). “Self-supervised learning of split invariant equivariant representations”. In: arXiv preprint arXiv:2302.10283.

      Hauri, Michael et al. (2026). “Dreamer-CDP: Improving Reconstruction-free World Models Via Continuous Deterministic Representation Prediction”. In: arXiv preprint arXiv:2603.07083.

      Oord, Aaron van den et al. (July 2018). “Representation Learning with Contrastive Predictive Coding”. In: arXiv:1807.03748 [cs, stat]. arXiv: 1807.03748.

      Bardes, Adrien et al. (2024). V-JEPA: Latent Video Prediction for Visual Representation Learning.

      Assran, Mido et al. (2025). “V-jepa 2: Self-supervised video models enable understanding, prediction and planning”. In: arXiv preprint arXiv:2506.09985.

      Drozdov, Katrina et al. (2024). “Video representation learning with joint-embedding predictive architectures”. In: arXiv preprint arXiv:2412.10925.

      LeCun, Yann (2022). “A Path Towards Autonomous Machine Intelligence Version 0.9.2, 2022-0627”. en. In.

      Asabuki, Toshitake et al. (2025). “Learning predictive signals within a local recurrent circuit”. In: Proceedings of the National Academy of Sciences 122.27, e2414674122. doi: 10.1073/pnas. 2414674122. eprint: https://www.pnas.org/doi/pdf/10.1073/pnas.2414674122.

      Yerxa, Thomas et al. (2024). “Contrastive-equivariant self-supervised learning improves alignment with primate visual area it”. In: Advances in neural information processing systems 37, pp. 96045–96070.

      Margalit, Eshed et al. (2024). “A unifying framework for functional organization in early and higher ventral visual cortex”. In: Neuron 112.14, pp. 2435–2451.

      Bakhtiari, Shahab et al. (2021). “The functional specialization of visual cortex emerges from training parallel pathways with self-supervised predictive learning”. In: Advances in Neural Information Processing Systems. Ed. by M. Ranzato et al. Vol. 34. Curran Associates, Inc., pp. 25164–25178.

      Niu, Julie Xueyan et al. (2024). “Learning predictable and robust neural representations by straightening image sequences”. In: Advances in Neural Information Processing Systems 37, pp. 40316– 40335.

      H´enaff, Olivier J et al. (2019). “Perceptual straightening of natural videos”. In: Nature neuroscience 22.6, pp. 984–991.

      Rossbroich, Julian et al. (2025). “Breaking Balance: Encoding local error signals in perturbations of excitation-inhibition balance”. In: bioRxiv, pp. 2025–05.

      Liu, Peng et al. (2025). “Layer-specific changes in sensory cortex across the lifespan in mice and humans”. In: Nature neuroscience 28.9, pp. 1978–1989.

      Carandini, Matteo et al. (2012). “Normalization as a canonical neural computation”. In: Nature reviews neuroscience 13.1, pp. 51–62.

    1. Reviewer #1 (Public review):

      The manuscript shows that different traits of adults and larvae correlate with Red List status. The authors argue that this shows a big gap in the conservation of amphibians and that the traits of all life stages should be taken into account in amphibian conservation. Specifically, amphibian conservation should do more for the habitats where the larvae live.

      The manuscript is well written and easy to understand. The methods are sound.

      While the study will make an interesting contribution to conservation science, there are many things that I disagree with.

      I don't think that amphibian larvae and their requirements are a "blind spot" as the title suggests. When reading the manuscript, I didn't learn how conservation practice should change in response to the results.

      I wonder whether the relationship between species traits and extinction risk is of great importance for conservation. If a species is Data Deficient on the IUCN Red List, then species traits could be used to predict its Red List category. However, for other conservation projects, I don't see how this would work. How would traits be linked to captive breeding, conservation translocation, pond construction or habitat management in general? In some cases, I can envision a link between species traits and pond hydroperiod.

      Species traits are body size and morphological traits. That makes sense. However, one of the species traits was microhabitat. I find it far-fetched to call habitat a species trait. This is standard habitat ecology. It is well known that habitats matter and that different habitat types face different threats, and consequently, the species that live in those habitats. Furthermore, habitat and morphology may be confounded. For example, tadpoles in lentic and lotic habitats have very different morphologies. So is it habitat or morphology?

      I don't know how the threat status of Chinese amphibians is determined. IUCN has multiple reasons why a species can be Red Listed. One reason is range size, and another reason is population decline. Personally, I don't think they should be pooled in an analysis because they are fundamentally different reasons why a species has a high extinction risk. A reduction in population size of greater than 30% in 10 years or 3 generations is not the same thing as a small distribution range. Another issue is that IUCN developed the Green Status of species. The Green Status shows that even a species which is LC on the Red List may be significantly depleted.

      The species traits in Table 1 are mostly functional/morphological and body size related (and microhabitat). While there may be correlations between traits and Red List status, it is unknown whether this is correlation or causation. In addition, it is difficult to know the conservation interventions that may be necessary now that we know that relative head with and Red List status are correlated.

      In the discussion, the authors explain why body size and other traits may affect extinction risk and whether there is a causal relationship. I agree that body size may have a direct effect because larger species are harvested more frequently (it was interesting to learn that tadpoles are harvested as well). However, as macroecological studies show, smaller species often have larger populations than larger species. Abundance may matter.

      I found it much harder to understand why relative head length and tympanum size correlated with Red List status. I wasn't convinced by the arguments in the discussion. Typanum size may be related to hearing and anthropogenic noise. Several studies are cited which show that frogs alter their calling behaviour in response to noise. Crucially, however, they describe changes in behaviour or properties of the advertisement call, yet none show that noise has effects on population viability. If some anthropogenic stressor affects individuals, then this does not mean that it will cause a population decline. When IUCN published the second global amphibian assessment, did they list noise as a major threat to amphibians?

      There are statements that the tadpole stage is the most important stage: "a critical period for amphibian survival" (line 78-79). While there is high mortality in the tadpole stage, tadpole survival is rather unlikely to affect population survival. Many population models show this. See, for example, Biek et al. 2002 in Conservation Biology. Other papers have argued that the postmetamorphic juvenile stage is most important (Petrovan and Schmidt 2009 Biological Conservation).

      The authors repeatedly make the statement that amphibian conservation should focus more on the tadpole stage. I don't understand why this statement is made. For example, a major activity in amphibian conservation is the restoration and de novo construction of ponds (see Calhoun et al. 2014 PNAS, Moor et al. 2022 PNAS). Ponds are habitats for tadpoles. Others removed fish from amphibian breeding sites because fish prey on tadpoles (and adults; see Vredenburg 2004 PNAS). Semlitsch (2002 in Conservation Biology) argued that the management of pond hydroperiod is a critical element of amphibian recovery plans. Ponds should be temporary because this effectively removes predators that consume tadpoles. Clearly, the tadpole stage is not a neglected stage in amphibian conservation.

    1. Author response:

      The following is the authors’ response to the original reviews

      eLife Assessment

      This important study fills a major geographic and temporal gap in understanding Paleocene mammal evolution in Asia and proposes an intriguing "brawn before bite" hypothesis grounded in diverse analytical approaches. However, the findings are incomplete because limitations in sampling design - such as the use of worn or damaged teeth, the pooling of different tooth positions, and the lack of independence among teeth from the same individuals - introduce uncertainties that weaken support for the reported disparity patterns. The taxonomic focus on predominantly herbivorous clades also narrows the ecological scope of the results. Clarifying methodological choices, expanding the ecological context, and tempering evolutionary interpretations would substantially strengthen the study.

      We have now thoroughly revised our manuscript in response to the editor and reviewer’s comments. In particular with regard to:

      (1) Sampling design: we clarified our methods section to indicate that we did not use worn or broken teeth in our initial analyses. We added the following sentence around line 690:

      “These tooth positions were selected from a broader examination of ~300 individual teeth from 72 specimens. We vetted the specimens and excluded 99 tooth positions (~33% of teeth initially chosen for possible inclusion) from our analyses because they either (1) were partially or completely broken at the crown, (2) were in an advanced stage of attritional wear where no cusps could be identified, or (3) possessed a combination of the two aforementioned conditions.”

      (2) Pooled versus by-tooth position analyses: we repeated the three major analyses (DTA & FEA variability through time, tooth size and variability through time, and DTA-FEA correlation through time) for individual molars (upper M1-3, lower m1-3) and select premolars (upper P3-P4 and lower p4; lower and upper p2 samples contained fewer than 5 specimens across the three time intervals, lower p3 contained only 2 specimens for the middle Paleocene, so they were excluded from the sub-partition analyses).

      For DTA & FEA variability through time (summarized as a new figure, Fig. S5, also pasted below), OPCR, DNE, and FEA trait data are supported in 78-100% of the per-tooth analyses for both the early-middle Paleocene and middle-late comparisons. By contrast, RFI and Slope data are replicated in only 22-56% of the per-tooth analyses. We qualified the main text reporting and discussion to include these sensitivity analyses so readers can assess nuances in the data when comparing pooled sample versus per-tooth analyses.

      For tooth size and variability through time (summarized in a new table, Table S3, also pasted below), we observed broad concordance in the pooled analyses and the per-tooth partitioned analyses. Different tooth positions provide strong support for different aspects of the observed trends, with the lower fourth premolar being the strongest driver of the overall trend. All of the significant trends in per-tooth analyses are in the same direction (i.e., decreasing size disparity and size mean through time) as the pooled sample. We added qualifying clarification in the text to bring attention to these refined results.

      For DTA-FEA correlation through time, we generated per-tooth correlation plots in three new figures (Figs. S9-11, only Fig. S10 shown here as an example). We observed that upper M1 patterns general reflect the trend recovered from analysis of the overall dataset, but M2 and M3 results display inconsistent DTA-FEA correlations, possibly due to small sample sizes. Lower molar patterns generally replicate those recovered in the overall analyses, but lower M1 and M2 signals appear to be stronger than those for lower M3. Finally, low sample sizes make premolar correlations unstable, with general pattern showing EP-MP strengthening then MP-LP stasis or weakening. Given these findings, it appears that the results in the pooled sample correlation plots are mainly driven by lower molar signals. It is not possible to conclude the other tooth position display different patterns because of the limited sample sizes.

      (3) Ecological scope of the study: although carnivorans and mesonychids are recorded from some of the time intervals examined in this study, our sampling choice of pantodonts and anagalids reflects the high abundance of available dental specimens in those clades, permitting us to make the strongest statistical inference given the incomplete fossil record. Additionally, all sampled taxa come from archaic clades that have not been determined to be specifically herbivorous; we included an additional paragraph in the introduction to explain this:

      “A major challenge with expanding analyses of post K-Pg recovery to Paleocene mammal assemblages elsewhere in the world is the generally stratigraphically limited nature of early Cenozoic sequences. In Asia, Paleocene localities in China represent the best studied to date[11]. From the earliest Paleocene, highly regional and endemic faunas are known from a handful of sedimentary basins (Fig. S1A). Among the faunal elements, only the archaic clades Anagalida and Pantodonta are consistently sampled across the major subdivisions of the Paleocene[11]. An additional complication with ecomorphological analysis of these early mammals is the uncertainty in their dietary ecology, as they are beyond the reach of conventional phylogenetic bracketing approaches to dietary reconstruction. Phenomic analysis of the placental radiation supports insectivory as the ancestral diet of the hypothetical placental ancestor, but uncertainty in the post K-Pg availability of insects and plants in some regions leave some doubt as to the accuracy of this ancestral state reconstruction[1]. Herein we treat the archaic Paleocene taxa in our analyses as having generalized diets rather than categorizing them as insectivores, herbivores, or carnivores.”

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This work provides valuable new insights into the Paleocene Asian mammal recovery and diversification dynamics during the first ten million years post-dinosaur extinction. Studies that have examined the mammalian recovery and diversification post-dinosaur extinction have primarily focused on the North American mammal fossil record, and it's unclear if patterns documented in North America are characteristic of global patterns. This study examines dietary metrics of Paleocene Asian mammals and found that there is a body size disparity increase before dietary niche expansion and that dietary metrics track climatic and paleobotanical trends of Asia during the first 10 million years after the dinosaur extinction.

      Strengths:

      The Asian Paleocene mammal fossil record is greatly understudied, and this work begins to fill important gaps. In particular, the use of interdisciplinary data (i.e., climatic and paleobotanical) is really interesting in conjunction with observed dietary metric trends.

      Weaknesses:

      While this work has the potential to be exciting and contribute greatly to our understanding of mammalian evolution during the first 10 million years post-dinosaur extinction, the major weakness is in the dental topographic analysis (DTA) dataset.

      There are several specimens in Figure 1 that have broken cusps, deep wear facets, and general abrasion. Thus, any values generated from DTA are not accurate and cannot be used to support their claims. Furthermore, the authors analyze all tooth positions at once, which makes this study seem comprehensive (200 individual teeth), but it's unclear what sort of noise this introduces to the study. Typically, DTA studies will analyze a singular tooth position (e.g., Pampush et al. 2018 Biol. J. Linn. Soc.), allowing for more meaningful comparisons and an understanding of what value differences mean. Even so, the dataset consists of only 48 specimens. This means that even if all the specimens were pristinely preserved and generated DTA values could be trusted, it's still only 48 specimens (representing 4 different clades) to capture patterns across 10 million years. For example, the authors note that their results show an increase in OPCR and DNE values from the middle to the late Paleocene in pantodonts. However, if a singular tooth position is analyzed, such as the lower second molar, the middle and late Paleocene partitions are only represented by a singular specimen each. With a sample size this small, it's unlikely that the authors are capturing real trends, which makes the claims of this study highly questionable.

      With regard to sampling design: we clarified our methods section to indicate that we did not use worn or broken teeth in our initial analyses. We added the following sentence around line 690:

      “These tooth positions were selected from a broader examination of ~300 individual teeth from 72 specimens. We vetted the specimens and excluded 99 tooth positions (~33% of teeth initially chosen for possible inclusion) from our analyses because they either (1) were partially or completely broken at the crown, (2) were in an advanced stage of attritional wear where no cusps could be identified, or (3) possessed a combination of the two aforementioned conditions.”

      With regard to pooled versus by-tooth position analyses: we repeated the three major analyses (DTA & FEA variability through time, tooth size and variability through time, and DTA-FEA correlation through time) for individual molars (upper M1-3, lower m1-3) and select premolars (upper P3-P4 and lower p4; lower and upper p2 samples contained fewer than 5 specimens across the three time intervals, lower p3 contained only 2 specimens for the middle Paleocene, so they were excluded from the sub-partition analyses).

      For DTA & FEA variability through time (summarized as a new figure, Fig. S5, also pasted below), OPCR, DNE, and FEA trait data are supported in 78-100% of the per-tooth analyses for both the early-middle Paleocene and middle-late comparisons. By contrast, RFI and Slope data are replicated in only 22-56% of the per-tooth analyses. We qualified the main text reporting and discussion to include these sensitivity analyses so readers can assess nuances in the data when comparing pooled sample versus per-tooth analyses.

      For the tooth size and variability through time (summarized in a new table, Table S3, also pasted below), we observed broad concordance in the pooled analyses and the per-tooth partitioned analyses. Different tooth positions provide strong support for different aspects of the observed trends, with the lower fourth premolar being the strongest driver of the overall trend. All of the significant trends in per-tooth analyses are in the same direction (i.e., decreasing size disparity and size mean through time) as the pooled sample. We added qualifying clarification in the text to bring attention to these refined results.

      For DTA-FEA correlation through time, we generated per-tooth correlation plots in three new figures (Figs. S8-10, only Fig. S9 shown here as an example). We observed that upper M1 patterns general reflect the trend recovered from analysis of the overall dataset, but M2 and M3 results display inconsistent DTA-FEA correlations, possibly due to small sample sizes. Lower molar patterns generally replicate those recovered in the overall analyses, but lower M1 and M2 signals appear to be stronger than those for lower M3. Finally, low sample sizes make premolar correlations unstable, with general pattern showing EP-MP strengthening then MP-LP stasis or weakening. Given these findings, it appears that the results in the pooled sample correlation plots are mainly driven by lower molar signals. It is not possible to conclude the other tooth position display different patterns because of the limited sample sizes.

      Reviewer #2 (Public review):

      Summary:

      This study uses dental traits of a large sample of Chinese mammals to track evolutionary patterns through the Paleocene. It presents and argues for a 'brawn before bite' hypothesis - mammals increased in body size disparity before evolving more specialized or adapted dentitions. The study makes use of an impressive array of analyses, including dental topographic, finite element, and integration analyses, which help to provide a unique insight into mammalian evolutionary patterns.

      Strengths:

      This paper helps to fill in a major gap in our knowledge of Paleocene mammal patterns in Asia, which is especially important because of the diversification of placentals at that time. The total sample of teeth is impressive and required considerable effort for scanning and analyzing. And there is a wealth of results for DTA, FEA, and integration analyses. Further, some of the results are especially interesting, such as the novel 'brawn before bite' hypothesis and the possible link between shifts in dental traits and arid environments in the Late Paleocene. Overall, I enjoyed reading the paper, and I think the results will be of interest to a broad audience.

      Weaknesses:

      I have four major concerns with the study, especially related to the sampling of teeth and taxa, that I discuss in more detail below. Due to these issues, I believe that the study is incomplete in its support of the 'brawn before bite' hypothesis. Although my concerns are significant, many of them can be addressed with some simple updates/revisions to analyses or text, and I try to provide constructive advice throughout my review.

      (1) If I understand correctly, teeth of different tooth positions (e.g., premolars and molars), and those from the same specimen, are lumped into the same analyses. And unless I missed it, no justification is given for these methodological choices (besides testing for differences in proportions of tooth positions per time bin; L902). I think this creates some major statistical concerns. For example, DTA values for premolars and molars aren't directly comparable (I don't think?) because they have different functions (e.g., greater grinding function for molars). My recommendation is to perform different disparity-through-time analyses for each tooth position, assuming the sample sizes are big enough per time bin. Or, if the authors maintain their current methods/results, they should provide justification in the main text for that choice.

      With regard to pooled versus by-tooth position analyses: we repeated the three major analyses (DTA & FEA variability through time, tooth size and variability through time, and DTA-FEA correlation through time) for individual molars (upper M1-3, lower m1-3) and select premolars (upper P3-P4 and lower p4; lower and upper p2 samples contained fewer than 5 specimens across the three time intervals, lower p3 contained only 2 specimens for the middle Paleocene, so they were excluded from the sub-partition analyses).

      For DTA & FEA variability through time (summarized as a new figure, Fig. S5, also pasted below), OPCR, DNE, and FEA trait data are supported in 78-100% of the per-tooth analyses for both the early-middle Paleocene and middle-late comparisons. By contrast, RFI and Slope data are replicated in only 22-56% of the per-tooth analyses. We qualified the main text reporting and discussion to include these sensitivity analyses so readers can assess nuances in the data when comparing pooled sample versus per-tooth analyses.

      For the tooth size and variability through time (summarized in a new table, Table S3, also pasted below), we observed broad concordance in the pooled analyses and the per-tooth partitioned analyses. Different tooth positions provide strong support for different aspects of the observed trends, with the lower fourth premolar being the strongest driver of the overall trend. All of the significant trends in per-tooth analyses are in the same direction (i.e., decreasing size disparity and size mean through time) as the pooled sample. We added qualifying clarification in the text to bring attention to these refined results.

      For DTA-FEA correlation through time, we generated per-tooth correlation plots in three new figures (Figs. S8-10, only Fig. S9 shown here as an example). We observed that upper M1 patterns general reflect the trend recovered from analysis of the overall dataset, but M2 and M3 results display inconsistent DTA-FEA correlations, possibly due to small sample sizes. Lower molar patterns generally replicate those recovered in the overall analyses, but lower M1 and M2 signals appear to be stronger than those for lower M3. Finally, low sample sizes make premolar correlations unstable, with general pattern showing EP-MP strengthening then MP-LP stasis or weakening. Given these findings, it appears that the results in the pooled sample correlation plots are mainly driven by lower molar signals. It is not possible to conclude the other tooth position display different patterns because of the limited sample sizes.

      Also, I think lumping teeth from the same specimen into your analyses creates a major statistical concern because the observations aren't independent. In other words, the teeth of the same individual should have relatively similar DTA values, which can greatly bias your results. This is essentially the same issue as phylogenetic non-independence, but taken to a much greater extreme.

      It seems like it'd be much more appropriate to perform specimen-level analyses (e.g., Wilson 2013) or species-level analyses (e.g., Grossnickle & Newham 2016) and report those results in the main text. If the authors believe that their methods are justified, then they should explain this in the text.

      Based on the per-tooth partition analyses we performed and reported above, the results now show that the overall trends described in the previous draft of the study is a composite of signals from different regions of the dentition. For example, the OPCR, DNE, and FEA trends persist across most tooth positions, whereas the Slope and RFI trends are mainly driven by lower fourth premolar patterns. The tooth size results are also mainly driven by lower fourth premolar patterns, but tooth disparity trends are broadly supported across tooth positions. These observations indicate that the overall trends remain valid, but there are nuances as to which tooth positions are driving which components of the trends. As such, we deem the overall results to be valid, and focused our revision on providing the nuances so readers can assess through-time patterns in more detail than in the previous version of the study.

      (2) Maybe I misunderstood, but it sounds like the sampling is almost exclusively clades that are primarily herbivorous/omnivorous (Pantodonta, Arctostylopida, Anagalida, and maybe Tillodonta), which means that the full ecomorphological diversity of the time bins is not being sampled (e.g., insectivores aren't fully sampled). Similarly, the authors say that they "focused sampling" on those major clades and "Additional data were collected on other clades ... opportunistically" (L628). If they favored sampling of specific clades, then doesn't that also bias their results?

      If the study is primarily focused on a few herbivorous clades, then the Introduction should be reframed to reflect this. You could explain that you're specifically tracking herbivore patterns after the K-Pg.

      We appreciate the reviewer’s suggestion that our sampling may have focused on putative herbivorous clades more than others. However, at the early stage of placental evolution during the Paleocene, and in particular among the endemic forms we studied from south China, it is unclear to us that such clearcut ecomorphological categories were present amongst the fossil mammals. Thus, we take a more agnostic approach and do not define the dietary categories of the sample taxa (and by extension, those of the unsampled taxa). Although we recognize that representatives of certain clades, such as Carnivora, may be more reasonably interpreted as carnivores/insectivores/omnivores and, in the current context, remains unsampled, we point out the fact that including tooth samples from rare taxa such as carnivores likely would have biased the analyses temporally. Chinese Paleocene carnivores are known only from one of the three time intervals analyzed (representing only a handful of specimens), and so would potentially inflate the disparity in that time interval relative to the others (if dentitions specialized for carnivory is assumed to be present in the Paleocene). To clarify this point, we added a paragraph in the introduction:

      “A major challenge with expanding analyses of post K-Pg recovery to Paleocene mammal assemblages elsewhere in the world is the generally stratigraphically limited nature of early Cenozoic sequences. In Asia, Paleocene localities in China represent the best studied to date[11]. From the earliest Paleocene, highly regional and endemic faunas are known from a handful of sedimentary basins (Fig. S1A). Among the faunal elements, only the archaic clades Anagalida and Pantodonta are consistently sampled across the major subdivisions of the Paleocene[11]. An additional complication with ecomorphological analysis of these early mammals is the uncertainty in their dietary ecology, as they are beyond the reach of conventional phylogenetic bracketing approaches to dietary reconstruction. Phenomic analysis of the placental radiation supports insectivory as the ancestral diet of the hypothetical placental ancestor, but uncertainty in the post K-Pg availability of insects and plants in some regions leave some doubt as to the accuracy of this ancestral state reconstruction[1]. Herein we treat the archaic Paleocene taxa in our analyses as having generalized diets rather than categorizing them as insectivores, herbivores, or carnivores.”

      (3) There are a lot of topics lacking background information, which makes the paper challenging to read for non-experts. Maybe the authors are hindered by a short word limit. But if they can expand their main text, then I strongly recommend the following:

      a) The authors should discuss diets. Much of the data are diet correlates (DTA values), but diets are almost never mentioned, except in the Methods. For example, the authors say: "An overall shift towards increased dental topographic trait magnitudes ..." (L137). Does that mean there was a shift toward increased herbivory? If so, why not mention the dietary shift? And if most of the sampled taxa are herbivores (see above comment), then shouldn't herbivory be a focal point of the paper?

      We edited the introduction to say that “We used dental topographical traits as indicators of ecomorphological diversity[28] and examined temporal shifts in tooth crown complexity, curvature, and height and their association with tooth performance in terms of deformation resistance using topographic and simulation analyses.” And also added the following to the methods section, in order to clarify that we are using DTA as a general ecomorphological proxy, and not a direct dietary proxy.

      “Overall, we use these DTA traits as indicators of ecomorphological capacity, but do not link them explicitly to dietary categories. The craniodental morphology of archaic placental clades in general have not been demonstrated to share the same structure-function linkages as crown mammals, so the aforementioned linkages between DTA and dietary ecology in extant species only serve as evidence that DTA is a potentially useful ecomorphological proxy, without the application of those DTA-diet relationships to the Paleocene fossil mammal dataset.”

      b) The authors should expand on "we used dentitions as ecological indicators" (L75). For non-experts, how/why are dentitions linked to ecology? And, again, why not mention diet? A strong link between tooth shape and diet is a critical assumption here (and one I'm sure that all mammalogists agree with), but the authors don't provide justification (at least in the Introduction) for that assumption. Many relevant papers cited later in the Methods could be cited in the Introduction (e.g., Evans et al. 2007).

      We added the following sentence to clarify our usage of tooth crowns as ecomorphological proxies: “Teeth are among the most well-preserved parts of fossil mammals, and the fact that they interface directly with the environment through mastication makes them suitable elements for studying potential ecology-morphology linkages.”

      c) Include a better introduction of the sample, such as explicitly stating that your sample only includes placentals (assuming that's the case) and is focused on three major clades. Are non-placentals like multituberculates or stem placentals/eutherians found at Chinese Paleocene fossil localities and not sampled in the study, or are they absent in the sampled area?

      We modified the following sentence to indicate our sampling focus on placentals: “Our analyses focused on placental mammals from three of the most fossiliferous and biogeographically isolated Paleocene sedimentary sequences in paleotropical Asia: The Nanxiong, Qianshan, and Chijiang Basins in present-day south China 23–27 (Fig. S1)”

      d) The way in which "integration" is being used should be defined. That is a loaded term which has been defined in different ways. I also recommend providing more explanation on the integration analyses and what the results mean.

      If the authors don't have space to expand the main text, then they should at least expand on the topics in the supplement, with appropriate citations to the supplement in the main text.

      We replaced all mentions of “integration” with “covariation” to avoid using the loaded terminology. Covariation more accurately reflects the correlation between two sets of traits (DTA vs FEA) without invoking developmental mechanisms implied by modularity/integration.

      (4) Finally, I'm not convinced that the results fully support the 'brawn before bite' hypothesis. I like the hypothesis. However, the 'brawn before ...' part of the hypothesis assumes that body size disparity (L63) increased first, and I don't think that pattern is ever shown. First, body size disparity is never reported or plotted (at least that I could find) - the authors just show the violin plots of the body sizes (Figures 1B, S6A). Second, the authors don't show evidence of an actual increase in body size disparity. Instead, they seem to assume that there was a rapid diversification in the earliest Paleocene, and thus the early Paleocene bin has already "reached maximum saturation" (L148). But what if the body size disparity in the latest Cretaceous was the same as that in the Paleocene? (Although that's unlikely, note that papers like Clauset & Redner 2009 and Grossnickle & Newham 2016 found evidence of greater body size disparity in the latest Cretaceous than is commonly recognized.) Similarly, what if body size disparity increased rapidly in the Eocene? Wouldn't that suggest a 'BITE before brawn' hypothesis? So, without showing when an increase in body size diversity occurred, I don't think that the authors can make a strong argument for 'brawn before [insert any trait]".

      Although it's probably well beyond the scope of the study to add Cretaceous or Eocene data, the authors could at least review literature on body size patterns during those times to provide greater evidence for an earliest Paleocene increase in size disparity.

      We added a sentence in the discussion of body size during the Paleocene to note that the largest late Cretaceous fossil mammals in China are shrew- to gopher-sized, whereas the largest early Paleocene Chinese Endemic Pantodonts are dog-sized:

      “Dog-sized CEPs such as Bemalambda reached sizes not seen in late Cretaceous mammals from China such as Zhangolestes and Kryptobaatar, which are shrew- to gopher-sized [Meng 2014]”

      Reference: Meng, J. (2014). Mesozoic mammals of China: implications for phylogeny and early evolution of mammals. Natl. Sci. Rev. 1, 521–542. 10.1093/nsr/nwu070.

      Furthermore, we tempered our discussion to restrict the “brawn before bite” hypothesis to post K-Pg recovery in the Paleocene. Body size patterns shifted in the Eocene as crown clades replaced the archaic endemic clades analyzed in our study, and much larger taxa began to appear after the PETM. Such body size shift patterns are based on different clades and likely different dynamics compared to the 10-million year interval examined in our study, so we refrain from commenting on post-Paleocene times.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In regard to the DTA dataset: Was there a method used to 'fix' these teeth before dental topographic analyses were implemented? If so, this should be explicitly stated. If not, the authors should explain why broken, worn, or abraded teeth were used.

      We excluded the incomplete teeth from our analyses. We added the following sentence for clarification: “These tooth positions were selected from a broader examination of ~300 individual teeth from 72 specimens. We vetted the specimens and excluded 99 tooth positions (~33% of teeth initially chosen for possible inclusion) from our analyses because they either (1) were partially or completely broken at the crown, (2) were in an advanced stage of attritional wear where no cusps could be identified, or (3) possessed a combination of the two aforementioned conditions.”

      (2) The authors should explicitly explain why all tooth positions were analyzed together. Again, this is not something that is typically done, and some explanation would be helpful for readers.

      We added a paragraph in the methods section to explain both our pooled sampling approach, as well as the per-tooth analyses added in this revised manuscript:

      “Given the rarity of Paleocene fossil material from China, we combined data from different tooth positions into three pooled samples, one for each of the time intervals examined (early, middle, late Paleocene). We treated the pooled samples as representative of the range of dental topographic features and bite performance traits available to the mammal taxa under study. In this way, the variance estimates are interpreted as measures of the morphological and performance heterogeneity present in each time interval dataset. To further tease out the possibility of specific tooth positions driving the overall trends observed in the pooled samples, we also performed the DTA, FEA, DTA-FEA correlation, and tooth size through-time analyses using per-tooth data partitions.”

      (3) I think the authors should hedge their claims a bit more and recognize the limitations of their study (e.g., sample size and tooth preservation).

      We thank the reviewer for raising this important point. We carefully read through the main text and further tempered our interpretations based on the limitations of our data. Additionally, we added a paragraph in the supplemental text to summarize the major sources of uncertainty in the sample:

      “Sample and methodological limitations

      The highly fragmentary nature of early Cenozoic mammal fossils in Asia means that even the best preserved faunas studied herein contain much missing information. First, the absence of a high-resolution chronological framework prevents the fossil data from being analyzed on a continuous time axis; the binning of the samples into three main intervals within a 10-million-year period hinders additional hypotheses about the environmental and climatic correlations of the dental structure-performance results presented. Second, the uneven sampling of the available mammalian assemblage throughout the Paleocene sites in China limits the breadth of ecomorphological categories included in the analyses; rarer taxa representing more specialized carnivore, insectivore, or herbivore forms were not included in our sampling. Third, the spatial discontinuity of stratigraphically younger (Eocene) and older (Cretaceous) mammal assemblages means that body size and ecomorphological shifts bracketing the Paleocene cannot currently be analyzed alongside the dataset presented. These limitations should be taken into account when considering the interpretations made in the main text.”

      Reviewer #2 (Recommendations for the authors):

      I'm including my Line Comments here as recommendations for the authors. But note that many of my recommendations are also in my Public Review.

      L22: "3% of sites"? Do you mean 3% of global sites?

      Yes, we revised the sentence to indicate 3% of global sites. Thank you for this suggestion.

      L35: This is nitpicky because it's not crucial to your study, but I can't help but point out that the Long Fuse, etc, hypotheses are specifically about the DIVERGENCE TIMES for Placentalia and major subclades, NOT the 'adaptive radiation' of placentals like you imply in your text. Adaptive radiations include ecomorphological diversification and are driven by ecological opportunity (e.g., Schluter 2000). (Emphasis on 'ecological.') The long fuse, short fuse, and explosive models do not include an ecological component - i.e., the diversifications could have occurred without ecological diversification. Instead, for hypotheses that are specifically on the adaptive/ecological radiation of mammals, see the Early Rise, Suppression (or Dinosaur Incumbency; Benevento et al. 2023 Palaeontology), and Late Rise hypotheses (Grossnickle et al. 2019 TREE). These hypotheses apply broadly to all mammals, not just placentals (see Box 1's figure in Grossnickle et al. 2019), but they can still be applied to mammalian subclades like eutherians/placentals (e.g., see Thomas Halliday papers).

      Thank you for helping to clarify the adaptive radiation vs. divergence time concepts. We edited this sentence to mention the adaptive radiation hypotheses instead, adding in the references provided by the reviewer.

      L39-40: I think your comment is probably accurate. But keep in mind that advocates of the Early Rise and Delayed Rise hypotheses (see citations within Grossnickle et al. 2019) might argue that other time periods, other than the Paleocene, are equally or more important.

      We added a reference to Grossnickle et al. 2019 to bring attention to potential arguments otherwise. Thank you for the suggestion.

      L48: I think the inclusion of "at higher latitudes" is a little distracting or misleading and should be erased. It implies that the taxonomic diversification was ONLY rapid at higher latitudes. But many of the references that you cite include analyses at the global or continental scale (e.g., Alroy 1999, Grossnickle & Newham 2016) and don't distinguish patterns at different latitudes. If you want to keep the point about latitudes, then I recommend inserting a separate sentence on that point.

      We removed “at higher latitudes”.

      L50: Isn't "stem lineages and those with no living relatives" somewhat redundant? Or do you mean something like "stem placental/eutherian lineages and extinct placental subgroups"?

      Yes, we adopted the suggested phrasing. Thank you.

      L53: I recommend starting a new paragraph around here (maybe starting with "Distinct from ...") that focuses specifically on introducing the 'brawn before [ecomorphological trait]' hypothesis.

      Done.

      L56: "large herbivores and their predators"? Are you just referring to mammals? Wilson (2013), which you cite, and Grossnickle & Newham (2016) argued that dietary specialists were targeted at the K-Pg, but none of the herbivores were "large" (at least relative to Cenozoic herbivores). And most faunivorous mammals at the time were probably insectivorous and not preying on herbivorous mammals, besides maybe a few outlying taxa (e.g., Altacreodus, Nanocuris). I'd revise your sentence for clarity.

      We removed “disproportionately impacting large herbivores and their predators” for clarity.

      L63: I'd replace "ecometric" with "ecomorphological". Ecometrics commonly refers to using fossil traits to infer paleo environments/climate (e.g., see papers by David Polly, Michelle Lawing, etc), which I don't think is what you're referring to here. (E.g., I don't think that brain size or jaw shape patterns were/are used to infer paleo environments.)

      Revised. Thank you.

      L85: I strongly advise against making conclusions like this: "Dental height and sharpness variability ... [spiked] in the middle Paleocene corresponding to a short-lived negative excursion in global temperature." That implies that the change in dentitions is linked to global temperature changes, which I don't think your results support. Later in the text you highlight the temporal uncertainty of your time bin ages (L650) and say that the middle Paleocene bin could be as old as ~62 Ma (L646), which is well before the negative excursion (and looks to be more in line with a positive excursion!), at least according to the Figure 1 time scale (see comment below). So, I don't think that your results even support your statement.

      We reworded this sentence to say “Dental height and sharpness variability were low in the beginning and end of the time interval, with a peak in the middle Paleocene. This pattern is observed both when dentitions are considered holistically and by tooth position in the lower dentition (Fig. S5; upper teeth display the opposite pattern).”

      L144: Using variance for disparity seems fine. But keep in mind that other disparity metrics, such as range (or sum-of-ranges for multivariate data), might produce different results. For instance, variance of RFI and Slope spike in the middle Paleocene, like you point out, but based on the values in Figure 1A, it looks like the ranges stay relatively constant through the Paleocene (although I realize that the ranges might change with bootstrapping). So, your choice of disparity metric might have a big influence on your conclusions. Alternatively, you could calculate disparity using multiple metrics (e.g., Brusatte et al. 2012 Nature Communications; Grossnickle & Newham 2016 supplemental analyses), even if it's just for supplemental analyses.

      Thank you for bringing the choice of disparity measures to our attention. We conducted a parallel set of bootstrapped disparity calculation and comparison analyses using range lengths (maximum trait value – minimum trait value for a given trait) and summarized the through-time trends as for variance-based results (Fig. S5). Overall, very similar trends are observed, providing support for the variance-based data interpretation presented in the main text. We added explanation of this additional sensitivity testing both in the main text and in the supplemental text.

      L147: "body size disparity ... (Fig. 1B, S6A, Table 1, Data S5)." But I don't see disparity calculated or plotted in any of the figures/tables that you cite. You test for differences in disparity between time bins (Table 1), but that doesn't provide the actual disparity patterns.

      We generated a new figure (Fig. S8) to show the tooth size variance and range levels across time and data partitions, and modified this sentence to say that “Over the same time interval examined, body size disparity and mean were higher in the early Paleocene than in subsequent time intervals (Fig. S8, Table S3; also supported by premolar 4 and upper molar partition analyses), indicating that substantial increases in the disparity of dental complexity, curvature, and height lagged behind maximum size disparity tooth size during the Paleocene.”

      L151-153: Maybe. But you're basing this on a much narrower temporal range (Paleocene) than the brain and jaw studies, and I think those studies observed big increases in brain/jaw disparity in the Eocene, which you don't sample. And as I explained elsewhere, I'm not convinced that your results strongly support the same pattern. At a minimum, I recommend tempering your conclusions to better reflect the uncertainty of your results.

      We tempered our statements here to say that “This suggests a ‘brawn before bite’ pattern in endemic Asian mammals, partially mirroring the endocranial and jaw functional morphology patterns identified in their North American and European counterparts [21,22]. These findings raise the possibility that an initial size-driven post-K-Pg recovery followed by ecomorphological radiation was a global phenomenon, even as regional tectonic events such as the initial collision of the Indian subcontinent with Asia and Deccan Traps volcanism influenced local mammal evolution.”

      L170: I'm not well-versed in integration (and modularity) studies, so maybe this reflects my ignorance, but I had trouble understanding sentences like this: "These findings indicate that form-function malleability, the coexistence of distinct topography-performance relationships in each time and taxon partition while overall integration between the two trait groups increases between time bins, was present throughout the Paleocene." If there is space, I recommend revising and/or breaking apart long, jargon-y sentences like that (throughout the paper) so that they're more digestible for readers.

      We simplified complex sentences such as the one the reviewer noted, in order to communicate our findings and interpretations more clearly. Thank you for the suggestion.

      L183: It's probably fine to assume most placental orders arose in the Paleocene based on fossil evidence. But keep in mind that molecular studies often argue that many orders arose in the Late Cretaceous.

      We revised the statement to indicate a “Cretaceous/Paleocene” origin of many modern mammal orders.

      L200-207: Again, this might just reflect my ignorance concerning integration analyses, but I recommend expanding on this text to better explain how your integration results support this conclusion. It seems really interesting, and I like the Garden of Eden hypothesis. It's just not immediately clear to me how your results support that hypothesis. A little more background on how to interpret the integration results would be helpful.

      We expanded the discussion here to say that “Such flexibility in dental form-function linkage permits ‘mix and match’ trait combinations rather than evolutionary change as a single unit, potentially enhancing the evolvability of feeding ecological traits as new environmental conditions arose [Goswami et al. 2015]”

      Reference: Goswami, A., Binder, W.J., Meachen, J., and O’Keefe, F.R. (2015). The fossil record of phenotypic integration and modularity: A deep-time perspective on developmental and evolutionary dynamics. Proc. Natl. Acad. Sci. 112, 4891–4896. 10.1073/pnas.1403667112.

      L218: "reached maximum tooth size disparity early". Again, I don't see size disparity plotted or reported. And without baseline comparisons (Late K or Eocene), it's hard to interpret your results and evaluate what 'maximum' means (Figure 1B).

      We revised the sentence to now say “In response, Paleocene mammal clades in south China between dental topography and bite performance later, all the while maintaining high levels of variability in dental complexity and convexity (Fig. 1).”

      Figure 1A: The time scale in the top left of the figure looks off. Shouldn't the K-Pg be at 66 Ma (not 65 Ma) and the P-E boundary at 56 Ma (not ~54 or 55)?

      We revised Fig. 1 to fix the time scale so that K-Pg is at 65.5 Ma and the P-E boundary at 56 Ma. Thank you for catching this.

      Figure 1A: Is there a different y-axis scale for the variance (red line) results?

      Yes, the y axes for the variance curves were missing. We added them back in. Thank you.

      L628-629: As I explained above, it feels like you focused your sampling just on herbivorous/omnivorous groups, and, if true, this is an important point that should be discussed at the forefront of the paper. Does your sample truly represent the total ecological diversity of the mammalian faunas at the time?

      We agree with the reviewer about the potential partial sampling of the range of ecomorphological diversity when only the most abundant clades are included in the analyses. However, we refrain from interpreting the dietary groupings represented in the dataset using an assumption of functional morphology from crown/extant clades. We added a paragraph in the introduction to bring attention to the inherent uncertainty in the ecological diversity of the dataset:

      “A major challenge with expanding analyses of post K-Pg recovery to Paleocene mammal assemblages elsewhere in the world is the stratigraphically limited nature of early Cenozoic sequences that produce fossil mammals. In Asia, Paleocene localities in China represent the best studied to date 11. From the earliest Paleocene, highly regional and endemic faunas are known from a handful of sedimentary basins (Fig. S1A). Among the faunal elements, only the archaic placental clades Anagalida and Pantodonta are consistently sampled across the major subdivisions of the Paleocene 11. An additional complication with ecomorphological analysis of these early mammals is the uncertainty in their dietary ecology, as they are beyond the reach of conventional phylogenetic bracketing approaches to dietary reconstruction. Phenomic analysis of the placental radiation supports insectivory as the ancestral diet of the hypothetical placental ancestor, but uncertainty in the post K-Pg availability of insects and plants in some regions leave some doubt as to the accuracy of this ancestral state reconstruction 1. Herein we treat the archaic Paleocene taxa in our analyses as having uncharacterized diets rather than categorizing them as insectivores, herbivores, or carnivores. “

      L653: Sorry if this is mentioned elsewhere, but did you avoid using teeth with especially worn or broken cusps? You might expand on how you chose teeth for your sample.

      We left out this detail in the original submission. Thank you for pointing this out. We had to exclude a third of the teeth because they were too worn or broken. We added the following explanation to the methods section:

      “These tooth positions were selected from a broader examination of ~300 individual teeth from 72 specimens. We vetted the specimens and excluded 99 tooth positions (~33% of teeth initially chosen for possible inclusion) from our analyses because they either (1) were partially or completely broken at the crown, (2) were in an advanced stage of attritional wear where no cusps could be identified, or (3) possessed a combination of the two aforementioned conditions.”

      L654: "specimens" should be "teeth", correct? In the preceding sentence, you say that there are 200 teeth from only 48 specimens.

      Corrected.

    1. Author response:

      The following is the authors’ response to the previous reviews

      eLife Assessment

      This important work demonstrates the role of physically linking the core and CTD kinase modules of TFIIH via separate domains of subunit Tfb3 in confining RNA Polymerase II Serine 5 CTD phosphorylation to promoter regions of transcribed genes in budding yeast. The main findings, resulting from analyses of viable Tfb3 mutants in which the linkage between TFIIH core and kinase modules has been severed, are supported by solid evidence from in vitro and in vivo experiments. The new findings raise the intriguing possibility that the Tfb3-mediated connection between core and kinase modules of TFIIH is an evolutionary addition to an ancestral state of physically unconnected enzymes.

      After consultation with the referees, we would like to suggest that you insert text into the RESULTS section acknowledging two limitations of your findings remaining in the revised manuscript, as follows:

      (i) It remains possible that Kin28 abundance was reduced by splitting Tfb3, which could be a factor in reducing its occupancies at gene promoters.

      In response, the paper now contains the following sentence:

      “Kin28 levels in extracts were below the limit of detection for our antibody, so we cannot rule out that the drop in ChIP signal is partly due to reduced Kin28 levels in the split Tfb3 strains. However, the viability of the cells (Figure 2) and the Tfb3-TAP purifications (Figure 3) argue against a complete loss of Kin28.”

      (ii) Lower than wild-type expression of the Tfb3 truncations might contribute to their mutant phenotypes shown in Figs. 2 & 5.

      In response, the paper now contains the following sentence:

      “There was some variation in protein expression levels (Figure 3A, left panel, lanes 1-4), and reduced levels of the split Tfb3 may contribute to the slow growth phenotypes.”

      Public Reviews:

      Reviewer #1 (Public review):

      Giordano et al. demonstrate that yeast cells expressing separated N- and C-terminal regions of Tfb3 are viable and grow well. Using this creative and powerful tool, the authors effectively uncouple CTD Ser5 phosphorylation at promoters and assess its impact on transcription. This strategy is complementary to previous approaches, such as Kin28 depletion or the use of CDK7 inhibitors. The results are largely consistent with earlier studies, reinforcing the importance of the Tfb3 linkage in mediating CTD Ser5 phosphorylation at promoters and subsequent transcription.

      Notably, the authors also observe effects attributable to the Tfb3 linker itself, beyond its role as a simple physical connection between the N- and C-terminal domains. These findings provide functional insight into the Tfb3 linker, which had previously been observed in structural studies but lacked clear functional relevance. Overall, I am very positive about the publication of this manuscript and offer a few minor comments below that may help to further strengthen the study.

      We appreciate the reviewer’s positive assessment of our work and suggestions for improvement.

      Page 4 PIC structures show the linker emerging from the N-terminal domain as a long alpha-helix running along the interface between the two ATPase subunits, followed by a turn and a short stretch of helix just N-terminal to a disordered region that connects to the C-terminal region (see schematic in Fig. 1A).

      The linker helix was only observed in the poised PIC (Abril-Garrido et al., 2023), not other fully-engaged PIC structures.

      Thanks for clarifying. We note that some structures of TFIIH alone also see the long helix. Accordingly, we modified this section to read:

      “In many TFIIH and PIC structures the linker is not visible, presumably due to flexibility. However, when it is seen (Abril-Garrido et al., 2023; Greber et al., 2019), the linker emerges from the N-terminal domain as a long alpha-helix running along the interface between the two ATPase subunits…”

      Page 8 Recent structures (reviewed in (Yu et al., 2023)) show that the Kinase Module would block interactions between the Core Module and other NER factors. Therefore, TFIIH either enters into the NER complex as free Core Module, or the Kinase Module must dissociate soon after.

      To my knowledge, this is still controversial in the NER field. I note the potential function on the kinase module is likely attributed to the N-terminal region of Tfb3 through its binding to Rad3.

      We are not experts on NER, but in reviews of the field this appears to be a widely held assumption. A 2008 paper from the Egly lab (Coin et al., DOI 10.1016/j.molcel.2008.04.024) is usually cited, which shows that the interaction between XPD (metazoan Rad3) and XPA is likely incompatible with XPD-MAT1 interaction. In addition to the Yu 2023 review, we now also cite a more recent publication that more extensively reviews the models for core TFIIH interactions (van Sluis et al, 2025). We looked at the multiple recently published structures of various TCR-NER and GG-NER intermediate complexes, and none of them show the CAK module or even the Tfb3/Mat1 N-term, even though those proteins were typically included during assembly. We also consulted with our colleagues Johannes Walter and Lucas Farnung, who are studying various TC-NER intermediates biochemically and structurally. Although the CAK module is included in their assembly reactions, it is not visible in their cryoEM structures. They tell me that the presence of CAK would be compatible with early TC-NER intermediates, but is predicted to overlap with later interactions of XPD with the TC-NER factor STK19 (see Mevissen et al., Cell 2024). To be conservative, we modified the sentence to say “Recent structures … suggest” rather than “show”.

      Because the yeast strains used in Fig. 6 retain the N-terminal region of Tfb3, the UV sensitivity assay presented here is unlikely to directly address the contribution of the kinase module to NER.

      We agree that our experiment only shows that the connection between Tfb3 N- and C-term domains is not necessary for NER. The individual domains might still be able to function independently. Accordingly, we changed the heading of that section from “Disconnected core TFIIH does not cause an NER defect” to “Split Tfb3 does not cause an NER defect.” This more closely matches the figure legend title.

      Page 11. Notably, release of the Tfb3 Linker contact also results in the long alpha-helix becoming disordered (Abril-Garrido et al., 2023), which could allow the kinase access to a far larger radius of area. This flexibility could help the kinase reach both proximal and distal repeats within the CTD, which can theoretically extend quite far from the RNApII body.

      Although the kinase module was resolved at low resolution in all PIC-Mediator structures, these structural studies consistently reveal the same overall positioning of the kinase module on Mediator, indicating that its localization is constrained rather than variable. This observation suggests that the linker region may help position the kinase module at this specific site, likely through direct interactions with the PIC or Mediator. This idea is further supported by numerous cross-links between the linker region and Mediator (Robinson et al., 2016).

      That is true. But please note that this sentence was meant to describe movement of the kinase module AFTER release from Mediator (see previous sentence). Re-reading the passage, we realized the confusion is because we propose multiple possible pathways in that paragraph. In the first half, we suggest the capture of the kinase module by Mediator might trigger the conformation changes in the linker. In the second half (where it says “Alternatively….”) we suggest the Mediator-CAK interaction could instead come first, and the release of this contact could free the CAK module to move around. We have modified the paragraph to make it clear these are two different distinct models.

      Comments on revisions:

      Revised ms clarified all my points, including those I previously misunderstood.

      Thanks again for helping us improve the manuscript.

      Reviewer #2 (Public review):

      Summary:

      This work advances our understanding of how TFIIH coordinates DNA melting and CTD phosphorylation during transcription initiation. The finding that untethered kinase activity becomes "unfocused," phosphorylating the CTD at ser5 throughout the coding sequence rather than being promoter-restricted, suggests that the TFIIH Core-Kinase linkage not only targets the kinase to promoters but also constrains its activity in a spatial and temporal manner.

      Strengths:

      The experiments presented are straightforward and the model for coupling initiation and CTD phosphorylation and for evolution of these linked processes are interesting and novel. The results have important implications for the regulation of initiation and CTD phosphorylation.

      Comments on revisions:

      The revised version with revisions to figures, text and new data has addressed all of our prior comments.

      We thank the reviewer for helping us improve the paper.

      Reviewer #3 (Public review):

      Summary:

      Eukaryotic gene transcription requires a large assemblage of protein complexes that govern the molecular events required for RNA Polymerase II to produce mRNAs. One of these complexes, TFIIH, comprises two modules, one of which promotes DNA unwinding at promoters, while the other contains a kinase (Kin28 in yeast) that phosphorylates the repeated motif at the C-terminal domain (CTD) of the largest subunit of Pol II. Kin28 phosphorylation of Ser5 in the YSPTSPS motif of the CTD is normally highly localized at promoter regions, and marks the beginning of a cycle of phosphorylation events and accompanying protein association with the CTD during the transition from initiation to elongation.

      The two modules of TFIIH are linked by Tfb3. Tfb3 consists of two globular regions, an N-terminal domain that contacts the Core module of TFIIH and a C-terminal domain that contacts the kinase module, connected by a linker. In this paper, Giordano et al. test the role of Tfb3 as a connector between the two modules of TFIIH in yeast. They show that while no or very slow growth occurs if only the C-terminal or N-terminal region of Tfb3 is present, near normal growth is observed when the two unlinked regions are expressed. Consistent with this result, the separate domains are shown to interact with the two distinct TFIIH modules. ChIP experiments show that the Core module of TFIIH maintains its localization at gene promoters when the Tfb3 domains are separated, while localization of the kinase module, and of Ser5 phosphorylation on the CTD of Pol II, is disrupted. Finally, the authors examine the effect of separating the Tfb3 domains on another function of TFIIH, namely nucleotide excision repair, and find little or no effect when only the N-terminal region of Tfb3 or the two unlinked domains are present.

      Strengths:

      Experiments involving expression of Tfb3 domains in yeast are well-controlled and the data regarding viability, interaction of the separate Tfb3 domains with TFIIH modules, genome-wide localization of the TFIIH modules and of phosphorylated Ser5 CTDs, and of effects on NER, are convincing. The experiments are consistent with current models of TFIIH structure and function and support a model in which Tfb3 tethers the kinase module of TFIIH close to initiation sites to prevent its promiscuous action on elongating Pol II.

      We appreciate that the reviewer finds that our main conclusions are convincing.

      Weaknesses:

      The work is limited in scope and does not provide major insights into the mechanism of transcription. The main addition to current models of transcription is that tethering of Kin28 to Tfb3 may limit kinase action from occurring downstream from the initiation site.

      The first described experiment, which purports to show that three kinases cannot function in place of Kin28 when tethered (by fusion) to Tfb3 is missing the crucial control of showing that Kin28 can support viability in the same context. This result also does not connect with the rest of the manuscript, although the experiment apparently motivated the subsequent studies reported here.

      We elected not to do this control experiment for several reasons. As reviewer 3 points out, this kinase fusion experiment turned out to be somewhat disconnected from the rest of the paper. Even though it didn’t work, we included it in the paper because the results led us to the realization that the Tfb3 C-term was actually not fully essential for viability as reported, which in turn led us to the idea of splitting Tfb3. Structural studies (https://doi.org/10.1126/sciadv.abd4420, https://doi.org/10.1073/pnas.2009627117, https://doi.org/10.7554/eLife.44771) show that, in addition to providing linkage to the core module, the C-term of Tfb3 induces a conformation change in Kin28/Cdk7 necessary for full kinase activity (which is likely why the strains without C-term are just barely viable). If we were to pursue why the fusions didn’t work, we could tether Kin28 directly to the Tfb3 linker (and may try this in the future), but then would need to also express the C-term separately for its activating function. Even then, this would be an imperfect control for the fusion experiments in Figure 1. Because were trying to best mimic Kin28 being tethered via the accessory subunit Tfb3/Mat1, in the Figure 1 experiment we did not directly attach the kinases to Tfb3. For Ctk1/Cdk12, we fused the Tfb3 linker to the Ctk3 accessory subunit (analogous to Tfb3), and for Bur1/Cdk9, we fused to the cyclin subunit Bur2 (there is no known third subunit in this complex). The one exception was Mpk1, which has no partner subunits and is not a CDK. There are many reasons why this high-risk protein fusion experiment may not have worked, but chose not to pursue it further at this time.

      Finally, the authors present the interesting and reasonable speculation that the TFIIH complex and connecting Tfb3 found in mammals and yeast may have evolved from an earlier state in which the two TFIIH subdomains were present as unconnected, distinct enzymes. It will be interesting to have this idea tested more thoroughly as more molecular evolutionary data becomes available.

      Comments on revisions:

      For the most part, the authors have satisfactorily addressed my previous critique. In particular, they have added to their discussion of evolutionary implications, and performed an experiment casting doubt on the assertion of a dominant negative effect, and as a consequence removed this claim from the manuscript. I also pointed out that the fusion experiments that lead off the Results section are missing the crucial control of including a Tfb3-Kin28 fusion. The authors have elected not to perform this control experiment, pointing out that even this control would be imperfect in some respects, and agreeing that this experiment is somewhat disconnected from the rest of the paper. The reason for including it, in spite of its somewhat tangential nature, is that it provides something of a rationale for the experiments that follow. I don't so much mind their retaining the experiment, as the absence of this control (and indeed, the results) does not so much impact the later results. However, I think if it is to be included, this shortcoming should be explicitly recognized, especially as a service to younger scientists who could benefit from an exposition that includes a thorough consideration of potential control experimenents.

      We thank the reviewer for helping us improve the paper.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors report the results of a tDCS brain stimulation study (verum vs sham stimulation of left DLPFC; between-subjects) in 46 participants, using an intense stimulation protocol over 2 weeks, combined with an experience-sampling approach, plus follow-up measures after 6 months.

      Strengths:

      The authors are studying a relevant and interesting research question using an intriguing design, following participants quite intensely over time and even at a follow-up time point. The use of an experience-sampling approach is another strength of the work.

      Weaknesses:

      There are quite a few weaknesses, some related to the actual study and some more strongly related to the reporting about the study in the manuscript. The concerns are listed roughly in the order in which they appear in the manuscript.

      We truly appreciate your dedicating time and efforts to review our manuscript. Yes, we do perceive that those weaknesses you raised all make sense. We agree with you on almost all the suggestions that you detailed below, particularly in clarifying statistics and sample size determination. Please see specific responses below.

      Major Comments

      (1) In the introduction, the authors present procrastination nearly as if it were the most relevant and problematic issue there is in psychology. Surely, procrastination is a relevant and study-worthy topic, but that is also true if it is presented in more modest (and appropriate) terms. The manuscript mentions that procrastination is a main cause of psychopathology and bodily disease. These claims could possibly be described as 'sensationalized'. Also, the studies to support these claims seem to report associations, not causal mechanisms, as is implied in the manuscript.

      Thank you for this very practical suggestion. We agree that the current statements to underline the importance of procrastination are somewhat overreaching. Upon revision, we have overall toned down such claims by explicitly stating them as “associative evidence”, and rewritten a portion of terms in a more modest and balanced style. Please see specific revisions in the main text below:

      Introduction Section (Page 5, Line 64-81)

      “Procrastination is increasingly becoming a prevalent behavioral problem around the world, which reflects the irrational voluntary postponement of scheduled tasks albeit being worse off for such delays (Blake, 2019; Steel, 2007). In the epidemiological investigations, more than 15% of adults were identified as having chronic procrastination problems, and the situation for students was worse as 70-80% of undergraduates engaged in procrastination (American College Health Association, 2022; Ferrari et al., 2005). Moreover, the behavioral genetic evidence indicates a certain heritability of procrastination in human beings as well (Gustavson et al., 2017; Gustavson et al., 2014, 2015). In addition to its prevalence, the undesirable associations between procrastination behavior and health also warrant cautions. There is cumulative evidence to show the close associations between procrastination behavior and working performance, financial status, interpersonal relationships, and subjective well-being (Ferrari, 1994; Pychyl & Sirois, 2016; Steel et al., 2021). Further, as the prospective cohort studies indicated, many mental health problems emerge alongside procrastination, particularly in sleep problems, depression, and anxiety (Hairston & Shpitalni, 2016; Johansson et al., 2023). Even worse, chronic procrastination behavior has been observed to impair general health, as manifested by the intimate associations with close system disruption, gastrointestinal disturbance, as well as a high risk of hypertension and cardiovascular disease (Sirois, 2015; Sirois, 2016). ... ”

      (2) It is laudable that the study was pre-registered; however, the cited OSF repository cannot be accessed and therefore, the OSF materials cannot be used to (a) check the preregistration or to (b) fill in the gaps and uncertainties about the exact analyses the authors conducted (this is important because the description of the analyses is insufficiently detailed and it is often unclear how they analyzed the data).

      We are sorry to encounter a serious technical barrier making our preregistration invisible and inaccessible. The OSF has disabled my OSF account, as it claimed to detect “suspicious user’s activities” in my account (please see the screenshot below). This results in no access to all materials already deposited in this OSF account, including this preregistration. We have contacted the OSF team, but received no valid technical solution to recover this preregistered report. We reckon that this may be triggered by my affiliation change to the Third Military Medical University of the People’s Liberation Army (PLA).

      To address this unexpected circumstance and to ensure transparency, we have explicitly reported this case in the main text, and added the “Reconstructed Preregistration Statement” into the Supplemental Materials (SM). Also, as it has been out of best practices in preregistration, in addition to transparently reporting this case, we have removed this statement regarding preregistration elsewhere throughout the whole revised manuscript. Furthermore, we fully understand the gaps of comprehending the statistics of this study, resulting from inadequate methodological details in the reporting. Therefore, we have clearly reported extensive details in the Methods section to clarify how to conduct those analyses, favoring the smooth evaluations of our conclusions. Please see what we have added in the lines below (Comments #4-9).

      Methods Section (Page 5, Line 186-191)

      “This study fully adhered to CONSORT reporting guidelines, and was originally preregistered in the OSF repository (10.17605/OSF.IO/Y3EDT). However, due to the technical constraint related to OSF account service (see SM), this OSF page is no longer accessible. For transparency and best practices of open science, based on the original protocol documentations, a preregistration statement has been reconstructed to clarify aprior hypotheses, sample size determinations, and analysis plans for this study (Table S1).”

      (3) Related to the previous point: I find it impossible to check the analyses with respect to their appropriateness because too little detail and/or explanation is given. Therefore, I find it impossible to evaluate whether the conclusions are valid and warranted.

      Again, we apologize for confusing you because of inadequate statistical and methodological details. As you may know, this manuscript has ever been reviewed by Nature Human Behaviour, which editorially constrained the paper length. Thus, a substantial number of details had to be omitted or removed. As you kindly suggested, we have diligently added extensive descriptions to clarify how we carried out statistical analyses in the present study. Please see specific instances underneath.

      (4) Why is a medium effect size chosen for the a priori power analysis? Is it reasonable to assume a medium effect size? This should be discussed/motivated. Related: 18 participants for a medium effect size in a between-subjects design strikes me as implausibly low; even for a within-subjects design, it would appear low (but perhaps I am just not fully understanding the details of the power analysis).

      Thank you for raising this crucial question. We have determined this a priori effect size based on the existing work we published previously (Xu et al., 2023, J Exp Psychol Gen;152(4):1122-1133). In our pilot study (Xu et al., 2023), we identified a significant interaction effect between the single-session tDCS stimulation (active vs sham) and time (pre-test vs post-test) (t = 2.38, p = .02, n = 27; 95% CI [0.14, 1.49]) for changing procrastination willingness in the laboratory settings, indicating a medium effect size. Therefore, this pilot study provides supportive evidence to determine this effect size a priori. To clarify, we have explicitly justified the selection of this effect size in the Methods section.

      Methods Section (Page 5, Line 206-215)

      “A full randomized block design was used to assign participants to both groups (active neuromodulation group, NM; sham-control group, SC) (see Fig. 2C). As the pilot study probing into the effect of single-session tDCS stimulation to change procrastination willingness indicated (t = 2.38, p = .02, 95% CI [0.14, 1.49]; Xu et al., 2023), statistical power was predetermined by G*Power at a relatively medium effect size (1-β err prob = 0.80, f = 0.25), yielding the total sample size at 18 to reach acceptable power (see SM Methods and Fig. S1)....”

      We fully understand that this sample size to reach a medium effect size is seemingly low, and that the18 participants for each group are apparently limited in any case. Upon double-checking these power analyses, we confirmed that this sample size requirement is indeed correct. Please see the G*Power outputs in Author response image 1.

      Author response image 1.

      Despite the absence of algorithmic errors in the power analysis here, we are aware that this limited sample size may hamper statistical robustness. To tackle this weakness, we have clearly warranted such cautions in the Limitation section:

      Limitations Section (Page 12, Line 637-640)

      “... In addition to technical limitations, given the apparently limited size of the sample (total N = 46), it warrants caution in generalizing these findings elsewhere, and necessitates further validations in a large-scale cohort.”

      (5) It remains somewhat ambiguous whether the sham group had the same number of stimulation sessions as the verum stimulation group; please clarify: Did both groups come in the same number of times into the lab? I.e., were all procedures identical except whether the stimulation was verum or sham?

      Yes, we fully followed the CONSORT pipeline to carry out this double-blind trial, and thus confirmed that all the participants in both groups had the same number of stimulation sessions in our lab. That is to say, except for the stimulation type (verum vs sham), all the procedures, equipment and even the room were identical for all the participants. For clarification, we have clearly stated this in the main text:

      Results Section (Page 9, Line 419-423)

      “In both groups, almost all participants (93.2%, 41/44) reported perceiving acceptable pain stemming from current stimulation, and believed they were receiving treatment (91.30% (21/23) for active neuromodulation group (NM), 86.95% (20/23) for sham control group (SC), x<sup>2</sup> = 0.224, p = .636). All the participants were engaged in the identical experimental procedures excepting to stimulation’s type (active vs sham). ...”

      (6) The TDM analysis and hyperbolic discounting approach were unclear to me; this needs to be described in more detail, otherwise it cannot be evaluated.

      We apologize for the inadequate details, which hindered a precise understanding of the TDM and the hyperbolic discounting model. The Temporal Decision Model (TDM) was originally proposed by our team (Xu et al., 2023; Zhang et al., 2019, 2020, 2021), which theoretically conceptualizes procrastination as the failure of trade-off between task outcome value (i.e., motivation to take actions now for pursuing task reward) and task aversiveness (i.e., motivations to take away from playing actions now for avoiding negative experiences). Once task aversiveness overrides the pursuit of task outcome values, the procrastination emerges. One overarching hypothesis in this theoretical model is that the task aversiveness is hyperbolically discounted when approaching the deadline: it would be discounted sharply when far from the deadline but discounted slowly when nearing the deadline (Zhang et al., 2019). Considering the nonlinear dynamics inherent in this hyperbolic discounting, we therefore employed a log-spaced temporal sampling scheme (Myerson et al., 2001) to strengthen curve-fitting performance (please see the schematic diagram (https://uen.pressbooks.pub/behavioraleconomics/chapter/the-reality-of-homo-sapiens, where each point indicates a sampling time)):

      Specifically, based on the log-spaced temporal sampling rule, five time points were first selected to fulfill the statistical prerequisites for hyperbolic model fitting, with increasing sampling density toward the deadline (e.g., for a task due at 20:00: sampling occurred at 10:00, 16:00, 18:00, 19:30, 20:00). At each time point, participants reported task aversiveness (A) on a 0–100 Visual Analog Scale (VAS). Then, task aversiveness discounting was calculated as 1- (A<sub>t</sub> / A<sub>earliest</sub>), where t<sub>earliest</sub> was the earliest sampling point (e.g., 10:00), serving as the reference for immediate execution. Subsequently, using the GraphPad Prisma software (v9, 525), we estimated the AUC from these five data points based on the Myerson algorithm (Myerson et al., 2001), which was computed as the trapezoidal integration of task aversiveness discounting over time. By this modelling method, a higher AUC reflects stronger temporal discounting of task aversiveness, which means that participants experience a faster decline in subjective aversiveness as execution is delayed, yielding lower effective aversiveness and reduced avoidance behavior. That is to say, if a participant showcases a greater discounting of task aversiveness as reflected by a higher AUC, she/he experiences a more pronounced reduction in subjective aversiveness upon postponement, plausibly yielding less procrastination. As you kindly suggested, we have added these details to explicitly clarify how to use the hyperbolic discounting approach for determining sampling time points and for calculating AUC of task aversiveness discounting.

      Methods Section (Page 6, Line 268-283)

      “On the Task day, we developed a mobile app to implement experience sampling method (ESM) for tracking one’s real-time evaluation of task aversiveness and task outcome value (see Fig. 1). The task aversiveness describes how disagreeable one perceives when performing a given real-life task to be, whereas outcome value refers to the subjective benefits of the task outcome brought about by completing the task before the deadline (Zhang & Feng, 2020). As theoretically conceptualized by the temporal decision model (TDM) of procrastination, the perceived task aversiveness is hyperbolically discounted when approaching deadline, showing sharply discounting when faring away from deadline but slowly discounting once nearing deadline (Zhang & Feng, 2020; Zhang et al., 2021). Thus, considering this nonlinear dynamics inherent in this hyperbolic discounting, the five recording moments of ESM were selected per task a priori by using a log-spaced temporal sampling scheme (Myerson et al., 2001), with increasing sampling density toward the deadline, such as moments of 10:00 (earliest), 16:00, 18:00, 19:30, 20:00 (deadline). The five sampling points could meet statistical prerequisite in the hyperbolic model fitting, requiring ≥ 4 points (Green & Myerson, 2004). To do so, recording moments of tasks were individually tailored for each task per participant in this ESM procedure.”

      Methods Section (Page 7, Line 318-334)

      “... As articulated temporal decision theoretical model above, the task aversiveness evoked by executing a task was temporally dynamic in a hyperbolic discounting pattern, with sharply discounting in faring away from deadline but slowly discounting in nearing deadline (Zhang & Feng, 2020). To quantitatively characterize the task aversiveness with consideration for its dynamics, the model-free area under the curve (AUC) was calculated. Specifically, based on the log-spaced temporal sampling rule, task aversiveness was measured by 100-point visual analog scale at the five sampling moments. Then, the task aversiveness discounting (A) was calculated as 1- (A(t) / A(earliest)), where t(earliest) was the earliest sampling point, serving as the reference for immediate execution. Subsequently, using the GraphPad Prisma software (v9, 525), the AUC was computed as the trapezoidal integration between task aversiveness discounting and time across five data points, basing on the Myerson algorithm (Myerson et al., 2001). By doing so, a higher AUC reflects stronger temporal discounting of task aversiveness along with nearing deadline, which means that participants experience a faster decline in subjective aversiveness as execution is delayed, yielding lower effective aversiveness and reduced avoidance behavior. As for the task outcome value, it was theoretically posited as a relatively stable evaluation of the task (Zhang & Feng, 2020; Zhang et al., 2021).”

      References

      Myerson, J., Green, L., & Warusawitharana, M. (2001). Area under the curve as a measure of discounting. Journal of the experimental analysis of behavior, 76(2), 235–243. https://doi.org/10.1901/jeab.2001.76-235

      Xu, T., Zhang, S., Zhou, F., & Feng, T. (2023). Stimulation of left dorsolateral prefrontal cortex enhances willingness for task completion by amplifying task outcome value. Journal of experimental psychology. General, 152(4), 1122–1133. https://doi.org/10.1037/xge0001312

      Zhang, S., Verguts, T., Zhang, C., Feng, P., Chen, Q., & Feng, T. (2021). Outcome Value and Task Aversiveness Impact Task Procrastination through Separate Neural Pathways. Cerebral cortex (New York, N.Y. : 1991), 31(8), 3846–3855. https://doi.org/10.1093/cercor/bhab053

      Zhang, S., Liu, P., & Feng, T. (2019). To do it now or later: The cognitive mechanisms and neural substrates underlying procrastination. Wiley interdisciplinary reviews. Cognitive science, 10(4), e1492. https://doi.org/10.1002/wcs.1492

      Zhang, S., & Feng, T. (2020). Modeling procrastination: Asymmetric decisions to act between the present and the future. Journal of experimental psychology. General, 149(2), 311–322. https://doi.org/10.1037/xge0000643

      (7) Coming back to the point about the statistical analyses not being described in enough detail: One important example of this is the inclusion of random slopes in their mixed-effects model which is unclear. This is highly relevant as omission of random slopes has been repeatedly shown that it can lead to extremely inflated Type 1 errors (e.g., inflating Type 1 errors by a factor of then, e.g., a significant p value of .05 might be obtained when the true p value is .5). Thus, if indeed random slopes have been omitted, then it is possible that significant effects are significant only due to inflated Type 1 error. Without more information about the models, this cannot be ruled out.

      Thank you for sharing this very timely and crucial comment. After careful scrutiny, we identified this statistical flaw you pointed out - each participant was not yet modeled as random slopes but as random intercepts merely. As you kindly suggested, we have reanalyzed all the statistics by adding random slopes (i.e., (1 + day|SubjectID)). Results showed a statistically significant interaction effect for both procrastination willingness (β = -7.8, SE = 1.8, DF = 45.6, p < .001) and actual procrastination rates (β = -7.4, SE = 2.4, DF = 46.6, p = .004), indicating the effectiveness of multi-session neuromodulation in mitigating procrastination. In the post-hoc simple effect analyses, participants who engaged in active neuromodulation (NM) showed a significant increase in task-execution willingness (i.e., decreased procrastination willingness; NM-before: 35.65 ± 30.20, NM-after: 80.43 ± 19.92, t.ratio = 5.4, p < .0001, Tukey correction) and a decrease in actual procrastination rates (NM-before: 43.26 ± 39.09, NM-after: 0.00 ± 0.00, t.ratio = 5.1, p < .0001, Tukey correction), while no such effects were identified for participants in the sham control group (for willingness, SC-before: 37.57 ± 26.46, SC-after: 47.35 ± 30.49, t.ratio =0.3, p = .77, Tukey correction; for actual procrastination, SC-before: 46.47 ± 40.75, SC-after: 33.34 ± 37.82, t.ratio = 0.7, p = .48, Tukey correction). Taken together, we do appreciate your pointing out this definitely crucial statistical weakness, and have confirmed that our findings remain reliable after adjusting for Type 1 error by adding random slopes. Moreover, as you kindly suggested, we have incorporated these statistical details, particularly those concerning the GLMM, into the main text to facilitate your evaluation. Please see specific revisions below:

      Methods Section (Page 8, Line 381-401)

      “To clarify whether multiple-session HD-tDCS neuromodulation can reduce procrastination, the generalized mixed-effects linear model (GLMM) was constructed with full factorial design for subjective procrastination willingness (i.e., self-reported visual analog scores) and actual procrastination behavior (i.e., real-world task-completion rate before deadline). Here, sex, age and socioeconomic status (SES) were modeled as covariates of no interest. As the National Bureau of Statistics (China) issued (https://www.stats.gov.cn/sj/tjbz/gjtjbz/), on the basis of per capita annual household income, the SES was divided into seven hierarchical tiers from 1 (poor) to 7 (rich). To obviate subjective rating bias stemming from individual daily mood, we separately measured participants’ daily emotional fluctuation at 10:00 and 16:00 using a self-rating visual analog item (i.e., “How do feel for your mood today?”, 0 for “completely uncomfortable” and 100 for “definitely happy”). By doing so, the averaged score of those self-rating emotions at the two time points was modeled into the GLMM as covariate of no interests, yielding the final expression of “outcome ~ Group*Treatment_Day + Age + Gender + SES + Emotions + (1 + Treatment_Day | SubjectID)” in the statistical model”. This analysis was implemented using the “lme4” and “lmerTest” packages. Employing “emmeans” package, simple effects were also tested at baseline and post-last-intervention using Tukey-adjusted pairwise comparisons of estimated marginal means from the full GLMM, controlling for covariates and random-effects structure. To validate statistical robustness, instead of continuous outcomes for parametric tests, we also conducted a between-group comparison for the number of tasks that procrastination emerges by using the nonparametric x<sup>2</sup> test with φ correction or Fisher exact test....”

      Results Section (Page 9, Line 428-449)

      “To identify whether ms-tDCS targeting the left DLPFC can alleviate subjective procrastination willingness and actual procrastination behavior, a generalized linear mixed-effects model with Scatterthwaite algorithm was built, with task-execution willingness and actual procrastination rates (PR) as primary outcomes, respectively. For procrastination willingness, results showed a statistically significant interaction effect between multi-session neuromodulations and groups (β = -7.8, SE = 1.8, DF = 45.6, p < .001; Fig. 3A). In the post-hoc simple effect analysis, it demonstrated a significantly increased task-execution willingness (i.e., decreased procrastination willingness) after neuromodulation in the active neuromodulation group (NM-before: 35.65 ± 30.20, NM-after: 80.43 ± 19.92, t.ratio = 5.4, p < .0001, Tukey correction), but no such effects were identified in the sham control group (SC-before: 37.57 ± 26.46, SC-after: 47.35 ± 30.49, t.ratio =0.3, p = .77, Tukey correction) (Fig. 3B-C). A linear uptrend for task-execution willingness was further observed across multiple sessions in the active NM group, indicating gradually increasing neuromodulation effects (Fig. 3D; p < .01, Mann-Kendall test). For actual procrastination behavior, changes to actual procrastination rates across all the sessions have been detailed in the Fig. 3E. Similarly, a statistically significant interaction effect was identified here (β = -7.4, SE = 2.4, DF = 46.6, p = .004), and the simple effect analysis further revealed decreased actual procrastination rates after ms-tDCS in the active neuromodulation group (NM-before: 43.26 ± 39.09, NM-after: 0.00 ± 0.00, t.ratio = 5.1, p < .0001, Tukey correction), but no such prominent changes found in the sham control group (SC-before: 46.47 ± 40.75, SC-after: 33.34 ± 37.82, t.ratio = 0.7, p = .48, Tukey correction) (Fig. 3F-G). Also, a significant downtrend for procrastination rates across all the sessions was identified in the active NM group (Fig. 3H; p < .01, Mann-Kendall test).”

      (8) Related to the previous point: The authors report, for example, on the first results page, line 420, an F-test as F(1, 269). This means the test has 269 residual degrees of freedom despite a sample size of about 50 participants. This likely suggests that relevant random slopes for this test were omitted, meaning that this statistical test likely suffers from inflated Type 1 error, and the reported p-value < .001 might be severely inflated. If that is the case, each observation was treated as independent instead of accounting for the nestedness of data within participants. The authors should check this carefully for this and all other statistical tests using mixed-effects models.

      Thank you for underlining this very timely and helpful comment. As you correctly pointed out above, we did not include random slopes in the original GLMM, highly risking the inflation of the false-positive rate (i.e., Type-I error). By adding the random slopes, we reanalyzed all the statistics from the GLMM, and confirmed that all the findings are still reliable from those new GLMMs with random slopes. Again, thank you for this crucial statistical advice, and please see the above response for full details regarding what we have revised to address this comment you kindly raised.

      (9) Many of the statistical procedures seem quite complex and hard to follow. If the results are indeed so robust as they are presented to be, would it make sense to use simpler analysis approaches (perhaps in addition to the complex ones) that are easier for the average reader to understand and comprehend?

      We do thank you for this practical and helpful comment. In the original manuscript, we incorporated a joint model of longitudinal and survival data (JM-LSD), in conjunction with machine learning algorithms, to strengthen the robustness of our statistical findings. Nevertheless, we all agree with you on this point: there is no need to complicate the analyses by repeatedly probing the same research question to increase methodological robustness, at the expense of compromising readability and intelligibility for a broader audience. As you suggested, we have removed these complicated statistical methods, and merely maintained the primary ones - GLMM and X<sup>2</sup> cross-tab test, as well as a complementary one - Mann-Kendall linear trend test. Thus, we have almost rewritten the whole Results section. Please see the specific instances below:

      Results Section (Page 9, Line 468-485)

      “Ms-tDCS changes task aversiveness and task-outcome value

      Both task aversiveness and task outcome value serve as key pathways determining whether one would procrastinate. To this end, we further utilized a generalized linear mixed-effects model to examine the effects of ms-tDCS on changes in task aversiveness and task outcome value. Task aversiveness changes across all the sessions are shown in the Fig. 4A and 4C. We demonstrated a statistically significant decrease in task aversiveness and an increase in task outcome value via ms-tDCS in the neuromodulation group (Task aversiveness: interaction effect, β = -0.12, SE = 0.04, DF = 46.7, p = .002; simple effect, NM-before <sub>(AUC)</sub>: 1.13 ± 0.53, NM-after <sub>(AUC)</sub>: 1.95 ± 0.85, t.ratio = 4.5, p < .001, Tukey correction; Outcome value: β = -6.8, SE = 1.74, DF = 46.2, p < .001; simple effect, NM-before: 35.86 ± 27.82, NM-after: 73.08 ± 23.33, t.ratio = 5.0, p < .001, Tukey correction; see Fig. 4B), but not in the sham control group (Task aversiveness: SC-before <sub>(AUC)</sub>: 1.07 ± 0.51, SC-after <sub>(AUC)</sub>: 1.28 ± 0.46, t.ratio = 1.3, p = .20, Tukey correction; Outcome value: SC-before: 34.00 ± 25.17, SC-after: 40.13 ± 28.94, t.ratio = 0.8, p = .41, Tukey correction; see Fig. 4D). In the neuromodulation (NM) group, task aversiveness steadily decreased with the cumulative number of stimulation sessions, while perceived task outcome value increased significantly (see Fig. 4E-F, p < .05, Mann-Kendall test). Thus, it provides causal evidence clarifying that neuromodulation to left DLPFC reduces task aversiveness and enhances task-outcome value meanwhile.”

      Results Section (Page 10, Line 525-542)

      “Long-term effects of ms-tDCS

      We have also attempted to conduct a follow-up investigation to test the long-term retention of ms-tDCS in reducing actual procrastination. Almost all the participants had undergone follow-up except one in the neuromodulation group after last neuromodulation for 6 months (N<sub>NM</sub> = 22, N<sub>SC</sub> = 23). Thus, the GLMM was constructed, with the PR before first neuromodulation vs. PR after last neuromodulation for 6 months as covariates of interest. Results showed the statistically significant group*time interaction effects (β = 16.5, SE = 9.9, p = .049). Simple-effect model demonstrated a decrease in actual procrastination rates in the active neuromodulation group after last stimulation for 6 months compared to baseline (β = -22.05, SE = 10.0, p = .038, Tukey correction; NM-before: 40.68 ± 37.96, NM-after<sub>6-months</sub>: 18.63 ± 29.80), and revealed null effects in the SC group (β = 1.26, SE = 9.78, p = .99, Tukey correction; SC-before: 46.47 ± 40.75, SC-after<sub>6-months</sub>: 47.73 ± 39.18) (see Fig. 6).. Furthermore, using a nonparametric x<sup>2</sup> test to compare differences in the number of procrastinated tasks, we still found a statistically significant reduction in procrastination frequency in NM group after neuromodulation for 6 months compared to baseline (x<sup>2</sup> = 3.30, p = .035, NM-before: 68.19% (15/22), NM-after<sub>6-months</sub>: 40.91% (9/22)), while no significant changes were observed in the SC group (x<sup>2</sup> = 0.11, p = .74, SC-before: 69.56% (16/23), SC-after<sub>6-months</sub>: 73.91% (17/23)). Therefore, beyond to short-term effects, the benefits of ms-tDCS neuromodulation to reduce procrastination pose the long-term retention.”

      (10) As was noted by an earlier reviewer, the paper reports nearly exclusively about the role of the left DLPFC, while there is also work that demonstrates the role of the right DLPFC in self-control. A more balanced presentation of the relevant scientific literature would be desirable.

      We are grateful to you for noticing the unbalanced presentation of the literature on left DLPFC. As you kindly suggested, we have added literature to support the association between self-control and the right lateralization of the DLPFC. Please see below for what we have revised:

      Introduction Section (Page 4, Line 137-143)

      “...In addition to the left lateralization, there is solid evidence indicating significant associations between self-control and the right DLPFC indeed, particularly given that this region specifically functions in top-down regulation, future self-continuity representation and social decisions (Huang et al., 2025; Lin and Feng, 2024; Knoch & Fehr, 2007). Despite this case, Xu and colleagues demonstrated null effects of anodally stimulating the right DPFC to modulate either value evaluation or emotional regulation for changing procrastination willingness (Xu et al., 2023).”

      (11) Active stimulation reduced procrastination, reduced task aversiveness, and increased the outcome value. If I am not mistaken, the authors claim based on these results that the brain stimulation effect operates via self-control, but - unless I missed it - the authors do not have any direct evidence (such as measures or specific task measures) that actually capture self-control. Thus, that self-control is involved seems speculation, but there is no empirical evidence for this; or am I mistaken about this? If that is indeed correct, I think it needs to be made explicit that it is an untested assumption (which might be very plausible, but it is still in the current study not empirically tested) that self-control plays any role in the reported results.

      We truly appreciate your pointing out this weakness with regard to conceptualization. Yes, you are correct in understanding this causal chain: we conceptually speculate that the HD-tDCS stimulation over the left DLPFC operates self-control to change procrastination, rather than empirically validating this component in the chain: brain stimulation→increased self-control→increased task outcome value→decreased procrastination. In this causal chain, we did not collect data to directly measure self-control at either baseline or post-neuromodulation times. Therefore, we all agree with your suggestion to explicitly claim this case in the main text. Following this advice, we have redrawn a portion of the Conclusion by clearly pointing out the hypothesis-generating role of self-control in mitigating procrastination, and have further claimed this case in the Limitation section:

      Abstract Section (Page 2, Line 55-57)

      “... This establishes a precise, value-driven neurocognitive pathway to account the conceptualized roles of self-control on procrastination, and offers a validated, theory-driven strategy for interventions.”

      Results Section (Page 10, Line 489-492 and 520-522)

      “Given the dual neurocognitive pathways identified above—reduced task aversiveness and increased task-outcome value—we proposed that these changes, conceptually driven by enhanced self-control via ms-tDCS over left DLPFC, account for how neuromodulation reduces procrastination. ...”

      “In summary, these findings demonstrated a mechanistic pathway underlying procrastination: the self-control that was conceptualized to be governed by left DLPFC mitigate procrastination by plausibly increasing task-outcome value.”

      Discussion Section (Page 13, Line 642-645)

      “Moreover, this study did not collect data for assessing participants’ self-control at either baseline or post-neuromodulation, thereby limiting our ability to determine whether the effects on procrastination were uniquely attributable to neuromodulation-induced changes in self-control. ...”

      (12) Figures 3F and 3H show that procrastination rates in the active modulation group go to 0 in all participants by sessions 6 and 7. This seems surprising and, to be honest, rather unlikely that there is absolutely no individual variation in this group anymore. In any case, this is quite extraordinary and should be explicitly discussed, if this is indeed correct: What might be the reasons that this is such an extreme pattern? Just a random fluctuation? Are the results robust if these extreme cells are ignored? The authors remove other cells in their design due to unusual patterns, so perhaps the same should be done here, at least as a robustness check.

      Thank you for raising this highly important and helpful comment. Indeed, we fully understand that this result is somewhat extraordinary, a fact that was equally striking to us when unblinding the data. After carefully scrutinizing the data and statistics, we are thrilled to confirm that this pattern is true. In support of this observation, we were gratified to receive numerous thank-you letters from participants who engaged in active neuromodulation. They expressed gratitude to us, and reported that they have substantially ameliorated procrastination behavior in real-life activities after completing the trial. While this does not constitute formal scientific evidence, we are also glad to see the benefits of this neuromodulation for those procrastinators.

      Two reasons could account for this pattern herein. One interpretation is to attribute this pattern to “scalar inflation”. In the present study, the procrastination rate was calculated as 1 minus the task-completion rate (e.g., 80%, 60%, 40%) by the deadline. At sessions # 6 and #7, all the participants completed their real-life tasks before the deadline, yielding a 0% (1 minus 100% completion rate) procrastination rate, without any between-individual variation. Thus, rather than there being no individual variation in procrastination, this scalar – the procrastination rate - is too insensitive to capture subtle differences per se. For instance, although participants #1 and #2 both showed a 0% procrastination rate - meaning that both completed their tasks before the deadline - Participant #1 might have completed it 3 hours before the deadline, whereas Participant #2 might have completed it only 10 minutes before. In this case, the “scalar inflation” emerges to let us perceive that both participants have equivalent procrastination rates, although participant #2 may have a higher procrastination level than #1. As conceptually defined in the field, procrastination is contextualized as “not completing a task before the deadline”. Thus, if this task is completed before the deadline, regardless of whether it was finished close to or far in advance of the deadline, this case is defined as “no procrastination”. In the present study, the primary outcome is whether a participant procrastinated on a real-life task before the deadline in real-world settings, irrespective of when she/he completed this task. Thus, this scalar - procrastination rate - fits our conceptualization of procrastination.

      Another reason is the potential accumulative effects from sequential multi-session tDCS stimulation. As shown in Mann-Kendall trend tests, the procrastination rates show a significant linear downtrend in the active neuromodulation group across sessions, even after removing sessions #6 and #7. This indicates that the improvements of going against procrastination may be sequentially accumulative along with the increase in sessions, implying a potential “dose-dependent effect”. Despite a speculative interpretation, this “dose-dependent effect” in neuromodulation has been well-documented in previous studies, showing the robustly linear association between the number of sessions and effectiveness (c.f., Cole et al., 2020; Hutton et al., 2023; Sabé et al., 2024; Schulze et al., 2018). Therefore, although this extreme pattern is somewhat extraordinary compared to previous observations, it makes sense.

      Yes, this is a definitely great idea to carry out a robustness check by removing sessions #6, #7, or both. We do believe that this analysis could support statistical robustness to go against potential biases from extreme cells. By doing so, we found that all the group*treatment_day interaction effects remained significant when removing either session #6 or session #7 (or even both, all p-values < .05), indicating high statistical robustness. Please see Supplementary table S3 and S4

      Taken together, in spite of their being extraordinary, we confirm that those findings are statistically robust to extreme outliers. As you kindly suggested, we have added those findings of the robustness check into the revised Supplemental Materials section.

      References

      Cole, E. J., Stimpson, K. H., Bentzley, B. S., Gulser, M., Cherian, K., Tischler, C., Nejad, R., Pankow, H., Choi, E., Aaron, H., Espil, F. M., Pannu, J., Xiao, X., Duvio, D., Solvason, H. B., Hawkins, J., Guerra, A., Jo, B., Raj, K. S., Phillips, A. L., … Williams, N. R. (2020). Stanford Accelerated Intelligent Neuromodulation Therapy for Treatment-Resistant Depression. The American journal of psychiatry, 177(8), 716–726. https://doi.org/10.1176/appi.ajp.2019.19070720

      Hutton, T. M., Aaronson, S. T., Carpenter, L. L., Pages, K., Krantz, D., Lucas, L., Chen, B., & Sackeim, H. A. (2023). Dosing transcranial magnetic stimulation in major depressive disorder: Relations between number of treatment sessions and effectiveness in a large patient registry. Brain stimulation, 16(5), 1510–1521. https://doi.org/10.1016/j.brs.2023.10.001

      Sabé, M., Hyde, J., Cramer, C., Eberhard, A., Crippa, A., Brunoni, A. R., Aleman, A., Kaiser, S., Baldwin, D. S., Garner, M., Sentissi, O., Fiedorowicz, J. G., Brandt, V., Cortese, S., & Solmi, M. (2024). Transcranial Magnetic Stimulation and Transcranial Direct Current Stimulation Across Mental Disorders: A Systematic Review and Dose-Response Meta-Analysis. JAMA network open, 7(5), e2412616. https://doi.org/10.1001/jamanetworkopen.2024.12616

      Schulze, L., Feffer, K., Lozano, C., Giacobbe, P., Daskalakis, Z. J., Blumberger, D. M., & Downar, J. (2018). Number of pulses or number of sessions? An open-label study of trajectories of improvement for once-vs. twice-daily dorsomedial prefrontal rTMS in major depression. Brain stimulation, 11(2), 327–336. https://doi.org/10.1016/j.brs.2017.11.002

      (13) The supplemental materials, unfortunately, do not give more information, which would be needed to understand the analyses the authors actually conducted. I had hoped I would find the missing information there, but it's not there.

      Sorry to offer uninformative supplemental materials (SM) in the original submission. As you suggested, we have added a substantial number of details to clarify how we conducted data analyses in the main text, and also tightened the whole SM section to improve readability and comprehensibility. We do hope that this revised manuscript could offer clear and adequate information in understanding methods and statistics for broader readers.

      In sum, the reported/cited/discussed literature gives the impression of being incomplete/selectively reported; the analyses are not reported sufficiently transparently/fully to evaluate whether they are appropriate and thus whether the results are trustworthy or not. At least some of the patterns in the results seem highly unlikely (0 procrastination in the verum group in the last 2 observation periods), and the sample size seems very small for a between-subjects design.

      Thank you for this very helpful summary. As you kindly suggested above, we have overhauled this manuscript to address those points that you listed here, particularly where we added relevant literature to balance our claims, added a huge amount of details to sufficiently/transparently report statistics, and conducted a robustness check to confirm the statistical robustness of our findings to those plausible extreme patterns (sessions #6 and #7), as well as justified how we determined this sample size fulfilling medium statistical power in a priori. Please see above for full details regarding how we addressed those comments, point-by-point.

      Reviewer #2 (Public Review):

      Chen and colleagues conducted a cross-sectional longitudinal study, administering high-definition transcranial direct stimulation targeting the left DLPFC to examine the effect of HD-tDCS on real-world procrastination behavior. They find that seven sessions of active neuromodulation to the left DLPFC elicited greater modulation of procrastination measures (e.g., task-execution willingness, procrastination rates, task aversiveness, outcome value) relative to sham. They report that tDCS effects on task-execution willingness and procrastination are mediated by task outcome value and claim that this neuromodulatory intervention reduces procrastination rates quantified by their task. Although the study addresses an interesting question regarding the role of DLPFC on procrastination, concerns about the validity of the procrastination moderate enthusiasm for the study and limit the interpretability of the mechanism underlying the reported findings.

      Strengths:

      (1) This is a well-designed protocol with rigorous administration of high-definition transcranial direct current stimulation across multiple sessions. The approach is solid and aims to address an important question regarding the putative role of DLPFC in modulating chronic procrastination behavior.

      (2) The quantification of task aversiveness through AUC metrics is a clever approach to account for the temporal dynamics of task aversiveness, which is notoriously difficult to quantify.

      Thank you for taking your invaluable time to review our manuscript, warmly applauding the strength in research design and the conceptualization of scaling task aversiveness, as well as kindly sharing such helpful and insightful evaluations. As you correctly pointed out, we are aware of the absence of detailed, clear and understandable reporting of measures (e.g., real-world procrastination), statistics and methods, in the original manuscript. Following all your suggestions, we have thoroughly revised this manuscript to address those comments that you kindly made, point-by-point. Please see the full response underneath.

      Weaknesses:

      (1) The lack of specificity surrounding the "real-world measures" of procrastination is problematic and undermines the strength of the evidence surrounding the DLPFC effects on procrastination behavior. It would be helpful to detail what "real-world tasks" individuals reported, which would inform the efficacy of the intervention on procrastination performance across the diversity of tasks. It is also unclear when and how tasks were reported using the ESM procedure. Providing greater detail of these measures overall would enhance the paper's impact.

      We genuinely appreciate your raising this very crucial comment. We are sorry for omitting a tremendous number of methodological details to comply with the editorial requirement on the manuscript’s length, which hampered the comprehension of how we measure “real-life tasks” and “real-world procrastination”.

      As shown in the schematic diagram for experimental procedure (Fig. 1), the experimental protocol alternated between Neuromodulation Days (Days 2, 4, 6, 8, 10, 12, 14) and Task Days (Days 1, 3, 5, 7, 9, 11, 13, 15). On each Neuromodulation Day, participants received either active or sham HD-tDCS, and—critically—before stimulation—were instructed to specify a real-life task they were required to complete the following day, with a deadline between 18:00 and 24:00. This ensured ≥24 hours between neuromodulation and task execution, isolating offline after-effects. For instance, on Day #2 (Neuromodulation Day), before carrying out stimulation, participants were asked to report a real-life task that has a deadline within 18:00 - 24:00 for tomorrow’s “task day” (Day #3) (please see the schematic diagram in Author response image 2).

      Author response image 2.

      There are some real-life tasks that they reported in our experiment as examples: “Complete and submit a homework assignment”, “Complete a standardized English proficiency test”, “Complete an online course module required for applying a Class C driver’s license”, “Prepare slides for a seminar presentation”, “Practice guitar”, “Practice Chinese calligraphy”, and “Do the laundry”. Reported tasks spanned academic (e.g., submitting an assignment), occupational (e.g., preparing a presentation), administrative (e.g., applying for a license), self-improvement (e.g., practicing guitar for ≥30 min), domestic (e.g., laundry), and health-related domains (e.g., running ≥ 2,000m for exercise), indicating a plausible task diversity.

      On each “task day”, participants engaged in an intensive Experience Sampling Method (iESM) protocol via a custom-built mobile app. Using this app, participants were required to report a subjective task-execution willingness score (i.e., a one-item 100-point visual analog scale, “How willing are you to do this task?”, 0 for “I will definitely procrastinate this task” and 100 for “I will take action to complete this task immediately”; procrastination willingness = 100 – the task-execution willingness score), the subjective task aversiveness (i.e., a one-item 100-point visual analog scale), the subjective task outcome value (i.e., a one-item 100-point visual analog scale), and the objective procrastination rate, respectively.

      Rather than self-reported scores from those one-item visual analog scales, we asked participants to report real “task completion rate” for the objective quantification of the “real-world procrastination behavior”. Specifically, at the deadline, each participant was asked to report whether she/he had completed this task. If she/he reported not having yet completed the task (i.e. procrastination behavior emerged), she/he was further required to report the percentage of the task completed (1% - 99%), which was defined as the task completion rate. By doing so, we could calculate the real-world procrastination rate for the real-life task as the “1 – the task completion rate”. For instance, if a participant did not complete her/his real-life task before the deadline (i.e. she/he procrastinated this task) and reported completing 75% of this task at the deadline, her/his real-world procrastination rate was computed as the 25% (1 - 75%) (Please see the schematic diagram in Author response image 3).

      Moreover, rather than merely a self-reported task completion rate, each participant was also asked to upload proof (e.g., screenshots of submitted assignments, photos of printed documents, system timestamps) to the ESM digital system for validation.

      Author response image 3.

      To determine the sampling time points for this mobile app in the ESM, we capitalized on both the conceptual temporal decision model and the statistical Myerson algorithm. Specifically, the Temporal Decision Model (TDM) was originally proposed by our team (Xu et al., 2023; Zhang et al., 2019, 2020, 2021), which theoretically conceptualizes procrastination as the failure of the trade-off between task outcome value (i.e., motivation to take actions now for pursuing task reward) and task aversiveness (i.e., motivations for avoiding taking action now for avoiding negative experiences). Once task aversiveness overrides the pursuits of task outcome values, procrastination emerges. One overarching hypothesis in this theoretical model is that the task aversiveness is hyperbolically discounted when approaching the deadline: it would be discounted sharply when far from the deadline but discounted slowly when nearing the deadline (Zhang et al., 2019). To maximize statistical power to fit dynamic motivational curves, we employed a log-spaced temporal sampling scheme (Myerson et al., 2001) (please see the schematic diagram in https://uen.pressbooks.pub/behavioraleconomics/chapter/the-reality-of-homo-sapiens, where each point indicates a sampling time):

      By this fitting algorithm (Myerson et al., 2001), five time points were selected to fulfill the statistical prerequisites for hyperbolic model fitting, with increasing sampling density toward the deadline (e.g., for a task due at 20:00: sampled at 10:00, 16:00, 18:00, 19:30, 20:00). Once the task-specific five sampling time points were determined per participant, this mobile app sent a digital message to ask her/him to immediately report the task aversiveness and the task outcome value then. As the primary outcomes, the procrastination rate (i.e., 1 – the task completion rate) and the procrastination willingness were sampled at the deadline point.

      Furthermore, yes, we fully concur with you on this great idea, that is, transparency about task diversity strengthens the generalizability of our findings. In response, we have tabulated these real-life tasks that were reported in this experiment in the independent Appendix 1, with automatic translations from Chinese to English via Qwen GPT. Please see below for what we have added to the main text:

      Methods Section (Page 6-7, Line 238-308)

      “Nested cross-sectional longitudinal design

      This study used a nested cross-sectional longitudinal design to investigate whether the multiple-session anodal HD-tDCS targeting the left DLPFC could reduce actual procrastination behavior and to probe how this effect manifests. To assess procrastination in daily life, we implemented a 15-day protocol alternating between Neuromodulation Days (Days 2, 4, 6, 8, 10, 12, 14) and Task Days (Days 1, 3, 5, 7, 9, 11, 13, 15). On the Neuromodulation days, the 20-min anodal HD-tDCS neuromodulation targeting the left DLPFC was performed for HD-tDCS active group at intervals of 2 days, while the sham-control group received sham HD-tDCS training. This HD-tDCS training was repeated for a total of seven sessions, and lasted 15 days (see Fig. 1a). Crucially, to capture procrastination in ecologically valid contexts, prior to receiving either active or sham HD-tDCS (administered between 09:00–18:00), participants were instructed to specify a real-life task they were personally obligated to complete the following day, with a self-defined deadline strictly constrained to 18:00–24:00 to ensure ≥24 hours between stimulation offset and task deadline, thereby isolating offline after-effects. This task should meet the following three criteria: (a) it should be already assigned in the real-world settings; (b) deadline should be constrained to 18:00-24:00 (see above); (c) it should be more likely to induce procrastinate. By doing so, more than 300 real-life tasks were collected, spanning academic (e.g., “submit a statistics homework assignment”), occupational (e.g., “draft and email a project proposal”), administrative (e.g., “complete online application for Class C driver’s license”), self-improvement (e.g., “practice guitar for ≥30 minutes”), domestic (e.g., “do laundry ”), and health-related (e.g., “running 2,000m for exercise”). Full task list has been tabulated in the Appendix 1. As primary outcomes, all the participants were required to reported task-execution willingness (TEW) (Zhang & Feng, 2020; Zhang, Liu, et al., 2019), for a real-life task 24 hours post-neuromodulation. Thus, procrastination willingness was quantified as 100-TEW score (see underneath for details). Furthermore, we asked participants to report the actual task completion rate (CR) of the task at the deadline (e.g. participant A finished 90% homework at deadline and reported this situation to us at deadline). In this vein, the actual procrastination rate (PR) was quantified as 1-CR.

      On the Task day, we developed a mobile app to implement experience sampling method (ESM) for tracking one’s real-time evaluation of task aversiveness and task outcome value (see Fig. 1). The task aversiveness describes how disagreeable one perceives performing a given real-life task to be, whereas outcome value refers to the subjective benefits of the task outcome brought about by completing the task before the deadline (Zhang & Feng, 2020). As theoretically conceptualized by the temporal decision model (TDM) of procrastination, the perceived task aversiveness is hyperbolically discounted when approaching deadline, showing sharply discounting when faring away from deadline but slowly discounting once nearing deadline (Zhang & Feng, 2020; Zhang et al., 2021). Thus, considering this nonlinear dynamics inherent in this hyperbolic discounting, the five recording moments of ESM were selected per task a prior by using a log-spaced temporal sampling scheme (Myerson et al., 2001), with increasing sampling density toward the deadline, such as moments of 10:00 (earliest), 16:00, 18:00, 19:30, 20:00 (deadline). The five sampling points could meet statistical prerequisite in the hyperbolic model fitting (requiring ≥ 4 points; Green & Myerson, 2004). To do so, recording moments of tasks were individually tailored for each task per participant in this ESM procedure. To obviate the confounds of daily emotions in task aversiveness evaluation, we used the averaged scores of PANAS at 10:00 (noon) and 16:00 (afternoon) as anchoring points to quantify one’s daily emotions by using this ESM app. Before each session of HD-tDCS training, each participant was required to report a real-life task whose deadline is tomorrow. To obtain the long-term effect of HD-tDCS (i.e., the interval between HD-tDCS and task completion is at least 24 hours), the task deadline that participants reported was required to be between 18:00 - 24:00. Once a sampling time reached, this app would send a digital message to require participants to fill online form for data collection.

      Quantification of covariates of interests

      Outcome variables of this study were twofold: one is task-execution willingness and another is procrastination rate (PR). Task-execution willingness is used to evaluate one’s subjective inclination to avoid procrastination (Zhang & Feng, 2020). In this vein, we used a 100-point scale to require participants to report their task-execution willingness (0 for “I will definitely procrastinate this task” and 100 for “I will take action to complete this task immediately”). This metric was recorded 24 hours after neuromodulation to examine its long-term effects. PR is used to quantify the extent to which one task has been procrastinated, and was calculated as 1 - CR (task completion rate). Critically, at the precise deadline, the app prompted participants to (a) indicate task completion status (yes/no), and if incomplete, (b) report the percentage completed (1–99%), defined as the Task CR, while simultaneously uploading objective evidence (e.g., screenshots of submitted files, photos of physical outputs, system-generated logs, or app-exported records). If the task was actually completed before the deadline, the CR would be 100% and the PR would be calculated as 0% (1-CR). PR was recorded at the actual task deadline for each participant. We were also interested in re-investigating their actual procrastination by using PR 6 months after the last neuromodulation to test the long-term retention of this neuromodulation effect.”

      References

      Myerson, J., Green, L., & Warusawitharana, M. (2001). Area under the curve as a measure of discounting. Journal of the experimental analysis of behavior, 76(2), 235–243. https://doi.org/10.1901/jeab.2001.76-235

      Xu, T., Zhang, S., Zhou, F., & Feng, T. (2023). Stimulation of left dorsolateral prefrontal cortex enhances willingness for task completion by amplifying task outcome value. Journal of experimental psychology. General, 152(4), 1122–1133. https://doi.org/10.1037/xge0001312

      Zhang, S., Verguts, T., Zhang, C., Feng, P., Chen, Q., & Feng, T. (2021). Outcome Value and Task Aversiveness Impact Task Procrastination through Separate Neural Pathways. Cerebral cortex (New York, N.Y. : 1991), 31(8), 3846–3855. https://doi.org/10.1093/cercor/bhab053

      Zhang, S., Liu, P., & Feng, T. (2019). To do it now or later: The cognitive mechanisms and neural substrates underlying procrastination. Wiley interdisciplinary reviews. Cognitive science, 10(4), e1492. https://doi.org/10.1002/wcs.1492

      Zhang, S., & Feng, T. (2020). Modeling procrastination: Asymmetric decisions to act between the present and the future. Journal of experimental psychology. General, 149(2), 311–322. https://doi.org/10.1037/xge0000643

      (2) Additionally, it is unclear whether the reported effects could be due to differential reporting of tasks (e.g., it could be that participants learned across sessions to report more achievable or less aversive task goals, rather than stimulation of DLPFC reducing procrastination per se). It would be helpful to demonstrate whether these self-reported tasks are consistent across sessions and similar in difficulty within each participant, which would strengthen the claims regarding the intervention.

      Thank you for raising this very crucial comment. We indeed agree with you on this point that the reported effects may vary with task difficulties and task-execution proficiency, which potentially confound the effects of stimulation on mitigating procrastination. As you correctly comment, given no data collection on difficulties or other relevant characteristics of tasks, we cannot completely rule out this confounder in interpreting our findings on the one hand. As a result, we have explicitly claimed this limitation in the Discussion section.

      On the other hand, despite no quantitative evidence, this risk of confounding main effects with disparities in task characteristics was controlled experimentally. As we reported above, all the reported tasks were mandated to meet three criteria: (a) they were already assigned in the real-world settings; (b) the deadline was constrained to 18:00-24:00; (3) they were likely to lead to procrastinate. To do so, each participant was clearly instructed to report a real-life task that was more likely to be procrastinated in real-world settings, and was not allowed to report easy, achievable and cost-less tasks. Supporting this case, those reported tasks were found spanning academic (e.g., submitting an assignment), occupational (e.g., preparing a presentation), administrative (e.g., applying for a license), self-improvement (e.g., practicing guitar for ≥30 min), domestic (e.g., laundry), and health-related domains (e.g., running ≥ 2,000m for exercise), indicating a plausible task diversity and difficulty. This was resonated by observing the high within-subject task homogeneity. For instance, for Participant #5, she/he reported the tasks that were almost all around academic activities across all the sessions. Therefore, as the task list reported (please see Appendix 1), these self-reported tasks were plausibly consistent across sessions and similar in difficulty within each participant.

      In addition, as we tested, almost all the participants reported they were receiving treatment, with 91.30% (21/23) for the active neuromodulation group (NM) and with 86.95% (20/23) for the sham control group (SC) (x<sup>2</sup> = 0.224, p = .636), indicating the effectiveness of the double-blinding methods. If participants learned across sessions to report more achievable or less aversive task goals, their procrastination willingness and procrastination rates for their reported tasks would all increasingly decrease, irrespective of whether they were in the active neuromodulation-effect group or the sham group. However, no such effects - procrastination willingness and procrastination rates for their reported tasks increasingly decreasing across sessions - existed in the sham control group (Mann-Kendall test, for procrastination willingness, tau = 0.60, p = .13; for procrastination rate, tau = 0.61, p = .13), indicating no statistically significant learning effect or strategic effect on task performance. Again, thank you for this very crucial comment, and we do hope these clarifications could address it.

      Limitations Section (Page 12, Line 637-640)

      “In addition, despite instructing to report valid real-life tasks with high probabilities to procrastinate, we had not yet measured the task difficulty and consistency across sessions for each participant. Consequently, interpreting the effects of neuromodulation to mitigate procrastination as “unique contributions” should warrant cautions. ...”

      (3) It would be helpful to show evidence that the procrastination measures are valid and consistent, and detail how each of these measures was quantified and differed across sessions and by intervention. For instance, while the AUC metric is an innovative way to quantify the temporal dynamics of task-aversiveness, it was unclear how the timepoints were collected relative to the task deadline. It would be helpful to include greater detail on how these self-reported tasks and deadlines were determined and collected, which would clarify how these procrastination measures were quantified and varied across time.

      We do appreciate your highlighting the importance of clarifying how to measure procrastination, substantially helping readers to interpret these findings. As reported above, the primary outcomes of this experiment included subjective procrastination willingness and objective actual procrastination rate. For the subjective procrastination willingness, using the purpose-built mobile app, participants were required to report subjective task-execution willingness score (i.e., one-item 100-point visual analog scale, “How willing are you to do this task?”, 0 for “I will definitely procrastinate this task” and 100 for “I will take action to complete this task immediately”). Thus, the procrastination willingness was computed as “100 – the task-execution willingness score”. For the objective procrastination rate, rather than self-reported scores from those one-item visual analog scales, we asked participants to report the real “task completion rate from 1% to 99%” for the objective quantification of the “real-world procrastination behavior”. Full details can be found in Response #1.

      For determining sampling time points for the quantification of AUC, we capitalized on both the conceptual Temporal Decision Model and the statistical Myerson algorithm. Specifically, the Temporal Decision Model (TDM) was originally proposed by our team (Xu et al., 2023; Zhang et al., 2019, 2020, 2021), which theoretically conceptualizes procrastination as the failure of the trade-off between task outcome value (i.e., motivation to take actions now for pursuing task reward) and task aversiveness (i.e., motivations for avoiding taking action now for avoiding negative experiences). Once task aversiveness overrides the pursuits of task outcome values, the procrastination emerges. One overarching hypothesis in this theoretical model is that the task aversiveness is hyperbolically discounted when approaching the deadline: it would be discounted sharply when being far from the deadline but discounted slowly when nearing the deadline (Zhang et al., 2019). To maximize statistical power to fit dynamic motivational curves, we employed a log-spaced temporal sampling scheme (Myerson et al., 2001). By this fitting algorithm (Myerson et al., 2001), five time points were selected to fulfill the statistical prerequisites for hyperbolic model fitting, with increasing sampling density toward the deadline (e.g., for a task due at 20:00: sampled at 10:00, 16:00, 18:00, 19:30, 20:00).

      Once the task-specific five sampling time points were determined per participant, this mobile app sent a digital message to ask her/him to immediately report the task aversiveness and the task outcome value then. After capturing the task aversiveness from those five time points, the task aversiveness discounting was calculated as 1- (A(t) / A(earliest)), where t(earliest) was the earliest sampling point (e.g., 10:00), serving as the reference for immediate execution. Subsequently, using the GraphPad Prisma software (v9, 525), we estimated the AUC from those five data points based on the Myerson algorithm (Myerson et al., 2001), which was computed via the trapezoidal integration between task aversiveness discounting and time. By this modelling method, a higher AUC reflects stronger temporal discounting of task aversiveness, which means that participants experience a faster decline in subjective aversiveness as execution is delayed, yielding lower effective aversiveness and reduced avoidance behavior. That is to say, if a participant showcases a greater discounting of task aversiveness as reflected by a higher AUC, she/he experiences a more pronounced reduction in subjective aversiveness upon postponement, plausibly yielding less procrastination.

      Taken together, following your suggestion, we have added a substantial number of details to clarify how to measure procrastination, when to sample the data and how to estimate the AUC into the revised manuscript. Please see them in Response #1.

      (4) There are strong claims about the multi-session neuromodulation alleviating chronic procrastination, which should be moderated, given the concerns regarding how procrastination was quantified. It would also be helpful to clarify whether DLPFC stimulation modulates subjective measures of procrastination, or alternatively, whether these effects could be driven by improved working memory or attention to the reported tasks. In general, more work is needed to clarify whether the targeted mechanisms are specific to procrastination and/or to rule out alternative explanations.

      Yes, we fully agree with you on this consideration: we should tone down the conclusions currently claimed in the main text, given the inherent shortcomings mentioned above. As you helpfully suggested, we have moderated our overall claims regarding the effects of multi-session neuromodulation in alleviating chronic procrastination. Please see specific instances below:

      Abstract Section (Page 2, Line 55-57)

      “... This establishes a precise, value-driven neurocognitive pathway to account the conceptualized roles of self-control on procrastination, and potentially offers a validated, theory-driven strategy for interventions.”

      Conclusion Section (Page 13, Line 657-664)

      “In conclusion, this study potentially provides an effective way to reduce both procrastination willingness and actual procrastination behavior by using neuromodulation on the left DLPFC. Furthermore, such effects have been observed for 2-day-interval long-term after-effects, and were also found for 6-month long-term retention in part. More importantly, this study identified that the ms-tDCS neuromodulation could decrease task aversiveness and increase task outcome value while, and further demonstrated that the increased task outcome value could predict decreased procrastination, a relationship conceptually driven by enhancing self-control. In this vein, the current study enriches our understanding of neurocognitive mechanism of procrastination by showing the prominent role of increased task outcome value in reducing procrastination. Also, it may provide an effective method for intervening in human procrastination.”

      Moreover, yes, as we clarified above, in addition to the objective measure of procrastination behavior, we also leveraged a one-item visual analog scale (i.e. one-item 100-point visual analog scale, “How willing are you to do this task?”, 0 for “I will definitely procrastinate this task” and 100 for “I will take action to complete this task immediately”) to measure subjective procrastination willingness. Results demonstrated that the subjective procrastination willingness significantly decreased across neuromodulation sessions in the active group, but not in the sham control group, consistent with the observed reduction in the objective procrastination measure. In addition, we all perceive it as helpful and crucial to note that we cannot draw the conclusion that the effects of neuromodulation on mitigating procrastination are contributed by increasing task outcome value uniquely. Given no measures or evidence of other factors, such as working memory and attention, we cannot rule out other neurocognitive pathways. To address this point, we have removed or rephrased such statements throughout the whole revised manuscript, and explicitly constrained to interpret this neurocognitive mechanism (i.e., increased task outcome value) within the theory-driven framework of the temporal decision model.

      Reviewer #3 (Public review):

      This manuscript explores whether high-definition transcranial direct current stimulation (HD-tDCS) of the left DLPFC can reduce real-world procrastination, as predicted by the Temporal Decision Model (TDM). The research question is interesting, and the topic - neuromodulation of self-regulatory behavior - is timely.

      Many thanks for kindly dedicating time to review our manuscript, and for the helpful comments detailed below. Thank you for appreciating the novelty of this study.

      However, the study also suffers from a limited sample size, and sometimes it was difficult to follow the statistics.

      Thank you for pointing out these crucial concerns. As you correctly raised, the sample size is somewhat small in any case, but we confirm that this sample size is adequate to obtain medium statistical power.

      For estimating the sample size, we determined the a priori effect size based on the existing work we published (Xu et al., 2023, J Exp Psychol Gen;152(4):1122-1133). In this pilot study, we identified a significant interaction effect between single-session tDCS stimulation (active vs sham) and time (pre-test vs post-test) (t = 2.38, p = .02, n = 27; 95% CI [0.14, 1.49]) for changing procrastination willingness in laboratory settings, indicating a medium effect size. Therefore, this pilot study provides supportive evidence to determine this effect size a priori.

      Using the GPower software with an estimation of a medium effect size, we determined that a total sample size of N<sub>total</sub> = 34 could reach adequate statistical power. Please see outputs of the GPower in Author response image 1.

      As for the statistics, we genuinely acknowledge that the vague methodological descriptions and complex algorithms indeed complicated the understanding of the methods and statistics. To address this, echoing the comment raised by Reviewer #1, we have removed the complicated statistics and methods, and further clarified how we used the generalized linear mixed-effect model (GLMM) for statistical analysis. Please see the specific revisions below:

      Methods Section (Page 8, Line 378-403)

      “Statistics

      All the statistics were implemented by R (https://www.rstudio.com/) and R-dependent packages.

      To clarify whether multiple-session HD-tDCS neuromodulation can reduce procrastination, the generalized mixed-effects linear model (GLMM) was constructed with full factorial design for subjective procrastination willingness (i.e., self-reported visual analog scores) and actual procrastination behavior (i.e., real-world task-completion rate before deadline). Here, sex, age and socioeconomic status (SES) were modeled as covariates of no interest. As the National Bureau of Statistics (China) issued (https://www.stats.gov.cn/sj/tjbz/gjtjbz/), on the basis of per capita annual household income, the SES was divided into seven hierarchical tiers from 1 (poor) to 7 (rich). To obviate subjective rating bias stemming from individual daily mood, we separately measured participants’ daily emotional fluctuation at 10:00 and 16:00 using a self-rating visual analog item (i.e., “How do feel for your mood today?”, 0 for “completely uncomfortable” and 100 for “definitely happy”). By doing so, the averaged score of those self-rating emotions at the two time points was modeled into the GLMM as covariate of no interests, yielding the final expression of “outcome ~ Group*Treatment_Day + Age + Gender + SES + Emotions + (1 + Treatment_Day | SubjectID)” in the statistical model”. This analysis was implemented using the “lme4” and “lmerTest” packages. Employing “emmeans” package, simple effects were also tested at baseline and post-last-intervention using Tukey-adjusted pairwise comparisons of estimated marginal means from the full GLMM, controlling for covariates and random-effects structure. To validate statistical robustness, instead of continuous outcomes for parametric tests, we also conducted a between-group comparison for the number of tasks that procrastination emerges by using the nonparametric x<sup>2</sup> test with φ correction or Fisher exact test. Regarding the 6-month follow-up investigation, this GLMM was also built to examine the long-term retention of neuromodulation on reducing actual procrastination.”

      The preregistration and ecological design (ESM) are commendable, but I was not able the find the preregistration, as reported in the paper.

      We are sorry to encounter a serious technical barrier that has rendered our preregistration invisible and inaccessible. The OSF has disabled my OSF account, as it claimed to detect “suspicious user’s activities” in my account. This has prevented access to all materials deposited in this OSF account, including this preregistration. We have contacted the OSF team, but received no valid technical solution to recover this preregistered report (please see the screenshot below). We reckon that this may be due to my affiliation change to the Third Military Medical University of People’s Liberation Army (PLA).

      To address this unexpected circumstance and to ensure transparency, we have explicitly reported this case in the main text, and added the “Reconstructed Preregistration Statement” to the Supplemental Materials (SM). Also, as it has been out of best practices in preregistration, in addition to transparently reporting this case, we have removed this statement regarding preregistration elsewhere throughout the revised manuscript.

      Overall, the paper requires substantial clarification and tightening.

      We are grateful for your evaluation, and we fully agree with you. In response, we have added a tremendous number of details to clarify how to measure procrastination, how to conduct the statistical analyses, and how to collect real-life tasks, as well as other experimental materials. Please see the revisions in the Methods section of the revised manuscript. Again, thank you for those helpful suggestions.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In the Supplemental Materials, page 4, lines 163 to 167 seem to be from a different manuscript (as the section talks about neural markers, significant clusters, and brain networks).

      We are sorry for erroneously embedding this irrelevant section here. We have removed it, and have double-checked the document to avoid such mistakes.

      (2) I'm no expert here, but some of the trace and density plots in the SOM look problematic (e.g., Figure S5 top panel). But it's not made clear to which model/analysis these plots belong, so they are not very helpful without that information.

      Thank you for bringing these potentially problematic plots to our attention. Following your great suggestion, these results have been removed from the SM to amplify readability and comprehensibility.

      (3) Table S1 reports side effects "from the neurostimulation" (this is also the language used in the main manuscript), but having the flu is rather unlikely to be a side effect from the stimulation, isn't it? Thus, this language is highly confusing, and when reading the main text, it's not clear that these are just life events that are most likely unrelated to the stimulation, but have the potential to affect the measured variables (i.e., ultimately, they seem a source of noise).

      We apologize for this confusing wording. Here, the “side effects” are defined as confounding effects deriving from unexpected life events that uncontrollably disrupt task execution and task performance, such as “having the flu”, or “an unexpected mandatory CCP (Communist Party of China) meeting assignment”. To obviate misunderstanding, we have rephrased “side effects” as “unexpected life events disrupting task execution” in both the main text and the SM section both.

      (4) The use of the English language could be improved.

      Thank you for your very practical suggestion. As you kindly suggested, we have invited a proofreading editor to edit and polish the English of the revised manuscript.

      Reviewer #2 (Recommendations for the authors):

      (1) It would be helpful to include greater detail about the ESM procedure and details of the self-reported tasks. This would help rule out potential confounds of difficulty or learning (e.g., participants may have learned to identify more achievable and less difficult tasks across the sessions, which would mean they are learning to perform the task better rather than to procrastinate less). Further elaboration on the quantification of procrastination measures would help clarify the mechanism underlying this behavior, which is important for clarifying how these effects arise and what aspect of procrastination behavior is being targeted by the tDCS intervention (and rule of alternative explanations).

      We wholeheartedly appreciate your sharing this very crucial recommendation. As we mentioned above, we fully followed your helpful suggestions, particularly by adding massive details to fully report how to collect real-life tasks (with consistent and plausible difficulty across sessions), how to determine sampling time points, and how to quantify metrics (e.g., subjective procrastination willingness score, objective procrastination rate, AUC of task aversiveness, and task outcome value) to the revised manuscript. We do believe that these revisions and clarifications are imperative and necessary. By including these details, we do believe that the readability and clarity have been substantially improved in the current form. Please see the specific revisions and clarifications above.

      (2) It would be helpful to proofread for grammatical and spelling typos (e.g., DLPFC is spelled incorrectly in line 140, Satterwaite is spelled incorrectly in Line 415).

      Thank you for your kind suggestion. Both spelling typos have been corrected, and we have double-checked the revised manuscript to ensure no such typos remain. As you kindly suggested, we have invited a proofreading editor to edit and polish the English of the revised manuscript.

      (3) Please clarify in Figure 4 that a higher AUC is associated with lower task aversiveness (which is stated in the methods but not clearly in the figure).

      Many thanks to you for your helpful suggestion. As you kindly suggested, we have clarified this case in the figure legend.

      Reviewer #3 (Recommendations for the authors):

      I want to see the preregistration.

      Thank you for your helpful recommendation. As we replied above, a serious technical issue on OSF occurred, making our preregistration invisible and inaccessible. OSF has disabled my account, claiming to detect “suspicious user’s activities” in my account. As a result, there is no access to all materials that were already deposited in this OSF account, including this preregistration. We have reconstructed this preregistration based on archived documents, and reported it in the SM. As we reported above, although this partially addresses the problem, it no longer fulfills the best practices of preregistration. Consequently, in addition to transparently reporting this case, we have removed all the preregistration statements throughout the revised manuscript.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This interesting paper probes the problematic relationships between the classical "spiralian" taxa, i.e., annelids, molluscs, brachiopods, platyhelminths and nemerteans, and shows that the branches leading to them are so short as to be unreliable guides to their relationships. This, in turn, has important implications for how we view the origin of the animal phyla.

      Strengths:

      A very careful analysis of a famous old problem with quite significant results. The results seem to be robust and support their conclusions.

      It often passes uncommented that many different trees are published about animal relationships, yet some parts of the tree seem extremely difficult to resolve; the spiralians are perhaps the most difficult case. More recently, problems about sponges or ctenophores as sister groups to the rest of the animals have alerted us to major areas of uncertainty in large-scale phylogenetic reconstruction; this paper is a welcome reminder that other, perhaps even harder, problems exist which may be difficult to ever resolve with the (molecular) data we have.

      Weaknesses:

      The paper could have perhaps drawn out some of the implications of its results in a clearer manner.

      Reviewer #2 (Public review):

      Summary:

      The relationships among the phyla making up Spiralia - a major clade of animals including molluscs, annelids, flatworms, nemerteans and brachiopods - have been challenging from a phylogenomic perspective despite decades of molecular phylogenetic effort. Every topology uniting subsets of these phyla has been recovered with apparent support in at least one study, yet no consensus has emerged even from large-scale genomic datasets. Serra Silva and Telford set out to determine whether this instability reflects a genuine biological signal being obscured by analytical limitations, or whether it reflects a rapid, near-simultaneous origin of these phyla that has left behind in modern genomes far too little phylogenetic information to resolve. They focused deliberately on five phyla, reducing the problem to a tractable set of 15 unrooted and 105 rooted topologies, and applied a suite of complementary approaches across two independent datasets and multiple substitution models to test whether any topology is significantly preferred over alternatives.

      Strengths:

      (1) The conceptual framing of the problem is excellent, and the study makes a convincing case across several lines of evidence. By enumerating all possible topologies and demonstrating empirically that every one of the 15 unrooted arrangements has been recovered as the preferred solution in at least one published study, the authors make a strong argument about the state of the field. The use of two entirely independent datasets as a consistency check is great, and convergence between them, where it occur,s substantially strengthens confidence in the conclusions.

      (2) It is my view that the simulation framework is a particular strength. Generating data on a fully unresolved star tree and scoring those data under both correctly-specified and misspecified substitution models provides convincing evidence that the strong preference for rooting Spiralia on the flatworm branch is, at least partly, an analytical artefact driven by the exceptionally long branch in combination with compositional heterogeneity across sites. This is an important methodological demonstration with implications beyond spiralian phylogenetics, as the same issue is likely to affect other deep, long-branched lineages in the animal tree of life.

      (3) The randomised taxon-jackknifing approach is a very nice addition here. The demonstration that preferred topologies shift depending on which species happen to be sampled (even within the same phylum) is a convincing indicator of weak signal, and provides a practical caution for future studies that may report strong support for a particular spiralian arrangement based on a fixed taxon sample.

      (4) The branch-length analyses, benchmarking internal interphylum branches against the already disputed and extremely short branch uniting deuterostomes (work also by this group), are well-conceived and solid.

      (5) I think it is worth highlighting the notable intellectual honesty throughout the paper: the authors do not overstate their results, correctly acknowledging that while the unrooted topology grouping molluscs with brachiopods and flatworms with nemerteans emerges most consistently, this preference is not statistically significant under more adequate substitution models and may itself carry some artefactual component.

      Weaknesses:

      (1) The restriction to five phyla is the most significant limitation, as the authors acknowledge this and give a clear computational justification, but readers should be aware that the paper's convincing conclusions apply specifically to the five focal phyla and the evidence remains incomplete with respect to spiralian phylogeny as a whole.

      (2) The treatment of substitution model adequacy, while commendably thorough for site-heterogeneous models, is necessarily bounded. The authors note that models accounting for non-stationarity, across-lineage compositional heterogeneity, or mixtures of tree histories might yield different results, and that even the most sophisticated currently available approaches have not produced consistent spiralian topologies across studies. This is not a criticism of what has been done here - the analytical scope is reasonable and well-implemented - but it means the paper cannot be read as a definitive demonstration that no model will ever resolve these relationships. The distinction between a true hard polytomy and a radiation that is effectively unresolvable given current data and methods could be drawn more sharply in the discussion.

      (3) The reticulation-aware coalescent analyses are presented somewhat briefly relative to the likelihood-based topology scoring. The finding that flatworms are recovered within a paraphyletic jaw-bearing animal clade in both summary trees - interpreted as long-branch attraction - is striking, and its implications for gene-tree-based approaches to spiralian rooting deserve more discussion than they currently receive.

      (4) The central conclusions - that interphylum branches in Spiralia are extraordinarily short, that topological preferences are strongly model-dependent and taxon-sampling-sensitive, and that an ancient rapid radiation is the most parsimonious explanation - are convincingly supported by the evidence presented. The identification of flatworm long-branch attraction as an important confounding factor in rooting analyses is itself an important and well-demonstrated result.

      Conclusion:

      This paper clearly makes an important contribution to the ongoing debate about spiralian relationships and, more broadly, to methodological discussions about how to handle anciently diversified clades where phylogenetic signal is genuinely limited. The exhaustive topology-scoring framework combined with taxon-jackknifing and simulation under unresolved trees is a valuable methodological template that could usefully be applied to other notoriously difficult nodes in the animal tree. I thoroughly enjoyed the discussion of the implications of these findings for interpreting Cambrian fossils and the evolutionary history of shells, segmentation, larval types and other characters - it is both thoughtful and thought-provoking and will be of broad interest well beyond the phylogenomics and zoology communities. From a very practical perspective, the data and scripts provided make the work useful to researchers wishing to apply similar approaches to other groups.

      Reviewer #3 (Public review):

      Summary:

      This paper addresses the controversial internal relationships within the Spiralia, a major clade of invertebrate animals including molluscs, annelids, brachiopods and flatworms.

      Strengths:

      Performs a range of empirical analyses and simulations that address the core question. Although a favoured unrooted topology finds some support, this is not strongly endorsed in the paper.

      Weaknesses:

      (1) Only considers a subset of relevant phyla (e.g. gastrotrichs are relevant to the phylogenetic position of Platyhelminthes), although how this would change the scale of the analyses (i.e. number of topologies) is addressed in the paper.

      (2) Discussion of Spiralia evolution and broader context, particularly the relevance for the fossil record. Line 448: our current understanding of the early spiralian fossil record is quite consistent with the main results of this paper. For example, there are very few claims for fossils that sit on the short branch leading to Spiralia (or Lophotrochozoa as defined here) that this paper discusses. Many of the key fossils that inform on the characters discussed in the introduction, which have unusual character combinations, have an apomorphy of one of the phyla discussed, and so are resolved as members of the stem lineages of particular phyla.

      (3) This is what you would expect with long phylum stem lineages (line 148) and a short spiralia stem lineage. For example, the mollusc Wiwaxia has chaetae, but a mollusc like Radula (Smith 2012), the conchiferan mollusc Pelagiella has chaetae and a coiled shell (Thomas et al. 2020). The only fossil groups that are routinely discussed as belonging to the stem lineage of more than one phylum are the tommotiids, which have chaetae, segmentation and a complex mineralised skeleton (but not shells in the brachiopod/mollusc sense, see Guo et al 2023) but they sit on the lophophorate stem lineage, a synapomorphy rich group the monophyly of which the present paper endorses (e.g. line 435). The fossil record is consistent with the scenario presented in line 442, e.g. convergent loss or reduction of chaetae and segmentation and convergent evolution of shells in molluscs and brachiopods.

      We thank the reviewers for their kind comments. Please see below for detailed responses to all identified weaknesses.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Some minor comments that might help improve the paper:

      (1) Abstract L17. "Most analyses on the 15 unrooted trees showed a preference for the same topology but the support over other solutions was non significant" - I don't really understand this sentence in the context of the paper; it makes it sound as if the tree is, after all, well resolved! Non-significant, or not significant better than non significant?

      Having read the rest of the paper I see what this refers to (uT4), but still I don't understand the second clause.

      Re-written to clarify.

      (2) Introduction L31. This makes it sound as if phoronids are actually part of brachiopods, and while that was recovered by Cohen and Weydmann 2005, I'm not sure if it's really a general result. In addition, rather than using "brachiopods plus phoronids" everywhere, you could use "Brachiozoa" (Cavalier-Smith 1998, Biol. Rev).

      We have updated our text and figures to use Brachiozoa.

      (3) L36-37. Yes, but the presence of Chaetagnatha in this clade is suggestive that their primitive body size is not small.

      Have made clear that chaetognaths are not all tiny.

      (4) L85. Kumar et al. may have claimed that Spiralia are as old as 670, but many other analyses would suggest a range of different results. Why choose just this one? In addition, this age seems rather incompatible with your results.

      We agree this maximum age is highly improbable (the principal point remains the deep age of the protostomes). We have used a different reference and refer to a generally acceptable minimum age only.

      (5) L88. The key part of this sentence, "proving a hard polytomy", comes at the end of a long set of references that makes it hard to connect to the lead-in "given the age of", so I would suggest rephrasing.

      Rephrased for clarity.

      (6) L109. It is unclear what this means in the context: "and even support multiple topologies".

      Re-worded for clarity.

      (7) Figure 1. Why did you choose to indicate brachiopods plus phoronids as a larval form, unlike the other clades? Perhaps it's because we don't know what the last common ancestor of the two looked like (unless P is an ingroup of B), but that's arguably true for some of the other clades as well!

      Apologies, this was laziness as we already had a line drawing of an actinotroch larva. Have improved the images in figures 1 and 5 where required.

      (8) L164. Reticulation-aware analyses. As I understand it, this would include introgression, hybridization, etc. However, incomplete lineage sorting has also been invoked, not just for Cambrian-explosion age events but also for other major radiations, such as for angiosperms and birds. How significant might ILS be for generating the results you get?

      Section title amended. Results section updated to reflect this. We now explicitly mention the potential impact of ILS and introgression on spiralian relationships in our discussion.

      Unrooted trees analysis:

      (9) L405 on. Maybe it would be worth including a figure showing the relative branch lengths of uT4. All the images of trees show similar-length branches, which gives off the wrong impression within the context of the paper!

      We understand the motivation, but we worry that showing uT4 as the sole phylogram may end up with this being interpreted by a casual reader as being the main result of the paper. Hopefully the figures with branch lengths encompass this information well enough and with no danger of misinterpretation.

      (10) L430 on. Why is this a "conservative" interpretation?

      Yes agreed not clear. Have changed to “We interpret our results as showing that…”

      (11) You mention synapomorphy accumulation time and implicitly equate shortness of branches with shortness of time. However, other options are available under varying diversification rate models (e.g. ClaDs, Barido-Sottani et al. 2023 Syst. Biol.; CET, Budd and Mann 2025, Syst.Biol.). In particular, the latter paper shows that when unusually large clades are selected for study (as is arguably the case here), then those clades are likely to have started with very high "evolutionary tempo", which speeds up all aspects of evolution, including diversification rates.

      In the Budd and Mann scenario large clades begin with high tempo of cladogenesis, high substitution rate and high diversification rate (rapid origin of new characters). This would suggest that the period of the radiation was extra rapid (even less time than in a ‘normal’ period during which smaller clades emerge) so we feel the point stands.

      (12) L449. Maybe refer to the Song et al. paper again here on scaphopods plus bivalves, as it makes the same sort of points, albeit in a slightly different context.

      We thank the reviewer for the suggestion and have added the citation where relevant.

      (13) Finally, to return to L20. You mention implications for the Cambrian fossil record, but then fail to deliver any!

      We have hopefully addressed this remark in the discussion better (at least to the extent we are qualified to).

      Yet if you are correct, then synapomorphy accumulation would unite groups of phyla, and would surely lead to a scenario highly incompatible with clock models suggesting deep origins of clades (as they would all be more fossilisable).

      Apologies but we don’t completely understand this point as ‘synapomorphy accumulation would unite groups of phyla’ is a little ambiguous. Of course, this is generally true, but our results suggest there was little opportunity to accumulate identifiable synapomorphies linking pairs, triplets or quartets of our 5 spiralian phyla.

      In addition, clock results suggest rather long periods of time leading to the phyla, which would imply that there would have to be extremely slow rates of molecular evolution to yield the short early branches here. Also, it might be worth referring to papers compatible with this view, such as Wernström, J.V. et al., EvoDevo 13, 17 (2022). https://doi.org/10.1186/s13227-022-00202-8 or some of the palaeo literature, such as Budd and Jackson 2016, Phil Trans.

      The referee refers to clock results suggesting a (deep) Ediacaran origin of Lophotrochozoa/Spiralia. We interpret the spiralian radiation itself as rapid but, in the absence of a clock analysis, we cannot comment on when it took place.

      Reviewer #2 (Recommendations for the authors):

      (My not very) Major points - as I feel this is an excellent paper.

      (1) The coalescent-based summary tree analyses warrant expansion. The recovery of flatworms within a paraphyletic jaw-bearing animal clade in both summary trees is a striking result attributed to long-branch attraction, but this interpretation would be strengthened by examining whether pruning or downweighting the longest-branching taxa within those groups affects the outcome, or by reporting per-node quartet scores more fully. This would make the reticulation-aware results more directly informative and would bring this section into better balance with the detailed likelihood-based analyses.

      We thank the reviewer for the suggestion of the expanded analyses. We have now done these, and they yielded essentially the same results as the unpruned analyses. Additionally, while not discussed, we ran the Astral analyses on the subset of gene-trees where all groups of interest (spiralian phyla and superphyletic Ecdysozoa, Deuterostomia, etc.) were monophyletic and found no changes to interphylum quartet scores beyond those due to enforced (super)phylum monophyly, with Platyhelminths still recovered within Gnathifera.

      We have expanded our description of the results slightly as well as our discussion. Location of the tables with detailed quartet scores and local posterior probabilities has been added to Fig. S1’s legend.

      (2) It would strengthen the paper to include at least a brief analysis or explicit discussion of whether any currently available models accounting for non-stationary or across-lineage compositional heterogeneity show any change in the pattern of support, even if only tested on a subset of topologies. A null result here would itself be informative and would make the conclusions more robust to the concern that unexamined model classes might behave differently.

      We thank the reviewer for the suggestion, but this represents a considerable amount of new work and we think it falls outside the scope of the present work. We have, as suggested, included this as a discussion point.

      (3) The authors note that topologies grouping flatworms with ribbon worms appear among the higher-scoring arrangements even under model misspecification in simulations. It would be helpful to comment explicitly on whether the apparent signal for this grouping should therefore be regarded with particular scepticism, or whether it survives artefact correction in any of the analyses, as this is a grouping that has appeared repeatedly in the literature and readers will want guidance on how to interpret it.

      We do state that the nemertean+platyhelminth grouping seems likely to be at the least emphasised by an artefact (as the referee points out it is common to the higher scoring trees in the star tree simulations). We state that this suggests “…that this grouping derives some support from systematic errors.” We now return briefly to this in the discussion.

      Writing and presentation

      (1) The abstract states that rooting Spiralia on the flatworm branch "is a long-branch artefact" - this is slightly stronger than the language used in the body of the paper, where the authors correctly write that this preference is "at least enhanced by" the artefact. The abstract phrasing should be softened to reflect the more nuanced conclusion in the text.

      Good point. Done.

      (2) A brief signposting sentence near the start of the Results, setting out the overall analytical logic before the individual sections begin, would help orient readers. The strategy - score all topologies, test robustness to model choice and taxon sampling, then use simulation to identify artefactual signals - is clear in retrospect but would benefit from being made explicit upfront.

      We have taken this suggestion on board. The summary seemed in the end better placed as the final part of the introduction.

      (3) Figure 3 is complex and would be easier to interpret with a brief explanatory note in the legend clarifying what a wide versus narrow range of log-likelihood scores across topologies means in practical terms for statistical resolution between trees.

      Added sentence to legend.

      Minor Corrections:

      (1) The Figure 2 legend contains a typographical error: "shorter than the short, disputed deuterostome branch" should read "shorter than."

      Done

      (2) At least one reference appears to carry a future publication year (Ishii et al., 2026) and should be verified for accuracy before final submission.

      This reference is correct per the journal’s website. We did find Google Scholar to list it as being from 2025.

      Reviewer #3 (Recommendations for the authors):

      (1) Abstract/SI definitions of Spiralia/Lophotrochozoa

      While I don't have strong feelings about this, if Spiralia is being used as an apomorphy-based name, then it still might be equivalent to Lophotrochozoa, as spiral cleavage in Gnathostoniula jenneri was illustrated by Riedl (1969). Although no other studies have replicated this observation, this should at least be mentioned.

      Sorry this reference to gnathostomulid spiral cleavage was included in a longer version of the discussion of nomenclature. This was first reduced in length (which was when the mention of gnathostomulid spiral cleavage was dropped) then finally moved to the supplementary material. We have now re-included mention of this in the discussion in supplementary info.

      The SI text suggests that the name Lophotrochozoa, as used in its original form by Halanych et al. (1995), was a node-based definition, and that this name is for the sister group of Ecdysozoa. However, in that paper, the name is actually defined as "as the last common ancestor of the three traditional lophophorate taxa, the molluscs, and the annelids, and all of the descendants of that common ancestor". This definition would exclude Gnathifera, and depending on the internal relationships of the non-Gnathiferan phyla, may be equivalent (or not) to the usage of the name Spiralia adopted in the present paper. The perils of mixing node and apomorphy-based definitions of clades are clear, and the situation is less straightforward than the paper suggests, and (somewhat unhelpfully given the subject of the paper) may only become clearer if the relationships of non-ecdysozoan protostomes are resolved.

      We believe that the community universally understood the definition of Lophotrochozoa following the 1997 paper (by the authors who also provided the original 1995 definition). This 1997 definition included both chaetognaths and rotifers as examples of the Gnathifera. The Spiralia, in contrast, began life not even as a name for a clade but a description of a character shared by some apparently unrelated taxa – similar to a grouping of ‘carnivores’. The introduction of a new name was, we suggest, unhelpful. We hope that by defining our terms up front the meaning in the current paper is clear.

      (2) Introduction

      Line 76. Some references needed regarding claims that there was a polymeric brachiopod ancestor, e.g. Gutman (1978), Temereva and Malakhov (2011), Guo et al. (2023). Likewise for the chaetae of brachiopods, annelids and molluscs, e.g. Schiemann (2017), as it's key to trace where these ideas originated.

      Added

      Figure 1. This is a nice illustration of the uncertainty in the relationships of these groups. However, I kept checking which thumbnail image was which for nemerteans and annelids. A minor suggestion, but perhaps a polychaete instead for the annelid?

      We have replaced the rather poor image of an earthworm with a polychaete and also now include labels. We hope the improved images are more helpful. Good point.

      (3) Results

      Branch length comparison. I understand why the deuterostome stem was chosen as the branch for comparison from the point of view of phylogenetic uncertainty. However, what about the branch leading to ecdysozoa or the branch subtending lophotrochozoan and/or gnathifera? Given that the short internodes are used as an argument underpinning uncertain relationships, can we be sure that Gnathifera is not nested within the group of interest, especially given that Gnathifera contains many long-branched taxa and the root may be misplaced within the group?

      We have added the Lophotrochozoa and Ecdysozoa median lengths to our plots and now discuss both the lophotrochozoan branch in our results.

      Line 249. Given that Spiralia is the group of interest, why were the Gnathiferans also chosen at random?

      The point of the experiment was to see the effect of taxon sampling on the consistency of the resulting topology. Random sampling across the tree seems helpful in this context. We chose Gnathifera as one group to sample from as this ensured they would be present in all trees. This seems appropriate as they are the sister group of the clade of interest and as such their inclusion reflects a choice a typical investigator might make when choosing which species to include. Additionally, as noted in the reviewer’s earlier comment, Gnathifera includes many long-branched taxa and we wanted to ensure our root-placement results were robust to this aspect of taxon sampling.

      (4) Discussion

      Line 448. Our current understanding of the early spiralian fossil record is quite consistent with the main results of this paper. For example, there are very few claims for fossils that sit on the short branch leading to Spiralia (or Lophotrochozoa as defined here) that this paper discusses. Many of the key fossils that inform on the characters discussed in the introduction that have unusual character combinations have an apomorphy of one of the phyla discussed, and so are resolved as members of the stem lineages of particular phyla.

      This is what you would expect with long phylum stem lineages (line 148) and a short spiralia stem lineage. For example, the mollusc Wiwaxia has chaetae, but a mollusc like radula (Smith 2012), the conchiferan mollusc Pelagiella has chaetae and a coiled shell (Thomas et al. 2020). The only fossil groups that are routinely discussed as belonging to the stem lineage of more than one phylum are the tommotiids, which have chaetae, segmentation and a complex mineralised skeleton (but not shells in the brachiopod/mollusc sense, see Guo et al 2023) but they sit on the lophophorate stem lineage, a synapomorphy rich group the monophyly of which the present paper endorses (e.g. line 435). The fossil record is consistent with the scenario presented in line 442, e.g. convergent loss or reduction of chaetae and segmentation and convergent evolution of shells in molluscs and brachiopods.

      We accept these points (though are clearly not experts on these fossils). We have (slightly tentatively given our lack of expertise) expanded our discussion to include these fossil taxa with their combinations of characters.

  3. bafybeihwigujdzh7xrbwmf2t2zv5eku6cr3reb5qzqmhgrpnfdd2ryhh7y.ipfs.dweb.link bafybeihwigujdzh7xrbwmf2t2zv5eku6cr3reb5qzqmhgrpnfdd2ryhh7y.ipfs.dweb.link
    1. Who is doing the job of helping you to map the expanding frontier of your knowledgeparaphrased: Who is doing the job of creating a map of the Web frontier as you explore it. (200????) Or indeed a map of the territory already explored, ready to resume exactly where you left off.  How Hyperpost addresses these problemsDeep rearrangability and repurposabilty supported by a new "Cosmology for Computing' Capture Intertwingularity as scaffoldings of everything you care about in one placeAdd new capabilities at the Meta LevelHyperPost: The Thought Processor for Google+Google+: interest based social networking serviceSocial Knowledge Network: Intersection of Knowledge Graph, Google+ Circles and Thought GraphsGoogle+: interest based social networking serviceCircles: entire saffolding: Vannevar Bush: American electrical engineer and science administratorMemex: hypothetical proto-hypertext system that Vannevar Bush described in 1945HyperPost: The Thought Processor for Google+trails: Trail blazing: StubMemex: hypothetical proto-hypertext system that Vannevar Bush described in 1945Connected neighborhoods of nodes thus conveyed contain not only the information presented in the narrative trails, but they also contain as it were the entire scaffolding  with which they were erected.  Trail blazing  as in the  Memex  Thought Vectors in Concept Space  kernel for  tinkerable  Hypermedia Direct manipulation interfaces to suit personal needsthe Lively Kernel project.tinkerable: through associations: "The Human mind works by association" As We May Think - The Atlantickernel: main component of most computer operating systemsLively Kernel: StubDirect manipulation interface: StubHypermedia: Hypermedia, an extension of the term hypertext, is a nonlinear medium of information that includes graphics, audio, video, plain text and hyperlinks.To have sufficient built in capability in the  kernel  that support  tinkerable  Hypermedia formats incorporating Direct manipulation interfaces to suit personal needs, as it was done in the Lively Kernel project.  Thought Graph Search for Things as you writeThe sentences that you write are Nodes Structural linksHyperPost: The Thought Processor for Google+search and mention: entity: something that existswrite about things: Node: network conceptThought Graph: HyperPost  invites us to  search and mention  all the things that are important in the context of our thoughts that are related to the things we write about. The sentences you write down are turned into  Nodes in a  Thought Graph    Public Knowledge Graph Incorporate Entities from Google's Knowledge GraphWikiData auto suggest boxesThing: Wikidata: free knowledge database project hosted by Wikimedia and edited by volunteersPersonal Knowledge Graph: Google: American multinational Internet and technology corporationKnowledge Graph: knowledge base used by Google to enhance its search engine's search resultsWhen you want to mention some  Thing  the search box autosuggests matching entities drawn   Wikidata.A new node in the user's  Personal Knowledge Graph  is created that references the node in the  Google's   Knowledge Graph. Personal Entities When you reach the edge of your recorded knowledgeThe Wiki GambitCreate your own on the flyAutomatic contextualizationfor thoughts and discovered web resourcesFocus on what you write, not where you put itPersonal Entity: wiki: type of website that visitors can editIn case no public entity matches the user's search a new  Personal Entity  node is created in the user's Personal Knowledge Graph. This is analogous to the greatest gambit of the  wiki.  When you reach the edges of your knowledge just create a new page for it. Here it is more fine grained, it is just a node. You do not need to think up a name for a page. Nor would you need to worry about where it is created, because the identity of the node is independent from where you put it.  Context of discovery and Justification Like the eval and apply of LISPContext of justification: refers to the later or final phase of research when evidence is applied to and compared with a hypothesis.Context of discovery: StubThe Lakatos's term  Context of discovery  can be created by marking trails during your web research with HyperPost, whereas in the   Context of justification  linking to web resources discovered completes the circle. Blaze Trails Attach Narrative Trails to entity nodeslink to web resourcesThe context for a sentence automatically contextualizes linked resourceDiscussion Threads: It is possible to attach  Narrative Trails  to any entity node so that more information about it can be further elaborated. These narrative trails comprise sequences of paragraph, which in turn, consist of sentences for individual thoughts. In addition links to web resources can be attached so that they are linked to relevant contexts and will not be lost. Deep Re-arrangability and Re-purposing Reuse through transclusion any trails or contextproduce every sentence is a node, it can be moved, transcluded in any contextsocial media    Posts,  blog  posts,  Presentations, Project Plans, Issue Trackers rooted in your own graph of all your  articulated knowledgetransclusion: technical method of including some or all of one stored document in another document, without having to copy the data itselfDeep Rearrangeabilty: Ted Nelson: American information technologist, philosopher, and sociologist; coined the terms "hypertext" and "hypermedia"immitationg paper: social media: interaction among people in which they create, share, and/or exchane information and ideas in virtual communities and networksPosts: blog: discussion or informational site published on the World Wide WebPresentation slide: A slide is a single page of a presentation. Collectively, a group of slides may be known as a slide deckBy providing suitable structural links all kinds of presentation format's like  social media    Posts,  blog  posts,  Presentation slides,  etc can be applied to arbitrary network of nodes in the Thought Graph. Combine that with  transclusion  and we have "Deep Rearrangeabilty"  ref  required to solve  Ted Nelson's problem with "immitating paper"  ref   Capture Intertwingularity as scaffoldings of everything you care about in one placeAdd new capabilities at the Meta LevelHyperPost: The Thought Processor for Google+Google+: interest based social networking serviceSocial Knowledge Network: Intersection of Knowledge Graph, Google+ Circles and Thought GraphsGoogle+: interest based social networking serviceCircles: entire saffolding: Vannevar Bush: American electrical engineer and science administratorMemex: hypothetical proto-hypertext system that Vannevar Bush described in 1945HyperPost: The Thought Processor for Google+trails: Trail blazing: StubMemex: hypothetical proto-hypertext system that Vannevar Bush described in 1945Connected neighborhoods of nodes thus conveyed contain not only the information presented in the narrative trails, but they also contain as it were the entire scaffolding  with which they were erected.  Trail blazing  as in the  Memex  Demo This presentation was created in HyperPostPosts can be derived from it and will be publishedword processor: computer program used for writing and editing documentsHyperPost is used to generate the presentation it remains the master.Working with it preserves all the familiar characteristics of  a word processor augmented to accommodate thoughts and knowledge in their native associative graph model.  ConclusionHyperPost shows the way how to overcome the problem with paperIt is put forward as one possible way forward to reinvent hypertext for Academia Availibility Hyperpost landing page: Landing Page | hyperPostThis presentation will shortly be  available at  Hyperpost landing page  For people who sign up for the beta an extended version will be made available presenting a much larger graph, containing our development road map. It will be dynamically extended. Thanks And Thanks for all the fish

      map the expanding frontier

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Comments on revised version:

      The authors have appropriately addressed my comments and questions from the initial review process. My remaining concern relates to the lack of evidence to confirm proteasomal inhibition by lactacystin in both promastigotes and amastigotes. The immunoblotting experiment newly presented does not reveal a clear increase in the levels of poly-ubiquitylated proteins in treated parasites. In fact, poly-Ub levels were lower at both the 4h and 18h timepoints of treatment. If alternative antibodies or additional immunoblots are not available, the manuscript would benefit from an expanded discussion of this observation and potential explanations. In particular, the interpretation that lactacystin stabilizes ama- and pro-specific degradation would be greatly strengthened by such validation.

      Reviewer #2 (Public review):

      General comments on the revisions:

      My view is that the authors have made significant, satisfactory changes that address the comments and queries I made on the original manuscript (Review Commons).

      There are two areas where the authors had to make major changes/justifications where further comment is merited, these were:

      RNA-seq.

      The most significant issue was the originally underpowered RNA-seq which had only two replicates. This has been repeated with four replicates now. This has not led to changes in the interpretation of the data between the original study and this one. One comment that the authors make in the response to this was : "Given the robustness of the stage-specific transcriptome, and the legal constrains associated with the use of animals, we chose to limit the number of replicates to the necessary". Ensuring that animal experiments are properly powered and that maximum robustness of the data from the minimum sample size is an important part of experimental design for ethical use of animal models. Essentially the replication here could have been avoided if the original study had used 1 more animal. However, the new version of RNA-seq brings appropriate confidence to the interpretation of the data.

      Phosphoproteomics.

      The authors provide a robust justification of their strategy for the phosphoproteomics and highlight the inclusion criteria for phosphosites: "Phosphosites were only considered if detected with high confidence (identification FDR<1%) and high localisation confidence (localisation probability >0.75) in at least one replicate". The way missing values were dealt with is explained "For statistical analyses, missing values within a given condition were imputed with a well-established algorithm (MLE) only when at least one observed value was present in that condition." This fills in some of the gaps I was missing from the original manuscript, and I am satisfied that the data analysis is entirely appropriate for a discovery/system -based approach such as this one. The authors also edit the manuscript to reflect that "occupancy" or "stoichiometry" might not be the best description of what they were presenting and switched to the terminology of "normalised phosphorylation level" - I think this is an appropriate response.

      Overall, in the absence of follow up experiments on specific individual examples, some of the claims in the original submission were toned down and reflect a more neutral description of the data now. Significantly, the data still underpin a key role for regulation of the ribosome between the amastigote and promastigote stages (and during the differentiation process). The recursive and reciprocal links between the phosphorylation and ubiquitination systems are interesting and present many opportunities for future investigation.

      Reviewer #3 (Public review):

      Summary:

      The authors proposed to use 5-layer systems level analysis (genomics, transcriptomics, proteomics / protein degradation, metabolomics, phosphoproteomics) to uncover how post-transcriptional mechanisms regulate stage differentiation in Leishmania donovani.<br /> This enabled the identification of several potential regulatory networks, including the regulation of stage-specific gene clusters by RNA stabilisation or decay, proteasomal degradation and protein phosphorylation.

      In the new version of this manuscript, the authors have addressed all questions raised by the reviewers.

      Strengths:

      Although some observations in this study have already been described in the literature, the integrated analysis applied here provides a novel view on how different levels of post-transcriptional networks regulate Leishmania differentiation. This "5-layer system" represents the first analysis of this depth in kinetoplastid parasites.

      The revised version with an increased sample number for the RNA-seq now made the authors assumptions adequate to their obtained data.

      The use of a proteasomal inhibitor adds an interesting insight in how protein degradation is involved in the parasite differentiation, confirming previous observations in the literature, and help to explain the discrepancies between mRNA and protein expression in the different stages.

      Weaknesses:

      While this work provides an impressive and foundational dataset, it opens the door for future research to rigorously validate these initial findings and conclusions.

      Significance and Impact in the field.

      The different datasets generated in this study will be of great interest to the parasitology community, either to be used for hypothesis generation, to validate data from other sources, etc.

      The multi-layered analysis performed here identified a series of potential feedback loops and regulatory networks to be further explored in organisms that lack transcriptional control.

      According to the reviewers’ comments, we made the following minor changes:

      As suggested by reviewer 1, we have extended the discussion of the results related to the analysis of the ubiquitination pattern by Western blot analysis as follows: “Proteasome inhibition blocked amastigote-to-promastigote differentiation, without inducing rapid global accumulation of ubiquitinated proteins (Figure S7C, upper panel) consistent with a quiescent-like state and low basal ubiquitin–proteasome system activity in amastigotes. After 18 h, ubiquitination levels remained similar to untreated cells, indicating that protein turnover and ubiquitin accumulation are primarily driven by developmental remodeling rather than acute proteasome inhibition. In promastigotes, the lack of detectable change (Fig. S7C, lower panel) may also reflect high basal ubiquitination, engagement of compensatory pathways such as autophagy, and/or only partial proteasome inhibition.”

      Recommendations for the authors:

      Reviewer #3 (Recommendations for the authors):

      Minor comments:

      - Supplementary figure 3 is not referenced in the main text.

      - The authors removed the "infinite" sign from figures 3 and 4 to better present the data according to their chosen approach to missing values when LFQ=0. However, the sign is still present in the respective figure legends, please adjust.

      Supplementary Figure 3 (Figure S3) is now referenced in the main text as requested.

      The "infinite" sign has been removed from the legends of Figures 3 and 4 as requested.

    1. Author response:

      Reviewer #1 (Evidence, reproducibility and clarity):

      Summary:

      This manuscript reports the identification of putative orthologues of mitochondrial contact site and cristae organizing system (MICOS) proteins in Plasmodium falciparum - an organism that unusually shows an acristate mitochondrion during the asexual part of its life cycle and then this develops cristae as it enters the sexual stage of its life cycle and beyond into the mosquito. The authors identify PfMIC60 and PfMIC19 as putative members and study these in detail. The authors at HA tags to both proteins and look for timing of expression during the parasite life cycle and attempt (unsuccessfully) to localise them within the parasite. They also genetically deleted both gene singly and in parallel and phenotyped the effect on parasite development. They show that both proteins are expressed in gametocytes and not asexuals, suggesting they are present at the same time as cristae development. They also show that the proteins are dispensible for the entire parasite life cycle investigated (asexuals through to sporozoites), however there is some reduction in mosquito transmission. Using EM techniques they show that the morphology of gametocyte mitochondria is abnormal in the knockout lines, although there is great variation.

      Major comments:

      The manuscript is interesting and is an intriguing use of a well studied organism of medical importance to answer fundamental biological questions. My main comments are that there should be greater detail in areas around methodology and statistical tests used. Also, the mosquito transmission assays (which are notoriously difficult to perform) show substantial variation between replicates and the statistical tests and data presentation are not clear enough to conclude the reduction in transmission that is claimed. Perhaps this could be improved with clearer text?

      We would like to thank the reviewer for taking the time to review our manuscript. We are happy to hear the reviewer thinks the manuscript is interesting and thank the reviewer for their constructive feedback.

      To clarify the statistical analyses used, we included a new supplementary dataset with all statistical analyses and p-values indicated per graph. Furthermore, figure legends now include the information on the exact statistical test used in each case.

      Regarding mosquito experiments, while we indeed reported a reduction in transmission and oocysts numbers, we are aware that this effect might be due to the high variability in mosquito feeding assays. To highlight this point, we deleted the sentence “with the transmission reduction of [numbers]….” and we included the sentence “The high variability encountered in the standard membrane feeding assays, though, partially obstructs a clear conclusion on the biological relevance of the observed reduction in oocyst numbers“

      More specific comments to address:

      Line 101/Fig1E (and figure legend) - What is this heatmap showing. It would be helpful to have a sentence or two linking it to a specific methodology. I could not find details in the M+M section and "specialized, high molecular mass gels" does not adequately explain what experiments were performed. The reference to Supplementary Information 1 also did not provide information.

      We added the information “high molecular mass gels with lower acrylamide percentage” to clarify methodology in the text. Furthermore, we extended the figure legend to include all relevant information. Further experimental details can be found in the study cited in this context, where the dataset originates from (Evers et al., 2021).

      Line 115 and Supplementary Figure 2C + D - The main text says that the transgenic parasites contained a mitochondrially localized mScarlet for visualization and localization, but in the supplementary figure 2 it shows mitotracker labelling rather than mScarlet. This is very confusing. The figure legend also mentions both mScarlet and MitoTracker. I assume that mScarlet was used to view in regular IFAs (Fig S2C) and the MitoTracker was used for the expansion microscopy (Fig S2D)?

      Please clarify.

      We thank the reviewer for pointing this out – this was indeed incorrectly annotated. We used the endogenous mito-mScarlet signal in IFA and mitoTracker in U-ExM. The figure annotation has now been corrected.

      Figure 2C - what is the statistical test being used (the methods say "Mean oocysts per midgut and statistical significance were calculated using a generalized linear mixed effect model with a random experiment effect under a negative binomial distribution." but what test is this?)?

      The statistic test is now included in the material and method section with the sentence “The fitted model was used to obtain estimated means and contrasts and were evaluated using Wald Statistics”. The test is now also mentioned in the figure legend.

      Also the choice of a log10 scale for oocyst intensity is an unusual choice - how are the mosquitoes with 0 oocysts being represented on this graph? It looks like they are being plotted at 10^-1 (which would be 0.1 oocysts in a mosquito which would be impossible).

      As the data spans three orders of magnitude with low values being biologically meaningful, we decided that a log scale would best facilitate readability of the graph. As the 0 values are also important to show, we went with a standard approach to handle 0s in log transformed data and substituted the 0s with a small value (0.001). We apologize for not mentioning this transformation in the manuscript. To make this transformation transparent, we added a break at the lower end of the log-scaled y-axis and relabelled the lowest tick as ‘0’. This ensures that mosquitoes with zero oocysts are shown along the x-axis without being assigned an artificial value on the log scale. We would furthermore like to highlight that for statistics we used the true value 0 and not 0.001.

      Figure 2D - it is great that the data from all feeding replicates has been shared, however it is difficult to conclude any meaningful impact in transmission with the knock-out lines when there is so much variation and so few mosquitoes dissected for some datapoints (10 mosquitoes are very small sample sizes). For example, Exp1 shows a clear decrease in mic19- transmission, but then Exp2 does not really show as great effect. Similarly, why does the double knock out have better transmission than the single knockouts? Sure there would be a greater effect?

      We agree with the reviewer and with the new sentence added, as per major point, we hope we clarified the concept. Note that original Figure 2D has been moved to the supplementary information, as per minor comment of another reviewer.

      Figure 3 legend - Please add which statistical test was used and the number of replicates.

      Done

      Figure 4 legend - Please add which statistical test was used and the number of replicates.

      Done. Regarding replicates, note that while we measured over 100 cristae from over 30 mitochondria, these all stem from the same parasite culture.

      Figure 5C - the 3D reconstructions are very nice, but what does the red and yellow coloring show?

      Indeed, the information was missing. We added it to the figure legend.

      Line 352 - "Still, it is striking that, despite the pronounced morphological phenotype, and the possibly high mitochondrial stress levels, the parasites appeared mostly unaffected in life cycle propagation, raising questions about the functional relevance of mitochondria at these stages."

      How do the authors reconcile this statement with the proven fact that mitochondria-targeted antimalarials (such as atovaquone) are very potent inhibitors of parasite mosquito transmission?

      Our original sentence was reductive. What we wanted to state was related to the functional relevance of crista architecture and overall mitochondrial morphology rather than the general functional relevance of the mitochondria. We changed the sentence accordingly.

      Furthermore, even though we do not discuss this in the article, we are aware of mitochondria targeting drugs that are known to block mosquito transmission. We want to point out that it is difficult to discern the disruption of ETC and therefore an impact on energy conversion with the impact on the essential pathway of pyrimidine synthesis, highly relevant in microgamete formation. Still, a recent paper from Sparkes et al. 2024 showed the essentiality of mitochondrial ATP synthesis during gametogenesis so it is very likely that the mitochondrial energy conversion is highly relevant for transmission to the mosquito.

      Reviewer #1 (Significance):

      This manuscript is a novel approach to studying mitochondrial biology and does open a lot of unanswered questions for further research directions. Currently there are limitations in the use of statistical tests and detail of methodology, but these could be easily be addressed with a bit more analysis/better explanation in the text.

      This manuscript could be of interest to readers with a general interest in mitochondrial cell biology and those within the specific field of Plasmodium research.

      My expertise is in Plasmodium cell biology.

      We thank the reviewer for the praise.

      Reviewer #2 (Evidence, reproducibility and clarity):

      Major comments:

      (1) In my opinion, the authors tend to sensationalize or overinterpret their results. The title of the manuscript is very misleading. While MICOS is certainly important for crista formation, it is not the only factor, as ATP synthase dimer rows make a highly significant contribution to crista morphology. Thus, one can argue with equal validity that ATP synthase should be considered the 'architect', as it's the conformation of the dimers and rows modulate positive curvature. Secondly, while cristae are still formed upon mic60/mic19 gene knockout (KO), they are severely deformed, and likely dysfunctional (see below). Thus, I do not agree with the title that MICOS is dispensable for crista formation, because the authors results show that it clearly is essential. So, the title should be changed.

      We thank the reviewer for taking the time to review our manuscript.

      Based on the reviewers’ interpretation we conclude the title does not come across as intended. We have changed the title to: “The role of MICOS in organizing mitochondrial cristae in malaria parasites”

      The Discussion section starting from line 373 also suffers from overinterpretation as well as being repetitive and hard to understand. The authors infer that MICOS stability is compromised less in the single KOs (sKO) in compared to the mic60/mic19 double KO (dKO). MICOS stability was never directly addressed here and the composition of the MICOS complex is unaddressed, so it does not make sense to speculate by such tenuous connections. The data suggest to me that mic60 and mic19 are equally important for crista formation and crista junction (CJ) stabilization, and the dKO has a more severe phenotype than either KO, further demonstrating neither is epistatic.

      We do agree with the reviewer’s notion that we did not address complex stability, and our wording did not make this sufficiently clear. We shortened and rephrased the paragraph in question.

      The following paragraphs (line 387 to 422) continues with such unnecessary overinterpretation to the point that it is confusing and contradictory. Line 387 mentions an 'almost complete loss of CJs' and then line 411 mentions an increase in CJ diameter, both upon Mic60 ablation. I do not think this discussion brings any added value to the manuscript and should be shortened. Yes, maybe there are other putative MICOS subunits that may linger in the KOS that are further destabilized in the dKO, or maybe Mic60 remains in the mic19 KO (and vice versa) to somehow salvage more CJs, which is not possible in the dKO. It is impossible to say with confidence how ATP synthase behaves in the KOs with the current data.

      We shortened this paragraph.

      (2) While the authors went through impressive lengths to detect any effect on lifecycle progression, none was found except for a reduction in oocyte count. However, the authors did not address any direct effect on mitochondria, such as OXPHOS complex assembly, respiration, membrane potential. This seems like a missed opportunity, given the team's previous and very nice work mapping these complexes by complexome profiling. However, I think there are some experiments the authors can still do to address any mitochondrial defects using what they have and not resorting to complexome profiling (although this would be definitive if it is feasible):

      i) Quantification of MitoTracker Red staining in WT and KOs. The authors used this dye to visualize mitochondria to assay their gross morphology, but unfortunately not to assay membrane potential in the mutants. The authors can compare relative intensities of the different mitochondria types they categorized in Fig. 3A in 20-30 cells to determine if membrane potential is affected when the cristae are deformed in the mutants. One would predict they are affected.

      Interesting suggestion. As our staining and imaging conditions are suitable for such analysis (as demonstrated by Sarazin et al., 2025, https://www.biorxiv.org/content/10.1101/2025.11.27.690934v1), we performed the measurements on the same dataset which we collected for Figure 3. We did, however, not detect any difference in mitotracker intensity between the different lines. The result of this analysis is included in the new version of Supplementary figure S6.

      ii) Sporozoites are shown in Fig S5. The authors can use the same set up to track their motion, with the hypothesis that they will be slower in the mutants compared to WT due to less ATP. This assumes that sporozoite mitochondria are active as in gametocytes.

      While theoretically plausible and informative, we currently do not know the relevance of mitochondrial energy conversion for general sporozoite biology or specifically features of sporozoite movement. Given the required resources and time to set this experiment up and the uncertainty whether it is a relevant proxy for mitochondrial functioning, we argue it is out of scope for this manuscript.

      iii) Shotgun proteomics to compare protein levels in mutants compared to WT, with the hypothesis that OXPHOS complex subunits will be destabilized in the mutants with deformed cristae. This could be indirect evidence that OXPHOS assembly is affected, resulting in destabilized subunits that fail to incorporate into their respective complexes.

      While this experiment could potentially further our understanding of the interaction between MICOS and levels of OXPHOS complex subunits we argue that the indirect nature of the evidence does not justify the required investments.

      To expedite resubmission, the authors can restrict the cell lines to WT and the dKO, as the latter has a stronger phenotype that the individual KOs and conclusions from this cell line are valid for overall conclusions about Plasmodium MICOS.

      I will also conclude that complexome/shotgun proteomics may be a useful tool also for identifying other putative MICOS subunits by determining if proteins sharing the same complexome profile as PfMic60 and Mic19 are affected. This would address the overinterpretation problem of point 1.

      (3) I am aware of the authors previous work in which they were not able to detect cristae in ABS, and thus have concluded that these are truly acristate. This can very well be true, or there can be immature cristae forms that evaded detection at the resolution they used in their volumetric EM acquisitions. The mitochondria and gametocyte cristae are pretty small anyway, so it not unreasonable to assume that putative rudimentary cristae in ABS may be even smaller still. Minute levels of sampled complex III and IV plus complex V dimers in ABS that were detected previously by the authors by complexome profiling would argue for the presence of miniscule and/or very few cristae.

      I think that authors should hedge their claim that ABS is acristate by briefly stating that there still is a possibility that miniscule cristae may have been overlooked previously.

      We acknowledge that we cannot demonstrate the absolute absence of any membrane irregularities along the inner mitochondrial membrane. At the same time, if such structures were present, they would be extremely small and unlikely to contain the full set of proteins characteristic of mature cristae. For this reason, we consider it appropriate to classify ABS mitochondria as acristate. To reflect the reviewer’s point while maintaining clarity for readers, we have slightly adjusted our wording in the manuscript, changing ‘fully acristate’ to ‘acristate’.

      This brings me to the claim that Mic19 and Mic60 proteins are not expressed in ABS. This is based on the lack of signal from the epitope tag; a weak signal is detected in gametocytes. Thus, one can counter that Mic19 and Mic60 are also expressed, but below the expression limits of the assay, as the protein exhibits low expression levels when mitochondrial activity is upregulated.

      We agree with the reviewer that the absence of a detectable epitope-tag signal does not definitively exclude low-level expression, and we have therefore replaced the term ‘absent’ with ‘undetectable’ throughout the manuscript. In context with previous findings of low-level transcripts of the proteins in a study by Lopez-Berragan et al. and Otto et al., we also added the sentence “The apparent absence could indicate that transcripts are not translated in ABS or that the proteins’ expression was below detection limits of western blot analysis.” to the discussion. At the same time, we would like to clarify that transcript levels for both genes fall within the <25th percentile, suggesting that these low values likely represent background signal rather than biologically meaningful expression. This interpretation is further supported by proteomic datasets in PlasmoDB, which report PfMIC19 and PfMIC60 expression in gametocyte and mosquito stages, but not in asexual blood stages.”

      To address this point, the authors should determine of mature mic60 and mic19 mRNAs are detected in ABS in comparison to the dKO, which will lack either transcript. RT-qPCR using polyT primers can be employed to detect these transcripts. If the level of these mRNAs are equivalent to dKO in WT ABS, the authors can make a pretty strong case for the absence of cristae in ABS.

      We appreciate the reviewer’s suggestion. As noted in the Discussion, existing transcriptomic datasets already show detectable MIC19 and MIC60 mRNAs in ABS. For this reason, we expect RT-qPCR to reveal low (but not absent) levels of both transcripts, unlike the true loss expected to be observed in the dKO. Because such residual signals have been reported previously and their biological relevance remains uncertain, we do not believe transcript levels alone can serve as a definitive indicator of cristae absence in ABS.

      They should highlight the twin CX9C motifs that are a hallmark of Mic19 and other proteins that undergo oxidative folding via the MIA pathway. Interestingly, the Mia40 oxidoreductase that is central to MIA in yeast and animals, is absent in apicomplexans (DOI: 10.1080/19420889.2015.1094593).

      Searching for the CX9C motifs is a valuable suggestion. In response to the reviewer´s suggestion we analysed the conservation of the motif in PfMIC19 and included this in a new figure panel (Figure 1 F).

      Did the authors try to align Plasmodium Mic19 orthologs with conventional Mic19s? This may reveal some conserved residues within and outside of the CHCH domain.

      In response to this comment we made Figure 1 F, where we show conserved residues within the CHCH domains of a broad range of MIC19 annotated sequences across the opisthokonts, and show that the Cx9C motifs are conserved also in PfMIC19. Outside the CHCH domain, we did not find any meaningful conservation, as PfMIC19 heavily diverges from opisthokont MIC19.

      (5) Statistical significance. Sometimes my eyes see population differences that are considered insignificant by the statistical methods employed by the authors, eg Fig. 4E, mutants compared to WT, especially the dKO. Have the authors considered using other methods such as student t-test for pairwise comparisons?

      The graphs in figures 3, 4 and 5 got a makeover, such that they now are in linear scale and violin plots (also following a suggestion from further down in the reviewer’s comments). We believe that this improves interpretability. ANOVA was kept as statistical testing to assure the correction for multiple comparisons that cannot be performed with standard t-test. A full overview of statistics and exact pvalues can also be found in the newly added supplementary information 2.

      Minor comments:

      Line 33. Anaerobes (eg Giardia) have mitochondria that do produce ATP, unlike aerobic mitochondria

      We acknowledge that producing ATP via OXPHOS is not a characteristic of all mitochondria-like organelles (e.g. mitosomes), which is why these are typically classified separately from canonical mitochondria. When not considering mitochondria-like organelles, energy conversion is the function that the mitochondrion is most well-known for and the one associated with cristae.

      Line 56: Unclear what authors mean by "canonical model of mitochondria"

      To clarify we changed this to “yeast or human” model of mitochondria.

      Lines 75-76: This applies to Mic10 only

      We removed the “high degree of conservation in other cristate eukaryotes” statement.

      Line 80: Cite DOI: 10.1016/j.cub.2020.02.053

      Done

      Fig 2D: I find this table difficult to read. If authors keep table format, at least get rid of 'mean' column' as this data is better depicted in 2C. I suggest depicted this data either like in 3B depicting portion of infected vs unaffected flies in all experiments, then move modified Table to supplement. Important to point out experiment 5 appears to be an outlier with reduced infectivity across all cell lines, including WT.

      To clarify: the mean reported in the table indicates the mean per replicate while the mean reported in figure 2C is the overall mean for a given genotype that corrects for variability within experiments. We agree that moving the table to the supplementary data is a good idea. We decided to not include a graph for infected and non-infected mosquitoes as this information would be partially misleading, highlighting a phenotype we argue to be influenced by the strong variability.

      Fig. 3C-G: I feel like these data repeatedly lead to same conclusions. These are all different ways of showing what is depicted in Fig 2B: mitochondria gross morphology is affected upon ablation of MICOS. I suggest that these graphs be moved to supplement and replaced by the beautiful images.

      Thank you for the nice comment on our images. We have now moved part of the graphs to supplementary figure 6 and only kept the Relative Frequency, Sphericity and total mitochondria volume per cell in the main figure.

      Line 180: Be more specific with which tubulin isoform is used as a male marker and state why this marker was used in supplemental Fig S6.

      We have now specified the exact tubulin isoform used as the male gametocyte marker, both in the main text and in Supplementary Fig. S6. This is a commercial antibody previously known to work as an effective male marker, which is why we selected it for this experiment. This is now clearly stated in the manuscript.

      Line 196 and Fig 3C: the word 'intensities' in this context is very ambiguous. Please choose a different term (puncta, elements, parts?). This is related to major point 2i above.

      To clarify the biological effect that we can conclude form the measurement, we added an explanation about it in the respective section of the results, and we decided to replace the raw results of the plug-in readout with the deduced relative dispersion.

      Line 222: Report male/female crista measurements

      We added Supplementary information 2, which contains exact statistical test and outcomes on all presented quantifications as well as a per-sex statistical analysis of the data from figure 4. Correspondingly, we extended supplementary information 2 by a per-sex colour code for the thin section TEM data.

      Fig. 4B-E: depict data as violin plots or scatter plots like Fig. 2C to get a better grasp of how the crista coverage is distributed. It seems like the data spread is wider in the double KO. This would also solve the problem with the standard deviation extending beyond 0%.

      We changed this accordingly.

      Lines 331-333: Please clarify that this applies for some, but not all MICOS subunits. Please also see major point 1 above. Also, the authors should point out that despite their structural divergence, trypanosomal cryptic mitofilins Mic34 and Mic40 are essential for parasite growth, in contrast to their findings with PfMic60 (DOI: https://doi.org/10.1101/2025.01.31.635831).

      This has been changed accordingly.

      Line 320: incorrect citation. Related to point 1above.

      Correct citation is now included in the text.

      Lines 333-335. This is related to the above. Again, some subunits appear to affect cell growth under lab conditions, and some do not. This and the previous sentence should be rewritten to reflect this.

      This has been changed accordingly.

      Line 343-345: The sentence and citation 45 are strange. Regarding the former, it is about CHCHD10, whose status as a bona fide MICOS subunit is very tenuous, so I would omit this. About the phenomenon observed, I think it makes more sense to write that Mic60 ablation results in partially fragmented mitochondria in yeast (Rabl et al., 2009 J Cell Biol. 185: 1047-63). A fragmented mitochondria is often a physiological response to stress. I would just rewrite as not to imply that mitochondrial fission (or fusion) is impaired in these KOs, or at least this could be one of several possibilities.

      The sentence has been substituted following the indication of the reviewer. Though we still include the data of the human cells as this has also been shown in Stephens et al. 2020.

      Line 373: 'This indicates' is too strong. I would say 'may suggest' as you have no proof that any of the KOs disrupts MICOS. This hypothesis can be tested by other means, but not by penetrance of a phenotype.

      Done

      Line 376-377; 'deplete functionality' does not make sense, especially in the context of talking about MICOS subunit stability. In my opinion, this paragraph overinterprets the KO effects on MICOS stability. None of the experiments address this phenomenon, and thus the authors should not try to interpret their results in this context. See major point 1.

      We removed the sentence. Also, the entire paragraph has been shortened, restructured and wording was changed to address major point 1.

      Other suggestions for added value

      (1) Does Plasmodium Sam50 co-fractionate with Mic60 and Mic19 in BN PAGE (Fig. 1E)

      While we did identify SAMM50 in our BN PAGE, the protein does not co-migrate with the MICOS components but instead comigrates with other components of a putative sorting and assembly machinery (SAM) complex. As SAMM50, the SAM complex and the overarching putative mitochondrial membrane space bridging (MIB) complex are not mentioned in the manuscript, we decided to not include the information in Author response image 1.

      Author response image 1.

      Reviewer #2 (Significance):

      The manuscript by Tassan-Lugrezin is predicated on the idea that Plasmodium represents the only system in which de novo crista formation can be studied. They leverage this system to ask the question whether MICOS is essential for this process. They conclude based on their data that the answer is no, which the authors consider unprecedented. But even if their claim is true that ABS is acristate, this supposed advantage does not really bring any meaningful insight into how MICOS works in Plasmodium.

      First the positives of this manuscript. As has been the case with this research team, the manuscript is very sophisticated in the experimental approaches that are made. The highlights are the beautiful and often conclusive microscopy performed by the authors. Only the localization of Mic60 and Mic19 was inconclusive due to their very low expression unfortunately.

      The examination of the MICOS mutants during in vitro life cycle of Plasmodium falciparum is extremely impressive and yields convincing results. Mitochondrial deformation is tolerated by life cycle stage differentiation, with a modest but significant reduction of oocyte production, being observed.

      However, despite the herculean efforts of the authors, the manuscript as it currently stands represents only a minor advance in our understanding of the evolution of MICOS, which from the title and focus of the manuscript, is the main goal of the authors.

      In its current form, the manuscript reports some potentially important findings:

      (1) Mic60 is verified to play a role in crista formation, as is predicted by its orthology to other characterized Mic60 orthologs.

      (2) The discovery of a novel Mic19 analog (since the authors maintain there is no significant sequence homology), which exhibits a similar (or the same?) complexome profile with Mic60. This protein was upregulated in gametocytes like Mic60 and phenocopies Mic60 KO.

      (3) Both of these MICOS subunits are essential (not dispensable) for proper crista formation

      (4) Surprisingly, neither MICOS subunit is essential for in vitro growth or differentiation from ABS to sexual stages, and from the latter to sporozoites. This says more about the biology of plasmodium itself than anything about the essentiality of Mic60, i.e. plasmodium life cycle progression tolerates defects to mitochondrial morphology. But yes, I agree with the authors that Mic60's apparent insignificance for cell growth in examined conditions does differ with its essentiality in other eukaryotes. But fitness costs were not assayed (e.g. by competition between mutants and WT in infection of mosquitoes)

      (5) Decreased fitness of the mutants is implied by a reduction of oocyte formation.

      While interesting in their own way, collectively they do not represent a major advance in our understanding of MICOS evolution. Furthermore, the findings bifurcate into categories informing MICOS or Plasmodium biology. Both aspects are somewhat underdeveloped in their current form.

      This is unfortunate because there seem to be many missed opportunities in the manuscript that could, with additional experiments, lead to a manuscript with much wider impact. For me, what is remarkable about Plasmodium MICOS that sets it apart from other iterations is the apparent absence of the Mic10 subunit. Purification of plasmodium MICOS via the epitope tagged Mic60 and Mic19 could have verified that MICOS is assembled without this core subunit. Perhaps Mic60 and Mic19 are the vestiges of the complex, and thus operate alone in shaping cristae. Such a reduction may also suggest the declining importance of mitochondria in plasmodium.

      Another missed opportunity was to assay the impact of MICOS-depletion of OXPHOS in plasmodium.

      This is a salient issue as maybe crista morphology is decoupled from OXPHOS capacity in Plasmodium, which links to the apparent tolerance of mitochondrial morphology in cell growth and differentiation. I suggested in section A experiments to address this deficit.

      Finally, the authors could assay fitness costs of MICOS-ablation and associated phenotypes by assaying whether mosquito infectivity is reduced in the mutants when they are directly competing with WT plasmodium. Like the authors, I am also surprised that MICOS mutants can pass population bottlenecks represented by differentiation events. Perhaps the apparent robustness of differentiation may contribute plasmodium's remarkable ability to adapt.

      I realize that the authors put a lot of efforts into their study and again, I am very impressed by the sophistication of the methods employed. Nevertheless, I think there is still better ways to increase the impact of the study aside from overinterpreting the conclusions from the data. But this would require more experiments along the lines I suggest in Section A and here.

      We thank the reviewer for their extensive analysis of the significance of our findings, including the compliments on our microscopy images and the sophisticated experimental approaches. We hope we have convincingly argued why we could or could not include some of the additional analyses suggested by the reviewer in section 1 above.

      With regard to the significance statement, we want to point out that our finding that PfMICOS is not needed for initial formation of cristae (as opposed to organization thereof), is a confirmation of something that has been assumed by the field, without being the actual focus of studies. We argue that the distinction between formation and organization of cristae is important and deserves some attention within the manuscript. The result of MICOS not being involved in the initial formation of cristae, we argue to be relevant in Plasmodium biology and beyond. As for the insights into how MICOS works in Plasmodium we have confirmed that the previously annotated PfMIC60 is indeed involved in the organization of cristae. Furthermore, we have identified and characterized PfMIC19. These findings, we argue, are indeed meaningful insights into PfMICOS.

      Reviewer #3 (Evidence, reproducibility and clarity):

      Summary:

      MICOS is a conserved mitochondrial protein complex responsible for organising the mitochondrial inner membrane and the maintenance of cristae junctions. This study sheds first light on the role of two MICOS subunits (Mic60 and the newly annotated Mic19) in the malaria parasite Plasmodium falciparum, which forms cristae de novo during sexual development, as demonstrated by EM of thin section and electron tomography. By generating knockout lines (including a double knockout), the authors demonstrate that knockout of both MICOS subunits leads to defects in cristae morphology and a partial loss of cristae junctions. With a formidable set of parasitological assays, the authors show that despite the metabolically important role of mitochondria for gametocytes, the knockout lines can progress through the life stages and form sporozoites, albeit with diminished infection efficiency.

      We thank the reviewer for their time and compliment.

      Major comments:

      (1) The authors should improve to present their findings in the right context, in particular by:

      i) giving a clearer description in the introduction of what is already known about the role of MICOS. This starts in the introduction, where one main finding is missing: loss of MICOS leads to loss of cristae junctions and the detachment of cristae membranes, which are nevertheless formed, but become membrane vesicles. This needs to be clearly stated in the introduction to allow the reader to understand the consistency of the authors' findings in P. falciparum with previous reports in the literature.

      We extended the introduction to include this information.

      iii) at the end to the introduction, the motivating hypothesis is formulated ad hoc "conclusive evidence about its involvement in the initial formation of cristae is still lacking" (line 83). If there is evidence in the literature that MICOS is strictly required for cristae formation in any organism, then this should be explained, because the bona fide role of MICOS is maintenance of cristae junctions (the hypothesis is still plausible and its testing important).

      To clarify we rephrased the sentence to: “Although MICOS has been described as an organizer of crista junctions, its role during the initial formation of nascent cristae has not been investigated.”

      (2) Line 96-97: "Interestingly, PfMIC60 is much larger than the human MICOS counterpart, with a large, poorly predicted N-terminal extension." This statement is lacking a reference and presumably refers to annotated ORFs. The authors should clarify if the true N-terminus is definitely known - a 120kDa size is shown for the P. falciparum but this is not compared to the expected length or the size in S. cerevisiae.

      To solve the reference issue, we added the uniprot IDs we compared to see that the annotated ORF is bigger in Plasmodium. We also changed the comparison to yeast instead of human, because we realized it is confusing to compare to yeast all throughout the figure, but then talk about human in this specific sentence.

      Regarding whether the true N-terminus is known. Short answer: No, not exactly.

      However, we do know that the Pf version is about double the size of the yeast protein.

      As the reviewer correctly states, we show the size of 120kDa for the tagged protein in Figure 1G. Considering that we tagged the protein C-terminally, and observed a 120kDa product on western blot, it is safe to conclude that the true N-terminus does not deviate massively from the annotated ORF, and hence, that there is a considerable extension of the protein beyond a 60kDa protein. We do not directly compare to yeast MIC60 on our western blots, however, that comparison can be drawn from literature: Tarasenko et al., 2017 showed that purified MIC60 running at ~60kDa on SDS-PAGE actively bends membranes, suggesting that in its active form, the monomer of yeast MIC60 is indeed 60kDa in size.

      To clarify, we now emphasize that we ran the Alphafold prediction on the annotated open reading frame (annotated and sequenced by Bohme et al. and Chapell et al. now cited in the manuscript), and revised the wording to make clear what we are comparing in which sentence.

      (3) lines 244-245: "Furthermore, our data indicates the effect size increases with simultaneous ablation of both proteins?". The authors should explain which data they are referring to, as some of the data in Fig 3 and 4 look similar and all significance tests relate to the wild type, not between the different mutants, so it is not clear if any overserved differences are significant. The authors repeat this claim in the discussion in lines 368-369 without referring to a specific significance test. This needs to be clarified.

      As a reply to this and other comments from the reviewers we added the multiple testing within all samples. In addition, to clarify statistics used we included a supplementary dataset with all p-values and statistical tests used.

      (4) lines 304-306: "Though well established as the cristae organizing system, the role of MICOS in initial formation of cristae remains hidden in model organisms that constitutively display cristae.". This sentence is misleading since even in organisms that display numerous cristae throughout their life cycle, new cristae are being formed as the cells proliferate. Thus, failure to produce cristae in MICOS knockout lines would have been observable but has apparently not been reported in the literature. Thus, the concerted process in P. falciparum makes it a great model organism, but not fundamentally different to what has been studied before in other organisms.

      We deleted this statement.

      (5) lines 373-378. "where ablation of just MIC60 is sufficient to deplete functionality of the entire MICOS (11, 15),". The authors' claim appears to be contrary to what is actually stated in ref 15, which they cite:

      "MICOS subunits have non-redundant functions as the absence of both MICOS subcomplexes results in more severe morphological and respiratory growth defects than deletion of single MICOS subunits or subcomplexes."

      This seems in line with what the authors show, rather than "different".

      This sentence has been removed.

      (6) lines 380-385: "... thus suggesting that membrane invaginations still arise, but are not properly arranged in these knockout lines. This suggests that MICOS either isn't fully depleted,...". These conclusions are incompatible with findings from ref. 15, which the authors cite. In that study, the authors generated a ∆MICOS line which still forms membrane invaginations, showing that MICOS is not required at all for this process in yeast. Hence the authors' implication that MICOS needs to be fully depleted before membrane invaginations cease to occur is not supported by the literature.

      This sentence has been deleted in the revised version of the manuscript.

      Minor comments:

      (1) The authors should consider if the first part of their title could be seen as misleading: It suggests that MICOS is "the architect" in cristae formation, but this is not consistent with the literature nor their own findings.

      Title is changed accordingly

      - Line 43, of the three seminal papers describing the discovery of MICOS in 2011, the authors only cite two (refs 6 and 7), but miss the third paper, Hoppins et al, PMID: 21987634, which should probably be corrected.

      Done, the paper is now cited

      - Page 2, line 58: for a more complete picture the authors should also cite the work of others here which shows that although at very low levels, e.g. complex III (a drug target) and ATP synthase do assemble (Nina et al, 2011, JBC).

      Done

      - Page 3, line 80: "Irrespective of the shape of an organism's cristae, the crista junctions have been described as tubular channels that connect the cristae membrane to the inner boundary membrane (22, 24)." This omits the slit-shaped cristae junctions found in yeast (Davies et al, 2011, PNAS), which the authors should include.

      The paper and concept have been added to the manuscript, though the sentence has been moved up in the introduction, when crista junctions are first introduced.

      - Line 97: "poorly predicted N-terminal extension", as there is no experimental structure, we don't know if the prediction is poor. Presumably the authors mean either poorly ordered or the absence of secondary structure elements, or the poor confidence score for that region in the prediction? This should be clarified or corrected.

      We were referring to the poor confidence score. To address this comment as well as major point 2, we rewrote the respective paragraph. It now clearly states that confidence of the prediction is low, and we mention the tool that was used to identify conserved domains (Topology-based Evolutionary Domains).

      - Line 98: "an antiparallel array of ten β-sheets". They are actually two parallel beta-sheets stacked together. The authors could find out the name of this fold, but the confidence of the prediction is marked a low/very low. So, its existence is unknown, not just its "function".

      We adapted the domain description to “a stack of two parallel beta-sheets" and replaced the statement on unknown function by the statement “Because this domain is predicted solely from computational analysis, both its actual existence in the native protein and its biological function remain unknown.”

      - Fig 1B: The authors show two alphafold predictions of S. cerevisiae and P. falciparum Mic60 structures. There is however an experimental Mic60/19 (fragment) structure from the former organism (PMID: 36044574), which should be included if possible.

      We appreciate the reviewer’s suggestion and note that the available structural data indeed provides valuable insight into how MIC60 and MIC19 interact. However, these structures represent fusion constructs of limited protein fragments and therefore capture only a small portion of each protein, specifically the interaction interface. Because our aim in Fig. 1B is to compare the overall domain architecture of the full-length proteins, we believe that including fragment-based structures would be less informative in this context.

      - Line: 318-321: "The same trend was observed for PfMIC19 and PfMIC60. Although transcriptomic data suggested that low-level transcripts of PfMIC19 and PfMIC60 are present in ABS (38), we did not detect either of the proteins in ABS by western blot analysis. While this statement is true, the authors should comment on the sensitivity of the respective methods - how well was the antibody working in their hands and how do they interpret the absence of a WB band compared to transcriptomics data?

      The HA antibody used in our experiments is a standard commercial reagent that performs reliably in both WB and IFA, although it shows a low background signal in gametocytes. We agree that the sensitivity of the method and the interpretation of weak or absent bands should be addressed explicitly. Transcript levels for both PfMIC19 and PfMIC60 in asexual blood stages fall within the <25 percentile, suggesting that these signals likely represent background. Nevertheless, we acknowledge that low-level protein expression below the detection limit of western blot analysis cannot be excluded. To reflect these considerations, we added the sentence: ‘The apparent absence could indicate that transcripts are not translated in ABS or that the proteins’ expression was below detection limits of western blot analysis.

      - Lines 322-323: would the authors not typically have expected an IFA signal given the strength of the band in Western blot? If possible, the authors should comment if the negative fluorescence outcome can indeed be explained with the low abundance or if technical challenges are an equally good explanation.

      Considering the nature of the investigated proteins (embedded in the IMM and spread throughout the mitochondria) difficulties in achieving a clear signal in IFA or U-ExM are not very surprizing. While epitopes may remain buried in IFA, U-ExM usually increases accessibility for the antibodies. However, U-ExM comes at the cost of being prone to dotty background signals, therefore potentially hiding low abundance, naturally dotty signals such as the signal of MICOS proteins that localize to distinct foci (at the CJ) along the mitochondrion. Current literature suggests that, in both human and yeast, STED is the preferred method for accurate spatial resolution of MICOS proteins (https://www.ncbi.nlm.nih.gov/pubmed/32567732,https://www.ncbi.nlm.nih.gov/pubmed/3206734 4). Unfortunately, we do not have experience with, nor access to, this particular technique/method.

      - Lines 357-365: the authors describe limitations of the applied methods adequately. Perhaps it would be helpful to make a similar statement about the analysis of 3D objects like mitochondria and cristae from 2D sections. E.g. the apparent cristae length depends on whether cristae are straight (e.g. coiled structures do not display long cross sections despite their true length in 3D).

      The limitations of other methods are described in the respective results section.

      We added a clarifying sentence in the results section of Figure 4:

      “Note that such measurements do not indicate the true total length or width of cristae, as the data is two-dimensional. The recorded values are to be considered indicative of possible trends, rather than absolute dimensions of cristae.“

      This statement refers to the length/width measurements of cristae.

      In the context of Figure 4D we mention the following (see preprint lines 229 – 230): “We expect this effect to translate into the third dimension and thus conclude that the mean crista volume increases with the loss of either PfMIC19, PfMIC60, or both.”

      For Figure 5, we included a clarifying statement in the results section of the preprint (lines 269 – 273): “Note that these mitochondrial volumes are not full mitochondria, but large segments thereof. As a result of the incompleteness of the mitochondria within the section, and the tomography specific artefact of the missing wedge, we were unable to confirm whether cristae were in fact fully detached from the boundary membrane, or just too long to fit within the observable z-range.”

      - Line 404: perhaps undetected or similar would be a better description than "hidden"?

      The sentence does not exist in the revised manuscript.

      Reviewer #3 (Significance):

      The main strength of the study is that it provides the first characterisation of the MICOS complex in P. falciparum, a human parasite in which the mitochondrion has been shown to be a drug target. Mic60 and the newly annotated Mic19 are confirmed to be essential for proper cristae formation and morphology, as well as overall mitochondrial morphology. Furthermore, the mutant lines are characterised for their ability to complete the parasite life cycle and defects in infection effectivity are observed. This work is an important first step for deciphering the role of MICOS in the malaria parasite and the composition and function of this complex in this organism. The limitation of the study stems from what is already known about MICOS and its subunits in great detail in yeast and humans with similar findings regarding loss of cristae and cristae defects. The findings of this study do not provide dramatic new insight on MICOS function or go substantially beyond the vast existing literature in terms of the extent of the study, which focuses on parasitological assays and morphological analysis. Exploring the role of MICOS in an early-divergent organism and human parasite is however important given the divergence found in mitochondrial biology and P. falciparum is a uniquely suited model system. One aspect that would increase the impact of the paper would be if the authors could mechanistically link the observed morphological defects to the decreased infection efficiency, e.g. by probing effects on mitochondrial function. This will likely be challenging as the morphological defects are diverse and the fitness defects appear moderate/mild.

      As suggested by Reviewer 2, we examined mitochondrial membrane potential in gametocytes using MitoTracker staining and did not observe any obvious differences associated with the morphological defects. At present, additional assays to probe mitochondrial function in P. falciparum gametocytes are not sufficiently established, and developing and validating such methods would require substantial work before they could be applied to our mutant lines. For these reasons, a more detailed mechanistic link between the observed morphological changes and the reduced infection efficiency is currently beyond reach.

      The advance presented in this study is to pioneer the study of MICOS in P. falciparum, thus widening our understanding of the role of this complex to different model organism. This study will likely be mainly of interest for specialised audiences such as basic research parasitologists and mitochondrial biologists. My own field of expertise is mitochondrial biology and structural biology.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, the role of the insulin receptor and the insulin growth factor receptor was investigated in podocytes. Mice, where both receptors were deleted, developed glomerular dysfunction and developed proteinuria and glomerulrosclerosis over several months. Because of concerns about incomplete KO, the authors generated and studied podocyte cell lines where both receptors were deleted. Loss of both receptors was highly deleterious with greater than 50% cell death. To elucidate the mechanism of cell death, the authors performed global proteomics and found that spliceosome proteins were downregulated. They confirmed this directly by using long-read sequencing. These results suggest a novel role for insulin and IGF1R signaling in RNA splicing in podocytes.

      This is primarily a descriptive study and no technical concerns are raised. The mechanism of how insulin and IGF1 signaling regulates splicing is not directly addressed but implicates potentially the phosphorylation downstream of these receptors. In the revised manuscript, it is shown that the mouse KO is incomplete potentially explaining the slow onset of renal insufficiency. Direct measurement of GFR and serial serum creatinines might also enhance our understanding of progression of disease, proteinuria is a strong sign of renal injury. An attempt to rescue the phenotype by overexpression of SF3B4 would also be useful but may be masked by defects in other spliceosome genes. As insulin and IGF are regulators of metabolism, some assessment of metabolic parameters would be an optional add-on.

      Significance:

      With the GLP1 agonists providing renal protection, there is great interest in understanding the role of insulin and other incretins in kidney cell biology. It is already known that Insulin and IGFR signaling play important roles in other cells of the kidney. So, there is great interest in understanding these pathways in podocytes. The major advance is that these two pathways appear to have a role in RNA metabolism.

      Comments on revised version:

      I'm satisfied with the revised manuscript and the responses to my previous concerns.

      Thank you.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, submitted to Review Commons (journal agnostic), Coward and colleagues report on the role of insulin/IGF axis in podocyte gene transcription. They knocked out both the insulin and IGFR1 mice. Dual KO mice manifested a severe phenotype, with albuminuria, glomerulosclerosis, renal failure and death at 4-24 weeks.

      Long read RNA sequencing was used to assess splicing events. Podocyte transcripts manifesting intron retention were identified. Dual knock-out podocytes manifested more transcripts with intron retention (18%) compared wild-type controls (18%), with an overlap between experiments of ~30%.

      Transcript productivity was also assessed using FLAIR-mark-intron-retention software. Intron retention w seen in 18% of ciDKO podocyte transcripts compared to 14% of wild-type podocyte transcripts (P=0.004), with an overlap between experiments of ~30% (indicating the variability of results with this method). Interestingly, ciDKO podocytes showed downregulation of proteins involved in spliceosome function and RNA processing, as suggested by LC/MS and confirmed by Western blot.

      Pladienolide (a spliceosome inhibitor) was cytotoxic to HeLa cells and to mouse podocytes but no toxicity was seen in murine glomerular endothelial cells.

      The manuscript is generally clear and well-written. Mouse work was approved in advance. The four figures are generally well-designed, bars/superimposed dot-plots.

      Methods are generally well described.

      Comments on revised version:

      Coward and colleagues have done an excellent job of responding to all the reviewer comments.

      Thank you.

      Reviewer #4 (Public review):

      Summary and background:

      This report entitled "The insulin/IGF axis is critically important (for) controlling gene transcription in the podocyte" from Hurcombe et al is based on a mouse double knockdown of the IR and IGF1R and a parallel cultured mouse podocyte model. Insulin/IGF signaling system in mammals evolved as three gene reduplicated peptides (insulin, IGF-1, and IGF-2) and their two receptors IR and IGF1R that cross-react to variable extents with the peptides, are ubiquitously expressed, and signal through parallel pathways. The major downstream effect of insulin is to regulate glucose uptake and metabolism, while that of the IGF pathways is to regulate growth and cell cycling in part through mTORC1. The GH-IGF-1-IGF1R pathway regulates post-natal growth. IGF-2 signaling is thought to play a major role in regulating intrauterine growth and development, although IGF-2 is also present at high levels in post-natal life. Thus, one would anticipate that reducing IR/IGF1R signaling in any cell would slow growth and cell cycling by reducing growth factor and metabolic mTORC1-mediated and other processes including the splicing of RNA for protein synthesis.

      Thank you for this new extra review and assessing our paper with new suggestions (we addressed the previous suggestions to the satisfaction of other reviewers). Of note -regarding this introduction – the podocyte is a terminally differentiated cell and may have unique responses to insulin / IGF as it is accepted it does not generally proliferate (hence we consider understanding the actions of insulin / IGF and their receptors to be of interest). Indeed, we have recently shown a contrasting effect of IGF signalling in the podocyte. Partial suppression of the IGF1 receptor is beneficial in contrast to near complete suppression that results in mitochondrial dysfunction (PMID:38706850).

      Mouse IR/IGF1R double knockdown model:

      A double knockdown mouse model was generated by interbreeding mice with different genetic backgrounds carrying floxed sites for IR and IGF-1R to produce mixed background offspring with both floxed IR and IGF-1R genes. These mice were crossed so that the podocin promoter driven-Cre (that comes on at about embryonic day 12 bas podocytes are developing) would delete IR and IGF-1R genes. Since podocin is believed to be an absolutely podocyte-specific protein, this podocin promoter this is predicted to specifically knock down the IR and IGF1R genes only in podocytes. The weight and growth of double KO offspring was not different from controls, but some proportion of the double knockdown mice subsequently developed proteinuria by 6 months and 20% died, although no specific data is provided to identify the cause of the deaths since eGFR was not decreased. Surviving mice were evaluated at 6 months of age. The efficacy of knockdown was not demonstrated in the mouse model itself, although a temperature-sensitive cell line developed from these double knockdown mice showed that expression of IR and IGF-1R proteins in the Cre-treated cell line were both reduced by about 50% (no statistical analysis of this result provided).

      In the knockout mice, proteinuria was significantly increased by 6 months, but not at earlier time points. Histologic analysis showed proteinaceous casts, glomerulosclerosis and interstitial fibrosis. Podocyte number was stated to be reduced by about 30% in double knockdown mice, although the method by which this was evaluated seems to have been by counting WT1 positive nuclei in glomerular cross-sections, an approach that is well-known not to be a reliable way of assessing true podocyte number. No information is provided about podocyte size, density or glomerular volume.

      Comment: If IR/IGF1R deletion plays a significant role in normal podocyte function sufficient to cause proteinuria and glomerulosclerosis then the effect of reduced IR and IGF1R protein expression on podocyte function would have been expected to produce a phenotype before 6 months. A more likely scenario to explain the overall result is that deleting the IR and IGF1R genes at about embryonic day12 impacted podocyte development to a variable extent such that some mice developed fewer podocytes per glomerulus than other mice. As mice grow and their glomeruli and glomerular capillary area increases, those mice with fewer podocytes would not be able to completely cover the filtration surface with foot processes and would develop proteinuria and glomerulosclerosis. If reduced podocyte number per glomerulus is the proximate cause of the observed proteinuria, then modulation of the body and kidney growth rate by calorie restriction to slow growth (lower circulating IGF-1 levels) would be expected to be protective, while a high protein high calorie diet (higher circulating IGF-1 levels) or uni-nephrectomy to increase kidney growth rate would be expected to enhance proteinuria and glomerulosclerosis.

      Thank you for these comments. In response to them:

      (1) WT1 as a marker of podocyte number. We agree may not be the most accurate way of precisely measuring podocyte number but is widely accepted in the field (PMID:33655004 / PMID:38542564) and we think convincingly shows fewer podocytes at 6-months.

      (2) Podocyte size and density was not measured. This was not the focus of the paper and the histology obviously showed a significant phenotype in several mice (Figs 1D-F). Of note we did objectively assess a glomeruloscleorosis index (Fig 1D). We took the approach to understand mechanism through non-biased proteomics and phospho-proteomics of conditionally immortalised podocytes in which we had convincingly knocked down the insulin and IGF1 receptors (Figure 2)

      (3) You did not study the mice earlier to ascertain the developmental phenotype. We concede we did not do this but there was no significant proteinuria detected early in the mice so elected not to increase mouse numbers by studying them then (which we consider good practice for reduction, replacement and refinement). We suspect there would have been subtle changes in those mice that had significantly reduced simultaneous IR and IGF1R knockdown. It was precisely because of this that we generated a conditionally immortalised podocyte cell line with robust simultaneous knock-down of both receptors.

      (4) You did not show significant insulin and IGF1 receptor knockdown in the conditionally immortalised cell line (reviewer states it was 50%). We clearly knocked both receptors down (insulin and IGF1R) in the podocyte line by >80% which was highly statistically significant (p<0.00001). Figure 2A. We agree this was crucial (and we made the cell line because of the variability in the mouse model).

      The model as used may be more representative of a variable degree of podocyte depletion than an effect of impaired IR/IGF1R signaling. Therefore, although the phenotype may be ultimately attributable to the IR/IGF1R gene deletions the proteinuria and glomerulosclerotic phenotype itself was probably a consequence of defective podocyte development. Examining podocyte number, size, density and glomerular volume at earlier time points (4 weeks) would help to answer this question. Therefore, a more appropriate title would be "The insulin/IGF axis is critically important (for) normal podocyte development and deployment". In this context the effect of the knockdowns on splicing would make more sense.

      Please see our response (above). We think our final conclusion that in the podocyte the insulin/IGF axis is important for spliceosome activity and control is valid. This is due to our findings (both total and phospho proteomics results) and considering recent other papers showing this axis can rapidly phosphorylate a variety of spliceosome proteins in different cell types (PMID:39939313 / PMID:32888406). All discussed in detail in the manuscript).

      Cell culture studies. A cell line was generated using a temperature sensitive SV40 system that has been previously reported from this laboratory. A detailed analysis is provided to show that double knockout cells exhibited abnormal spliceosome activity. This forms the basis for the conclusion that "The insulin/IGF axis is critically important (for) controlling gene transcription in the podocyte". There are several concerns that weaken this conclusion.

      (1) In the double knockdown cell culture system about 30% of cells were "lost" by 3 days and about 70% of cells were "lost" by 5days. The studies were done at the 3 day time point. It is not clear whether "lost" cells were in the process of dying, stress-induced detachment, or just growing more slowly than control due to reduced IR and IGF-1R signaling. These processes could have impacted splicing in a non-specific way independent of IR/IGF1R signaling itself.

      (2) Can a single cell line derived from the double floxed mice be relied on to provide an unbiased picture of the effect of deleting IR and IGF-1R? Presumably, the transfection and selection process will select for cells that survive thereby including unknown biases, possibly related to spliceosome function. Is a single cell line adequate? These investigators have extensive experience with this type of analysis, but this question is not addressed in the discussion.

      (3) To determine whether the effect is specific to reduced IR/IGFR signaling the deletion of IR and IGF-1R could be corrected by transfecting full length IR and IGF-1R cDNAs into the cells to restore normal IR/IGF1R signaling. If transfected cells with intact IR and IGF-1R expression and activity returns spliceosome activity to normal this would be evidence that receptors themselves play some role in spliceosome activity, as opposed to the downstream effect on growth limitation/stress on the cells.

      (4) Other ways of testing whether the splicing effect is specifically due to reduced IR/IGF-1R signaling would be to (a) block IR and IGF1R receptors using available inhibitors, (b) remove or reduce insulin, IGF-1 and IGF-2 levels in the culture medium, (c) use low glucose and amino acid culture medium to slow growth rate independent of receptor function, (d) or block intra-cellular signaling via the IR and IGF-1R receptors through mTORC1 inhibition using rapamycin or other signaling targets.

      (5) It would be useful to determine whether the cultured cells stressed in other ways (e.g. ischemia, toxins, etc.) also results in the same splicing abnormalities.

      Point 1. 70% cell loss was observed at day 7 (not day 5). We found approximately 20% loss at day 3. We opted to go for this early date hypothesising the key detrimental processes would be clear then. This 3 day time point also ensures there has been enough time to allow for the expression of Cre recombinase, receptor gene excision and degradation of existing endogenous IR/IGF1R following lentiviral transduction. Interestingly we did not find a major “death or apoptosis” signal in our data then but agree it should be considered. We think this is a specific pathway as we have examined several other conditionally immortalised detrimental podocyte cell line previously using proteomics with a much more severe phenotype of cell death (E.g. podocyte GSK3 alpha/beta knockdown) and we detected NO spliceosome signal (PMID:30679422). Furthermore, there are now other podocyte proteomics “stress” studies that have been published in which there is proteinuria and significant cell loss / death that also do not show spliceosome dysfunction. These include studying the detailed proteosomal signature of podocytes stressed with Doxorubicin and Lipopolysaccharide endotoxin LPS in mice (PMID:32047005) and bradykinin stimulation of rat podocytes (PMID:32518694).

      Point 2. Yes, we think it is valuable and reproducible. We generated a podocyte cell line from insulin receptor and IGF1 receptor homozygous floxed cells. Hence there is no selection bias in the cells when generating the line as both receptors are effectively intact. We then temporally “knocked down” the receptors with extrinsic lentiviral Cre.

      Importantly we validated our cell line findings both back in the cells (with Western blotting) and in our transgenic receptor knockdown mice and found evidence of spliceosomal dysregulation (Figure 3E and 3F). Also as discussed above the spliceosome has been identified in other models in the insulin/IGF pathway.

      Point 3. We don’t think the experiment of knocking down the receptors and then reconstituting them would prove this hypothesis. This is because if splicing abnormality was due to generalised cell dysfunction (which we do not think is the case in this situation) then putting the receptors back may simply restore cell health and the spliceosomal function (e.g. it does not prove it is via the receptors). Secondly, the process of transduction with multiple lentiviruses may be inherently stressful to the cell and there may be a high level of extrinsic receptor inserted which may also be confounding/detrimental. Finally, as discussed there are now several lines of evidence describing insulin / IGF signalling to spliceosomal proteins which we consider important (discussed in the paper in detail).

      Point 4. We think modulating the receptors using the Cre-lox approach is the cleanest approach (with fewer off-target effects) to interrogate the insulin / IGF axis. It allows us to differentiate the cells by thermo-switching (which is crucial for this terminally differentiated cell) and then robustly knocking down both receptors simultaneously to investigate mechanism. We agree these supplementary approaches may give some extra information if their limitations (eg off target effects of inhibitors) are also taken into consideration.

      Point 5. They do not. Please see response to point 1 above regarding GSK3, Doxorubicin, LPS and bradykinin challenge.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Johnston and Smith used linear electrode arrays to record from small populations of neurons in the superior colliculus (SC) of monkeys performing a memory-guided saccade (MGS) task. Dimensionality reduction (PCA) was used to reveal low-dimensional subspaces of population activity reflecting the slow drift of neuronal signals during the delay period across a recording session (similar to what they reported for parts of cortex: Cowley et al., 2020). This SC drift was correlated with a similar slow-drift subspace recorded from the prefrontal cortex, and both slow-drift subspaces tended to be associated with changes in arousal (pupil size). These relationships were driven primarily by neurons in superficial layers of the SC, where saccade sensitivity/selectivity is typically reduced. Accordingly, delay-period modulations of both spiking activity and pupil size were independent of saccade-related activity, which was most prevalent in deeper layers of the SC. The authors suggest that these findings provide evidence of a separation of arousal- and motor-related signals. The analysis techniques expand upon the group's previous work and provides useful insight into the power of large-scale neural recordings paired with dimensionality reduction. This is particularly important with the advent of recording technologies which allow for the measurement of spiking activity across hundreds of neurons simultaneously. Together, these results provide a useful framework for comparing how different populations encode signals related to cognition, arousal, and motor output in potentially different subspaces.

      Comments on revised manuscript:

      The authors have done a very good job of responding to all of the reviewers' concerns.

      No weaknesses to address.

      Reviewer #2 (Public review):

      Weaknesses:

      (1) The greatest weakness in the present research is the fact that arousal is a functionally less important non-motoric variable. The authors themself introduce the problem with a discussion of attention, which is without any doubt the most important cognitive process that needs to be functionally isolated from oculomotor processes. Given this introduction, one cannot help but wonder, why the authors did not design an experiment, in which spatial attention and oculomotor control are differentiated. Absent such an experiment, the authors should spend more time on explaining the importance of arousal and how it could interfere with oculomotor behavior.

      (2) In this context, it is particularly puzzling that one actually would expect effects of arousal on oculomotor behavior. Specifically, saccade reaction time, accuracy, and speed could be influenced by arousal. The authors should include an analysis of such effects. They should also discuss the absence or presence of such effects and how they affect their other results.

      (3) The authors use the analysis shown in Figure 6D to argue that across recording sessions the activity components capturing variance in pupil size and saccade tuning are uncorrelated. however, the distribution (green) seems to be non-uniform with a peak at very low and very high correlation specifically. The authors should test if such an interpretation is correct. If yes, where are the low and high correlations respectively? Are there potentially two functional areas in SC?

      Comments on revised manuscript:

      I remain somewhat concerned that the authors jump immediately into an analysis of the 'arousal-related' effects on SC activity. Before that, I would like to see a more detailed discussion justifying the use pupil size alone (i.e., w/o other indicators such as RT) as indicative of fluctuations in general arousal that are causal to concomitant changes in SC activity. Instead, in its current form, the authors find changes in SC activity and describe them immediately as 'arousal-related'.

      Other than this conceptual issue, I do not have major problems with the analysis per se.

      We agree with the reviewer that we may have advanced into discussing arousal-related effects in the previous version of the manuscript without providing a thorough explanation for why we think the slow drift axis is associated with changes in the monkey’s arousal levels. Arousal has been linked to the size of the pupil as well as movements of the eyes in numerous previous studies. We have made the following changes in the revised manuscript to address the reviewer’s concern:

      (1) When first describing how the spiking responses of SC neurons fluctuate over the course of a recording session (Lines 130-132), we have used the phrase "slow fluctuations in the spiking responses" rather than "arousal-related fluctuations in the spiking responses". Then, when describing these effects in more detail (Lines 136-147), we have explained why we think these fluctuations may be related to arousal. The following text has been added in the revised manuscript for clarification:

      “We found that this low-dimensional pattern of activity in the SC was also correlated with pupil size in the present study and with simultaneously recorded data in the prefrontal cortex (PFC), pointing to a link between this brain-wide fluctuation and changes in the monkeys’ arousal levels while performing the task.” (Lines 136-147)

      (2) We have changed the subheading in Line 183 of the revised manuscript from "Arousal-related fluctuations are present in the SC and correlated with pupil size and fluctuations in PFC activity" to "Slow fluctuations in SC spiking activity are correlated with pupil size and PFC activity". Given that we have not yet explained the results linking these fluctuations to arousal at this stage of the manuscript, we believe that this revised title is more accurate and avoids jumping too quickly to arousal-related fluctuations without first explaining the link between SC slow drift, pupil size and PFC activity.

      (3) We have provided additional justification for using pupil size and PFC activity to assess whether SC slow drift is associated with changes in the monkeys’ arousal levels. In a previous study, we computed an identical slow drift axis for spiking responses in visual cortex (V4) and PFC, and investigated how these low-dimensional neural activity patterns, which were themselves strongly correlated, were associated with various eye-related metrics (e.g., pupil size, microsaccade rate, reaction time, saccade velocity). Results showed that pupil size was the strongest predictor of slow drift in V4 and PFC. Given that the eye metrics were also strongly correlated with each other, we believe that the observed relationship between SC slow drift, pupil size and PFC activity provides sufficient evidence to suggest that the fluctuations observed in the SC are arousal-related. The following text has been added to the Results section of the revised manuscript:

      “Moreover, previous work in our laboratory computed a similar slow-drift axis using spiking activity in visual cortex (V4) and PFC, and investigated the relationship between these low-dimensional neural activity patterns and different eye-related metrics (e.g., pupil size, microsaccade rate, reaction time, saccade velocity). In addition to observing a strong correlation between V4 and PFC slow drift, we found that, relative to the other eye-related metrics, pupil size was the strongest predictor of these fluctuations (Johnston et al., 2022a). Thus, to further confirm the link between the SC slow drift axis and changes in the monkeys’ arousal levels while they performed the MGS task, we next sought to explore if projections onto the SC slow drift axis were associated with pupil size.” (Lines 236-344)

      Reviewer #3 (Public review):

      Summary:

      This study looked at slow changes in neuronal activity (on the order of minutes to hours) in the superior colliculus (SC) and prefrontal cortex (PFC) of two monkeys. They found that SC activity shows slow drift in neuronal activity like in the cortex. They then computed a motor index in SC neurons. By definition, this index is low if the neuron has stronger visual responses than motor response, and it is low if the neuron has weaker visual responses and stronger motor responses. The authors found that the slow drift in neuronal activity was more prevalent in the low motor index SC neurons and less prevalent in the high motor index neurons. In addition, the authors measured pupil diameter and found it to correlate with slow drifts in neuronal activity, but only in the neurons with lower motor index of the SC. They concluded that arousal signals affecting slow drifts in neuronal modulations are brain-wide. They also concluded that these signals are not present in the deepest SC layers, and they interpreted this to mean that this minimizes the impact of arousal on unwanted eye movements.

      Strengths:

      The paper is clear and well-written.

      Showing slow drifts in the SC activity is important to demonstrate that cortical slow drifts could be brain-wide.

      Weaknesses:

      The authors find that the SC cells with the low motor index are modulated by pupil diameter. However, this could be completely independent of an "arousal signal". These cells have substantial visual sensitivity. If the pupil diameter changes, then their activity should be influenced since the monkey is watching a luminous display. So, in this regard, the fact that they do not see "an arousal signal" in the most motor neurons (through the pupil diameter analyses) is not evidence that the arousal signal is filtered out from the motor neurons. It could simply be that these neurons simply do not get affected by the pupil diameter because they do not have visual sensitivity. So, even with the pupil data, it is still a bit tricky for me to interpret that arousal signals are excluded from the "output layers" of the SC.

      Of course, the general conclusion is that the motor neurons will not have the arousal signal. It's just the interpretation that is different in the sense that the lack of the arousal signal is due to a lack of visual sensitivity in the motor neurons.

      I think that it is important to consider the alternative caveat of different amounts of light entering the system. Changes in light level caused by pupil diameter variations can be quite large. Please also note that I do not mean the luminance transient associated with the target onset. I mean the luminance of the gray display. it is a source of light. if the pupil diameter changes, then the amount of light entering to the visually sensitive neurons also changes.

      Comments on revised manuscript:

      The authors have addressed my first primary comment. For the light comment, I'm still not sure they addressed it. At the very least, they should explicitly state the possibility that the amount of light entering from the gray background can matter greatly, and it is not resolved by simply changing the analysis interval to the baseline pre-stimulus epoch. I provide more clear details below:

      In line 194 of the redlined version of the article (in the Introduction), the citation to Baumann et al., PNAS, 2023 is missing near the citation of Jagadisan and Gandhi, 2022. Besides replicating Jagadisan and Gandhi, 2022, this other study actually showed that the subspaces for the visual and motor epochs are orthogonal to each other

      We thank the reviewer for this comment and apologize that the citation to Baumann et al., PNAS, 2023 was missing in the previous version of the manuscript. In addition to including this citation in the revised version, we have provided a much more comprehensive description of all three cited studies and clarified that, in addition to replicating the results of Jagadisan and Gandhi, Baumann et al., PNAS, 2023 showed that the subspaces for the visual and motor epochs are orthogonal to each other. The following lines have been added to the Introduction of the revised manuscript:

      “A similar separation has been observed for visual and motor responses in the SC (Jagadisan and Gandhi, 2022; Ayar et al., 2023; Baumann et al., 2023). For example, Jagadisan and Gandhi (2022) used linear microelectrode arrays to investigate why early eye movements are not triggered when neuronal responses to a visual target, presented before a delayed saccade to that target, cross a threshold. They found that population activity in the SC was less stable during the visual epoch of a delayed saccade task, relative to the saccade epoch. Moreover, saccades could be evoked more easily by patterned microstimulation when the temporal structure of the microstimulation was stable across electrodes, providing a potential explanation for how downstream regions differentiate between visual and motor responses. Similar results were reported by Baumann et al. (2023) who found that the strength of SC motor responses during a saccade to a visual image depends on the features of that image (e.g., contrast, orientation). When dimensionality reduction was applied to the spiking responses of neuronal populations in the SC, the population trajectory during the initial visual response to the image was orthogonal to that during the motor response. These findings replicate the separation in temporal population structure reported by Jagadisan and Gandhi (2022) and support the results of Ayar et al. (2023). They found that, although not completely orthogonal, population activity in the SC is distinct for visual and motor responses during the same oculomotor task and across different tasks, which could further facilitate the decoding of signals related to sensation, action and context by downstream regions.” (Lines 110-127)

      Line 683 (and around) of the redlined version of the article (in the Results): I'm very confused here. When I mentioned visual modulation by changed pupil diameter, I did not mean the transient changes associated with the brief onset of the cue in the memory-guided saccade task. I meant the gray background of the display itself. This is a strong source of light. If the pupil diameter changes across trials, then the amount of light entering the eye also changes from the gray background. Thus, visually-responsive neurons will have different amount of light driving them. This will also happen in the baseline interval containing only a fixation spot. The arguments made by the authors here do not address this point at all. So, please modify the text to explicitly state the possibility that the global luminance of the display (as filtered by the pupil diameter) alters the amount of light driving the visually-responsive neurons and could contribute to the higher effects seen in the more visual neurons.

      We apologize that our analysis did not fully address the reviewer’s concern that the presence of fluctuations in visual neurons and their absence in motor neurons may have arisen indirectly due to changes in the amount of light entering the eye caused by changes in pupil size. As per the reviewer’s suggestion, we have now raised the possibility that visual neurons in the SC may have firing rates that are monotonically related to slow trends in overall luminance induced by pupil size changes, whereas motor neurons do not. Although we believe this to be an unlikely explanation, the paragraph from lines 374-398 has been modified to better describe this possibility, including the following text:

      “Given that slow drift is found in traditionally defined visual areas (e.g., area V4) and in regions that show mixed selectivity for multiple task variables (e.g., PFC) (Cowley et al., 2020), it seems unlikely that slow drift is caused by luminance fluctuations alone and more likely that it reflects global changes in arousal. At the same time, these arousal-related fluctuations covary with changes in pupil size (Johnston et al., 2022a), which could modulate the amount of light entering the eye from the display. This might affect visual neurons but not motor neurons due to their lack of visual sensitivity. Because SC neurons exist on a continuum, with visual responses decreasing and motor responses increasing from the intermediate to deep layers (Massot et al., 2019; Heusser et al., 2022) and no clear categorical boundary for motor-only neurons, any readout strategy would still need to avoid corruption of the motor output by slow drift, even if it were caused by changes in the amount of light entering the eye.” (Lines 387-398)

      The figures (everywhere, including the responses to reviewers) are very low resolution and all equations in methods are missing.

      We thank the reviewer for bringing this to our attention. We believe this issue may have arisen during conversion of the manuscript file for review, as the figures were of sufficient quality and the equations visible in the version that appeared online (https://doi.org/10.7554/eLife.99278.2). In any case, we will ensure that high-resolution figures are submitted with the revised manuscript and apologize that they were low resolution in the previous version.

      I'm very confused by Fig. 2 - supplement 2. Panel B shows a firing rate burst aligned to *microsaccade* onset. Does that mean you were in the foveal SC? i.e. how can neurons have a motor burst to the target of the memory-guided saccade and also for microsaccades? And which microsaccade directions caused such a burst? And what does it mean to compute the motor index and spike count for microsaccades in panel C? if you were in the proper SC location for the saccade target, then shouldn't you *not* get any microsaccade-related burst at all? This is very confusing to me and needs to be clarified

      We agree that clarification is needed here and thank the reviewer for their comment. The eccentricity of the targets was set to match the endpoints of the evoked saccades, which for some sessions were relatively close to the fovea. The mean eccentricity of the targets across sessions was 4.52° (SD = 2.89°). These values are now reported in the Methods section of the revised manuscript (Line 637). For the neuron shown in Figure 2–figure supplement 2, the eccentricity of the targets was 3°. Previous research has shown that some SC neurons respond during microsaccades as well as slightly larger saccades (see Hafed & Krauzlis, 2012, J. Neurophysiol., Fig. 4B). This likely explains why the neuron shown in Figure 2–figure supplement 2, which had a receptive field at ~3° based on saccades evoked by microstimulation, also responded during microsaccades. We apologize that this was not explained in the previous version and agree that it could have been confusing for the reader. To address this, the legend for this supplementary figure has been edited in the revised version and now reads:

      “(B) PSTH for an SC neuron that responded around the time of a microsaccade. Firing rates were computed in 1ms bins, averaged across trials and smoothed using a Gaussian function (σ = 5ms). Note that the targets were set to 3º in this session based on saccades evoked by microstimulation (see Methods). Previous research has shown that some SC neurons respond during microsaccades as well as to slightly larger saccades (Hafed and Krauzlis, 2012). This likely explains why this SC neuron, which had a RF at ~3º based on saccades evoked by microstimulation, also responded around the time of a microsaccade.” (Lines 1026-1031)

    1. Author response:

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

      eLife Assessment

      This study explores how exogenous attention operates at the finest spatial scale of vision, within the foveola - a topic that has not been previously explored. The question is important for understanding how attention shapes perception, and how it differs between the periphery and the central regions of highest visual acuity. The evidence is compelling, as shown by carefully designed experiments with state-of-the-art eye tracking to monitor attended locations just a few tens of minutes of arc away from the fixation target, but additional clarification regarding analyses and implications for vision and oculomotor control would broaden the impact of the study.

      We thank the editors and reviewers for their thorough evaluation of our work. We have carefully revised the manuscript and substantially reworked the Discussion to address all of the points raised, eliminate redundancies, streamline the text, and clarify the implications of our findings for vision and oculomotor control. We have also expanded the documentation of our power analyses and conducted the additional analyses requested by the reviewers. Our point-by-point responses are provided.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The manuscript investigates how exogenous attention modulates spatial frequency sensitivity within the foveola. Using high-precision eye-tracking and gaze-contingent stimulus control, the authors show that exogenous attention selectively improves contrast sensitivity for low- to midrange spatial frequencies (4-8 cycles/degree), but not for higher frequencies (12-20 CPD). In contrast, improvements in asymptotic performance at the highest contrast levels occur across all spatial frequencies. These results suggest that, even within the foveola, exogenous attention operates through a mechanism similar to that observed in peripheral vision, preferentially enhancing lower spatial frequencies.

      Strengths:

      The study shows strong methodological rigor. Eye position was carefully controlled, and the stimulus generation and calibration were highly precise. The authors also situate their work well within the existing literature, providing a clear rationale for examining the fine-grained effects of exogenous attention within the foveola. The combination of high spatial precision, gazecontingent presentation, and detailed modeling makes this a valuable technical contribution.

      Weaknesses:

      The manipulation of attention raises some interpretive concerns. Clarifying this issue, together with additional detail about statistics, participant profiles, other methodological elements, and further discussion in relation to oculomotor control in general, could broaden the impact of the findings.

      We thank the reviewer for the helpful comments. In the Discussion, we have now considered additional factors that could have contributed to the observed attentional effects. First, the exogenous cue might have functioned as a temporal warning signal. However, the interval between cue and stimulus onset was fixed across trials, meaning that the cue did not provide temporal information beyond what participants could already anticipate. Furthermore, participants completed a large number of trials (≥ 4000), making it highly likely that the temporal relationship between trial onset and target onset was overlearned. These considerations indicate that the observed benefit in the valid condition was predominantly attributable to spatial reorienting induced by the cue, rather than to differences in the temporal predictability of the target across conditions.

      Another possibility is that the 100% validity of the exogenous cue could potentially have promoted endogenous attentional engagement. Yet, several characteristics of our task strongly limited the extent to which such endogenous engagement could meaningfully influence performance. Endogenous attentional benefits typically emerge only after ~150-200 ms (Posner & Petersen, 1990; Carrasco, 2011), whereas our cue-target SOA was 100 ms, and the target remained visible for only 50 ms. Under these temporal constraints, any voluntary, slow endogenous enhancement would primarily occur after the stimulus offset. Thus, although endogenous maintenance is theoretically possible given the cue’s validity, it is unlikely to have substantially contributed to the observed attentional benefits in our task.

      Regarding the points on statistical reporting and participant details, we followed the reviewer’s suggestions by adding post hoc power analyses and providing more comprehensive reporting of the linear model outputs (see Appendices 1 and 2). We also expanded the description of the training procedures conducted with participants prior to formal data collection in the Methods section.

      We appreciate the reviewer for raising the important question of how our findings may relate to oculomotor control. To address this, we analyzed trials excluded from the manuscript due to saccades. This analysis revealed that saccade latencies were shorter in the valid condition than in the neutral condition (see Figure 2 — Supplementary Figure 2). This earlier saccade onset may reflect exogenously triggered preparatory activity in the oculomotor system in response to the salient cue. Future studies are needed to examine whether this preparatory mechanism serves to efficiently guide microsaccades or saccades toward behaviorally relevant stimuli in everyday vision. We have incorporated this point into the Discussion, highlighting a potential mechanistic link between exogenous attention and oculomotor behavior.

      Reviewer #2 (Public review):

      Summary:

      This study aims to test whether foveal and non-foveal vision share the same mechanisms for endogenous attention. Specifically, they aim to test whether they can replicate at the foveola previous results regarding the effects of exogenous attention for different spatial frequencies.

      Strengths:

      Monitoring the exact place where the gaze is located at this scale requires very precise eyetracking methods and accurate and stable calibration. This study uses state-of-the-art methods to achieve this goal. The study builds on many other studies that show similarities between foveal vision and non-foveal vision, adding more data supporting this parallel.

      Weaknesses:

      The study lacks a discussion of the strength of the effect and how it relates to previous studies done away from the fovea. It would be valuable to know if not just the range of frequencies, but the size of the effect is also comparable.

      We thank the reviewer for raising these important issues. In response, we have expanded the Discussion to link our findings to prior work. First, we included a direct comparison of our effect sizes with those reported in previous studies. This analysis revealed that our effect sizes are highly comparable to those earlier studies (see Figure 3 — Supplementary Figure 4). Second, we contextualized our findings within the popular framework of normalization model of attention in the Discussion. We detected a mixture of contrast and response gain effects, consistent with predictions from the normalization framework given our experimental design. Finally, we extended the Discussion to consider potential underlying neural mechanisms. Specifically, we suggested that differences in attentional modulation, particularly the manifestation in response gain vs. contrast gain between the fovea and extrafovea, may reflect distinct characteristics of foveal neurons relative to those in extrafoveal regions.

      Reviewer #3 (Public review):

      Summary:

      This paper explores how spatial attention affects foveal information processing across different spatial frequencies. The results indicate that exogenously directed attention enhances contrast sensitivity for low- to mid-range spatial frequencies (4-8 CPD), with no significant benefits for higher spatial frequencies (12-20 CPD). However, asymptotic performance increased as a result of spatial attention independently of spatial frequency.

      Strengths:

      The strengths of this article lie in its methodological approach, which combines a psychophysical experiment with precise control over the information presented in the foveola.

      Weaknesses:

      The authors acknowledge that they used the standard approach of analyzing observeraveraged data, but recognize that this method has limitations: it ignores the uncertainty associated with parameter estimates and the relationships between different parameters of the psychometric model. This may affect the interpretation of attentional effects. In the future, mixed-effects models at the trial level could overcome these limitations.

      We thank the reviewer for this comment. Our Methods section continues to transparently discuss these limitations, as well as the fact that these limitations are shared with most published studies in psychophysics. Additionally, we now include measures of uncertainty for all key effects (see Appendices 1 and 2), and we have reported effect sizes throughout the Results section. Finally, we have added post hoc power analyses to the Methods. Following previous approaches to power calculation for related experiments, we found that our study was sufficiently powered to detect the main effect of attention and had moderate power to detect the interaction between attention and spatial frequency.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The manipulation of attention raises some interpretive concerns. Since only valid and neutral cue conditions were included, the results might reflect differences in temporal predictability rather than true spatial reorienting of attention. In other words, the valid cue could act mainly as a temporal warning signal that reduces uncertainty about stimulus onset. Without invalid trials or a non-predictive control cue, it remains difficult to separate spatial and temporal contributions to exogenous attention.

      We thank the reviewer for raising this point. In this regard, we would like to clarify that there was no temporal uncertainty in stimulus onset: across all conditions and trial types, the stimulus was presented at the same time relative to the start of the trial, i.e., 600 ms after the start. Yet, we acknowledge that the shorter temporal proximity between the cue and stimulus in valid trials could serve as an additional temporal warning signal, potentially conferring an advantage relative to the neutral condition. While we cannot completely rule out a contribution of such temporal cueing within the constraints of the current experimental design, we believe its impact was limited. Specifically, the fixed cue-stimulus interval reduced the cue’s ability to convey additional temporal information. Furthermore, observers completed a large number of trials (≥4000), and the temporal contingency between trial onset and target onset was likely overlearned. Taken together, these considerations indicate that the observed benefit in the valid condition was predominantly attributable to spatial reorienting induced by the cue, rather than to differences in the temporal predictability of the target across conditions. We now mention this in the revised Discussion (lines 309-318).

      We recognized that the original Figure 2 illustrating the experimental paradigm may have caused confusion regarding the timing structure of the task. We have therefore updated the figure to more explicitly illustrate the trial timeline in both conditions.

      (2) The reported effects seem small, and no power analysis is provided. With only seven participants, the study may not have enough statistical power to confirm that the observed differences are reliable or generalizable. Although the technical precision in gaze and stimulus control is impressive, it cannot offset the limitations of a small sample. The authors should include effect size estimates, confidence intervals, and ideally a post-hoc power analysis.

      The statistical results are reported only as χ² values from model comparisons, which do not show the direction or size of the effects. For clarity and transparency, these tests should be accompanied by fixed-effect estimates with their standard errors and confidence intervals, so readers can better assess both the reliability and perceptual relevance of the findings.

      The reviewer raised several important points regarding the study's statistical rigor.

      In the revised manuscript, we now report effect size estimates (Cohen’s d) in the Results section and Appendices. Effect sizes were in the medium-to-large range, including the effect of attention on contrast sensitivity at 4 and 8 CPD, and the difference in attentional benefit on contrast sensitivity between 4 and 12 CPD and between 8 and 12 CPD. We have also included the full model outputs, including standard errors and confidence intervals, in the Appendices.

      The sample size for the current study was determined based on the magnitude of the attentional effects observed in our previous work (Guzhang et al., 2021). The experimental design and dependent measures were highly similar across the two studies, and the prior study revealed a robust effect, which accounted for a substantial proportion of within-observer variance in a tightly controlled repeated-measures design.

      We have revised the manuscript, adding bootstrap-based power estimates, following the procedure described by Jigo and Carrasco (2020), using data from Guzhang et al. (2021). Assuming the effect size in our current study would be comparable to the prior one, 2 to 12 observers were randomly sampled with replacement, and a one-way repeated-measures ANOVA with attention as the main factor was used. This procedure was repeated 10,000 times, and power was estimated as the proportion of iterations yielding a significant main effect for each sample size. The results of this analysis indicate that a sample size of five observers would have been sufficient to achieve approximately 80% power to detect the main effect of attention in the prior study. Based on these estimates, the sample size used in the current study (seven observers) is adequately powered.

      We also conducted a post hoc power analysis to evaluate the power of our design to detect the main effects and their interaction. It was performed using the R package simr, which estimates statistical power for mixed-effects models through model-based simulation. Specifically, simr generated datasets based on the fixed- and random-effect structure of the fitted model, preserving the observed effect sizes and variance components. For each simulated dataset, the model was refit, and the effect of interest was tested. By repeating this procedure 501 times across different sample sizes, power was estimated as the proportion of simulations in which the effect was statistically significant. Based on these post hoc simulations, we estimated that our study had high power (>95%) to detect the main effects and moderate power (>65%) to detect the interaction. Although the estimated power for the interaction was lower than for the main effects, the observed effect size was substantial (as indexed by Cohen’s d), indicating that the interaction was not trivially small.

      We now describe these analyses in lines 501-532 in the Methods section.

      (3) The task seems quite demanding, requiring fine spatial discrimination, very small stimuli, and head stabilization with a bite bar. It is not clear whether participants were naïve or experienced observers. If they had prior psychophysical training, practice effects could have influenced the results, particularly given the lack of invalid trials. The manuscript would benefit from clarifying participants' experience level and describing any training or familiarization procedures.

      We appreciate the reviewer’s concern regarding potential training effects. All observers had prior experience with similar tasks, but were naïve to the scope of this study. Each participant underwent an initial familiarization phase of approximately 50 trials with the experimental setup of this study. They then completed an additional ~50 trials to estimate their individual contrast thresholds per spatial frequency level before we proceeded with data collection at the five predefined contrast levels.

      Based on our experience, we have found that, for experiments similar to the one described here, observers quickly adapt to the setup and are generally able to maintain reliable fixation and stable performance, even during the initial training phase. In addition, each participant completed approximately 400 trials before the data collection started. Even observers who began the session with no prior experience would have become practiced with the setup by the time the actual data-collection phase started, during which ~4000 trials were collected per observer. Therefore, whether an observer participated in previous experiments is unlikely to meaningfully affect the results, as the large number of trials ensures comparable levels of task familiarity across individuals.

      Crucially, valid and neutral trials were interleaved throughout the session. Any general learning or practice would therefore influence both conditions equally. Despite this, we still observed clear performance improvements in the valid condition relative to the neutral condition, indicating that the observed benefits cannot be attributed solely to practice and reflect an attentional enhancement. We have added elaboration on the training procedures in Methods (lines 411-429).

      Finally, we recognize that the lack of invalid trials may raise concerns given our 100% spatially predictive cue, as noted in Reviewer 3’s first comment. We refer the reader to our response to that point for a more detailed discussion of cue validity and the distinction between exogenous and endogenous influences in our paradigm.

      (4) The study would benefit from a clearer connection between the behavioral results and possible underlying neural mechanisms. How might the observed changes in contrast sensitivity relate to known physiological processes at the retinal, thalamic, or cortical level? The discussion could be strengthened by framing the findings within established models of attentional modulation or by referring to known effects of attention in the early visual cortex.

      This is an important point, and we agree that framing the findings within established models of attentional modulation can strengthen the discussion. We believe that the normalization model of attention (Reynolds and Heeger, 2009; Herrmann et al., 2010) offers a useful framework for interpreting our behavioral findings, especially the attention-related changes in contrast sensitivity and asymptotic performance observed at the foveal scale. We have now added a more detailed discussion linking our results to this model and considering, explicitly as speculation, how known physiological processes at different stages may contribute to the observed effects in Discussion (lines 264-307).

      (5) The ecological relevance of the results is not fully developed. The authors propose that the observed effects may resemble natural attentional shifts triggered by salient events, yet the brief, highly localized flashes used here are somewhat artificial. A more likely interpretation is that these mechanisms relate to oculomotor control within the fovea, perhaps reflecting preparatory activity for microsaccades or fine fixation adjustments. Considering this view could broaden the impact of the findings and link them to current discussions on the relationship between attention and oculomotor control.

      We thank the reviewer for raising this important point regarding the ecological relevance of our findings, which we did not sufficiently address in the original manuscript. Although we briefly motivated scenarios that engage exogenous attention at high spatial resolution, such as detecting road signs or traffic lights at a distance while driving, we did not fully elaborate on how such attentional processes may link to downstream visual and oculomotor functions.

      In our experiment, observers maintained fixation and avoided saccades throughout the trial. Nevertheless, in a subset of trials (on average 17% ± 3%), observers made saccades after stimuli disappeared and prior to providing a response. Typically, these movements were microsaccades with amplitudes smaller than 0.5°, directed toward the target location, in both valid and neutral trials. These saccades were discarded prior to the analyses performed in the manuscript. Inspired by the reviewer’s feedback, we decided to examine the saccade latency in these trials relative to the onset of the response cue to assess whether exogenous cueing influenced oculomotor timing. Notably, we observed an earlier onset of microsaccades in valid compared to neutral trials (71 ms ± 50 ms faster, P < 0.01). We have now added this observation as Figure 2 — Supplementary Figure 2 in the manuscript. Because the presence of an exogenous pre-cue was the only difference between the two trial types, the earlier microsaccade onset likely reflects exogenously triggered preparatory activity in the oculomotor system in response to the salient pre-cue. Such fine-grained attention may prime potential eye movements toward behaviorally relevant stimuli for further examination. This interpretation is consistent with the reviewer’s suggestion and supports a mechanistic link between exogenous attention and oculomotor behavior, extending the ecological relevance of our findings. This point has been added to the Discussion on lines 329 to 340.

      We also conducted analysis to examine ocular drift behavior following the response cue. Although trials included in the manuscript analyses were constrained such that fixation during target presentation remained within a small window (10’ radius) around the fixation marker, we did not assess whether gaze subsequently drifted closer to the target location after the response cue. One possibility is that exogenous attention might bias ocular drift, shifting the preferred locus of fixation closer to the target. To address this, we computed the average Euclidean distance between gaze position and the target location following response cue onset for valid and neutral trials. However, we found no significant difference in gaze-target distance between valid and neutral trials (p = 0.57).

      Although the spatial cueing approach has long been used to probe exogenous attention in a controlled manner in psychophysical experiments, we fully recognize the importance of understanding attention under more naturalistic viewing conditions that allow observers to freely move their eyes. Developing paradigms that incorporate more naturalistic, salient stimuli would be an important direction for future work, enabling investigation of exogenous attention in ecologically valid settings and its influence on sequential actions and processes, including oculomotor behavior.

      (6) There is no statement about the availability of the data and code used for the experiment.

      We have now added the data and code for the analysis pipeline to the Open Science Framework (OSF).

      Reviewer #2 (Recommendations for the authors):

      (1) The study could discuss the strength of the effect and how it relates to previous studies.

      We thank the reviewer for raising this point. To facilitate direct comparison with the study by Jigo and Carrasco (2020), we computed attentional benefit as the ratio of contrast sensitivity between the valid and neutral conditions (now shown in Figure 3 — Supplementary Figure 4). In their data, the attentional benefit at 0° eccentricity peaked just below 4 CPD, with a ratio of approximately 1.2, corresponding to a ~20% increase in contrast sensitivity. This magnitude closely matches the benefit we observed for fine-grained attentional shifts within the foveola at spatial frequencies between 4 and 8 CPD (17% ± 12% and 16% ± 14% for 4 and 8 CPD, respectively). We have added this comparison to the Discussion (lines 246-262).

      In addition, we acknowledge that prior studies have reported heterogeneous attentional effects, including pure contrast gain, pure response gain, or a mixture of the two. We now explicitly reference these findings in the Discussion and use the normalization model of attention (Reynolds and Heeger, 2009; Herrmann et al., 2010) to account for how differences in stimulus configuration, attention field size, and eccentricity may account for discrepancies between our findings and prior studies examining attention in the extrafovea or when broadly distributed across the fovea (lines 264-307).

      (2) Minor details:

      (a) The abstract mentions gaze-contingent-display, but if I understand correctly, the stimulus was not presented in a gaze-contingent manner.

      That’s correct. Although stimuli were not presented gaze-contingently, we used a gaze-contingent calibration procedure (see Methods, lines 386-389) to achieve higher precision in localizing the line of sight. This increased accuracy was essential for selecting trials in which stimuli remained at the intended eccentricity relative to the preferred locus of fixation. To avoid potential confusion, however, we have removed this detail from the abstract.

      (b) Line 361: What is the manual calibration the authors are referring to? It does not appear to be described.

      The text has been updated to explain more explicitly what auto and manual calibrations are.

      (c) Line 402: There may be a typo towards the end of the line "t0" should be "to"?

      Text has been updated. Thank you.

      (d) Line 405. What are the units of 30?

      It’s in arcminutes. Text has been updated.

      Reviewer #3 (Recommendations for the authors):

      I found this paper very interesting, with a solid methodological approach and excellent data analyses. The authors present a well-designed psychophysical study that contributes valuable insights into the mechanisms of attention in the foveola. The methodology is rigorous, and the analyses are thoughtfully conducted and clearly presented.

      That said, I would like to offer a few comments and suggestions for clarification and further consideration:

      (1) Exogenous attention:

      If a 100% spatially predictive cue is compared to a neutral cue, the observed attentional effect should not be described as (purely) exogenous, since the cue fully predicts where the post-cue will request a response. This situation represents a case in which attention is exogenously driven but endogenously maintained (see e.g., Chica et al., 2013, Behavioural Brain Research). I recommend clarifying this distinction in the manuscript (and title) to avoid conceptual ambiguity.

      We thank the reviewer for raising this important conceptual point. We agree that because the pre-cue was 100% spatially predictive, the resulting attentional allocation cannot be considered purely exogenous. Although the abrupt, salient onset of the cue obligatorily triggers an exogenous shift of attention, its validity could also promote endogenous maintenance of attention at the cued location. Yet, several characteristics of our task strongly limit the extent to which such endogenous engagement could meaningfully influence performance. Endogenous attentional benefits typically emerge only after ~150-200 ms (Posner & Petersen, 1990; Carrasco, 2011), whereas our cue-target SOA was 100 ms, and the target remained visible for only 50 ms. Under these temporal constraints, any voluntary, slow endogenous enhancement would primarily occur after the stimulus offset. Thus, although endogenous maintenance is theoretically possible given the cue’s validity, it is unlikely to have substantially contributed to perceptual encoding in our task.

      We also considered the possibility that our response cue (a retro-cue indicating the target location) might recruit endogenous attention to the internal perceptual representation. Importantly, however, this retro-cue was equally informative in valid and neutral conditions. Any enhancement driven by the retro-cue should therefore benefit both trial types to the same extent. The fact that we still observe a robust advantage in valid trials supports the conclusion that the performance improvements predominantly reflect fast, spatially specific exogenous facilitation rather than slower endogenous processes.

      We have revised the manuscript to clarify that although the cue obligatorily triggers an exogenous attentional shift, its 100% validity could allow for endogenous attention maintenance as shown by Chica et al. (2013). We also added an explanation detailing why such endogenous contributions are unlikely to drive our main results, given the rapid cue-target timing in our task in Discussion (lines 319-327). Finally, to further prevent ambiguity, we updated the manuscript title to refer to “exogenously triggered attention,” rather than simply “exogenous attention.”

      (2) Interpretation of statistical effects:

      The statement "Therefore, asymptotic performance showed only independent, additive effects of frequency and attention, without a systematic influence of spatial frequency on the attentional benefit" seems not to be supported by the data, as the main effect of frequency was not significant.

      We thank the reviewer for this helpful observation. We agree that the original phrasing did not accurately reflect the results, as the main effect of spatial frequency was not significant (p = .0545). We have revised the sentence to “Therefore, asymptotic performance reflected an effect of attention alone, with no detectable contribution of spatial frequency or of the interaction between spatial frequency and attention” to avoid implying such an effect (lines 210-211).

      If data from two participants were missing in one condition, the authors should consider replacing this data with new participants.

      We agree with the reviewer that having two observers with missing data in one condition is not ideal. However, the 20 cpd condition was deliberately positioned near the resolution limit at the tested eccentricity and was therefore extremely demanding. Observers also had to monitor two stimulus locations simultaneously, further increasing task difficulty. This condition was challenging for all observers and, despite testing up to the highest contrast, two of seven observers were unable to perform above chance, indicating that for a non-trivial fraction of observers, this condition was effectively unmeasurable with our paradigm. As noted in the manuscript, the 20 cpd condition also has a statistical limitation: thresholds clustered near the upper bound (approaching 100% contrast), compressing the dynamic range and markedly reducing variance relative to lower spatial frequencies, which violates the homoscedasticity assumption of linear models. For these reasons, we did not pursue additional data collection in this condition. Nevertheless, we report the data that were successfully obtained, as they remain informative about performance near the resolution limit.

      We finally note that even when setting aside the 20 CPD condition, our data support this conclusion: comparisons between 4 and 12 CPD, as well as between 8 and 12 CPD, revealed large differences in the magnitude of the attentional benefit (d = 0.65, 95% CI [0.11, 1.18] and d = 0.62, 95% CI [0.08, 1.14], respectively). To further quantify these effects, we have added Cohen’s d to report the effect sizes for these spatial-frequency comparisons across texts in Results as well as in tables in Appendices.

      (3) Sample size:

      As this is a psychophysical experiment with many trials and few participants, I am curious about how the authors determined the appropriate sample size and the number of trials required to detect the expected effects. Given that many effects were found to be significant, it seems that statistical power was adequate; however, it would be helpful if the authors could explain how this issue was addressed a priori during experimental planning.

      We appreciate that the reviewer raised this point. Please see the reply to the second point from Reviewer 1, who raised a related question about statistical power.

      (4) Figure 2 clarification:

      In Figure 2B, I do not fully understand the "Valid" and "Neutral" representation. Both conditions include a post-cue indicating the right position; however, in the neutral condition, there is a central fixation square, whereas in the valid condition, there is not. Please clarify this aspect of the figure. I think I understood the paradigm, but this part of the figure is misleading.

      Precue only exists in valid condition. But there is a mistake where fixation marker is missing in valid condition in panel B.

      We thank the reviewer for pointing this out. We have updated Figure 2 to explicitly show the sequence of valid vs. neutral trials. The fixation mark remained on the screen throughout the trial in both the valid and neutral conditions. After a 500 ms fixation period, an exogenous cue was presented for 30 ms in valid trials, followed by a 70 ms interval before stimulus onset. In neutral trials, no cue was presented, and the screen remained blank for 100 ms before the stimuli appeared. In conditions, a response cue would appear 50 ms after stimulus offset.

    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 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:

      (1a) 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.

      (1b) 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.

      (1c) 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.

      (1d) 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.

      (2) 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.

      (3) 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.

      (4) 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

      (1) 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.

      (2) 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): 

      (1) 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.

      (2) 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.

      (3) 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.

      Recommendations for the authors:

      (1A) Intracellular leucine can decrease from:

      inhibition of transport/uptake via semapimod as the authors claim or

      decreased uptake/requirement of many metabolites due to cells entering static growth arrest from challenge by semapimod

      To rule out the growth-inhibitory effect of semapimod on L-leucine uptake, we estimated intracellular L-leucine in Mtb after brief exposure of 24 hours to 50ng/ml semapimod (kindly refer Materials and Methods). We confirmed that 24 hours of treatment with 50ng/ml semapimod does not cause cells entering static growth arrest.

      (1B) increased consumption/utilization of leucine for some programmed response to semapimod challenge

      Our results show reduced expression of genes involved in leucine catabolism such as accD1, bkdA and bkdB in semapimod-treated cells, and thus the above hypothesis seems unlikely.

      (1C) Additional metabolites should be measured to determine the specificity of the semapimod challenge.

      As mentioned below, we measured intracellular valine in the semapimod-treated Mtb 6206 by LC-MS/MS, which shows no change in its level. These observations thus corroborate a specific effect of semapimod on L-leucine level in the cell.

      (2) The effect of Semapimod on L-leucine uptake is largely based on indirect evidence, without showing reduced transport of the amino acid. Gene expression data is not enough to prove that the amino acid transport is blocked. More compelling evidence is required to confirm this mechanism.

      The authors could perform leucine uptake assays to directly confirm the functioning of Semapimod, inhibiting L-leucine transport. Another possibility would be to try out measuring intra-bacterial leucine levels for drug-treated versus untreated M. tuberculosis strains.

      Data presented in the Fig. 3b shows lesser intracellular L-leucine upon semapimod treatment; in contrast, Sem<sup>R</sup> strain exhibits ~3-fold more intracellular L-leucine, as estimated by mass spectrometry (kindly refer our response to comment #6 below). Together, these observations indicate an inhibitory effect of semapimod on L-leucine uptake by the auxotroph.

      (3) The authors show that the overexpression of leuC-leuD restores Semapimod resistance in the auxotroph (Figs. 3C-3E). Is it possible to examine Semapimod resistance of WT-H37Rv or the complemented mutant grown in leucine-limiting conditions? This sort of evidence will be more direct on the specific drug-target beyond the auxotroph (mc<sup>2</sup> 6206).

      Because endogenous L-leucine synthesis pathway is functional in WT-H37Rv, as well as complemented auxotrophic strain, leucine-limiting conditions are unexpected to yield any effect on susceptibility to semapimod.

      Author response image 1.

      (4) Biolayer Interferometry (BLI) shows Semapimod binds to PpsB (Fig. 6); however, there is no clear evidence that it disrupts PDIM synthesis. More direct evidence would be to study the effect of Semapimod on a ppsB mutant (may be a knock-down). This would prove the specificity of Semapimod for PpsB. Likewise, it would be worth looking into the effect of Semapimod using mutant M. tuberculosis defective for PDIM synthesis.

      As recommended by the peer reviewer, we created the ppsB knockdown strain in the Mtb mc2 6206 by CRISPRi and examined its vulnerability to semapimod treatment. As can be seen in the Author response image 1, ppsB KD strain shows lesser susceptibility to semapimod when compared with the pDcas9-control strain which exhibits significant growth inhibition on the 7H11-OADS-PL agar plate containing 200nM semapimod.

      (5) Metabolomics experiments would benefit from including other control BCAAs like isoleucine and valine to determine if decreased intracellular levels of leucine are specific to semapimod or a general consequence of growth arrest from an antimicrobial agent.

      As suggested by the reviewer, we measured intracellular valine as well as proline levels in the semapimod-treated Mtb 6206 by LC-MS/MS; data presented in the supplimentry figure 5 clearly show no change in their levels upon semapimod treatment.

      (5) Figure 3c, pyrazinamide susceptibility assay could be included on the panCD strain to ensure complementation leads to functional panCD. Parent strain would be resistant to PZA, complement strain would be susceptible. (doi: 10.1038/s41467-019-14238-3).

      The wild-type Mtb 6206 is unable to grow in the absence of pantothenate. We verified resumption of growth of Mtb 6206 in 7H9-OADS-L-leucine medium lacking pantothenate upon PanCD overexpression, which provides more direct evidence of the expression of functional copies of panCD genes.

      (6) does the Sem-R mutant have increased levels of leucine?

      As can be seen in the supplimentry figure 7, Sem<sup>R</sup> strain shows ~3.0 fold increase in the intracellular L-leucine level when compared with the WT strain. In contrast, a comparable level of another BCAA– valine, is observed in both the strains

    1. In summary, we find striking mathematical similarity among animal ‘song’ vocalizations and human musical sounds regarding the stability of CES, along with some well-defined differences across evolutionary distant taxa that evolved singing behavior independently (i.e. anurans, birds, primates)

      I don't think you have yet shown enough to make this claim. The paper would greatly benefit from the use of null models. Given that all the data used in the paper share informational structure (i.e., they're way detectable in some way as "songs" to humans), are the relationships you identify actually surprising? It's very hard to gauge this without a null, either empirical or simulated, to compare to.

      Similarly, it's impossible to know whether the comparisons are fair without a deeper examination of how parameter choice (e.g., window sampling size) may differentially affect the CES estimation across song types. Even if you find significant similarity between human/animal song times compared to a null, how will you know if this isn't a product of bias in your CES estimation?

    1. Author response:

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

      Reviewer #1 (Public Review):

      Summary:

      Sun et al. generated germline-specific cKO mice for the Znhit1 gene and examined its effect on male meiosis. The authors found that the loss of Znhit1 affects the transcriptional activation of pachytene. Znhit1 is a subunit of the SRCAP chromatin remodeling complex and a depositor of H2AZ, and in cKO spermatocytes, H2AZ is not deposited into the gene region. The authors claim that this is why the PGA was not activated. These findings provide important insights into the mechanisms of transcriptional regulation during the meiotic prophase.

      Strengths:

      The authors used samples from their original mouse model, analyzing both the epigenome and the transcriptome in detail using diverse NGS analyses to gain new insights into PGA. The quality of the results appeared excellent.

      Weaknesses:

      Overall, the data is inconsistent with the authors' claims and does not support their final conclusions. In addition, the sample used may not be the most suitable for the analysis, but a more suitable sample would dramatically improve the overall quality of the paper.

      Thank you for your comprehensive summary of our study and your thoughtful insights into its strengths and weaknesses. We greatly appreciate this valuable feedback, which helps us further improve our work. Below, we provide a detailed response addressing each of the points you raised.

      Reviewer #1 (Recommendations For The Authors):

      Major revisions:

      Surprisingly, many genes were upregulated in the scRNA-seq results. How many XY genes are included? Discuss why many genes are up-regulated in Fig. 5E whereas bulk RNA-seq showed only 70 genes were down-regulated. Since apoptosis-related factors are up-regulated in Fig5E, could these up-regulated genes be due to the high content of the transcriptome of dead cells? As you know, cell death starts, but randomly and violently disrupts the transcriptome, so we think it is not desirable to analyze the transcriptome with dead cells in the mix. Describe this point appropriately in the text or generate new data without dead cells.

      We sincerely appreciate the reviewer’s critical points. Below, we address each point sequentially:

      (1) To address the question about XY-linked genes, we utilized scRNA-seq data to identify differentially expressed sex chromosome genes in spermatocytes at different stages. Our analysis revealed an aberrant activation of XY-linked genes relative to controls. Specifically, 120 XY-linked genes were aberrantly activated in zygotenestage spermatocytes, and 119 XY-linked genes showed aberrant activation in pachytene-stage spermatocytes (revised Fig. 4F). This observation directly indicates that Znhit1 knockout impairs Meiotic Sex Chromosome Inactivation (MSCI), a finding that aligns with our prior characterization of XY chromosome synapsis defects in Znhit1-deficient spermatocytes.

      (2) Two key reasons explain the discrepancy between scRNA-seq and bulk RNA-seq results:

      First, scRNA-seq employs a more permissive threshold for identifying DEGs (log2 fold change [log2FC] = 0.25), thereby enhancing sensitivity to subtle expression changes and enabling the detection of more upregulated genes. In contrast, bulk RNAseq uses a stricter threshold (log2FC = 1), which filters out these subtly upregulated transcripts, resulting in fewer DEGs overall.

      Second, scRNA-seq can capture cell subset-specific differential expression. In contrast, bulk RNA-seq averages signals across mixed cells, masking such subsetspecific expression changes.

      These clarifications have been included in the Data Analysis section of the revised manuscript.

      (3) We fully agree with the reviewer’s concern that dead cells could confound transcriptomic analyses. Before downstream analysis, we excluded non-viable cells via stringent QC: cells with mitochondrial RNA (mtRNA) content exceeding 15% were removed, as high mtRNA content is a well-established marker of cell death or compromised viability. To further validate that upregulated genes were not driven by dead cell contamination, we analyzed the correlation between the expression of apoptosis-related genes and mtRNA fractions in our data. This analysis revealed no significant correlation (Pearson correlation coefficient, r = -0.02; please see Author response image 1). These results collectively rule out dead cell transcriptome contamination as the primary cause of the observed gene upregulation.

      Author response image 1.

      Scatter Chart showing the Pearson correlation between apoptosisrelated genes and mitochondrial RNA fractions in scRNA-seq data.

      Line 280-286: The data in Figures 7I and J are confusing: as shown by KAS-seq, it is natural that ssDNA is not formed in the promoter region in Znhit1-cKO sample because transcription does not proceed, but why is ssDNA formed in the enhancer region in the first place in control and then lost in Znhit1-cKO sample? Generally, it is said that in the enhancer region, including the super-enhancer region, doublestranded DNA is not dissociated, thus not forming ssDNA. Discuss why the loss of ssDNA in the enhancer region affects transcription with appropriate citations. Also, show whether genes downstream of the missing ssDNA in the promoter region have abnormal transcriptional activity, along with the RNA-seq data. Furthermore, in the region shown in Figure 7I, why the chromatin is even more open, as shown by ATACseq in Znhit1-cKO. Discuss whether this is related to transcriptional progression or aberrant substitution with H2A. If the function of ZNHIT1 is to replace H2A with H2AZ for PGA, it is not necessary to show the H2A level in Znhit1-cKO.

      We appreciate the reviewer’s constructive comments.

      (1) ssDNA dynamics in enhancer regions: Emerging evidence demonstrates that active enhancers undergo transient DNA unwinding to form ssDNA, a process critical for transcriptional regulation by transcribing enhancer RNAs (eRNA). KAS‑seq is sufficiently sensitive to detect ssDNA in enhancer regions (Kim et al., 2010; Wu et al., 2020). It has been shown that H2A.Z (deposited by the ZNHIT1-SRCAP complex) is required for maintaining enhancer accessibility and dynamic unwinding (Sporrij et al., 2023). In this study, we found that Znhit1 deletion and defective H2A.Z incorporation impaired enhancer ssDNA formation, indicating that ZNHIT-H2A.Z plays an important role in the activity of both promoter and enhancer.

      (2) Impact of ssDNA loss on transcription: To address how missing ssDNA affects transcriptional activity, we further analyzed changes in KAS‑seq signals following Znhit1 knockout. Overall, KAS‑seq signals were significantly reduced upon Znhit1 depletion, confirming that Znhit1 is essential for ssDNA formation. Further examination of KAS‑seq signals at promoters of downregulated genes also revealed reduced signals (revised manuscript, Fig. S8). In contrast, KAS-seq signals of upregulated genes remained relatively low and showed no changes in both the control and knockout groups, and their upregulation probably results from indirect regulation. These results underscore the importance of ZNHIT1-mediated chromatin states in regulating ssDNA formation and gene expression.

      (3) Aberrant chromatin openness in Znhit1-cKO (ATAC-seq): The increased chromatin accessibility detected by ATAC-seq likely represents a disorganized, nonfunctional state rather than productive transcriptional openness. H2A.Z normally constrains chromatin dynamics to facilitate ordered transcriptional regulation (Cole et al., 2021); its absence in Znhit1-cKO leads to higher ATAC-seq signals, suggesting that this aberrant openness fails to support proper assembly of the transcriptional machinery.

      Minor revisions:

      Line 106. The text says that they looked for chromatin factors, but the legend says that they looked for epigenetic factors. The text must be consistent.

      We have corrected it in the revised manuscript (line 801).

      Line 107. Although it is stated that the transcriptional data published here were used, it appears from the cited references that they are scRNA-seq data. A clear explanation is required in the text or legend.

      We have revised this data as scRNA-seq data (line 107).

      Line 141-143: Using TUNEL analysis in Figure 4F, the authors show that Znhit1cKO testis cells contain many dead cells. Describe the type or stage of the apoptotic cells.

      We appreciate the reviewer’s suggestion. Specifically, we performed TUNEL staining on testes isolated from P14 mice, a critical time point for pachytene development (revised Fig. 2D). We tested this by showing that apoptosis-related genes were significantly upregulated in pachytene-stage spermatocytes in scRNA-seq data (revised Fig. 4D). To further validate this observation, we performed scRNA-seq from P35 testis samples. The results revealed a significant reduction in late pachytene-stage spermatocytes in Znhit1-cKO samples (revised Fig. 2F), consistent with apoptotic loss of pachytene cells. Collectively, these data confirm that Znhit1 knockout impairs pachytene-stage spermatocyte development.

      The authors claimed that the loss of Znhit1 lowers the transcription of a group of genes involved in homologous recombination, including Rnf212, causing a delay in homologous recombination; however, if the process of homologous recombination is delayed, homologous chromosome pairing and synapsis are affected unless DSB repair is completed. Provide a satisfactory explanation for the fact that DNA damage remains on autosomes despite complete synapsis, as shown in Figure 3C, which is likely not solely due to delayed homologous recombination.

      Thank you for this insightful comment. We fully agree that persistent autosomal DNA damage cannot be explained solely by delayed homologous recombination. To resolve this question, we further analyzed autosomal synapsis through SYCP1 and SYCP3 staining. While autosomal synapsis appeared morphologically complete, we identified subtle but significant synapsis defects in autosomal terminal regions (revised Fig. 3A). This suggests that Znhit1 knockout also results in autosomal synapsis defects. We speculate that these synapsis defects are associated with the unresolved autosomal DNA damage we observed.

      Lines 150-163. With regard to XY unpairing in Znhit1-cKO pachytene spermatocytes, there is insufficient discussion as to whether this is due to transcriptional aberrations.

      Thank you for highlighting the need to link transcriptional aberrations to XY unpairing in Znhit1-cKO pachytene spermatocytes. To address this, we analyzed sex chromosome transcription using scRNA-seq data. Relative to controls, 120 XYlinked genes were aberrantly activated at zygotene, and 119 were upregulated at pachytene in Znhit1-cKO spermatocytes (revised Fig. 4F), directly demonstrating Znhit1 knockout disrupts Meiotic Sex Chromosome Inactivation (MSCI). Given that intact MSCI is required to stabilize XY synapsis in pachytene spermatocytes, we conclude that the observed XY unpairing is likely a direct consequence of these sex chromosome transcriptional abnormalities. We add this information to the revised manuscript (lines 221-226).

      Line 187-194. Analysis of the scRNA-seq data is shown in Figure 4, but it lists several genes as stage-specific markers, some of which do not have well-understood meiotic functions. Please cite a reference paper that provides sufficient evidence to qualify this stage.

      In response to this comment, we have refined the presentation of marker genes used for cell annotation (revised Fig. S4B). We have incorporated relevant references supporting their utility as stage-specific markers for the meiotic stages (line 187).

      Line 225-233: If Znhit1 is important for H2AZ deposition and regulates PGA through it, how does it regulate HR-related genes that are expressed earlier through H2AZ deposition during the pachytene stage? For example, Rnf212 is not specifically expressed during the pachytene stage but is one of the targets of MEIOSIN, so it is expressed at an earlier stage.

      Thank you for this insightful comment. We fully acknowledge the reviewer’s key observation that HR-related genes such as Rnf212 are MEIOSIN targets that initiate transcription at earlier meiotic stages, before the pachytene stage. Our stage-resolved scRNA-seq data further showed that the expression of Ccnb1ip1 and Rnf212 was significantly upregulated from zygotene to pachytene, following their initial transcriptional onset. We next showed that the loss of H2A.Z deposition induced by Znhit1 deletion specifically impaired this pachytene-specific secondary transcriptional activation, rather than the early MEIOSIN-driven expression onset (please see Author response image 2).

      Author response image 2.

      Plots showing the expression level of indicated genes in scRNAseq data.

      Line 245-251: As shown in Figure 6E, more than 14,000 genes have H2AZ peaks. In contrast, only approximately 60% of the genes downregulated by Znhit1-cKO appeared to be directly affected by H2AZ. Are the remaining 40% of genes regulated in a different way that is not mediated by H2AZ? Also, only a few percent of the genes with H2AZ peaks are affected, but why are only genes with A-MYB involvement affected, as shown in Figure 7?

      Thank you for these insightful and constructive comments. For the ~40% of downregulated genes not directly linked to H2A.Z, they were likely regulated through indirect mechanisms. H2A.Z deposition mediated by ZNHIT1 may influence upstream transcriptional regulators (e.g., transcription factors or coactivators), whose dysregulation in turn affects these genes.

      The selective effect of H2A.Z loss on A-MYB target genes is explained by the strict context-dependent function of H2A.Z, which requires stage-specific partner transcription factors to exert its regulatory activity. During the zygotene-to-pachytene transition, A-MYB acts as the master regulator of pachytene gene activation and forms a functional collaborative complex with H2A.Z to drive target gene transcription. Disrupted H2A.Z deposition upon Znhit1 deletion specifically impairs the activity of this A-MYB-H2A.Z complex, leading to selective downregulation of A-MYB targets. Other H2A.Z peak-associated genes may rely on alternative cofactors and compensatory mechanisms.

      Line 245-256: Figures 6 and F show that the localization of H2AZ is reduced in Znhit1-cKO mice, which means that no substitution with H2A occurs. If so, show it in the data because the localization of H2A should be increased compared to that in the control.

      To clarify the status of H2A, we have now detected immunofluorescent staining against H2A. While H2A.Z deposition was clearly impaired following Znhit1 deletion, the global level of H2A did not change significantly (Author response image 3). We speculate that this observed absence of a compensatory increase in H2A is likely due to the intrinsically low abundance of the histone variant H2A.Z relative to canonical histone H2A under physiological conditions.

      Author response image 3.

      Immunostaining of SYCP3 and H2A in spermatocyte testis sections of control and Znhit1-sKO mice, Scale bar, 40 μm.

      Reviewer #2 (Public Review):

      Summary:

      The study demonstrates that Znhit1 regulates male meiosis, with deletion causing pachytene failure associated with defective expression of pachytene genes and subtle effects on X-Y pairing and DSB repair. The authors attribute this phenotype to the defective incorporation of the Znhit1 target H2A.Z into chromatin.

      Strengths:

      The paper and the figures are well presented and the narrative is clear. Evidence that the conditional deletion strategy removes Znhit1 is strong, with multiple orthogonal approaches used. Most of the meiotic phenotyping is well performed, and the omics analysis clearly identifies a dramatic effect on the meiotic gene expression program. The link to H2A.Z and A-MYB adds a mechanistic angle to the study.

      Weaknesses:

      (1) Current literature demonstrates that meiotic mutants arrest at one of two stages: midpachytene (stage IV of the seminiferous cycle) or metaphase I (stage XII of the seminiferous cycle). This study documents that in the Znhit1 KO the midpachytene marker H1t appears normally, but that cells arrest before diplotene. If this is true, then arrest must occur during late pachytene, which based on my knowledge has never been documented for a meiotic KO. To resolve this, the authors should present stronger histological substaging evidence to support their claim.

      Thank you for this insightful and constructive comment. To achieve highresolution tracking of cell lineage progression, we performed scRNA-seq analysis using P35 testes in this revised manuscript. scRNA-seq data showed that germ cells normally progressed through all meiotic stages and successfully gave rise to spermatids in control groups. By contrast, in the Znhit1 knockout group, late pachytene spermatocytes decreased significantly, and only very few subsequent germ cell types were observable (revised Fig. 2F, G). In scRNA-seq data, although very few diplotene spermatocytes and meiotic metaphase I cells were detectable, these cells still appeared abnormal, as evidenced by their extremely low Pou5f2 expression. We have revised our description of the meiotic arrest stage in the manuscript.

      (2) The authors overlooked the possible effects of Znhit1 deletion on MSCI. Defective MSCI is a well-established cause of pachytene arrest. Actually, the fact that they see X-Y pairing failure should alert them even more strongly to this possibility because MSCI failure is often associated with defective X-Y pairing. This could be easily addressed by examination of their RNAseq data.

      To address the concern that Znhit1 deletion may impact Meiotic Sex Chromosome Inactivation (MSCI), we analyzed XY-linked gene expression using scRNA-seq data from spermatocytes at distinct stages. Our analysis revealed aberrant activation of XY-linked genes in Znhit1-CKO spermatocytes relative to controls. Specifically, 120 XY-linked genes were activated at zygotene, and 119 XY-linked genes were upregulated at pachytene (revised Fig. 4F). This observation directly demonstrates that Znhit1-CKO impairs MSCI, which aligns with our prior characterization of defective X-Y chromosome synapsis in Znhit1-deficient spermatocytes. To explicitly resolve this concern, we have integrated these MSCIfocused RNA-seq analyses into the revised Results section (lines 221-226).

      (3) The recombination assays need attention.

      In the text the authors state that they studied RPA2 and DMC1, but the figures show RPA2 and RAD51.

      The RPA counts are not quantitated.

      The conclusion that crossover formation fails (based on MLH1 staining) is not justified. This marker does not appear in wt males until late pachytene, so if cells in this mutant are dying before that stage, MLH1 cannot be assessed.

      The authors state that gH2AZ persists in the KO, but I'm not convinced that they are comparing equivalent stages in the wt and KO. In Figure 3C, the pachytene cell is late, whereas in the mutant the pachytene cell is early or mid (when residual gH2AX is expected, even in wt males).

      Previous work (PMID: 23824539) has shown that antibodies reportedly detecting pATM in the sex body are non-specific. I therefore advise caution with the data shown in Figure 3D.

      We appreciate the reviewer’s detailed feedback on our recombination assays and have addressed each concern as follows:

      (1) Discrepancy between text and figures (RPA2/DMC1 vs. RPA2/RAD51): We have corrected this in the revised manuscript.

      (2) Quantitation of RPA2 foci: We have supplemented quantitative analysis of RPA2 foci (revised Fig. S3).

      (3) Conclusion on crossover failure: Single-cell RNA sequencing data from P35 testes definitively confirmed that Znhit1 knockout spermatocytes successfully progressed to the late pachytene stage, ruling out the possibility that our MLH1 staining results are confounded by cell death or arrest before this critical stage. In addition, analysis of transcriptome datasets revealed significant downregulation of important genes required for homologous recombination and crossover formation, including Ccnb1ip1 and Rnf212. Reduced expression of these essential factors may impair the assembly of MLH1 crossover foci. These data demonstrate that ZNHIT1 is essential for proper homologous recombination and crossover formation during male meiosis. We have revised the text to emphasize this context.

      (4) γH2AX persistence and stage matching: We have replaced the images with more representative, stage‑matched pachytene spermatocytes from wild‑type and Znhit1‑KO mice (revised Fig. 2C). Furthermore, prompted by the insightful comment from Reviewer 1, we carefully re‑examined autosomal synapsis and identified abnormal synapsis specifically at the terminal regions of autosomes in Znhit1‑deficient spermatocytes (revised Fig. 3A). These data together confirm that ZNHIT1 is essential for DSB repair during male meiotic prophase I.

      (5) pATM staining issue: Following the reviewer’s advice, we carefully reviewed the relevant literature (PMID: 23824539) and confirmed that the anti‑pATM antibody may exhibit non‑specific staining on the XY chromosomes. Accordingly, we have removed the pATM staining data presented in Figure 3D from the revised manuscript to ensure the accuracy and rigor of our results.

      (4) RNAseq data. The authors show convincingly that Znhit1 activates genes that are normally upregulated at the zyg-pachytene transition. They should repeat the analysis for genes normally upregulated at the prelep- lep and lep-zyg transition to show that this effect is really pachytene-gene specific.

      We appreciate this suggestion. To clarify the stage specificity of ZNHIT1’s regulatory role, we analyzed genes upregulated at the prelep-lep and lepzyg transitions. Our results showed that Znhit1 knockout had little impact on the overall expression levels of these genes (as shown in revised Fig. 4B). In contrast, as we previously reported, genes upregulated at the zygotene-pachytene transition were remarkably downregulated in Znhit1-cKO. These findings further confirm the specificity of ZNHIT1 in regulating pachytene gene expression.

      (5) I am puzzled that the title and overall gist of the study focuses on H2A.Z, when it is Znhit1 that has been deleted.

      We appreciate the reviewer’s observation and have revised the study title as suggested. Specifically, the title is now updated to “ZNHIT1-dependent H2A.Z deposition at meiotic prophase I underlies pachytene gene expression and meiotic progression during male meiosis.”

      Reviewer #3 (Public Review):

      Summary:

      Sun et al. present a manuscript detailing the phenotypic characterization of loss of Znhit1 in male germ cells. Znhit1 is a subunit of the chromatin regulating complex SRCAP that functions to deposit the histone variant H2A.Z. Given that meiosis, and specifically meiotic recombination, occurs in the context of the dynamic condensing of chromosomes, the role of chromatin regulators in general, and histone variants specifically, in mammalian meiosis is an active area of research. Previous work has shown that H2A.Z is found at the locations of recombination in plants, although H2A.Z was previously not found at recombination sites in mammalian meiosis. Here the authors use a conditional approach to ablate Znhit1 in spermatocytes and characterize a block in meiosis in prophase I in the transition from pachytene to diplotene stage.

      Strengths:

      The authors combine current methods in immunohistochemistry and functional genomics to provide strong evidence of meiotic block upon the loss of Znhit1. They find that loss of Znhit1 leads to reduced incorporation of the histone variant H2A.Z, specifically at promoters and enhancers. Further, RNA sequencing found more genes are down-regulated upon loss of Znhit1 compared to upregulated, suggesting that incorporation of H2A.Z is critical for the expression of genes necessary for successful meiotic progression.

      A strength of the manuscript is tying the locations of changes in H2A.Z deposition with binding of the transcription factor A-MYB, providing a mechanism that can potentially combine the changes in chromatin regulation with variable binding of a transcription factor in gene expression in pachytene stage spermatocytes.

      Weaknesses:

      A weakness in the single-cell RNA experiment using cells from 16-day-old male mice. The authors suggest that the rationale for the experiment was to determine where the Znhit1-sKO mutant showed an arrest in meiosis, and claim that this is the pachytene stage. However, in the 'first wave' of meiosis 16-day-old mice are just beginning to enter pachytene, so cells from later meiotic stages will be largely absent in these tubules. This is clear from the UMAP showing a similar pattern of cell distributions between wild-type and mutant mice. Using older mice would have better demonstrated where the mutant and wild-type mice differ in cell-type composition.

      We appreciate the reviewer’s constructive comment. To resolve this issue, we have added new scRNA‑seq data from testes of P35 mice, which harbor a full spectrum of meiotic stages, including late pachytene, diplotene, metaphase I spermatocytes, and post-meiotic spermatids. Compared with wild-type controls, Znhit1-sKO testes exhibited a marked reduction in late pachytene spermatocytes and a near-complete loss of post-pachytene cell types, directly validating the pachytenestage meiotic arrest (revised Fig. 2F, G). All updated analyses have been integrated into the manuscript to strengthen our conclusions.

      The authors use the term pachytene genome activation (PGS) in the manuscript to suggest a novel process by which genes are specifically increased in expression in the pachytene stage of meiotic prophase I, without reference to literature that establishes the term. If the authors are putting forward a new concept defined by this term, it would strengthen the manuscript to describe it further and delineate what the genes are that are activated and discuss potential mechanisms.

      We appreciate the reviewer’s valuable feedback on our use of the term "pachytene genome activation (PGA)".

      To address this, we have revised the text to explicitly frame PGA as a stage-specific transcriptional program observed in our data, defined by the coordinated upregulation of a distinct set of genes during the pachytene stage of meiotic prophase I.

      (1) Definition and Gene Set: Using the scRNA-seq dataset, we formally defined PGA as the transcriptional wave characterized by genes with increased expression in pachytene vs. zygotene spermatocytes (n = 1,560 genes). Functional enrichment analysis shows these genes are primarily involved in DNA repair, cilium organization, and spermatid development (Table S3), consistent with the biological process of germ cell development.

      (2) Relationship to existing literature: While PGA as a term is not widely established, our data align with prior observations of pachytene-specific transcriptional upregulation (Alexander et al., 2023; Ernst et al., 2019; Turner, 2015). Importantly, Alexander et al reveals that in late meiotic stages, starting from pachynema, chromatin has a ~3-fold increase in transcription. We have added these citations to clearly illustrate the relevant advances in the field (lines 68-71).

      (3) Regulation of pachytene-stage gene expression: We further delineate that PGA is regulated by ZNHIT1-dependent H2A.Z deposition. Znhit1 deletion resulted in significant downregulation of 70.1% (1,094 out of 1,560) of these genes. This links PGA to chromatin-based regulation, where ZNHIT1-dependent H2A.Z deposition enables pachytene-specific transcription.

      Generally speaking, the authors present solid evidence for a pachytene block in male germ cell development in mice lacking Znhit1 in spermatocytes. The evidence supporting a change in gene expression during pachytene, that more genes are downregulated in the mutant compared to increased expression, and changes in histone modification dynamics and placement of H2A.Z all support a role in alterations in meiotic gene regulation. However, the support that changes in H2A.Z impacting meiotic recombination (as suggested in the manuscript title) is less supported, rather than a general cell arrest in the pachytene stage leading to cell death. The conclusions around the role of Znhit1 influencing meiotic recombination directly could use further justification or mechanistic hypothesis.

      We acknowledge the reviewer’s comments. Indeed, existing data support the presence of a pachytene block in spermatocytes of Znhit1-deficient mice, along with aberrant pachytene gene expression and impaired H2A.Z deposition.

      In response, we made the following revisions: (1) we adjusted the manuscript title and conclusion to reduce emphasis on a direct H2A.Z-recombination link, and focus instead on ZNHIT1/H2A.Z in pachytene gene regulation and meiotic progression; (2) recombination defects may be indirect consequences of failed pachytene gene regulation, rather than a direct regulatory effect of ZNHIT1 on recombination machinery (lines 314-319).

      Reviewer #3 (Recommendations For The Authors):

      Quality of the images for meiotic spreads - images have low contrast and are tiny. It is difficult to see the SYCP3 results even when the images are magnified on the computer screen.

      We have provided new images with high resolution to ensure a clear visualization of SYCP3 signals.

      Line 165 - indicates the results for DMC1, although the figure suggests the results are for RAD51 foci.

      We have corrected this mistake.

      Line 306 - this manuscript 'confirms' that H2AZ is not found at mammalian recombination sites, a result already in the literature.

      We have corrected this mistake (lines 309-312).

      Reviewing Editor Comments:

      Major points and revisions highlighted by the reviewers:

      (1) Meiotic prophase in Znhit1KO: The main questions to clarify are the stage and status of progression, the analysis of apoptosis, and the consequences of gene expression on the X and Y. Additional analysis for DSB repair foci, gH2AX is also required. Those analysis are needed to answer to reviewer 2. Even if H2AZ was not detected at recombination hotspots, it may be possible that it plays a role in DSB repair but the level is too low for detection. This should be discussed as H2AZ was shown to be involved in DNA repair.

      We sincerely appreciate the reviewing editor’s constructive comments.

      (1) Stage and progression of meiotic prophase: We supplement P35 testes for scRNAseq. Results confirmed Znhit1-KO spermatocytes arrest at late pachytene, and postpachytene stages (diplotene, metaphase I) were nearly absent (revised Fig. 2F, G).

      (2) Apoptosis analysis: We studied this by demonstrating that apoptosis-related genes were upregulated in pachytene spermatocytes at the single-cell level (revised Fig. 4D). To further validate this finding, we performed scRNA-seq analysis on P35 testis samples. Our results revealed a marked reduction in late pachytene spermatocytes in Znhit1-cKO testes (revised Fig. 2F, G), consistent with apoptotic depletion of pachytene-stage cells. Together, these data confirm that Znhit1 ablation impairs pachytene-stage spermatocyte development.

      (3) X/Y gene expression consequences: To address this key point, we performed stage-resolved analysis of XY-linked gene expression using scRNA-seq data from different-stage spermatocytes. Compared with controls, we detected aberrant ectopic activation of XY-linked genes in Znhit1-KO spermatocytes: 120 XY-linked genes were inappropriately activated at zygotene, and 119 remained abnormally upregulated at pachytene (revised Fig. 4F). These results provide direct evidence that Znhit1 deletion impairs Meiotic Sex Chromosome Inactivation (MSCI).

      (4) DSB repair issue: We have replaced the images with more representative, stage‑matched pachytene spermatocytes (revised Fig. 3C). The revised images show consistently increased γH2AX signals in Znhit1-KO spermatocytes. Prompted by Reviewer 1’s comment, we identified abnormal synapsis at autosomal terminal regions in mutant cells. Together, these results confirm that ZNHIT1 is essential for DSB repair during male meiotic prophase I.

      (5) Potential role of H2A.Z in DSB repair: Though H2A.Z was nearly undetectable at recombination hotspots, we discuss two possibilities: (1) ZNHIT1-H2A.Z depletion dysregulated DSB repair-related genes; (2) Current ChIP-seq sensitivity may miss low-abundance H2A.Z at hotspots, which could support repair via chromatin remodeling. Future high-resolution assays (super-resolution imaging, DSB-targeted ChIP-seq) are proposed to validate this. We agree that recombination defects may be indirect consequences of failed pachytene gene regulation, rather than a direct regulatory effect of ZNHIT1 on recombination machinery.

      (2) Gene expression analysis. The first consequence of H2AZ depletion is gene expression downregulation. However, it may be not surprising that some genes are down and others upregulated. There are likely secondary and indirect effects including the upregulation of some genes. The authors should explain and discuss this point such as to answer to questions raised by reviewer 1 and 2.

      The primary consequence of H2A.Z depletion in pachytene spermatocytes is indeed widespread downregulation of genes. For the coexistence of upregulated genes, we explain this via three key points.

      (1) Technical differences between scRNA-seq and bulk RNA-seq (addressing Reviewer 1): scRNA-seq captures cell-type-specific differentially expressed genes that bulk RNA-seq masks (bulk averages signals across mixed cells, hiding changes in rare subsets). Additionally, scRNA-seq uses a lower log2(fold change) threshold (0.25 vs. 1 in bulk RNA-seq), detecting subtle upregulations missed by bulk analysis.

      (2) No dead cell contamination (addressing Reviewer 1): Stringent quality control excluded cells with >15% mitochondrial RNA. Apoptosis-related genes showed no significant correlation with mitochondrial RNA fractions (Pearson correlation coefficient, r = -0.02; please see Author response image 1), ruling out dead cell transcriptome interference.

      (3) Secondary/indirect effects (addressing Reviewers 1 & 2): Upregulated genes likely result from indirect regulatory cascades. H2AZ depletion may disrupt upstream transcription factors, leading to compensatory upregulation of their downstream genes or cell stress responses to meiotic arrest. Notably, Znhit1 knockout specifically impacts genes upregulated at the zygotene-pachytene transition, while genes upregulated at preleptotene-leptotene or leptotene-zygotene transitions remain largely unaffected (revised Fig. 4B), confirming the specificity of H2A.Z’s direct regulatory role and framing upregulation as non-targeted indirect effects.

      (3) The authors should also test the effect of Znhit1KO on the 1196 genes (up PreL/L) and 1325 (up L/Z) as shown in Figure 5D for the PGA. Also in Figure 5B, there is no evaluation of the statistical significance of the variation, this should be revised. X and Y genes should be analysed. KAS-Seq should be correlated with gene expression analysis, and several points as mentioned in the reviews below should be better explained and discussed.

      (1) Effect of Znhit1-KO on PreL/L- and L/Z-upregulated genes: we analyzed the 1196 genes upregulated at the PreL/L transition and 1325 genes upregulated at the L/Z transition. Znhit1 knockout had minimal effect on the expression of these early meiotic gene sets (revised Fig. 4B), whereas genes activated at the zygotene‑pachytene transition were strongly downregulated in Znhit1-KO spermatocytes. These results confirm the specific role of ZNHIT1 in regulating pachytene‑stage gene expression. We have also added a statistical evaluation for the variation shown in Fig. 4B.

      (2) X/Y-linked gene analysis: Analysis of stage‑resolved scRNA‑seq revealed aberrant ectopic activation of 120 XY‑linked genes at zygotene and 119 at pachytene in Znhit1-KO spermatocytes (revised Fig. 4F), demonstrating impaired Meiotic Sex Chromosome Inactivation (MSCI).

      (3) KAS-seq correlation with gene expression: We analyzed the link between KAS‑seq signals and gene expression, and we found that Znhit1 depletion caused a global reduction in KAS‑seq signals, especially at promoters of downregulated genes (revised Fig. S8). Genes with increased expression showed low KAS‑seq signals in both control and mutant groups, likely reflecting indirect regulation. These results highlight the essential role of ZNHIT1 in transcriptional regulation.

      (4) The title should refer to Znhit1, and the effect on meiotic recombination activities may be an indirect consequence of prophase progression arrest, even if some recombination genes are downregulated. This point is important as noted by reviewer 3.

      We fully acknowledge Reviewer 3’s key point and have revised the manuscript title to “ZNHIT1-dependent H2A.Z deposition at meiotic prophase I underlies pachytene gene expression and meiotic progression during male meiosis” to reduce emphasis on a direct H2A.Z-recombination link.

      Regarding meiotic recombination activities: The downregulation of recombinationrelated genes (e.g., Ccnb1ip1, Rnf212) stems from impaired pachytene-stage transcriptional programs caused by ZNHIT1-dependent H2A.Z deposition defects, which in turn leads to prophase progression arrest. Thus, the observed recombination abnormalities may be a secondary consequence of the meiotic prophase arrest, rather than a direct regulatory effect of ZNHIT1 on recombination machinery. This clarification has been integrated into the Discussion section (lines 314-318).

      (5) The recent structural analysis of SRCAP should be cited: Yu et al. Cell Discovery (2024) 10:15 https://doi.org/10.1038/s41421-023-00640-1.

      We have cited this reference in this revised manuscript (lines 234-236).

      (6) The authors should read and answer the specific revisions asked for by the reviewers.

      We have thoroughly read and systematically addressed all specific revisions requested by Reviewers 1, 2, and 3, as detailed in the revised manuscript and supplementary data.

      References

      Alexander, A.K., Rice, E.J., Lujic, J., Simon, L.E., Tanis, S., Barshad, G., Zhu, L., Lama, J., Cohen, P.E., and Danko, C.G. (2023). A-MYB and BRDT-dependent RNA Polymerase II pause release orchestrates transcriptional regulation in mammalian meiosis. Nature communications 14.

      Cole, L., Kurscheid, S., Nekrasov, M., Domaschenz, R., Vera, D.L., Dennis, J.H., and Tremethick, D.J. (2021). Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells. Nature communications 12, 2524.

      Ernst, C., Eling, N., Martinez-Jimenez, C.P., Marioni, J.C., and Odom, D.T. (2019). Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis. Nature communications 10, 1251.

      Kim, T.K., Hemberg, M., Gray, J.M., Costa, A.M., Bear, D.M., Wu, J., Harmin, D.A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010). Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187.

      Sporrij, A., Choudhuri, A., Prasad, M., Muhire, B., Fast, E.M., Manning, M.E., Weiss, J.D., Koh, M., Yang, S., Kingston, R.E., et al. (2023). PGE(2) alters chromatin through H2A.Z-variant enhancer nucleosome modification to promote hematopoietic stem cell fate. Proceedings of the National Academy of Sciences of the United States of America 120, e2220613120.

      Turner, J.M. (2015). Meiotic Silencing in Mammals. Annu Rev Genet 49, 395-412. Wu, T., Lyu, R., You, Q., and He, C. (2020). Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ.

      Nature methods 17, 515-523.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Al Asafen and colleagues apply a set of scanning fluorescence correlation spectroscopic approaches (Raster Image Correlation Spectroscopy (RICS), cross-correlation RICS, and pair-correlation function spectroscopy) to address the nuclear-cytoplasmic kinetics of the Dorsal (Dl) transcription factor in early Drosophila embryos. The Toll/Dl system has long been appreciated to establish dorsal-ventral polarity of the embryo through Tolldependent control of Dl nuclear localization, and provides an example of a morphogen gradient produced with high enough precision to yield robust biophysical measurements of general transcription factor activity and function. By measuring GFP-tagged Dl protein, either in wild-type embryos or in mutant embryos with low/medium/high levels of Toll signaling, the authors report diffusivity of Dl in nuclear and cytoplasmic compartments of the embryo, as well as the fraction of mobile and immobile Dl, which can be correlated with DNA binding through cross-correlation RICS. A model is presented where Cactus/IkB is implicated in preventing Dl from binding to DNA.

      Strengths:

      The experiments on wild-type GFP-tagged Dorsal are performed well, are mostly reported well, and are interpreted fairly.

      Weaknesses:

      The discrepancy between experiment and theory as pertains to Michaelis-Menten kinetics is not fully motivated in the text, and could benefit from a more clear presentation. The experiments performed to distinguish between the contribution of Toll-dependent phosphorylation and Cactus interaction models for limiting Dorsal DNA binding are possibly confounded by the presence of wild-type, GFP-tagged Dorsal protein.

      Thank you for your thoughtful feedback. Regarding the discrepancy between experiment and theory in relation to Michaelis-Menten kinetics, we recognize that our initial explanation may not have been explicit enough. Our intent was to illustrate that if DNA binding is a saturable process, then while the absolute concentration of Dl bound to DNA will increase with total Dl levels, the fraction of Dl bound to DNA will decrease. We used Michaelis-Menten kinetics only as a familiar example to convey this concept but did not intend to suggest that the system strictly follows Michaelis-Menten behavior. To clarify this point, we removed mention of Michaelis-Menten as an illustrative analogy and stuck specifically with discussing the system as “saturating.” This primarily affected text in the paragraph starting on Line 204, but also Lines 323-325.

      Regarding the concern about potential confounding effects due to the presence of wildtype GFP-tagged Dorsal (Dl[wt]-GFP): we understand the importance of addressing this point more directly. Therefore, we have imaged the Dorsal-GFP gradient in embryos expressing the UAS-dl[S280P]-GFP or the UAS-dl[S317A]-GFP constructs in the absence of the BAC-recombineered Dl-GFP construct. In both cases, the dl mutants by themselves were not able to recapitulate enough of the Dl gradient to test our hypotheses. We have added this analysis to Supplemental Figure 4 and mentioned this figure on Lines 333-336 and 354-358. Furthermore, we explicitly mention that it is possible the reason why we failed to reject the null hypothesis in the Toll phosphorylation mutant case may be due to the additional copy of Dl[wt]-GFP (the BAC recombineered construct), with text added to Lines 343-345, 365-369 (Results) and 408-418 (Discussion).

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Al Asafen, Clark et al., use fluorescence correlation spectroscopy (FCS) to quantitatively analyze the mobility of Dl along the DV axis of the early Drosophila embryo. Dl is essential for dorsal-ventral (DV) patterning and its gradient initiates the activation of several genes and thereby orchestrates the formation of the Drosophila body plan. While the mechanisms underlying the formation of the Dl gradient have been extensively studied by this group and others, there are some observations for which there is not yet a mechanistic explanation. For example, the peak of the Dl gradient grows continuously during nuclear cycles 10-14. This is likely due to Cact-dependent Dl diffusion and Dl binding to DNA. However, the biophysical parameters governing Dl nuclear dynamics that would support these claims have not been previously measured. In this work, the authors provide evidence that GFP-tagged Dl may be separated into a mobile pool and an immobile pool. Interestingly, the fraction of immobile Dl is position-dependent along the DV axis, revealing more binding to DNA in the ventral than in the dorsal nuclei. This is either due to higher binding affinity in ventral locations (due to Toll-dependent Dl phosphorylation) or to higher Dl-Cact binding in dorsal nuclei that would prevent Dl from binding to DNA. Using dl-mutant alleles, the authors support the latter hypothesis.

      Strengths:

      The manuscript is well written and their conclusions are convincingly supported by their methodology and analysis. As a quantitative study, the biophysical analysis seems rigorous, in general.

      Although this is not the first study that employs FSC to investigate the dynamics of a morphogen, it further exemplifies how these quantitative tools can be used to uncover mechanistic aspects of morphogen dynamics during development. In particular, the manuscript reports novel biophysical parameters of Dl dynamics that will be helpful in future hypotheses-driven modeling studies.

      Weaknesses:

      In my opinion, the main weakness of the manuscript is that the main biological implication of the study, namely that the asymmetry in the fraction of immobile Dl is a result of nuclear Dl-Cact binding which prevents Dl from binding DNA (Figure 5), occurs in a region of the embryo where there is very little Dl anyways (Figure 1A, 5A). While it is interesting that the fraction of immobile Dl increases (just a little, but significantly) in dorsal nuclei in mutants expressing a form of Dl with reduced Cact binding it is unclear what is the biological impact of this effect in a location where Dl is nearly absent. As can be seen in Figure 3F, the fraction of immobile is unaffected in Dl-mutant forms with reduced DNA binding, because it is already very low. It is unlikely that Dl binding to Cact in dorsal nuclei would affect shuttling as well since the fraction is very low anyway.

      We thank the reviewer for pointing out the places where we could strengthen our explanations. Here we first address the criticism, also raised by the other reviewer, that the fraction of immobile Dl increases only a small amount (Fig. 5A). [In our reply to the next comment, we address the question of biological implications.] We attempted to explain this small effect size in the manuscript; however, we understand that we could clarify further and, given the fact that eLife has no restraints on space, we added more explanation in the main text.

      In essence, even though the effect was statistically significant, the effect size was small because the mutation was “diluted” by the presence of a wildtype Dl protein tagged with GFP. We were willing to deal with this dilution because the alternative was that, according to previous literature, without any wildtype Dl, no Dl gradient would be present in the reduced Toll phosphorylation mutants, and only a very weak Dl gradient (weakened on both ends) would be present in mutants that reduced Cact binding. We were confident that, with our quantitative approaches, we would be able to detect the diluted effect.

      However, because both reviewers have criticized this diluted effect, in this resubmission, we have included analysis of GFP-tagged mutants without the presence of wildtype Dl protein. Unfortunately, these embryos lack a discernible Dl gradient and cannot be analyzed in such a way as to test the hypotheses that the mutants were generated for.

      Even so, the effect of the Cact-binding mutant was strong enough that we were able to statistically distinguish it from embryos expressing only wildtype Dl-GFP, even with the dilution effect. On the other hand we have also included a caveat that our failure to statistically distinguish Toll phosphorylation mutants from wildtype may be due to the dilution effect. We now also explicitly state the concerns about a lack of a discernible Dl gradient and have included figures of full mutants in the supplement. See also our discussion of Reviewer 1’s similar comment.

      While the authors have a very clear understanding of the biology of the Dl gradient, I feel that the manuscript is more written as a 'tools' paper (i.e., to exemplify how FSC methods and analysis can be used for biological discovery). This is ok, but I think that the authors should discuss further what are the biological implications of these findings other than the contribution to uncovering the biophysical parameters.

      Here we underscore the biological implications of our discovery that Cact is present in the nucleus on the dorsal side. The reviewer mentioned that Cact in the nucleus on the dorsal side appears to have little overall effect, because this is the location of the embryo where there is very little Dl in the first place, which raises the question of whether this discovery is impactful.

      While we previously used the final paragraph of the discussion to touch on the implications of this discovery, we acknowledge that we could have spent more time on the explanation. As such, we have expanded this final paragraph into two paragraphs. In the first of the two, we discuss in more detail the implications specifically of the Dl/Cact interactions in the dorsal-most nuclei, as understood by the results of this paper. In brief, knowing that Dl in the dorsal-most nuclei is bound by Cact results in an updated understanding of the Dl gradient, with increased dynamic range, robustness, and precision (but unknown shape).

      In the second of the two paragraphs, we discuss this result in light of our recent work on imaging Cact in live embryos, in which we have shown that Cact is present in all nuclei at roughly uniform levels. Taken together, we suggest that it is possible that Cact is bound to Dl in all nuclei (not just the dorsal-most), which would allow us to estimate the shape of the overall Dl gradient by subtracting off the fluorescence that stems from Dl/Cact complex.

      For example, I think that the implications of the rejected hypothesis (i.e., that Tolldependent Dl phosphorylation does not seem to have an impact on Dl binding affinities to DNA) are important and should be further discussed (even if no additional experiments are performed). What is then the role of Dl phosphorylation? Perhaps it could have an impact on patterning robustness in lateral regions. The authors should report in Figure 5 also what happens to the fraction of Dl bound to DNA in lateral regions in the reduced Cact binding and reduced Toll phosphorylation mutants.

      We appreciate the reviewer’s suggestion that the rejection of the hypothesis that phosphorylation of Dl by Toll impacts Dl/DNA binding could be expanded upon further. For the role of Dl phosphorylation by Toll: we previously mentioned that this phosphorylation is known to enhance the nuclear import or retention of Dl, and that mutation of serine 317 to an alanine abolishes Toll-mediated phosphorylation of Dl, which results in embryos with no Dl gradient. We had also mentioned that phosphorylation of Dl is not known to affect its DNA binding, which is the hypothesis we sought to test by creating the dl[S317A]-GFP mutants. We did not image any mutants, or the UAS-dl[wt]-GFP control, in the lateral regions, for two reasons. First, this region is easily the smallest of the three regions, in terms of the percentage of the DV axis (see Fig. 1A). Second, because of the dilution effect, we knew the effect size would be small, and as such, we imaged only on the extreme ends of the gradient so that the most clear conclusion could be drawn about the effect that Toll phosphorylation might have on DNA binding of Dl.

      The way that position along the DV axis is reported using the nuclear-cytoplasmic-ratio (NCR) in Figures 1-3 is not incorrect, but I wonder if it is the best way of doing it. The reason is that it spreads out a relatively small region of the embryo (the ventral-most locations) and shrinks a relatively large region of the embryo (lateral and dorsal regions), see Figure 1A. Perhaps reporting the NCR in log_2 units would be more appropriate.

      We agree that there is some distortion of the relative spatial extents of the Dorsal gradient when NCR is used as an independent variable on a plot. However, we prefer the NCR on the horizontal axis because it is closer the functional variable (Dl concentration, rather than spatial location) for the properties we studied.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I really enjoyed the first part of this paper and have only minor suggestions for improvement of the presentation. I am confused about the experimental approach for the final figure, distinguishing phosphorylation and cactus-dependent effects. I'll divide my comments between "First Part/General Suggestions", "Last Part", and finish with some minor typo observations.

      The gist of the issues with the last part of the paper could boil down to insufficient detail/explanation of the section. The discrepancy with expectation with Michaelis-Menten kinetics is presented in a total of three sentences and is not necessarily obvious to the general readership of eLife. The mutants chosen to distinguish the phosphorylation and cactus mechanisms could be described more (why these? aren't other residues phosphorylated?) and possibly why also having wild-type GFP-Dl in the measurements isn't confounding. Since there is unlimited space in this journal, it may be advisable to use this space to fill out these rationales and ideas.

      First part/General Suggestions:

      (1) For the RICS data, (Figures 1 and 2) there is a nice correlation between WT NC ratio and the selected low/med/hi Dl activity mutants. More-or-less the median values in, say, Figure 1E-G are reflected in Figure 1H. However, with the ccRICS data (Figure 3), it looks like there is less correspondence between the range of fraction bound estimates in, for instance, "ventral" in Figure 3D and '10b' in Figure 3E. Can the authors comment on this? Should the reader be able to make this kind of comparison, or does something about data collection for the wt/NCR measurements preclude direct comparison of magnitudes with the panel of mutants? (imaging setup, laser power, etc)?

      The reviewer is correct that there seems to be a discrepancy in the values of ψ between the wt embryos (ventral side) and the Toll10B embryos. It should be noted that the Toll10B embryos are not “ventral-like” in every way, in part because they have unknown activated Toll levels that might be above or below what is seen at the ventral midline in wildtype embryos, and in part because there is no DV gradient, and thus no shuttling in these embryos that would accumulate total Dorsal on the ventral midline. As such, comparisons between Toll10B embryos and the ventral side of wildtype embryos are not exactly one-toone, and we are more confident in comparing among the mutants in an allelic series. To address this question, we have added a sentence to the end of the second paragraph of the “Dorsal/DNA binding exhibits a spatial gradient” subsection of the Results (Lines 233235).

      (2) Materials and methods: Mounting and imaging of Drosophila embryos: the authors cite the "488 nm laser intensity ranged from 0.5% to 3.0%..." The values presented here are not useful for the general reader or an individual looking to replicate these conditions, as emission power produced from such values will vary from instrument to instrument. It is standard in these cases to report an estimated laser power (measured in watts) for each laser line, and a clear description of how such measurements were made (stationary beam, under scanning conditions, with what detector, etc). These measurements are valuable and the authors are strongly encouraged to report such measurements for their setup.

      We appreciate the reviewer’s suggestion and understand the importance of providing absolute laser power values for reproducibility. We have now included the laser power (in watts) for the laser lines on both microscopes used in this study. The revised text can be found in the Materials and Methods section, in the Lines 535-536 and 540.

      (3) The presentation of the data in Figure 4 is difficult to understand. Are the kymographs (A lower) representing the entire length of the big white arrow in A upper? Or do the dashed lines indicate the x-axis limits of the kymograph? It is difficult to tell from the figure legend, where the dashed lines are described as "areas where Dl-GFP movement is measured out of the nucleus." I believe that the authors can make these measurements and that Figure 4B reflects properties of "movement" of Dl out of the nucleus, but how they get there from these data is not clear to this reader. Perhaps a cartoon explaining the green lines and the orange lines in the kymograph or tightening the legend would help.

      We thank the reviewer for their feedback and understand the need for greater clarity in the text of the pCF section and in Figure 4. The widths of the kymographs in the lower panels correspond to the full widths of the images in the upper panels. The pCF measurements were taken at the y-coordinates at the level of the white arrows. The dashed vertical lines connecting the upper and lower panels illustrate two cases of locations along the x-axis of the image where Dl is crossing from inside a nucleus to outside. In the two illustrated cases, these crossings are accompanied by either zero Dl molecules being observed to cross the nuclear barrier (ventral image/kymograph on left) or delayed crossing of Dl molecules (dorsal image/kymograph on right). To address this concern, we have added more detail to the Fig. 4 legend and greatly expanded on a discussion of what pCF does in the text (the second and third paragraph of the section). We have also updated Fig. 4 to align with new explanations from the text: namely, describing the y-axis of the kymographs as Δt (instead of log(time)) and explicitly showing that the pair correlation is for pairs of pixels that are Δx = 6 pixels apart. Further details were also added to the relevant Methods section.

      (4) DV position in the wild-type imaging experiments is operationally determined through measurement of the Dorsal NC ratio. This makes sense, but the strategy is buried in the first paragraph of the results, and not discussed in the M & M. For readers unfamiliar with imaging the fly embryo or the nuances of the Dl gradient, perhaps a sentence or two explaining that embryos were oriented randomly along the DV axis, and DV positions of the imaging region were estimated by measuring the Dl NC ratio.

      We thank the reviewer for this helpful suggestion. To improve clarity, we have added a description of how DV position was determined to the Materials & Methods section (paragraph starting on Line 520). Specifically, we now state that embryos were randomly oriented along the DV axis and that we used the Dorsal NC ratio of intensity as a proxy for measuring the DV position in imaging experiments. Additionally, we have added a statement to the Results section to ensure that this strategy is more clearly introduced (Lines 143-144). We appreciate this recommendation, as it will help readers unfamiliar with fly embryo imaging better understand our approach.

      (5) It would be nice to report the corresponding NC-ratio values for Dl in each of the mutant conditions, perhaps as a supplement to Figure 1. Currently, Figure 1H relies on the (admittedly well-established) properties of the three mutants, but it feels that an additional nice quantitative link in the data can be drawn out here. Do the authors see the strict correlation between the wt and mutant diffusivity measurements at specific NC-ratios?

      We are hesitant to try to draw direct comparisons between the mutants and the behavior of the wildtype embryo at the corresponding NCR. This is because, in the context of these uniform mutants, the NCR is determined by a combination of at least three factors that we cannot measure or control for: the unknown strength of Toll signaling, the unknown capacity of Toll signaling (ie, the potential saturation of the cytoplasmic enzymes controlled by Toll signaling), and, most importantly, the lack of a shuttling mechanism that concentrates Dl on the ventral side of the embryo. As such, the NCR does not represent a continuous variable that transforms the behavior of one mutant into another (or from mutants into wt DV coordinates), as it does along the DV axis in wildtype embryo. This is why the mutant studies are presented as boxplots. At best, we were comfortable only in using the uniform mutants as an allelic series to produce gross trends. We have added a brief statement describing the shuttling caveat to the Results section (Lines 173-177).

      (6) In the section related to Dl nuclear export, the language used to describe Dl kinetics is ambiguous. The term "movement" is used seemingly as a catch-all for nuclear-importexport as distinguished from diffusion. However, diffusion is also a form of movement. Could this section be reworked to explicitly distinguish nuclear import-export and diffusive movements?

      We appreciate the reviewer’s suggestion and agree that the language used to describe Dl kinetics could be more precise. By way of explanation, the pCF analysis calculates the time scale on which Dl can exit the nucleus. pCF only gives a signal if it sees the same Dl molecule twice, at two different locations after some Δt amount of time has passed. Because of this, if a given Dl molecule in a ventral nucleus is being tracked, then that molecule has some probability that it is bound to DNA initially, which means it will take, on average, longer to exit the nucleus than a Dl molecule not initially bound to DNA. Therefore, on the ventral side, the time scale on which Dl exits the nucleus is longer than on the dorsal side (where DNA binding is not happening). This can be true even if the nuclear export rate constants are the same on the ventral side vs the dorsal side. As such, we were careful to choose language that did not imply that we were talking about a nuclear export rate constant. We have added this discussion to the end of the relevant Results section (Lines 308-315).

      We have also revised this section to explicitly distinguish between the mobility associated with exiting the nucleus and diffusive movement, while still trying to distinguish between the time scale of exiting the nucleus vs the nuclear export rate. Specifically, we now refer to ‘time scale of nuclear export’ when discussing transport across the nuclear envelope and reserve the term ‘diffusion’ for passive intracellular movement. Furthermore, we have edited a sentence in this section (Lines 291-293) to describe the distinction we are making between the time scale measured by pCF and the time scale commonly associated with nuclear export (that is, the reciprocal of the rate constant). We hope this clarification improves readability and conceptual clarity.

      Last Part:

      (1) There is an undersold argument centered on Michaelis-Menten kinetics that needs to be explicitly presented, especially since it motivates the final experiments of the paper, which are challenging. In the two sections describing how the data do not adhere to expectations based on Michaelis-Menten Kinetics, the assertion that "the fraction of immoble Dl is expected to decrease with increasing nuclear total Dl concentration" is only intuitively true if the system is saturated. Is the system demonstrably saturated? Another interpretation of this would be that these results demonstrate that the system is likely not saturated. In any case, the authors need to devote some space in the introduction and/or results and/or discussion to fully motivate this point.

      We agree that the reviewer has raised an important point: if the system is very far from saturation, then the fraction of immobile Dl is not expected to decrease with increasing nuclear total Dl concentration. But neither would it increase; it would instead stay flat. To correct this mistake, we have edited the sentences in question to acknowledge the farfrom-saturation scenario, saying “at best, [the fraction bound] remain[s] constant” (Line 209). As such, our original point, which is that in no case would the fraction immobile increase [unless something else is going on besides affinity-based binding to DNA], it still valid.

      (2) Wouldn't any argument on the basis of Michaelis-Menten need to rely on the assumption that the system is at steady-state? Reeves 2012 concludes that during the times measured here, Dl does not reach a steady state. It would be good, in the context of the point above, for the authors to clarify how this impacts the expectations of saturation and the application of M/M kinetics.

      We thank the reviewer for raising this important point. We apologize for not being clear on our points about M/M kinetics and would like to stress again that we are not claiming the system is has M/M kinetics. We appealed to M/M kinetics only as a simple, intuitive example of a saturating system to point out the difference between bound concentration vs bound fraction as functions of total concentration. We did this because previous feedback on our manuscript suggested that the difference between these two variables needed to be made clearer. Because this point seemed controversial with both reviewers, we removed all mention of M/M kinetics and simply refer to the system as “saturating.” For further explanation, see the first paragraph of our response to Reviewer 1’s “weaknesses” in the public review.

      (3) It is not clear to me how the inclusion of wild-type, GFP-tagged dorsal in the experimental setup for Figure 5 is not confounding. For the S317 (phospho-) mutant, GFPtagged alleles of both phospho- and wild-type Dl are expressed. The reasoning is that not enough phospho-mutant Dl gets into the nucleus, and this makes it difficult to distinguish the dorsal from the ventral side of the embryo, so in a dl mutant background, there is expression of wt GFP-dl from a BAC, and nos>Gal4 driven expression of a GFP-tagged S317A mutant dl. The measurements show that on the ventral side of the embryo, there is no difference in the fraction of bound Dl. Couldn't this be predominantly binding of wildtype GFP-Dl? How is this interpretable? Wouldn't it be easier to perform these measurements in a Tl 10b background (or to cross in UAS>Tl[10b]) and for the only GFPtagged dl to be S317A? The same goes for the S234 mutant (could be done in the pelle mutant background).

      We thank the reviewer for raising the point that the confounding effect of wildtype Dl makes it difficult to interpret the results from the 317A mutant. Under the circumstances of the experimental design, we can best conclude that, if the null hypothesis is incorrect, the effect size was too small to detect with our sample size. As such, we have modified our discussion of the results of this experiment to carefully explain this caveat (rather than confidently saying that Toll phosphorylation has no effect). For further explanation, see the second paragraph of our response to Reviewer 1’s “weaknesses” in the public review, as well as our response to the related question raised by Reviewer 2 in the public review.

      Minor issues/typo stuff:

      (1) This reviewer notes that the submitted materials contain neither line numbers nor page numbers.

      We appreciate the reviewer’s feedback. We have now included line numbers and page numbers in the revised manuscript for easier reference.

      (2) First paragraph of results: "We imaged small regions of the embryo..." The parenthetical statement only cites pixel size and directs the reader to the methods. Without the total number of pixels, the pixel size value does not clarify how "small" the imaged region is. Consider including the xy area, pixel dimensions, and pixel size here to assert the smallness of the imaged area.

      We have added the requested information.

      (3) Second paragraph, Introduction: "Dorsal, one of three (Drosophila) homologs to mammalian NF-kB" (Add Drosophila). Also, aren't these orthologs?

      We have made these changes.

      (4) Last sentence of last paragraph in the introduction: Kind of a throw-away sentence. Consider revising.

      We thank the reviewer for making this point; the sentence was originally constructed to state that our quantitative measurements resulted in a biologically significant discovery. However, because Reviewer 2 also mentioned the question of biological significance, we have changed this final sentence to explicitly mention of what the biological significance is: namely, an understanding of the Dl gradient that has superior dynamic range, spatial range, robustness, and precision.

      (5) Where is the median line in the S317A boxplot in Fig 5C?

      The median line is at ψ = 0. We have added an explanation of this to the Figure legend.

      (6) Materials & Methods: Fly transformation, typo: Drosophila embryos were injected with 0.5 µl of each pUAST construct..." The volume of an entire Drosophila embryo is less than 0.5 µl, please revise the units to reflect the value injected. Most likely an absolute volume unit was stated when rather a concentration of an injection solution, delivered at significantly smaller volumes was intended.

      We thank the reviewer for catching this typo. It was intended to indicate a concentration of 0.5 ng/μL, and we have made the appropriate changes.

      Reviewer #2 (Recommendations for the authors):

      (1) Perhaps this has been described in a prior publication (if this is the case, please simply state this somewhere in the Methods section where Dl-GFP embryos are described), but since Dl-GFP embryos have one copy of endogenous dl and one copy of Dl-GFP, how do potential differences in tagged vs. non-tagged Dl interactions with DNA or Cact affect their findings?

      The reviewer brings up a good point, and we acknowledge that any time a protein is tagged with GFP, the behavior of the protein may be affected. We have now explicitly added this caveat to our discussion in a new paragraph on Lines 420-429.

      (2) In the Discussion section, the authors argue that a major implication of their findings is the possibility that Cact binds Dl in the nuclei would imply that the true (active) Dl gradient may be unknown unless the unbounded Dl is separated from the Dl/Cact (inactive form). While this is an interesting point, this idea is not supported by the findings of Figure 5B where there is no effect in the fraction of Dl bound to DNA in the reduced Cactus binding mutants. The authors should report what happens in lateral regions in Figure 5 because perhaps there is an effect there (see comment on this in the Public Review).

      We thank the reviewer for the insight, as we did not directly discuss the implications of the middle column of Fig. 5B on our hypothesis. Indeed, our hypothesis is not supported by Fig. 5B; it is instead inconclusive (failure to reject H0). This is why we designed the second experiment (Fig. 5C) to test the Cactus hypothesis, because the effect size would be greater on the dorsal side.

      Furthermore, as pointed out by both reviewers, the presence of wildtype Dl-GFP in these experiments is confounding. We have discussed this elsewhere in our rebuttal, but briefly, this problem resulted in needing larger effect sizes to detect a statistically significant difference between wt and the mutant populations. This was a necessary evil that we were willing to deal with in order to ensure the Dl gradient could be established so that the dorsal vs ventral sides would be distinguishable. We have added a fuller discussion of these issues to the relevant Results section (Lines 333-336, 343-345, 354-359, 365-369) and also the Discussion section (Lines 412-418), including underscoring the fact that, from a falsification standpoint, the results in Fig. 5B do not allow us to reject either null hypothesis, possibly due to the confounding effect of wildtype Dl. We appreciate the reviewer’s point about this, and believe the changes suggested by the reviewer have improved the manuscript.

      On the other hand, we respectfully disagree with the reviewer that investigating either mutant in the lateral regions of the embryo would bear fruit. To the first approximation, it would be the average between the behaviors on the ventral vs. dorsal sides. For the S317A mutant, neither the ventral nor the dorsal side was conclusive in regards to our hypotheses. (Although we admit here that further investigation into why the S317A column in Fig. 5C was statistically different from wildtype, in the opposite direction from the S234P mutant, may be interesting in future work.) For the S234P mutant, the data were more conclusive on the side of the embryo where the effect size was expected to be large enough to detect a difference. In the lateral regions, the expectation would be that the effect size would be intermediate, which would make the interpretation of the results more difficult (i.e., more likely to be inconclusive). In contrast, as Fig. 5C is already conclusive, we are not confident there would be more information gained by imaging the lateral regions.

      (3) Is Figure 5A a wild-type embryo? If so, I think that the labels are misleading or unclear. Also, is it the same image as in Figure 1A? If so, I suggest replacing this with a schematic since it does not add any new data.

      We have eliminated the labels for the mutants and have added the following comment to the figure 5 legend “Same embryo as in Fig. 1A”.

      (4) Also in Figure 5, I suggest using labels to indicate the schematics instead of simply using their location. You could use 5A', 5A' and 5A', for example.

      We have made the suggested changes.

      (5) The use of some technical labels makes some figures difficult to read. I suggest using more simple labels for mutants in Figure 3F (replace R063C) or Figure 5B, C (replace S234P and S317A).

      We have made changes to Fig. 3F, Fig. 5B,C, and the corresponding places in the figure legends. We have labeled R063C as ↓DNA, S317A as ↓Toll, and S234P as ↓Cact.

      (6) I suggest reporting p-values consistently. For example, in Figure 4B, they use one or two asterisks to denote p-values less than 0.07 and 0.05, respectively, which is somehow arbitrary and unconventional. Why not report the actual values as in Figure 5C, for example? (By the way, I would report in Figure 5B the actual p-values as well, since a nonsignificant value is also reported in Figure 5C. Also in Figure 5C, report values in the same notation (decimal or scientific), i.e., either put 0.005 as 5x10^-3 or 10^-3 as 0.001).

      We have made the suggested changes.

    1. Author response:

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

      Reviewer #1 (Public review):

      This manuscript provides several important findings that advance our current knowledge about the function of the gustatory cortex (GC). The authors used high-density electrophysiology to record neural activity during a sucrose/NaCl mixture discrimination task. They observed population-based activity capable of representing different mixtures in a linear fashion during the initial stimulus sampling period, as well as representing the behavioral decision (i.e., lick left or right) at a later time point. Analyzing this data at the single neuron level, they observed functional subpopulations capable of encoding the specific mixture (e.g., 45/55), tastant (e.g., sucrose), and behavioral choice (e.g., lick left). To test the functional consequences of these subpopulations, they built a recurrent neural network model in order to "silence" specific functional subpopulations of GC neurons. The virtual ablation of these functional subpopulations altered virtual behavioral performance in a manner predicted by the subpopulation's presumed contribution.

      Strengths:

      Building a recurrent neural network model of the gustatory cortex allows the impact of the temporal sequence of functionally identifiable populations of neurons to be tested in a manner not otherwise possible. Specifically, the author's model links neural activity at the single neuron and population level with perceptual ability. The electrophysiology methods and analyses used to shape the network model are appropriate. Overall, the conclusions of the manuscript are well supported.

      Weaknesses:

      One potential concern is the apparent mismatch between the neural and behavioral data. Neural analyses indicate a clear separation of the activity associated with each mixture that is independent of the animal's ultimate choice. This would seemingly indicate that the animals are making errors despite correctly encoding the stimulus. Based solely on the neural data, one would expect the psychometric curve to be more "step-like" with a significantly steeper slope. One potential explanation for this observation is the concentration of the stimuli utilized in the mixture discrimination task. The authors utilize equivalent concentrations, rather than intensity-matched concentrations. In this case, a single stimulus can (theoretically) dominate the perception of a mixture, resulting in a biased behavioral response despite accurate concentration coding at the single neuron level. Given the difficulty of isointensity matching concentrations, this concern is not paramount. However, the apparent mismatch between the neural and behavioral data should be acknowledged/addressed in the text.

      We thank the Reviewer for the insightful comments and thoughtful suggestions. Our electrophysiological recordings show that GC dynamically encodes stimulus concentration of mixture elements, dominant perceptual quality, and decisions of directional lick. With regard to the encoding of mixtures, the clear separation of activity associated with each mixture (Figure 3) is present at a trial-averaged pseudo-population level, and average activities associated with more similar, intermediate mixtures are closer to each other in this space. At a single trial level activities evoked by similar, intermediate mixtures are much harder to separate. This increased similarity can lead to behavioral errors resulting from either incorrect encoding of the stimulus or from the inability to interpret the stimulus to guide the correct decision. The psychometric function, which shows that more distinct stimuli (100/0 vs 0/100) lead to fewer mistakes than more ambiguous, intermediate mixtures (55/45 vs 55/45), is consistent with the increased ambiguity of responses to intermediate mixtures.

      The Reviewer is correct that there could be a slight mismatch in the perceived intensity of the mixture components. This mismatch could be the reason for the slight asymmetry in our psychometric function (Figure 1B). However, it is not uncommon for mice in these 2AC tasks to also have a motor laterality bias in their responses that manifests itself for the more ambiguous stimuli. We chose not to model this bias given its subtlety and its unknown origin. Rather, we chose to model an ideal scenario in which stimuli have matched intensity and no motor bias exists. In the revised manuscript we discuss this issue.

      Reviewer #1 (Recommendations for the authors):

      (1) The apparent mismatch between neural and behavioral data. I am providing more details in this section to hopefully better illustrate my concern.

      (a) Based on the author's psychometric curve, sucrose appears to be a more salient signal causing the behavior to be shifted (e.g., a 50/50 mixture results in a >60% predicted behavioral performance). If both sucrose and salt were intensity-matched, a 50/50 mixture should result in a behavioral performance near 50%. The increased salience of sucrose could cause the animals to have lower overall performance despite accurate neural encoding. Alternatively, certain animals could display a strong side bias, skewing the data slightly. These issues have seemingly been fixed in the model data, which displays a more balanced psychometric curve. Accordingly, the model data seemingly displays a larger shift in error trials as compared to correct trials (Figure 6A).

      The reviewer is correct in observing that the average experimental psychometric curve in Figure 1B shows a slight shift in favor of the sucrose side with a 50/50 mixture. We fit psychometric curves to each session and the mean value of P(Sucrose choice | Stimulus = 50/50) across sessions was significantly different from 0.5 (one-sample t-test, p = 0.003), with 5 probabilities below 0.5 and 18 above it.

      This slight bias could be attributed to a slight mismatch in the perceived intensity of the mixture components and/or lateral motor biases. In any case, it is subtle and its origins were not a focus of this study.

      Models were not trained to match the animals’ psychometric curves, but rather to choose correctly in an ideal scenario where stimuli have matched intensities. This explains why the model simulations lack the bias observed in animal behavior data.

      We do not believe that there is a mismatch between the experimental behavioral and neural data, as trial-averaged pseudo-population trajectories are farther in neural space for more discriminable stimuli and closer in neural space for more similar stimuli, consistent with behavioral performance that is high for more discriminable stimuli and low for more similar stimuli. Moreover, as the model also shows, a clear separation of trial-averaged trajectories still results in a sigmoidal performance function for trial-to-trial behavior.

      Finally, subtle behavioral biases would not necessarily be expected to appear in our dPCA analyses since we used this technique to find a single axis that best separates all stimuli conditions regardless of choice when the pseudo-population data are projected upon it. Additional modes of activity that explain less overall variance might better reflect biases.

      (b) Although I am not an expert at these analyses, I wonder whether the elevated bump (i.e., >0) in Figure 3C of the 55/45 mixture that occurs early in the stimulus presentation further supports the hypothesis mentioned above and could indicate an early signal of salience/increased intensity?

      The reviewer is correct that the 55/45 trajectory features a brief positive wave right after stimulus delivery before going negative. While this may be related to stimuli not being explicitly balanced for intensity, it could also reflect a signal related to ambiguity or balanced mixtures. We are hesitant to interpret this positive deflection as conclusive evidence of a bias in neural activity, given its short duration and the natural variability of neural signals.

      (2) The increase in step-perception neurons after the decision period is confusing (Figure 4C). The text states (line 246) "the analysis reveals a small and time-invariant proportion of step-perception neurons". However, the proportion doubles after the decision-making process, which is seemingly a significant change. Why does this occur? This observation is noticeably missing from the network data. Could it be attributed to a mislabeling of "step-choice" neurons, given the correlation between the left/right decision and sweet/salty? Either way, it is very noticeable and should be addressed.

      We cannot be sure of the reason for the increase in step-perception neurons after decisions. One possibility is that they are acting as feedback for learning, encoding the percept to compare with choice and outcome to improve performance. The model, which presumably learns the task differently from the animals, does not seem to leverage this signal for its own learning. We have modified the text, now referring to a “small but consistently present proportion” of step-perception neurons, and included this proposed explanation in the Discussion.

      (3) Optional: I think the authors are missing an opportunity to analyze the temporal aspect of this multiplex code using their network-based modeling approach. A significant proportion of neurons fall into different categories (i.e., step-perception/linear, etc.) at different time points. However, the virtual ablation experiments remove any neuron that falls into one of these categories at any time. By limiting the cell-specific virtual ablation to specific time windows, you could (I think) provide stronger evidence for the temporal sequence of the encoding of these perceptual aspects.

      This was an excellent suggestion for an additional modeling experiment, so we performed it. A new supplemental figure (Figure S8) and additional text in the revised manuscript showcase the results. In summary:

      In terms of behavioral results, ablating the linear coding units in the beginning (that is, silencing all units that are labeled linear in any bin within the first 1.2 s after stimulus onset for the entirety of the 1.2 s) significantly reduces performance, as does ablating the step-perception or step-choice coding units at the end (1.2 s prior to choice). The remaining combinations of coding type and timing of the ablation do not affect performance.

      Regarding the dynamics of coding types (compare Figure 7A), stimulus coding activity was significantly blunted only by ablating the linear coding units in the beginning, whereas choice coding activity was diminished by ablating the choice coding units at the end or by ablating the linear coding units at either the beginning or the end.

      Reviewer #2 (Public review):

      Lang et al. investigate the contribution of individual neuronal encoding of specific task features to population dynamics and behavior. Using a taste-based decision-making behavioral task with electrophysiology from the mouse gustatory cortex and computational modeling, the authors reveal that neurons encoding sensory, perceptual, and decision-related information with linear and categorical patterns are essential for driving neural population dynamics and behavioral performance. Their findings suggest that individual linear and categorical coding units have a significant role in cortical dynamics and perceptual decision-making behavior.

      Overall, the experimental and analytical work is of very high quality, and the findings are of great interest to the taste coding field, as well as to the broader systems neuroscience field.

      I have a couple of suggestions to further enhance the authors' important conclusions:

      My main comment is the distinction between constrained and unconstrained units. The authors train a small percentage of units to match the real neural data (constrained units), and then find some unconstrained units that are similar to the real neural data and some that are not. As far as I could tell, the relative fraction of constrained and unconstrained units in the trained RNN is not reported; I assume the constrained ones are a much smaller population, but this is unclear. The selection of different groups of neurons for the RNN ablation experiments appears to be based on their response profiles only. Therefore, if I understood correctly, both constrained and unconstrained units are ablated together for a given response category (e.g., linear or step-perception). It would be useful, therefore, to separately compare the effects of constrained vs. unconstrained RNN units.

      We thank the Reviewer for the constructive feedback. The Reviewer is correct that ablations were carried out with respect to response categories only and included both constrained and unconstrained units.

      The ratio of total units to constrained units was fixed at 5.88, thus constrained units were ~17% of the network and unconstrained units were ~83%. This value is specified in the Methods (RNN: Components and dynamics), but we have reported it in the Results of the revised manuscript for clarity.

      We have also edited the Methods because they wrongly stated that the ratio of unconstrained (rather than total) units to constrained units was 5.88.

      Specifically:

      (1) For the analyses in the initial version of the manuscript, the authors should specify how many units in each ablation category are constrained and unconstrained.

      In the revised manuscript, we have specified the fractions of constrained and unconstrained units within each response category. For convenience, they are reported here: linear = 194 constrained and 691 unconstrained units; step-perception = 147 constrained and 840 unconstrained units; step-choice = 129 constrained and 814 unconstrained units; “other” = 353 constrained and 1739 unconstrained units.

      (2) The authors should repeat Figure 6, but only for unconstrained units to test how much of the effects in the initial version of Figure 6 are driven by constrained vs. unconstrained RNN units.

      In the revised version we have included two additional supplemental figures (Figures S5-6) where the analyses of Figure 6 are carried out separately for constrained and unconstrained units. In short, the results for the constrained units strongly resemble those for the experimental data, while the results for the unconstrained units strongly resemble those for all model units.

      (3) The authors should repeat Figure 7, but performing ablations separately on the constrained and unconstrained units to examine how the network behaves in each case and the resulting "behavioral" effect.

      The revised version includes a supplemental figure (Figure S7) with the results of these additional ablation simulations.

      In summary:

      In terms of behavioral performance, the prior results showing that ablating linear, step-perception, or step-choice units significantly impairs performance, while ablating “other” has no significant effect, hold even if ablation is restricted to only constrained or only unconstrained units. There is a significant main effect of constrained vs unconstrained; on average, ablating the unconstrained population impairs performance more, most likely due to their larger population size.

      In terms of dynamics, to impair stimulus coding by ablating step-choice units, you must ablate them all; to impair stimulus coding by ablating linear or step-perception units, however, ablating just the unconstrained ones suffices. As before, ablating linear, step-perception, or step-choice units significantly impairs choice coding activity, while ablating “other” units does not; these results hold even if ablation is restricted to only constrained or only unconstrained units. Finally, there is again a significant main effect of constrained vs unconstrained; on average, ablating the unconstrained population impairs dynamics more, most likely due to the larger population size.

      Reviewer #2 (Recommendations for the authors):

      (1) In addition to panel 5B, it would be informative to show data from individual mice and the corresponding RNNs trained on each mouse, to assess how closely they match. If available, including one representative example of a good match and one of a less accurate match would help the reader get a better sense of the data.

      Figure 5B shows the average behavioral performance of the model. Individual models were not trained directly on the psychometric curves of experimental sessions; they were trained to perform the task correctly. After successful training, model simulations were run with input noise to be able to produce a sigmoidal psychometric curve. However, although the input noise was tuned to capture the overall correct rate of the corresponding experimental session, we did not attempt to match the details of the psychometric curve. See also the next reply.

      (2) In addition to panel 5C, it would be useful to add examples of experimentally observed PSTHs and the corresponding activity trajectory for the units in the RNN trained to match them, for all the other coding patterns (step-perception and step-choice).

      We note that the PSTH in 5C is not an example of a linear coding unit as the Reviewer implies, but simply one with a good fit, and here the model’s output was produced in the absence of input noise. In order to classify step-perception and step-choice responses one needs error trials, but the model was trained without this input noise that induces errors (and produces a sigmoidal psychometric function) to match experimental PSTHs from correct trials only. Post-training simulations were then run with input noise to induce error trials, and model unit response profiles were classified based on this. However, there is no guarantee that error trials in the model match the error trials in the experiment; therefore, step-perception and step-choice units in the model may or may not be step-perception and step-choice units in the data. Despite this limitation, the revised manuscript includes additional examples, in Figure S2, of experimentally observed PSTHs and their corresponding model activity, to supplement Figure 5C and provide a better sense of the goodness-of-fit.

      (3) Electrophysiological data in Figure 2 - It would be helpful to provide statistics on how many neurons change their activity in each session.

      In the revised manuscript we have included across-session statistics for proportions of neurons that are taste-responsive and that show decision preparatory activity. We have also included tables (Tables S1 and S3) with the numbers of neurons that are taste-responsive and that show preparatory activity for each session in the experimental and model data.

      (4) Peak auROC selection - How was the peak auROC selected? Selecting only one bin for the peak could be potentially problematic and may result in the incorrect identification of an outlier that does not faithfully represent the neuron's overall activity. The peak selection could instead be based on several consecutive bins showing a consistent trend. If this approach was already implemented, the authors should explicitly describe it in the Methods section.

      Peak auROC was selected from a single bin (with average duration about 50ms). While it is true that this may result in outlier neurons that transiently prefer one stimulus strongly but more consistently prefer the other, we opted for a simple criterion to sort the neurons into two categories for visualization. Adopting more stringent criteria that consider multiple bins may result in neurons that cannot be placed in either category, and we wanted a way to examine the entire pseudo-population. Also, the entire auROC trace is visualized in the heatmap, so potential outliers are not hidden and can be assessed by eye.

      Reviewer #3 (Public review):

      Primary taste cortex neurons show a variety of dynamic response profiles during taste decision-making tasks, reflecting both sensory and decision variables. In the present study, Lang et al. set out to determine how neurons with distinct response profiles contribute to perceptual decisions about taste stimuli.

      The methods, with reference to the behavioral task and electrophysiological recordings/data analysis, are straightforward, solid, and appropriate. The computational model is presented in a clear and conceptually intuitive manner, although the details are outside of my area of expertise.

      The experimental design features a simple 2-alternative forced-choice design that yielded clear psychometric curves across a range of stimuli. In vivo recordings were performed using Neuropixels and yielded an appropriate sample of single neuron responses. The strength of the model lies in the fact that it consists of single neurons whose response profiles mimic those recorded in vivo, and allows neuron-selective manipulation.

      By virtually lesioning specific subsets of neurons in the network, the authors demonstrate that a relatively small population of neurons with specific tuning profiles was sufficient to produce the observed neural dynamics and behavioral responses. This effect was selective as lesioning other responsive neurons did not affect overall response dynamics or performance.

      These findings provide new insight into the relation between the response profiles of single neurons in sensory cortex, their population-level activity dynamics, and the perceptual decisions they inform.

      The approach is particularly innovative as it uses computational modeling to target functionally-defined "cell types", which cannot necessarily be targeted by more conventional genetic approaches.

      We thank the Reviewer for the positive assessment of our study.

      Reviewer #3 (Recommendations for the authors):

      (1) Introduction: I'm missing a clearly stated specific hypothesis and what is predicted on the basis of that hypothesis. What is the alternative?

      The null hypothesis is that single neuron activity patterns, even when clearly structured, do not matter for population activity or behavior. Alternatively, they do matter for these phenomena, and our model supports the alternative hypothesis. We have made this hypothesis clearer in the Introduction.

      (2) Discussion: Much of the text is a recap of the Introduction and Results sections. Please elaborate on the specific insights gained from the findings. The idea that tuned neurons in the sensory cortex are the basis for perception and perceptual decisions concerning the features being represented by those neurons is generally accepted. What the present study adds to this insight could be described more explicitly. On the other hand, the idea that small populations of tuned neurons are responsible for perception of taste/perceptual decisions about taste appears in contrast with previous accounts where stimulus features/decisions are reflected in correlated changes in activity across distributed populations of taste cortical neurons, including ones that are not necessarily tuned or even overtly responsive. How do the present findings relate to this idea?

      This is a very good point about reconciling these findings with past ones that have focused on coordinated changes across ensembles of neurons, i.e., metastable dynamics of internal (hidden) states. There is a brief mention of metastability toward the end of the Discussion, but we agree it deserves elaboration.

      This work does emphasize single unit activity, but in the context of, and as relevant to, population activity. We believe that the findings and frameworks of previous studies and those presented here are compatible rather than mutually exclusive. There is no reason why neurons with the coding patterns we studied here cannot coordinate with others to participate in the formation of different metastable states. The question of which—neurons with specific response profiles, or ensemble activity patterns that may involve these neurons?—is necessary and sufficient for producing perception and behavior during the mixture-based decision-making task is interesting but rather difficult to answer because of the single units’ contribution to both alternatives. One would need to utilize a manipulation that disrupts ensemble coordination without disrupting single unit activity to differentiate between them. We have made these points clearer in the Discussion.

      (3) Results: RNNs were based on data from single sessions -- how many neurons of each tuning type were observed in each session? In particular, there were 23 sessions but only 25 neurons total tuned to choice, suggesting that modelled choice neurons were based on ~1 neuron.

      The revised manuscript includes the session-by-session breakdown of response types for both experiment and model in two supplementary tables (Tables S2 and S4). We note that there are 25 neurons tuned to choice during the last 500 ms of the trial prior to decision, but 114 out of 626 neurons in total are tuned to choice in some time bin in the experimental data.

      (4) Minor: Indicate the time windows used for analysis of stimulus sampling, delay, and choice on the figures.

      The revised manuscript now includes the illustration of sampling and delay windows in Figure 2C-D, since we averaged the values over these windows for use in a 2-way ANOVA. All other figures either are associated with bin-by-bin analyses and have the first central and lateral licks (T and D) indicated, or have the time windows specified (e.g., Figure 4B, which uses [T, T + 0.5 s] and [D - 0.5 s, D]).

    1. Author response:

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

      eLife Assessment

      This study provides valuable insights with solid evidence into altered tactile perception in a mouse model of ASD (Fmr1 mice), paralleling sensory abnormalities in Fragile X and autism. Its main strength lies in the use of a novel tactile categorization task and the careful dissection of behavioral performance across training and difficulty levels, suggesting that deficits may stem from an interaction between sensory and cognitive processes. However, while the experiments are well executed, the reported effects are subtle and sometimes non-significant. The interpretation of results may be overextended given the nature of the data (solely behavioral), the reliance on repeated d′ measures may obfuscate some of the results without clearer psychometric or regressionbased analyses, and the absence of mechanistic, causal, or computational approaches limits the strength of the broader conclusions. The work will be relevant to those interested in autism, cognition, and/or sensory processing.

      We thank the editors for their positive assessment of the data quality and the novelty of our behavioral task, and for pointing out the limitations inherent in behavioral studies.

      We would like to clarify one important point regarding the use of d′ measures. While d′ was included to quantify sensitivity, our conclusions are not based solely on repeated d′ measures. In addition to d′, we analyzed raw behavioral data (correct and incorrect choice rates), and categorization performance was assessed using psychometric curves fitted with logistic regression models. These complementary analyses provide converging evidence and ensure that our interpretations are supported by multiple robust measures.

      In the revised manuscript, we have further strengthened the analyses by including additional regression-based assessments, reporting effect sizes for subtle effects, and refining the statistical methods for clarity and transparency.

      We fully acknowledge that this work is behavioral and does not directly reveal the underlying neural mechanisms. Nonetheless, the translational framework we have developed establishes a robust foundation for future studies. This platform can be directly applied in clinical research on autism and other neuropsychiatric conditions involving sensory-cognitive interactions, and provides a solid basis for subsequent mechanistic, causal, or computational investigations to uncover the neural circuits mediating these effects.

      We greatly appreciate the editors’ and reviewers’ guidance and believe the revisions have clarified and strengthened the manuscript.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study addresses the important question of how top-down cognitive processes affect tactile perception in autism - specifically, in the Fmr1-/y genetic mouse model of autism. Using a 2AFC tactile task in behaving mice, the study investigated multiple aspects of perceptual processing, including perceptual learning, stimulus categorization and discrimination, as well as the influence of prior experience and attention.

      We appreciate the reviewer’s statement highlighting the importance of our study.

      Strengths:

      The experiments seem well performed, with interesting results. Thus, this study can/will advance our understanding of atypical tactile perception and its relation to cognitive factors in autism.

      We thank the reviewer for recognizing the quality of our experiments and the relevance of our findings for understanding tactile perception and cognition in autism.

      Weaknesses:

      Certain aspects of the analyses (and therefore the results) are unclear, which makes the manuscript difficult to understand. Clearer presentation, with the addition of more standard psychometric analyses, and/or other useful models (like logistic regression) would improve this aspect. The use of d' needs better explanation, both in terms of how and why these analyses are appropriate (and perhaps it should be applied for more specific needs rather than as a ubiquitous measure).

      We thank the reviewer for these constructive comments. We acknowledge that aspects of the analyses were previously difficult to follow, and we have reworked the Results section to improve clarity and transparency.

      We would like to emphasize that all d′ measures are complemented by analyses of raw response rates (correct and incorrect choices), ensuring that our interpretations are not solely dependent on this metric. In addition, we applied standard psychometric analyses wherever possible. For the training phase, only two stimulus amplitudes were presented, which precluded the construction of full psychometric curves; however, for the categorization phase, psychometric analyses were feasible and are reported in Figure 3. Specifically, psychometric functions were fitted to the data using logistic regression, allowing us to estimate both categorization bias (threshold) and precision (slope) across stimulus intensities. These analyses revealed no evidence of categorization bias or precision in Fmr1<sup>-/y</sup> mice across stimulus strengths.

      Following the reviewer’s suggestion, we have also added general linear model analyses that account for trial history, providing a complementary perspective on decision-making dynamics. Finally, while the calculation of d′ is detailed in the Methods, we have revised the Results to clearly explain its use and appropriateness in each relevant analysis.

      These revisions aim to provide a clearer, more comprehensive picture of the data while ensuring that all conclusions are supported by multiple complementary measures.

      Reviewer #2 (Public review):

      Summary:

      This manuscript presents a tactile categorization task in head-fixed mice to test whether Fmr1 knockout mice display differences in vibrotactile discrimination using the forepaw. Tactile discrimination differences have been previously observed in humans with Fragile X Syndrome, autistic individuals, as well as mice with loss of Fmr1 across multiple studies. The authors show that during training, Fmr1 mutant mice display subtle deficits in perceptual learning of "low salience" stimuli, but not "high salience" stimuli, during the task. Following training, Fmr1 mutant mice displayed an enhanced tactile sensitivity under low-salience conditions but not high-salience stimulus conditions. The authors suggest that, under 'high cognitive load' conditions, Fmr1 mutant mouse performance during the lowest indentation stimuli presentations was affected, proposing an interplay of sensory and cognitive system disruptions that dynamically affect behavioral performance during the task.

      Strengths:

      The study employs a well-controlled vibrotactile discrimination task for head-fixed mice, which could serve as a platform for future mechanistic investigations. By examining performance across both training stages and stimulus "salience/difficulty" levels, the study provides a more nuanced view of how tactile processing deficits may emerge under different cognitive and sensory demands.

      We thank the reviewer for emphasizing the strengths of our task design and analysis approach, and we appreciate that the potential of this platform for future mechanistic investigations is recognized.

      Weaknesses:

      The study is primarily descriptive. The authors collect behavioral data and fit simple psychometric functions, but provide no neural recordings, causal manipulations, or computational modeling. Without mechanistic evidence, the conclusions remain speculative.

      We thank the reviewer for the careful reading of our manuscript and for these constructive comments. We agree that our study is purely behavioral, and we appreciate the opportunity to clarify the scope and interpretation of our findings. The primary goal of this work was to characterize behavioral patterns during tactile discrimination and categorization in a translationally relevant mouse model of autism.

      Although we did not include direct neural recordings, causal manipulations, or computational modeling, our analyses combining choice behavior, sensitivity measures from signal detection theory, psychometric curves, and regression-based models of trial history provide a detailed and robust characterization of perceptual learning, stimulus discrimination, categorization, and the interplay of cognitive processes with tactile perception. The manuscript has been revised to explicitly state that our conclusions are behavioral, emphasizing that this work establishes a foundation for future studies aimed at elucidating the neural and circuit mechanisms underlying these sensory–cognitive interactions.

      Second, the authors repeatedly make strong claims about "categorical priors," "attention deficits," and "choice biases," but these constructs are inferred indirectly from secondary behavioral measures. Many of the effects are based on non-significant trends, and alternative explanations (such as differences in motivation, fatigue, satiety, stereotyped licking, and/or reward valuation) are not considered.

      Alternative explanations for our findings including differences in motivation, fatigue, satiety, stereotyped licking, or reward valuation were carefully considered. As described in the Methods, only testing sessions with >70% correct performance on the training stimuli (12 µm and 26 µm) were included, excluding sessions with reduced motivation, fatigue, satiety, or stereotyped licking that could confound performance on low- or high-salience stimuli.

      Although differences in reward valuation could affect learning speed, we observed no genotype differences in training duration (Fig. 1B-D, Fig. S1C-D). Sessions with disengagement were analyzed only during epochs of active task performance (information added to the revised Methods section, lines 619-620). Reward-driven choice biases were unlikely, as no genotype differences were observed in categorization bias (Fig. 3F) and GLM analyses confirmed that previous reward outcome did not affect current choices (Fig. 4D).

      Finally, altered reward valuation could increase miss rates. Elevated miss rates in Fmr1<sup>-/y</sup> mice were restricted to the lowest-intensity stimulus (12 µm) under high cognitive load, demonstrating a salience- and context-specific effect inconsistent with generalized motivational or reward deficits. The Discussion has been updated to clarify these points and delimit the scope of our interpretations (lines 483-499).

      Third, the mapping of the behavioral results onto high-level cognitive constructs is tenuous and overstated. The authors' interpretations suggest that they directly tested cognitive theories such as Load Theory, Adaptive Resonance Theory, or Weak Central Coherence. However, the experiments do not manipulate or measure variables that would allow such theories to be tested. More specific comments are included below.

      This was not done intentionally. References to Load Theory were meant to provide conceptual inspiration for assessing attention in high cognitive load conditions during categorization, rather than to indicate a formal test. Moreover, we do not claim to have tested the Weak Central Coherence theory, although our results suggest reduced facilitation of across- category discrimination. Finally, we agree that citing Adaptive Resonance Theory, which is grounded in artificial neural network models, could be misleading, and we have revised the text accordingly.

      (1) The authors employ a two-choice behavioral task to assess forepaw tactile sensitivity in Fmr1 knockout mice. The data provide an interesting behavioral observation, but it is a descriptive study. Without mechanistic experiments, it is difficult to draw any conclusions, especially regarding top-down or bottom-up pathway dysfunctions. While the task design is elegant, the data remain correlational and do not advance our mechanistic understanding of Fmr1-related sensory and/or cognitive alterations.

      We thank the reviewer for this comment and agree that our study is purely behavioral and does not provide direct mechanistic evidence for top-down pathway dysfunction. In the first version of the manuscript, the term “top-down” was used at the behavioral level, referring to the influence of higher-order cognitive processes (e.g., categorization, attention, sensory and choice history integration) on tactile perception, rather than to imply specific neural circuits.

      We acknowledge that identifying the neural pathways underlying these effects would require extensive mechanistic experiments, including identifying the specific top-down pathway that modulates the influence of categorization on discrimination without directly altering categorization itself and performing pathway-specific recordings and manipulations. Such work represents a substantial mechanistic research program beyond the scope of the present study.

      To clarify that our study does not provide insights into the neural underpinnings of the studied behavioral processes, we have revised the manuscript, removing the term “top-down” or replacing it with “higher-order processes” where appropriate. We also explicitly noted that future work using neural recordings or causal manipulations will be needed to uncover the neural underpinnings of these behavioral phenomena (lines 508-510).

      (2) The conclusions hinge on speculative inferences about "reduced top-down categorization influence" or "choice consistency bias," but no neural, circuit-level, or causal manipulations (e.g., optogenetics, pharmacology, targeted lesions, modeling) are used to support these claims. Without mechanistic data, the translational impact is limited.

      We recognize that terms such as “reduced top-down categorization influence” and “choice consistency bias” are derived from behavioral observations. However, we respectfully note that these behavioral inferences are widely used in clinical studies to characterize cognitive tendencies (Soulières et al., 2007; Feigin et al., 2021) and are not inherently speculative.

      The translational impact of our work lies in the development of a robust behavioral platform that allows precise dissection of tactile perception and cognitive influences in a manner directly comparable to clinical studies. While we agree that neural, circuit-level, or causal manipulations would provide valuable mechanistic insight, the current study establishes a foundational behavioral framework that can guide and inform future investigations into the underlying neurobiological substrates.

      To ensure clarity, we have revised the manuscript throughout to explicitly indicate that all conclusions are based on behavioral measures and do not imply mechanistic evidence.

      (3) Statistical analysis:

      (a) Several central claims are based on "trends" rather than statistically significant effects (e.g., reduced task sensitivity, reduced across-category facilitation). Building major interpretive arguments on non-significant findings undermines confidence in the conclusions.

      We chose to present both statistically significant effects and trends to ensure transparency and to highlight that commonly used aggregate measures, such as d′, can sometimes obscure meaningful underlying patterns. In the text, p-values between 0.05 and 0.1 are described as trends without over-interpreting their significance. To further support interpretation, we have now computed effect sizes (Hedges’ g) for all subtle effects. In the revised manuscript, all interpretations of non-significant effects have been reworded to avoid overstatement.

      (b) The n number for both genotypes should be increased. In several experiments (e.g., Figure 1D, 2E), one animal appears to be an outlier. Considering the subtle differences between genotypes, such an outlier could affect the statistical results and subsequent interpretations.

      The number of mice used per genotype is consistent with standard practices in behavioral studies of sensory processing. To complement statistical analyses and account for small sample sizes, we have calculated effect sizes (Hedges’ g) for all subtle or trend-level effects (p ≈ 0.05–0.1), providing a measure of effect magnitude independent of sample size.

      As the reviewer correctly noted, no animals were excluded as outliers, since observed variability reflects true biological differences rather than experimental or technical errors. In the revised manuscript, we re-examined all datasets for potential outliers, and when identified, analyses were performed both with and without the data point. Any results sensitive to single animals are explicitly reported. This procedure is now detailed in the Methods section (lines 675-679).

      (c) The large number of comparisons across salience levels, categories, and trial histories raises concern for false positives. The manuscript does not clearly state how multiple comparisons were controlled.

      We thank the reviewer for highlighting this important point. To control for false positives arising from multiple comparisons, we applied the Bonferroni correction. This information has been added to the Methods section (line 682) to ensure transparency and reproducibility of all statistical tests.

      (d) The data in Figure 5, shown as separate panels per indentation value, are analyzed separately as t-tests or Mann-Whitney tests. However, individual comparisons are inappropriate for this type of data, as these are repeated stimulus applications across a given session. The data should be analyzed together and post-hoc comparisons reported. Given the very subtle difference in miss rates across control and mutant mice for 'low-salience' stimulus trials, this is unlikely to be a statistically meaningful difference when analyzed using a more appropriate test.

      We thank the reviewer for raising this point, as this was not done intentionally. In the revised manuscript, miss rates for high- and low-salience stimuli were reanalyzed using a mixedeffects linear model, which appropriately accounts for repeated measurements within sessions (Fig. 5; Results section: lines 320-340). This analysis confirmed that Fmr1<sup>-/y</sup> mice exhibit increased miss rates specifically at the 12 µm amplitude, with the effect disappearing at higher low-salience amplitudes (18 µm). Post-hoc comparisons with Bonferroni correction revealed a strong trend for increased misses at 12 µm (T-test: t = -2.8437, p = 0.058, Hedge’s g = 1.23), while no significant differences were found at other amplitudes. The Methods section has been updated to detail this statistical approach for analyzing miss rates (lines 686687).

      (4) Emphasis on theoretical models:

      The paper leans heavily on theories such as Adaptive Resonance Theory, Load Theory of Attention, and Weak Central Coherence, but the data do not actually test these frameworks in a rigorous way. The discussion should be reframed to highlight the potential relevance of these frameworks while acknowledging that the current data do not allow them to be assessed.

      As mentioned above, our goal was not to directly test theoretical frameworks such as Adaptive Resonance Theory, Load Theory of Attention, or Weak Central Coherence, but rather to provide a context for interpreting our behavioral findings. In the revised manuscript, we have removed references to the Load Theory from the Results section and reframed the Discussion to emphasize that our results are consistent with certain predictions from these cognitive theories, without implying that the experiments directly assessed them. This clarifies that the interpretations are based on observed behavioral patterns, while still acknowledging the potential relevance of these frameworks to better understand tactile perception and cognition in autism.

      Reviewer #3 (Public review):

      Summary:

      Developing consistent and reliable biomarkers is critically important for developing new pharmacological therapies in autism spectrum disorders (ASDs). Altered sensory perception is one of the hallmarks of autism and has been recently added to DSM-5 as one of the core symptoms of autism. Touch is one of the fundamental sensory modalities, yet it is currently understudied. Furthermore, there seems to be a discrepancy between different studies from different groups focusing on tactile discrimination. It is not clear if this discrepancy can be explained by different experimental setups, inconsistent terminology, or the heterogeneity of sensory processing alterations in ASDs. The authors aim to investigate the interplay between tactile discrimination and cognitive processes during perceptual decisions. They have developed a forepaw-based 2-alternative choice task for mice and investigated tactile perception and learning in Fmr1-/y mice.

      Strengths:

      There are several strengths of this task: translational relevance to human psychophysical protocols, including controlled vibrotactile stimulation. In addition to the experimental setup, there are also several interesting findings: Fmr1-/y mice demonstrated choice consistency bias, which may result in impaired perceptual learning, and enhanced tactile discrimination in low-salience conditions, as well as attentional deficits with increased cognitive load. The increase in the error rates for low salience stimuli is interesting. These observations, together with the behavioral design, may have a promising translational potential and, if confirmed in humans, may be potentially used as biomarkers in ASD.

      We appreciate the reviewer’s positive assessment regarding our study’s translational value and the importance of our behavioral findings.

      Weaknesses:

      Some weaknesses are related to the lack of the original raster plots and density plots of licks under different conditions, learning rate vs time, and evaluation of the learning rate at different stages of learning. Overall, these data would help to answer the question of whether there are differences in learning strategies or neural circuit compensation in Fmr1-/y mice. It is also not clear if reversal learning is impaired in Fmr1-/y mice.

      We thank the reviewer for these helpful suggestions. We agree that visualizing behavioral patterns, such as raster and density plots of licks, as well as learning rate over time, provides additional insights into learning dynamics. In response, we have added these analyses to the revised manuscript (Fig. S1, Fig. S2), which illustrate both individual and group-level learning trajectories and trial-by-trial licking patterns.

      There was no assessment of reversal learning in Fmr1<sup>-/y</sup> mice in this study. While this is an interesting and important question, and is motivated by previous preclinical and clinical findings, it falls outside the scope of the current manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Main Comments

      (1) This study addresses the important question of how top-down cognitive processes affect tactile perception in autism - specifically, in the Fmr1-/y genetic mouse model of autism vs. WT controls. Using a 2AFC tactile task in behaving mice, the study investigated multiple aspects of perceptual processing, including perceptual learning, stimulus categorization and discrimination, as well as the influence of prior experience and attention. The experiments seem well performed, with interesting results. I found certain aspects of the analysis not clearly explained, which made it difficult at times to understand.

      Please see specific details in the comments below.

      (2) To measure sensitivity, the authors present many comparisons of d' - sometimes between pairs of stimuli (or sometimes even for a single stimulus level).

      (a) Firstly, the calculation of d' for a single stimulus value is unclear (because the same proportion of high/low choices for a given stimulus can result from shifts in bias/criterion).

      We agree with the reviewer that calculating d′ for a single stimulus conflates sensitivity with response bias/criterion differences. For this reason, the panels showing d′ for individual stimulus amplitudes during training (Fig. 1F and 1G in the original manuscript) have been removed from the manuscript.

      In addition, we revised our d’ (Fig. 1E) and criterion calculations (Fig. 2A), treating the high amplitude stimuli as “signal” and low amplitude stimuli as “noise”, based on the Signal Detection Theory. The formulas used in the revised manuscript take into account correct responses during high amplitude stimuli and wrong responses during low amplitude stimuli to calculate the sensitivity and bias of the mice during discrimination in the training period.

      Sensitivity (d′) is now computed as:

      d' = z(lick right|high amplitude stimulus) - z(lick right|low amplitude stimulus)

      and the criterion (c) as:

      c = −1/2 × [z(lick right / high amplitude) + z(lick right / low amplitude)]

      (b) Secondly, while calculating d' makes sense for comparing two stimulus levels (like in the training condition), in the test condition (with a spread of stimuli), this becomes a little tedious - at times difficult to follow and unclear.

      I would have thought that sensitivity (at least for overall performance) would be better compared using data from all the stimuli - e.g. either using:

      (i) the sigma of the psychometric curve (although the downside of that approach is that it ignores history effects), or

      (ii) a logistic regression for the choices, given the stimuli, where the weights assigned to the stimulus magnitude indicate sensitivity (the advantage of that approach is that history effects, like the previous trials/choices can be used as regressors in the model). Accordingly, it can simultaneously also quantify the history effects. This could even be expanded to a GLMM (mixed effects for different mice).

      We thank the reviewer for this very valuable feedback. Indeed, during the testing phase, we calculated sensitivity d’ to probe the overall categorization sensitivity (Fig. 3H).

      (i) This analysis was only complementary to the psychometric curves (fitted on the rightward lick rate for each stimulus amplitude using a general linear model – Fig. 3A). As the reviewer proposes, we had calculated the sigma of the psychometric curve (Fig. 3G, slope) to assess categorization precision. Sensitivity calculations have also now been revised using the aforementioned formula (d' = z(lick right|high amplitude stimulus) - z(lick right|low amplitude stimulus).

      (ii) To incorporate history effects, we implemented generalized linear models (GLMs) with a binomial link function to predict high-salience licks (right-lick choices) based on the current stimulus, trial history, genotype, and their interactions. A main-effects model included current stimulus, previous stimulus, previous outcome, previous choice, and genotype, followed by interaction terms to assess genotype-specific modulation of history effects. These analyses are now presented in the new Figure 6.

      The resulting coefficients are shown in Fig. 6A. As expected, decisions were primarily driven by current stimulus amplitude (Fig. 6A, B). Both genotypes displayed a tendency to repeat previous choices (Fig. 6A, C), while previous reward outcomes did not influence current choice (Fig. 6A, D). Notably, stimulus amplitude history showed genotype-specific effects: WT mice were negatively influenced by the previous stimulus, whereas Fmr1<sup>-/y</sup> mice remained unaffected (Fig. 6A, E).

      To clearly visualize these findings, we plotted psychometric curves and marginal effects accounting for current stimulus, previous choice, previous outcome, and previous stimulus (Fig. 6B-E). These analyses are now fully integrated into the Methods (lines 688-702), Results (Fig. 6, lines 341-369), and Discussion (lines 469-479) sections of the revised manuscript.

      (3) I find some of the terminology used confusing/misleading:

      (a)The term "Categorization thresholds" can be misleading - in psychometric curves, "thresholds" often refer to the sigma (SD) of the fitted curve used to measure sensitivity (inversely related). Here, I think that the meaning is in terms of the PSE/ criterion. Perhaps the terminology can be improved to prevent confusion on this matter. E.g., I think that here the authors mean a measure of bias/criterion/PSE or similar. Correct? Not really a perceptual "threshold".

      We thank the reviewer for pointing this out. In our analysis, the term “threshold” referred to the inflection point (i.e., the midpoint parameter μ) of the fitted logistic psychometric function used to categorize high- versus low-amplitude stimuli. We termed it “threshold” in the categorization of high and low amplitude stimuli. We agree with the reviewer that we could also use the term “Categorization bias”. We originally opted to avoid this term, not to confuse the readers when referring to the criterion (signal detection theory) as “response bias”. However, seeing as the term “threshold” may be confusing as well, we adopted the term “Categorization bias” in the updated version of the manuscript (lines 282, 284, 637-638, 785, Fig. 3F).

      (b) Similarly, I think that "Categorization accuracy" can be misleading when describing the slope of the psychometric curve. Performance could have a steep slope but still be quite inaccurate (e.g., if there is a big bias). Perhaps "precision" is a better description of the slope?

      We thank the reviewer for this suggestion. The slope of the psychometric curve is often referred to as “sensitivity” in the literature (Carandini and Churchland, 2014), but in our original manuscript we used the term “accuracy” to avoid confusion with the d′ measure from signal detection theory. We have revised the manuscript and Figures with the term “precision” as the reviewer suggested (lines 282, 284, 637-638, 786, Fig. 3G).

      Minor Comments

      (1) Abstract: "determines how autistic individuals engage" - there are other factors too. So, I think that "determines" is a little strong. Perhaps "influences" is more appropriate.

      We have incorporated the reviewer’s suggestion (line 7).

      (2) Figure 1 F, G. On the one hand, d' is defined as "sensitivity (d') in discriminating between high- and low-salience stimuli" - that seems to make sense. But then d' is also calculated and presented for each salience level on its own. How was this done? Namely, percent correct (or proportion of choices high/low salience) could be affected by criterion shifts as well as sensitivity. This makes calculating the d' for a single (low or high) salience stimulus ambiguous. So, how do these authors make this conclusion?

      We agree that calculating d′ for a single stimulus amplitude is ambiguous, because the resulting value conflates true stimulus sensitivity with shifts in response bias or criterion. Consequently, all analyses and figures reporting d′ for individual high- or low-salience stimuli (e.g., Figures 1F and 1G) have been removed from the revised manuscript.

      In the updated analyses, d′ is calculated only across high- versus low-salience stimuli, following standard Signal Detection Theory procedures, ensuring that it reflects true discriminability between the two categories (Methods, line 631; Figure 1E).

      (3) "Our results showed comparable correct choice rates in Fmr1-/y and WT mice (Fig. 1H), for both high- and low-salience stimuli (Fig. S1C-D). In contrast, Fmr1-/y mice presented a significantly higher rate of incorrect choices (Fig. 1I)." - aren't correct choices and incorrect choices complementary (i.e., 1-x) in a 2AFC? How is this possible?

      We thank the reviewer for pointing this out. Correct and incorrect choices are complementary at the single-trial level if miss trials are excluded. However, in our analyses, correct and incorrect choice rates were calculated by normalizing the number of correct or incorrect responses to the total number of trials (including misses), which breaks this complementarity and contributes to the differences observed in Fig. 1H–I. This was clarified in the Methods section (lines 616-617). Moreover, incorrect responses were less frequent than correct ones and are thought to reflect lapses, response bias, and impulsive responding rather than sensory performance, making them more sensitive to genotype-dependent differences in behavioral control. Based on this concept, we further examined whether incorrect choices were preferentially associated with specific stimulus amplitudes and assessed response bias and prior effects.

      (4) The conclusion that "they showed a strong trend toward reduced sensitivity for lowsalience stimuli (Fig. 1G)" has a confound - it could be that there was a criterion shift (rather than differences in sensitivity)?

      We agree with the reviewer that the previously reported trend in sensitivity for low-salience stimuli could reflect a criterion shift rather than true differences in sensory sensitivity. Because sensitivity estimates for individual stimulus amplitudes are not well-defined in a 2AFC framework, we have removed the sensitivity calculations for high- and low-salience stimuli considered independently. Instead, we now present salience-specific differences using correct and incorrect response rates for each stimulus amplitude, which more directly capture performance differences without assuming changes in sensory sensitivity (Fig. 1G-I, S1E-F).

      (5) Figure 3D, E - I stumbled over this in comparison to Figure 3B, C. That is because (a) In D and E, the authors compare right-lick responses (reporting high salience) to stimuli of 12 μm and 14 μm amplitude (Figure 3D) and low-salience lick rates for the same (Figure 3E). I would have thought that these approaches are simply complementary (1-x) - see related minor question above/below. So, what is the advantage of presenting them both?

      We presented both panels to clarify the source of the observed differences in performance. Specifically, showing right-lick responses (reporting high-salience choices) alongside low salience lick rates allows us to distinguish whether reduced high-salience reporting arises from an actual shift in choice (e.g., increased leftward licking) versus an increase in miss trials at the lowest amplitude (12 µm). By presenting both, we can demonstrate that the effect is primarily driven by an increase in leftward choices rather than by missed responses, providing a more precise interpretation of behavioral changes. The complementary analysis for leftward choices has now been moved to the supplemental material (Fig. S5A) and the reason for this analysis has been clarified in the Results (lines 275-276).

      (b) In B and C, the authors compare two differences in stimulus magnitude (2 and 4 μm), but in Figure 3D and E, only one difference (2 μm) from two perspectives. I was expecting a comparison with stimuli differing by 4 μm in amplitude (comparable to the high stimulus comparison of 26 μm vs. 22 μm stimuli).

      We have indeed analyzed the 12 μm versus 16 μm stimulus pair, which corresponds to a 4 μm difference and is reliably discriminated by both genotypes. In the original manuscript, we did not include this comparison because of the differences already seen at a 2 μm amplitude difference. Based on the reviewer’s suggestion, we have now included the 12 μm vs. 16 μm comparison in the revised manuscript (Results, lines 270-272; Fig. 3E) to provide a complementary perspective consistent with the high-salience comparisons (26 μm vs. 22 μm).

      (c) "Sensitivity d' for high- and low-salience stimuli was calculated based on the Correct and Incorrect choice rate for high- and low-salience stimuli respectively." How were trials for which the animal did not respond taken into account? Were these part of the denominator? Or were these excluded when calculating proportions? (related to the Q regarding Figure 3 D,E above).

      Indeed, the Miss trials were part of the denominator. This is now clarified in the Methods section (line 631).

      (d) "c = d'(high)- d'(low)." - I did not understand this fully. There were several high and several slow stimuli - so how were these calculated? Pooled for high and pooled for low? Per stimulus difference?

      This was indeed calculated for pooled high and low amplitudes during testing. In the revised manuscript, criterion c has been recalculated based on the average correct high rate (for stimuli of 20-26 µm amplitude) and average incorrect low rate (for stimuli of 12-18 µm amplitude), using the same formula as in the analysis of the training dataset:

      c = −1/2 × [z(lick right / high amplitude) + z(lick right / low amplitude)]

      Pooling across amplitudes allows us to obtain a single summary measure of response bias toward the right lickport, independent of stimulus discriminability. This approach is consistent with standard signal detection theory practices when multiple stimulus levels are present.

      If the inter-trial interval is 5-10s, how is a 5s timeout a punishment?

      The 5 s timeout serves as a punishment by temporarily delaying access to the next trial and potential reward, thereby reducing the overall reward rate. Even though the inter-trial interval (ITI) varies between 5 and 10 s, the timeout increases the effective delay before the next opportunity to earn a reward, discouraging incorrect responses. This is consistent with standard operant conditioning procedures, where brief timeouts act as negative consequences without being overly severe. Across most trials, the timeout effectively reduces expected reward rate, though its impact is minimal when the ITI is already long.

      Reviewer #2 (Recommendations for the authors):

      Task-related questions:

      (1) What evidence is there that the 40 Hz, 12 μm stimulus is "low salience: while the 40 Hz, 26 μm stimulus is "high salience"? This seems like an arbitrary distinction without showing sensitivity curves across a group of animals. Better definitions of the stimuli and the actual forces applied are necessary.

      We thank the reviewer for this comment. Based on our previous work (Semelidou et al., bioRxiv; Accepted in Advanced Science), both the 40 Hz, 12 µm and 40 Hz, 26 µm stimuli are clearly suprathreshold. In the present study, however, stimulus salience is defined in a relative and operational manner within this suprathreshold range.

      Specifically, analysis of miss trials (Fig. S3E) shows that the 40 Hz, 12 μm stimulus consistently elicited a higher proportion of missed responses compared to the 40 Hz, 26 μm stimulus across animals, indicating lower behavioral performance for the lower-amplitude stimulus. We therefore refer to the 12 μm stimulus as “low salience” and the 26 μm stimulus as “high salience” to denote relative differences in perceptual strength and attentional engagement within the suprathreshold range, rather than differences in detectability or absolute sensory sensitivity. This definition has been clarified in the Methods (lines 583-587) and Results sections (lines 115-119; lines 225-227).

      (2) Sensitivity curves/detection thresholds for each mouse should be included in the study.

      We thank the reviewer for this suggestion. Sensitivity curves and detection thresholds for low-amplitude and low-frequency vibrotactile forepaw stimulation have been systematically characterized in our previous study (Semelidou et al., bioRxiv, Accepted in Advanced Science). In that work, we demonstrated that stimuli with similar amplitudes and even lower frequency (10Hz) than those used in the present study are reliably detectable by mice, confirming that both the 40 Hz, 12 µm and 40 Hz, 26 µm stimuli fall within the suprathreshold range.

      Because the goal of the present study was not to determine absolute detection thresholds but rather to examine discrimination and categorization performance within a suprathreshold range, we did not re-establish full psychometric detection curves for each mouse.

      We have clarified this rationale in the revised manuscript (Results, lines 108-113; Methods, lines: 577-579).

      (3) What force is being applied during stimulus presentations? 12 or 26 μm does not provide enough information about the stimuli applied. What are the physical parameters of the indenter? What material, what tip size?

      Vibrotactile stimuli were delivered to the forepaw via a piezoelectric actuator. A 12.7 mm stainless steel post (ThorLabs) was mounted on the actuator vertically and a 0.6 mm stainless steel rod (ThorLabs) was clamped horizontally onto this post. The horizontal rod served as the contact bar on which the animal rested its right forepaw.

      Stimuli were sinusoidal vibrations at 40 Hz with peak-to-peak displacements of 12 μm (low salience) or 26 μm (high salience). The actuator displacement was calibrated prior to experiments to ensure accurate vibration amplitudes.

      Animals were positioned in the setup to ensure stable and consistent forepaw contact with the rod delivering the vibration. Pilot experiments with an extra sensor to monitor forepaw placement confirmed that the mice did not remove their forepaws from the bar before stimulus delivery. All this information is now added in the Methods section (lines 552-555, 580-582).

      (4) Only one vibration stimulus was used (40 Hz) - this preferentially activates specific subsets of low-threshold mechanoreceptors and not others. A range of vibrotactile stimuli (with varying frequencies) would be more useful. From this limited range of stimuli, it is difficult to assess whether the findings would extrapolate to other types of stimuli.

      We agree that using a single vibration frequency limits the generalization of our findings across the full range of mechanoreceptor subtypes and vibrotactile stimulus conditions. In the present study, we deliberately focused on amplitude discrimination within the flutter range (<50 Hz), as this frequency preferentially activates subsets of low-threshold mechanoreceptors relevant for flutter perception and is commonly used in clinical studies of tactile amplitude discrimination (Puts et al., 2014, 2017; Asaridou et al., 2022). By holding frequency constant and varying only amplitude, we were able to isolate amplitude-dependent perceptual and decision-making processes while minimizing frequency-dependent variability and to facilitate direct translational comparisons with human studies using similar flutter stimuli.

      We acknowledge, however, that extending the paradigm to additional, high frequencies would help determine whether the observed effects generalize across mechanoreceptor channels. We have now added this point as a future direction in the Discussion section (lines 510-514).

      (5) The methods indicate that during the implementation of the water-restriction protocol, mice had access to a solid water supplement in their home cage. How did they control for how much water supplement was consumed by each mouse before the testing sessions?

      We thank the reviewer for raising this point. The solid water supplement was divided into premeasured individual portions, and each mouse received its allotted amount only after the daily training/testing session. Daily body weight measurements were used to monitor hydration and ensure that all animals maintained stable body weight. If necessary, supplemental water was adjusted to maintain animals within the approved weight range. This procedure is now described in the Methods section (line 567-571).

      (6) A control version of the test, perhaps using a different sensory modality, would be useful for making conclusions.

      We agree that testing other sensory modalities would provide a useful control for assessing the generalizability of the observed effects. However, in the present study, we intentionally focused on the tactile modality, as touch has been shown to play a critical role in autism across sexes and predict other core behavioral symptoms. This makes touch particularly relevant for investigating translational mechanisms in this model.

      By specifically targeting tactile perception, we aimed to investigate the link between sensory discrimination, decision-making, and cognitive modulation within a modality that is strongly implicated in autism. Previous studies in autistic individuals have demonstrated similar interactions between cognitive processes and perceptual decision-making in the visual domain, suggesting that such effects may not be modality-specific. Nevertheless, extending this paradigm to additional sensory systems would be valuable to directly test whether comparable cognitive influences on perception generalize across modalities. We have now incorporated this perspective as a future direction in the Discussion section (lines 514-518).

      Reviewer #3 (Recommendations for the authors):

      There are several questions:

      (1) It is important to show stimulus intensity-response curves representing tactile responses for both WT and Fmr1-/y mice.

      We thank the reviewer for this important comment. Detection sensitivity curves for lowamplitude and low-frequency vibrotactile stimulation of the forepaw have been characterized in detail in our previous study (Semelidou et al., bioRxiv; now accepted in Advanced Science). In that work, we showed that stimuli at or above 8 µm amplitude and 10Hz frequency are reliably detected by both WT and Fmr1<sup>-/y</sup> mice.

      Based on these findings, the current study employed vibrotactile stimuli at a higher frequency (40 Hz) and amplitudes of 12 µm and above, ensuring that all stimuli were well within the suprathreshold range for both genotypes. This experimental choice was made to specifically probe discrimination, categorization, and decision-making processes, rather than basic sensory detection. As a result, the behavioral effects reported here cannot be attributed to differences in stimulus detectability.

      We have clarified this rationale in the revised manuscript to make explicit that the absence of full intensity-response curves in the current study reflects a deliberate focus on suprathreshold perceptual and cognitive processes rather than sensory threshold differences (Results, lines 108-113; Methods, lines: 577-579).

      (2) There is no difference in the time it takes to learn the task between WT and Fmr1-/y mice. But how does the learning rate curve look? Is there a difference in the slope between WT and Fmr1-/y early vs late into learning?

      We thank the reviewer for this suggestion. To directly address whether learning dynamics differed between genotypes, we analyzed learning curves across training.

      We first computed the correct choice rate per day for each animal (Fig. S2A) and fit a mixedeffects model including training day, genotype, and their interaction. This analysis revealed no genotype differences in baseline performance or learning rate with minimal Genotype × Day interaction (Fig. S2A-top, Fig. S2C).

      We additionally computed the slope of the learning curve for each individual, which also showed no difference across genotypes (Fig. S2B). In addition, within-animal day-to-day performance variability was also comparable across groups (Fig. S2A-bottom, S2D).

      These analyses indicate that WT and Fmr1<sup>-/y</sup> mice exhibit similar learning trajectories during training. The learning curves are now included in Figure S2, described in the Results (lines 140–151) and detailed in the Methods (lines 644-658).

      (3) It would be useful to see raster plots of licks for different trials and the corresponding lick density plots for early vs late trials.

      We thank the reviewer for this suggestion. To visualize trial-by-trial behavior, we included example lick traces from an early 100-trial session and a late 100-trial session, alongside the corresponding raster plots of licks (Fig. S1A–B).

      (4) Consistent with the first question, examples of intermediate learning stages would help gain more insight into how both WT and Fmr1-/y mice learn.

      In line with the reviewer’s suggestion, we examined whether WT and Fmr1<sup>-/y</sup> mice showed different performance during intermediate stages of learning. To this end, we defined the middle three days of the training period of each animal as the intermediate learning phase. We compared both the mean correct-choice rate and individual learning slopes across this interval. Statistical analyses revealed no significant genotype differences in either measure, indicating comparable performance and learning dynamics during the intermediate phase of training (lines 152-156).

      (5) How does the learning rate change with increased cognitive load for both WT and Fmr1-/y mice?

      We thank the reviewer for this question. While our experimental design did not include a manipulation of cognitive load during the learning phase itself, we assessed whether increased cognitive load affected performance by analyzing behavior on the first day of testing, when animals were required to categorize and discriminate among a larger set of stimuli compared to training.

      Using performance on the training stimuli during this first testing session as a proxy, we found no significant difference between WT and Fmr1<sup>-/y</sup> mice in correct choice rate (Author response image 1). This indicates that increased cognitive load did not differentially affect performance on familiar stimuli across genotypes at this stage.

      Because this analysis does not reflect learning rate per se, but rather performance under increased task demands after learning had already occurred, we did not incorporate it into the main Results section. Instead, it is presented here to directly address the reviewer’s question.

      Author response image 1.

      Correct choice rate for the 12 µm and 26 µm stimuli during the first day of testing when the cognitive load is high.

      (6) How does the learning rate change if the sensory stimuli are more challenging for both WT and Fmr1-/y to detect?

      We thank the reviewer for this question. In the present study, animals were deliberately trained using well-separated, suprathreshold low- and high-salience stimuli to ensure reliable stimulus detection and to avoid confounding learning rate with perceptual difficulty or discrimination limits.

      A recent study (Heimburg et al., 2025) has shown that learning is slower when the difference between the two training stimuli is reduced. Based on these results, we would expect that decreasing the separation between low- and high-salience stimuli would similarly increase training duration for both WT and Fmr1<sup>-/y</sup> mice, since our results do not indicate any discrimination or categorization deficits in the mouse model of autism. However, directly testing how stimulus difficulty modulates learning rate would require a dedicated manipulation of stimulus spacing during training and was beyond the scope of the current study.

      Editor's note:

      Should you choose to revise your manuscript, if you have not already done so, please include full statistical reporting including exact p-values wherever possible alongside the summary statistics (test statistic and df) and, where appropriate, 95% confidence intervals.

      These should be reported for all key questions and not only when the p-value is less than 0.05 in the main manuscript.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      __ __We thank all reviewers for the valuable feedback and critical insight on our study. We acknowledge the concern that the manuscript, in its initial form, appeared descriptive and did not provide the mechanistic insight inferred from the current data. In the revised manuscript, we will (i) more clearly delineate what mechanistic inferences can be drawn from the existing data, (ii) expand our discussion of the caspase-independent mechanisms, and (iii) incorporate additional experiments/analyses aimed at identifying downstream effectors that mediate the observed phenotypes. In this revision plan, we have included six new figures addressing some of the major issues raised by reviewers.

      1. Specifically, to address questions about mechanistic insight, we generated stable ACSL1:HaloTag expressing hESCs. Currently presented as Figure 1A for reviewers____. __ACSL1 is a critical enzyme that catalyzes the first step of fatty acid oxidation at the outer mitochondrial membrane. Our previous analysis and work from the Opferman lab demonstrated that ACSL1 contains a BH3-like domain. Thus, we examined the effects of MCL-1 inhibition on the mitochondrial localization of this enzyme. Our findings pinpoint that MCL-1 inhibition is causing the displacement of ACSL1 from the mitochondria (__Figures 1B-C for reviewers). Our interpretations of the effects of MCL-1 inhibition are 2-fold: 1) as we show in our data, MCL-1 inhibition causes disruption of the mitochondrial cristae, altering the microenvironment for fatty acid oxidation, and 2) as seen in cancer cells, the MCL-1 inhibitor may also displace ACSL1 from the mitochondria. In the new version of the manuscript, we will focus on these 2 mechanisms as mechanistic outcomes of MCL-1 inhibition.
      2. We have included data of cells treated with Perhexilin (CPT1/2 inhibitor), and Etomoxir (CPT1a inhibitor) (Figure 2 for reviewers). This experiment determines whether direct perturbation the FAO pathway mimics the effects of the MCL-1i.
      3. We have assayed the effects of MCL-1 inhibition on oxygen consumption rates in NPCs. Currently presented as Figure 3 for reviewers.
      4. We will perform MCL-1:MICOS proximity ligation assays and/or immunoprecipitation assays to determine whether MCL-1 inhibitors disrupt the association of MCL-1 with MICOS. Preliminary data suggesting an association (albeit, very weak) are shown in Figure 4 for reviewers. __Reviewer #1____ (Evidence, reproducibility and clarity (Required)): __

      Summary: This study claims that beyond its canonical anti-apoptotic function, MCL-1 has essential non-apoptotic roles in human neurodevelopment. Pharmacologic inhibition of MCL-1 in human neural stem cells disrupts mitochondrial inner membrane architecture by destabilizing cristae and the OPA1-MICOS complex, leading to swollen mitochondria with disorganized cristae. These structural defects impair fatty acid oxidation and lipid droplet homeostasis, linking cristae integrity to metabolic competence. Independently of apoptosis or proliferation, MCL-1 inhibition selectively depletes intermediate neural progenitors, indicating a direct role in lineage progression. Overall, the work positions MCL-1 as a key regulator of mitochondrial structure-metabolism coupling that instructs neural progenitor identity and human neurogenesis.

      Overall: The study does a good job of using (in most assays) caspase inhibition (e.g., QVD treatment) to block apoptotic responses induced by MCL-1 inhibition. As a result, many of the phenotypes caused by inhibition are likely to be independent of caspase activation. As a result, this manuscript would be of interest to researchers that study the topics of the BCL-2 family and cell death signaling, mitochondrial bioenergetics and dynamics, neurodevelopment, and cellular metabolism. However, as currently presented the manuscript is only descriptive and lacks mechanistic insight.

      We thank Reviewer 1 for the insightful evaluation of our work. We are encouraged that the reviewer finds the study relevant to investigators in the fields of BCL-2 family biology, mitochondrial dynamics and bioenergetics, neurodevelopment, and cellular metabolism. We also thank the reviewer for pointing out the need to increase the mechanistic insight of our findings. As mentioned above, in the revised manuscript, we are proposing to address this.

      Major Concerns:

      1) The authors only use a single MCL-1 inhibitor and never use other non-targeting BH3-mimetics (such as venetoclax) as negative controls. This seems like a missed opportunity to demonstrate that the phenotypes observed are MCL-1 dependent.

      This is an excellent point. We will include venetoclax (ABT-199) to examine their effect on intermediate progenitors (TBR2 +) and early born neurons (BIII tubulin +).

      2) There is no mechanism proposed in this study other than reliance upon QVD as not affecting the phenotypes. As submitted, the manuscript only can speculate that these phenotypes are due to non-apoptotic roles of MCL-1 inhibition. The authors have missed an opportunity to explore MCL-1's non-apoptotic functions directly.

      Mechanistically, we propose MCL-1 is acting in 2 ways: 1) as we show in our data, MCL-1 inhibition causes disruption of the mitochondrial cristae, altering the microenvironment for fatty acid oxidation, and 2) as seen in cancer cells, MCL-1 inhibitors may also displace ACSL1 from the mitochondria.

      In the past few weeks, since receiving the initial reviews, we have focused on testing the 2nd possibility, since the accumulation of lipids was also seen in cancer cells (see PMID: 38503284). We have successfully generated stable ACSL1:HaloTag expressing hESCs (Figure 1A for reviewers). Our findings included here, ACSL1 is displaced from the mitochondria by MCL-1 inhibition in NPCs (Figures 1B-C for reviewers).

      Other concerns exist that weaken the impact of the study.

      1. Figure 1 should include the fact that QVD inhibition (shown in Sup Fig 2) does not obviate the phenotype induced by pharmacological inhibition of MCL-1 on mitochondrial morphology. We would like to clarify that QVD does prevent the phenotypes induced by MCL-1 inhibition on mitochondrial morphology. In Fig1B, we report an increase in volume and surface area at 24h and 48h along with a decrease in mitochondrial content at 48h when NPCs were treated with MCL-1i only. However, NPCs co-treated with QVD in Supp Fig 2B did not exhibit any significant morphological phenotypes on average or at min/max values. Reviewer 1 may be referring to Fig 1B’s corresponding min/max values presented in Supp Fig 2A where we reported an increase in __max __volume.

      Figure #

      Volume

      Surface Area

      Fig 1B (MCL-1i only, avg values)

      Increase (avg vol)

      increase (avg)

      Supp Fig 2B (MCL-1i+QVD)

      no change

      no change

      Supp Fig 2A (MCL-1i only, max/min values)

      increase (max vol)

      no change (max)

      For clarity, we will move Supplementary Fig 2A into Supplementary Fig 1.

      Figure 2 would benefit from evidence that caspase inhibition does not repress the phenotype on mitochondrial cristae morphology (volume and area). Furthermore, the FIB-SEM data are very hard to appreciate as the size precludes visualization of individual mitochondria.

      While we included the visualization of the segmented mitochondria and cristae (Figure 2C), as well as snapshots through the z-stack for segmented cristae only (Figure 2E) and segmented mitochondria separately (Supp Figure 3A) in the original manuscript, we are also now attaching the FIB-SEM 3D reconstruction videos (New Supplementary Videos 1-2 for reviewers) (1. Mito and cristae, 2. Cristae only, 3. Mito only) for ease of visualization purposes.

      Figure 3 reports that MIC60 and OPA1 appear to be downregulated in response to MCL-1 inhibition, but these appear to be more significant only when QVD is added. Why would the phenotype be obscured in the non-QVD setting (Fig. 2B&C). How does MCL-1 inhibition lead to changes in MIC60/MICOS/OPA1? This seems quite preliminary at this point.

      In Figures 3B and 3C, we report decreased protein levels of short-form OPA1 and MIC10 only, not MIC60. We argue that our data with QVD shows that the cell death function of MCL-1 (i.e., inhibiting cell death effectors from initiating the caspase cascade) is not the main trigger of the phenotypes we report (cristae dysregulation and fatty acid oxidation disruption), however, cells without a functional cristae and/or defects in FAO, may not be able to survive long-term. Thus, QVD treatment preserves these cells that may not survive the dismantling of such an essential structure. To confirm this, we have performed immunofluorescence of cleaved caspase 3 (Figure 5 for reviewers). These results show that indeed MCL-1 inhibition at the time points of our study doesn’t result in increased activation of Caspase-3. We reported similar results of MCL-1 inhibition in oligodendrocyte precursor cells (Gil and Hanna et al., Glia, 2025, PMID: 41420072)

      The loss of MIC60 and OPA1 should repress electron transport chain function, are such impacts observed in the cultured cells? This could be shown by assessing oxygen consumption, etc. Such data would enhance the authors' conclusion that MCL-1 inhibition leads to defects in mitochondrial physiology*. *

      We completely agree with this comment by Reviewer 1. In our revision, we will include an assessment of mitochondrial oxygen consumption rate, using the Seahorse analyzer (mitochondrial stress test), of NPCs treated with MCL-1i. Preliminary data (n=3) are currently presented as Figure 3 for reviewers. Interestingly, these data show a more nuanced cellular response. Consistent with our conclusion that MCL-1 inhibition does not cause apoptotic cell death, MCL-1i did not affect mitochondrial respiration at baseline. The specific deficits appear in spare respiratory capacity and maximal respiration, meaning cells can sustain routine mitochondrial function but lose the ability to respond to increased energetic demand. This suggests MCL-1 loss creates a mitochondrial reserve deficiency rather than a generalized bioenergetic failure. The results with caspase inhibitors show a near-zero OCR across both 24h and 48h timepoints, and significant reductions in maximal respiration, spare respiratory capacity, and non-mitochondrial OCR. Remarkably, these conditions are not detrimental to newborn neurons, as shown in Figure 7. This is very interesting because it suggests that, under severe bioenergetic failure, neural stem cells (PAX6+) can differentiate into newborn neurons in a TBR2-independent manner. More relevant to this study, our results unequivocally demonstrate that TBR2-positive cells depend on the non-apoptotic function of MCL-1

      In Figure 4, the differences between transcripts (qPCR data) and protein (immunoblot) data are often confusing and not well explained. Why do the authors propose that mRNA expression is decreasing whereas the protein expression is increasing? Example CPT1. Furthermore, it is unclear what these data mean functionally? Is this reflective of enhanced lipid oxidation or simply a response to inhibition of fatty acid oxidation? Clarification of the impact of these findings is necessary.

      We agree with Reviewer 1 that the results could be hard to interpret. However, the effects of MCL-1 inhibitors on the transcription of fatty acid oxidation genes have been widely cited by the work of Opferman and Walensky (PMID: 36198266). We speculate that the effects on transcription are triggered by mitochondrial signaling. The mechanistic insight into this phenomenon would be an interesting next step.

      In the case of CPT1, we addressed this comment and found that the difference is due to differential expression of isoforms The RT-qPCR shown in Figure 4, is on CPT1c, whereas the western blot is on CPT1a. Unfortunately, after trying several products, we determined that there are no good antibodies for CPT1c. Thus, since we can’t compare gene and protein expression, we will include CPT1a RT-qPCR data to complement the western blot.

      The increase in lipid droplet number induced by MCL-1 inhibition has been previously documented, but it is unclear whether this increase is related to an inability to oxidize lipid (defective fatty acid oxidation) that leads to increases in the cellular abundance or whether this indicates that MCL-1 inhibition leads to enhanced storage. Do other inhibitors of fatty acid oxidation lead to similar increases in lipid droplet size and abundance? Does QVD inhibition affect this phenotype?

      This is a great point raised by Reviewer 1, and one we have also wondered about. We conducted an experiment using C16 BODIPY to address this point (Figure 6 for Reviewers). We observed no changes in C16 lipid droplet accumulation in count, volume, or surface area when cells were treated with MCL-1 inhibitor for 24 hours total with or without a starvation period in the last 6 hours of treatment. However, we observed significant pan-lipid droplet accumulation in the same conditions. This contrast suggests that FAO of exogenous LC-fatty acids is not reliant on MCL-1. This finding does not discount from the requirement of MCL-1 for other FAO processes especially given the major limitation of how much C16 BODIPY (fluorescent palmitate) can be administered to the cells (10µM) which was 10-fold less than what we exogenously supplied to the cells for the pan-BODIPY experiment (100µM, see Figure 5). It is entirely possible that this small dose was not enough to detect any lipid droplet accumulation.

      We have now also included experiments using etomoxir and perhexiline to assess their effects on TBR2/PAX6 (Figure 2 for reviewers). The results indicate that inhibiting the FAO pathway does not fully mimic the effects of MCL-1i on TBR2. However, we show that MCL-1i displaces ACSL1 from the mitochondria, a step that is upstream of CPT1/2. We suggest a model in which the coordinated non-apoptotic function of MCL-1 at the outer mitochondrial membrane promotes ACSL1 activity and, in the inner mitochondrial membrane, regulates mitochondrial cristae morphology. While our data point to this model, we are limited by the tools to investigate it further, but it will be a great direction for future experiments.

      For Figure 6, while these data may be very meaningful, as presented they are very hard to appreciate. Insets that show the neuronal populations would help to convey the point that the differentiation is impacted. Also, are there other methods that could confirm these observations (qPCR to show changes in differentiation).

      We agree with Reviewer 1. In the new version of the manuscript, we will include panels that zoom into the cell populations we quantified. The current panels will go to a new Supplemental figure. We will also add the TUBB3 to the qPCR panel in the new version.

      Figure 7 is also very hard to appreciate. What is the reader to see? Can these be quantified? It seems that QVD may be rescuing in this figure, does this suggest that MCL-1 inhibition might be inducing death. All of this needs to be quantified.

      We will provide quantification of BIII tubulin branching, and it will be included next to the images provided.

      BCL-XL has also been implicated in affecting mitochondrial electron transport chain function (See PMID: 19255249, 21926988, 21987637). Can BCL-XL inhibitors affect any of the phenotypes associated here?

      We will include experiments to test the effect of BCL-2 and BCL-XL inhibitors on TBR2 cells to address this comment.

      Please be carefully avoid using the term "MCL-1 loss", when talking about pharmacological inhibition. Only genetic ablation (e.g. knockout, silencing, etc.) should be termed loss.

      We have now removed the reference to MCL-1 loss in line 199.

      __*Reviewer #1 (Significance (Required)):

      The study advances in human cells the impacts of MCL-1 inhibition. They replicate many impacts previously observed in mouse systems and refine analyses to impacts on MICOS complex, lipid droplet storage, and neuronal differentiation. While these findings are important and would be well received by a wide audience, the study fails to provide almost any mechanistic insight into how these phenotypes are being induced. The only common theme is that blocking caspase activation in many assays fails to block the phenotype.

      *__

      __Reviewer #2_ (Evidence, reproducibility and clarity (Required)): _*

      Summary: This manuscript by Hanna et al. investigates non-apoptotic roles of MCL-1 in human neural stem cells and connects MCL-1 inhibition to mitochondrial cristae formation and beta-oxidation. Connecting these roles to brain development, the authors also show a reduction in the number of progenitor cells upon MCL-1 inhibition, independently of caspase activity. Throughout their work, the authors make use of an impressive array of imaging techniques. While the methods used offer sufficient evidence to connect MCL-1 inhibition to cristae architecture, the mechanistic underpinnings of this effect remain unexplored. *__

      We thank Reviewer 2 for the thoughtful and positive assessment of our manuscript. We appreciate the reviewer’s recognition that our study reveals non-apoptotic roles of MCL-1 in human neural stem cells. We are also grateful for the acknowledgment of the imaging approaches employed, which allowed us to connect MCL-1 function to cristae architecture with multiple complementary techniques. We acknowledge the reviewer’s point that the mechanistic basis by which MCL-1 influences cristae structure remains insufficiently defined. In the revised manuscript, we will clarify the limitations of the current data, expand our discussion of potential mechanisms, and incorporate additional analyses to identify downstream effectors that mediate these structural and metabolic changes.

      Major comments:

      - In Fig. 1B, the very same representative images are shown for both conditions (DMSO and S63845) at 48 hours.

      We deeply appreciate Reviewer 2 for catching this unintentional duplication that occurred during figure preparation. We have now corrected this issue.

      - For Western Blot analysis, it looks like the authors only quantified the band density of their proteins of interest without considering varying levels of control protein (Actin) levels. Normalizing the protein levels to actin would account for any differences in loaded protein amounts (although a Ponceau staining might be preferable still to exclude this). This is especially relevant for Fig. 4E, where actin levels visibly differ between the conditions.

      All WB quantifications were normalized to Actin (this detail is now added to the y-axis of all band density graphs and figure legends). In addition, we will transform the data to a logarithmic scale to “normalize” for gel-to-gel variability.

      - The authors offer evidence that MCL-1 inhibition impedes proteolytic cleavage of OPA1-L into the OPA-1-S isoforms, yet do not explore the mechanism behind this. Since OPA1 is cleaved by both OMA1 and YME1L, determination of the levels of these proteases could help shed some light on the mechanism leading to cristae reorganization.

      We will follow up on Reviewer 2's comment with a WB analysis of OMA1 and YMEL in cells treated with an MCL-1 inhibitor.

      - Generally speaking, while the authors show all those effects (cristae defects, FAO dysfunction) upon MCL-1 inhibition, it would be interesting to see whether any of those effects can be rescued by blocking FA import e.g. through carnitine palmitoyl- transferase 1a (CPT1a) inhibition with etomoxir to understand if they are downstream of altered Fa supply. This could affect cristae morphology through altered Cardiolipin biogenesis.

      This is an excellent point, which was also raised by reviewer 1. We have now included experiments using etomoxir and perhexiline to assess their effects on TBR2/PAX6 (Figure 2 for Reviewers). As mentioned above, the results indicate that inhibiting the FAO pathway does not fully mimic the effects of MCL-1i on TBR2. However, we show that MCL-1i displaces ACSL1 from the mitochondria, a step that is upstream of CPT1 and 2. We suggest a model in which the coordinated non-apoptotic function of MCL-1 at the outer mitochondrial membrane promotes ACSL1 activity and, in the inner mitochondrial membrane, regulates mitochondrial cristae morphology. While our data point to this model, we are limited by the tools to investigate it further, but it will be a great direction for future experiments. The suggestion of Reviewer 2 that the effects on FAO could impact cardiolipin biogenesis is a very exciting possibility. However, difficult to test with the tools available.

      - In line 262 the authors discuss that mitochondria lose metabolic function upon MCL-1 inhibition. This claim would require additional experiments. While the authors look at lipid droplet accumulation and FAO enzymes, there are many more aspects to mitochondrial metabolic function that should be investigated. While measuring the oxygen consumption rate via Seahorse might require additional resources (optional), measurements of ATP production, ROS generation or determination of the mitochondrial membrane potential should be feasible.

      We fully agree with Reviewer 2's comment, which was also raised by Reviewer 1. In our revision, we will include an assessment of the mitochondrial oxygen consumption rate of NPCs treated with MCL-1i, measured using the Seahorse analyzer (mitochondrial stress test). These data are presented as Figure 3 for reviewers. Interestingly, these data show a more nuanced cellular response. While MCL-1i does not globally collapse mitochondrial respiration at baseline, the specific deficits appear in spare respiratory capacity and maximal respiration, meaning cells can sustain routine mitochondrial function but lose the ability to respond to increased energetic demand. This suggests MCL-1 loss creates a mitochondrial reserve deficiency rather than a generalized bioenergetic failure. The results with caspase inhibitors show a near-zero OCR across both 24h and 48h timepoints, and significant reductions in maximal respiration, spare respiratory capacity, and non-mitochondrial OCR. These conditions are detrimental for TBR2-positive NPCs (Figure 6) , but not for newborn neurons (Figure 7).

      - While the authors "propose a model in which MCL-1 associates with MICOS", they do not offer direct scientific to support this hypothesis. Co-immunoprecipitation experiments or e.g. proximity ligation assays would better support the proposed model.

      We agree with this statement. Preliminary, we have performed proximity ligation assays and immunoprecipitation analyses to test for this interaction (see below and ____Figure 4 for reviewers), and the results indicate an interaction, albeit very weak. In the revised version of the manuscript, we will attempt to repeat these experiments with MCL-1i.

      - While Fig. 7 shows representative images, quantification e.g. for the truncation of neuronal processes is missing.

      We will provide quantification of BIII tubulin branching, which will be included alongside the images provided.

      - In lines 219f. the authors state that they "observed a significant downregulation of PAX6 and EOMES at 24 hours that was not rescued by QVD co-treatment". While there is still a trend towards a downregulation, there is no statistical significance anymore. In fact, PAX6 levels almost mirror those of SOX2 which is not described as "downregulated" by the authors. In order to be more consistent, I would suggest rephrasing this part, or at least reword it to be less absolute.

      In the new version, we will clarify that while QVD rescued TBR2 and PAX6 transcript levels at 24h, it did not rescue them at 48h. We will also mention the downregulation of SOX2 at 48h that persists with co-treatment.

      - Brinkmann et al. (2025) also investigated cristae structure upon MCL-1 deletion in vivo and found no effect when MCL-1 was replaced with other Bcl-2 family members. It would be interesting to combine MCL-1 inhibition with overexpression of MCL-1 versus BCL-XL to reconsolidate some of the discrepant findings.

      While this is a great suggestion for future studies, there are some complications. Specifically, it is likely that the inhibitor may also target the overexpressed MCL-1 and thus, a mutant form is needed.

      To address this, we generated a Flag-tagged MCL-1 construct with a mutated BH3 domain, previously described by Kotschy et al. Nature 2016. We validated the construct in HeLa cells, but unfortunately the mutant protein appears to be significantly less stable than the WT construct, complicating analysis of this experiment.

      Minor comments:

      - In Supp. Fig. 1C the MCL-1 protein is shown both to run above 37kDa (upper panel) and below 37 kDa (lower panel). Could the authors please comment on why this is the case?

      The observed variation is caused by drift in the gel during electrophoresis. In Fig 1C, the protein ladder is on the edge of the gel, whereas in Fig 1E, the protein ladder is in the middle of the gel, and the last sample is on the edge and also exhibits edge drift.

      - In line 64 of the introduction the authors mention clinical trials yet do not give a citation for these trials making it hard to judge whether the content of these trials is actually related to the brain.

      This information is anecdotal, based on an Amgen press release.

      - MCL-1 as well as ACSL-1 are sometimes written without the hyphen both in the text and figures.

      We will carefully check the manuscript before submission.

      - Lines 92-94 and 106-108 essentially highlight the same existing knowledge gap. Maybe the content of these two paragraphs could be combined in order to avoid repetition.

      We thank Reviewer 2 for this suggestion. We will do this in the new version of the manuscript.

      - In Fig. 1A, the authors provide a schematic for their experimental design. While the figure legend is very thorough, some of this information (like the days of collection) could also be included in the figure itself. The same is true for schematics in the following figures.

      We agree with this and will incorporate the suggestion in the new version.

      - Fig. 2A includes a typo (analyze) but would maybe also be more suitable for the supplement figures or could even be combined with Fig. 1A as not much new content is added.

      We already incorporated these changes in the new version of the manuscript.

      - Regarding statistical analysis, could the authors please comment on why they did not consider one-sample t-tests suitable for the cases where control values were set at 1 (e.g. Fig. 4B, C for the relative expression).

      This is a valid suggestion. We will rerun RT-qPCR data using a one-sample t-test.

      - In lines 247f. the authors state that "inhibition of MCL-1 leads to [...] and disassembly of the MICOS complex as well as OPA1". This sounds like OPA1 is still cleaved upon MCL-1, which is not at all what the authors showed and further discuss. Rewording of the sentence would help in avoiding any misunderstandings.

      We agree with this comment and have now reworded the paragraph: “Inhibition of MCL-1 leads to structural collapse of the cristae likely due to the possible disassembly of the MICOS complex, as suggested by decreased MIC10 levels, and interruption of OPA1 cleavage, as suggested by decreased short-form OPA1, two scaffolds required for cristae maintenance.”

      - In lines 210f. the authors state that "quantitative imaging increased the average and maximum volume of lipid droplets". While there is definitely a trend towards an increase for the maximum volume, the increase is in fact not statistically significant. This should be reflected in the wording.

      We have reworded this to “Quantitative imaging revealed a significant increase in average lipid droplet volume and a trending increase in maximum volume of lipid droplets.”

      - In Fig. 6 the overlap between TBR2 and PAX6 is hard to judge when printed out. Including a zoom-in may make it easier to judge.

      We agree with Reviewer 2. In the new version of the manuscript, we will include panels that zoom into the cell populations we quantified. The current panels will go to a new Supplemental figure. We will also add the TUBB3 to the qPCR panel in the new version.

      - In Fig. 7 the color-coding is listed in the figure legend but is missing from the figure itself. If the authors could include this, as they did for the other figures, it would further improve this figure.

      We agree. We have specified the channel color in the new figure.

      - Line 238 should reference Fig. 7A, as Fig 7B does not exist.

      Thanks for catching this. It is already corrected

      - In the figure legends the authors state that biological replicates were used. Were technical replicates also performed?

      Yes, technical replicates were performed for RT-qPCR.

      Reviewer #2 (Significance (Required)):____ Significance

      The authors make use of a wide array of imaging techniques to further elucidate non-apoptotic roles of MCL-1. The study has the potential to offer new insights into mitochondrial biology on the level of basic research rather than translational. While the methods used offer sufficient evidence to connect MCL-1 inhibition to cristae architecture, the mechanistic underpinnings of this effect remain unexplored. Nevertheless, the study offers additional knowledge on the role of MCL-1 in human neural stem cells, whereas previous research mostly focused on cardiomyocytes or cancer cells.

      Reviewer #3____ (Evidence, reproducibility and clarity (Required)):

      Summary: ____ In this study, Gama et al. describe a non-canonical role for the anti-apoptotic protein Myeloid Cell Leukemia-1 (MCL-1) in mitochondrial cristae organization and suggest a role of MCL-1 in regulating metabolism and neuronal differentiation. Using fluorescence microscopy imaging and electron microscopy, the authors show changes to mitochondrial morphology upon treatment with MCL-1 inhibitor S63845. MCL-1 inhibition results in altered protein and transcript levels of some key proteins involved in mitochondrial cristae organization and fatty acid metabolism. While some of the findings are interesting and indeed point towards a non-canonical role of MCL-1, several key conclusions of the authors are not sufficiently supported by the data shown in the manuscript.

      We thank Reviewer 3 for the careful evaluation of our manuscript. We appreciate the reviewer’s recognition that our study identifies a potential non-canonical role for MCL-1 in mitochondrial cristae organization, metabolism, and neuronal differentiation. As with Reviews 1 and 2, we are encouraged that the reviewer finds these observations interesting and suggestive of previously unappreciated functions for MCL-1. We agree that stronger evidence is required to firmly link MCL-1 inhibition to specific changes in MICOS organization and metabolic regulation. In the revised manuscript, we will (i) more clearly distinguish between observations and mechanistic inferences, (ii) temper conclusions where appropriate, and (iii) incorporate additional analyses and controls to better substantiate the proposed model.

      Major comments:

      1. The authors try to disentangle the apoptotic and non-apoptotic role of MCL-1 through addition of a caspase inhibitor. However, I am not convinced that phenotypes found under the addition of caspase inhibitor are necessarily caused by non-canonical functions independent of apoptosis. It could also be that the observed changes happen upstream of caspase activation. In addition, many of the described finding, such as CPT1 expression changes, only happen in the presence of the caspase inhibitor. If one follows the logic of the authors, changes associated by non-canonical MCL-1 functions should happen under MCL-1 inhibition and caspase inhibition, but not with MCL-1 inhibition only____. __ The reviewer is right that we expected non-canonical functions to happen under MCL-1 inhibition and caspase inhibition. Our data with QVD shows that the cell death function of MCL-1 (i.e., inhibiting cell death effectors from initiating the caspase cascade) is not the main trigger of the phenotypes we report (cristae dysregulation and fatty acid oxidation disruption), however, cells without a functional cristae and/or defects in FAO, may not be able to survive long-term. Thus, QVD treatment preserves these cells that may not survive the dismantling of such an essential structure. To confirm this, we performed immunofluorescence of cleaved caspase 3 (__Figure 5 for reviewers). These results show that, indeed, MCL-1 inhibition at the time points of our study doesn’t result in increased Caspase-3 activation. We reported similar results of MCL-1 inhibition in oligodendrocyte precursor cells (Gil and Hanna et al., Glia, 2025, PMID: 41420072).

      The authors show no data on the viability of the cells in response to the MCL-1 inhibitor. To exclude secondary effects of the inhibitor, at least some of the results should be validated with an MCL-1 knock down.

      We will include this experiment in our revised manuscript. To check the effects of MCL-1 knockdown on TBR2 positive cells, we tested 5 different ASOs for MCL-1. Knockdown efficiency with ASOs was very low (on average In Figure 1, the authors show immunofluorescence data of mitochondria and nucleus staining and conclude that MCL-1 inhibition alters mitochondrial morphology. Based on the images shown in Fig. 1, I do not think that individual mitochondria can be segmentd to measure their volume and length. In addition, some metrics such as mitochondrial content are not explained in the text or methods.

      We can achieve mitochondrial segmentation with a SoRa Spinning Disk Confocal Microscope, which has a lateral (XY) resolution of approximately 120 nm to 150 nm and an axial (Z) resolution of approximately 300 nm–320 nm. All images are first denoised prior to sharpening using the Richardson-Lucy deconvolution algorithm. Additionally, the FIB-SEM data are consistent with the IF data (both show increase in mitochondrial volume and surface area).

      We agree with Reviewer 3 that we need to explain some metrics in the revised version. We will specify the meaning of mitochondrial content (count of all mitochondria in FOV, not normalized to Hoechst).

      In Fig. 2 B-D, the authors show TEM and FIB-SEM imaging to demonstrate alterations in the cristae architecture upon treatment with MCL-1 inhibitor. However, based on the images shown, it looks that cristae area and density is reduced under S63845 treatment in TEM images, while the FIB-SEM data come to the opposite conclusion. In addition, the quantification of cristae volume quantified as cristae volume in percentage is unclear to me.

      We apologize for the confusion. No conclusions about the cristae area and density were made using the TEM data, because TEM data represent a single snapshot section of a mitochondrion without a discernible orientation. Cristae from TEM were described as “aberrant” and preliminarily revealed changes in cristae and were followed up with FIB-SEM, 3D reconstruction of intact mitochondria, and quantification of volume.

      In the new version of the manuscript, we will specify that the cristae volume is normalized to the volume of its respective mitochondria (i.e., how much of the mitochondrial volume is attributed to cristae).

      The change in CPT1/2 protein levels (Fig. 4) is interesting but does not directly proof that fatty acid oxidation is altered, as concluded by the authors. For this, the authors would need to directly measure fatty acid oxidation for example using Seahorse or metabolic tracing experiments. Also, to prove that the MCL-1 inhibition affects neural differentiation through fatty acid oxidation, a rescue experiment should be performed through CPT1 overexpression.

      We agreed that this is an important point. We have optimized the fatty acid oxidation test using Seahorse and will make sure to include it in the revised version of the manuscript.

      In Figure 6, the authors show decreased intermediate progenitor cells after MCL-1 inhibition by immunofluorescence staining. I am not convinced that this can be concluded from the data shown, since the concentration of intermediate progenitor cells is very close to the noise levels. Since the MCL-1 treated cells look much less sparse, I don't think the percentages can be compared (total counts are between 2-20). Although this data might give some indication that differentiation could be impaired, the measured effect could be very well due to lower viability of the cells. The authors need to control for this or come up with a different method for measuring differentiation.

      The number of TBR2 is low, but we disagree with the reviewer’s assessment of noise levels. We focused on cells expressing only TBR2 and rigorously examined this population of cells. The percentages are compared to account for the lower density of the MCL-1i-treated cultures, as the IPC counts are normalized to the Hoechst total cell count within the FOV. Moreover, the immunofluorescence images are complemented with RT-qPCR, which shows significant downregulation of EOMES (gene encoding TBR2).

      Figure 7 is missing quantification

      We will include this quantification in the revised version of the manuscript.

      Reviewer #3 (Significance (Required)):

      General assessment____: The manuscript reports an interesting finding, which suggest a non-canonical role of MCL-1 in mitochondrial remodeling, regulation of fatty acid oxidation and neuronal fate. While this finding would be highly interesting and relevant, the presented data do not sufficiently support this conclusion. Further experiments would have to be performed to proof causality. ____ Advance: Should the authors manage to proof their hypothesis by additional experiments, this would indeed advance the field on mitochondrial remodeling and its effect on neuronal differentiation by

      identifying a novel molecular player. ____ Audience: mitochondrial biology, cell biology, developmental neuroscience Own expertise: mitochondrial biology, cell biology, advanced imaging techniques

    1. Reviewer #3 (Public review):

      Summary:

      The authors aim to compare proposal models of perceptual decision making using a joint modeling approach, where they fit models to both behavioral outcomes as well as CPP. Most notably, they compare a standard evidence accumulation model with models that track the evidence without integrating it over time (extrema detection). The authors report that the joint CPP-behavioral data do not discriminate between two of their proposals.

      Strengths:

      This is an interesting finding that reinforces the idea that what we believe to see based on aggregation over trials may not be what happens on every single trial. The models are creative, and the simulations are convincing, relating the models to multiple neural markers of decision formation. These include the CPP but also mu/beta power spectra.

      Weaknesses:

      The paper makes some strong points, and the work seems generally well-executed. The weaknesses that I identified are twofold:

      (1) Embedding in the literature/exposition of the main argument.

      The focus in the introduction is on the noise-free nature of the stimulus and the prolonged presentation time. However, after reading the paper, I felt these were mostly experimental design choices that enable comparison of the different models using the CPP. Perhaps my misreading of the goals of the paper stems from two other observations:

      a) The fact that the stimulus is noise-free does not entail that perception is noise-free. Thus, the argument that using a noise-free stimulus precludes the necessity of temporal integration seems not completely valid. Of course, one could argue that noise is limited in this case, but that makes a noise-free stimulus more of a design choice.

      b) The focus on prolonged stimulus presentation, but at the same time the contrast with expanded judgement, did not make sense to me. Perhaps, as a non-native speaker, I am misreading the subtle difference between "protracted sampling" and "longer sampling", but again, the longer duration seems mostly a design choice.

      More could be said about the optimality of the extrema detection methods. In particular, decades of work (centuries?) have shown that evidence integration is an optimal decision-making procedure: For example, the Sequential Probability Ratio Test is Bayes-optimal wrt mean RT (Wald, 1946); evidence accumulation together with collapsing threshold serves to maximize rewards in repeated choices (e.g., Bogacz et al., PsychRev, 2006; Boehm et al. APP, 2020). Given all this work, why would the brain have evolved to adopt a different mechanism? I realize that the paper is not about optimal decision making, but some discussion of this point seems warranted.

      (2) Modeling choices.

      The authors introduce a parameter, sampT, that represents uncertainty in the sampling onset time. It was not clear to me whether this parameter represented an offset of all trials, or a distribution (probably the latter). I wonder how exactly this parameter was integrated into the models, and in particular, if and how it interacts with the starting-point parameters. My intuition is that on a single-trial, IF early sampling occurs, you can model that with either a negative sampT and z at 0, or with sampT at 0 but a shift in z. This would suggest trade-offs between these parameters, making them hard to estimate independently. Since the paper does not depend on the identification of parameter estimates, this may not be a huge problem, but nevertheless it is good to explore the consequences.

      The way the Bounded Integration model (BIntg) is formulated seems very close to the EZ-diffusion model (Wagenmakers et al., PBR, 2007). This model states that the proportion of correct responses Pc = 1/(1+exp(-B*D/s^2), with B and D the bound and drift rate parameters, respectively. However, filling in the numbers for the high contrast condition from Table 2, and assuming that s=2 (because the model description states that dt=2, with s undefined), I get a Pc of 80% for the 1.6H condition. This seems substantially less than what Figure 2 suggests.

      On some occasions, it is unclear to me what modeling choices are being made:

      a) It seems as if the models are fit on accuracy data alone (before introducing the neural data). This seems suboptimal given that the authors do report differences in RT.

      b) Are the models fit on all data combined, or on the data of individual participants? Fitting individual participant data is preferred, as combined or aggregated data may be distorted by individual differences.

      c) The authors seem to suggest that the diffusion coefficient s is estimated (in the section "Integration models"). Most likely, however, this is set to a fixed value. Obviously, it matters for the model comparison using AIC whether this parameter was freely estimated or not.

      Not really a weakness, but I wondered about the effect of stimulus duration on RT. In particular, what hypothesis (or post hoc explanation) do the authors have for these RT effects? I could think of at least three hypotheses that are consistent with the behavioral data:

      a) H1: The shorter the evidence duration, the more likely participants are to require a double-check before response execution, reflecting their uncertainty about their decision.<br /> b) H2: There is a collapsing threshold that initiates at stimulus offset, leading to quicker responses on trials where there is more evidence.<br /> c) H3: motor preparation is correlated with the evidence signal, which leads to faster responses on trials with more evidence.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Here, the authors have addressed the recruitment and firing patterns of motor units (MUs) from the long and lateral heads of the triceps in the mouse. They used their newly developed Myomatrix arrays to record from these muscles during treadmill locomotion at different speeds, and they used template-based spike sorting (Kilosort) to extract units. Between MUs from the two heads, the authors observed differences in their firing rates, recruitment probability, phase of activation within the locomotor cycle, and interspike interval patterning. Examining different walking speeds, the authors find increases in both recruitment probability and firing rates as speed increases. The authors also observed differences in the relation between recruitment and the angle of elbow extension between motor units from each head. These differences indicate meaningful variation between motor units within and across motor pools and may reflect the somewhat distinct joint actions of the two heads of triceps.

      Strengths:

      The extraction of MU spike timing for many individual units is an exciting new method that has great promise for exposing the fine detail in muscle activation and its control by the motor system. In particular, the methods developed by the authors for this purpose seem to be the only way to reliably resolve single MUs in the mouse, as the methods used previously in humans and in monkeys (e.g. Marshall et al. Nature Neuroscience, 2022) do not seem readily adaptable for use in rodents.

      The paper provides a number of interesting observations. There are signs of interesting differences in MU activation profiles for individual muscles here, consistent with those shown by Marshall et al. It is also nice to see fine-scale differences in the activation of different muscle heads, which could relate to their partially distinct functions. The mouse offers greater opportunities for understanding the control of these distinct functions, compared to the other organisms in which functional differences between heads have previously been described.

      The Discussion is very thorough, providing a very nice recounting of a great deal of relevant previous results.

      We thank the Reviewer for these comments.

      Weaknesses:

      The findings are limited to one pair of muscle heads. While an important initial finding, the lack of confirmation from analysis of other muscles acting at other joints leaves the general relevance of these findings unclear.

      The Reviewer raises a fair point. While outside the scope of this paper, future studies should certainly address a wider range of muscles to better characterize motor unit firing patterns across different sets of effectors with varying anatomical locations. Still, the importance of results from the triceps long and lateral heads should not be understated as this paper, to our knowledge, is the first to capture the difference in firing patterns of motor units across any set of muscles in the locomoting mouse.

      While differences between muscle heads with somewhat distinct functions are interesting and relevant to joint control, differences between MUs for individual muscles, like those in Marshall et al., are more striking because they cannot be attributed potentially to differences in each head's function. The present manuscript does show some signs of differences for MUs within individual heads: in Figure 2C, we see what looks like two clusters of motor units within the long head in terms of their recruitment probability. However, a statistical basis for the existence of two distinct subpopulations is not provided, and no subsequent analysis is done to explore the potential for differences among MUs for individual heads.

      We agree with the Reviewer and have revised the manuscript to better examine potential subpopulations of units within each muscle as presented in Figure 2C. We performed Hartigan’s dip test on motor units within each muscle to test for multimodal distributions. For both muscles, p > 0.05, so we can not reject the null hypothesis that the units in each muscle come from a multimodal distribution. However, Hartigan’s test and similar statistical methods have poor statistical power for the small sample sizes (n=17 and 16 for long and lateral heads, respectively) considered here, so the failure to achieve statistical significance might reflect either the absence of a true difference or a lack of statistical resolution.

      Still, the limited sample size warrants further data collection and analysis since the varying properties across motor units may lead to different activation patterns. Given these results, we have edited the text as follows:

      “A subset of units, primarily in the long head, were recruited in under 50% of the total strides and with lower spike counts (Figure 2C). This distribution of recruitment probabilities might reflect a functionally different subpopulation of units. However, the distribution of recruitment probabilities were not found to be significantly multimodal (p>0.05 in both cases, Hartigan’s dip test; Hartigan, 1985). However, Hartigan’s test and similar statistical methods have poor statistical power for the small sample sizes (n=17 and 16 for long and lateral heads, respectively) considered here, so the failure to achieve statistical significance might reflect either the absence of a true difference or a lack of statistical resolution.”

      The statistical foundation for some claims is lacking. In addition, the description of key statistical analysis in the Methods is too brief and very hard to understand. This leaves several claims hard to validate.

      We thank the Reviewer for these comments and have clarified the text related to key statistical analyses throughout the manuscript, as described in our other responses below.

      Reviewer #2 (Public review):

      The present study, led by Thomas and collaborators, aims to describe the firing activity of individual motor units in mice during locomotion. To achieve this, they implanted small arrays of eight electrodes in two heads of the triceps and performed spike sorting using a custom implementation of Kilosort. Simultaneously, they tracked the positions of the shoulder, elbow, and wrist using a single camera and a markerless motion capture algorithm (DeepLabCut). Repeated one-minute recordings were conducted in six mice at five different speeds, ranging from 10 to 27.5 cm·s⁻¹.

      From these data, the authors reported that:

      (1) a significant portion of the identified motor units was not consistently recruited across strides,

      (2) motor units identified from the lateral head of the triceps tended to be recruited later than those from the long head,

      (3) the number of spikes per stride and peak firing rates were correlated in both muscles, and

      (4) the probability of motor unit recruitment and firing rates increased with walking speed.

      The authors conclude that these differences can be attributed to the distinct functions of the muscles and the constraints of the task (i.e., speed).

      Strengths:

      The combination of novel electrode arrays to record intramuscular electromyographic signals from a larger muscle volume with an advanced spike sorting pipeline capable of identifying populations of motor units.

      We thank the Reviewer for this comment.

      Weaknesses:

      (1) There is a lack of information on the number of identified motor units per muscle and per animal.

      The Reviewer is correct that this information was not explicitly provided in the prior submission. We have therefore added Table 1 that quantifies the number of motor units per muscle and per animal.

      (2) All identified motor units are pooled in the analyses, whereas per-animal analyses would have been valuable, as motor units within an individual likely receive common synaptic inputs. Such analyses would fully leverage the potential of identifying populations of motor units.

      Please see our answer to the following point, where we address questions (2) and (3) together.

      (3) The current data do not allow for determining which motor units were sampled from each pool. It remains unclear whether the sample is biased toward high-threshold motor units or representative of the full pool.

      We thank the Reviewer for these comments. To clarify how motor unit responses were distributed across animals and muscle targets, we updated or added the following figures:  

      Figure 2C

      Figure 4–figure supplement 1

      Figure 5–figure supplement 2

      Figure 6–figure supplement 2

      These provide a more complete look at the range of activity within each motor pool, suggesting that we do measure from units with different activation thresholds within the same motor pool, rather than this variation being due to cross-animal differences. For example, Figure 2C illustrates that motor units from the same muscle and animal show a wide variety of recruitment probabilities. However, the limited number of motor units recorded from each individual animal does not allow a statistically rigorous test for examining cross-animal differences.

      (4) The behavioural analysis of the animals relies solely on kinematics (2D estimates of elbow angle and stride timing). Without ground reaction forces or shoulder angle data, drawing functional conclusions from the results is challenging.

      The Reviewer is correct that we did not measure muscular force generation or ground reaction forces in the present study. Although outside the scope of this study, future work might employ buckle force transducers as used in larger animals (Biewener et al., 1988; Karabulut et al., 2020) to examine the complex interplay between neural commands, passive biomechanics, and the complex force-generating properties of muscle tissue.

      Major comments:

      (1) Spike sorting

      The conclusions of the study rely on the accuracy and robustness of the spike sorting algorithm during a highly dynamic task. Although the pipeline was presented in a previous publication (Chung et al., 2023, eLife), a proper validation of the algorithm for identifying motor unit spikes is still lacking. This is particularly important in the present study, as the experimental conditions involve significant dynamic changes. Under such conditions, muscle geometry is altered due to variations in both fibre pennation angles and lengths.

      This issue differs from electrode drift, and it is unclear whether the original implementation of Kilosort includes functions to address it. Could the authors provide more details on the various steps of their pipeline, the strategies they employed to ensure consistent tracking of motor unit action potentials despite potential changes in action potential waveforms, and the methods used for manual inspection of the spike sorting algorithm's output?

      This is an excellent point and we agree that the dynamic behavior used in this investigation creates potential new challenges for spike sorting. In our analysis, Kilosort 2.5 provides key advantages in comparing unit waveforms across multiple channels and in detecting overlapping spikes. We modified this version of Kilosort to construct unit waveform templates using only the channels within the same muscle (Chung et al., 2023), as clarified in the revised Methods section (see “Electromyography (EMG)”):

      “A total of 33 units were identified across all animals. Each unit’s isolation was verified by confirming that no more than 2% of inter-spike intervals violated a 1 ms refractory limit. Additionally, we manually reviewed cross-correlograms to ensure that each waveform was only reported as a single motor unit.”

      The Reviewer is correct that our ability to precisely measure a unit’s activity based on its waveform will depend on the relationship between the embedded electrode and the muscle geometry, which alters over the course of the stride. As a follow-up to the original text, we have included new analyses to characterize the waveform activity throughout the experiment and stride (also in Methods):

      “We further validated spike sorting by quantifying the stability of each unit’s waveform across time (Figure 1–figure supplement 1). First, we calculated the median waveform of each unit across every trial to capture long-term stability of motor unit waveforms. Additionally, we calculated the median waveform through the stride binned in 50 ms increments using spiking from a single trial. This second metric captures the stability of our spike sorting during the rapid changes in joint angles that occur during the burst of an individual motor unit. In doing so, we calculated each motor unit’s waveforms from the single channel in which that unit’s amplitude was largest and did not attempt to remove overlapping spikes from other units before measuring the median waveform from the data. We then calculated the correlation between a unit’s waveform over either trials or bins in which at least 30 spikes were present. The high correlation of a unit waveform over time, despite potential changes in the electrodes’ position relative to muscle geometry over the dynamic task, provides additional confidence in both the stability of our EMG recordings and the accuracy of our spike sorting.”

      We have included a supplementary to Figure 1 to highlight the effectiveness of our spike sorting.

      (2) Yield of the spike sorting pipeline and analyses per animal/muscle

      A total of 33 motor units were identified from two heads of the triceps in six mice (17 from the long head and 16 from the lateral head). However, precise information on the yield per muscle per animal is not provided. This information is crucial to support the novelty of the study, as the authors claim in the introduction that their electrode arrays enable the identification of populations of motor units. Beyond reporting the number of identified motor units, another way to demonstrate the effectiveness of the spike sorting algorithm would be to compare the recorded EMG signals with the residual signal obtained after subtracting the action potentials of the identified motor units, using a signal-to-residual ratio.

      Furthermore, motor units identified from the same muscle and the same animal are likely not independent due to common synaptic inputs. This dependence should be accounted for in the statistical analyses when comparing changes in motor unit properties across speeds and between muscles.

      We thank the Reviewer for this comment. Regarding motor unit yield, as described above the newly-added Table 1 displays the yield from each animal and muscle.

      Regarding spike sorting, while signal-to-residual is often an excellent metric, it is not ideal for our high-resolution EMG signals since isolated single motor units are typically superimposed on a “bulk” background consisting of the low-amplitude waveforms of other motor units. Because these smaller units typically cannot be sorted, it is challenging to estimate the “true” residual after subtracting (only) the largest motor unit, since subtracting each sorted unit’s waveform typically has a very small effect on the RMS of the total EMG signal. To further address concerns regarding spike sorting quality, we added Figure 1–figure supplement 1 that demonstrates motor units’ consistency over the experiment, highlighting that the waveform maintains its shape within each stride despite muscle/limb dynamics and other possible sources of electrical noise or artifact.

      Finally, the Reviewer is correct that individual motor units in the same muscle are very likely to receive common synaptic inputs. These common inputs may reflect in sparse motor units being recruited in overlapping rather than different strides. Indeed, in the following text added to the Results, we identified that motor units are recruited with higher probability when additional units are recruited.

      “Probabilistic recruitment is correlated across motor units

      Our results show that the recruitment of individual motor units is probabilistic even within a single speed quartile (Figure 5A-C) and predicts body movements (Figure 6), raising the question of whether the recruitment of individual motor units are correlated or independent. Correlated recruitment might reflect shared input onto the population of motor units innervating the muscle (De Luca, 1985; De Luca & Erim, 1994; Farina et al., 2014). For example, two motor units, each with low recruitment probabilities, may still fire during the same set of strides. To assess the independence of motor unit recruitment across the recorded population, we compared each unit’s empirical recruitment probability across all strides to its conditional recruitment probability during strides in which another motor unit from the same muscle was recruited (Figure 7). Doing this for all motor unit pairs revealed that motor units in both muscles were biased towards greater recruitment when additional units were active (p<0.001, Wilcoxon signed-rank tests for both the lateral and long heads of triceps). This finding suggests that probabilistic recruitment reflects common synaptic inputs that covary together across locomotor strides.”

      (3) Representativeness of the sample of identified motor units

      However, to draw such conclusions, the authors should exclusively compare motor units from the same pool and systematically track violations of the recruitment order. Alternatively, they could demonstrate that the motor units that are intermittently active across strides correspond to the smallest motor units, based on the assumption that these units should always be recruited due to their low activation thresholds.

      One way to estimate the size of motor units identified within the same muscle would be to compare the amplitude of their action potentials, assuming that all motor units are relatively close to the electrodes (given the selectivity of the recordings) and that motoneurons innervating more muscle fibres generate larger motor unit action potentials.

      We thank the Reviewer for this comment. Below, we provide more detailed analyses of the relationships between motor unit spike amplitude and the recruitment probability as well as latency (relative to stride onset) of activation.

      We generated Author response image 1 to illustrate the relationship between the amplitude of motor units and their firing properties. As suspected, units with larger-amplitude waveforms fired with lower probability and produced their first spikes later in the stride. If we were comfortable assuming that larger spike amplitudes mean higher-force units, then this would be consistent with a key prediction of the size principle (i.e. that higher-force units are recruited later). However, we are hesitant to base any conclusions on this assumption or emphasize this point with a main-text figure, since EMG signal amplitude may also vary due to the physical properties of the electrode and distance from muscle fibers. Thus it is possible that a large motor unit may have a smaller waveform amplitude relative to the rest of the motor pool.

      Author response image 1.

      Relation between motor unit amplitude and (A) recruitment probability and (B) mean first spike time within the stride. Colored lines indicate the outcome of linear regression analyses.

      Currently, the data seem to support the idea that motor units that are alternately recruited across strides have recruitment thresholds close to the level of activation or force produced during slow walking. The fact that recruitment probability monotonically increases with speed suggests that the force required to propel the mouse forward exceeds the recruitment threshold of these "large" motor units. This pattern would primarily reflect spatial recruitment following the size principle rather than flexible motor unit control.

      We thank the Reviewer for this comment. We agree with this interpretation, particularly in relation to the references suggested in later comments, and have added the following text to the Discussion to better reflect this argument:

      “To investigate the neuromuscular control of locomotor speed, we quantified speed-dependent changes in both motor unit recruitment and firing rate. We found that the majority of units were recruited more often and with larger firing rates at faster speeds (Figure 5, Figure5–figure supplement 1). This result may reflect speed-dependent differences in the common input received by populations of motor neurons with varying spiking thresholds (Henneman et al., 1965). In the case of mouse locomotion, faster speeds might reflect a larger common input, increasing the recruitment probability as more neurons, particularly those that are larger and generate more force, exceed threshold for action potentials (Farina et al., 2014).”

      (4)    Analysis of recruitment and firing rates

      The authors currently report active duration and peak firing rates based on spike trains convolved with a Gaussian kernel. Why not report the peak of the instantaneous firing rates estimated from the inverse of the inter-spike interval? This approach appears to be more aligned with previous studies conducted to describe motor unit behaviour during fast movements (e.g., Desmedt & Godaux, 1977, J Physiol; Van Cutsem et al., 1998, J Physiol; Del Vecchio et al., 2019, J Physiol).

      We thank the Reviewer for this comment. In the revised Discussion (see ‘Firing rates in mouse locomotion compared to other species’) we reference several examples of previous studies that quantified spike patterns based on the instantaneous firing rate. We chose to report the peak of the smoothed firing rate because that quantification includes strides with zero spikes or only one spike, which occur regularly in our dataset (and for which ISI rate measures, which require two spikes to define an instantaneous firing rate, cannot be computed). Regardless, in the revised Figure 4B, we present an analysis that uses inter-spike intervals as suggested, which yielded similar ranges of firing rates as the primary analysis.

      (5)    Additional analyses of behaviour

      The authors currently analyse motor unit recruitment in relation to elbow angle. It would be valuable to include a similar analysis using the angular velocity observed during each stride, re broadly, comparing stride-by-stride changes in firing rates with changes in elbow angular velocity would further strengthen the final analyses presented in the results section.

      We thank the Reviewer for this comment. To address this, we have modified Figure 6 and the associated Supplemental Figures, to show relationships in unit activation with both the range of elbow extension and the range of elbow velocity for each stride. These new Supplemental Figures show that the trends shown in main text Figure 6C and 6E (which show data from all speed quartiles on the same axes) are also apparent in both the slower and faster quartiles individually, although single-quartile statistical tests (with smaller sample size than the main analysis) not reach statistical significance in all cases.

      Reviewer #3 (Public review):

      Summary:

      Using the approach of Myomatrix recording, the authors report that:

      (1) Motor units are recruited differently in the two types of muscles.

      (2) Individual units are probabilistically recruited during the locomotion strides, whereas the population bulk EMG has a more reliable representation of the muscle.

      (3) The recruitment of units was proportional to walking speed.

      Strengths:

      The new technique provides a unique data set, and the data analysis is convincing and well-performed.

      We thank the Reviewer for the comment.

      Weaknesses:

      The implications of "probabilistical recruitment" should be explored, addressed, and analyzed further.

      Comments:

      One of the study's main findings (perhaps the main finding) is that the motor units are "probabilistically" recruited. The authors do not define what they mean by probabilistically recruited, nor do they present an alternative scenario to such recruitment or discuss why this would be interesting or surprising. However, on page 4, they do indicate that the recruitment of units from both muscles was only active in a subset of strides, i.e., they are not reliably active in every step.

      If probabilistic means irregular spiking, this is not new. Variability in spiking has been seen numerous times, for instance in human biceps brachii motor units during isometric contractions (Pascoe, Enoka, Exp physiology 2014) and elsewhere. Perhaps the distinction the authors are seeking is between fluctuation-driven and mean-driven spiking of motor units as previously identified in spinal motor networks (see Petersen and Berg, eLife 2016, and Berg, Frontiers 2017). Here, it was shown that a prominent regime of irregular spiking is present during rhythmic motor activity, which also manifests as a positive skewness in the spike count distribution (i.e., log-normal).

      We thank the Reviewer for this comment and have clarified several passages in response. The Reviewer is of course correct that irregular motor unit spiking has been described previously and may reflect motor neurons’ operating in a high-sensitivity (fluctuation-driven) regime. We now cite these papers in the Discussion (see ‘Firing rates in mouse locomotion compared to other species’). Additionally, the revision clarifies that “probabilistically” - as defined in our paper - refers only to the empirical observation that a motor unit spikes during only a subset of strides, either when all locomotor speeds are considered together (Figure 2) or separately (Figure 5A-C):

      “Motor units in both muscles exhibited this pattern of probabilistic recruitment (defined as a unit’s firing on only a fraction of strides), but with differing distributions of firing properties across the long and lateral heads (Figure 2).”

      “Our findings (Figure 4) highlight that even with the relatively high firing rates observed in mice, there are still significant changes in firing rate and recruitment probability across the spikes within bursts (Figure 4B) and across locomotor speeds (Figure 5F). Future studies should more carefully examine how these rapidly changing spiking patterns derive from both the statistics of synaptic inputs and intrinsic properties of motor neurons (Manuel & Heckman, 2011; Petersen & Berg, 2016; Berg, 2017).”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      As mentioned above, there are several issues with the statistics that need to be corrected to properly support the claims made in the paper.

      The authors compare the fractions of MUs that show significant variation across locomotor speeds in their firing rate and recruitment probability. However, it is not statistically founded to compare the results of separate statistical tests based on different kinds of measurements and thus have unconstrained differences in statistical power. The comparison of the fractional changes in firing rates and recruitment across speeds that follow is helpful, though in truth, by contemporary standards, one would like to see error bars on these estimates. These could be generated using bootstrapping.

      The Reviewer is correct, and we have revised the manuscript to better clarify which quantities should or should not be compared, including the following passage (see “Motor unit mechanisms of speed control” in Results):

      “Speed-dependent increases in peak firing rate were therefore also present in our dataset, although in a smaller fraction of motor units (22/33) than changes in recruitment probability (31/33). Furthermore, the mean (± SE) magnitude of speed-dependent increases was smaller for spike rates (mean rate<sub>fast</sub>/rate<sub>slow</sub> of 111% ± 20% across all motor units) than for recruitment probabilities (mean p(recruitment)<sub>fast</sub>/p(recruitment)<sub>slow</sub> of 179% ± 3% across all motor units). While fractional changes in rate and recruitment probability are not readily comparable given their different upper limits, these findings could suggest that while both recruitment and peak rate change across speed quartiles, increased recruitment probability may play a larger role in driving changes in locomotor speed.”

      The description in the Methods of the tests for variation in firing rates and recruitment probability across speeds are extremely hard to understand - after reading many times, it is still not clear what was done, or why the method used was chosen. In the main text, the authors quote p-values and then state "bootstrap confidence intervals," which is not a statistical test that yields a p-value. While there are mathematical relationships between confidence intervals and statistical tests such that a one-to-one correspondence between them can exist, the descriptions provided fall short of specifying how they are related in the present instance. For this reason, and those described in what follows, it is not clear what the p-values represent.

      Next, the authors refer to fitting a model ("a Poisson distribution") to the data to estimate firing rate and recruitment probability, that the model results agree with their actual data, and that they then bootstrapped from the model estimates to get confidence intervals and compute p-values. Why do this? Why not just do something much simpler, like use the actual spike counts, and resample from those? I understand that it is hard to distinguish between no recruitment and just no spikes given some low Poisson firing rate, but how does that challenge the ability to test if the firing rates or the number of spiking MUs changes significantly across speeds? I can come up with some reasons why I think the authors might have decided to do this, but reasoning like this really should be made explicit.

      In addition, the authors would provide an unambiguous description of the model, perhaps using an equation and a description of how it was fit. For the bootstrapping, a clear description of how the resampling was done should be included. The focus on peak firing rate instead of mean (or median) firing rate should also be justified. Since peaks are noisier, I would expect the statistical power to be lower compared to using the mean or median.

      We thank the Reviewer for the comments and have revised and expanded our discussion of the statistical tests employed. We expanded and clarified our description of these techniques in the updated Methods section:

      “Joint model of rate and recruitment

      We modeled the recruitment probability and firing rate based on empirical data to best characterize firing statistics within the stride. Particularly, this allowed for multiple solutions to explain why a motor unit would not spike within a stride. From the empirical data alone, strides with zero spikes would have been assumed to have no recruitment of a unit. However, to create a model of motor unit activity that includes both recruitment and rate, it must be possible that a recruited unit can have a firing rate of zero. To quantify the firing statistics that best represent all spiking and non-spiking patterns, we modeled recruitment probability and peak firing rate along the following piecewise function:

      Eq. 1:

      Eq. 2:

      where y denotes the observed peak firing rate on a given stride (determined by convolving motor unit spike times with a Gaussian kernel as described above), p denotes the probability of recruitment, and λ denotes the expected peak firing rate from a Poisson distribution of outcomes. Thus, an inactive unit on a given stride may be the result of either non-recruitment or recruitment with a stochastically zero firing rate. The above equations were fit by minimizing the negative log-likelihood of the parameters given the data.”

      “Permutation test for joint model of rate and recruitment and type 2 regression slopes

      To quantify differences in firing patterns across walking speeds, we subdivided each mouse’s total set of strides into speed quartiles and calculated rate (𝜆, Eq. 1 and 2, Fig. 5A-C) and recruitment probability terms (p, Eq. 1 and 2, Fig. 5D-F) for each unit in each speed quartile. Here we calculated the difference in both the rate and recruitment terms across the fastest and slowest speed quartiles (p<sub>fast</sub>-p<sub>slow</sub> and 𝜆<sub>fast</sub>-𝜆<sub>slow</sub>). To test whether these model parameters were significantly different depending on locomotor speed, we developed a null model combining strides from both the fastest and slowest speed quartiles. After pooling strides from both quartiles, we randomly distributed the pooled set of strides into two groups with sample sizes equal to the original slow and fast quartiles. We then calculated the null model parameters for each new group and found the difference between like terms. To estimate the distribution of possible differences, we bootstrapped this result using 1000 random redistributions of the pooled set of strides. Following the permutation test, the 95% confidence interval of this final distribution reflects the null hypothesis of no difference between groups. Thus, the null hypothesis can be rejected if the true difference in rate or recruitment terms exceeds this confidence interval.

      We followed a similar procedure to quantify cross-muscle differences in the relationship between firing parameters. For each muscle, we estimated the slope across firing parameters for each motor unit using type 2 regression. In this case, the true difference was the difference in slopes between muscles. To test the null hypothesis that there was no difference in slopes, the null model reflected the pooled set of units from both muscles. Again, slopes were calculated for 1000 random resamplings of this pooled data to estimate the 95% confidence interval.”

      The argument for delayed activation of the lateral head is interesting, but I am not comfortable saying the nervous system creates a delay just based on observations of the mean time of the first spike, given the potential for differential variability in spike timing across muscles and MUs. One way to make a strong case for a delay would be to show aggregate PSTHs for all the spikes from all the MUs for each of the two heads. That would distinguish between a true delay and more gradual or variable activation between the heads.

      This is a good point and we agree that the claim made about the nervous system is too strong given the results. Even with Author response image 2 that the Reviewer suggested, there is still not enough evidence to isolate the role of the nervous system in the muscles’ activation.

      Author response image 2.

      Aggregate peristimulus time histogram (PSTH) for all motor unit spike times in the long head (top) and lateral head (bottom) within the stride.

      In the ideal case, we would have more simultaneous recordings from both muscles to make a more direct claim on the delay. Still, within the current scope of the paper, to correct this and better describe the difference in timing of muscle activity, we edited the text to the following:

      “These findings demonstrate that despite the synergistic (extensor) function of the long and lateral heads of the triceps at the elbow, the motor pool for the long head becomes active roughly 100 ms before the motor pool supplying the lateral head during locomotion (Figure 3C).”

      The results from Marshall et al. 2022 suggest that the recruitment of some MUs is not just related to muscle force, but also the frequency of force variation - some of their MUs appear to be recruited only at certain frequencies. Figure 5C could have shown signs of this, but it does not appear to. We do not really know the force or its frequency of variation in the measurements here. I wonder whether there is additional analysis that could address whether frequency-dependent recruitment is present. It may not be addressable with the current data set, but this could be a fruitful direction to explore in the future with MU recordings from mice.

      We agree that this would be a fruitful direction to explore, however the Reviewer is correct that this is not easily addressable with the dataset. As the Reviewer points out, stride frequency increases with increased speed, potentially offering the opportunity to examine how motor unit activity varies with the frequency, phase, and amplitude of locomotor movements. However, given our lack of force data (either joint torques or ground reaction forces), dissociating the frequency/phase/amplitude of skeletal kinematics from the frequency/phase/amplitude of muscle force. Marshall et al. (2022) mitigated these issues by using an isometric force-production task (Marshall et al., 2022). Therefore, while we agree that it would be a major contribution to extend such investigations to whole-body movements like locomotion, given the complexities described above we believe this is a project for the future, and beyond the scope of the present study.

      Minor:

      Page 5: "Units often displayed no recruitment in a greater proportion of strides than for any particular spike count when recruited (Figures 2A, B)," - I had to read this several times to understand it. I suggest rephrasing for clarity.

      We have changed the text to read:

      “Units demonstrated a variety of firing patterns, with some units producing 0 spikes more frequently than any non-zero spike count (Figure 2A, B),...”

      Figure 3 legend: "Mean phase ({plus minus} SE) of motor unit burst duration across all strides.": It is unclear what this means - durations are not usually described as having a phase. Do we mean the onset phase?

      We have changed the text to read:

      “Mean phase ± SE of motor unit burst activity within each stride”

      Page 9: "suggesting that the recruitment of individual motor units in the lateral and long heads might have significant (and opposite) effects on elbow angle in strides of similar speed (see Discussion)." I wouldn't say "opposite" here - that makes it sound like the authors are calling the long head a flexor. The authors should rephrase or clarify the sense in which they are opposite.

      This is a fair point and we agree we should not describe the muscles as ‘opposite’ when both muscles are extensors. We have removed the phrase ‘and opposite’ from the text.

      Page 11: "in these two muscles across in other quadrupedal species" - typo.

      We have corrected this error.

      Page 16: This reviewer cannot decipher after repeated attempts what the first two sentences of the last paragraph mean. - “Future studies might also use perturbations of muscle activity to dissociate the causal properties of each motor unit’s activity from the complex correlation structure of locomotion. Despite the strong correlations observed between motor unit recruitment and limb kinematics (Fig. 6, Supplemental Fig. 3), these results might reflect covariations of both factors with locomotor speed rather than the causal properties of the recorded motor unit.”

      For better clarity, we have changed the text to read:

      “Although strong correlations were observed between motor unit recruitment and limb kinematics during locomotion (Figure 6, Figure 6–figure supplement 1), it remains unclear whether such correlations actually reflect the causal contributions that those units make to limb movement. To resolve this ambiguity, future studies could use electrical or optical perturbations of muscle contraction levels (Kim et al., 2024; Lu et al., 2024; Srivastava et al., 2015, 2017) to test directly how motor unit firing patterns shape locomotor movements.The short-latency effects of patterned motor unit stimulation (Srivastava et al., 2017) could then reveal the sensitivity of behavior to changes in muscle spiking and the extent to which the same behaviors can be performed with many different motor commands.”

      Reviewer #2 (Recommendations for the authors):

      Minor comments:

      Introduction:

      (1) "Although studies in primates, cats, and zebrafish have shown that both the number of active motor units and motor unit firing rates increase at faster locomotor speeds (Grimby, 1984; Hoffer et al., 1981, 1987; Marshall et al., 2022; Menelaou & McLean, 2012)." I would remove Marshall et al. (2022) as their monkeys performed pulling tasks with the upper limb. You can alternatively remove locomotor from the sentence and replace it with contraction speed.

      Thank you for the comment. While we intended to reference this specific paper to highlight the rhythmic activity in muscles, we agree that this deviates from ‘locomotion’ as it is referenced in the other cited papers which study body movement. We have followed the Reviewer’s suggestion to remove the citation to Marshall et al.

      (2) "The capability and need for faster force generation during dynamic behavior could implicate motor unit recruitment as a primary mechanism for modulating force output in mice."

      The authors could add citations to this sentence, of works that showed that recruitment speed is the main determinant of the rate of force development (see for example Dideriksen et al. (2020) J Neurophysiol; J. L. Dideriksen, A. Del Vecchio, D. Farina, Neural and muscular determinants of maximal rate of force development. J Neurophysiol 123, 149-157 (2020)).

      Thank you for pointing out this important reference. We have included this as a citation as recommended.

      Results:

      (3) "Electrode arrays (32-electrode Myomatrix array model RF-4x8-BHS-5) were implanted in the triceps brachii (note that Figure 1D shows the EMG signal from only one of the 16 bipolar recording channels), and the resulting data were used to identify the spike times of individual motor units (Figure 1E) as described previously (Chung et al., 2023)."

      This sentence can be misleading for the reader as the array used by the researchers has 4 threads of 8 electrodes. Would it be possible to specify the number of electrodes implanted per head of interest? I assume 8 per head in most mice (or 4 bipolar channels), even if that's not specifically written in the manuscript.

      Thank you for the suggestion. As described above, we have added Table 1, which includes all array locations, and we edited the statement referenced in the comment as follows:

      “Electrode arrays (32-electrode Myomatrix array model RF-4x8-BHS-5) were implanted in forelimb muscles (note that Figure 1D shows the EMG signal from only one of the 16 bipolar recording channels), and the resulting data were used to identify the spike times of individual motor units in the triceps brachii long and lateral heads (Table 1, Figure 1E) as described previously (Chung et al., 2023).“

      (4) "These findings demonstrate that despite the overlapping biomechanical functions of the long and lateral heads of the triceps, the nervous system creates a consistent, approximately 100 ms delay (Figure 3C) between the activation of the two muscles' motor neuron pools. This timing difference suggests distinct patterns of synaptic input onto motor neurons innervating the lateral and long heads."

      Both muscles don't have fully overlapping biomechanical functions, as one of them also acts on the shoulder joint. Please be more specific in this sentence, saying that both muscles are synergistic at the elbow level rather than "have overlapping biomechanical functions".

      We agree with the above reasoning and that our manuscript should be clearer on this point. We edited the above text in accordance with the Reviewer suggestion as follows:

      "These findings demonstrate that despite the synergistic (extensor) function of the long and lateral heads of the triceps at the elbow, …”

      (5) "Together with the differences in burst timing shown in Figure 3B, these results again suggest that the motor pools for the lateral and long heads of the triceps receive distinct patterns of synaptic input, although differences in the intrinsic physiological properties of motor neurons innervating the two muscles might also play an important role."

      It is difficult to draw such an affirmative conclusion on the synaptic inputs from the data presented by the authors. The differences in firing rates may solely arise from other factors than distinct synaptic inputs, such as the different intrinsic properties of the motoneurons or the reception of distinct neuromodulatory inputs.

      To better explain our findings, we adjusted the above text in the Results (see “Motor unit firing patterns in the long and lateral heads of the triceps”):

      “Together with the differences in burst timing shown in Figure 3B, these results again suggest that the motor pools for the lateral and long heads of the triceps receive distinct patterns of synaptic input, although differences in the intrinsic physiological properties of motor neurons innervating the two muscles might also play an important role.”

      We also included the following distinction in the Discussion (see “Differences in motor unit activity patterns across two elbow extensors”) to address the other plausible mechanisms mentioned.

      “The large differences in burst timing and spike patterning across the muscle heads suggest that the motor pools for each muscle receive distinct inputs. However, differences in the intrinsic physiological properties of motor units and neuromodulatory inputs across motor pools might also make substantial contributions to the structure of motor unit spike patterns (Martínez-Silva et al., 2018; Miles & Sillar, 2011).”

      (6) "We next examined whether the probabilistic recruitment of individual motor units in the triceps and elbow extensor muscle predicted stride-by-stride variations in elbow angle kinematics."

      I'm not sure that the wording is appropriate here. The analysis does not predict elbow angle variations from parameters extracted from the spiking activity. It rather compares the average elbow angle between two conditions (motor unit active or not active).

      We thank the Reviewer for this comment and agree that the wording could be improved here to better reflect our analysis. To lower the strength of our claim, we replaced usage of the word

      ‘predict’ with ‘correlates’ in the above text and throughout the paper when discussing this result.

      Methods:

      (7) "Using the four threads on the customizable Myomatrix array (RF-4x8-BHS-5), we implanted a combination of muscles in each mouse, sometimes using multiple threads within the same muscle. [...] Some mice also had threads simultaneously implanted in their ipsilateral or contralateral biceps brachii although no data from the biceps is presented in this study."

      A precise description of the localisation of the array (muscles and the number of arrays per muscle) for each animal would be appreciated.

      (8) "A total of 33 units were identified and manually verified across all animals." A precise description of the number of motor units concurrently identified per muscle and per animal would be appreciated. Moreover, please add details on the manual inspection. Does it involve the manual selection of missing spikes? What are the criteria for considering an identified motor unit as valid?

      As discussed earlier, we added Table 1 to the main text to provide the details mentioned in the above comments.

      Regarding spike sorting, given the very large number of spikes recorded, we did not rely on manual adjusting mislabeled spikes. Instead, as described in the revised Methods section, we verified unit isolation by ensuring units had >98% of spikes outside of 1ms of each other. Moreover, as described above we have added new analyses (Figure 1–figure supplement 1) confirming the stability of motor unit waveforms across both the duration of individual recording sessions (roughly 30 minutes) and across the rapid changes in limb position within individual stride cycles (roughly 250 msec).

      Reviewer #3 (Recommendations for the authors):

      Figure 2 (and supplement) show spike count distributions with strong positive skewness, which is in accordance with the prediction of a fluctuation-driven regime. I suggest plotting these on a logarithmic x-axis (in addition to the linear axis), which should reveal a bell-shaped distribution, maybe even Gaussian, in a majority of the units.

      We thank the Reviewer for the suggestion. We present the requested analysis (Author response image 3), which shows bell-shaped distributions for some (but not all) distributions. However, we believe that investigating why some replotted distributions are Gaussian and others are not falls beyond the scope of this paper, and likely requires a larger dataset than the one we were able to obtain.

      Author response image 3.

      Spike count distributions for each motor unit on a logarithmic x-axis.

      Why not more data? I tried to get an overview of how much data was collected.

      Supplemental Figure 1 has all the isolated units, which amounts to 38 (are the colors the two muscle types?). Given there are 16 leads in each myomatrix, in two muscles, of six mice, this seems like a low yield. Could the authors comment on the reasons for this low yield?

      Regarding motor unit yield, even with multiple electrodes per muscle and a robust sorting algorithm, we often isolated only a few units per muscle. This yield likely reflects two factors. First, because of the highly dynamic nature of locomotion and high levels of muscle contraction, isolating individual spikes reliably across different locomotor speeds is inherently challenging, regardless of the algorithm being employed. Second, because the results of spike-train analyses can be highly sensitive to sorting errors, we have only included the motor units that we can sort with the highest possible confidence across thousands of strides.

      Minor:

      Figure captions especially Figure 6: The text is excessively long. Can the text be shortened?

      We thank the Reviewer for this comment. Generally, we seek to include a description of the methods and results within the figure captions, but we concede that we can condense the information in some cases. In a number of cases, we have moved some of the descriptive text from the caption to the Methods section.

      References

      Berg, R. W. (2017). Neuronal Population Activity in Spinal Motor Circuits: Greater Than the Sum of Its Parts. Frontiers in Neural Circuits, 11. https://doi.org/10.3389/fncir.2017.00103

      Biewener, A. A., Blickhan, R., Perry, A. K., Heglund, N. C., & Taylor, C. R. (1988). Muscle Forces During Locomotion in Kangaroo Rats: Force Platform and Tendon Buckle Measurements Compared. Journal of Experimental Biology, 137(1), 191–205. https://doi.org/10.1242/jeb.137.1.191

      Chung, B., Zia, M., Thomas, K. A., Michaels, J. A., Jacob, A., Pack, A., Williams, M. J., Nagapudi, K., Teng, L. H., Arrambide, E., Ouellette, L., Oey, N., Gibbs, R., Anschutz, P., Lu, J., Wu, Y., Kashefi, M., Oya, T., Kersten, R., … Sober, S. J. (2023). Myomatrix arrays for high-definition muscle recording. eLife, 12, RP88551. https://doi.org/10.7554/eLife.88551

      De Luca, C. J. (1985). Control properties of motor units. Journal of Experimental Biology, 115(1), 125–136. https://doi.org/10.1242/jeb.115.1.125

      De Luca, C. J., & Erim, Z. (1994). Common drive of motor units in regulation of muscle force. Trends in Neurosciences, 17(7), 299–305. https://doi.org/10.1016/0166-2236(94)90064-7

      Farina, D., Negro, F., & Dideriksen, J. L. (2014). The effective neural drive to muscles is the common synaptic input to motor neurons. The Journal of Physiology, 592(16), 3427–3441. https://doi.org/10.1113/jphysiol.2014.273581

      Hartigan, P. M. (1985). Algorithm AS 217: Computation of the Dip Statistic to Test for Unimodality. Applied Statistics, 34(3), 320. https://doi.org/10.2307/2347485

      Henneman, E., Somjen, G., & Carpenter, D. O. (1965). FUNCTIONAL SIGNIFICANCE OF CELL SIZE IN SPINAL MOTONEURONS. Journal of Neurophysiology, 28(3), 560–580. https://doi.org/10.1152/jn.1965.28.3.560

      Karabulut, D., Dogru, S. C., Lin, Y.-C., Pandy, M. G., Herzog, W., & Arslan, Y. Z. (2020). Direct Validation of Model-Predicted Muscle Forces in the Cat Hindlimb During Locomotion. Journal of Biomechanical Engineering, 142(5), 051014. https://doi.org/10.1115/1.4045660

      Kim, J. J., Wyche, I. S., Olson, W., Lu, J., Bakir, M. S., Sober, S. J., & O’Connor, D. H. (2024). Myo-optogenetics: Optogenetic stimulation and electrical recording in skeletal muscles. https://doi.org/10.1101/2024.06.21.600113

      Lu, J., Zia, M., Baig, D. A., Yan, G., Kim, J. J., Nagapudi, K., Anschutz, P., Oh, S., O’Connor, D., Sober, S. J., & Bakir, M. S. (2024). Opto-Myomatrix: μLED integrated microelectrode arrays for optogenetic activation and electrical recording in muscle tissue. https://doi.org/10.1101/2024.07.01.601601

      Manuel, M., & Heckman, C. J. (2011). Adult mouse motor units develop almost all of their force in the subprimary range: A new all-or-none strategy for force recruitment? Journal of Neuroscience, 31(42), 15188–15194. https://doi.org/10.1523/JNEUROSCI.2893-11.2011

      Marshall, N. J., Glaser, J. I., Trautmann, E. M., Amematsro, E. A., Perkins, S. M., Shadlen, M. N., Abbott, L. F., Cunningham, J. P., & Churchland, M. M. (2022). Flexible neural control of motor units. Nature Neuroscience, 25(11), 1492–1504. https://doi.org/10.1038/s41593-022-01165-8

      Martínez-Silva, M. de L., Imhoff-Manuel, R. D., Sharma, A., Heckman, C. J., Shneider, N. A., Roselli, F., Zytnicki, D., & Manuel, M. (2018). Hypoexcitability precedes denervation in the large fast-contracting motor units in two unrelated mouse models of ALS. eLife, 7(2007), 1–26. https://doi.org/10.7554/eLife.30955

      Miles, G. B., & Sillar, K. T. (2011). Neuromodulation of Vertebrate Locomotor Control Networks. Physiology, 26(6), 393–411. https://doi.org/10.1152/physiol.00013.2011

      Petersen, P. C., & Berg, R. W. (2016). Lognormal firing rate distribution reveals prominent fluctuation–driven regime in spinal motor networks. eLife, 5. https://doi.org/10.7554/elife.18805

      Srivastava, K. H., Elemans, C. P. H., & Sober, S. J. (2015). Multifunctional and Context-Dependent Control of Vocal Acoustics by Individual Muscles. The Journal of Neuroscience, 35(42), 14183–14194. https://doi.org/10.1523/JNEUROSCI.3610-14.2015

      Srivastava, K. H., Holmes, C. M., Vellema, M., Pack, A. R., Elemans, C. P. H., Nemenman, I., & Sober, S. J. (2017). Motor control by precisely timed spike patterns. Proceedings of the National Academy of Sciences of the United States of America, 114(5), 1171–1176. https://doi.org/10.1073/pnas.1611734114

    1. Author response:

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

      We are pleased that Reviewer 3 appreciated our findings and found the temporal lag between the expression of TFF1 and TFF3 during signaling particularly interesting. The reviewer also advised us not to overemphasize that this lag arises from phase separation of ERα at the TFF1 locus, as the use of 1,6-hexanediol alone is not sufficient to conclusively establish whether ERα condensates undergo liquid–liquid phase separation. We agree with this assessment and have revised the manuscript accordingly. Specifically, we have modified the title to remove reference to phase separation and have updated the text throughout the manuscript to avoid claiming that the observed condensates are a result of phase separation. The revised title is: “Ligand-dependent Enhancer Activation Indirectly Modulates Non-target Promoters in a Chromatin Domain.”

      With these changes, we are proceeding with the Version of Record using revised version of the manuscript.

      ———

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

      Reviewer #1:

      Summary:

      The manuscript by Bohra et al. describes the indirect effects of ligand-dependent gene activation on neighboring non-target genes. The authors utilized single-molecule RNA-FISH (targeting both mature and intronic regions), 4C-seq, and enhancer deletions to demonstrate that the non-enhancer-targeted gene TFF3, located in the same TAD as the target gene TFF1, alters its expression when TFF1 expression declines at the end of the estrogen signaling peak. Since the enhancer does not loop with TFF3, the authors conclude that mechanisms other than estrogen receptor or enhancer-driven induction are responsible for TFF3 expression. Moreover, ERα intensity correlations show that both high and low levels of ERα are unfavorable for TFF1 expression. The ERa level correlations are further supported by overexpression of GFP-ERa. The authors conclude that transcriptional machinery used by TFF1 for its acute activation can negatively impact the TFF3 at peak of signaling but once, the condensate dissolves, TFF3 benefits from it for its low expression.

      Strengths:

      The findings are indeed intriguing. The authors have maintained appropriate experimental controls, and their conclusions are well-supported by the data.

      Weaknesses:

      There are some major and minor concerns that related to approach, data presentation and discussion. But I think they can be fixed with more efforts.

      We thank the reviewer for their positive comments on the paper. We have addressed all their specific recommendations below.  

      The deletion of enhancer reveals the absolute reliance of TFF1 on its enhancers for its expression. Authors should elaborate more on this as this is an important finding.

      We thank the reviewer for the comment. We have now added a more detailed discussion on the requirement of enhancer for TFF1 expression in the revised manuscript (line 368-385).  

      In Fig. 1, TFF3 expression is shown to be induced upon E2 signaling through qRT-PCR, while smFISH does not display a similar pattern. The authors attribute this discrepancy to the overall low expression of TFF3. In my opinion, this argument could be further supported by relevant literature, if available. Additionally, does GRO-seq data reveal any changes in TFF3 expression following estrogen stimulation? The GRO-seq track shown in Fig.1 should be adjusted to TFF3 expression to appreciate its expression changes.

      We have now included a browser shot image of TFF3 region showing GRO-Seq signal at E2 time course (Fig. S1C). We observed an increased transcription towards the 3’ end of TFF3 gene body at 3h.  The increased transcription at 3h, corroborates with smFISH data. The relative changes of TFF3 expression measured by qRT-PCR and smFISH for intronic transcripts are somewhat different, we speculate that such biased measurements that are dependent on PCR amplifications could be more for genes that express at low levels and smFISH using intronic probes may be a more sensitive assay to detect such changes.    

      Since the mutually exclusive relationship between TFF1 and TFF3 is based on snap shots in fixed cells, can authors comment on whether the same cell that expresses TFF1 at 1h, expresses TFF3 at 3h? Perhaps, the calculations taking total number of cells that express these genes at 1 and 3h would be useful.

      Like pointed out by the reviewer, since these are fixed cells, we cannot comment on the fate of the same cell at two time points. To further address this limitation, future work could employ cells with endogenous tags for TFF1 and TFF3 and utilize live cell imaging techniques. In a fixed cell assay, as the reviewer suggests, it can be investigated whether a similar fraction shows high TFF3 expression at 3h, as the fraction that shows high TFF1 expression at 1 h. To quantify the fractions as suggested by the reviewer, we plotted the fraction of cells showing high TFF1 and TFF3 expression at 1h and 3h. We identify truly high expressing cells by taking mean and one standard deviation (for single cell level data) at E2-1hr as the threshold for TFF1 (80 and above transcript counts) and mean and one standard deviation (for single cell level data) at E2-3hr as the threshold for TFF3 (36 and above transcript counts). The fraction with high TFF1 expression at 1h  (12.06 ± 2.1) is indeed comparable to that with high TFF3 expression at 3h (12.50 ± 2.0) (Fig. 2C and Author response image 1). We should note that if the transcript counts were normally distributed, a predetermined fraction would be expected to be above these thresholds and comparable fractions can arise just from underlying statistics. But in our experiments, this is unlikely to be the case given the many outliers that affect both the mean and the standard deviation, and the lack of normality and high dispersion in single cell distributions. Of course, despite the fractions being comparable, we cannot be certain if it is the same set of cells that go from high expression of TFF1 to high expression of TFF3, but definitely that is a possibility. We thank the reviewer for pointing out this comparison.

      Author response image 1.

      The graph represents the percent of cells that show high expression for TFF1 and TFF3 at 1h and 3h post E2 signaling. The threshold was collected by pooling in absolute RNA counts from 650 analyzed cells (as in Fig. 2C). The mean and standard deviation over single cell data were calculated. Mean plus one standard deviation was used to set the threshold for identifying high expressing cells. For TFF1, as it maximally expresses at 1h the threshold used was 80. For TFF3, as it maximally expresses at 3h the threshold used was 36. Fraction of cells expressing above 80 and 36 for TFF1 and TFF3 respectively were calculated from three different repeats. Mean of means and standard deviations from the three experiments are plotted here.

      Authors conclude that TFF3 is not directly regulated by enhancer or estrogen receptor. Does ERa bind on TFF3 promoter? 

      The ERa ChIP-seq performed at 1h and 3h of signaling suggests that TFF3 promoter is not bound by ERa as shown in supplementary Fig. 1B and S1B. However, one peak upstream to TFF1 promoter is visible and that is lost at 3h. 

      Minor comments:

      Reviewer’s comment -The figures would benefit from resizing of panels. There is very little space between the panels.

      We have now resized the figures in the revised manuscript.

      The discussion section could include an extrapolation on the relationship between ERα concentration and transcriptional regulation. Given that ERα levels have been shown to play a critical role in breast cancer, exploring how varying concentrations of ERα affect gene expression, including the differential regulation of target and non-target genes, would provide valuable insights into the broader implications of this study.

      This is a very important point that was missing from the manuscript. We have included this in the discussion in the revised manuscript (line 426-430).

      Reviewer #2:

      Summary:

      In this manuscript by Bohra et al., the authors use the well-established estrogen response in MCF7 cells to interrogate the role of genome architecture, enhancers, and estrogen receptor concentration in transcriptional regulation. They propose there is competition between the genes TFF1 and TFF3 which is mediated by transcriptional condensates. This reviewer does not find these claims persuasive as presented. Moreover, the results are not placed in the context of current knowledge.

      Strengths:

      High level of ERalpha expression seems to diminish the transcriptional response. Thus, the results in Fig. 4 have potential insight into ER-mediated transcription. Yet, this observation is not pursued in great depth however, for example with mutagenesis of ERalpha. However, this phenomenon - which falls under the general description of non monotonic dose response - is treated at great depth in the literature (i.e. PMID: 22419778). For example, the result the authors describe in Fig. 4 has been reported and in fact mathematically modeled in PMID 23134774. One possible avenue for improving this paper would be to dig into this result at the single-cell level using deletion mutants of ERalpha or by perturbing co-activators.

      We thank the reviewer for pointing us to the relevant literature on our observation which will enhance the manuscript. We have discussed these findings in relations to ours in the discussion section (Line 400-413). We thank the reviewer for insight on non-monotonic behavior.

      Weaknesses:

      There are concerns with the sm-RNA FISH experiments. It is highly unusual to see so much intronic signal away from the site of transcription (Fig. 2) (PMID: 27932455, 30554876), which suggests to me the authors are carrying out incorrect thresholding or have a substantial amount of labelling background. The Cote paper cited in the manuscript is likewise inconsistent with their findings and is cited in a misleading manner: they see splicing within a very small region away from the site of transcription. 

      We thank the reviewer for this comment, and apologize if they feel we misrepresented the argument from Cote et al. This has now been rectified in the manuscript. However, we do not agree that the intronic signals away from the site of transcription are an artefact. First, the images presented here are just representative 2D projections of 3D Z-stacks; whereas the full 3D stack is used for spot counting using a widely-used algorithm that reports spot counts that are constant over wide range of thresholds (Raj et al., 2008). The veracity of automated counts was first verified initially by comparison to manual counts. Even for the 2D representations the extragenic intronic signals show up at similar thresholds to the transcription sites. 

      The signal is not non-specific arising from background labeling, explained by following reasons:

      • To further support the time-course smFISH data and its interpretation without depending on the dispersed intronic signal, we have analyzed the number of alleles firing/site of transcription at a given time in a cell under the three conditions. We counted the sites of transcription in a given cell and calculated the percentage of cells showing 1,2,3,4 or >4 sites. We see that the percent of cells showing a single site of transcription for TFF1 is very high in uninduced cells and this decreases at 1h. At 1h, the cells showing 2, 3 and 4 sites of transcription increase which again goes down at 3h (Author response image 2A). This agrees with the interpretation made from mean intronic counts away from the site of transcription. Similarly, for TFF3, the number of cells showing 2,3 and 4 sites of transcription increase slightly at 3hr compared to uninduced and 1hr (Author response image 2B).  We can also see that several cells have no alleles firing at a given time as has been quantified in the graphs on right showing total fraction of cells with zero versus non-zero alleles firing (Author response image 2A-B). A non-specific signal would be present in all cells.

      • There is literature on post-transcriptional splicing of RNA beyond our work, which suggests that intronic signal can be found at relatively large distances away from the site of transcription. Waks et al. showed that some fraction of unspliced RNA could be observed up to 6-10 microns away from the site of transcription suggesting that there can be a delay between transcription and (alternative) splicing (Waks et al., 2011). Pannuclear disperse intronic signals can arise as there can be more than one allele firing at a time in different nuclear locations. The spread of intronic transcripts in our images is also limited in cells in which only 1 allele is firing at E2-1 hour (Author response image 2C) or uninduced cells (Author response image 2D). Furthermore, Cote et al. discuss that “Of note, we see that increased transcription level correlates with intron dispersal, suggesting that the percentage of splicing occurring away from the transcription site is regulated by transcription level for at least some introns. This may explain why we observe posttranscriptional splicing of all genes we measured, as all were highly expressed.” This is in line with our interpretation that intron signal dispersal can occur in case of posttranscriptional splicing (Coté et al., 2023). Additionally, other studies have suggested that transcripts in cells do not necessarily undergo co-transcriptional splicing which leads us to conclude that intronic signal can be found farther away from the site of transcription. Coulon et al. showed that splicing can occur after transcript release from the site and suggested that no strict checkpoint exists to ensure intron removal before release which results in splicing and release being kinetically uncoupled from each other (Coulon et al., 2014). Similarly, using live-cell imaging, it was shown that splicing is not always coupled with transcription, and this could depend on the nature and structural features of transcript (such as blockage of polypyrimidine tract which results in delayed recognition) (Vargas et al., 2011). Drexler  et al. showed that as opposed to drosophila transcripts that are shorter, in mammalian cells, splicing of the terminal intron can occur post-transcriptionally (Drexler et al., 2020). Using RNA polymerase II ChIP-Seq time course data from ERα activation in the MCF-7 cells, Honkela et al. showed that large number of genes can show significant delays between the completion of transcription and mRNA production (Honkela et al., 2015). This was attributed to faster transcription of shorter genes which results in splicing  delays suggesting rapid completion of transcription on shorter genes can lead to splicing-associated delays (Honkela et al., 2015). More recently, comparisons of nascent and mature RNA levels suggested a time lapse between transcription and splicing for the genes that are early responders during signaling (Zambrano et al., 2020). The presence of significant numbers of TFF1 nascent RNA in the nucleus in our data corroborates with above observations. 

      • Uniform intensities across many transcripts suggests these are true signal arising from RNA molecules which would not be the case for non-specific, background signal (Author response image 2E).

      • Splicing occurs in the nucleus and intron containing pre-transcripts should be nuclear localized. Thus, intronic signals should remain localized to the nucleus unlike the mature mRNA which translocate to the cytoplasm after processing and thus exonic signals can be found both in the nucleus and the cytoplasm. In keeping with this, we observe no signal in the cytoplasm for the intronic probes and it remains localized within the nucleus as expected and can be seen in Author response image 2F, while exonic signals are observed in both compartments. This suggests to us that the signal is coming from true pre-transcripts. There is no reason for non-specific background labelling to remain restricted to the nucleus.

      • We observe that the mean intronic label counts for both the genes TFF1 and TFF3 increases upon E2-induction compared to uninduced condition (Fig. 2B). Similarly, the mean intronic count for both genes reduce drastically in the TFF1-enhancer deleted cells (Fig. 3C, D). This change in the number of intronic signal specifically on induction and enhancer deletion suggests that the signal is not an artefact and arises from true nascent transcripts that are sensitive to stimulus or enhancer deletion.

      • We expect colocalization of intronic signal with exonic signals in the nucleus, while there can be exonic signals that do not colocalize with intronic, representing more mature mRNA. Indeed, we observe a clear colocalization between the intronic and exonic signals in the nucleus, while exonic signals can occur independent of intronic both in the nucleus and the cytoplasm. This clearly demonstrates that the intronic signals in our experiments are specific and not simply background labelling (Author response image 2G).

      These studies and the arguments above lead us to conclude that the presence of intronic transcripts in the nucleus, away from the site of transcription is not an artefact. We hope the reviewer will agree with us. These analyses have now been included in the manuscript as Supplementary Figure 6 and have been added in the manuscript at line numbers 106-111, 201204,  215-217 and line 231-235. We thank the reviewer for raising this important point.

      Author response image 2.

      Dynamic induction and RNA localization of TFF1 and TFF3 transcription across cell populations using smRNA FISH A. Bar graph depicting the percentage of cells with 1,2,3,4, or greater than 4 sites of transcription for TFF1 (left) is shown. The graph shows the mean of means from different repeats of the experiment, and error bars denote SEM (n>200, N=3). Only the cells with at least one allele firing were counted and cells with no alleles were not included in this. The graph on right shows the number of cells with zero or non-zero number of alleles firing. B. Bar graph depicting the percentage of cells with 1,2,3,4 or greater than 4 sites of transcription for TFF3 (left) is shown. The graph shows the mean of means from different repeats of the experiment, and error bars denote SEM (n>200, N=3). Only the cells with at least one allele firing were counted and cells with no alleles were not included in this. The graph in the middle shows the number of cells with 2,3,4 or greater than 4 sites of transcription for TFF3.The graph on the right shows the number of cells with zero or non-zero number of alleles firing. C. Images from single molecule RNA FISH experiment showing transcripts for InTFF1 in cells induced for 1 hour with E2. The image shows that when a single allele of TFF1 is firing, the transcripts show a more spatially restricted localisation. The scale bar is 5 microns. D. Images from single molecule RNA FISH experiment showing transcripts for InTFF1 in uninduced cells. The image shows that when a single allele of TFF1 is firing and transcription is low, the transcripts show a more spatially restricted localisation. The scale bar is 5 microns. E. Line profile through several transcripts in the nucleus show uniform and similar intensities indicating that these are true signals. F. 60X Representative images from a single molecule RNA FISH experiment showing transcripts for InTFF1 and ExTFF1 (top) and InTFF3 and ExTFF3 (bottom). The image shows that there is no intronic signal in the cytoplasm, while exonic signals can be found both in the nucleus and the cytoplasm. The scale bar is 5 microns. G. 60X Representative images from single molecule RNA FISH experiment showing transcripts for InTFF1 and ExTFF1. The image shows that all intronic signals are colocalized with exonic signals, but all exonic signals are expectedly not colocalized with intronic signals, representing more mature mRNA. The scale bar is 5 microns.

      One substantial way to improve the manuscript is to take a careful look at previous single cell analysis of the estrogen response, which in some cases has been done on the exact same genes (PMID: 29476006, 35081348, 30554876, 31930333). In some of these cases, the authors reach different conclusions than those presented in the present manuscript. Likewise, there have been more than a few studies that have characterized these enhancers (the first one I know of is: PMID 18728018). Also, Oh et al. 2021 (cited in the manuscript) did show an interaction between TFF1e and TFF3, which seems to contradict the conclusion from Fig. 3. In summary, the results of this paper are not in dialogue with the field, which is a major shortcoming. 

      We thank the reviewer for pointing out these important studies. The studies from Prof. Larson group are particularly very insightful (Rodriguez et al., 2019). We have now included this in the discussion (line 106-111 and line 420-424) where we suggest the differences and similarities between our, Larson’s group and also Mancini’s group (Patange et al., 2022; Stossi et al., 2020). 

      The 4C-Seq data from the manuscript Oh et al. 2021 is exactly consistent with our observation from Fig 3 as they also observed little to no interaction between TFF1e and TFF3p in WT cells, only upon TFF1p deletion, did the TFF1e become engaged with the TFF3p. In agreement with this, we also observe little to no interaction between TFF1e and TFF3p in WT cells (Fig.3A). This is also consistent with our competition model for resources between these two genes. Oh et al. shows interaction between TFF1e and TFF3 when the TFF1 promoter is deleted showing that when the primary promoter is not available the enhancer is retargeted to the next available gene (Oh et al., 2021). It does not show that in WT or at any time point of E2 signalling does TFF1e and TFF3 interact.

      In the opinion of this reviewer, there are few - if any - experiments to interrogate the existence of LLPS for diffraction-limited spots such as those associated with transcription. This difficulty is a general problem with the field and not specific to the present manuscript. For example, transient binding will also appear as a dynamic 'spot' in the nucleus, independently of any higher-order interactions. As for Fig. 5, I don't think treating cells with 1,6 hexanediol is any longer considered a credible experiment. For example, there are profound effects on chromatin independent of changes in LLPS (PMID: 33536240).  

      We are cognizant of and appreciate the limitations pointed out by the reviewer. We and others have previously shown that ERa forms condensates on TFF1 chromatin region using ImmunoFISH assay (Saravanan et al., 2020).  The data below shows the relative mean ERα intensity on TFF1 FISH spots and random regions clearly showing an appearance of the condensate at the TFF1 site. Further, the deletion of TFF1e causes the reduction in size of this condensate. Thus, we expect that these ERα condensates are characterized by higher-order interactions and become disrupted on treatment with 1,6-hexanediol. These condensates are the size of below micron as mentioned by the reviewer, but most TF condensates are of the similar sizes. We agree with the reviewer that 1,6- hexanediol treatment is a brute-force experiment with several irreversible changes to the chromatin. Although we have tried to use it at a low concentration for a short period of time and it has been used in several papers (Chen et al., 2023; Gamliel et al., 2022). The opposite pattern of TFF1 vs. TFF3 expression upon 1,6- hexanediol treatment suggests that there is specificity. Further, to perturb condensates, mutants of ERa can be used (N-terminus IDR truncations) however, the transcriptional response of these mutants is also altered due to perturbed recruitment of coactivators that recognize Nterminus of ER, restricting the distinction between ERa functions and condensate formation.

      References:

      Chen, L., Zhang, Z., Han, Q., Maity, B. K., Rodrigues, L., Zboril, E., Adhikari, R., Ko, S.-H., Li, X., Yoshida, S. R., Xue, P., Smith, E., Xu, K., Wang, Q., Huang, T. H.-M., Chong, S., & Liu, Z. (2023). Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions. Molecular Cell, 83(19), 3438-3456.e12. https://doi.org/10.1016/j.molcel.2023.08.027

      Coté, A., O’Farrell, A., Dardani, I., Dunagin, M., Coté, C., Wan, Y., Bayatpour, S., Drexler, H. L., Alexander, K. A., Chen, F., Wassie, A. T., Patel, R., Pham, K., Boyden, E. S., Berger, S., Phillips-Cremins, J., Churchman, L. S., & Raj, A. (2023). Post-transcriptional splicing can occur in a slow-moving zone around the gene. eLife, 12. https://doi.org/10.7554/eLife.91357.2

      Coulon, A., Ferguson, M. L., de Turris, V., Palangat, M., Chow, C. C., & Larson, D. R. (2014). Kinetic competition during the transcription cycle results in stochastic RNA processing. eLife, 3, e03939. https://doi.org/10.7554/eLife.03939

      Drexler, H. L., Choquet, K., & Churchman, L. S. (2020). Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores. Molecular Cell, 77(5), 985-998.e8. https://doi.org/10.1016/j.molcel.2019.11.017

      Gamliel, A., Meluzzi, D., Oh, S., Jiang, N., Destici, E., Rosenfeld, M. G., & Nair, S. J. (2022). Long-distance association of topological boundaries through nuclear condensates. Proceedings of the National Academy of Sciences of the United States of America, 119(32), e2206216119. https://doi.org/10.1073/pnas.2206216119

      Honkela, A., Peltonen, J., Topa, H., Charapitsa, I., Matarese, F., Grote, K., Stunnenberg, H. G., Reid, G., Lawrence, N. D., & Rattray, M. (2015). Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays. Proceedings of the National Academy of Sciences of the United States of America, 112(42), 13115. https://doi.org/10.1073/pnas.1420404112

      Oh, S., Shao, J., Mitra, J., Xiong, F., D’Antonio, M., Wang, R., Garcia-Bassets, I., Ma, Q., Zhu, X., Lee, J.-H., Nair, S. J., Yang, F., Ohgi, K., Frazer, K. A., Zhang, Z. D., Li, W., & Rosenfeld, M. G. (2021). Enhancer release and retargeting activates disease-susceptibility genes. Nature, 595(7869), Article 7869. https://doi.org/10.1038/s41586-021-03577-1

      Patange, S., Ball, D. A., Wan, Y., Karpova, T. S., Girvan, M., Levens, D., & Larson, D. R. (2022). MYC amplifies gene expression through global changes in transcription factor dynamics. Cell Reports, 38(4). https://doi.org/10.1016/j.celrep.2021.110292

      Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A., & Tyagi, S. (2008). Imaging individual mRNA molecules using multiple singly labeled probes. Nature Methods, 5(10), Article 10. https://doi.org/10.1038/nmeth.1253

      Rodriguez, J., Ren, G., Day, C. R., Zhao, K., Chow, C. C., & Larson, D. R. (2019). Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity. Cell, 176(1–2), 213-226.e18. https://doi.org/10.1016/j.cell.2018.11.026

      Saravanan, B., Soota, D., Islam, Z., Majumdar, S., Mann, R., Meel, S., Farooq, U., Walavalkar, K., Gayen, S., Singh, A. K., Hannenhalli, S., & Notani, D. (2020). Ligand dependent gene regulation by transient ERα clustered enhancers. PLOS Genetics, 16(1), e1008516. https://doi.org/10.1371/journal.pgen.1008516

      Stossi, F., Dandekar, R. D., Mancini, M. G., Gu, G., Fuqua, S. A. W., Nardone, A., De Angelis, C., Fu, X., Schiff, R., Bedford, M. T., Xu, W., Johansson, H. E., Stephan, C. C., & Mancini, M. A. (2020). Estrogeninduced transcription at individual alleles is independent of receptor level and active conformation but can be modulated by coactivators activity. Nucleic Acids Research, 48(4), 1800. https://doi.org/10.1093/nar/gkz1172

      Vargas, D. Y., Shah, K., Batish, M., Levandoski, M., Sinha, S., Marras, S. A. E., Schedl, P., & Tyagi, S. (2011). Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing. Cell, 147(5), 1054–1065. https://doi.org/10.1016/j.cell.2011.10.024

      Waks, Z., Klein, A. M., & Silver, P. A. (2011). Cell-to-cell variability of alternative RNA splicing. Molecular Systems Biology, 7(1), 506. https://doi.org/10.1038/msb.2011.32

      Zambrano, S., Loffreda, A., Carelli, E., Stefanelli, G., Colombo, F., Bertrand, E., Tacchetti, C., Agresti, A., Bianchi, M. E., Molina, N., & Mazza, D. (2020). First Responders Shape a Prompt and Sharp NF-κB-Mediated Transcriptional Response to TNF-α. iScience, 23(9), 101529. https://doi.org/10.1016/j.isci.2020.101529

    1. Author response:

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

      eLife Assessment

      This study provides a valuable characterization of individual sarcomere's contractility and synchrony in spontaneously beating cardiomyocytes as a function of substrate stiffness. The authors, however, provide an incomplete explanation for the observed heterogeneous and stochastic dynamics, so that the work remains mainly descriptive. The work will be of interest to scientists working on muscle biophysics, nonlinear dynamics, and synchronization phenomena in biological systems.

      We appreciate the reviewer’s insightful comments. A detailed explanation of the described phenomena in the form of a theoretical model and simulations was not included in our manuscript, because we believed it would be most impactful to present a detailed quantitative statistical description of the experiments in one manuscript and then introduce the model, which we already had in preparation, in a separate manuscript to avoid diluting the overall message.

      However, following the reviewers’ advice, we have now included a comprehensive model into the revised manuscript. This model qualitatively and quantitatively explains the experimentally observed phenomena and introduces a novel class of coupled relaxation oscillators based on a non-monotonic force-velocity relationship of individual sarcomeres. We believe that this addition significantly strengthens the manuscript.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In this manuscript, the authors experimentally demonstrated the heterogeneous behavior of sarcomeres in cardiomyocytes and that a stochastic component exists in their contractile activity, which cancels out at the level of myofibrils.

      Strengths:

      The experiments and data analysis are robust and valid. With very good statistics and unbiased methods, they show cellular activity at the individual level and highlight the heterogeneity between biological networks. The similarity of the results to the study cited in [24] demonstrates the validity of the in vitro setup for answering these questions and the feasibility of such in-vitro systems to extend our knowledge of physiology.

      Weaknesses:

      Compared to the current literature ([24]), the study does not show a high degree of innovation. It mainly confirms what has been established in the past. The authors complemented the published experiments by developing an in vitro setup with stem cells and by changing the stiffness of the substrate to simulate pathological conditions. However, the experiments they performed do not allow them to explain more than the study in [24], and the conclusions of their study are based on interpretation and speculation about the possible mechanism underlying the observations.

      We thank the reviewer for contextualizing our work with the literature. We appreciate the comparison to the study by Kobirumaki-Shimozawa et al. which we cite prominently. They observed stochastically varying beating patterns of individual sarcomeres on a beat-to-beat basis. They propose that this arises from a "titin-based mechanism" operating stochastically, which they interpret as being fundamentally linked to sarcomere-length-dependent effects. This interpretation differs from our model. We feel that the inclusion of our comprehensive model in the revised manuscript will emphasize the significance and novelty of our findings. Our work proposes a distinct alternative mechanistic explanation for the observed stochasticity, grounded in the force-velocity relationship and intrinsic stochasticity, and presents additional novel dynamic phenomena (such as popping and high-frequency oscillations) not reported in the literature yet. We outline the key advancements of our study below:

      (1) Physiologically Relevant Human Model System: Our study utilizes human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Using a human cell model provides direct relevance for understanding human cardiac physiology and pathophysiology, overcoming limitations inherent in translating findings from rodent models. The hiPSC-CMs exhibit key physiological differences from the mouse ventricular myocytes observed in [24], most notably beating at a significantly lower frequency (~1 Hz or 60 bpm) compared to mice (~5-8 Hz or 300-500 bpm). This difference in timescale is critical as it allowed us to resolve complex intra-beat dynamics that may be different and also harder to observe in mouse cardiomyocytes.

      (2) Advanced Experimental Methodology and Resolution: We developed a novel assay incorporating our SarcAsM algorithm for high-throughput tracking and analysis of individual sarcomere dynamics. This approach gave us spatial resolution better than 20 nm at significantly higher sampling rates than previous studies, including Kobirumaki-Shimozawa et al. Furthermore, our high-throughput in vitro approach made it possible to analyze vastly larger datasets than, e.g., the study by Kobirumaki-Shimozawa et al. (which reports observations from fewer than 20 myofibrils, encompassing less than 200 sarcomeres in total). While we recognize that in-vivo tissue studies present unique experimental challenges, the substantially greater statistical power of our study is crucial for reliably characterizing the complex, stochastic dynamics we report. The enhanced resolution and statistical robustness are not merely incremental; they enable the detailed identification and analysis of heterogeneous behaviors that were previously inaccessible or could not be characterized with the same level of confidence.

      (3) Novel Observed Phenomena: Our high-resolution data reveals specific dynamic behaviors, such as sarcomere "popping" and high-frequency oscillations during contraction, which, to our knowledge, have not been previously reported or characterized in cardiomyocytes. The resolution limitations and the high beating frequency in mouse models may not have permitted the observation of these subtle, but potentially important phenomena.

      (4) Distinct Mechanistic Explanation and Model: Kobirumaki-Shimozawa et al. propose a qualitative model where sarcomere motion variability primarily arises from length-dependent activation. This view is essentially a static one, based on a long history of isometric skeletal muscle experiments, where time-dependent forces are not relevant. We argue that in highly dynamic cardiomyocytes this may not be the most useful approach. While we acknowledge length dependence can play a role, our integrated experimental-theoretical work proposes a different primary mechanism. Our model demonstrates that the observed stochastic heterogeneity and beat-to-beat variations, including the oscillatory motion and popping, can be quantitatively explained by dynamic instabilities arising from a non-monotonic force-velocity relationship of individual sarcomeres in conjunction with intrinsic sarcomere-level stochastic fluctuations. The model emphasizes the active, transient nature of force generation rather than solely assuming length dependence. Our model provides an alternative explanation for the observed dynamics, and a quantitative, mechanism-based understanding.

      Reviewer #2 (Public Review):

      Summary:

      Sarcomeres, the contractile units of skeletal and cardiac muscle, contract in a concerted fashion to power myofibril and thus muscle fiber contraction.

      Muscle fiber contraction depends on the stiffness of the elastic substrate of the cell, yet it is not known how this dependence emerges from the collective dynamics of sarcomeres. Here, the authors analyze the contraction time series of individual sarcomeres using live imaging of fluorescently labeled cardiomyocytes cultured on elastic substrates of different stiffness. They find that reduced collective contractility of muscle fibers on unphysiologically stiff substrates is partially explained by a lack of synchronization in the contraction of individual sarcomeres.

      This lack of synchronization is at least partially stochastic, consistent with the notion of a tug-of-war between sarcomeres on stiff sarcomeres. A particular irregularity of sarcomere contraction cycles is 'popping', the extension of sarcomeres beyond their rest length. The statistics of 'popping' suggest that this is a purely random process.

      Strengths:

      This study thus marks an important shift of perspective from whole-cell analysis towards an understanding of the collective dynamics of coupled, stochastic sarcomeres.

      Weaknesses:

      Further insight into mechanisms could be provided by additional analyses and/or comparisons to mathematical models.

      We thank the reviewer for the feedback. We have enhanced the manuscript by a comprehensive dynamic model, that we also contrast with previously proposed models.

      Reviewer #3 (Public Review):

      Summary:

      The manuscript of Haertter and coworkers studied the variation of length of a single sarcomere and the response of microfibrils made by sarcomeres of cardiomyocytes on soft gel substrates of varying stiffnesses.

      The measurements at the level of a single sarcomere are an important new result of this manuscript. They are done by combining the labeling of the sarcomeres z line using genetic manipulation and a sophisticated tracking program using machine learning. This single sarcomere analysis shows strong heterogeneities of the sarcomeres that can show fast oscillations not synchronized with the average behavior of the cell and what the authors call popping events which are large amplitude oscillations. Another important result is the fact that cardiomyocyte contractility decreases with the substrate stiffness although the properties of single sarcomeres do not seem to depend on substrate stiffness.

      The authors suggest that the cardiomyocyte cell behavior is dominated by sarcomere heterogeneity. They show that the heterogeneity between sarcomeres is stochastic and that the contribution of static heterogeneity (such as composition differences between sarcomeres) is small.

      Strengths:

      All the results are to my knowledge new and original and deserve attention.

      Weaknesses:

      However, I find the manuscript a bit frustrating because the authors only give very qualitative explanations of the phenomena that they observe. They mention that popping could be explained by a nonlinear force-velocity relation of the sarcomere leading to a rapid detachment of all motors. However, they do not explicitly provide a theoretical description. How would the popping depend on the parameters and in particular on the substrate stiffness? Would the popping statistics be affected by the stiffness? It is also not clear to me how the dependence on the soft gel stiffness of the cardiomyocyte cell can be explained by the stochasticity of the sarcomere properties. Can any of the results found by the authors be explained by existing theories of cardiomyocytes? The only one I know is that of Safran and coworkers.

      I also found the paper very difficult to read. The authors should perhaps reorganize the structure of the presentation in order to highlight what the new and important results are.

      We are grateful for this detailed and critical feedback. The observed phenomena (stochastic heterogeneity, popping, high-frequency oscillatory motion) can indeed be explained by a nonmonotonic force-velocity relation along with stochastic fluctuations of individual sarcomeres. At the time of initial submission of this manuscript, we already had a theoretical model in preparation, which both qualitatively and quantitatively explains the observed phenomena. As a result, we included certain interpretations preemptively, which caused some lack of clarity in the absence of the full model. We have now added the model to this manuscript, providing a mechanistic interpretation of our findings. The model is different from prior models in that it emphasizes time-dependent forces, typically disregarded in models built to understand isometric skeletal muscle experiments.

      We have shortened, streamlined and restructured our manuscript to improve the readability and accessibility of our study.

      Recommendations for the authors:

      There is a consensus among reviewers that the link between the stiffness dependence of the observed stochastic dynamics and the proposed tug-of-war mechanism is unclear. More quantitative support and discussion is required, possibly using theoretical modeling.

      We are grateful for the insightful and comprehensive feedback by both editor and reviewers. As suggested, we have now added a comprehensive model explaining the observed phenomena and presenting a new conceptual view on cardiac muscle dynamics.

      Reviewer #1 (Recommendations For The Authors):

      The authors addressed an interesting question related to the dynamics of cardiac cells and their multiscale dynamics. They did a good job in terms of experimental design and data analysis. However, I fear that they do not contribute enough new information to the topic.

      The authors should refer to the study in [24] and explain better the difference between these two studies. Although the different approaches are quite obvious, it is not clear to me what additional insights they add to the problem. They conducted their experiments with different stiffnesses. However, the conclusions they draw from the study are based on speculation (e.g. about the behavior of myosin heads in relation to shortening and relaxation), while their data mainly confirm previous studies. They need to address more explicitly the novelty of their study.

      Novelty and Comparison with Previous Studies: We understand the concern about distinguishing our contribution from prior work, specifically Kobirumaki-Shimozawa et al., 2021.

      As detailed in our public response, these are the key advances:

      Use of a medically relevant human iPSC-CM model vs. mouse cardiomyocytes.

      Superior spatial and temporal resolution via our SarcAsM algorithm, revealing novel phenomena like popping and high-frequency oscillations not previously reported.

      Significantly greater statistical power due to our high-throughput in vitro assay.

      We added a distinct mechanistic explanation based on the dynamic force-velocity relationship and sarcomere-level stochasticity, contrasting with the static, deterministic titin/length-dependence focus of previous studies.

      Interpretation and Speculation: We acknowledge that without the explicit model, some interpretations in the initial submission appeared speculative. As noted in our public response, we had already started to develop a theoretical model explaining our observations at the time of submission, targeting a second follow-up publication. Including interpretations based on this unpublished model prematurely clearly caused confusion. We now include the full model in the revised manuscript.

      Integration of the Theoretical Model: We have now fully integrated the model into the revised manuscript. The model explicitly demonstrates how the non-monotonic force-velocity relationship of individual sarcomeres leads to dynamic instabilities around a critical force threshold. This instability along with stochasticity drives a 'tug-of-war' between coupled sarcomeres, generating complex emergent behaviors.

      Mechanistic Explanation Beyond Length-Dependence: Our model quantitatively reproduces all key experimental findings (stochastic heterogeneity, popping, oscillations) without relying on length-dependent activation effects. This strongly supports our conclusion that the active, transient dynamics of individual sarcomeres governed by the force-velocity relationship are fundamental drivers of these complex contractile patterns. We believe this provides a significant conceptual advance, highlighting a potentially underappreciated aspect of sarcomere dynamics. Previous models focused mostly on length-dependence, historically based on skeletal muscle fiber experiments that were often done under static, isometric conditions. We feel that the new model represents a substantial paradigm shift in understanding highly dynamic muscles such as heart muscle.

      We are confident that the inclusion of the model addresses the majority of the reviewer's concerns.

      Additional comments:

      The authors write of a tug-of-war competition between the sarcomeres, and I'm not sure what they mean by that. I would spend more words explaining this point, especially because it seems to be an important point to describe their results. Similarly, they talked about an all-or-nothing phenomenon when they described the elongation of sarcomeres. What do they mean by this?

      We have revised the manuscript where clarification was needed and now define the terms mentioned more explicitly.

      (1) "Tug-of-War": We used this term metaphorically to describe the mechanical competition between linearly coupled sarcomeres within a myofibril, especially when contracting against rigid external boundary conditions. While it is not a perfect analogy, the metaphor intuitively captures the inherent instability of this interaction: similar to how a team in a real tug-of-war might suddenly yield when one person tires and the rest of team gets overloaded, rather than steadily losing ground, the dynamic instability arising from the non-monotonic force-velocity relationship (detailed in our model, lines 300ff) can cause individual sarcomeres to abruptly change state (e.g., shorten or rapidly lengthen) while under tension from their neighbors. We have removed the term from the title and now use it more sparingly within the manuscript to better reflect its role as an illustrative analogy.

      (2) "All-or-Nothing" Elongation (Popping): The term "popping" describes our experimental observation of sudden, rapid, and extensive elongation of individual sarcomeres. This typically occurs late in the contraction cycle during early relaxation, when overall force may be declining, but individual sarcomeres can still experience significant tension from their neighbors. We described this specific type of rapid elongation in the original manuscript as an "all-or-nothing" phenomenon because, typically, sarcomeres in these events yield rapidly and strongly overshoot their resting length without recovering in a given activation cycle. The speed of popping events is substantially higher than the speed of coordinated gradual shortening observed during systoles that is driven by bound myosin heads. This observation strongly suggests an instability-driven, avalanche-like unbinding of myosin heads from the actin filaments during these events.

      We agree that the term "all-or-nothing" is not precise, and we have removed it, as it is not essential for describing the observed "popping" dynamics.

      The authors claim that the popping frequency increases as a function of stiffness. However, Figure 4E does not really seem to be a common practice in terms of statistical significance. A better description could help to remove this doubt.

      We clarified the presentation of popping frequency data and its statistical interpretation.

      (1) Popping Frequency vs. Substrate Stiffness (previously Figure 4D, now Figure 3G):

      We first corrected that the dependence of popping frequency on substrate stiffness was presented in Figure 4D, not 4E. In the revised, shortened manuscript it can be now found in Fig. 3G. Due to the large number of observations (N) in our dataset, the slight upward trend in popping frequency with increasing substrate stiffness shown in Figure 4D does reach statistical significance using standard tests. For details see Figure captions.

      (2) Popping Frequency vs. Sarcomere Resting Length (previously Figure 4E, now Figure 3H):

      Figure 4E addresses the relationship between popping frequency and the individual sarcomere's resting length. To generate this plot, we binned sarcomeres based on their measured resting length (in intervals of 0.02 µm) and calculated the mean popping frequency within each bin across all conditions. We have now clarified this in the figure caption.

      (3) Interpretation of Length Dependence:

      While Figure 3H clearly shows that longer sarcomeres are more prone to popping, we argue this is likely a modulating factor rather than the sole underlying cause. Two key observations support this interpretation:

      Even very short sarcomeres (e.g., < 1.65 µm resting length) exhibit a non-zero popping frequency (around 5-10%), indicating that popping is not exclusive to long sarcomeres.

      The distribution of resting lengths, now added to the graph, is narrower than the wide range (1.6-2.0 µm) plotted in Figure 3H. Popping still occurs stochastically within a myofibril of sarcomere with relatively similar resting lengths.

      Therefore, while length clearly influences the probability of popping, the phenomenon itself appears to be fundamentally stochastic, occurring across a range of lengths. This is consistent with our model in which dynamic instabilities (driven by the non-linear force-velocity relationship) and stochastic fluctuations are the primary triggers, while length affects probability of occurrence.

      Changes in Manuscript:

      We have revised the text associated with Figures 3G and 3H to clarify the distinction between stiffness and length dependence.

      We have added a statement in the Methods section and figure legends (e.g., Legend for Fig 3) explaining our approach to statistical analysis and interpretation for large datasets where standard p-values may be less informative.

      We believe these clarifications directly address the reviewer's concerns about the data presentation and interpretation in Figure 3.

      Reviewer #2 (Recommendations For The Authors):

      This is an interesting study, which however could and should be extended, see below. The current manuscript contains much less information than its length suggests; its figures contain partially redundant data.

      Taking into account this critical feedback, we have restructured, streamlined and shortened the manuscript to improve readability and accessibility.

      (1) How regular are the cellular contraction cycles?

      Have the authors computed a coefficient of variation of cycle durations?

      Does this regularity depend on substrate stiffness?

      We have substantially improved the detection accuracy of contraction intervals compared to our initial submission (details see SarcAsM, https://www.biorxiv.org/content/10.1101/2025.04.29.650605v1). We calculated the beating rate variability (defined as the standard deviation of cycle durations), and found a low variability of on average less than 0.05 s across the tested conditions. The distribution of this variability is positively skewed, with the majority of values clustering near zero. We have added new panels showing these results to Fig. S2B.

      (2) Which experiments could the authors perform to identify the origin of the apparent 3-Hz oscillations?

      Would these oscillations persist even if the cardiomyocytes would not beat?

      We now address these questions in the revised manuscript.

      (1) Active Nature: The ~3 Hz oscillations are clearly linked to active contraction. They are absent in quiescent, non-beating cardiomyocytes observed under identical conditions, confirming that they are not passive fluctuations or baseline cellular tremors.

      (2) Signal Fidelity: We are confident these are genuine physiological events, not artifacts. Our high temporal resolution (~15 ms frame time) and tracking accuracy (< 20 nm) allow reliable detection because events are well above system noise. This is now explained in the revised manuscript.

      (3) Can the authors augment their study by modeling?

      For example, could the experimental data be fitted by a Kuramoto-type model of the form d phi_i / dt = eps*sin( Omega - phi_i ) + lambda*sin( phi_i - phi_i+1 ) + xi_i, combining phase-locking of sarcomere oscillations with phase phi_i to intracellular calcium oscillations with phase Omega, and anti-phase synchronization between neighboring sarcomeres, as well as noise xi?

      If yes, how would the coupling strength depend on subtrate stiffness?

      We now added a model. While a Kuramoto-type phase model is powerful for studying synchronization, we determined that a more mechanistic approach was required. Crucially, sarcomeres are mechanically coupled in series within a myofibril, and this direct physical linkage is not well-represented by the abstract, phase-based coupling of a Kuramoto model.

      Instead, our model comprises serially coupled sarcomeres, each governed by an underdamped Langevin equation. This framework allowed us to infer the force-velocity relation without any prior assumptions directly from our experimental data, revealing a critical non-monotonic characteristic. As we now emphasize in the revised manuscript, this behavior is mathematically equivalent to a Van-der-Pol relaxation oscillator, which reflects the instability-driven nature of the system.

      Furthermore, and in line with the reviewer's suggestion, our model incorporates a stochastic noise term which we found essential for reproducing the observed phenomena. Without this noise term, the characteristic sarcomere dynamics do not emerge (Fig. 5).

      (4) What is the maximally extended length of titin, and how does this length correspond to the maximal length of popping sarcomeres?

      The force-extension curves of titin have been measured in single-molecule experiments (and the packing density of titin is known) - can the authors use this information to infer the forces acting inside sarcomeres?

      We thank the reviewer for this thoughtful question. While sarcomere length during popping can be measured, inferring the corresponding intra-sarcomeric force is not straightforward in a living, contracting cardiomyocyte. The relationship between extension and force is complex and dynamic, involving multiple molecular components.

      Our data show elongations up to 0.5 μm during popping events. While this magnitude is plausibly within the extensibility range of titin and other mechanically relevant components (Caporizzo & Prosser, 2021; Loescher & Linke, 2023), directly inferring force from this observation is challenging. In such a multi-component system with both active and passive elements, total force comprises several factors that cannot be disentangled from a simple length measurement alone. First, the system is dominated by active, velocity-dependent force generation of cross-bridges, which our model shows is non-monotonic. Second, titin exhibits a restoring force that is strongly strain-rate dependent (Rief et al., 1997), critical during rapid elongation. Third, viscous drag forces within the sarcomere are also highly strain-rate dependent, contributing significantly during rapid length changes. Fourth, other structural elements such as microtubules and intermediate filaments contribute to viscoelastic properties, particularly at high strains (Caporizzo & Prosser, 2021). This complex interplay makes it impossible to map a given sarcomere length to a unique force value using single-molecule titin data alone.

      (5) I urge the authors to make their raw data openly available.

      We agree on the importance of data availability. While the complete raw imaging dataset is several hundred gigabytes and thus impractical to deposit, we have uploaded a comprehensive dataset to Zenodo to ensure full reproducibility. This repository includes a representative subset of raw imaging data (50 cells per condition), with corresponding sarcomere motion data provided in a readable JSON format. Crucially, the deposition also contains the complete aggregated data underlying all figures and statistical analyses presented in the manuscript. All provided data can be programmatically accessed and analyzed using our `SarcAsM` Python API. The data can be accessed at: https://doi.org/10.5281/zenodo.17564384.

      Minor

      (1) How did the authors determine the start and end of contraction cycles when analyzing their data?

      The start and end points of each contraction cycle were identified using ContractionNet, a custom convolutional neural network we developed for this purpose. This method, used for all analyses in the revised manuscript, detects contraction intervals with high accuracy directly from sarcomere dynamics time-series data and significantly outperforms the threshold-based approach used previously. The complete methodology, algorithm description, and validation of ContractionNet are detailed in our companion paper on the SarcAsM analysis software

      (www.biorxiv.org/content/10.1101/2025.04.29.650605v1, see Fig. S6).

      (2) What are the measurement errors in determining Delta_SL?

      The measurement error for the Z-band trajectories is approximately 17 nm. This high tracking accuracy is achieved with our deep-learning-based Z-band segmentation approach, which employs a 3D convolutional neural network (3D U-Net) to leverage both spatial and temporal context for robust Z-band segmentation in noisy, high-speed recordings. A full description of this validation is available in our SarcAsM companion paper (see Figure S3 therein).

      (3) Does popping occur while other sarcomeres are still contracting?

      This is an important point. Yes, popping frequently occurs while other sarcomeres within the same myofibril are still actively shortening. This simultaneity is clearly visualized in the newly added Movie M1, which displays a phase-space plot (velocity vs. length change relative to rest) for all tracked sarcomeres over time. In this visualization, popping events appear as trajectories moving into the top-right quadrant (rapid elongation), while concurrently, other sarcomeres are represented by points in the left quadrants (negative velocity), indicating ongoing shortening. We have included Movie M1 as supplementary material.

      (4) The authors argue that their data on popping sarcomeres is consistent with homogeneous popping probabilities.

      (5) Can the authors assess in simulations how dispersed the popping probabilities of individual sarcomeres could be before they would notice a statistically significant difference to the homogeneous case?

      This question touches on a key challenge in analyzing these complex dynamics. A direct statistical test of popping probability for each individual sarcomere is not feasible, as the number of events per sarcomere over our observation time is too low for robust single-unit analysis. Consequently, our approach relies on testing the cumulative distributions of inter-event spatial distances and temporal gaps across all sarcomeres within a given region (LOI).

      In nearly half of the analyzed LOIs, these cumulative distributions were statistically indistinguishable (p > 0.05) from the geometric distribution expected for a single, homogeneous stochastic process. This provides strong support for our primary conclusion that popping is fundamentally a random phenomenon.

      For the cases that deviate from the homogeneous model, we argue that this does not refute the underlying stochasticity of the events. Instead, we propose this is the expected statistical signature of pooling data from a population of sarcomeres that have slight, intrinsic variations in their individual popping probabilities due to factors like resting length or structural integrity. Even if each sarcomere's popping is a locally random event, a cumulative test performed on a population with varied baseline probabilities is expected to detect a deviation from a simple, homogeneous model.

      Regarding the requested simulation study: While we agree this would be methodologically informative, the sensitivity to detect probability dispersion depends on multiple interacting factors (number of sarcomeres per LOI, observation time, event rates, and the assumed form of heterogeneity). Any single simulation scenario would therefore be highly model-dependent and of limited generality. Rather than introducing additional assumptions, we base our conclusions on the observed agreement with the homogeneous model in approximately half of LOIs and the correlation of deviations with measurable properties (Fig. 4E). A comprehensive statistical analysis would constitute a substantial methodological study beyond the scope of this mechanistically focused manuscript.

      (6) Can the authors measure sarcomere rest length and check if this rest length is correlated with the popping probability of individual sarcomeres?

      Yes, we performed this analysis. As shown in Figure 3H (previously Fig. 4E), we found a positive correlation between sarcomere resting length and popping frequency, confirming that longer sarcomeres have a higher probability of popping.

      Importantly, however, the popping probability remains non-zero even for shorter sarcomeres. As detailed in our response to Reviewer #1 regarding this figure, we interpret resting length as a significant modulating factor that influences popping probability, rather than the sole determinant of the phenomenon.

      (7) Several mathematical models of sarcomere contraction exist (e.g., crossbridge models).

      (8) Could the authors perform computer simulations of several such stochastic sarcomere models coupled in series?

      Alternatively, could the authors discuss this?

      As I understand, references 16-18 model myofibril contraction assuming static variability of sarcomeres, but do not account for stochasticity in the contractility of individual sarcomeres.

      We thank the reviewer for this excellent suggestion. We have performed such simulations, and the theoretical model is a central component of our revised manuscript (new Figures 4 and 5; manuscript lines 316ff).

      As the reviewer points out, previous models (e.g., refs 12 and 14 in our manuscript) have often relied on predefined static variability between sarcomeres to explain heterogeneous behavior. Our work takes a fundamentally different approach. We model the myofibril as a chain of serially coupled sarcomeres, where the dynamics of each unit are governed by an underdamped Langevin equation. This formulation inherently incorporates stochasticity and describes the interplay between a non-monotonic, velocity-dependent active force, a length-dependent passive force, and the mechanical coupling to its neighbors.

      Crucially, the model parameters were not assumed, but were instead inferred by fitting the model directly to our experimental data using a gradient-free optimization algorithm. This data-driven stochastic model was sufficient to quantitatively reproduce key observed phenomena, including high-frequency oscillations and popping events. Our central finding is that these complex behaviors emerge naturally from the coupled system, driven by the non-monotonic force-velocity relationship and intrinsic stochastic fluctuations. This demonstrates that predefined static heterogeneity is not required to explain the observed dynamics.

      (9) The manuscript could be shortened (e.g., lines 52-56 in the introduction provide little extra value).

      We have significantly revised the entire manuscript to improve clarity and readability. We have removed sentences in the introduction as suggested and substantially restructured major sections. One of the main reasons for this was the integration of our theoretical model, which was originally prepared as a separate manuscript. This required us to completely reframe the introduction and reorganize the figures and results.

      We are confident that these extensive changes have resulted in a stronger, more concise and impactful paper that now integrates our experimental findings with a theoretical model.

      (10) Figure 2 is overloaded with data. Several panels could be moved to the SM without compromising the key message.

      Introducing the notation in panels Figures 2A-C does not seem ideal to me; maybe add a cartoon?

      We agree that the Fig. 2 was dense. We have redesigned panels A-F to improve clarity and better guide the reader. We now use a consistent color-coding scheme to link the extrema in the phase portraits (A-C) to the corresponding distributions of individual sarcomeres (E-G). We have also revised the accompanying text to make the figure's logic more transparent.

      We have considered moving panels A-C to the supplementary materials. However, we believe their placement in the main text is crucial for two reasons:

      (1) Revealing Core Dynamics: The length-velocity phase portrait is the first visualization that reveals the underlying near-oscillatory dynamics of individual sarcomeres. This was not an assumed behavior but a critical experimental observation that directly motivated our entire theoretical modeling effort. We now also provide animated versions of these plots (Movies X-Y) to further illustrate these complex dynamics.

      (2) Enabling Model-Experiment Comparison: A phase portrait is a standard tool for comparing experimental data with theoretical models. Retaining it in the main text allows us to directly compare data and model in our new Figures 4 and 5, providing a clear validation of our model.

      (11) Similarly, Figures 4F, G, and H seem dispensable to me.

      (I also wonder how clear the analogy of a coin flip is if a biased coin with probabilities p and 1-p needs to be used.)

      We agree that the previous Figure 4F, which served a purely illustrative purpose, was dispensable and have removed it. The "coin flip" analogy was potentially confusing and we have removed it.

      As part of a broader restructuring of the manuscript, the quantitative analyses from the original Figures 4G and 4H are now presented as Figures 3I and 3J. They provide important supporting evidence for the stochastic nature of the resulting popping events. We believe retaining this quantitative analysis is valuable, and we hope that by streamlining the figure and removing the analogy, we have addressed the reviewer's concerns.

      (12) Equation (1) is unnecessarily complicated. The same holds for Equation (2).

      It might make sense to separate definitions for serial and mutual correlations.

      (This would also simplify the axes labels in Figure 3C.)

      (13) The notation used in Equation (1) is not fully clear.

      I assume t denotes a unit-less time index and T is the unit-less duration of a contraction cycle, measured in multiples of a fixed time interval?

      Regarding comments (12) and (13):

      We thank the reviewer for these helpful suggestions. In response to comment (12), we have separated the definitions for the mutual (r<sub>m</sub>) and serial (r<sub>s</sub>) correlation coefficients, presenting them as distinct calculations rather than as special cases of a single, more complex formula. This makes their definitions more direct and explicit. The calculation for the serial correlation coefficient has also been streamlined into a concise inline definition.

      In response to comment (13), we have clarified the notation in Equation (1). In the manuscript text (lines 208f), we now explicitly state that 𝑡 represents the discrete, unitless time index (i.e., the frame number) within a time-series, and 𝑇 is the total number of frames (i.e., the total duration in frames) of a given contraction cycle.

      While Equation (1) itself is the standard definition for the uncentered correlation coefficient and cannot be algebraically simplified, we have added text to specify this and justify its use. This metric (equivalent to cosine similarity) is appropriate for our analysis as it assesses the similarity in the shape of motion patterns, independent of their mean values.

      Finally, to further streamline the paper, we have removed the velocity correlation analysis and the corresponding parts of Figure 3.

      (14) The authors should make clear in all figures what is experiment and what is simulation.

      We have now clarified the nature of each graph in the figure captions.

      (15) The caption of Figure 3C could be simplified.

      We have simplified all figure captions.

      (16) I found Figure 3A hard to understand.

      We concluded that Figure 3A was confusing and did not add essential information to the manuscript. We have removed it entirely.

      Reviewer #3 (Recommendations For The Authors):

      In conclusion, l think that the manuscript would gain a lot if some more precise and more quantitative interpretation of the results were given. This might require a collaboration with theorists.

      We have integrated a novel theoretical framework into the revised manuscript (new Figures 4 and 5; manuscript lines 300ff as described above.

      This new section introduces a data-driven, stochastic dynamical model that simulates the myofibril as a chain of serially coupled sarcomeres. Each sarcomere's motion is governed by an underdamped Langevin equation, a formulation that inherently accounts for stochasticity. Crucially, our model incorporates a non-monotonic force-velocity relationship inferred directly from our experimental data, rather than relying on predefined static variability between sarcomeres a key distinction from previous theoretical work.

      This integrated model successfully and quantitatively reproduces all major experimental phenomena described in the paper, including high-frequency oscillations and stochastic "popping" events. It demonstrates that these complex behaviors emerge naturally as dynamic instabilities from the coupled system. This addition elevates the manuscript from a descriptive study to one that provides a predictive, mechanism-driven framework for understanding sarcomere dynamics.

    1. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The factors that create and maintain diversity in host-associated microbiomes remain poorly understood. A better understanding of these factors will help in the efforts to leverage the adaptive potential of the microbiome to help solve pressing problems in health and agriculture.

      Experimental evolution provides a promising path forward as we can track the causes and consequences in the emergence of novel variants, but experimental evolution remains underutilized in host-microbiome interactions. Here, Gracia-Alvira utilizes a long-term experimental evolution study in Drosophila simulans under hot and cold temperature regimes to identify strain-level variation in an important fly bacterium, Lactiplantibacillus plantarum. They identify three strains of L. plantarum, which are most prevalent in their respective three temperature regimes, suggesting that these are locally adapted bacteria. Then, using a combination of genomics, in vitro, and in vivo, Gracia-Alvira et al attempt to understand the factors that led to the differentiation of the hot and cold L. plantarum and their impacts on the fly host.

      Strengths:

      This is an excellent use of experimental evolution to track the emergence of novelty in the microbiome. The genomic analyses are all solid and appropriate for the data sets. It is especially striking that the comparisons with the other, independent experimental evolution studies in different labs (and across continents between Portugal and South Africa) show a consistent response to temperature. Many have disregarded the microbiome as it is something that is too sensitive to seemingly innocuous variables (particularly in the fly microbiome), such that we cannot find generalities. However, this finding highlights the potential for experimental evolution to uncover these dynamics. The question of how strains emerge and are maintained is timely and is one of the key open questions in host-microbiome evolution currently.

      Weaknesses:

      (1) The framing in the title and throughout the discussion about "subspecies competition" does not match the data that was collected. The subspecies competition requires actually tracking the competitive outcomes between the hot, cold, and unevolved L. plantarum. In the in vivo work, I can see that mixes of the strains were made, but they did not track whether the cold strain outcompeted the hot strain in vivo under cold conditions, for example.

      We thank the reviewer for the honest concern and take this opportunity to defend our claim of "subspecies competition used across the manuscript. As the reviewer states, subspecies competition requires tracking the competitive outcomes between the three clades, and this is what we did by sampling and sequencing across ten years of experimental evolution (Figures 4 and S3). For this reason, we point that the subspecies competition assessment comes from the direct observation of changes in relative abundance across the time series, and not from the follow-up experiments in vivo or in vitro.

      While Figure 4 is suggestive that there is ongoing competition in the hot temperature regime, this is not necessarily shown in the cold, which is dominated by the C clade. It could also be that the bacteria cannot survive in the flies at the different temperatures. The growth curve assays hint that the bacteria can grow, but the plate reader couldn't actually maintain the 18 {degree sign}C temperature (line 455). So all of this evidence is very indirect and insufficient to say that strain competition is driving these patterns.

      We thank the reviewer for the alternative hypothesis that could explain the observed subspecies dynamic. We rule out that dominance of clade C in the cold occurs because the other two clades cannot grow in this regime based on three pieces of evidence:

      (1) In the time series, clades H and U decrease, but never disappear (Figures 4 and S3), even showing some peaks of abundance in specific replicate populations (Figure S3).

      (2) We isolated individuals belonging to clade H in the cold-evolved populations, as shown in figure 2. This is a direct evidence that clade H prevails in the cold-evolved populations, although in low abundance.

      (3) We did grow the three taxa in fly food petri dishes incubated at both temperature regimes, observing growth in all cases.

      We will include the food growth experiment in the revised manuscript as further supporting evidence for growth in both regimes.

      (2) The in vivo results are interesting in that there appears to be a fitness cost of clade C, but the explanation is underdeveloped. I say under-developed because in Figure 4, the cold L. plantarum remains much higher throughout adaptation to the hot temperature regime than the hot L. plantarum in the cold regime. The hot L. plantarum is low abundance throughout the cold regime. I felt like this observation was not explained, but it seems relevant to understanding the strain dynamics.

      We acknowledge that a strong fitness cost of clade C is observed in axenic D. melanogaster. In the native host, D. simulans, with reduced microbiome, we observed delayed development that could even be an advantage depending on the situation, as pointed out by reviewer 3 in the recommendations.

      Even if we assume that flies colonized with clade C are less fit in the experimental evolution, another caveat is whether the flies can actively select for the L. plantarum clade. Under this assumption, a clade that imposes a fitness cost to the fly (clade C) should be selected against over time because the flies colonized by this clade will have less offspring, or develop later than the rest. Alternatively, as the microbiome is shared among all the individuals in the population, the host might not be able to “purge” the pernicious clade, and L. plantarum dynamics might be controlled solely by the relative fitness between clades in the given experimental treatment. We will discuss this hypothesis in the revision as a way to explain the relationship between the abundance of each clade and the effect on the host.

      I will also note that this is not the first time that L. plantarum or other Lactobacillus have been shown to exert fitness costs to Drosophila. Gould, PNAS, 2018, shows that both Lactobacillus plantarum and Lactobacillus brevis in mono-association have lower fitness (measured through Leslie matrix projections using lifespan and fecundity) than axenic flies. Many studies of wild Drosophila fail to find Lactobacillus, or it is low abundance (e.g., Chandler, PLoS Genetics, 2014; Wang, Environmental Microbiology Reports, 2018; Henry & Ayroles, Molecular Ecology, 2022; Gale, AEM, 2025). This might help provide useful context for the in vivo results.

      We thank the reviewer for the references. These observations will be compared to our phenotypic results and discussed in the revised version of the manuscript.

      (3) The data in Figure 4 are compelling to focus on the L. plantarum variants. However, I can see from the methods that the competitive mapping included only other strains of Wolbachia.

      We appreciate the thorough reading of the methods by the reviewer. The competitive mapping comprised two steps: first we discarded the reads that mapped to Drosophila, Wolbachia and additional potential contaminants from sequencing facitilies (human, dog...). This step leaves the reads originated from whole the external microbiome of the flies, including L. plantarum. The second competitive mapping step recruits the reads that map any clade of L. plantarum.

      It is not clear how other members of the microbiome changed in response to the temperature regimes. As I note in point #2, given that Lactobacillus is often rare, it is not clear what the rest of the microbiome looks like over the course of adaptation. Indeed, it seems like Mazzucco & Schlotterer, PRSB, 2021 did a broader analysis of the microbiome and found that Acetobacter is by far the most common bacterium (I think this data is also part of the data shown here?). Expanding on why or why not in this context is important and will improve this study, particularly if the focus is on connecting these evolutionary dynamics to ecological competition to explain the emergence of strain diversity.

      We acknowledge that the rest of the Drosophila microbiome is not addressed in this study, as we wanted to focus the storyline around the intraspecific dynamics found in L. plantarum. We consider that a complete characterization of the whole Drosophila microbiome would unnecessarily elongate the paper and thus we treat it as a constant biotic factor.

      We must point out that our dataset is not the one reported by Mazzucco & Schlötterer, which was done in D. melanogaster, rather than D. simulans. Nevertheless, both experiments share the same infrastructure, temperature regimes and fly maintenance.

      We will include a list of taxa that were isolated from the populations, as well as to report L. plantarum prevalence and abundance across the experiment in order to provide context of the microbiome, beyond L. plantarum, to the readership.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Gracia-Alvira et al. investigated how environmental temperature affects competition among members of the microbiome, with a focus on intraspecific diversity, using the Drosophila model. Notably, the authors identified three clades of Lactiplantibacillus plantarum from a natural population of Drosophila simulans collected in Florida. They tracked the dynamics of these three bacterial clades under two temperature conditions over the course of more than ten years. Using comparative genomics and phylogeny, they showed that these three bacterial clades likely adapted to their host independently in a temperature-specific manner. Further, by combining in vitro culture and in vivo mono-association assays, they demonstrated the functional divergence of these three bacterial clades phenotypically, including their growth dynamics and effects on host fitness. Lastly, they performed pathway analysis and speculated on key genomic variance supporting such functional divergence.

      Strengths:

      The laboratory evolutionary experiment in response to cold or hot environmental temperature is impressive, given its more than ten years of experimental time period. This collection of achieved microbiome samples paired with the fly host data can be a valuable resource for the field.

      Weaknesses:

      The laboratory evolutionary experiment can be limited due to its artificial experimental setup. For example, wild flies rely on a more diverse set of food sources and are constantly exposed to new bacterial inoculations, whereas under laboratory conditions, flies live in a more restricted ecosystem. In addition, environmental temperatures differ among different locations, but they also involve seasonal changes within the same region. This manuscript can be strengthened with further discussions that elaborate on these limitations.

      As the reviewer has correctly noted, our experimental setting is not exempt from limitations. Lab-reared flies are fed with a defined standard diet. Furthermore, although the system is not completely close to bacterial migration, this is limited as replicate populations are not allowed to mix during the maintenance of the flies. For this reason, we consider our laboratory setting as a compromise between observing wild populations, which undergo all biotic and abiotic stresses but cannot be manipulated, and evolving the bacteria in absence of the host, or in gnobiotic hosts, in which biotic interactions are not fully considered. We will extend on this in the new version of the manuscript.

      Moreover, the extent of host effects involved in these experiments remains ambiguous, because it is unclear whether these Lactiplantibacillus plantarum mostly reside within fly guts or on Drosophila medium. The laboratory evolutionary experiment possibly favored better colonizers on Drosophila medium under either cold or hot temperatures, which subsequently can saturate fly guts. As fully dissociating these variables can be experimentally tedious, the authors may want to comment more on these aspects in the discussion. Or they may want to consider some measurements. For example, measuring the growth rate of these bacteria on Drosophila medium under different temperatures, in addition to the current MRS culture experiments, or measuring the portion of the Lactiplantibacillus on Drosophila medium versus these stably colonizing fly guts.

      The reviewer's point was briefly addressed in the Results chapter: "Phenotypic differences in liquid culture".

      Reviewer #3 (Public review):

      Summary:

      The study presents an analysis of 297 pangenomes derived from 20 populations of Drosophila simulans, at 19 time points for fast-reproducing individuals in a hot environment, or at 10 time points for slow-reproducing individuals in a cold environment, over a period of more than 10 years. The authors select a particular microbial component of the pangenomes and study the dynamics of Lactiplantibacillus plantarum strains in two environments. They discover that the revealed operational taxonomic units could be divided into three phylogenetic clades, which have their own genomic and genetic features, different adaptive capabilities that depend on the environment, and have a distinct impact on the fitness of the host.

      Strengths:

      The authors prove that bacterial microbiome components are sensitive to the environment and could rapidly (years) be fixed in eukaryotic populations. This study establishes a tractable model that potentially enables the study of variability of the physiological influence of distinct strains of an important commensal species, Lactiplantibacillus plantarum, on the Drsosophila host. It is clearly shown that this single species consists of several phylogenetically and functionally diverse strains. The authors did not limit their interest to their own model, but rather they have integrated a comparative approach by analysing phylogenetic relationships among 92 described L.plantarum strains.

      Overall, the study is novel and delivers important discoveries of a longitudinal, well-replicated experiment, generating a substantial amount of genomic data. It highlights an important dimension of research that environmental selection operates at the subspecies level.

      Weaknesses:

      Even though the authors show only one particular example by conducting their longitudinal experiment, they honestly acknowledge failures important for interpretation of the biological significance of the results (gnotobiotic mono-association experiments was done with D.melanogaster, but not D. simulans) and therefore they state limitations of their conclusions (weaker effects in the non-axenic flies are due to the presence of other taxa or to higher-order interactions with other members of the microbiome). These interactions could significantly affect bacterial growth, metabolism, and physiological influence on the host.

      We agree with the reviewer in that the use gnobiotic animals is a limitation, as by "tuning" the flies' microbiome we are modifying the interactions between members, which can potentially change the phenotypic outcome. Nevertheless, we use it as a complementary approach, rather than the only inference in our study.

      The authors exploit the results of their experiment to speculate about a wide range of evolutionary phenomena, like within-species competition, ecological adaptation and evolution of the host, fitness advantage of bacteria to the host, the benefits of parasitism or mutualism, the domestication of the microbiome, etc. At the end, they conclude that their study "highlights that even subspecies diversity plays a key role in adaptation to environmental temperature". However, the potential mechanisms of such adaptation are barely discussed, so that the focus of the study shifts from the temperature-induced changes in microbial population structures toward metabolism-related adaptations of clade representatives that enable them to diversify their carbon and nitrogen sources. The role of the temperature factor remains elusive.

      We acknowledge that our study does not fully resolve the mechanism by which a different clade ends up dominating each temperature regime. The MRS liquid experiment was an attempt to answer whether differences in optimal growth temperature could explain the temperature-specific abundance of the two clades. Our experiments showed, however, thatthis was not the case. Beyond this point, it is hard to disentangle the role of the temperature, as it could also act indirectly on the bacteria, for example, through the host or the food.

      A second observation in our time series was that a third clade, U, was unfit in both regimes despite starting the experiment in high abundance. For this reason we also studied what made this clade less fit. Based on our analyses, we propose that the decrease of clade U was driven by the shift to a laboratory diet, shared by all experimental populations.

      In addition to that, the paper has a clearly minimalistic experimental approach to address functional properties of the revealed L.plantarum strains, so that their own fitness, or their relationship with the Drosophila host, is characterised superficially. Therefore, the authors' discourse can be speculative rather than factual (especially when the authors use the expression "likely" to share their guesses in the "Results" section). Nevertheless, these minor drawbacks do not underscore the novelty of the discovered phenotypes and the importance of their further investigation.

      We consider the reviewer's concern and will tone down the phrasing when reporting our findings in the revised version of the manuscript.

    1. R0:

      Reviewer #1:

      This paper examines factors associated with Shigella-attributed diarrhea among children aged 6–35 months in Malawi, including a novel assessment of seasonal effect modification. The analyses are technically rigorous and appropriately applied to the observational dataset, and the findings provide valuable evidence to guide targeted interventions, including the forthcoming Shigella vaccine rollout. I recommend publication pending a few minor revisions noted below.

      • The introduction explicitly situates the burden of Shigella in an economic context, but are there any other lenses, perhaps more human-centric, through which we can think about the implications of this burden? • Please include references for the categorization methods of diarrhea severity and WASH in the “Predictor Variables” section of the Methods. • How did you approach producing age group bins for this study? Was it data driven or decided a priori based on some contextual motivation? • Please add a statement justifying Poisson regression as the chosen analytic method. • Given that some samples were tested by culture, some by qPCR, and some by both it would be beneficial to add more clarification in the methods about the different testing procedures and results classification. For the samples tested by both methods, what happened if one result was positive and the other negative? In the discussion you state “Notably, 43% of qPCR-positive cases were also culture-positive, supporting the clinical relevance of the qPCR-detected cases”, however only 43% overlap between the two methods actually seems quite low – can you point to any other studies that have looked at this? • I believe when using generalized estimating equations (GEE) to account for clustering it is standard to report the number of clusters and distribution of cluster size. • These analyses rely on an assumption of missing data at random/completely at random, however the complete case analysis conducted excludes 32% of children with missing vaccination data. Please elaborate on this missingness in the limitations beyond reduction in sample size to include the potential bias introduced if the data is not in fact missing randomly. Alternatively, it may be worthwhile to consider inclusion of the observations with unknown vaccination status as a third category – which may still have relevant interpretation given the reality of often not knowing children’s vaccination status when designing interventions. • Was there any consideration of prior antibiotic use among patients reporting to the clinic with diarrhea? Please elaborate how this may or may not influence these results (perhaps in the limitations). • Please standardize spelling of “enrollment” throughout the manuscript (sometimes one vs two ls). • In Table 1 the Wasting “None” group percentage needs a decimal instead of a comma.

      Reviewer #2:

      The findings are interesting but it need through revision considering the following critical points. • Clearly mention the inclusion and exclusion criteria for selection of patients in the current study? • What was the limitation of the study? • Shigella were isolated and identified using culturing. What was the specie distribution of Shigella? • Mention the duration of the study (months/years) in the abstract. • Briefly describe how the culture and qPCR were used for detection of Shigella. Is Shigella DNA directly detected in fecal sample or it is detected from culture? • Define the criteria of Household drinking water source categorization: Improved, Unimproved?? • The abbreviations used in the tables should be defined in the table’s foot note.

      Academic Editor:

      Two reviewers have evaluated your manuscript and provided their comments below. In particular, please provide more detail in the methods section on the microbiological methods for Shigella detection and add information on any missing critical variables e.g. in the table footnotes. In addition and given the high missingness for vaccination status, conducting a sensitivity analysis for the multivariable models while excluding vaccination would aid with the interpretation of the study findings.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Reviewer #1

      Evidence, reproducibility and clarity

      1) Summary

      This study investigates the mechanochemistry of Arp2/3-mediated branched actin networks at the level of individual branch junctions under load. Using microfluidic single-filament/branch force assays (including constant-force flow and open-chamber imaging) the authors quantify debranching, re‑nucleation, and mother- vs daughter‑interface stability across nucleotide states of Arp2/3 (ADP-Pi, ADP, and an ADP-BeFx proxy for ADP-Pi). They further test effects by two branch regulators (GMF and cortactin). Key findings include: (i) ADP-Pi and ADP complexes share similar force dependence but differ markedly (~20×) in intrinsic dissociation rate; (ii) phosphate turnover on the Arp2/3 complex is rapid ii) affinity for Pi drops when Arp2/3 loses its daughter filament; (iii) quantification from model fits uncovers large stability differences between daughter and mother interfaces of the Arp2/3 complex; (iv) extraordinary high stability of ADP-Pi-like Arp2/3 on the mother filament; and (v) distinct effects of GMF and cortactin on force‑dependent stability. Overall, the work combines technically demanding measurements with mechanistic modeling to probe how nucleotide state and regulatory factors tune branch mechanics.

      2) Major comments:

      1. Low force kinetics and completeness of survival curves (Figure 1). "For all forces, the surviving curves exhibited a clear single exponential behavior...." While the data can be fitted to monoexponential decay curves, data at low forces is clearly incomplete. >90% of branches have not dissociated by the end of the experiment. For the particular data shown in 1C (F00nN, n=60 total branches) it means that the time information is coming from

      Essential; experiment might already be performed. Otherwise straightforward to do (weeks time).

      In figure 1B, we indeed show a Survival curve for ADP-Arp2/3 complex branch dissociation at 0 pN up to 900 seconds. As now shown in updated supp figure S2, the data was in fact acquired for at least 5000 seconds for ADP-Arp2/3 and ADP-Pi states (N=2 repeats for each condition, with n = 60 and 90 branches for ADP-Arp2/3 branches, and 90 and 132 branches for ADP-Pi-Arp2/3 branches). The debranching rates reported in the initial submission were already obtained by fitting the surviving curves over the whole duration of the experiments.

      1. Stability Analysis (Figure 4). I can follow much of the arguments presented in the stability analysis of the daughter vs mother interfaces, which is in principle extremely interesting! However, there are some concerns here:

      i) The authors emphasize the zero force ratio derived from fits (which is linked to the stability difference of the two interfaces in the absence of force) despite this being only weakly constrained by data. Intuitively in the model, the stability difference should grow to very large values as the re-nucleation ratio approaches 1 at low force. This combined with the noise in the data poses an issue in my opinion. Looking at the data and the error margin, I think that the authors cannot state with high confidence that there is a real difference between the relative stability of the daughter and mother interfaces between the two nucleotide states of the complex.

      Essential; analysis and textual revision only

      We thank the reviewer for this comment. The difference in stability between the two interfaces is strongly constrained by the shape of the branch renucleation ratio versus force curve, and its value at 0 pN. This is illustrated in the figure shown below (new Supp Fig. S8), showing the dissociation rates of the two interfaces (in 'dashed' and 'point-dashed' style) that contribute to the overall debranching rate in each nucleotide condition. Despite the limited force range at which we probed the debranching rate, the branch renucleation ratio curve informs us on which interface is the weakest, and how this evolves with force.

      We have assessed the confidence intervals of the parameters obtained from the fits, taking into account the error bars on our experimental datapoints. It seems to indicate that the simultaneous fits of the debranching rate and the branch renucleation ratio curves indeed constrain the parameters quite strongly. These confidence intervals are now reported in the main text and in the summarizing table.

      We have repeated branch renucleation experiments for ADP-BeFx- and ADP-Pi-Arp2/3 complex branches (see new figure 4C&D, and our response to the next point). We believe these new measurements allow a better assessment of the relative stability between the two interfaces for Arp2/3 complex branch junctions in the ADP-BeFx state.

      Still, we agree with the reviewer that the dispersion of the experimental data does not allow us to have a strong confidence on the crossover force and relative stability difference of the interfaces. Therefore, we have slightly toned down the way we present and discuss the differences in stability when comparing the two nucleotide states.

      ii) For ADP-Pi, the renucleation ratio essentially remains flat over the measured force range. Hence, the data can only provide little leverage to estimate both the zero force ratio and, more importantly, the differential distance to the transition state in the slip-bond model in my opinion, which will show in the crossover force. Consequently, the quoted ">100×" stability difference at F=0 and the crossover force >20pN are driven largely by extrapolation rather than direct constraint by data. Given the high number of free parameters in the model, I would anticipate that several crossover forces and differential distances might explain the data nearly equally well. Instead of loosely reporting exact number from fits, I would have hoped for some sort of sensitivity analysis, for instance relying on profile likelihoods. Also parameter values could be reported as bounds (e.g crossover force≫measured range) rather than precise point estimates. This issue re-occurs (albeit not as drastically) for the cortactin experiments (Figure 6).

      Essential; analysis and textual revision only

      As mentioned in our response to the previous point, we have repeated renucleation experiments for ADP-BeFx- (and also for Arp2/3 complex branches in the presence of 50 mM Pi) (see new figure 4C&D) to better characterize the differential distance between to the transition force. The crossover force for the ADP-BeFx state is now 13.5 pN and the ratio of the stability between the two interfaces is roughly 100 times.

      We agree with the reviewer that the dispersion of the experimental data does not allow us to have a strong confidence on the crossover force and relative stability difference of the interfaces. We have thus toned down the way we report these values. We do believe though that the difference we report between the ADP and ADP-BeFx state appears to be significant and needs to be acknowledged.

      As a side note, it has proven to be challenging to pull on branches at forces higher than 7 pN. To apply a large force on the branch junction, we need to have a high flow rate. In this case, it appeared that the height of the filaments (both mother and daughter filaments) above the surface seem to deviate from what we have established in our previous studies (Jegou et al, Nat. Comm. 2013 & Wioland et al, PNAS 2019). This may originate from the fact branched filaments have a more complex shape than an individual filament. Characterizing accurately the evolution of the branch height as a function of the flow rate and applied force would require quite extensive additional characterization, which, we believe, is beyond the current focus of this study on the stability of Arp2/3 complexes.

      iii) One important expectation from the "two slip bond" model is that branch dissociation rates should not necessarily scale mono-exponentially as they mostly do over the accessible force range of the paper. However, once the "minor" pathway of dissociation from the mother starts to dominate at high forces, rates become more force sensitive. This is nicely recaptured by the model fits in Figure S6 but deserves some explanation in the text. Otherwise, people will simply remember the "ADP-Pi is 20-fold more stable than ADP at all forces" message.

      Essential; textual revision only

      We now have rephrased the key sentences (in the Abstract and Results sections) to more clearly state that the debranching rate is not increasing mono-exponentially with force.

      In the Abstract: "Remarkably, we find that branch junctions are over 30-fold more stable when the Arp2/3 complex is in the ADP-Pi rather than ADP state, and that force accelerates debranching with similar exponential factors in both states."

      In the Results section: "The debranching rate seems to increase exponentially with the applied pulling force, in the range of 0 to 6 pN (Fig. 1F; see more refined analysis below). This behaviour is predicted by the Bell-Evans model for a slip bond."

      iv) One important prerequisite for the model is that isolated Arp2/3 complexes (without a daughter filament) should dissociate with equal rates from mother filaments at all flow rates. Since the Arp2/3 complex prefers mother filament curvature, forces experienced by the mother might change its off-rate. It would be good to refer to this assumption in the text and experimentally verify it. I could not find it in the paper nor in Ghasemi et al 2024.

      Essential; simple experiment (a weeks time).

      We thank the reviewer for this important comment.

      First, we investigated whether the viscous drag force, applied on the ADP-Arp2/3 complexes which remain bound to mother filaments could affect their stability. We have performed branch renucleation experiments at different flow rates but with the same pulling force on branch junctions (average force 3.9 pN) by adapting the length of the daughter filament. As shown in new supp. figure S11 (shown below), we did not observe any significant differences between 'low' and 'high' flow rates. If the off-rate of the surviving Arp2/3 was significantly affected by the flow, this would have led to a variation of the renucleation ratio with the flow rate.

      Second, we have investigated the impact of the tension experienced by the mother filament at the location of the branch junction for ADP-Arp2/3 complex branches, with the same pulling force on the branches (average 4.1 pN pulling force on branches). We have quantified the debranching rate from three groups of branches depending on their position along mother filaments. As shown in new supp. figure S12 (shown below), we can observe a small trend, where the debranching rate decreases with the tension on the mother filament at the branching point.

      Doubling the tension on the mother filament from 15 to 30 pN decreases the debranching rate by a third. Though, pairwise logrank tests performed between the survival fractions of the three binned groups do not report any statistical significant difference (all p values > 0.05). One possible explanation for this is the height of the mother filament in the microfluidics flow that increases linearly from the anchoring point to the free barbed end. As a consequence the pulling force on the branches will be higher, as branches experience faster flows.

      For these same groups, upon branch dissociation, all remaining-bound Arp2/3 complexes are exposed to the same flow rate; the branch renucleation ratios were similar. Thus branch renucleation ratio seems to not significantly depend on the tension experienced by the mother filament at the branching point.

      Similarly, Pandit et al PNAS 2020, Extended figure S1, also reported no detectable impact of the mother filament tension on the debranching rate in their assay.

      v) The force dependence of the branch re-nucleation rate (Fig 3D) has been measured previously by the same group (Ghasemi et al). While the data in the older paper has not been fitted by a model, the trend of the data in the previous paper looks conspicuously different. Are there any explanations for this? I speculate that it might be related to actin and ATP not being saturated (low-force re-nucleation rate rarely exceeds 80%) in Ghasemi et al., but it would be good to know what the authors think about this. Essential; textual revision only

      This is a good point. We have plotted the data of the renucleation ratio from ADP-Arp2/3 complex from figure 1F of Ghasemi et al, Sc. Adv. 2024 (performed at 0.3 and 1 µM actin), together with the data of the current study from figure 4D (performed at 1.5 µM actin). We feel this comparison could be of interest to the readers, and have thus integrated it in the manuscript as new supp. figure S13 (shown below).

      As expected, the branch renucleation ratio is lower with lower concentrations of actin. The experimental data points from Ghasemi et al are similarly well fitted by the branch renucleation function obtained for 1.5 µM multiplied by a scaling parameter, which reflects the fact that the branch renucleation ratio is actin concentration dependent (Fig. 6A in Ghasemi et al). This scaling parameter was the only free parameter of those fits.

      Since the branch renucleation ratio depends on the actin concentration as follows, 0.97.kon.([actin] - Cc)kon.([actin] - Cc)+koffATP-Arp2/3 , with kon = 3.4 µM-1.s-1 and koff ATP-Arp2/3 = 0.66 s-1 from (Ghasemi et al. 2024), the scaling parameter obtained by the fits give estimates of the actin concentration in these experiments, of 0.6({plus minus}0.05) and 0.9({plus minus}0.2) µM for the experiments performed at 0.3 and 1 µM respectively in (Ghasemi et al. 2024).

      1. Stability of the authentic ADP-Pi-Arp2/3 complex on the mother filament. The extraordinary stability of the isolated ADP-BeFx-Arp2/3 complex on mother filaments is surprising, especially considering that both ATP and ADP states are much more labile (Ghasemi et al 2024). I would recommend repeating this experiment in the authentic ADP-Pi state with labelled Arp2/3 complexes as a more direct readout, even if this would require working with very high phosphate concentrations.

      Essential; simple experiment (a weeks time).

      We have followed the recommendation of the reviewer and have performed new experiments using fluorescent Arp2/3 complexes for ADP, ADP-BeFx and ADP-Pi states, now displayed in new figure 5C (also shown below).

      For fluorescent Arp2/3 complexes remaining bound to the mother filament, the Arp2/3 complex - mother filament interface is ~ 100 times more stable in the ADP-BeFx state (0.0046 s-1) compared to the ADP state (0.56 s-1). We also assessed the dissociation of surviving ADP-BeFx-Arp2/3 complexes using unlabelled Arp2/3 complexes (previously in figure 4B, repeated experiment shown in new supp. figure S10), which also indicates a remarkable stability.

      The dissociation curve of surviving Arp2/3 complexes in the presence of 50 mM Pi and 200 µM ATP in solution reflects the mixture of Arp2/3 dissociating in the ADP/ATP state and ADP-Pi-Arp2/3 that can either dissociate in the ADP-Pi state or lose their Pi and dissociate in the ATP state. Despite the presence of 50 mM Pi, the rate at which ADP dissociates and ATP reloads rate is much faster than Pi binding. Fitting this survival curve with a function that accounts for the initial double populations and the evolution of the ADP-Pi population (see Methods) gives a good estimate of the Pi release rate.

      OPTIONAL: Further, but beyond the scope of the present paper, would be titrating phosphate in these experiments, which would even allow the authors to independently verify the reduced Pi affinity for Arp2/3 in the mother filament. Of note, this affinity difference is needed to satisfy detailed balance in the reaction scheme (Fig 4 D)!

      We thank the reviewer for this suggestion. High concentrations of phosphate in the buffer renders glass surfaces quite sticky in our assays. We've tried several different passivation strategies (BSA, PLL-PEG, K-casein, ...) but none gave satisfactory results. So titrating phosphate, by going beyond 50 mM phosphate, proved to be quite challenging.

      Detailed balance, considering the two possible routes connecting the ADP-Pi-Arp2/3 complex branch junction state and the surviving ADP-Arp2/3 complex state, can be written as KPi rel.branch junction . Kdebranching ADP-Arp2/3 = KdebranchingADP-Pi-Arp2/3 . KPi rel.surviving Arp2/3.. Some of these affinity constants are not known, because of the inability to determine reverse reactions rates such as the rebinding of a daughter filament to a surviving Arp2/3. It is thus hard to determine how the affinity of Pi for Arp2/3 complex changes between Arp2/3 complexes at branch junctions and surviving Arp2/3 complexes on mother filaments.

      While we cannot determine the affinity constant of Pi for a surviving Arp2.3 complex, our data indicates that the dissociation rate of Pi is higher from Arp2/3 complexes at branch junction (koff = 0.21 s-1) than from surviving Arp2/3 complexes (koff = 0.05 s-1). This unexpected finding indicates that surviving Arp2/3 complexes adopt a conformation where the nucleotides are readily exchanged, but where the 'back door' for Pi release is less open. We now discuss this point in our revised manuscript.

      1. Importance of "surviving" ADP-Pi-Arp2/3 complexes. The authors show a) rapid turnover of Pi on the ADP-Arp2/3 complex in both branch- or mother filament-bound state and b) the lowered Pi affinity of the latter. Nonetheless, they emphasize the importance of long-lived "surviving" ADP-Pi bound complexes on the mother (even stated in the abstract). I understand that this fraction shows under some experimental conditions (BeFx), but unless I am missing something, most complexes should rapidly lose their phosphate and either exchange nucleotide or dissociate from the mother under physiological conditions. Please clarify or tone done.

      Essential; textual revision only

      We thank the reviewer for their remark. We have tried to clarify this aspect in the manuscript.

      As shown now with the departure rate of fluorescent surviving Arp2/3 complexes together with branch renucleation data, we show that surviving ADP-Pi-Arp2/3 complexes are quite stable on mother filaments, because they detach and release their Pi slowly, such that branch regrowth will occur provided there is actin in solution. In the absence of actin monomers, as the reviewer correctly points out, the surviving ADP-Pi-Arp2/3 will predominantly release its Pi and thus become a surviving ADP-Arp2/3 complex. We have modified the text to avoid any confusion.

      1. GMF mechanism. The authors claim that GMF "...accelerates the departure of the surviving Arp2/3 complex from the mother...". I assume that they infer this from decrease in the re-nucleation ratio. However, alternatively GMF could simply dwell on the complex, inhibiting re-nucleation without promoting dissociation from the mother. The authors should either monitor Arp2/3 dwell times directly to discriminate between these possibilities or be more cautious in their conclusions.

      Essential; simple experiment (a weeks time) or textual revision.

      In Ghasemi et al. Sci. Adv. 2024, we examined the departure of Arp2/3 from the mother filament after GMF-induced debranching using fluorescent Arp2/3. Most of the fluorescent Arp2/3 dissociated from mother filaments within the same frame as the branch, i.e. within 0.5 seconds after the debranching event, and none were visible after another second . This could be due to Arp2/3 departing with the branch or an accelerated departure after branch dissociation. In any case, this rules out the possibility that GMF would dwell on the surviving complex for a substantial amount of time without promoting dissociation from the mother.

      In the present manuscript, we now show that increasing the ATP concentration 10-fold (from 0.2 to 2 mM) is sufficient to restore the branch renucleation ratio to its level without GMF. This shows that GMF does not cause Arp2/3 to leave with the branch, but rather that it (also) acts on the surviving Arp2/3 complex, in a way that is countered by high concentrations of ATP. More specifically, it suggests that GMF accelerates the departure of the surviving ADP-Arp2/3 complex, either directly and by hindering the reloading of ATP, and that GMF does not affect the surviving Arp2/3 complex once it has reloaded ATP.

      We now discuss these two non-mutually exclusive possibilities for the accelerated dissociation of the surviving ADP-Arp2/3 complex in the manuscript.

      6.Cortactin mechanism and the "leash model". I must say that the cortactin data are the most puzzling part of the paper and hard to reconcile with what we know from structure. I was hoping to find some of this resolved in the discussion. However, I do not understand the "leash model" in the discussion section for cortactin-mediated branch stabilization: "This would explain the observed increase in branch survival compared to the absence of cortactin. As the pulling force is increased, this rebinding mechanism becomes less efficient." According to my understanding of the data, this is opposite to what happens. Cortactin only stabilizes the labile interface at elevated forces! Some re-writing might help here.

      Essential; textual revision.

      We thank the reviewer for having us think more thoroughly about the model we initially proposed. We now believe that our 'leash' mechanism is not able to fully recapitulate our observations in a simple and satisfactory manner.

      We now propose a much simpler model, where the binding of cortactin to the Arp2/3 complex at the branch junction simply changes the energy landscape of the Arp2/3-daughter interface without the need to invoke a rebinding of the daughter filament upon branch departure. We have updated our interpretation of the data in the Discussion section accordingly.

      Overall, our results on the impact of cortactin on branch renucleation highlights a surprising behaviour that would require further investigation to fully decipher the underlying molecular mechanism.

      3) Minor comments

      Organization: - I do not want to impose on how to best tell the story, but I felt that Fig1 A-D and Fig 2 A-B belong to one logical unit (nucleotide dependence), whereas Fig 1 E-F and Fig 2 C belong to the other (Pi binding and exchange). Perhaps consider re-organizing to streamline presentation?

      We thank the reviewer for their suggestion. We agree that it flows more naturally as suggested, and have made the changes! Thank you.

      Semantics/Typos: - Abstract: „... ADP-Pi and ADP-Arp2/3 detach with the same exponential increase as a function of force...". Increase should refer to the dissociation rate, which should be added to the sentence.

      We have corrected this.

      Results page 8: "...and the majority of Arp2/3 complexes detach from the mother filament while remaining bound to the branch at the debranching time." "Branch" should likely be daughter here, as there is no branch after dissociation of either interface.

      We have corrected this, thank you.

      Results page 13: "Exposing ADP-BeFx-Arp2/3 complex branch junctions to a saturating amount of GMF...". It is strange to imply saturation, because GMF likely simply does not bind to the complex in this nucleotide state with appreciable affinity. Suggest to change to "high".

      We have made the changes accordingly.

      Discussion page 18: "Moreover, in mammalian Arp2/3, His80 in Arp3 (corresponding to His73 in mammalian actin) is not methylated, and corresponds to residue N77 in Arp3, which is also not modified." N77 likely belongs to Arp2?

      We have made the changes accordingly.

      Discussion page 19: "We showed that Pi affinity for Arp2/3 complexes at branch junctions is around 3.7 mM (Fig. 1), a value which lies within the reported 1-10 mM Pi concentration measured in the cytosol in different mammalian cell types". Notably, this is not too different from F-actin, which should be mentioned. By this measure alone, free inorganic phosphate could also directly regulate actin filament stability!

      We now mention this and discuss that intracellular Pi can also impact actin filament nucleotide state.

      Future interest (non essential): - It would be utterly exciting (but beyond current scope) to quantify how instantaneous debranching rates evolve for naturally aging branches starting from ATP-Arp2/3 complexes!

      We thank the reviewer for this remark. It is indeed quite beyond the scope of the current study, as this would require a way to probe ATP-Arp2/3 complex branches while daughter filaments are still quite short (so pulling on them is difficult). An interesting alternative could be to use ATP analogs, such as App-NHp (aka AMP-PNP), to stabilize this state. However, some studies have mentioned that App-NHp is not very stable.

      Significance

      General assessment:

      This is a compelling and carefully executed study that delivers a clear mechanistic framework for how Arp2/3 branch junctions fail and re‑form under load. The central strength is the tight integration of state‑of‑the‑art reconstitutions with careful and original kinetic analysis. The experimental design is elegant and experiments have been carried out to a masterful standard. The figures are clear, the statistics are appropriate with some exceptions as detailed above. There are very few labs in the world that could have achieved this feat!

      A few aspects could be further strengthened, most notably the explanation and application of the "two slip bond" model as well as slightly more restraint in speculating around specific regulatory mechanisms. However, these are minor refinements that do not detract from the important contributions of the paper.

      Overall, the clearly work merits publication with high priority after revision; most requested changes are textual/analytical with very few targeted experiments, which would substantially strengthen core claims.

      We thank the reviewer for their positive evaluation of our manuscript. We hope that our responses to the detailed points above, along with the corresponding revisions of the manuscript, will alleviate their concerns.

      Advance relative to prior literature: The major novel findings of the paper are already summarized above. There is some recent work done on the subject of branch mechanics by the authors (Ghasemi et al 2024, PMID: 38277459) and others (Pandit et al 2020 PMID: 32461373), but the focus of the present work is clearly unique and the there is plenty of novel insight.

      Audience and impact: Primary audience: specialists in cytoskeleton dynamics, in vitro reconstitution single molecule biophysics, and mechanobiochemistry. Secondary: researchers in cell motility, morphogenesis and mechanobiology, physicists working on active matter and modelers studying force producing and load-bearing biopolymer networks. The results and analysis framework should inform quantitative models of branched network turnover under load and the interpretation of regulatory factor action in vivo and in cells.

      Reviewer expertise: Actin dynamics; biochemical reconstitution; single molecule approaches; biophysics.

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      Xiao et al examine the molecular events occurring when Arp2/3 complex-mediated actin filament branches are removed from mother actin filaments. They do this using microfluidics assay with purified proteins combined with single filament TIRF imaging of branched actin filaments with distinct fluorescent labels. The contribution of different nucleotide states of Arp2/3 complex are tested in conjunction with the relationship force exerted on the branches and regulatory protein involvement from GMF and cortactin. The data seem comprehensive and highly quantified in response to concentration, force, fraction of branches and survival times and branching rates. They find that ADP-BeFx and high phosphate concentrations (leading to the ADP-Pi state) leads to a slower debranching rate at a given level of force applied. The ability to rapidly switch the buffer gives powerful information about response times of debranching compared with other actin remodelling events. They use renucleation experiments to determine that the previous debranching event most often occurs at the Arp2/3 complex/daughter interface, showing that filaments will be ready to re-branch in the stable ADP-Pi bound state. GMF addition allows debranching of the ADP state to occur at a lower force. Cortactin acts similarly to the ADP-Pi state to increase branch stability.

      Specific comments

      The pulling force on the branches seems to arise from different flow rates in the microfluidics. Viscous drag is mentioned and I can see there is methylcellulose in the buffer. It would be helpful to have the explanation of the conversion between flow and force, even if it has been standard in previous work.

      We apologize if this was unclear: in microfluidics experiments, the buffer does not contain methylcellulose. Methylcellulose is only used for 'open chamber' experiments, where no force is applied to Arp2/3 branches, to maintain them in the TIRF field of excitation (Figure S2).

      To better clarify the conversion between flow and force, we have rephrased and extended the Methods section to explain how the force on the branch junction is computed based on the local flow velocity and the length of the daughter filament.

      Pg 5 - what was the motivation to titrate phosphate? It seems a stretch that intracellular Pi levels are tuning branching inside cells more than protein-mediated control (GMF or cortactin) - can the authors evidence this at all?

      We are not claiming that the level of Pi plays a stronger regulatory role than proteins. We show that inorganic phosphate tunes the state of the Arp2/3 complex, which in turn modulates the action of regulatory proteins, such as GMF and cortactin.

      Nonetheless, we do show that the contribution of inorganic phosphate is quite central as it can (1) strongly stabilize branch junctions (~30-fold decrease in the dissociation rate), and (2) tune the activity of GMF and cortactin on Arp2/3 complexes at branch junctions as well as on the 'surviving' Arp2/3 complexes that remain bound to mother filaments.

      We thus titrated phosphate and found that its impact on Arp2/3 complex stability is significant in the range of Pi concentration that is explored in cells. For the sake of completeness, and following a comment from reviewer #1, we now also mention the affinity of Pi for actin subunits in filaments in the Discussion, and discuss the impact of intracellular Pi on actin itself.

      Minor comments

      • In the introduction, while the structural and mutagenesis evidence is clearly stated, in other cases a bit more detail would be helpful e.g. 'biochemical studies', which referred measurement of hydrolysis rates using radiolabelling

      We have made changes to more precisely define which biochemical assays were used in previous studies.

      • Page 3 Figures shouldn't be referenced in the introduction

      We have removed the references to the figures from the introduction.

      • Page 3 slip bond behaviour needs explanation

      We now explain the concept when first using this concept in the manuscript, as follows: "The debranching rate seems to increase exponentially with the applied pulling force, in the range of 0 to 6 pN (Fig. 1F; see more refined analysis below). This behaviour of accelerated debranching with the increase of the applied force is similar to the 'slip bond' concept, as predicted by the Bell-Evans model of the force-dependent lifetime of the interaction between two proteins".

      • Figure 1B seems to be a theoretical schematic which is superfluous

      We suppose that the reviewer is actually referring to figure 3B of the initial manuscript, describing the energy potential of a molecular interaction as a function of the reaction coordinate. We agree with the reviewer that it is not absolutely required and we have removed it.

      • Figure 4D is helpful, different weight lines might help even more to explain the dominant pathways

      We have made modifications to the biochemical reaction scheme in this figure (now figure 5F in the revised version). We hope we succeeded in improving its readability. Since the different paths depend on mechano-chemical parameters, there is no real dominant pathway per se.

      **Referee cross-commenting**

      Rev1 sounds like the specialist here. I can't comment on their requests. Some similar points arise between the reviewers which need addressing.

      Reviewer #2 (Significance (Required)):

      Significance

      Taking a look at references 16 and 19, I do not find it clear what is achieved differently in the current work compared to these papers and what agrees and what disagrees. If it's a species difference I might expect the two species would be analysed side-by-side in this paper.

      We thank the reviewer for this important comment. The goal of our study was not to compare the behaviour of mammalian and yeast Arp2/3 complexes.

      We now try to better explain that the motivation of the present work is to address how the nucleotide state of the Arp2/3 complex tunes actin branch mechanosensitive stability, and regulates interactions with well known Arp2/3 complex binding proteins. Most of the reactions are quantified here for the first time. Moreover, the experiments with branch junctions in different nucleotide states are done under controlled mechanical conditions, providing the first direct measurements of the force-dependence of the debranching reactions. Our detailed kinetic analysis of the full reaction scheme allows us to model the different binding interfaces of the Arp2/3 complex.

      In addition, it is worth noting that:

      1. Species matter and this is why ref 16 and 19 can give the impression to disagree on the ability to renucleate branches thanks to the stability of surviving Arp2/3 complexes on mother filaments.
      2. In ref 16 (Pandit et al, PNAS 2020) species are mixed (yeast Arp2/3 and mammalian alpha actin from skeletal muscle), likely leading to a different behaviour compared to the only mammalian protein situation we examine in our current work. In particular, with mixed species one misses the ability to renucleate, as shown in our previous study Ghasemi et al (ref 19). However, since mixing species does not correspond to anything physiological, we do not think it is worth repeating these conditions alongside our experiments.
      3. Further, the analysis carried out in ref 16 suffers from important limitations: the force was unknown (not calibrated) and the data was fitted by a model that compounded several reactions, providing only an indirect estimation of the rates, in particular at zero force. In contrast, we have worked with calibrated forces (including dedicated experiments at zero force) and we have carried out specific experiments to directly measure several rates.
      4. In ref 19 (our earlier work) we did not investigate the impact of the nucleotide state of the branch junction at all, and we did not systematically measure the dissociation rates as a function of force. Contrary to Pandit et al, we directly measure the difference in branch stability at zero force between ADP and ADP-Pi states and show that the ~ 30 fold difference holds true at all probed forces. Last, the force dependence of the branch renucleation success rate gives us crucial information on which of the two Arp2/3 complex interfaces ruptures first.

      I'm not understanding how the authors can distinguish effects of adding phosphate and BeFx on Arp 2 and 3 compared to effects on actin. Importantly, are possible accompanying changes in the actin filament a confounding factor?

      We have checked that the nucleotide state (ADP-BeFx and ADP-Pi versus ADP) of the mother and daughter filaments have no impact on branch stability:

      • In the experiments shown in figure 2F, where the buffer condition to which branches are exposed is quickly changed from phosphate buffer to buffer without phosphate, we observe a rapid change of branch stability. Actin subunits at the branch junction are in F-actin conformation according to recent cyroEM observations (ref. Chavani et al, Nat Comm. 2024; Liu et al, NSMB 2024). These actin subunits, initially in the ADP-Pi state, are expected to age and become ADP with a rate of ~ 0.007 s-1 (ie half-time of 100 s; ref. Jegou et al, PLoS Biology 2011, Ooosterhert et al, NSMB 2023), a much lower rate than the observed change of the debranching rate (0.21 s-1). This means that the debranching rate is independent of the nucleotide state of daughter and mother filaments.

      • In new supp. Figure S4, we show that the debranching rate is similar for ADP-Arp2/3 complex branch junctions initiated from ADP- or ADP-BeFx-actin mother filaments.

      • In new supp. Figure S9, we initially exposed branch junctions to a BeFx solution then monitored debranching and branch renucleation in our standard buffer (ie without BeFX or Pi). We observed multiple rounds of branch renucleation, the first with ADP-BeFx-actin daughter filaments, and the following with daughter filaments never exposed to BeFx. They all had the same debranching rates and renucleation success rates.

      The paper is quite specialist to read and the advance appears to be incremental. My expertise is in molecular pathways to actin regulation outside the main area of the paper.

      The results we present in this study are often unexpected, and some go counter long-standing assumptions. The regulation of Arp2/3-nucleated branches is of importance for the stability and the force-generating capabilities of many actin networks in cells. Last, most of the measurements that we present had never been done, mainly because experiments are difficult to achieve, and require specific tools to monitor several events while controlling the applied force.

      We believe our results are of broad interest as they go counter long-standing assumptions. We have rewritten the text in several instances to convey our message more clearly.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      Please find enclosed the review of the manuscript "Inorganic phosphate in Arp2/3 complex acts as a rapid switch for the stability of actin filament branches" by Xiao et al.

      The authors provide a detailed investigation of how the nucleotide bound to the Arp2/3 complex affects branch stability under flow force. From a kinetic perspective, this is an elegant study with generally high-quality data, although some conclusions rest on assumptions rather than direct experimental evidence.

      We thank the reviewer for their positive feedback. We have improved our manuscript and performed important additional experiments to provide more direct experimental evidence of our conclusions.

      A key question concerns the physiological relevance of these findings. For instance, the concept of branch regrowth may not be applicable in cellular contexts, since forces by actin polymerization would displace existing branches away from sites where they generate this active forces. The authors should clarify the relevance of regrowth during active force generation by branched networks.

      We thank the reviewer for this comment. Our in vitro results indeed point to a previously unreported property of branched actin networks, i.e. the ability of Arp2/3 complexes to readily renucleate branches in the ADP-Pi state and that it does require reloading ATP within Arp2/3.

      Branched actin networks, especially the lamellipodia or endocytotic patches, do exert active force thanks to actin polymerization of the individual branches at the forefront. Though, the whole actin network is exposed to stress, and the architecture of the network (inter-branch distance, crosslink between branches, ...) presumably strongly impact its mechanical properties.

      In the case of other types of branched actin networks, such as the actin cortex, myosin motor put the whole network under tension. Such pulling forces on actin branches, depending on the amplitude of the pulling force, can lead to branch regrowth, and network self-repair.

      We have modified the text to make the physiological relevance clearer.

      Additionally, all experiments employ flow conditions that branches would probably not experience in cells-notably, the flow direction in the cellular context would be reversed. Altering the flow direction relative to the branches could affect not only the relationship between flow rate and branch stability, but potentially other system properties as well.

      We agree with the reviewer that in cells branches will not experience flow conditions similar to the ones we use in our in vitro assay. Nonetheless, in cells we expect mechanical stress on the branch junction to be applied in all directions. In lamellipodia, the compressive force applied at the leading edge is expected to result in diverse local orientations of the force on individual branch junctions within the network (as explained in Lappalainen et al. Nat Rev MBC 2022). Also, branch junctions are found in the cell cortex, where they are exposed to pulling forces resulting from the action of myosin motors and crosslinkers on mother and daughter filaments.

      This impact of the direction of the flow was addressed in our previous publication (Ghasemi et al, Sc. Adv. 2024, figure 2) and, to a lesser extent, by the lab of Enrique de la Cruz in Pandit et al, PNAS 2020 (ref. 16). We reported that flow direction has a minimal effect, if any, on branch dissociation rate and renucleation ratio.

      Reviewer #3 (Significance (Required)):

      Furthermore, the study appears not to account for the mother filament (particularly its nucleotide state) or the actin subunit bound to the Arp2/3 complex. The authors should discuss why their interpretation focuses exclusively on the Arp2/3 complex rather than on the actin filaments or Arp2/3-bound actin subunit.

      We have checked that the nucleotide state (ADP-BeFx and ADP-Pi versus ADP) of the mother and daughter filaments has no impact on branch stability :

      • In the experiments shown in figure 2F, where the buffer condition to which branches are exposed is quickly changed from phosphate buffer to buffer without phosphate, we observe a rapid change of branch stability. Actin subunits at the branch junction are in F-actin conformation according to recent cyroEM observations (ref. Chavani et al, Nat Comm. 2024; Liu et al, NSMB 2024). These actin subunits, initially in the ADP-Pi state, are expected to age and become ADP with a rate of ~ 0.007 s-1 (ie half-time of 100 s; ref. Jegou et al, PLoS Biology 2011, Ooosterhert et al, NSMB 2023), a rate much lower than the observed change of the debranching rate (0.21 s-1). This means that the debranching rate is independent of the nucleotide state of daughter and mother filaments.

      • In new supp. Figure S4, we show that the debranching rate is similar for ADP-Arp2/3 complex branch junctions initiated from ADP- or ADP-BeFx-actin mother filaments.

      • In new supp. Figure S9, we initially exposed branch junctions to a BeFx solution then monitored debranching and branch renucleation in a regular buffer. We observed multiple rounds of branch renucleation, the first with ADP-BeFx-actin daughter filaments, and the following with daughter filaments never exposed to BeFx. They all had the same debranching rates and renucleation success rates.

      An important concern involves the use of KPi (inorganic phosphate). Based our experience, KPi appears to have effects beyond simply impacting nucleotide state-actin filaments seem to assemble differently in the presence of KPi. The authors should exercise caution in their interpretation of KPi-based experiments.

      Concentration of KPi (up to 50 mM Pi) did not slow down barbed end elongation rate in our experiments.

      Overall, while the technical quality and kinetic analyses are state-of-the-art, relating this work to physiological contexts remains challenging, and some conclusions appear overstated.

      We have made changes in the discussion to try to more clearly relate our in vitro observations and conclusions with the cellular context where branch renucleation could have a strong impact on the architecture and mechanics of actin networks.

    1. Reviewer #3 (Public review):

      Summary:

      In this manuscript, Okuno et al. re-analyze whole-brain imaging data collected in another paper (Brezovec et al., 2024) in the context of the two currently available Drosophila connectome datasets: the partial "FlyEM" (hemibrain) dataset (Scheffer et al., 2020) and the whole-brain "FlyWire" dataset (Dorkenwald et al., 2024). They apply existing fMRI signal processing algorithms to the fly imaging data and compute function-structure correlations across a variety of post-processing parameters (noise reduction methods, ROI size), demonstrating an inverse relationship between ROI size and FC-SC correlation. The authors go on to look at structural connectivity amongst more polarized or less polarized neurons, and suggest that stronger FC-SC correlations are driven by more polarized neurons.

      Strengths:

      (1) The result that larger mesoscale ROIs have higher correlation with structural data is interesting. This has been previously discussed in Drosophila in Turner et al., 2021, but here it is quantified more extensively.

      (2) The quantification of neuron polarization (PPSSI) as applied to these structural data is a promising approach for quantifying differences in spatial synapse distribution. The revision now uses morphological cable length for some analyses rather than straight-line distance, which improves the realism and interpretability of these results.

      Weaknesses:

      One should not score noise/nuisance removal methods solely by their impact on FC-SC correlation values, because we do not know a priori that direct structural connections correspond with strong functional correlations. In fact, work in C. elegans, where we have access to both a connectome and neuron-resolution functional data, suggests that this relationship is weak (Yemini et al., 2021; Randi et al., 2023). Similarly, I don't think it's appropriate to tune the confidence scores on the EM datasets using FC-SC correlations as an output metric. While it is likely that some FC-SC relationship does exist at large scales, it does not in my view justify use of this metric for evaluating noise removal methods, since such methods may inadvertently remove real neural correlates. This concern remains unaddressed in the revision.

      Any discussion of FC-SC comparisons should include an analysis of excitatory/inhibitory neurotransmitters, which are available in the fly connectome dataset. The authors examine the ratios of input and output neurotransmitters in different defined regions. However, I think it would be more useful to integrate the neurotransmitter information more fully into the assessment of SC, for instance: examining the signed weight (excitatory - inhibitory), or by examining the excitatory and inhibitory networks separately.

      Comparisons between fly and human MRI data are also premature here. Firstly, the fly connectomes, which are derived from neuron-scale EM reconstructions, are a qualitatively different kind of data from human connectomes, which are derived from DSI imaging of large-scale tracts. Likewise, calcium data and fMRI data are very different functional data acquisition methods-the fact that similar processing steps can be used on time-series data does not make them surprisingly similar, and does not in my view constitute evidence of "similar design concepts."

      The comparison of FlyEM/FlyWire connectomes concludes that differences are more likely a result of data processing than of inter-individual variability. If this is the case, the title should not claim that the manuscript covers individual variability.<br /> The analysis of the wedge-AVLP neuron strikes me as highly speculative, given that the alignment precision between the connectome and the functional data is around 5 microns (Brezovec* et al, PNAS 2024).

    2. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this paper, the authors analyze connectome data from Drosophila and compare the physical wiring with functional connectivity estimated from calcium imaging data. They quantify structure-function relationships as a correlation of the two connectivity modalities. They report correlations roughly comparable to what has been described in the literature on sc/fc relationships in mammalian connectome data at the meso-scale. They then repeat their analysis, focusing on segregated versus unsegregated synapses. They derive separate connectomes using one or the other class of synapse. They show differential contributions to the sc/fc relationships by segregated versus unsegregated synapses.

      Strengths:

      There is nice synthesis of multimodal imaging data (Ca and EM data from flies and meso-scale data from human and marmoset).

      Thank you very much for your comments.

      Weaknesses:

      (1) The paper is written in an unusual way. The introduction intermingles results with background, making it hard to figure out what precisely is being tested.

      Thank you for pointing this out. We have revised the introduction to make it more concise.

      (2) There are also major methodological gaps. Though the mammalian connectomes are used as a point of reference, no descriptions of their origins or processing are included.

      The reanalysis of marmoset data is presented in Ext. Data Figure. However, as pointed out by other reviewers, the data was obtained in [10], and the processing is also described in [10]. Therefore, we have revised the caption and removed the Ethics Declaration.

      (3) A major weakness stems from the actual calculation of the sc/fc correlation. In general, SC is sparse. In the case of the EM connectomes, it is *exceptionally* sparse (most neural elements are not connected to one another). The authors calculated sc/fc coupling by correlating the off-diagonal elements of sc (the logarithm of its edge weights) and fc matrices with one another. The logarithmic transformation yields a value of infinity for all zero entries. The authors simply impute these elements with 0. This makes no sense and, depending on whether these zero elements are distributed systematically versus uniformly random, could either inflate or deflate the sc/fc correlations. Care must be taken here.

      Thank you for pointing this out. As you mentioned, the SC matrix becomes increasingly sparse as the number of ROIs increases (Ext. Data Fig.2-2b). In contrast, the FC matrix may contain values even when there are no direct connections between ROIs (indirect connections). We conducted an investigation into this issue. To deal with this issue, Honey et al. (2009) [6] resampled the elements of the SC matrix in rank order using a Gaussian distribution and calculated the FC-SC correlation between this resampled SC and FC.

      Ext. Data Fig.2-2a shows a comparison between resampled SC (Honey et al.’s method) and log-scaled SC (our method). Up to 200 ROIs, the proportion of SC matrix elements that are zero is less than 10% (Ext. Data Fig.2-2b), and there is little zero replacement of logarithmic elements. In this situation, replacing with Gaussian arithmetic tends to increase the correlation coefficient (Ext. Data Fig.2-2a). On the other hand, with 10,000 ROIs, where sparsity is extremely high, the proportion of SC matrix elements that are zero exceeds 70%. In this situation, 70-80% of the zeros are randomly assigned from the smaller end of the Gaussian distribution, which causes a lowering of the correlation coefficient (Ext. Data Fig.2-2a, c, d). For these reasons, we believe that log-scaled SC has less bias than resampling with a Gaussian distribution, and conclude that using log-scaled SC as is in this paper is reasonable. Log-scaled SC has also been used in previous studies [9, 68] and is considered a simple method for showing the relationship (correlation) between FC and SC. To show that we have considered this issue, Ext. Data Fig.2-2 has been added to the manuscript.

      (4) Further, in constructing the segregated versus unsegregated connectomes, they use absolute thresholds for collecting synapses. It is unclear, however, whether similar numbers of synapses were included in both matrices. If the number is different, that might explain the differential relationship with fc; one matrix has more non-zero entries (and as noted earlier, those zero entries are problematic).

      Author response image 1.

      a, Sparsity rate histogram of SC matrix with cPPSSI (0-0.1) and subsampled null SC matrices corresponding Fig.4e. Red line indicates sparsity rate of SC matrix with cPPSSI (0-0.1). b, Sparsity rate histogram of SC matrix with cPPSSI (0.9-1) and subsampled null SC matrices corresponding Fig.4f. c, Sparsity rate histogram of SC matrix with reciprocal synapse (≤2𝜇𝑚) and subsampled null SC matrices corresponding Fig.4i.

      Thank you for pointing this out. The number of synaptic connections in the SC matrix shows a large difference between those extracted from cPPSSI (0-0.1) and cPPSSI (0.9-1) (Fig. 4e, f). However, when null SC matrices (99) were generated for each and compared with the cPPSSI-extracted matrices, the FC-SC correlation was significantly higher or lower. At this point, since the sparsity rates of the null SC matrices differed a lot from that of the SC matrices extracted by cPPSSI, we regenerated the null SC matrices in Fig. 4e and 4i. As shown in Author response image 1, we ensured that the extracted SCs (red lines) fit within the null-generated matrices. This figure was added to Ext. Data Fig.4-5, and the main text was also revised. The sparsity rates are 0.52 for cPPSSI (0-0.1) and 0.123 for cPPSSI (0.9-1). Since both cases involve comparisons with null SC matrices that have closely similar sparsity rates, we believe comparison using log-scaled SC is appropriate.

      (5) There was also considerable text (in the results) describing the processing of the Ca data. In this section, the authors frequently refer to some pipelines as "better" or "worse" (more or less effective). But it is not clear what measures they adopted to assess the effectiveness of a pipeline.

      Detailed registration flow of Ca data is described in “Preprocessing of D. melanogaster calcium imaging data” in Materials and Methods section (Ext. Data Fig. 1-1a). Then, optimal nuisance factor removal methods and smoothing size were investigated. We used both correlation analysis (FC-SC correlation) and ROC curve analysis (FC-SC detection). Since signals are assumed to be transmitted between regions based on SC, when SC is treated as the ground truth, we considered a pipeline with a FC-SC higher similarity and higher detection to be better. We updated the Results section to include this point.

      Reviewer #2 (Public review):

      Summary:

      Okuno et al. investigate the structure-function relationship in the fruit fly Drosophila melanogaster. To do so, they combine published data from two recent synapse-level connectomes ("hemibrain" and "FlyWire") with a dataset comprising functional whole-brain calcium imaging and behavioural data. First, they investigate the applicability of fMRI pre-processing techniques on data from calcium imaging. They then cross-correlate this pre-processed functional data with structural data extracted from the connectomes, including a comparison to humans. The authors proceed to compare the two connectomes and find significant differences, which they attribute to differences in the accuracy of the synapse detections. Next, they present a novel algorithm to quantify whether neurons are segregated (pre- and postsynapses are spatially separate) or unsegregated (pre- and postsynapses are mixed). Using this approach, they find that unsegregated neurons may contribute more to function than segregated neurons. Applying a general linear model to the functional dataset suggests that activity in two brain areas (Wedge and AVLP) is suppressed during walking. The authors identify a GABAergic neuron in the connectome that could be responsible for this effect and suggest it may provide feedback to the fly's "compass" in the central complex.

      Strengths:

      The study tackles a relevant question in connectomics by exploring the relationship between structural and functional connectivity in the Drosophila brain. The authors apply a range of established and adapted analytical methods, including fMRI-style preprocessing and a novel synaptic segregation index. The effort to integrate multiple datasets and to compare across species reflects a broad and methodical approach.

      Thank you very much for your comments.

      Weaknesses:

      The manuscript would benefit from a clearer overarching narrative to unify the various analyses, which currently appear somewhat disjointed. While the technical methods are extensive, the writing is often convoluted and lacks crucial details, making it difficult to follow the logic and interpret key findings. Additionally, the conclusions are relatively incremental and lack a compelling conceptual advance, limiting the overall impact of the work.

      (1) The introduction currently contains a number of findings and conclusions that would be better placed in the results and discussion to clearly delineate past findings from new results and speculations.

      Thank you for pointing this out. We have revised the introduction to make it more concise.

      (2) The narrative would benefit greatly from some clear statements along the lines of "we wanted to find out X, therefore we did Y".

      Thank you for pointing this out. In many biology papers, the problem is clear, but as you say, this paper starts by comparing the very fine SC and FC of flies, which makes the problem unclear and the results sporadic. We have revised the structure of the introduction.

      (3) More concise terminology would be helpful. For example, the connectomes are currently referred to as either "hemibrain", "FlyEM", "whole-brain", or "FlyWire".

      Thank you for pointing this out. We revised the manuscript to separate "hemibrain" and "whole-brain" from "connectome." "hemibrain" and "whole-brain" retain their original meanings.

      (4) The abstract claims "a new, more robust method to quantify the degree of pre- and post-synaptic segregation". However, the study fails to provide evidence that this method is indeed more robust than existing methods.

      We apologize, but this information was not included in the main figures or the Results section. It is presented in the Methods section and Ext. Data Fig. 4-1i, j. We moved related texts from the Methods to the Results section.

      (5) The authors define unsegregated neurons as having mixed pre- and postsynapses in the same space. However, this ignores the neurons' topology: a neuron can exhibit a clearly defined dendrite with (mostly) postsynapses and a clearly defined axon with (mostly) presynapses, which then occupy the same space. This is different from genuinely unsegregated neurons with no distinct dendritic and axonal compartments, such as CT1.

      Thank you for pointing this out. Regarding this point, we think it is difficult to discuss the neuron’s topology in this paper. We defined PPSSI and demonstrated only that unsegregated neurons with mixed pre- and post-synapses are scattered throughout the brain (Ext. Data Fig. 4-2e). Further research is needed to determine the relationship with morphology in individual neurons.

      One possibility is that inhibitory, non-spiking unsegregated neurons, such as CT1 amacrine cell [24, 27, 28] or interneurons in Antennal Lobe [29], may be widely used throughout the brain (WAGN is also a candidate for this). Grimes et al. [34] mentioned “The retina is a beautiful example of a neural network that optimizes signal processing capacity while minimizing cellular cost.” To maintain the signal dynamic range, A17 amacrine cells must optimize the processing units and wiring costs. If one unit equaled one cell, an enormous number of cell bodies would be required, reducing the number of processing units per volume and increasing the energy cost during development. To optimize this, they proposed arranging units capable of parallel processing within a single cell, thereby maximizing the processing units and wiring costs per volume.

      Signal bursts might also occur in the central nervous system (CNS), in which case CNS neurons also require dynamic range adjustment. The concept of optimizing processing units per volume is highly compelling and is thought to apply not only to the retina but throughout the entire brain.

      (6) It is not entirely clear where the marmoset dataset originates from. Was it generated for this study? If not, why is there a note in the Ethics Declaration?

      Marmoset data were reported in [10] and it was not generated for this study. We therefore removed the Ethics Declaration.

      (7) On the differences between hemibrain and FlyWire: What is the "18.8 million post-synapses" for FlyWire referring to? The (thresholded) FlyWire synapse table has 130M connections (=postsynapses). Subsetting that synapse cloud to the hemibrain volume still gives ~47M synapses. Further subsetting to only connections between proofread neurons inside the hemibrain volume gives 19.4M - perhaps the authors did something like that? Similarly, the hemibrain synapse table contains 64M postsynapses. Do the 21M "FlyEM" post-synapses refer to proofread neurons only? If the authors indeed used only (post-)synapses from proofread neurons, they need to make that explicit in results and methods, and account for differences in reconstruction status when making any comparisons. For example, the mushroom body in the hemibrain got a lot more attention than in FlyWire, which would explain the differences reported here. For that reason, connection weights are often expressed as, e.g., a fraction of the target's inputs instead of the total number of synapses when comparing connectivity across connectomic datasets. Furthermore, in Figure 3b, it looks like the FlyWire synapse cloud was not trimmed to the exact hemibrain boundaries: for example, the trimmed FlyWire synapse cloud seems to extend further into the optic lobes than the hemibrain volume does.

      Thank you for pointing this out. FlyEM connectome data version 1.2 was downloaded and used as described in Data Availability. This data is provided in the format defined by https://neuprint.janelia.org/public/neuprintuserguide.pdf, and we extracted neurons and synapses from it.

      The entire segmentation body is 28M segmentations, and there were 99,644 Traced proofread neurons. In addition, there were 73M (pre- or post- alone) synapses, 87M records in synapseSets and 128M records in synapseSet-to-synapse. When we extracted post-synapses between Traced neurons, the total number was 21.4M (i.e., connections from Traced neurons to other body fragments like Orphans were excluded).

      The FlyWire dataset (v783) was downloaded from the flywire codex and Zenodo. This dataset contained 139,255 proofread neurons and 54.5M (pair of pre- and post-) synapses, as described in Dorkenwald et al. [13], with 18.8M post-synapses in the regions corresponding to the hemibrain primary ROIs. We have updated the Results and Methods sections by taking into account your comment.

      In Fig. 3b, these images were created using a mask that extended the boundaries of the hemibrain primary ROIs, making the boundaries unclear. Therefore, we corrected the images in Fig. 3b by adjusting the mask so that the boundaries were properly aligned.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript, Okuno et al. re-analyze whole-brain imaging data collected in another paper (Brezovec et al., 2024) in the context of the two currently available Drosophila connectome datasets: the partial "FlyEM" (hemibrain) dataset (Scheffer et al., 2020) and the whole-brain "FlyWire" dataset (Dorkenwald et al., 2024). They apply existing fMRI signal processing algorithms to the fly imaging data and compute function-structure correlations across a variety of post-processing parameters (noise reduction methods, ROI size), demonstrating an inverse relationship between ROI size and FC-SC correlation. The authors go on to look at structural connectivity amongst more polarized or less polarized neurons, and suggest that stronger FC-SC correlations are driven by more polarized neurons.

      Strengths:

      (1) The result that larger mesoscale ROIs have a higher correlation with structural data is interesting. This has been previously discussed in Drosophila in Turner et al., 2021, but here it is quantified more extensively.

      (2) The quantification of neuron polarization (PPSSI) as applied to these structural data is a promising approach for quantifying differences in spatial synapse distribution.

      Thank you very much for your comments.

      Weaknesses:

      One should not score noise/nuisance removal methods solely by their impact on FC-SC correlation values, because we do not know a priori that direct structural connections correspond with strong functional correlations. In fact, work in C. elegans, where we have access to both a connectome and neuron-resolution functional data, suggests that this relationship is weak (Yemini et al., 2021; Randi et al., 2023). Similarly, I don't think it's appropriate to tune the confidence scores on the EM datasets using FC-SC correlations as an output metric.

      Thank you for pointing this out. We believe that the FC in C. elegans uses cell body dynamics, which is different from the synaptic population dynamics in a region of fly calcium imaging or fMRI data (BOLD [Blood Oxygenation Level Dependent] signal). The BOLD signal in a region is thought to correspond to the neurovascular coupling of synaptic population dynamics. Furthermore, compartmentalization of a neuron has been observed in C. elegans (Hendricks et al., 2012)*, showing different dynamics across neuron compartments. Thus, the dynamics of the cell body and the dynamics of the synaptic population in other regions are different in C. elegans. We speculate that there is some relationship between FC-SC between regions, because the FC-SC correlation in the fly brain reached r=0.87 with 20 ROIs (Fig. 2d). We believe that this result is different from the cell body dynamics in C. elegans.

      *Hendricks et al., “Compartmentalized calcium dynamics in a C. elegans interneuron encode head movement,” Nature 487, 99-103 (2012)

      Any discussion of FC-SC comparisons should include an analysis of excitatory/inhibitory neurotransmitters, which are available in the fly connectome dataset. However, here the authors do not perform any analyses with neurotransmitter information.

      A comparison between FC-SC and neurotransmitter has been written in the Results section. We investigated the ratios of neurotransmitter input (ExtFig.3-2a) and output (Fig. 3f) in each region, and investigated the relationship between this ratio and FC-SC correlation in each neurotransmitter. This revealed significant correlations for acetylcholine (r=0.39, p=0.0013) and GABA (r=-0.25, p=0.046) (Fig. 3g). That is, the higher the percentage of excitatory connections, the higher the FC-SC correlation; conversely, the higher the percentage of inhibitory connections, the lower the FC-SC correlation.

      Comparisons between fly and human MRI data are also premature here. Firstly, the fly connectomes, which are derived from neuron-scale EM reconstructions, are a qualitatively different kind of data from human connectomes, which are derived from DSI imaging of large-scale tracts. Likewise, calcium data and fMRI data are very different functional data acquisition methods-the fact that similar processing steps can be used on time-series data does not make them surprisingly similar, and does not in my view, constitute evidence of "similar design concepts."

      Thank you for pointing this out. As you say, fiber bundles of DTI and EM connectome are completely different. Nevertheless, the fact remains that the FC-SC correlation is high in both the fly and human brains. As mentioned above, both regional signal from calcium imaging and BOLD signal from fMRI are based on synaptic population dynamics. It was estimated that 43% of the energy consumption in the gray matter is due to synaptic activity of neurons (Harris et al., 2012), and the BOLD signal fluctuates greatly due to this activity. Furthermore, synaptic activity is thought to be much faster than the activity of microglia and astrocytes, so the FC of fMRI is thought to mainly capture the regional correlation of synaptic activity. In other words, in both flies and humans, although the size is different, the pre-synaptic activity in one region and the pre-synaptic activity in another region via neural fibers are being compared in a common manner in the form of FC-SC.

      In addition, non-spiking unsegregated neuron exists in mammals as well, such as the amacrine cell of the retina [34], and even pyramidal cells in the neocortex show local mixtures of pre- and post-synapses (Ext. Data Fig.1-2). If a functional unit is realized by local compartment in a neuron as mentioned in [34], the fly will be a powerful model organism for investigating them, and its functional “design concept” may also be useful for mammals.

      Harris et al., “The Energetics of CNS White Matter,” J. Neurosci., 2012, 32 (1) 356-371

      The comparison of FlyEM/FlyWire connectomes concludes that differences are more likely a result of data processing than of inter-individual variability. If this is the case, the title should not claim that the manuscript covers individual variability.

      Thank you for pointing this out. Inter-individual variability is relevant to both SC and FC. Regarding SC, we think the difference in the number of synapses between the two individuals is due to the difference in detection power caused by differences in the resolution of the electron microscope. Regarding FC, as stated in the Results section, “Spatial smoothing is useful for absorbing inter-individual variability and conducting second-level group analysis.” Increasing the smoothing size improves the correlation and AUC between group-averaged FC and SC, indicating the presence of inter-individual variability in FC (Fig. 2b, Ext. Data Fig. 2-1b, especially when the number of ROIs is high). We added this text in the Introduction and Results sections to address your comment.

      The analysis of the wedge-AVLP neuron strikes me as highly speculative, given that the alignment precision between the connectome and the functional data is around 5 microns (Brezovec* et al, PNAS 2024).

      As you mentioned, functional analysis has limitations in spatial resolution. In particular, the resolution in the Z axis is 4 μm, which is 1,000 times lower than the resolution of electron microscopy data. This makes it difficult to perfectly match synaptic activity to a synapse in the structural data. Furthermore, spatial smoothing is applied to functional images to absorb inter-individual variability, which can only provide blurred results for group analyses. These are considered limitations of the methods used in fMRI analysis. Despite these limitations, we applied GLM analysis to walking behavior and observed clear inactivity region. This region roughly corresponds to the synaptic cloud of a neuron named WAGN (Fig.5b and c). This neuron also connects to WPNb and ANs in the connectome data, suggesting a possibility that it is related to walking behavior. This is merely a screening reference; therefore, further biological experimentation is needed to pursue this topic.

      Recommendations for the authors:

      Reviewing Editor Comments:

      We should emphasize that the reviewers encouraged revision and resubmission. If the reviewers' comments were to be addressed in full in a revision to strengthen the evidence, this would significantly increase the impact of the findings and the relevance of the work to the fly neuroscience community and to the connectomics field more broadly.

      Thank you very much for your comments.

      Major Issues:

      (1) Structural correlation and functional correlation measure very different aspects of network data, yet a simple correlation between the off-diagonal elements of the two is used. It would be expected that this would not be directly proportional, and it's not clear why this would be a sensible measure. The authors need a better solution for dealing with the zero entries in the SC matrix. Replacing the infinities with zeros and then running the linear regression to get an SC/FC relationship is not appropriate. Even with a better metric, given that both intuition and other studies have shown a weak correlation between FC and SC, using FC-SC correlation as a quality descriptor for other properties is not proper. Furthermore, the authors don't account for neurotransmitter identity in the structural data, which would have strong implications for the relationships between FC and SC.

      Thank you for pointing this out. To investigate this issue we compared the FC-SC correlation between the Gaussian resampled SC approach used in Honey et al. (2009) [6] and the log-scaled SC used in this study (Ext. Data Fig.2-2a). With a small number of ROIs, the sparsity rate is low (Ext. Data Fig.2-2b), resulting in less zero replacement. Therefore, log-scaled SC is likely to more accurately represent the FC-SC relationship. Furthermore, with a large number of ROIs, the sparsity rate exceeds 70%, and Gaussian resampled SC randomly assigns a large number of zero elements from the smaller end of the distribution. This tends to lower the correlation (Ext. Data Fig.2-2c, d), suggesting that log-scaled SC provides fairer results. Log-scaled SC has been used in previous studies [9, 68] and is considered a simple method for showing the relationship (correlation) between FC and SC. When zero replacement is undesirable, using connection weights (the proportion of connections originating from the target region among all connections) can yield results similar to log-scaled SC (data not shown). It may be possible to compare various methods, but this is outside the scope of this study and requires further research.

      The C. elegans studies presented by Reviewer #3 showed a weak correlation between FC and SC. However, C. elegans neurons do not fire and exhibited different calcium fluctuations depending on the region (Hendricks et al., 2012). This suggested that the cell body and various synaptic terminal regions have different FCs, which is consistent with the objective of our study (neuronal compartmentalization). If a functional unit is locally composed of multiple neurons and synapses, it is expected that SC and FC from that region will show a strong relationship. Larger regions would include multiple functional units, and a relationship between SC and FC would also be found, which is consistent with the results of our study. The C. elegans study compared FC of the cell body (a region) with SC of whole cell (not a same region), which would be inconsistent.

      (2) Synaptic segregation on neurons can be topologically present even if pre- and post-synaptic synapses are present in similar regions of space, as an axon branch and dendrite branch can overlap in space but remain distinct along the arbor. The authors emphasize a region-based definition that does not reflect cellular anatomy. Moreover, the authors do not make an argument for their claim of better robustness of their new synaptic segregation measures.

      Author response image 2.

      Distance calculation for DBSCAN. a, Example synapse pair (black dot) of distance calculation. Red line shows the straight-line distance, and green line shows the morphology-based distance. DBSCAN will places two synapses in the same cluster based on straight-line distance, but they will be in different clusters based on the morphology-based distance.

      Thank you for pointing this out. We changed from using DBSCAN based on the straight-line distance between synapses to DBSCAN based on the morphology-based distance via the branch nearest to the synapse (Author response image 2a). This resulted in a synaptic segregation measure that incorporates cellular anatomy. We updated all related figures, such as Figure.4, Ext. Data Figure.4-1, 4-2, 4-3, 4-4, Figure.5h. Also, we updated related text in the Results and Methods sections.

      (3) Reviewers found the overall structure of the paper is difficult to follow, with sections appearing disjoint and the aims of different sections not well described. This extended to the paper organization as well, with the introduction not clearly setting up the questions and being distinct from the results. The manuscript would benefit from a clearer overarching narrative to unify the various analyses.

      Thank you for pointing this out. We have revised the introduction to make it more concise.

      (4) Similarly, there are several descriptions of data and analysis that are unclear or lacking, including the source of the marmoset data and how the FlyWire synapse was subsampled.

      As pointed out by other reviewers, the marmoset data was obtained in [10], and the processing is also described in [10]. Therefore, we have revised the caption and removed the Ethics Declaration.

      We have updated the Results and Methods sections regarding the extraction of "traced" neurons and synapses in FlyEM connectome data, and the extraction of post-synapses in hemibrain primary ROIs in FlyWire connectome data.

      (5) Comparisons between FlyWire and Hemibrain have shown many similarities and some clear examples of inter-individual variability. There was concern that technical decisions with handling FlyWire synapse sampling were responsible for some of the differences observed between the datasets.

      In response to Reviewer #2's question, we answered that both FlyEM and FlyWire use proofread neurons and their connecting synapses. We also updated Fig. 3b and the Results and Methods sections.

      Reviewer #1 (Recommendations for the authors):

      The paper is written in an unusual way. It would be helpful if the introduction read more like a standard introduction. Describe the relevant background that the reader needs to understand the results that come later. Frame the experiments in terms of a question or hypothesis. Results should be relegated to the results section (or, if you like, a final paragraph that summarizes the findings). They should not be intermingled throughout the introduction.

      Thank you for pointing this out. We have revised the introduction to make it more concise.

      The authors must be more attentive in terms of how they construct the segregated/unsegregated connectomes. I suggest exploring various thresholds/bins, but also considering proportionality thresholds that match the number of synapses.

      Thank you for pointing this out. As pointed out by other reviewers, we changed from using DBSCAN based on the straight-line distance between synapses to DBSCAN based on the morphology-based distance via the branch nearest to the synapse (Author response image 2a). This resulted in a synaptic segregation measure that incorporates cellular anatomy.

      We also considered about the sparsity rates of the SC matrices. Since the sparsity rates of the null SC matrices differed a lot from that of the SC matrices extracted by cPPSSI, we regenerated the null SC matrices, shown in Fig. 4e and 4i. As shown in Author response image 1, we ensured that the extracted SCs fit within the null-generated matrices. This figure was added to Ext. Data Fig.4-5, and the main text was also revised.

      The authors need a better solution for dealing with the zero entries in the sc matrix. Replacing the infinities with zeros and then running the linear regression to get an sc/fc relationship is not appropriate.

      Thank you for pointing this out. To investigate this issue, as pointed out by other reviewers, we compared the FC-SC correlation between the Gaussian resampled SC approach used in Honey et al. (2009) [6] and the log-scaled SC used in this study (Ext. Data Fig.2-2a). With a small number of ROIs, the sparsity rate was low (Ext. Data Fig.2-2b), resulting in less zero replacement. Therefore, log-scaled SC is likely to more accurately represent the relationship. Furthermore, with a large number of ROIs, the sparsity rate exceeds 70%, and resampled SC randomly assigns a large number of zero elements from the smaller end of the distribution. This tends to lower the correlation (Ext. Data Fig.2-2c, d), suggesting that log-scaled SC provides fairer results. Using connection weights (the proportion of connections originating from the target region among all connections) can yield results similar to log-scaled SC (data not shown), because this matrix can also be very sparse. It may be possible to compare various methods, but this is outside the scope of this study and requires further research.

      It would be useful to include a description of where the human/marmoset datasets came from. It would be useful to describe the processing of those datasets and whether they're comparable to how the fly data was processed.

      As pointed out by other reviewers, the marmoset data was obtained in [10], and the processing is also described in [10]. Therefore, we have revised the caption and removed the Ethics Declaration.

      The pre-processing of fly calcium imaging data is described in the Methods section. Unfortunately, this processing method is not comparable to that used in humans/marmosets as it was highly customized.

      The authors report sc/fc correlations for the human/marmoset datasets based on single papers. However, in the human case, especially, the strength of sc/fc correlations is highly variable. Not just based on number/size of parcels, but based on amount of data, processing pipeline, single-subject versus group averaged (incidentally, single-subject sc/fc is ‘much’* lower than group-averaged, which has big implications for this study, where the fly datasets are, in essence, N=1 studies).

      Yes, there are numerous FC-SC correlation studies. We think Honey et al. (2009) [6] to be a highly representative study. It showed r = 0.39 to 0.48 for individual participants in 998 ROIs, and r = 0.36 for averaged one, but it increased r = 0.53 excluding absent or inconsistent structural connections. So, single-subject may not be much lower than group-averaged. Since the SC for a fly is an N=1 study, the FC-SC correlation for the same individual cannot be calculated. We think further research will be necessary.

      Reviewer #2 (Recommendations for the authors):

      Abstract:

      Please introduce the term "ROI"

      Thank you for pointing this out. We have revised the Abstract.

      Introduction:

      (1) On a general note: the introduction reads like an extended abstract (i.e., a mix of results and discussion).

      Thank you for pointing this out. We have revised the introduction to make it more concise.

      (2) Line 43: Does this mean FC-SC correlation is higher in flies but not significantly so? Please clarify.

      We performed Mann-Whitney U test and it was not significant (p= 0.2667).

      (3) Line 51: The "confidence" score does not indicate the degree of synaptic detection.

      In the NeuPrint user guide, https://neuprint.janelia.org/public/neuprintuserguide.pdf it states “confidence - The certainty that an annotated synapse is correct and valid.” Since “degree of synaptic detection” may be difficult to understand, we changed it to “certainty of an annotated synapse.”

      (4) Line 59-61: This statement needs refining: post-synapses do not "receive" neurotransmitters, action potentials aren't conducted along nerve fibres.

      We changed “receive” to “sense.” About “action potentials,” we changed “conduct an action potential” to “graded potentials”, and removed “along nerve fibers.”

      (5) Line 61: calcium activity as detected via GCaMP correlates with (electric) neuronal activity - please cite relevant GCaMP literature here.

      We added F. Helmchen and J. Waters, "Ca2+ imaging in the mammalian brain in vivo," Eur J Pharmacol., vol. 447, pp. 119-129, 2002.

      (6) Line 76: "interconnected" is rather vague; just say "many Drosophila neurons are reciprocally connected".

      Thank you for pointing this out. Lin et al., (2024) showed motif analysis and there are many reciprocal, three-node and rich-club connections. However, introduction was updated and this sentence was removed.

      (7) Line 77: comparing unsegregated vs reciprocal synapses is overly simplistic; these are separate features of the same object - i.e., a synapse can be reciprocal and at the same time be segregated in the presynaptic neuron but unsegregated in the postsynaptic neuron.

      Thank you for pointing this out. As you say, the relationship is complicated. In this paper, we are concerned with the degree of segregation of pre- and post-synapses, and we are looking at the segregation within a neuron. In this case, nearby reciprocal synapses (<=2 μm) are included in unsegregated synapses. We have made a correction to the sentence.

      (8) Line 79: I don't understand how we get from unsegregated synapses to local activity.

      Retinal amacrine cells have extensive unsegregated synapses, which provide local feedback inhibition of burst inputs [34]. We changed the text around these descriptions.

      (9) Line 80: What does "more essential function" mean?

      We removed this sentence.

      (10) Line 85: "as shown earlier": Is this based on results in this study or prior work? See also the general above note on mixing results/discussion into the introduction.

      Thank you for pointing this out. We have revised the introduction to make it more concise.

      (11) Line 85-87: I don't understand how the applicability of certain fMRI analysis methods in turn means that functional activity is locally compartmentalized. Did you mean to say something along the lines of "we applied common fMRI methods which showed functional activity is locally compartmentalized"?

      These sentences discuss the commonality between fMRI (BOLD signal) and calcium signal, which both represent presynaptic population dynamics within a local region (voxel). Furthermore, unsegregated synapses are widespread throughout the fly brain (Ext. Data Fig.4-2) and can also be observed in human pyramidal cells (Ext. Data Fig.1-2). Unsegregated synapses suggest local compartment activity [33, 34, 39, 40] and contribute more to functional activity (Fig.4b). Therefore, the similar trend in FC-SC correlation (Fig.2d) between humans and flies suggest that both species exhibit localized compartmental activity via unsegregated synapses throughout the entire brain.

      Because these sentences contain many conclusions, they have been moved from the Introduction to the Discussion section.

      (12) Line 87: Please provide a reference for "common among various species".

      Thank you for pointing this out. Because these sentences contain many conclusions, they have been moved from the Introduction to the Discussion section.

      Results:

      (1) Line 91-92:

      (a) Please explain where the calcium data came from, how it was generated, etc.

      We added the data source and a reference (Brezovec et al. [14]).

      (b) Please clarify: what registration method?

      This is not simple. Please see the Methods section and Ext. Data Fig.1-1. This is also indicated in the text.

      (c) "calcium image" → "calcium image data"?

      We changed “calcium image” to “calcium imaging data”.

      (d) What is the "FDA template"?

      This is a brain template created by Brezovec et al. [14]. JRC2018 is a well-known brain template, but it was created by immunostaining postmortem brains and did not fit well with calcium imaging data from living flies. Therefore, we used the FDA template.

      (2) Line 93: Please introduce the term "ROI".

      We added “(Region of Interest)” in Line 38.

      (3) Line 94: Ito et al., Neuron (2014) "A systematic nomenclature for the insect brain" is a better reference for Drosophila neuropils; for the hemibrain, the ROIs were generated to match that original atlas

      Thank you for pointing this out. We added a reference.

      (4) Line 95/96: It is unclear what was used as the basis for the k-means/distance-based clustering

      This was because we wanted to investigate whether nuisance factor removal methods are robust, even for such diverse types of ROI. We added this point to the text.

      (5) Line 120ff: I'm not sure how the total number of ROIs is relevant for comparing flies and humans, given (a) the huge difference in brain size and (b) the difference in resolution of the functional data.

      Indeed, the fly brain and the human neocortex are completely different. We are investigating whether there are commonalities between them using a metric called FC-SC correlation. As described in our answer for (11), both the fMRI (BOLD signal) and calcium signal represent presynaptic population dynamics within a local region (voxel). FC represents the synchronization of synaptic activity between regions, and SC represents the structural connectivity of neurons. Both flies and humans showed high SC-FC correlation and showed similar trends (Fig. 2d), so we believe it would be interesting to investigate this phenomenon.

      (6) Line 123: "by contrast" is misleading here since, as you say, there isn't really a difference.

      We changed “by contrast” to “and.”

      (7) Line 141: I'm somewhat worried that the differences between FlyWire and hemibrain synapse counts are due to the issues mentioned above.

      Thank you for the comment but we are not sure about “the issues mentioned above” is referring to.

      (8) Line 148: There is no evidence that any differences in synapse are due to the resolution or anisotropy (as suggested in the introduction).

      We apologize that we don’t have direct evidence for it. We changed this to the sentence “This may be caused by differences in detection accuracy resulting from the resolution of EM scanning, but not to inter-individual variability.”

      (9) Line 155: References "39,45" have no brackets.

      These are not referencing numbers, but brain regions of Brodmann area 39 and 45.

      (10) Line 155-157: I don't think we can infer the composition of brain areas in humans based on a tenuous correlation in flies; this is highly speculative and really should be in the discussion.

      In humans, there are areas with strong and weak FC-SC correlations [8], which may be due to the E-I (Excitatory-Inhibitory) balance of connections. We investigated this possibility by comparing the correlation between neurotransmitters and FC-SC correlations in the fly brain. We slightly changed this sentence.

      (11) Line 159: I find the first 2-3 sentences in this paragraph confusing. Are you saying that you did all these things in the prior results sections, or that you wanted to look at X and therefore you did Y? Maybe there is an issue with the tense here?

      We changed the sentences around this description.

      (12) Line 161: "whole-brain" = FlyWire?

      We changed “whole-brain” to “FlyWire”.

      (13) Line 163: Please explain the "PPSSI" acronym.

      This is now explained on Line 75.

      (14) Line 165: The description of how the cPPSSI was calculated is hard to follow. For example, what's the "fraction of synapse number".

      We changed our sentences around this description to be clearer. The cPPSSI is the degree of segregation within a cluster and is also assigned to each synapse. The PPSSI is then the average of the cPPSSI values of all synapses in a neuron.

      (15) Line 166: Is there a difference between "cPPSSI" and "PPSSI"?

      Yes, there is. Please see our answer for (14).

      (16) Line 167: "The result showed a histogram resembling a normal distribution" → I suggest running a normality test.

      Thank you for pointing this out. We tested it by Lilliefors test and the result was p=0.001 (significantly not a normal distribution). Since there are numerous values with PPSSI=1, it is not judged to be a normal distribution. We therefore changed this description.

      (17) Line 173: I am somewhat worried about a selection bias in your correlation of segregated vs unsegregated synapses. First, it seems like only a small fraction of neurons are in the 0-0.1 and 0.9-1 PPSSI range. I would suggest running a proper correlation between PPSSI and FC-SC correlation instead of looking at just the two extremes. Second, your examples for segregated neurons (APL + CT1) are large neurons that densely innervate spatially close and functionally very similar neuropils. If the sample of unsegregated neurons consists mainly of these large interneurons, I'm not at all surprised that they contributed strongly to FC-SC correlation.

      Thank you for pointing this out. For this work we investigated synapses (not neurons), extracting those with cPPSSI of 0-0.1 and 0.9-1, and performed a rank text with the FC-SC correlation of random sub-sampled synapses. We aimed to demonstrate that unsegregated synapses in particular, strongly contribute to FC-SC, and we hope to investigate overall trends in a future study.

      (18) Line 185: I don't think the function of reciprocal synapses is "considered to be clear". There are examples of feedback inhibition through reciprocal synapses, in particular in the visual system, but that does not mean that this is true across the board.

      We changed “considered to be clear” to “considered to be clearer than unsegregated synapses.” Of course, the function of reciprocal synapses is unknown for the whole brain, but we think it is more well-studied than unsegregated synapses.

      (19) Line 188 / Figure 4h: that figure panel does not appear to show transmitter pairs.

      Figure 4h (FlyWire) showed transmitter pairs. Ext. Data Fig.4-1g did not, because FlyEM does not have transmitter information.

      (20) Line 192: Please clarify "functionally common".

      We changed our sentences to clarify this.

      (21) Line 199: "ventral nerve code" → "ventral nerve cord".

      We fixed this typo.

      (22) Line 201: I don't think you can use "conversely" here.

      We changed “Conversely” to “Moreover.”

      (23) Line 201: How certain are you that the WAGN neuron is the only candidate? Also, it would be nice to provide the neuron IDs so that people can identify them in the connectome.

      Thank you for pointing this out. We added Root ID: 720575940644632087 in the text. Actually, we found several GABA neuron candidates, such as 720575940637611365, 720575940644632087, 720575940613552947, 720575940640333109 and 720575940612264817. We investigated whether ER1(L) was present in these downstream connections and found that 720575940644632087 had the strongest connection with the largest number of synapses, so we adopted this.

      (24) Line 207: When you say "the left WAGN was strongly connected", are those connections not also present for the right WAGN?

      There is a right WAGN (Root ID: 720575940624377224), but it does not have strong interconnections with WPNb tier 2/3 (left) neurons. For the right WAGN, there are few inputs from WPNb tier 2/3 (left). We added “(left)” in the text.

      (25) Line 212: I don't think you can use "however" here.

      We removed “however.”

      (26) Line 214: "well unsegregated" → "very unsegregated"?

      This sentence was removed, because we recalculated Fig. 5h.

      Ethics Declaration:

      It seems the marmoset data were reported on in [10], so why is there a reference to the generation of the dataset?

      Yes, marmoset data were reported in [10], so we removed the Ethics Declaration.

      Reviewer #3 (Recommendations for the authors):

      (1) In my opinion, the title and framing of this manuscript dramatically overstate the results presented here. Also, the results presented in the different figures in this manuscript seem disjointed and are not very related to each other.

      Thank you for pointing this out. We have rewritten our manuscript slightly to address this. Inter-individual variability is relevant to both SC and FC. Regarding SC, we think the difference in the number of synapses between the two individuals is due to the difference in detection power caused by differences in the resolution of the electron microscope. Regarding FC, as stated in the Results section, “Spatial smoothing is useful for absorbing inter-individual variability and conducting second-level group analysis.” Increasing the smoothing size improves the correlation and AUC between group-averaged FC and SC, indicating the presence of inter-individual variability in FC (Fig. 2b, Ext. Data Fig. 2-1b, especially when the number of ROIs is high). We added this text in the Introduction and Results sections.

      (2) There are multiple ways to compute structural correlation matrices-the methods the authors implemented should be discussed in greater detail in the manuscript.

      Thank you for pointing this out. To investigate this issue, as pointed out by other reviewers, we compared the FC-SC correlation between the Gaussian resampled SC approach, used in Honey et al. (2009) [6] and the log-scaled SC approach, used in this study (Ext. Data Fig.2-2a). With a small number of ROIs, the sparsity rate was low (Ext. Data Fig.2-2b), resulting in fewer zero replacement. Therefore, log-scaled SC is likely to more accurately represent the relationship in our study. Furthermore, with a large number of ROIs, the sparsity rate exceeds 70%, and resampled SC randomly assigns a large number of zero elements from the smaller end of the Gaussian distribution. This tends to lower the correlation (Ext. Data Fig.2-2c, d), suggesting that log-scaled SC provides fairer results. Using connection weights (the proportion of connections originating from the target region among all connections) can yield results similar to log-scaled SC (data not shown), because this matrix can be also very sparse. The log-scaled SC aprroach has been used in previous studies [9, 68] and is considered a simple method for showing the relationship (correlation) between FC and SC. It may be possible to compare various methods in-depth, but this is outside the scope of this study and requires further research.

      (3) The use of the FC-SC detection score defined by the authors should be discussed and justified more extensively in the text.

      Thank you for pointing this out. This has already been discussed in [10]. We defined our own “FC-SC detection score,” but we consider the overall approach to be well established in the literature. For example, Stafford et al. (2014) carried out FC-SC detection for 168 mouse cortical regions, and obtained 78.26% sensitivity and 81.69% specificity for the top 1% of SC. Hori et al. (2020) also investigated FC-SC detection for 55 cortical regions of the marmoset brain left hemisphere, achieving an AUC of 0.72. We think FC-SC detection is an index that evaluates the relationship between FC and SC from a different angle than FC-SC correlation and is worthwhile.

      Hori et al., (2020). Comparison of resting-state functional connectivity in marmosets with tracer-based cellular connectivity. NeuroImage, 204, 116241.

      Stafford et al., (2014). Large-scale topology and the default mode network in the mouse connectome. Proc. Natl. Acad. Sci. U.S.A., 111(52), 18745-18750.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      • *

      Background and unknown in the field:

      This study investigates how fibroblast alignment influences the migration of intestinal epithelial cells, contributing to tissue integrity and repair. It is well established that intestinal fibroblasts are important regulators in the tissue through their ability to secrete essential paracrine factors for the epithelium. However, it is less well understood if they also play additional structural, tissue architecture instructing role and how the communication between the fibroblasts and the epithelia is regulated.

      Advance over state of the art:

      Here the authors have set-up an elegant three-component system to investigate this. They have gone beyond the recent advances of culturing intestinal and colonic organoids in 2D (in a manner that preserves- and villus-like organization) and bioengineered epithelial-stromal model comprising organoid-derived intestinal epithelial cells (IECs), primary intestinal fibroblasts, and a basement membrane matrix. Using this model, they have uncovered fibroblasts enhancing the directed and persistent migration of intestinal epithelial cells (IECs). They used scRNAseq to carefully analyse the stromal cell populations present in their co-cultures of primary mouse intestinal subepithelial fibroblasts and organoid-derived intestinal mouse epithelial cells. They observed that this reflected well the stromal cell-type composition as well as the paracrine activity previously reported for these cells in tissue. Using a clever system with Matrigel and an elastomeric barrier, the authors were able to induce non-epithelial gaps in different scenarios (IECs alone or with fibroblasts or with conditioned media) and observe the wound-closure as well as the presence of specific cell types. They observed that the epithelial monolayers showed significant gap closure when in direct contact with fibroblasts compared to controls. Interestingly, the enhanced efficiency of epithelial migration and gap closure, in the presence of fibroblasts, was independent of PGE-EP4 signaling and was not due to differences in cell proliferation. Instead, the imaging revealed that the fibroblasts were in direct contact with the epithelium. The authors observed that in the absence of fibroblasts the migration properties of cells in the villus and the crypt regions were dramatically different and the fibroblast presence was necessary to efficiently synchronize these to support gap closure. In addition, the presence of fibroblasts enhanced the directionality of the epithelial cell migration. Detailed imaging and image analyses revealed that gap closure involved activation of the fibroblasts and co-ordinated coalignment of IECs and fibroblasts. They also explored matrix deposition of the fibroblasts during the process and found that they deposited aligned ECM fibers that guide epithelial migration. Mere cell-derived matrix (devoid of live fibroblasts) was able to partially recapitulate the fibroblast-coordinated epithelial migration that the fibroblast generated matrix and its alignment are key contributors to the phenotype.

      Comments:

      This is overall a very interesting and well-written study. The imaging and the image analysis are state-of-the art and the bioengineered model is an exciting advancement over current methods developed by these researchers and others. This study meets all the criteria for a publication in the since that all the experiments seem to be carefully conducted, with appropriate controls and sufficient quantifications and statistics. The claims made by the authors are supported by the data. This is currently suitable to be published as a method/protocol and as a descriptive study uncovering interesting cross-talk and co-dependencies of epithelial and stromal cells during injury repair. There are of course aspects that could improve the study further like more mechanistic insight into the underpinnings of the direct epithelia-fibroblast interaction and its involvement in the directed IEC migration. However, these may be topics to investigate in a future study.

      • *

      Reviewer #1 (Significance (Required)):

      • *

      The strengths of the study are the highly in vivo relevant model system that is amendable to imaging and detailed image analysis of distinct cell populations. This may be adapted by others in in the field and has the potential to transform the way cell dynamics in the intestinal epithelium are visualized and investigated in vitro

      • *

      We thank the reviewer for their thoughtful and positive assessment of our work, and their recognition of the relevance of the bioengineered epithelial-stromal model and its potential for quantitative imaging and analysis of epithelial and fibroblast dynamics.

      We agree that further mechanistic insight into epithelial-fibroblast crosstalk would strengthen the study. While the current manuscript establishes this tractable system and identifies a role for fibroblast organization and matrix alignment in coordinating epithelial migration, we also aim to deepen the mechanistic understanding in the revision. As outlined in our response to Reviewer 2, we will perform additional experiments to further investigate the epithelial-fibroblast crosstalk and force-dependent interactions underlying this process.

      We believe that these additions will complement the current findings and strengthen the conceptual contribution of the study beyond its methodological advances.

      • *

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      • *

      Please find enclosed my review comments on the manuscript entitled "Fibroblast alignment coordinates epithelial migration and maintains intestinal tissue integrity" by Jordi Comelles et al.

      In this manuscript, the authors use a bioengineered epithelial-stromal system composed of organoid-derived intestinal epithelial cells, primary intestinal fibroblasts, and a basement membrane matrix to show that direct physical interactions between fibroblasts and epithelial cells drive a large-scale organization of the fibroblast network. This spatial reorganization, in turn, promotes persistent and oriented migration of epithelial cells, ultimately enabling restoration of the intestinal epithelium in an in vitro gap-closure assay. Overall, while the authors use an elegant in vitro model to study intestinal wound closure, and more specifically the role of fibroblasts in this context, I find this manuscript not suitable for publication in its present form. The data are overinterpreted, the novelty is limited, and the molecular mechanisms underlying WAE-fibroblast interactions are insufficiently addressed.

      • *

      We thank the reviewer for their contribution to the revision process with their valuable assessments. We will address their specific points below.

      • *

      Figure 1 - What are the units of the "fraction gap closure" shown in panels d and e? Is it expressed as a percentage?

      We thank the reviewer for pointing this out. The "fraction of gap closed" was calculated as (A(t = 0h)-A(t))/A(t = 0h), where A(t = 0h) corresponds to the initial gap area and A(t) is the area of the gap measured at the time point t. With this definition, the fraction of gap closed is dimensionless, it is 0 at the initial time point, will reach 1 if the gap is fully closed and will have negative values if the gap area increases beyond the initial size, as observed in some replicates of the control condition. To avoid misinterpretation, we will express this quantity as a percentage (i.e., multiplied by 100), as suggested by the reviewer. Moreover, we realized it was ill defined in the methods section. This will be corrected as well in the revised version.

      • *

      "Actually, epithelial monolayers achieved the most effective gap closure when cultured in direct physical contact with fibroblasts (Figure 1e and Movies 2 and 3)." From the data shown in panels c, d, and e, it appears that fibroblast-conditioned medium alone promotes efficient gap closure, comparable to the + fibroblast condition.

      We agree with the reviewer that the original closing sentence overstated the effect. While both fibroblast-conditioned medium and direct fibroblast contact promote efficient gap closure compared to control conditions, the data do not support a consistent difference between these two conditions. We will therefore remove this statement in the revised version to more accurately reflect the results.

      • *

      Figure 2 - The use of a cell proliferation inhibitor during the gap-closure assay would help determine the contribution of cell proliferation at the migration front.

      We agree with the reviewer that inhibiting proliferation would help assess the contribution of cell proliferation to gap closure. However, in the 2D gap-closure assay, our Ki67 immunostaining showed no significant differences in the proportion of proliferative cells between conditions, either within the monolayer or at the migration front. This suggests that differential proliferation is unlikely to account for the differences in gap closure observed between control and fibroblast-containing conditions.

      We note that, in a separate 3D organoid assay, fibroblast-derived signals induced a WAE-like transcriptional program associated with reduced Ki67 mRNA expression, indicating that fibroblasts can promote a more migratory epithelial state without increasing proliferation. Thus, while proliferation may contribute to epithelial homeostasis and repair, our data do not point it as the main determinant of the differences observed in the 2D gap-closure phenotypes.

      In addition, pharmacological inhibition of proliferation would likely perturb the homeostasis of the organoid-derived epithelial monolayers, in which proliferative crypt compartments are essential, and would be difficult to restrict to epithelial cells without also affecting fibroblasts in co-culture. For these reasons, although such experiments could inform the general contribution of proliferation to gap closure, we do not think they would directly clarify the differences observed between conditions in our system.

      • *

      Figure 2f and 2g - Has a dose-dependent effect of PGE2 been tested?

      We thank the reviewer for pointing this out. We did not perform a dose-response analysis of PGE2 in this study, as our aim was to assess the involvement of the PGE2-EP4 axis rather than to characterize its quantitative dynamics. We therefore selected a concentration based on previous work demonstrating dose-dependent induction of the WAE program in 3D organoid systems (Miyoshi et al., 2017). In that study, 1 µM PGE2 was sufficient to induce a significant increase in the WAE marker Cldn4, and we used this concentration as a biologically relevant reference condition. We will clarify this in the methods section.

      • *

      Figure 2i - The + fibroblast + EP4i condition (pink) is missing.

      We thank the reviewer for pointing this out. The + fibroblast + EP4i condition is present in the plot but not visually distinguishable because it overlaps with the + fibroblast condition and is therefore masked by it. As shown in Figure S4e, the + fibroblast + EP4i condition falls within the variability range of the + fibroblast condition. To improve clarity, we will revise the figure to ensure that this condition is visually identifiable.

      • *

      "This suggests a mechanical or contact-mediated role for fibroblasts in preserving epithelial integrity and promoting coordinated migration beyond their paracrine signaling." While PGE2-EP4 signaling does not appear to be involved in the fibroblast-mediated enhancement of gap-closure efficiency, the conclusion that physical interactions are more important than paracrine effects is overstated. For instance, an experimental condition in which fibroblast-conditioned medium is inactivated (boiling for 5 minutes) would strengthen this conclusion. In addition, inhibition of actomyosin contractility in fibroblasts would be informative.

      Figure 3 - The data presented here do not convincingly support the dismissal of conditioned medium as a contributing factor. The differences between the + fibroblast-conditioned medium and + fibroblast conditions are modest. In both cases, epithelial cells migrate and gaps close.

      We agree with the reviewer that inhibition of actomyosin contractility in fibroblasts would provide valuable insight into the role of force-dependent interactions in epithelial-stromal coupling. However, pharmacological inhibitors of the Rho-ROCK-myosin pathway (e.g., blebbistatin, ML-7, or the ROCK inhibitor Y-27632) would also affect epithelial contractility in our co-culture system, making it difficult to specifically attribute any observed effects to fibroblast mechanics.

      We also agree that paracrine signaling plays an important role in epithelial gap closure. Indeed, supplementation of control media with PGE improves gap closure compared to control conditions, although it does not reach the levels observed with fibroblast-conditioned medium, suggesting that additional soluble factors contribute beyond the PGE-EP4 axis. However, time-lapse imaging revealed direct and dynamic interactions between fibroblasts and epithelial cells (Movie 6; Figure S5a-d; Movie 7), which prompted us to further investigate the contribution of physical interactions, as addressed in Figure 3.

      In Figure 3, we analyzed migration at the single-cell level, in contrast to the tissue-level measurements used for gap closure quantification. In organoid-derived intestinal monolayers, two distinct compartments can be identified: crypt-like and villus-like regions. In vivo, these compartments exhibit different migration behaviors: cells in the crypt are primarily displaced due to crowding, whereas cells in the villus actively migrate, as suggested by the presence of cryptic lamellipodia (Krndija et al., 2019). Consistent with this, tracking individual cells revealed that crypt cells are largely static, while villus cells migrate toward the gap. This compartmentalized behavior was observed in both control and fibroblast-conditioned medium conditions. Strikingly, in the presence of fibroblasts, this differential behavior was reduced, resulting in coordinated migration of both crypt and villus regions.

      This mismatch between compartments in control conditions may contribute to the appearance of discontinuities ("holes") within the epithelial layer during migration. In control experiments, these defects failed to close, whereas in conditioned medium they closed slowly or incompletely. In contrast, in the presence of fibroblasts, these disruptions were rapidly and efficiently resolved, indicating improved tissue integrity.

      Additionally, analysis of individual trajectories near the migration front showed that cells exhibit significantly increased directional persistence (i.e., movement aligned with the direction of gap closure) in the presence of fibroblasts compared to conditioned medium alone.

      Taken together, while paracrine signaling from fibroblasts contributes to epithelial migration and gap closure, the physical presence of fibroblasts induces qualitative changes in epithelial behavior, including coordinated migration across compartments, improved hole closure, and enhanced directional persistence.

      • *

      Figure 4a - "Upon removal of the barrier (t = 0 h), fibroblasts at the epithelial front were small and evenly distributed, with no prominent α-SMA fibers present." Here, fibroblasts are α-SMA positive but not elongated. α-SMA may therefore not be the most appropriate marker. What are the levels of phosphorylated MLC2? These may increase during wound closure. Also, fibroblasts culture promotes aSMA expression, therefore, it may be possible that the fibroblasts used in this assay may not represent the healthy fibroblasts found in vivo.

      We agree with the reviewer that fibroblasts are α-SMA positive at early time points but are not yet elongated. In our system, we observe that α-SMA is already present at t = 0 h, while fibroblasts progressively elongate and reorganize α-SMA into prominent fiber structures over time. This suggests that changes in α-SMA organization, rather than its initial presence, are associated with fibroblast activation during gap closure.

      We note that baseline α-SMA expression may be influenced by in vitro culture conditions prior to the assay, which could differ from the state of fibroblasts in vivo. We will clarify this point in the Discussion to better contextualize our observations relative to native fibroblast populations.

      In addition, we agree that assessing phosphorylated myosin light chain 2 (pMLC2) levels would provide complementary information on contractile activity. We will therefore perform pMLC2 staining, as suggested, to further evaluate force generation by fibroblasts during the wound closure process.

      • *

      Figure 5 - Fibroblast alignment could also result from paracrine signals secreted by epithelial cells. This possibility should be tested.

      We thank the reviewer for this suggestion. To test whether fibroblast alignment could be driven by epithelial-derived paracrine signals, we will culture fibroblasts in conditioned medium collected from epithelial monolayers undergoing gap closure (control condition without fibroblasts) and quantify their alignment over time. This will be compared to fibroblasts maintained in standard fibroblast medium.

      This experiment will directly assess whether epithelial-derived soluble factors are sufficient to induce fibroblast alignment, or whether direct physical interactions are required.

      • *

      In summary, this manuscript demonstrates that epithelial cells migrate more efficiently on extracellular matrix proteins deposited and oriented by fibroblasts. This concept is not novel. Identifying the molecular mechanisms governing interactions between WAE and subepithelial fibroblasts would significantly enhance the novelty and impact of this study.

      • *

      Reviewer #2 (Significance (Required)):

      • *

      In this manuscript, the authors use a bioengineered epithelial-stromal system composed of organoid-derived intestinal epithelial cells, primary intestinal fibroblasts, and a basement membrane matrix to show that direct physical interactions between fibroblasts and epithelial cells drive a large-scale organization of the fibroblast network. This spatial reorganization, in turn, promotes persistent and oriented migration of epithelial cells, ultimately enabling restoration of the intestinal epithelium in an in vitro gap-closure assay. Overall, while the authors use an elegant in vitro model to study intestinal wound closure, and more specifically the role of fibroblasts in this context, I find this manuscript not suitable for publication in its present form. The data are overinterpreted, the novelty is limited, and the molecular mechanisms underlying WAE-fibroblast interactions are insufficiently addressed.

      *We thank the reviewer for this thorough and critical assessment. We have clarified the overstatements in the rebuttal and we will modify the text to address concerns regarding overinterpretation and clearly acknowledge the limitations of our approach. In particular, we will refine the framing of the study to better distinguish between the contributions of paracrine signaling and physical epithelial-stromal interactions. *

      *To address the reviewer's concerns regarding mechanism and novelty, we will perform additional experiments aimed at further characterizing epithelial-stromal cross-talk, and experiments to assess fibroblast contractility and its contribution to epithelial coordination. *

      We believe that these revisions and proposed experiments will strengthen the manuscript and clarify its conceptual contribution.

      • *

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      • *

      Summary:

      - Provide a short summary of the findings and key conclusions (including methodology and model system(s) where appropriate).

      The study by Comelles et al. focuses on how primary intestinal fibroblasts contribute to organoid-derived intestinal epithelial migration in wound healing assays. Using fibroblast-epithelial co-cultures in a 2D in vitro gap closure system, the authors found that direct interaction with fibroblasts drives cohesive and directed migration of intestinal epithelia toward the gap. They further propose that long-range fibroblast alignment promotes the deposition of extracellular matrix (ECM) proteins in an oriented fashion, contributing to directed epithelial migration.

      Major comments:

      - Are the key conclusions convincing?

      Some of the key conclusions of this manuscript are not entirely convincing given the available data. The manuscript would benefit from additional evidence and/or clarifications to support their conclusions. See comments below.

      • *

      - Should the authors qualify some of their claims as preliminary or speculative, or remove them altogether?

      (Fig 4a) The authors claim that fibroblasts become activated during gap closure as evidenced by the enhanced assembly of a-SMA fibers 24 hours following barrier removal. Yet, long a-SMA fibers are also observed when fibroblasts are cultured in the absence of epithelial cells or barrier removal (Fig. S1b). To support this conclusion, the authors should consider including additional controls to account for potential time-dependent assembly of a-SMA fibers (e.g., fibroblast-only control).

      We thank the reviewer for pointing this out. We agree that a fibroblast-only control would be important to account for potential time-dependent assembly of α-SMA fibers. We will therefore perform additional experiments monitoring α-SMA organization in fibroblasts cultured alone over time, which will allow us to better interpret the dynamics observed in the co-culture conditions.

      • *

      (Fig. 5a) The authors conclude that fibroblasts align parallel to the direction of epithelial migration during gap closure. While quantifications are convincing, again, a fibroblast-only control accounting for time-dependent spreading and elongation (as seen in Fig. S1) is missing. Including such a control would strengthen their claim that alignment is specific to the gap closure context rather than a time-dependent phenotype.

      We agree with the reviewer that, given the intrinsic ability of fibroblasts to form ordered domains with long-range alignment, this control would be highly informative. We will therefore quantify fibroblast alignment over time in fibroblast-only cultures, which will allow us to determine to what extent the long-range organization observed in co-culture is specific to the gap closure context.

      • *

      (Fig 6) The authors claim that fibroblast-derived aligned ECM drives directional epithelial migration. While fibronectin fibers appear scarce and weakly aligned with the direction of migration, laminin and type IV collagen fibers are barely detectable (Fig. 6f). This may reflect a defect in ECM deposition rather than fiber alignment, which contrasts with Fig. S1, where fibroblasts are shown to deposit and assemble laminin and type IV collagen fibers. One possible explanation is that primary fibroblasts were not cultured long enough to allow robust ECM deposition. Alternatively, the observed effect may be specific to fibronectin, which is consistent with fibroblasts being its major source. The authors should revise their interpretation or provide additional evidence to support their current claim.

      We thank the reviewer for this important point. We agree that differences in ECM signal within the gap may reflect not only fiber alignment but also differences in the amount of protein deposited. In the +fibroblast condition, fibroblasts in the gap have more time to secrete ECM compared to the "empty gap" condition, where fibroblasts remain confined beneath the epithelium.

      In addition, the presence of Matrigel likely masks the contribution of certain ECM components, making laminin or type IV collagen more apparent than fibronectin. We will therefore revise the interpretation of these results to explicitly acknowledge the contribution of ECM abundance in addition to alignment.

      • *

      (Fig 6i) The authors propose that the presence of ECM alone within the gap enhances epithelial gap closure compared to empty gap conditions, although gap closure remains less effective than in the presence of primary fibroblasts. From the figure legend and methods, it seems that the decellularized ECM condition is generated using NIH-3T3 fibroblasts cultured for 8 days, whereas the other conditions used primary fibroblasts cultured for 1 day (Fig. 6a-h). This comparison is confounded by differences in cell source and ECM deposition time. If I am misunderstanding this, please clarify, otherwise consider repeating the decellularized ECM condition using primary fibroblasts and matching culture times for a fair comparison. Along these lines, please include images showing that ECM fibers remain intact following decellularization.

      We thank the reviewer for this suggestion. We will include additional staining to confirm that ECM fibers remain intact after decellularization in the revised version.

      Regarding the use of NIH-3T3 fibroblasts for CDM generation, this choice was made to minimize potential residual paracrine signaling from primary intestinal fibroblasts after decellularization. We acknowledge that this introduces differences in cell source.

      Concerning culture time, we followed established protocols for CDM formation, which recommend extended culture periods ({greater than or equal to}8 days) to allow robust ECM deposition (Cukierman et al., 2001; Franco-Barraza et al., 2016; Godeau et al., 2020). We will clarify these points in the revised manuscript and discuss the limitations associated with these differences.

      • *

      - Would additional experiments be essential to support the claims of the paper? Request additional experiments only where necessary for the paper as it is, and do not ask authors to open new lines of experimentation.

      Yes. The additional experiments outlined above would help support the current conclusions of the manuscript, rather than to explore new directions beyond its scope.

      • *

      - Are the suggested experiments realistic in terms of time and resources? It would help if you could add an estimated cost and time investment for substantial experiments.

      Yes, the additional experiments primarily involve the inclusion of controls and additional immunofluorescence imaging to their existing experimental setups. They should be relatively straightforward to implement (~2-3 months).

      • *

      - Are the data and the methods presented in such a way that they can be reproduced?

      Yes.

      • *

      - Are the experiments adequately replicated and statistical analysis adequate?

      Overall, yes. But some plot legends should specify the number of replicates analyzed (e.g. Fig. 2b, Fig. 2d, Fig. 3h).

      We will review and correct these issues.

      • *

      Minor comments:

      - Specific experimental issues that are easily addressable.

      (Fig. 1c-e) The authors state that intestinal epithelial monolayers exhibit the most effective gap closure when in direct contact with fibroblasts. However, fibroblast-conditioned media and co-cultures show comparable gap closure efficiencies (Fig. 1e). The authors should consider revising this interpretation based on the provided data.

      We thank the reviewer for pointing this out, which was also raised by Reviewer 2. As discussed above, we agree that the original statement overstated the effect. Both fibroblast-conditioned medium and direct fibroblast contact promote efficient gap closure compared to control conditions, and we will revise the text accordingly to reflect that no consistent quantitative difference is observed between these two conditions.

      • *

      (Fig. 3b) The authors suggest that crypt-like epithelial cells undergo migration when grown on fibroblasts, but not in conditioned media alone. This is interesting, but it is not clear how they identify crypt-like cells for tracking. The authors should clarify if crypt-like cells are defined based on markers or inferred from their morphology.

      We thank the reviewer for this comment. In these tracking analyses, crypt-like cells were identified based on morphology. As shown in Figure S3 and in Larrañaga et al., 2025, crypt-like cells, defined by specific molecular markers, are significantly smaller than villus-like cells and form high-density regions. These features allow their identification based on morphology in fluorescently labeled monolayers. We will clarify this criterion in the Methods section of the revised manuscript.

      • *

      (Fig 3f-h) The authors conclude that fibroblasts promote directed epithelial cell motility based on cell trajectory analysis. Although they state that this analysis is performed on epithelial monolayers, their tdTomato epithelial population appears sparse in some conditions (control and conditioned media; Fig. S6a). Such variability in cell density may bias measurements of migration directionality at the cell-level, unless a mixed population is being used for tracking. The authors should clarify whether this analysis was indeed conducted on confluent monolayers.

      We thank the reviewer for this comment. For trajectory analysis, we used a mixed population of tdTomato-positive and non-fluorescent epithelial cells in some experiments to facilitate individual cell tracking. Importantly, epithelial monolayers were confluent in all conditions analyzed. We will clarify this in the Methods section.

      • *

      (Fig 6b) Their gap closure experimental setup indicates that fibroblasts are cultured on a Matrigel-coated surface, which should already contain abundant laminin and type IV collagen. Thus, it is unclear why type IV collagen is not detected underneath fibroblasts. The authors should explain why this is the case for clarity.

      We thank the reviewer for pointing out this observation. Indeed, fibroblasts are cultured on a Matrigel-coated surface which contains laminin and collagen type IV among many other components. We observed thick collagen-rich structures between the fibroblasts and the epithelia that we atributed, not only to fibroblasts' secreted collagen, but also a rearrengement of the collagen available in the coated surface. We will clarify this in the discussion of the revised version for clarity.

      • *

      - Are prior studies referenced appropriately?

      Yes

      • *

      - Are the text and figures clear and accurate?

      Mostly. Figures 6d and 6g seem to be duplicated by mistake.

      We thank the reviewer for noting this. We will correct this mistake.

      • *

      - Do you have suggestions that would help the authors improve the presentation of their data and conclusions?

      There are some missing frames in Movie 2. If they are not available, it's okay to include black frames, so that the sequence remains consistent with the timestamps.

      The authors may consider using asterisks as significance indicators instead of reporting precise p-values directly on their plots. Having this format would facilitate visual comparison of statistical significance across conditions.

      Displaying single channels of experiments where co-cultures are used would help to better interpret their data.

      We thank the reviewer for pointing out these issues and for their valuable suggestions. We will correct the errors in the movie and improve the presentation as suggested where possible.

      • *

      Reviewer #3 (Significance (Required)):

      • *

      - Describe the nature and significance of the advance (e.g. conceptual, technical, clinical) for the field.

      This study provides a valuable contribution to understanding how fibroblasts influence intestinal epithelial migration. The main advance lies in the use of a co-culture system combining organoid-derived intestinal epithelial cells that assemble into a crypt-villus organization with primary intestinal fibroblasts in a 2D gap closure system. This approach allows the authors to examine epithelial-fibroblast interactions in a more physiologically relevant context compared to prior work.

      We thank the reviewer for their positive assessment of the significance of our work.

      • *

      - Place the work in the context of the existing literature (provide references, where appropriate).

      Addressed above.

      • *

      - State what audience might be interested in and influenced by the reported findings.

      Cell and developmental biology, extracellular matrix biology, tissue regeneration.

      • *

      - Define your field of expertise with a few keywords to help the authors contextualize your point of view. Indicate if there are any parts of the paper that you do not have sufficient expertise to evaluate.

      Tissue morphogenesis, cell motility, extracellular matrix dynamics.

      We thank the reviewer for their positive assessment and for their suggestions to improve the manuscript.

      • *
    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      (1) They start by incubating LFA-1 with iRBCs and show by flow analysis that a substantial population of these iRBCs binds to the LFA-1 (Figure 1C). They do conduct the control with uninfected RBCs, but put this in the supplementary material. As this is a critical control, I think that it should be moved to Figure 1C as it is essential to allow interpretation of the iRBC data. The authors also do not state which strain of P. falciparum they used (line 144). This is critical information as different strains have different variant surface antigens and should be included. With these changes, this data seems convincing.

      We thank the reviewer for this important suggestion. We agree that the uninfected RBC (uRBC) control is critical for interpreting the specificity of LFA-1 αI-Fc binding. In the revised manuscript, we have ensured that these control data are clearly presented and appropriately referenced in the main text; however, we have retained them in the Supplementary Information (Supplementary Figure S1) to maintain clarity and avoid overcrowding Figure 1, while still ensuring their visibility and accessibility to the reader. Importantly, these data demonstrate negligible binding of LFA-1 αI-Fc to uRBCs compared to iRBCs, supporting specificity. We have explicitly stated the parasite strain used (Plasmodium falciparum 3D7) in the Methods section (line 475).

      (2) They next incubated LFA-1 with the iRBCs, cross-linked and conducted a pulldown, identifying GP130 as a binding partner. Using cross-linkers is a dangerous strategy as it risks non-specific cross-linking. Did they try without cross-linking and find an interaction?

      We agree that cross-linking can introduce potential artefacts. To mitigate this, we included hIgG control pulldown experiments performed under identical conditions. Proteins identified in the control eluate were excluded as background (summarized in Supplementary Table S1). Importantly, PfGBP-130 was the only protein specifically enriched in the LFA-1 αI-Fc pulldown across all three biological replicates (Fig. 2A, Venn Diagram). While cross-linking was used to stabilize transient interactions, consistent enrichment of PfGBP-130 across the three biological replicates precludes any concerns of non-specificity.

      (3) They raised antibodies to PfGBP and showed IFA, which reveals that these antibodies stain iRBCs (Figure 2Ciii). This experiment lacks a critical control of uninfected RBCs, which needs to be included to show that the staining is specific. Without this, it is not possible to conclude that there is iRBC-specific staining with PfGBP.

      The question pertains to Fig. 2Biii. The IFA images include both infected and neighboring uninfected erythrocytes within the same field. No PfGBP-130 staining is observed in uninfected cells. PfGARP staining, specifically done to verify parasite-infected cell and surface localisation, shows complete resonance with PfGBP-130 staining. This unequivocally shows that the antibodies raised specifically recognise only infected RBCs.

      (4) They then conduct a pulldown using LFA-Fc, which does show GP130 only in the presence of the LFA-Fc, but not when empty beads are used. This is convincing. BLI measurements are also used to study this interaction (Figure 2Ci). The BLI data is presented in such a way that any association phase is obscured by the y-axis, which makes it impossible to know whether there is binding here. I think that the data needs to be shown with some baseline before the addition of the ligand so that the association can be seen. The data is also a bit messy with a downward drift and the curves showing different shapes, for example, with the 1.0uM curve seeming to have a different association rate. Also, is this n=1? I think that this data needs to be repeated and replicated. As this is the only data which shows a direct interaction between LFA1and GBP, as pulldowns are done with lysates, which might mean bridging components. I think that it is important to repeat the BLI or use additional biophysical methods to assess binding, to obtain more convincing data.

      We sincerely thank the reviewer for highlighting this important concern regarding the BLI data presentation and interpretation. We would like to clarify that the baseline signal prior to ligand addition was subtracted during data processing; therefore, the plotted curves represent the net response following ligand association. However, we agree that this may have obscured the visualization of the association phase. Accordingly, in the revised manuscript, we have re-plotted the data with adjusted y-axis scaling to better capture the association kinetics. In addition, to ensure robustness and reproducibility, the BLI experiments were performed in multiple independent replicates (n ≥ 3) using independently purified protein batches. The original figure showed a representative dataset; we have now included averaged sensorgrams along with standard deviation in the calculated KD values [K<sub>D</sub> = (1.7 ± 0.22) × 10<sup>-8</sup> M] (Figure 2C (i)). These revisions provide a clearer and more accurate representation of the binding interaction.

      (5) The authors next do some modelling of the putative complex. This is done by homology modelling and docking, which is not the most up-to-date method and is over-interpreted. Personally, I would remove this data as I did not find it convincing, and it is not important for the story. If the authors wish to include it, then I think that they should validate the modelling by mutagenesis to show that the residues which the models indicate might bind are involved in the interaction.

      We thank the reviewer for this thoughtful comment regarding the modelling analysis. We agree that computational docking and homology-based modelling have inherent limitations and should not be over-interpreted. In our study, these analyses were included strictly as supporting evidence to provide a structural framework for the PfGBP-LFA-1 interaction, while the primary conclusions are based on direct biochemical and functional validation, including pull-down, BLI measurements, receptor knockdown, and cellular inhibition assays. Importantly, the use of docking approaches such as ClusPro, followed by interface analysis and MD simulations, is a widely accepted and routinely used strategy to generate testable hypotheses for protein-protein interactions, particularly when experimental structures are unavailable (e.g., Comeau et al., 2004; Weng et al., 2019). We believe that the current modelling serves as a useful complementary analysis that is consistent with, and supportive of, the experimentally validated interactions.

      (6) They next made GP130 and tested the binding of this to THP-1 cells, which are often used as a model for macrophages. They observe greater binding of PfGBP-Fc to these cells when compared with hIgG and show that LFA-1 siRNA reduces this binding. I was a little confused about how the flow plots related to the graph in the bottom right corner of Figure 3Bii. In the flow plots, hIgG control shows 12.8% of cells in the gated region, while the unstained cells has 5.63%, but the MFI data shows a decrease in binding for hIgG vs unstained cells. How is this consistent? Also, the siRNA reduces the number of cells in the gated region from 66.6% to 25.9%, which is still substantially more that 5.63% in the unstained control. This also doesn't seem quite consistent with the MFI data. Could the authors explain this? Also, perhaps an additional experiment would be to add soluble LFA-1 into this assay as an additional control to determine whether this blocks PfGBP binding to the THP-1 cells? It could be that there are additional mechanisms of binding which indicate why the siRNA has a partial effect. The same is true for the NK cell experiments in Figure 3Ci, in which the siRNA has a partial effect. The authors also test binding to HEK, HepG2 and 'stem' cells and claim' only background levels of binding', but in each case, there is more binding to these cells by PfGBP-Fc than by hIgG, albeit less than in THP-1 and NK cells. Why have the authors decided that these increases are not significant? All in all, these experiments do indicate a role for the GBP-LFA1 interaction in the binding of immune cells to iRBCs, but perhaps not as absolutely as is suggested.

      We thank the reviewer for this insightful comment. The apparent discrepancy arises because the flow plots depict the percentage of cells within a defined positive gate, whereas the graphs quantify mean fluorescence intensity (MFI) across the entire population. We have revised figure legend accordingly to indicate the same. Regarding the partial reduction in binding upon LFA-1 (CD11a) knockdown, we agree that this indicates LFA-1 is a major but not exclusive contributor, which is biologically plausible given incomplete siRNA depletion and the known avidity-dependent nature of integrin interactions. Importantly, our conclusion is supported by multiple orthogonal approaches (αI-domain binding, LC-MS/MS identification, BLI, docking, receptor knockdown, and functional blockade). We also appreciate the suggestion of soluble LFA-1 competition, which we acknowledge as an important future experiment. Finally, we have revised the text regarding HEK293T, HepG2, and stem cells to reflect that PfGBP-Fc binding is minimal but not absent, consistent with low/non-expression of LFA-1 in non-immune cells. Overall, we have moderated our claims to state that PfGBP-LFA-1 interaction is a dominant and functionally relevant mechanism, while not excluding additional low-affinity or accessory interactions.

      Figure legend change: Representative flow plots depict the percentage of cells within a predefined positive gate, whereas the accompanying summary graph quantifies fluorescence intensity across the analyzed population. These two metrics report distinct properties of the distribution and are therefore not expected to be numerically identical.

      (7) The authors next produce CHO cells with PfGBP on the surface. These cells bind toLFA-1 specifically. When these cells were incubated with primary NK cells, they did see increases in activation markers, which were reduced by the addition of anti-CD11a, suggesting these to be specific. They also conduct the same experiment with anti-GBP with iRBCs, but this is in a different figure. It would be easier for the reader if Figure 5B were in the same figure as Figure 4B, as it is related data using the same method. I found this data convincing, showing that the LFA1:GBP interaction does contribute to immune cell recognition and activation.

      We thank the reviewer for this positive assessment and helpful suggestion regarding figure organization. We agree that the CHO-PfGBP and iRBC-based NK cell activation assays represent conceptually related experiments that both address LFA-1-PfGBP dependent activation using similar readouts. We have retained separate panels to distinguish the reductionist CHO-based system from the physiologically relevant iRBC context. We believe that the combined evidence from both systems strengthens the conclusion that PfGBP-LFA-1 interaction is a key contributor to NK cell recognition and activation.

      (8) The authors next conduct an experiment in which they assess parasite growth in the presence of NK cells and in the presence of anti-GBP. They use Heochst staining as a measure of parasite growth and claim that NK cells reduce the number of parasites, but that anti-GBP abolishes this effect (Figure 5A). I found this experiment very unconvincing as there are small effects and no demonstration of significance. More commonly used approaches to study parasite growth are lactate dehydrogenase GIA assays or calcein-AM labelling. I did not find this experiment convincing and would either remove or supplement with additional data using a more robust assay, with repeats and tests of statistical significance.

      We respectfully disagree that the assay should be removed, because flow-cytometric quantification of P. falciparum parasitemia using DNA dyes such as Hoechst is a widely used, accepted, and high-throughput approach for measuring infected erythrocytes and parasite growth, with clear separation of infected from uninfected RBCs and good reproducibility across malaria studies (Dent et. al., 2009; Jang et. al., 2014). Importantly, closely related immune-cell killing experiments in the malaria field have used the same general strategy, co-culture with effector cells followed by flow-cytometric enumeration of parasitemia to infer parasite control, including the seminal NK-cell study by Chen et. al., 2014, which our assay design follows conceptually, and later work showing reduced parasitemia after co-incubation with cytotoxic lymphocytes measured by nucleic-acid dye flow cytometry. We therefore believe the experiment is methodologically valid and directly relevant to the biological question, namely whether disrupting PfGBP-LFA-1 engagement alters NK-cell-mediated restriction of parasite expansion.

      Reviewer #2 (Public review):

      (1) PfGBP-130 is proposed to be a membrane protein based on a single predicted transmembrane domain. Figures 2b and 3a show ribbon schematics with this TM domain at residues 51-68, in agreement with TM prediction algorithms such as TMHMM 2.0 and Phobius. However, this predicted TM is upstream of the PEXEL motif (residues 84-88, sequence RILAE), a conserved sequence for parasite protein export to host cytosol that is proteolytically processed at its 4th residue. Thus, residues 1-87are removed from PfGBP-130 prior to export, yielding a mature protein without predicted TMs. Prior studies have determined that the mature PfGBP-130 lacks TMs and is retained as a soluble protein in host cell cytosol (PMID: 19055692, 35420481). Thus, the authors' model of PfGBP-130 as a surface-exposed membrane protein conflicts with both computational analysis of the mature protein and these prior reporter studies. An important simple experiment would be to evaluate PfGBP-130membrane association in immunoblots using the authors' PfGBP-130 antibody after hypotonic lysis (PMID: 19055692) and after alkaline extraction (e.g. 100 mM NaCO3, pH 11 as frequently used, PMID: 33393463). If the prior studies and computational analyses are correct, the protein will be predominantly in the soluble and/or alkaline supernatant fractions.

      We thank the reviewer for this important observation regarding PfGBP-130 topology and export. We agree that the presence of a PEXEL motif supports proteolytic processing and that the mature protein may lack a classical transmembrane domain. However, consistent with our model of surface accessibility, we would like to clarify that in an independent proteomic study performed in our laboratory on the membrane-enriched fraction of Plasmodium falciparum-infected erythrocytes, PfGBP-130 was reproducibly identified by LC-MS/MS among membrane-associated proteins (data not shown; can be provided upon request). These findings support the conclusion that, irrespective of the absence of a canonical transmembrane domain, PfGBP-130 is associated with the iRBC membrane compartment, likely via peripheral or protein-complex–mediated interactions, as described for several exported Plasmodium proteins.

      (2) Many findings rely on the specificity of antibodies generated against PfGPB-130 or NK cell receptors. Although the authors have included key controls (use of isotype control antibodies, lack of anti-PfGBP-130 binding to uninfected cells), cross-reactivity between P. falciparum antigens is well-recognized and could significantly undermine the interpretation of experiments (PMID: 2654292 and 1730474 provide key examples of antigens recognized by antibodies raised against other proteins). For example, the surface localization in IFA experiments (Figure 2B(iii)) could reflect anti-PfGBP-130binding to an unrelated parasite surface antigen, a possibility not addressed by any of the authors’ controls. As another example, the iRBC lysate immunoblot using this antibody in Fig. 2B(iv) suggests a MW of 95 kDa, which corresponds to the unprocessed pre-protein before export; cleavage in the PEXEL motif yields a processed mature protein of 85 kDa, which should be readily resolved from the pre-protein in immunoblots (PMID: 19055692). A better immunoblot using immature infected cell stages might show both the pre-protein and the mature protein as a doublet band.

      We thank the reviewer for raising this important concern regarding antibody specificity. We agree that cross-reactivity among P. falciparum antigens is a known issue and have taken multiple steps to ensure specificity in our study. First, the anti-PfGBP-130 antibodies were generated against a defined recombinant fragment and show no detectable binding to uninfected RBCs and no signal in hIgG control immunoprecipitates, supporting specificity. Importantly, in our LC-MS/MS analysis of LFA-1 αI-domain pull-downs, PfGBP-130 was specifically enriched and consistently identified across replicates, independently validating the target recognized by the antibody. Furthermore, the same antibody detects a single dominant band in both iRBC lysates and αI pull-down fractions, arguing against widespread cross-reactivity. Regarding the apparent molecular weight (~95 kDa), we agree that this likely corresponds to the precursor form, and that a processed form (~85 kDa) may not be well resolved under our current conditions.

      (3) PfGBP-130 is not essential for in vitro cultivation (PMID: 18614010 and MIS of 1.0 in the piggyBac mutagenesis screen as tabulated on plasmodb.org, indicating a highly dispensable gene). The authors should use the knockout line as a control in their IFA localization experiments to address antibody specificity. More fundamentally, their model predicts that NK cells should not recognize or kill infected cells from the knockout line when compared to their untransfected parent. Such results with the knockout line would compellingly support the authors' model without reliance on antibodies that may cross-react with other parasite antigens. PMID: 18614010reported that the PfGBP-130 knockout exhibited increased membrane rigidity, suggesting an intracellular scaffolding protein rather than a surface localization and use as a ligand for LFA-1 interaction and NK cell-mediated killing.

      We agree that a PfGBP-130 knockout line would provide a powerful genetic validation of both antibody specificity and the proposed functional role of PfGBP-130 in NK cell recognition. At present, such experiments were not included in this study, and we acknowledge this as an important limitation. However, we would like to emphasize that our conclusion does not rely on antibody-based localization alone; rather, it is supported by multiple orthogonal approaches, including LFA-1 αI-domain pull-down coupled to LC-MS/MS, biophysical interaction analysis, receptor knockdown, and functional blocking assays. In addition, in one of our previous proteomic analyses of the membrane-enriched fraction of infected erythrocytes, PfGBP-130 was identified among the proteins present in the membrane fraction, supporting its association with the iRBC membrane compartment despite lacking a classical mature transmembrane domain.

      (4) PfGBP-130 non-essentiality raises the question of why the gene would be retained if it triggers NK cell-mediated killing of infected cells in vivo. Presumably, this killing would pose strong selective pressure against retention of PfGBP-130. Some speculation is warranted to support the model.

      We thank the reviewer for this thoughtful evolutionary question. We agree that if PfGBP-130 enhances NK-cell recognition, its retention likely reflects a context-dependent fitness trade-off rather than a simple benefit or cost. This situation is not unusual in P. falciparum: several exported or surface-associated proteins are retained despite being immunogenic because they also provide advantages in other settings, such as erythrocyte remodeling, cytoadhesion, niche adaptation, immune modulation, or transmission. The clearest precedent is the PfEMP1/var system, in which highly immunogenic surface antigens are nevertheless strongly maintained because they mediate sequestration and in vivo fitness, while antigenic variation limits continuous immune exposure (Chew et. al., 2022). Similarly, other variant surface antigens such as STEVOR and RIFIN are retained despite immune recognition because they contribute to erythrocyte binding, antigenic diversity, and immune evasion or modulation (Niang et. al., 2009; Sakoguchi et. al., 2025). More broadly, many P. falciparum genes that appear dispensable in standard in vitro culture are nevertheless preserved because culture does not recapitulate the selective pressures present in vivo, including splenic clearance, endothelial interactions, immune attack, and within-host competition.

      Reviewer #3 (Public review):

      (1) Anti-GBP130 antibodies are used in the cellular assays to block the interaction between GBP130 and LFA1. They should therefore also block interactions betweenGBP130 and LFA1 recombinant proteins in the biolayer interferometry experiment. Do the authors have data to show this? Similarly, the anti-CD11a antibodies used to block the interaction in the cellular assays should also block the in vitro interaction between recombinant LFA1 and GBP130.

      We thank the reviewer for this insightful suggestion. We agree that demonstrating antibody-mediated inhibition of the recombinant PfGBP-LFA-1 interaction would provide an additional orthogonal validation of the interface. While such blocking experiments were not included in the original BLI dataset, our current study already establishes the specificity of this interaction through multiple independent approaches, including αI-domain pull-down and LC-MS/MS identification, BLI-derived high-affinity binding (KD ~10<sup>-8</sup> M), structural docking, receptor knockdown, and antibody-mediated inhibition in cellular systems. We note that antibody-mediated blocking in a purified biophysical system is not always directly comparable to cellular assays, as epitope accessibility, orientation on biosensor surfaces, and conformational states of integrins (which are known to undergo activation-dependent structural changes) can influence inhibition efficiency. Nonetheless, we fully agree that this represents an important validation experiment.

      (2) The structural modelling analysis of the predicted complex between GBP130 andLFA1 (Figure 2cii) predicts that the majority of the important GBP130 interface residues are located in the region D509-N607. However, the authors present BLI data for the GBP130-LFA1 interaction, which used the N-terminal fragment of GBP (residues 69-270), which does not include the GBP130 residues predicted to be important for the formation of the complex between the two proteins. Could the authors provide an explanation for how an interaction was observed with theGBP130-N fragment, which does not contain the residues predicted to be important for interacting with LFA1?

      We thank the reviewer for this important observation. We agree that the structural model predicts a major interaction interface within the D509-N607 region of PfGBP-130; however, this does not preclude the existence of additional or auxiliary binding determinants within the N-terminal region used in our BLI assays (aa 69-270). PfGBP-130 is a multi-domain, repeat-containing protein, and such proteins frequently exhibit distributed or multivalent interaction interfaces, where individual regions can independently engage binding partners with lower affinity while the full-length protein achieves higher avidity through cooperative interactions. In our study, the BLI data using the N-terminal fragment demonstrate that this region is sufficient to mediate direct interaction with the LFA-1 αI domain, whereas the structural model based on full-length predictions likely captures a dominant or higher-affinity interface in the C-terminal region. Importantly, the interaction is supported by multiple orthogonal datasets, including pull-down/LC-MS/MS, cellular binding assays, and functional inhibition, indicating that the observed binding is not an artefact of fragment choice.

      Author response image 1.

      To further examine this, we performed docking and binding energy analyses comparing the full-length PfGBP-130-LFA-1 complex with the N-terminal domain-LFA-1 complex. Using the PRODIGY server, the predicted binding affinity for the full-length complex was -9.8 kcal/mol, whereas the N-terminal domain complex exhibited a still favorable binding energy of -5.6 kcal/mol. Similarly, HawkDock (v2) analysis yielded binding energies of -22.2 kcal/mol for the full-length complex and -14.1 kcal/mol for the domain-only complex. While reduced relative to the full-length protein, these values remain well within the range of stable protein-protein interactions, supporting the ability of the N-terminal region to independently contribute to binding. These energy calculations take into account all non-covalent interactions. For clarity, hydrogen bonds have been specifically highlighted in the figure to represent key interaction interface.

      (3) There is no section in the materials and methods describing how the BLI was performed; this should be added. The highest concentration ofGBP130 used in the interaction measurements is 1.4uM, almost 100x the measured Kd (0.015uM) for the GBP130-LFA1 interaction. At these high concentrations ofGBP130, I would expect to start seeing saturation of binding, but the interferometry curves show that saturation is not close to being reached. This strongly suggests that the binding of GBP130 to LFA1 is non-specific.

      We thank the reviewer for raising these important technical points. We have included a detailed description of the biolayer interferometry (BLI) methodology in the Materials and Methods section in the manuscript. Regarding the concern about lack of saturation at higher analyte concentrations, we respectfully disagree that this necessarily indicates non-specific binding. In BLI assays, incomplete saturation can arise from several well-recognized factors, including suboptimal orientation or partial inaccessibility of immobilized ligand on the biosensor, mass transport limitations, or heterogeneous binding populations particularly relevant for integrins such as LFA-1, whose αI domain exists in multiple conformational states with distinct affinities. Importantly, the interaction exhibits clear concentration-dependent association and dissociation kinetics that fit a 1:1 binding model with a KD in the nanomolar range, which is inconsistent with non-specific interactions that typically show poor fitting and minimal dissociation. Furthermore, the specificity of the PfGBP-LFA-1 interaction is supported by multiple independent lines of evidence in our study, including selective enrichment in αI-domain pull-downs, absence in IgG controls, reduction upon CD11a knockdown, and functional inhibition by blocking antibodies in cellular assays. We have now clarified these points in the revised manuscript and tempered the interpretation to acknowledge potential experimental constraints of BLI while maintaining that the cumulative data strongly support a specific interaction.

      Minor points:

      (1) For the pulldown experiments, can the authors confirm that cross-linking was also performed for the protein A beads + hIgG control?

      Yes, DTSSP cross-linking was performed identically in the protein A beads + hIgG control arm. This is consistent with the control design described in the manuscript.

      (2) If the recombinant CD11a I subdomain used as a probe is correctly folded and functional, it should bind ICAM1. Do the authors have this data?

      We agree that ICAM-1 binding is an important functional validation for the recombinant CD11a αI probe (Hogg et. al., 1998). The isolated αI domain of LFA-1 is well established as the principal ICAM-1-binding module, and soluble αI-domain reagents have previously been shown to bind/block ICAM-1 interactions. We did not include this control in the current version.

      (3) Were the authors able to perform the reciprocal pull-down, using pfGBP130-N-Fc to pull down LFA1 from cell surfaces?

      We did not perform a reciprocal pull-down with PfGBP130-N-Fc and native cell-surface LFA-1 in the present study; we agree this would be a useful orthogonal experiment.

      (4) After identifying GBP130 as a co-purifying protein in the LFA-1 pull-down experiments, the authors select an N-terminal fragment of GBP130 to recombinantly express and use. How did the authors narrow down which region of GBP130interacted with LFA-1?

      The N-terminal PfGBP130 fragment (aa 69-270) was selected empirically as a tractable, soluble recombinant segment containing a defined repeat-containing extracellular region, rather than because we had already mapped the full LFA-1-binding interface. We agree with the reviewer that our structural model suggests that additional residues, including a likely dominant interface outside this fragment, may contribute to the full interaction, and we have clarified that the N-terminal fragment should be interpreted as a minimal binding-competent region, not necessarily the sole binding site.

      (5) As erythrocytes age, their surface undergoes biochemical changes, most notably a drop in levels of sialylation, decreasing the net repulsive negative charge, and they generally become more adherent. Can the authors exclude the possibility that, rather than binding to a parasite-derived ligand, LFA alpha 1 is instead binding to a marker of older erythrocytes? In the data presented, increased binding of LFA alpha 1 is observed as parasites progress through the life cycle, but the host erythrocytes will be ageing during parasite replication, which could account for the increased levels of LFA alpha 1 binding. To rule out this explanation, data from LFA alpha 1 staining of age-matched uninfected erythrocytes could be provided.

      We agree that erythrocyte aging can alter surface sialylation and adhesiveness, and loss of sialic acid is known to reduce erythrocyte surface charge and increase adhesiveness. However, our data argue against aging alone explaining the signal, because LFA-1 αI-Fc binding was compared with uninfected RBC controls and the interaction led to enrichment of a parasite-derived ligand, PfGBP130, in pull-down/MS analyses.

      (6) Figure 3b(i) Surface staining of THP1 cells was performed using GBP-130 Fc as a probe, which should detect all LFA1-positive cells. But no accompanying staining data using an anti-LFA1 antibody are shown, so it is not possible to determine whether staining profiles with GBP-130 Fc match staining profiles with anti-LFA1 antibodies. This is important to show what proportion of LFA1-positive cells can recognise parasite-derived GBP-130 Fc.

      (7) Figure 3c(i) Surface staining of peripheral NK cells is performed using GBP-130 Fc as a probe, which should detect all LFA1-positive cells. Here, as well, there are no staining data using an anti-LFA1 antibody. This would allow a comparison between cell population LFA1 staining with an anti-LFA1 antibody and cell population LFA1 staining with GBP-130 Fc. The two staining profiles should be similar as both probes bind the same surface marker. However, it appears this might not be the case because the staining data using GBP-130 Fc show that only a minor proportion of NK cells (~20%) stain positive, but the majority of peripheral NK cells usually express CD11a, as it is a key adhesion molecule in the formation of immune synapses with target cells. This suggests that GBP-130 can only bind to a subset of NK cells, and if it is binding LFA1, then it can only play a role in mediating the formation of an immune synapse with this subpopulation of NK cells. Could the authors include a comment in the manuscript making clear that the GBP-130 only assists a small proportion of NK cells in adhering to parasite-infected erythrocytes? Are there any reasonable hypotheses as to whyGBP-130 was only able to stain a small subpopulation of LFA1-expressing NK cells?

      For minor comment 6 and 7

      We agree that parallel staining with anti-CD11a would help relate PfGBP130-Fc binding to total LFA-1-positive THP-1 and NK-cell populations. Importantly, LFA-1 expression and ligand binding competence are not equivalent, because integrin binding depends strongly on activation/conformation and avidity state; in NK cells, only a subset can display LFA-1 in a partially activated conformation at baseline despite broader CD11a expression. Thus, a smaller PfGBP130-Fc-positive subset than the total CD11a-positive population is biologically plausible and does not imply inconsistency.

    1. Author response:

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

      eLife Assessment

      This important study examines the evolution of virulence and antibiotic resistance in Staphylococcus aureus under multiple selection pressures. The evidence presented is convincing, with rigorous data that characterizes the outcomes of the evolution experiments. However, the manuscript's primary weakness is in its presentation, as claims about the causal relationship between genotypes and phenotypes are based on correlational evidence. The manuscript needs to be revised to address these limitations, clarify the implications of the experimental design, and adjust the overall narrative to better reflect the nature of the findings.

      Thank you for your feedback. Here, we summarize the major changes made in the revised manuscript:

      (1) We did not test causality between mutations and phenotypes in our study. We were intentional about not using causal wording (“mutation X caused/led to/resulted in phenotype Y”), and only discussed these results using the terms “correlation” and “association”, and only when they were statistically significant. We understand that some readers may view these terms as being equivalent to “causation”, thus in the revision, we have modified our wording as suggested (please see below for specific lines).

      (2) We agree that experimental evolution in nematodes is not a direct simulation of evolution in humans. The goal of our study was first and foremost, a test of how multiple selective pressures can shape pathogen evolution. This point was presented in the first paragraph, the second to last paragraph of the Introduction (which included our hypotheses), and the last paragraph of the manuscript. References to humans and other mammalian systems were intended to point out similarities between our findings and what had already been found in S. aureus outside the lab. Despite differences between mammals and nematodes, several parallels arose at both the phenotypic and genomic levels, which is interesting from an evolutionary standpoint. We understand that more experiments and tests would be needed before we can make claims about the selective pressures acting on S. aureus outside the lab. We presented some information in the context of humans because a large part of the literature on S. aureus is on its role as a major bacterial pathogen; we did not want to neglect this aspect of its natural life history.

      In the revised manuscript, we are more explicit in stating these points, as well as tempering some language regarding human infection, and removing some references to humans. Please see below for specific lines as well as justification for specific references to humans/mammalian systems.

      (3) We have including additional details on the experimental design below. We hope this is sufficiently clarifying.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors investigate how methicillin-resistant (MRSA) and sensitive (MSSA) Staphylococcus aureus adapt to a new host (C. elegans) in the presence or absence of a low dose of the antibiotic oxacillin. Using an "Evolve and Resequence" design with 48 independently evolving populations, they track changes in virulence, antibiotic resistance, and other fitness-related traits over 12 passages. Their key finding is that selection from both the host and the antibiotic together, rather than either pressure alone, results in the evolution of the most virulent pathogens. Genomically, they find that this adaptation repeatedly involves mutations in a small number of key regulatory genes, most notably codY, agr, and saeRS.

      Strengths:

      The main advantage of the research lies in its strong and thoroughly replicated experimental framework, enabling significant conclusions to be drawn based on the concept of parallel evolution. The study successfully integrates various phenotypic assays (virulence, growth, hemolysis, biofilm formation) with whole-genome sequencing, offering an extensive perspective on the adaptive landscape. The identification of certain regulatory genes as common targets of selection across distinct lineages is an important result that indicates a level of predictability in how pathogens adapt.

      Thank you very much.

      Weaknesses:

      (1) The main limitation of the paper is that its findings on the function of specific genes are based on correlation, not cause-and-effect evidence. While the parallel evolution evidence is strong, the authors have not yet performed the definitive tests (i.e., reconstruction of ancestral genes) to ensure that the mutations identified in isolation are enough to account for the virulence or resistance changes observed. This makes the conclusions more like firm hypotheses, not confirmed facts.

      We have replaced instances of “association” and “correlation” with wording similar to that suggested where applicable, including:

      L 342 – 344: “The loss of SCCmec and ACME was more often identified in populations exhibiting an increase in total growth from the ancestor outside the host…”

      L 371 – 375: “Mutations in three genes were regularly identified in populations exhibiting significant increases in virulence from the ancestor: codY, gdpP, and pbpA. Mutations in agr in general were not associated with changes in overall virulence, but MSSA populations harboring mutations in this gene were more likely to exhibit greater virulence compared to MRSA populations (Wilcoxon rank sum exact test P = 0.045).”

      L 377: “Mutations in specific genes were often found in populations able to hemolyze red blood cells…”

      L 379 – 381: “There were also significant differences between the mutations regularly identified in oxacillin-resistant populations evolved from the MSSA ancestor...”

      L 384 – 385: “By contrast, mutations in agr were often in populations exhibiting loss of hemolytic activity, consistent with previous findings...”

      L 409 – 410: “Mutations that arose during experimental evolution are regularly found in strains associated with human systemic infections.”

      We have also stated that ancestral reconstruction is needed:

      L 553 – 555: “Future experiments may include introducing these mutations into the ancestral background to directly link the mutations in these genes to evolved virulence.”

      (2) In some instances, the claims in the text are not fully supported by the visual data from the figures or are reported with vagueness. For example, the display of phenotypic clusters in the PCA (Figure 6A) and the sweeping generalization about the effect of antibiotics on the mutation rates (Figure S5) can be more precise and nuanced. Such small deviations dilute the overall argument somewhat and must be corrected.

      In reference to Fig. 6A, we have revised the statement as suggested: “…where populations exposed to host and sub-MIC oxacillin clustered together, largely separating from all other treatments…” Line 442

      In reference to Fig. S5, we conducted statistics to include both MRSA and MSSA populations and examined the effect of oxacillin on the number of mutations. While oxacillin had a significant effect on the number of mutations, we agree with the reviewer that this may be driven by the MRSA populations and have clarified: “Sub-MIC oxacillin selection also resulted in more mutations than in its absence ( = 5.92, P = 0.015), although this is likely driven by MRSA populations.” Lines 310 – 311

      Reviewer #2 (Public review):

      Summary:

      The manuscript describes the results of an evolution experiment where Staphylococcus aureus was experimentally evolved via sequential exposure to an antibiotic followed by passaging through C. elegans hosts. Because infecting C. elegans via ingestion results in lysis of gut cells and an immune response upon infection, the S. aureus were exposed separately across generations to antibiotic stress and host immune stress. Interestingly, the dual selection pressure of antibiotic exposure and adaptation to a nematode host resulted in increased virulence of S. aureus towards C. elegans.

      Strengths:

      The data presented provide strong evidence that in S. aureus, traits involved in adaptation to a novel host and those involved in antibiotic resistance evolution are not traded off. On the contrary, they seem to be correlated, with strains adapted to antibiotics having higher virulence towards the novel host. As increased virulence is also associated with higher rates of haemolysis, these virulence increases are likely to reflect virulence levels in vertebrate hosts.

      Weaknesses:

      Right now, the results are presented in the context of human infections being treated with antibiotics, which, in my opinion, is inappropriate. This is because

      (1) exposure to the host and antibiotics was sequential, not simultaneous, and thus does not reflect the treatment of infection, and

      (2) because the site of infection is different in C. elegans and human hosts.

      We have removed the two sentences referencing site of infection:

      Introduction: “In the host, antibiotic concentrations will gradually decline after administration due to metabolism and excretion.”

      Discussion: “…in addition to infection of antibiotic-treated hosts, where there is uneven distribution of drugs across tissues.”

      For our rationale for discussing humans in general, please see below.

      Nevertheless, the results are of interest; I just think the interpretation and framing should be adjusted.

      Thank you very much.

      Reviewer #3 (Public review):

      Summary:

      Su et al. sought to understand how the opportunistic pathogen Staphylococcus aureus responds to multiple selection pressures during infection. Specifically, the authors were interested in how the host environment and antibiotic exposure impact the evolution of both virulence and antibiotic resistance in S. aureus. To accomplish this, the authors performed an evolution experiment where S. aureus was fed to Caenorhabditis elegans as a model system to study the host environment and then either subjected to the antibiotic oxacillin or not. Additionally, the authors investigated the difference in evolution between an antibiotic-resistant strain, MRSA, and an isogenic susceptible strain, MSSA. They found that MRSA strains evolved in both antibiotic and host conditions became more virulent, and that strains evolved outside these conditions lost virulence. Looking at the strains evolved in just antibiotic conditions, the authors found that S. aureus maintained its ability to lyse blood cells. Mutations in codY, gdpP, and pbpA were found to be associated with increased virulence. Additionally, these mutations identified in these experiments were found in S. aureus strains isolated from human infections.

      Strengths:

      The data are well-presented, thorough, and are an important addition to the understanding of how certain pathogens might adapt to different selective pressures in complex environments.

      Thank you very much.

      Weaknesses:

      There are a few clarifications that could be made to better understand and contextualize the results. Primarily, when comparing the number of mutations and selection across conditions in an evolution experiment, information about population sizes is important to be able to calculate the mutation supply and number of generations throughout the experiment. These calculations can be difficult in vivo, but since several steps in the methodology require plating and regrowth, those population sizes could be determined. There was also no mention of how the authors controlled the inoculation density of bacteria introduced to each host. This would need to be known to calculate the generation time within the host. These caveats should be addressed in the manuscript.

      While the population sizes within hosts and generation time could be determined, we would need to conduct additional experiments (e.g., infecting nematodes with S. aureus, then crushing, plating, and counting colony forming units across time intervals) in order to obtain measurements for pathogen growth in hosts across time. For experimental evolution, we crushed a set number of dead nematodes (30) and all bacteria that were released were allowed to grow in liquid media before an aliquot (25%) was used to seed the next passage. Picking and crushing nematodes across 48 populations for one time point was an arduous task. The additional steps of picking, crushing, and plating nematodes across multiple time intervals at the same time experimental evolution was being performed would not be logistically sound.

      In terms of the inoculation density of bacteria, all nematodes were placed on abundant lawns of S. aureus. Nematodes were exposed to full lawns the entire infection step; bacteria remained in abundance. While we do not know the exact inoculum each individual nematode was exposed to, we know that they ingested the bacteria because of the high mortality rate. Furthermore, we followed the same procedure for every replicate across every host-associated treatment. Host individuals within and across passages were also genetically identical to one another. Altogether, these factors allowed for more consistency across the experiment, such that relative inoculum size should be similar across individual hosts. Please refer to the evolution experiment diagram (Author response image 1) for more details.

      Ultimately, while knowing the absolute population size, inoculum size, and generation time within the host is interesting, the rounds of selection (the number of times each population was exposed to the selective pressures) is also important in addressing our major question. Every treatment, which started out from one ancestral clone (MRSA or MSSA), was exposed to the same number of bouts of selection (passages), yet we see significant divergence in terms of traits and mutations. Future directions would certainly involve determining the number of steps (e.g., number of generations within hosts) required to reach these end points, but not knowing exactly how many steps were required do not detract from addressing the larger question of determining how pathogens respond to multiple selective pressures.

      Another concern is the number of generations the populations of S. aureus spent either with relaxed selection in rich media or under antibiotic pressure in between the host exposure periods. It is probable then that the majority of mutations were selected for in these intervening periods between host infection. Again, a more detailed understanding of population sizes would contribute to the understanding of which phase of the experiment contributed to the mutation profile observed.

      We conducted every step of the evolution experiment on the same timeline. For example, all replicates across treatments were grown in liquid media at the same time (see Author response image 1.). All populations were exposed to the same selective pressures at this step of the experiment. We can then compare populations that were subsequently exposed to hosts against those that were not. Populations passaged without a host served as the control. Mutations that were solely unique to host-exposed populations would more likely contribute to the traits of interest, compared to mutations that were in common between the host-exposed and no-host treatments. Similar comparisons could be made with the oxacillin-exposed and no-oxacillin populations.

      In general, the only differences between treatments would be driven by the treatments themselves. Given that we are interested in treatment-level effects, any differences in population size or generation time between treatments could contribute to the treatment effects we observe, and thus were not something we aimed to hold uniform across our experiment.

      Author response image 1.

      Schematic of procedural steps involved in one passage of S. aureus through nematodes (+host -ox) compared to without nematodes (-host -ox).

      Recommendations for the authors:

      Reviewing Editor Comments:

      We encourage you to address all other comments raised by the reviewers; however, the review team has identified the following points as the most critical and fundamental to improve your manuscript:

      (i) Reframing the narrative: You will need to adjust the narrative so that the study is presented as a "proof of principle" rather than a direct simulation of a human infection.

      While we referenced human infection, we believe the study had been presented as a proof of principle. Examples include:

      (1) We discussed the gap of knowledge in the first paragraph: “It is unclear how virulence evolves in the face of more than one selective pressure and whether this trait is constrained or facilitated by antibiotic resistance.” Lines 86 – 88

      (2) In the second to last paragraph in the Introduction, we presented the main hypotheses: “Adaptation may require resources to be expended toward either virulence or antibiotic resistance, leading to a trade-off between these traits (Ferenci, 2016). Alternatively, weaker selection from sub-MIC antibiotics may interact synergistically with hosts and facilitate the evolution or maintenance of high virulence and antibiotic resistance.” Lines 176 – 179

      (3) The last paragraph concluded with “Our findings ultimately emphasize the importance of considering the host context in the evolution of antibiotic resistance. Integrating multiple traits, such as virulence, antibiotic resistance, and fitness may be critical in identifying the factors that facilitate host shifts and persistence of drug-resistant pathogens.” Lines 613 – 616

      These paragraphs, which set up the context for our work, did not primarily discuss human infections.

      In the revised manuscript, we have further tempered language regarding human infection:

      L 169 - 172: “Experimentally evolving S. aureus in C. elegans thus allows us to track the early stages of virulence and antibiotic resistance evolution in novel host populations with the potential to identify conserved genomic regions underlying evolved traits.”

      L 595 – 596: “Additional direct tests are needed to evaluate the role of these mutations in adaptation of S. aureus to different infection sites.”

      L 610 – 611: “Pathogen evolution in a tractable invertebrate animal model yielded phenotypes and genotypes similar to those identified in mammalian hosts, highlighting the utility of evolution experiments to identify potential ecological and genetic mechanisms that may give rise to pathogen traits conserved across systems.”

      And removed some references to humans:

      In the Introduction: “In the host, antibiotic concentrations will gradually decline after administration due to metabolism and excretion.”

      In the Discussion: “…in addition to infection of antibiotic-treated hosts, where there is uneven distribution of drugs across tissues.”

      Otherwise, our rationale for referencing humans/mammalian systems in our Introduction include:

      Setting the context of our study system: we discussed humans and clinical significance when we first introduced S. aureus (lines 132 – 151) and experimental evolution (lines 153 – 172). Much of what is known about S. aureus outside the lab is when it is interacting with humans, thus we weaved in relevant information that has been discovered in other organisms.

      Hemolysis: This ability is important for S. aureus virulence toward C. elegans (Sifri et al., 2003).

      S. aureus genomic database: we intended to leverage this large-scale database of genomes isolated from S. aureus outside the lab to compare patterns emerging from experimental evolution to those in existing isolates. Due to its relevance as a major bacterial pathogen, most of the isolates happen to be from clinical settings.

      (ii) Adjusting the causal language: You will need to soften the language so that correlational claims do not appear to be causal.

      We have adjusted language as noted above.

      (iii) Clarifying methodological aspects: You will need to provide more details on the methodology, such as population sizes, and clarify the implications of these in the conclusions of the work.

      We have provided additional explanation of methodology and the role of control (no host) treatments above.

      Reviewer #1 (Recommendations for the authors):

      The paper is robust, and the study is of great significance. Tackling the subsequent issues would greatly enhance the paper and elucidate its findings.

      Major Recommendations:

      (1) Revising Causal Language: The main flaw of the manuscript lies in its presentation of correlational data as if it were causal. We highly suggest a thorough review of the text to soften causal language when connecting genotypes to phenotypes. The absence of ancestral reconstruction should be recognized as a constraint. Assertions ought to be presented as robust, evidence-based hypotheses. For instance, rather than saying a mutation "associated with significant increases in virulence," you might say "was regularly identified in groups that developed increased virulence, strongly suggesting this gene's role in the adaptation." This will more precisely clarify the contribution of the work.

      We have softened language and stated that ancestral reconstruction is needed as noted above.

      (2) Expand on Parallel Mutations: The examination of parallel evolution in Figure 4A is intriguing but would be notably stronger with additional details. I suggest including an additional supplementary figure or table detailing the specific non-synonymous mutations identified in the highly parallel genes (e.g., codY, agr, gdpP). It is essential for the reader to understand whether parallel evolution is happening at the gene level (different mutations in a single gene) or at the nucleotide level (the precise same mutation appearing again). Kindly specify if any of these mutations were nonsense mutations, as this suggests that the loss-of-function is advantageous.

      The full table of mutations is in fig share (10.6084/m9.figshare.28745558). We have added a Supplemental Table (Table S2) containing mutations in genes occurring in more than two populations. Many of these mutations were not the same, indicating parallel evolution at the gene level (lines 315 – 317).

      Minor Recommendations for Clarity and Accuracy:

      (1) Introduction:

      Lines 176-177: Please add a citation for the statement describing the function of the SCCmec cassette, as this is established knowledge.

      Done.

      (2) Results:

      Section Title (Line 254): The title "Host and sub-MIC antibiotic promoted growth..." is imprecise. Figure 3B shows that it is the combination of these factors that promotes growth in MRSA, while oxacillin alone is detrimental. Please revise the title to reflect this synergistic effect.

      “Synergistically” has been added to the title: “Host and sub-MIC antibiotic synergistically promoted growth of MRSA…” Lines 269 – 270

      Lines 261-263: The description of Figure 3B is incomplete. The text should explicitly state that the -host+ox treatment resulted in the lowest growth for MRSA, which provides a critical contrast and suggests a fitness cost.

      We have added “By contrast, exposure to sub-MIC oxacillin alone yielded the lowest growth, suggesting a fitness cost.” Lines 277 – 278

      Line 294: The claim that "Sub-MIC oxacillin selection also resulted in more mutations" is a generalization not supported for the MSSA genotype, according to Figure S5. Please revise this sentence to specify that this effect was observed in the MRSA populations.

      We have clarified: “Sub-MIC oxacillin selection also resulted in more mutations than in its absence ( = 5.92, P = 0.015), although this is likely driven by MRSA populations.” Lines 310 – 311

      Lines 419-421: The claim that the +host+ox populations in Figure 6A "formed a distinct cluster" is an overstatement, as there is visible overlap with one other treatment (e.g., host-ox). Please revise this to more accurately describe the visual data (e.g., "clustered together, largely separating...").

      We have revised the statement as suggested: “…where populations exposed to host and sub-MIC oxacillin clustered together, largely separating from all other treatments…” Lines 442 – 443

      Lines 422-424: The interpretation of the MRSA PCA (Figure 6A) focuses on the correlation between virulence and sub-MIC growth. However, the correlation between "biofilm production" and "growth without oxacillin" appears visually stronger. Please address this correlation as well for a more complete interpretation.

      We have added “For MRSA populations, biofilm production and growth without oxacillin also appeared to be positively correlated.” Lines 447 – 448

      (3) Discussion:

      Lines 469-470: The statement that "exposure to oxacillin resulted in pathogens causing the greatest host mortality" is imprecise. The data in Figure 2A show that it is the combination of host and oxacillin. Please revise this for accuracy and add a direct citation to Figure 2A here.

      We have added clarification: “Nonetheless, we observed differing evolutionary trajectories, where exposure to oxacillin in host-associated treatments resulted in pathogens causing the greatest host mortality.” Lines 496 – 498

      Reviewer #2 (Recommendations for the authors):

      After reviewing the paper and reading the previous reviews from PLoS Biology, my biggest criticism of the paper is the way the story is told. In principle, the results are interesting and relevant, but the analogy to human infection and immune system/ antibiotic treatment strategies does not fit entirely with the experimental design or the results. I think the motivation needs to be reframed. In the study, antibiotic exposure is purely environmental, i.e., not in the host. How does environmental antibiotic use affect in vivo evolution, as this is not tested? As previous reviewers have pointed out, S. aureus is not an enteric pathogen in humans but most often causes skin infections. Furthermore, much of the results and discussion is focused on haemolysis of red blood cells, a cell type that C. elegans does not have. What the paper does present, on the other hand, and something that is interesting and novel, is a test in a model system of how a bacterial pathogen evolves to competing selection pressures. I might have hypothesised a priori that these competing pressures result in trade-offs, something which there is no evidence of, even though growth rate does not appear to be negatively impacted as a consequence of selection for drug resistance and virulence together. Instead, many traits are correlated and seemingly at the mechanistic level. This is cool and is a proof of principle, even if the system does not completely mirror reality, and I think the story should be told as such.

      We agree entirely with the reviewer that testing how pathogens respond to multiple selective pressures and the resulting lack of trade-offs are significant and interesting. We presented this question (lines 86 – 88) and our hypothesis about such trade-off in the Introduction (lines 176 – 179). As stated above, we had framed our paper to highlight these points and have removed references to antibiotic concentrations in treated humans.

      We measured and discussed hemolysis because it is important for virulence toward C. elegans (lines 195 – 197) (Sifri et al., 2003). We believe our manuscript contained a reasonable discussion of this trait. For example, three panels of the main figures presented the main hemolysis results (Figures 2B, 2C, and 2D), whereas 23 other panels did not at all involve hemolysis. In the Discussion, hemolysis took up half of the shortest paragraph (lines 509 – 519) and an additional sentence (line 589 – 591), out of seven total paragraphs.

      Specific comments:

      (1) L137-138. Can S. aureus really survive for long periods of time outside of the host? Can you clarify this statement? Do you mean it is an opportunistic pathogen and can also replicate in the environment?

      S. aureus can form biofilms and persist for weeks on inert surfaces (Kramer et al., 2024; Tran et al., 2023), indicating that it may replicate in non-host environments. We have included the phrase “opportunistic pathogen” to clarify (line 145).

      (2) L187 - to ascertain

      Corrected.

      (3) Figure 2B - there seems to be a benefit of haemolysis activity to oxacillin resistance, perhaps a crossover in mechanism? In MSSA, without a host, it goes to complete fixation, whereas it is completely lost when antibiotics aren't present. I know this is discussed later, but I would appreciate a more detailed hypothesis of why this could be.

      Antibiotics have been found to induce expression of virulence traits, such as in the case of oxacillin and hemolysis. Thus, it is reasonable that exposure to oxacillin during evolution would maintain MSSA’s hemolytic ability. We hypothesize that the loss of hemolysis in the absence of oxacillin may be due to the cost of hemolysis expression without a stimulant (oxacillin), hemolysis may not be expressed as often and be subject to deleterious mutations. Alternatively, the stress that cells were under favored virulence in some way, rather than the direct action of the antibiotic.

      (4) L225-228 - As C. elegans do not have red blood cells, why would we expect this? Do you see increased lysis of C. elegans gut cells? Or could it be due to iron accumulation as you are growing the staph on BHI?

      We measured and correlated nematode mortality with hemolytic ability because hemolysis had been found to be involved in virulence toward C. elegans (Sifri et al., 2003). The hemolysis phenotype is a surrogate for S. aureus virulence gene expression.

      (5) Figure 3A - There seems to be a growth cost of evolving oxacillin resistance in the absence of a host. Why might this be?

      MRSA populations exposed to oxacillin without a host during evolution visually exhibited the lowest growth rate. While this is an interesting question, the result was not statistically significant, so we cannot speculate in the manuscript.

      Reviewer #3 (Recommendations for the authors):

      (1) Some claims in the introduction are either non cited or not correctly stated. The second sentence has a claim about the interplay between antibiotic resistance and virulence with no citation listed. Additionally, there is a claim about S. aureus "evading detection" by attacking the host's immune cells. That is by definition not avoiding detection. Perhaps phrasing it as resisting host immune function would make it clearer.

      We have added a citation (lines 80 – 81) and clarified our wording: “Once inside the host, S. aureus resists host immune function by hindering or lysing immune cells.” Lines 140 – 141

      (2) Once in the introduction and in the discussion, the authors referred to S. aureus as a novel pathogen for C. elegans, I do not think enough is known to make this statement.

      This S. aureus strain is novel because it was isolated from humans, so at least in its recent evolutionary past, it has not interacted with C. elegans. Furthermore, we used a C. elegans isolate (N2) that had been frozen and maintained in the lab on E. coli, and had not been exposed to other microbes in its recent evolutionary past. Finally, S. aureus has not been found to be a native pathogen of C. elegans in nature (Ekroth et al., 2021).

      (3) Key suggestion: Change Figure 1C to reflect the design better. So you could have the +OXA before the host and then have an arrow looping back again to show the cycle of each step. So a figure that would have something like: MRSA > +OXA > +host>+OXA --> MRSA .

      We have updated the figure as suggested.

      (4) Suggest changing "greatest" on line 191, section header to greater.

      Done.

      (5) Line 258: Rich media can still provide selective pressures that are difficult to quantify - fast growth, cofactor and other nutrient limitations due to that fast growth

      We have adjusted our wording: “Importantly, rich media reduced the risk of introducing additional selective pressures than those being tested.” Lines 273 – 274

      (6) Why were intergenic mutations routinely ignored? These can often be very important phenotypically.

      We had focused on genes because there was a sufficient number of genes to discuss, but we have added a Supplemental Table (Table S2) containing all mutations (including intergenic and synonymous) appearing in more than 2 populations. We have also added information regarding mecA, an accessory gene, highlighting the role non-core genes may have in shaping bacterial evolution:

      “Despite evolving in similar environments, MRSA and MSSA populations differing only in the presence of an intact accessory gene (mecA)—proceeded on divergent evolutionary paths…” Lines 66 – 68

      “Carriage of Staphylococcal cassette chromosome mec (SCCmec), which encodes mecA, an accessory gene that provides resistance…” Lines 187 – 188

      “As MRSA and MSSA only differed in the presence of an intact mecA gene at the start of the experiment, accessory genes may play important roles in shaping bacterial evolution (Jackson et al., 2011).” Lines 472 – 474

      (7) Line 294: more mutations than what?

      We have clarified the sentence: “Sub-MIC oxacillin selection also resulted in more mutations than in its absence…” Lines 310 – 311

      (8) Lines 295-297: wording is pretty confusing. It seems that the discussion is about increased mutation rates, possibly due to hypermutators resulting from mutL or recA mutations, but this isn't well-thought out and much is implied here. Furthermore, see the above comment about comparing mutations across conditions - it's hard to make inferences of mutation rates without knowing the mutation supply as a result of varying population sizes across conditions and through the experiment.

      We have clarified the sentence: “…there were only two mutations in DNA and mismatch repair genes (mutL and recA), suggesting repair genes were not the sole mechanism involved.” Lines 313 – 314

      Because all populations evolved from one ancestral clone (either MRSA or MSSA), all mutations that are found at the end of the experiment would have arisen de novo from that ancestor. Since all populations experienced the same number of passages/rounds of selection, we determined mutation rate by counting the number of mutations that were found at the last passage for each replicate population. Populations that acquired significantly more mutations had a higher mutation rate in terms of # of mutations/# of selection rounds.

      (9) Line 486: typo "Mutations genes".

      Corrected.

      (10) Line 487: "antibiotics may allow" is awkward; suggest changing to more precise language, possibly relating to pleiotropy if that is what was meant here.

      We had intended to mean “adaptation [to antibiotics] may allow”. We have clarified: “Mutations in genes involved in resistance to antibiotics were found more often in populations with increased virulence, suggesting that antibiotic adaptation may also favor evolution of virulence.” Lines 514 – 516

      REFERENCES

      Ekroth AKE, Gerth M, Stevens EJ, Ford SA, King KC. 2021. Host genotype and genetic diversity shape the evolution of a novel bacterial infection. ISME Journal 15:2146–2157. DOI: https://doi.org/10.1038/s41396-021-00911-3, PMID: 33603148

      Kramer A, Lexow F, Bludau A, Köster AM, Misailovski M, Seifert U, Eggers M, Rutala W, Dancer SJ, Scheithauer S. 2024. How long do bacteria, fungi, protozoa, and viruses retain their replication capacity on inanimate surfaces? A systematic review examining environmental resilience versus healthcare-associated infection risk by “fomite-borne risk assessment.” Clinical Microbiology Reviews. PMID: 39388143

      Sifri CD, Begun J, Ausubel FM, Calderwood SB. 2003. Caenorhabditis elegans as a model host for Staphylococcus aureus pathogenesis. Infection and Immunity 71:2208–2217. DOI: https://doi.org/10.1128/IAI.71.4.2208-2217.2003, PMID: 12654843

      Tran NN, Morrisette T, Jorgensen SCJ, Orench-Benvenutti JM, Kebriaei R. 2023. Current therapies and challenges for the treatment of Staphylococcus aureus biofilm-related infections. Pharmacotherapy 43:816–832. DOI: https://doi.org/10.1002/phar.2806, PMID: 37133439

    1. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Gosselin et al., develop a method to target protein activity using synthetic single-domain nanobodies (sybodies). They screen a library of sybodies using ribosome/ phage display generated against bacillus Smc-ScpAB complex. Specifically, they use an ATP hydrolysis deficient mutant of SMC so as to identify sybodies that will potentially disrupt Smc-ScpAB activity. They next screen their library in vivo, using growth defects in rich media as a read-out for Smc activity perturbation. They identify 14 sybodies that mirror smc deletion phenotype including defective growth in fast-growth conditions, as well as chromosome segregation defects. The authors use a clever approach by making chimeras between bacillus and S. pnuemoniae Smc to narrow-down to specific regions within the bacillus Smc coiled-coil that are likely targets of the sybodies. Using ATPase assays, they find that the sybodies either impede DNA-stimulated ATP hydrolysis or hyperactivate ATP hydrolysis (even in the absence of DNA). The authors propose that the sybodies may likely be locking Smc-ScpAB in the "closed" or "open" state via interaction with the specific coiled-coil region on Smc. I have a few comments that the authors should consider:

      Major comments:

      (1) Lack of direct in vitro binding measurements:

      The authors do not provide measurements of sybody affinities, binding/ unbinding kinetics, stoichiometries with respect to Smc-ScpAB. Additionally, do the sybodies preferentially interact with Smc in ATP/ DNA-bound state? And do the sybodies affect the interaction of ScpAB with SMC?

      It is understandable that such measurements for 14 sybodies is challenging, and not essential for this study. Nonetheless, it is informative to have biochemical characterization of sybody interaction with the Smc-ScpAB complex for at least 1-2 candidate sybodies described here.

      We agree with the reviewer that adding such data would be reassuring and that obtaining solid data using purified components is not trivial, even for a smaller selection of sybodies. We have now incorporated ELISA data as new Table S1, which shows that most sybodies support clear binding to Smc-ScpAB. Curiously, while (only) some sybodies show a clear preference for ATP-bound or unbound Smc, this is not a strong predictor of the strength of phenotype observed in vivo. We have also attempted to characterize the binding of Smc to sybodies by other methods including pull-downs, cross-linking, and by biophysical methods (GCI). However, we prefer to not include these data as the outcomes are not clear due to inconsistencies in the behaviour of purified sybodies.

      (2) Many modes of sybody binding to Smc are plausible

      The authors provide an elaborate discussion of sybodies locking the Smc-ScpAB complex in open/ closed states. However, in the absence of structural support, the mechanistic inferences may need to be tempered. For example, is it also not possible for the sybodies to bind the inner interface of the coiled-coil, resulting in steric hinderance to coiled-coil interactions. It is also possible that sybody interaction disrupts ScpAB interaction (as data ruling this possibility out has not been provided). Thus, other potential mechanisms would be worth considering/ discussing. In this direction, did AlphaFold reveal any potential insights into putative binding locations?

      We have attempted to map the binding by structure prediction, however, so far, even the latest versions of AlphaFold are not able to clearly delineate the binding interface that we have confidently identified by the mapping using chimeric proteins. Indeed, many ways of binding are possible, including disruption of ScpAB interaction. However, since the mapped binding sites are located on the SMC coiled coils, the later scenario seems unlikely and would be an indirect consequence of altered coiled coil configuration, consistent with our current interpretation.

      (3) Sybody expression in vivo

      Have the authors estimated sybody expression in vivo? Are they all expressed to similar levels?

      We have tagged selected sybodies with gfp and performed live cell imaging. This shows that sybodies without strong phenotypes are similarly expressed at least at low inducer concentration. Moreover, many sybodies localize as foci in the cell presumably by binding to Smc complexes loaded onto the chromosome at ParB/parS sites. We have included example data in the revised version of the manuscript as Figure S4 and Figure S5. Notably, a sybody (Sb007) with a weak growth phenotype shows focal localization at low inducer concentration and high expression levels when fully induced, comparable to sybodies with strong phenotypes. Altogether, this suggests that the lack of phenotype is not due to absence of sybody expression or localization.

      (4) Sybodies should phenocopy ATP hydrolysis mutant of Smc

      The sybodies were screened against an ATP hydrolysis deficient mutant of Smc, with the rationale that these sybodies would interfere this step of the Smc duty cycle. Does the expression of the sybodies in vivo phenocopy the ATP hydrolysis deficient mutant of Smc? Could the authors consider any phenotypic read-outs that can indicate whether the sybody action results in an smc-null effect or specifically an ATP hydrolysis deficient effect?

      As alluded to above, we think that our selection gave rise to sybodies that bind various, possibly multiple Smc conformations. Consistent with this idea, the phenotypes of sybody expression are similar to null mutant rather than the ATP-hydrolysis defective EQ mutant, which display even more severe growth phenotypes in B. subtilis. To highlight this point, we have added the following notes to the text:

      “These conditions favour ATP-engaged particles alongside the typically predominant ATP-disengaged rod-shaped state.”

      “ELISA data revealed that nearly all clones bind purified Smc-ScpAB (Table 1). However, the ELISA signals of only few Sybodies showed clear dependence on the presence or absence of ATP and DNA (Table S1).”

      Significance:

      Overall, this is an impressive study that uses an elegant strategy to find inhibitors of protein activity in vivo. The manuscript is clearly written and the experiments are logical and well-designed. The findings from the study will be significant to the broad field of genome biology, synthetic biology and also SMC biology. Specifically, the coiled coil domain of SMC proteins have been proposed to be of high functional value. The authors have elegantly identified key coiled-coil regions that may be important for function, and parallelly exhibited potential of the use of synthetic sybody/designed binders for inhibition of protein activity.

      Reviewer #2 (Public review):

      Summary:

      Structural Maintenance of Chromosome proteins (SMCs), a family of proteins found in almost all organisms, are organizers of DNA. They accomplish this by a process known as loop extrusion, wherein double-stranded DNA is actively reeled in and extruded into loops. Although SMCs are known to have several DNA binding regions, the exact mechanism by which they facilitate loop extrusion is not understood but is believed to entail large conformational changes. There are currently several models for loop extrusion, including one wherein the coiled coil (CC) arms open, but there is a lack of insightful experimentation and analysis to confirm any of these models. The work presented aims to provide much-needed new tools to investigate these questions: conformation-selective sybodies (synthetic nanobodies) that are likely to alter the CC opening and closing reactions.

      The authors produced, isolated, and expressed sybodies that specifically bound to Bacillus subtilis Smc-ScpAB. Using chimeric Smc constructs, where the coiled coils were partly replaced with the corresponding sequences from Streptococcus pneumoniae, the authors revealed that the isolated sybodies all targeted the same 4N CC element of the Smc arms. This region is likely disrupted by the sybodies either by stopping the arms from opening (correctly) or forcing them to stay open (enough). Disrupting these functional elements is suggested to cause the Smc-dependent chromosome organization lethal phenotype, implying that arm opening and closing is a key regulatory feature of bacterial Smc-ScpAB.

      Significance:

      The authors present a new method for trapping bacterial Smc's in certain conformations using synthetic antibodies. Using these antibodies, they have pinpointed the (previously suggested) 4N region of the coiled coils as an essential site for the opening and closing of the Smc coiled coil arms and that hindering these reactions blocks Smc-driven chromosomal organization. The work has important implications for how we might elucidate the mechanism of DNA loop extrusion by SMC complexes.

      Reviewer #3 (Public review):

      Summary:

      Gosselin et al. use the sybody technology to study effects of in vivo inhibition of the Bacillus subtilis SMC complex. Smc proteins are central DNA binding elements of several complexes that are vital for chromosome dynamics in almost all organisms. Sybodies are selected from three different libraries of the single domain antibodies, using the "transition state" mutant Smc. They identify 14 such mutant sybodies that are lethal when expressed in vivo, because they prevent proper function of Smc. The authors present evidence suggesting that all obtained sybodies bind to a coiled-coil region close to the Smc "neck", and thereby interfere with the Smc activity cycle, as evidenced by defective ATPase activity when Smc is bound to DNA.

      The study is well done and presented and shows that the strategy is very potent in finding a means to quickly turn off a protein's function in vivo, much quicker than depleting the protein.

      The authors also draw conclusions on the molecular mode of action of the SMC complex. The provide a number of suggestive experiments, but in my view mostly indirect evidence for such mechanism.

      My main criticism is that the authors have used a single - and catalytically trapped form of SMC. They speculate why they only obtain sybodies from one library, and then only identify sybodies that bind to a rather small part of the large Smc protein. While the approach is definitely valuable, it is biassed towards sybodies that bind to Smc in a quite special way, it seems. Using wild type Smc would be interesting, to make more robust statements about the action of sybodies potentially binding to different parts of Smc.

      The reviewer reports (Rev. #1 and Rev. #3) made us realize that the manuscript text was misleading on the this point. Although we used the purified ATP hydrolysis–deficient Smc protein for sybody isolation, this is not expected to restrict the selection to a specific conformation. As described in detail in Vazquez-Nunez et al. (Figure 5), this mutant displays the ATP-engaged conformation only in a smaller fraction of complexes (~25% in the presence of ATP and DNA), consistent with prior in vivo observations reported by Diebold-Durand et al. (Figure 5). Rather than limiting the selection to a particular configuration, our aim was to reduce the prevalence of the predominant rod state in order to broaden the range of conformations represented during sybody selection. Consistent with this interpretation, only a small number of isolated sybodies show strong conformation-specific binding in the presence or absence of ATP/DNA, as observed by ELISA (now included in the manuscript). Notably, the effect size of ATP/DNA on ELISA signals was not a strong predictor to the strength of phenotypes observed in vivo. The text has been revised accordingly. See line 84 and line 92.

      We are thus quite confident based prior work (and on the now included ELISA data) that the Smc ATPase mutation did not strongly bias the selection in one way or another. The surprising bias towards coiled coil binding sites has likely other explanations, as they likely form a preferred epitope recognized by sybodies from the loop library.

      Line 105: Alternatively, the other libraries did not produce good binders or these sybodies were 106 not stably expressed in B. subtilis. This could be tested using Western blotting - I am assuming sybody antibodies are commercially available. However, this test is not important for the overall study, it would just clarify a minor point.

      While there are antibody fragments available to augment the size of sybodies (PMID: 40108246), these recognize 3D-epitopes and are thus not suited for Western blotting. We did not follow up on the negative results of two of the three libraries but would like to point out again that there are several biases that likely emerge for the same reason (bias to library, bias to coiled coil binding site). If correct, then sybodies are likely ineffective in inactivating Smc in B. subtilis, with the notable exceptions of the sybodies that we have isolated and characterized in this manuscript. We have added this notion to the manuscript.

      Fig. 2B: is odd to count Spo0J foci per cells, as it is clear from the images that several origins must be present within the fluorescent foci. I am fine with the "counting" method, as the images show there is a clear segregation defect when sybodies are expressed, I believe the authors should state, though, that this is not a replication block, but failure to segregate origins.

      We agree that this is an important point. We have added the following statement to clarify this point: “These elongated cells are known to harbour expanded nucleoids, consistent with delayed oriC separation rather than delayed DNA replication”

      Testing binding sites of sybodies to the SMC complex is done in an indirect manner, by using chimeric Smc constructs. I am surprised why the authors have not used in vitro crosslinking: the authors can purify Smc, and mass spectrometry analyses would identify sites where sybodies are crosslinked to Smc. Again, I am fine with the indirect method, but the authors make quite concrete statements on binding based on non-inhibition of chimeric Smc; I can see alternative explanations why a chimera may not be targeted.

      We have made several attempts of testing direct binding with mixed outcomes and decided to not include those results in the light of the stronger and more relevant in vivo mapping. However, we have added ELISA results (new Table S1) that support a direct interaction.

      Smc-disrupting sybodies affect the ATPase activity in one of two ways. Again, rather indirect experiments. This leads to the point Revealing Smc arm dynamics through synthetic binders in the discussion. The authors are quite careful in stating that their experiments are suggestive for a certain mode of action of Smc, which is warranted.

      In line 245, they state More broadly, the study demonstrates how synthetic binders can trap, stabilize, or block transient conformations of active chromatin-associated machines, providing a powerful means to probe their mechanisms in living cells. This is off course a possible scenario for the use of sybodies, but the study does not really trap Smc in a transient conformation, at least this is not clearly shown.

      We agree and have simplified the statement by removing “stabilize” and “transient”.

      Overall, it is an interesting study, with a well-presented novel technology, and a limited gain of knowledge on SMC proteins.

      We respectfully disagree with the last point, since our unique results highlight the importance of the Smc coiled coils. which are less well represented in the SMC literature (when compared to the heads and hinge domains for example), likely (at least in part) due the mild effect of single point mutations on coiled coil dynamics.

      Significance:

      The work describes the gaining and use of single-binder antibodies (sybodies) to interfere with the function of proteins in bacteria. Using this technology for the SMC complex, the authors demonstrate that they can obtain a significant of binders that target a defined region is SMC and thereby interfere with the ATPase cycle.

      The study does not present a strong gain of knowledge of the mode of action of the SMC complex.

      As pointed out above, we respectfully disagree with this assertion.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Lumen formation is a fundamental morphogenetic event essential for the function of all tubular organs, notably the vertebrate vascular network, where continuous and patent conduits ensure blood flow and tissue perfusion. The mechanisms by which endothelial cells organize to create and maintain luminal space have historically been categorized into two broad strategies: cell shape changes, which involve alterations in apical-basal polarity and cytoskeletal architecture, and cell rearrangements, wherein intercellular junctions and positional relationships are remodeled to form uninterrupted conduits. The study presented here focuses on the latter process, highlighting a unique morphogenetic module, junction-based lamellipodia (JBL), as the driver for endothelial rearrangements.

      Strengths:

      The key mechanistic insight from this work is the requirement of the Arp2/3 complex, the classical nucleator of branched actin filament networks, for JBL protrusion. This implicates Arp2/3-mediated actin polymerization in pushing force generation, enabling plasma membrane advancement at junctional sites. The dependence on Arp2/3 positions JBL within the family of lamellipodia-like structures, but the junctional origin and function distinguish them from canonical, leading-edge lamellipodia seen in cell migration.

      Weaknesses:

      The study primarily presents descriptive observations and includes limited quantitative analyses or genetic modifications. Molecular mechanisms are typically interrogated through the use of pharmacological inhibitors rather than genetic approaches. Furthermore, the precise semantic distinction between JAIL and JBL requires additional clarification, as current evidence suggests their biological relevance may substantially overlap.

      We have previously analyzed the effects of different ve-cadherin (cdh5) mutant alleles on EC rearrangements (Paatero et al., 2018; Sauteur et al., 2014).These mutants show complex defects (e.g. hypersprouting, reduced contact inhibition during anastomosis) in EC behavior early in vascular tube formation. We find that analysis of JBL dynamics and function is very difficult in such situations. The use of small molecule inhibitors allows acute interventions within a defined time-window and to avoid pleiotropic effects of genetic ablations. We have expanded our discussion on the distinction between JAIL and JBL and hope that this will clarify why – in our opinion – these terms should be used differentially in different cell biological contexts (see below and lines 348-374 in the manuscript).

      Reviewer #2 (Public review):

      Summary:

      In Maggi et al., the authors investigated the mechanisms that regulate the dynamics of a specialized junctional structure called junction-based lamellipodia (JBL), which they have previously identified during multicellular vascular tube formation in the zebrafish. They identified the Arp2/3 complex to dynamically localize at expanding JBLs and showed that the chemical inhibition of Arp2/3 activity slowed junctional elongation. The authors therefore concluded that actin polymerization at JBLs pushes the distal junction forward to expand the JBL. They further revealed the accumulation of Myl9a/Myl9b (marker for MLC) at the junctional pole, at interjunctional regions, suggesting that contractile activity drives the merging of proximal and distal junctions. Indeed, chemical inhibition of ROCK activity decreased junctional mergence. With these new findings, the authors added new molecular and cellular details into the previously proposed clutch mechanism by proposing that Arp2/3-dependent actin polymerization provides pushing forces while actomyosin contractility drives the merging of proximal and distal junctions, explaining the oscillatory protrusive nature of JBLs.

      Strengths:

      The authors provide detailed analyses of endothelial cell-cell dynamics through time-lapse imaging of junctional and cytoskeletal components at subcellular resolution. The use of zebrafish as an animal model system is invaluable in identifying novel mechanisms that explain the organizing principles of how blood vessels are formed. The data is well presented, and the manuscript is easy to read.

      Weaknesses:

      While the data generally support the conclusions reached, some aspects can be strengthened. For the untrained eye, it is unclear where the proximal and distal junctions are in some images, and so it is difficult to follow their dynamics (especially in experiments where Cdh5 is used as the junctional marker). Images would benefit from clear annotation of the two junctions. All perturbation experiments were done using chemical inhibitors; this can be further supported by genetic perturbations.

      We have added annotations to several figures and paid particular attention to the proximal and distal junctions.

      We have previously analyzed the effects of different ve-cadherin (cdh5) mutant alleles on EC rearrangements (Paatero et al., 2018; Sauteur et al., 2014). These mutants show complex defects (e.g. hypersprouting, reduced contact inhibition during anastomosis) in EC behavior early in vascular tube formation. We find that analysis of JBL dynamics and function is very difficult in such situations. The use of small inhibitors allows acute interventions within a defined time-window and to avoid pleiotropic effects of genetic ablations.

      Reviewer #3 (Public review):

      The paper by Maggi et al. builds on earlier work by the team (Paatero et al., 2018) on oriented junction-based lamellipodia (JBL). They validate the role of JBLs in guiding endothelial cell rearrangements and utilise high-resolution time-lapse imaging of novel transgenic strains to visualise the formation of distal junctions and their subsequent fusion with proximal junctions. Through functional analyses of Arp2/3 and actomyosin contractility, the study identifies JBLs as localized mechanical hubs, where protrusive forces drive distal junction formation, and actomyosin contractility brings together the distal and proximal junctions. This forward movement provides a unique directionality which would contribute to proper lumen formation, EC orientation, and vessel stability during these early stages of vessel development.

      Time-lapse live imaging of VEC, ZO-1, and actin reveals that VEC and ZO-1 are initially deposited at the distal junction, while actin primarily localizes to the region between the proximal and distal sites. Using a photoconvertible Cdh5-mClav2 transgenic line, the origin of the VEC aggregates was examined. This convincingly shows that VE-cadherin was derived from pools outside the proximal junctions. However, in addition to de novo VEC derived from within the photoconverted cell, could some VEC also be contributed by the neighbouring endothelial cell to which the JBL is connected?

      Yes, the green (non-converted) VE-cadherin can indeed originate from either of the two cells. The main point we want to make, based on our observations, is that the red (converted) VE-cadherin from the proximal junction (as defined by the ROI) does not contribute to the distal junction.

      As seen for JAILs in cultured ECs, the study reveals that Arp2/3 is enhanced when JBLs form by live imaging of Arpc1b-Venus in conjunction with ZO-1 and actin. Therefore Arp2/3 likely contributes to the initial formation of the distal junction in the lamellopodium.

      Inhibiting Arp2/3 with CK666 prevents JBL formation, and filopodia form instead of lamellopodia. This loss of JBLs leads to impaired EC rearrangements.

      Is the effect of CK666 treatment reversible? Since only a short (30 min) treatment is used, the overall effect on the embryo would be minimal, and thus washing out CK666 might lead to JBL formation and normalized rearrangements, which would further support the role of Arp2/3.

      We have performed washout experiments and find that the ectopic filopodia disappear when the inhibitor is removed. This experiment is shown in supplementary Figure 3 and supplementary Movies 12 and 13.

      From the images in Figure 4d it appears that ZO-1 levels are increased in the ring after CK666 treatment. Has this been investigated, and could this overall stabilization of adhesion proteins further prevent elongation of the ring?

      This is an interesting thought and we haven take a closer look. There is quite a bit of sample-to-sample variation in the ZO1 signal. The quantification (Author response image 1) indicates that there is no increase in the CK666 treated embryos on average.

      Author response image 1.

      To explore how the distal and proximal junctions merge, imaging of spatiotemporal imaging of Myl9 and VEC is conducted. It indicates that Myl9 is localized at the interjunctional fusion site prior to fusion. This suggests pulling forces are at play to merge the junctions, and indeed Y 27632 treatment reduces or blocks the merging of these junctions.

      For this experiment, a truncated version of VEC was use,d which lacks the cytoplasmic domain. Why have the authors chosen to image this line, since lacking the cytoplasmic domain could also impair the efficiency of tension on VEC at both junction sites? This is as described in the discussion (lines 328-332).

      This line was used because it labels the entire JBL protrusion more clearly. We have also included an example using the VE-cad-Venus line (supplementary Figure 4b), which shows a Myl-Cherry pattern consistent with the other examples.

      Since the time-lapse movies involve high-speed imaging of rather small structures, it is understandable that these are difficult to interpret. Adding labels to indicate certain structures or proteins at essential timepoints in the movies would help the readers understand these.

      We have added annotations and labels to all movies. We have also improved annotations in several figures (i.e. Figs. 1, 2, 5, 6 and 7)

      Recommendations for the authors:

      Reviewing Editor Comments:

      Overall, the reviewers are supportive of the manuscript but identify a number of areas where the clarity of the presented data could be improved, and further quantification could be provided to strengthen your conclusions. We would encourage you to address these minor concerns as best you can and to consider the recommendations of all three reviewers when deciding how to revise your manuscript.

      Reviewer #1 (Recommendations for the authors):

      Lumen formation is a fundamental morphogenetic event essential for the function of all tubular organs, notably the vertebrate vascular network, where continuous and patent conduits ensure blood flow and tissue perfusion. The mechanisms by which endothelial cells organize to create and maintain luminal space have historically been categorized into two broad strategies: cell shape changes, which involve alterations in apical-basal polarity and cytoskeletal architecture, and cell rearrangements, wherein intercellular junctions and positional relationships are remodeled to form uninterrupted conduits. The study presented here focuses on the latter process, highlighting a unique morphogenetic module, junction-based lamellipodia (JBL), as the driver for endothelial rearrangements.

      JBL are described as oscillating membrane protrusions emerging at endothelial junctions, operating in a ratchet-like manner to mediate convergent cell movements. This ratchet mechanism allows endothelial cells to approach each other, thereby aligning and joining local luminal segments into a continuous vascular structure. The study employs in vivo high-resolution time-lapse imaging, a technically demanding method that captures spatiotemporal dynamics of cytoskeletal and adhesion complexes during JBL activity with unprecedented detail.

      The key mechanistic insight from this work is the requirement of the Arp2/3 complex, the classical nucleator of branched actin filament networks, for JBL protrusion. This implicates Arp2/3-mediated actin polymerization in pushing force generation, enabling plasma membrane advancement at junctional sites. The dependence on Arp2/3 positions JBL within the family of lamellipodia-like structures, but the junctional origin and function distinguish them from canonical, leading-edge lamellipodia seen in cell migration.

      An intriguing observation is that a novel junction arises at the distal pole of a JBL. This distal junction is formed from a pool of VE-cadherin that is spatially redistributed from regions outside the initial JBL domain. The distal junction then merges with the proximal junction through a process dependent on actomyosin contractility, as was judged by Myl9 recruitment.

      The alternation between pushing forces (Arp2/3-dependent JBL protrusion) and pulling forces (actomyosin-driven junction fusion) defines JBL as a bidirectional mechanical module. Inhibition of actomyosin prevents merging of proximal and distal junctions, thereby stalling lumen continuity. This two-phase system, actin-based extension followed by actomyosin-mediated constriction, ensures both elongation and maturation of endothelial arrangements, ultimately securing vascular patency.

      This manuscript represents a robust and thoughtfully executed study that advances our understanding of lumen formation during vascular development. The overarching conclusions are well substantiated, and the results section provides a clear and detailed exposition of the key findings. I appreciate the explanatory movie at the end. Nevertheless, I offer several remarks for further improvement:

      (1) The fluorescent images presented are visually compelling, yet lack quantitative analysis in the initial figure. Although quantification is included in Figure 3, it is advisable to incorporate this analysis into Figure 1 as well. Early presentation of quantification will help the reader to appreciate the impact and significance of the findings from the outset.

      We appreciate the reviewer’s suggestion and have now added line graphs to measure the spatiotemporal intensities of the Utrophin and ZO-1 reporters in Figure 1b. These measurements demonstrate the sequence of F-actin protrusion and subsequent junctional movement. In Figure 1a, we have added a double-headed arrow which shows the overall movement of the junction towards the dorsal side of the forming DLAV.

      (2) For the fluorescence images, further quantitative analysis of membrane overlap, either in terms of width or pixel overlap, would enhance the rigor of the study. Temporal quantification of overlap may provide valuable insights into the stability and reproducibility of the process across experimental replicates.

      JBL are quite heterogenous with respect to size, shape and dynamics, which makes quantifications of membrane overlap (JBL size) across experimental replicates difficult. We have published some quantifications on JBL orientation and oscillation in our previous paper (Paatero et al., 2018, Nat. comm. Figures 1 and 2), which are in agreement with our current study.

      (3) When referencing the role of Arp2/3, the authors employ an ArpC1b transgenic fish. The results section should thus specifically address the involvement of ArpC1b, rather than generalizing to Arp2/3. In the discussion, it would be appropriate to speculate on the potential involvement of the complete Arp2/3 complex. Notably, the use of CK is acknowledged as a broadly accepted inhibitor of actin polymerization.

      As ArpC1b is a subunit of an active Arp2/3 complex (Padrick et al., 2011), we have used an ArpC1b-Venus as a readout for Arp2/3 localization. The construct has been validated before in cell culture (Law et al., 2021) as well as in zebrafish (Malchow et al., 2024) and the spatiotemporal distribution of the reporter shown to be consistent with Arp2/3 complex. We are stating this in the results section (lines 173-178) and subsequently use the term Arp2/3 to facilitate reading of the text. In the corresponding figure legends, we are maintaining the term ArpC1b. CK666 interferes with the dimerization of Arp2 and Arp3 subunits and thus prevents activity of the Arp2/3 complex.

      (4) The discussion regarding JAIL versus JBL involvement remains challenging to interpret. If JAIL structures arise from the loss of cell-cell contacts, both JAIL and JBL resemble membrane protrusions and are likely governed by similar molecular mechanisms, predominantly actin polymerization and Arp2/3 activity, with probable contribution from Rac1 signaling. The precise semantic distinction between JAIL and JBL warrants further clarification, as their biological relevance may be overlapping.

      We agree with the reviewer. Below we outline the reasons why lamellipodial protrusions that emanate from cell-cell junctions should not be indiscriminately called JAIL, but that JAIL and JBL constitute different cellular activities acting in different tissue contexts. We have modified the text in the Discussion (lines 348-374).

      (1) JAIL have originally been described in cell culture experiments (Abu-Taha et al., 2014). According to this and subsequent papers by the same group, local dissolution of endothelial adherens junctions (i.e. downregulation of VE-cadherin) triggers the formation of lamellipodia-like structures. These protrusions eventually retract, followed by the reestablishment of EC junctions.

      (2) In our in vivo studies, we observed lamellipodial protrusions during endothelial cell rearrangements, and we call these structures JBL (Paatero et al., 2018). While JBL appear very similar to JAIL in general (i.e. regulation by Arp2/3 and its localization), we also observe two critical differences. For one, JBL form while maintaining the original (proximal) junction. Moreover, a distal junction is formed at the front edge of the JBL, leading to a “double junction” configuration. In our current manuscript, we have examined the role of actomyosin contractility and find that it correlates with and is required for the merging of proximal and distal junctions during JBL cycles. These observations indicates that the proximal and distal junctions are essential components of JBL function during endothelial cell elongation and rearrangements. These salient and distinct features prompted us to adopt the term junction-based-lamellipodia (JBL), in order to differentiate them from JAIL.

      (3) We like to argue that JAIL and JBL represent similar but different lamellipodia-like protrusions. JAILs are associated with the maintenance of endothelial integrity, and control permeability and trans-endothelial cell migration, as has been suggested by several publications (Cao et al., 2017; Kipcke et al., 2025; Seebach et al., 2021; Taha et al., 2014). In contrast, JBL drive cell rearrangements, by step-wise elongation of cell junctions leading to convergent cell movements.

      (4) Although JAIL have also been implicated in endothelial cell migration (Cao and Schnittler, 2019; Cao et al., 2017; Seebach et al., 2021), neither junctional patterns nor junctional dynamics have been analyzed in this context. We therefore propose that JAIL and JBL are actin-based protrusions forming at endothelial cell-cell junctions, but act in different contexts to provide cell motility (JBL) or endothelial integrity (JAIL).

      (5) Some of the quantification plots, specifically in figures 5d and 6c, do not display significant differences or distribution patterns. It would be beneficial to revise these graphs to clearly represent statistical significance and underlying data distributions.

      Because of the spatiotemporal heterogeneity, it is difficult to perform statistical quantifications across samples. In Figure 5c/d, we have imaged/analyzed myl9-EGFP in a mosaic situation, in which only one of interacting cells expresses high levels of myl9-EGFP. This is a rare situation and we managed to image only this example. Nevertheless, it is consistent with our other expression data of myl9-reporters and also with our previous photoconversion experiments using photoconvertible UCHD (Paatero et al., 2018, Figure 4), which shows that actin-rich JBL form at the front end of the endothelial cell in the direction of junction elongation. In Figure 5d, we have quantified the average intensity of GFP signal within the region of interest. The newly added error bars indicate the standard deviation between pixel intensities within the ROI.

      In Figure 6c, we have analyzed the Myl9b-mCherry intensities and find that it is redistributed during a JBL cycle. The spatial distribution is evident from the heat-map and we have not included a standard deviation. Myl9b-mCherry levels are very heterogenous and is not possible to quantify intensities across samples. We have, however, included four more examples of Myl9b-mCherry distribution in Supplementary Figure 4. The patterns observed in these samples are consistent with those in Figure 6.

      (6) The observation of myosin recruitment does not inherently imply a concomitant increase in actomyosin contractile activity. The inclusion of phospho-MLC staining would considerably strengthen the evidence for enhanced actomyosin activity.

      This is a good suggestion and we have extensively tried different anti-P-Myl antibodies (and protocols), but did not get them to work reliably on zebrafish embryos. We therefore rely on published work that has established the correlation between the recruitment of myosin light chain and increased actomyosin tension (Fernandez-Gonzalez et al., 2009; Munjal et al., 2015).

      Reviewer #2 (Recommendations for the authors):

      (1) Figure 1a is not described/mentioned in the Results.

      The have corrected this (lines 102-108). We have also added measurements to better present the different dynamics of F-actin (UCHD) and ZO1 within the JBL and the relative endothelial cell movements (see Figure 1b), as suggested by reviewer#1.

      (2) In Figure 3a, the authors claim that Arp2/3 is deposited at the distal side of the junction ring. While it is clear where the proximal junction is (ZO1-rich), the distal junction is less so (hardly any ZO1). It is therefore difficult to agree based on this time-lapse imaging that Arpc1b-Venus is at the distal junction. Can the authors please include panels showing merged channels and annotate where the proximal and distal junctions are?

      The activation of the Arp2/3 complex and the formation of the distal junction are sequential events. We see that ArpC1b oscillates with an accumulation at the onset and during JBL protrusion. In contrast, the distal junction is formed when the protrusive activity has been stopped. One caveat of the analysis shown in Figure 3a is that our ZO1 reporters label the distal junction only very weakly – this is in particular the case for the ZO1-tdTomato knock-in. The distal junction is better visible in VE-cadherin and UCHD reporters, as shown in Figures 5 to 7.

      (3) In Figures 3b and c, it is also difficult to distinguish proximal and distal junctions in these images. Please mark the boundaries in the image panels (Figure 3b) and indicate on the x-axis where the proximal and distal junctions are (Figure 3c).

      In Figure 3b, we show ArpC1b-Venus and mRuby-UCHD side-by-side. This Figure demonstrates that the Arp2/3 complex maintains its position at the front of the JBL during the protrusive phase (always distal to the UCHD signal). The imaging is done at very short intervals (1/30sec), which makes it difficult to follow entire oscillations due to photo-bleaching of the ArpC1b reporter.

      (4) The treatment of CK666 resulted in perturbed localization of Arpc1b-Venus. Therefore, the inhibition of junctional elongation can also be explained by the mislocalization of Arp2/3, rather than the inhibition of Arp2/3 activity at the junctions. Can the authors discuss this or perform another experiment that is more specific to manipulating Arp2/3 activity?

      CK666 is a well-established inhibitor of Arp2/3. Structural and functional analyses have shown that CK666 interferes with the interaction between Arp2 and Arp3, thereby preventing the activation of the complex (Hetrick et al., 2013; Padrick et al., 2011). We therefore conclude that the phenotypes we observe in CK666 treatment are due to Arp2/3 inhibition.

      It is possible that CK666 prevents ArpC1b binding to the Arp2/3 complex. However, published work suggests that ArpC1b can bind to Arp2/3 also in its inactive state (Chou et al., 2022). Thus, we can only speculate why we lose localization ArpC1b under CK666. We prefer not to do so.

      (5) In Figures 5d and 6c, is the quantification of Myl9 intensity of one cell only? If so, can the authors show the dynamics of average Myl9 intensity i) between forwarding and non-forwarding JBL poles and ii) as the proximal and distal junctions merge several endothelial cells?

      Figure 5c/d depicts two interacting cells, expressing different levels of Myl9a-EGFP. This is a rare experimental situation and we managed to image only this example. We quantified the average signal at both poles of the junctional ring within a region of interest. The newly added error bars indicate the standard deviation between pixel intensities within the ROI. The analysis has been done on immunofluorescent images, therefore a dynamic analysis over time is not possible.

      In Figure 6c, we have analyzed the Myl9b-mCherry intensities and find that it is redistributed during a JBL cycle. The spatial distribution is evident from the heat-map and we have not included a standard deviation. Myl9b-mCherry levels are very heterogenous and is not possible to quantify intensities across samples. We have, however, included four more examples of Myl9b-mCherry distribution in Supplementary Figure 4. The patterns observed in these samples are consistent with those in Figure 6.

      (6) Figure 5. The 'f' in the figure legend should be 'e' since there is no panel 'f'.

      We have corrected this.

      (7) Figure 7. As the boundaries for proximal and distal junctions are not always clear, especially when Cdh5 appears as clusters, how do you determine where the two junctions are in order to measure the interjunctional space? Please offer a clearer explanation in the Methods.

      We have added the following in the M&M. “Junctional merging tracking Speed of junctional merge was evaluated by monitoring isolated junctional rings during DLAV formation. Inhibitor treatment Y-27632 (75 μM) or DMSO (1%) were applied 30 min before mounting. The same concentrations of chemicals were applied to the low-melting-point agarose mounting medium and the E3 medium on top of it before imaging and imaging the junctions for 10-15 min on an Olympus SpinSR spinning disc microscope. Distances were measured using Fiji software. In each frame, the interjunctional distance was defined as the maximum distance between the proximal and distal junctions. A line was manually drawn between the proximal and distal junctions in Fiji, and its length was recorded. The same proximal and distal junction landmarks were used consistently across all time points.”

      (8) One would think that upon the inhibition of junctional mergence (by ROCK inhibition), actin polymerization would persist to push the distal junction forward to elongate the JBL. However, there is instead a decrease in junctional elongation (Figure 7b). Can the authors speculate why? Additionally, junction elongation can probably be achieved by continuous "pushing" of the distal junction alone (through actin polymerization). Can the authors speculate why there is a need/what is the benefit of merging proximal and distal junctions for junction elongation?

      These are all very interesting questions, but they are quite complex and would require extensive and speculative answers, which is outside the scope of this study. Nevertheless, here are a few quick thoughts on these issues.

      (1) When endothelial cells elongate, they have to overcome tensile forces at the junctions (generated by the subjunctional actomyosin belt). JBL are providing a tractive and deforming force, which overcomes the tensile force and thus promotes junctional elongation.

      (2) The distal junction is then providing an anchor to which the actin cytoskeleton can attach. The space between proximal and distal junction becomes a compartment of local actomyosin contraction, which provides the force for the ratchet to move the proximal junction forward  junctional mergence.

      (3) Thus, it is not the protrusion (pushing) itself that elongates the cell but the elongation of the junction (driven by actomyosin contraction)!

      (4) The maintenance of the proximal junction is most likely needed to ensure endothelial integrity during the JBL cycles.

      (5) How the frequency and the size of JBLs is regulated is not known. One possible player that might be involved is an internal clock mechanism (e.g. a feedback loop via small GTPases (such as Rac)  Arp2/3 regulation). Another possibility is that JBL size is limited by it sweeping up basally localized VE-cadherin (in cis-configuration). Increasing cell-cell adhesion (by VE-cad trans-interactions between the JBL and the underlying cell) eventually stop the protrusion. It is also possible that an cell-autonomously controlled mechanism of F-actin polymerization (actin pulses) are involved in the regulation of the JBC cycle length.

      (9) The animation showing the molecular mechanism of JBL function during endothelial junction elongation (Video 25) is very helpful in understanding the dynamic coupling between junctional proteins, actomyosin cytoskeleton, and junction remodelling. However, I wonder why there are no Myosin II proteins binding to the actin bundles during the merging of proximal and distal junctions (between 0:25 and 0:28), since this is one of the main findings by the authors in this study.

      Since we show two JBL cycles, we want to spread the information over both of them.

      References:

      Cao, J. and Schnittler, H. (2019). Putting VE-cadherin into JAIL for junction remodeling. J. Cell Sci. 132.

      Cao, J., Ehling, M., März, S., Seebach, J., Tarbashevich, K., Sixta, T., Pitulescu, M. E., Werner, A. C., Flach, B., Montanez, E., et al. (2017). Polarized actin and VE-cadherin dynamics regulate junctional remodelling and cell migration during sprouting angiogenesis. Nat. Commun. 8, 1–20.

      Chou, S. Z., Chatterjee, M. and Pollard, T. D. (2022). Mechanism of actin filament branch formation by Arp2/3 complex revealed by a high-resolution cryo-EM structure of the branch junction. Proc. Natl. Acad. Sci. U. S. A. 119, e2206722119.

      Fernandez-Gonzalez, R., Simoes, S. de M., Röper, J. C., Eaton, S. and Zallen, J. A. (2009). Myosin II Dynamics Are Regulated by Tension in Intercalating Cells. Dev. Cell 17, 736–743.

      Hetrick, B., Han, M. S., Helgeson, L. A. and Nolen, B. J. (2013). Small molecules CK-666 and CK-869 inhibit actin-related protein 2/3 complex by blocking an activating conformational change. Chem. Biol. 20, 701–712.

      Kipcke, J. P., Odenthal-Schnittler, M., Aldirawi, M., Franz, J., Bojovic, V., Seebach, J. and Schnittler, H. (2025). TNF-α induces VE-cadherin-dependent gap/JAIL cycling through an intermediate state essential for neutrophil transmigration. Front. Immunol. 16,.

      Law, A. L., Jalal, S., Pallett, T., Mosis, F., Guni, A., Brayford, S., Yolland, L., Marcotti, S., Levitt, J. A., Poland, S. P., et al. (2021). Nance-Horan Syndrome-like 1 protein negatively regulates Scar/WAVE-Arp2/3 activity and inhibits lamellipodia stability and cell migration. Nature Communications 2021 12:1 12, 5687-.

      Malchow, J., Eberlein, J., Li, W., Hogan, B. M., Okuda, K. S. and Helker, C. S. M. (2024). Neural progenitor-derived Apelin controls tip cell behavior and vascular patterning. Sci. Adv. 10, 1174.

      Munjal, A., Philippe, J. M., Munro, E. and Lecuit, T. (2015). A self-organized biomechanical network drives shape changes during tissue morphogenesis. Nature 524, 351–355.

      Paatero, I., Sauteur, L., Lee, M., Lagendijk, A. K., Heutschi, D., Wiesner, C., Guzmán, C., Bieli, D., Hogan, B. M., Affolter, M., et al. (2018). Junction-based lamellipodia drive endothelial cell rearrangements in vivo via a VE-cadherin-F-actin based oscillatory cell-cell interaction. Nat. Commun. 9,.

      Padrick, S. B., Doolittle, L. K., Brautigam, C. A., King, D. S. and Rosen, M. K. (2011). Arp2/3 complex is bound and activated by two WASP proteins. Proc. Natl. Acad. Sci. U. S. A. 108, E472–E479.

      Sauteur, L., Krudewig, A., Herwig, L., Ehrenfeuchter, N., Lenard, A., Affolter, M. and Belting, H. G. (2014). Cdh5/VE-cadherin promotes endothelial cell interface elongation via cortical actin polymerization during angiogenic sprouting. Cell Rep. 9, 504–513.

      Seebach, J., Klusmeier, N. and Schnittler, H. (2021). Autoregulatory “Multitasking” at Endothelial Cell Junctions by Junction-Associated Intermittent Lamellipodia Controls Barrier Properties. Front. Physiol. 11,.

      Taha, A. A., Taha, M., Seebach, J. and Schnittler, H. J. (2014). ARP2/3-mediated junction-associated lamellipodia control VE-cadherin-based cell junction dynamics and maintain monolayer integrity. Mol. Biol. Cell 25, 245–256.

    1. Reviewer #2 (Public review):

      Summary:

      The authors analyzed the temporal dynamics of gene expression patterns within the inflammatory response transcriptome following TNF stimulation, and proposed that the splicing rate of certain introns is a key mechanism of regulating mature mRNA expression rate.

      Strengths:

      The measurement strategy is generally well-designed to understand the core question of splicing rate and gene expression. The following computation analysis, as well as the mutation or repair studies, further supported the claims. The writing and presentation of the results are also generally clear and easy to follow. I think this manuscript will be of interest to a wide audience.

      Weaknesses: 

      I do have some questions regarding some of the results and conclusions, and I think either more analysis or more explanation and discussion can make the claims more solid. Please see below for details:<br /> <br /> (1) On the hybrid capture method and the RNA coverage results: The strategy of enriching for the last exon before sequencing does have significance in linking pre-mRNA and mature mRNA. If I understand correctly, this enriches for pre-mRNA molecules that are about to finish the full-length elongation of RNA polymerase. However, is this strategy biased towards measuring the splicing rate variation on introns closer to the 3-prime end? For example, if a gene takes 5 minutes for the RNA polymerase to elongate through the full length of the gene, for intron #1 that's very close to the 5' end, you can't tell if it takes 20s to be spliced out or 4 minutes, as both will show as fully spliced out in the sequencing library. In other words, for introns near the 5' end, a consistent "CoSI=1" pattern in the data doesn't necessarily suggest a true consistent fast splicing of that intron. Do you observe any general pattern of the measured "slowliness" in relation to the 5'-3' location of the introns? If so, should the 5' introns be specially considered or even excluded from certain analyses that use all introns?<br /> <br /> (2) Following on my last point, it may benefit the readers if the author can provide a more detailed comparison of possible sequencing library construction choices. For example, is it feasible to also enrich for other exons for the sequencing library, etc?<br /> <br /> (3) Figure 1C: Are there biological replicates, and should there be error bars and statistics on the plot? Similarly, in places like Figure 2, Supplemental Figure 4C, Supplemental Figure 6, etc., is there any statistical analysis that can be done to show if the claimed differences are statistically significant?<br /> <br /> (4) The logic behind measuring the half-lives of introns seems a little unclear to me.  From the time-dependent RNA coverage plots in Figure 2, it seems that, if we assume a constant transcription elongation rate, then the splicing rate of a specific intron can vary across time after TNF stimulation, as represented by the temporal change of CoSI values, or the heights of the coverage plot relative to neighboring exons. This means the splicing rate or half-life of an intron is not necessarily constant but may be time-dependent, at least in the case of TNF stimulation. Shouldn't the half-life measurements be designed in a way to measure the half-life at multiple time points after TNF stimulation? And maybe the measured half-lives of some introns will show as time-dependent?<br /> <br /> (5) In Supplemental Figure 6, the interpretation is a little confusing to me: If delayed splicing is causing delayed expression of the corresponding gene, shouldn't the non-immediate gene groups (early/intermediate/Late) have low CoSI beginning from the early time points (e.g. 4 minutes)? Why does the slowdown of splicing seem to peak at a later time point? Does it mean immediately after TNF stimulation, there's a different mechanism in delaying the expression of the non-immediate gene groups? Maybe it's better to have more explanation or use a different visualization to show what non-immediate gene groups are experiencing at very early time points.<br /> <br /> (6) On the fine-tuning of the deep sequence model: it's a little unclear whether the input and output are time-dependent. It's stated that expression at multiple time points is used for training, but it's unclear whether the model outputs time-dependent expression patterns and whether the time information is used as input.

    1. Author response:

      The following is the authors’ response to the previous reviews

      eLife Assessment

      This study presents results supporting a model that tumorous germline stem cells (GSCs) in the Drosophila ovary mimic the stem cell niche and inhibit the differentiation of neighboring cells. The valuable findings show that GSC tumors often contain non-mutant cells whose differentiation is suppressed by the GSC tumorous cells. However, the evidence showing that the GSC tumors produce BMP ligands to suppress differentiation of non-mutant cells is incomplete due to concerns about the new HCR data.

      Thanks for this assessment. All concerns raised by the reviewers regarding the HCR data and others are followed by our responses below.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This preprint from Shaowei Zhao and colleagues presents results that suggest tumorous germline stem cells (GSCs) in the Drosophila ovary mimic the ovarian stem cell niche and inhibit the differentiation of neighboring non-mutant GSC-like cells. The authors use FRT-mediated clonal analysis driven by a germline-specific gene (nos-Gal4, UASp-flp) to induce GSC-like cells mutant for bam or bam's co-factor bgcn. Bam-mutant or bgcn-mutant germ cells produce tumors in the stem cell compartment (the germarium) of the ovary (Fig. 1). These tumors contain non-mutant cells - termed SGC for single-germ cells. 75% of SGCs do not exhibit signs of differentiation (as assessed by bamP-GFP) (Fig. 2). The authors demonstrate that block in differentiation in SGC is a result of suppression of bam expression (Fig. 2). They present data suggesting that in 73% of SGCs BMP signaling is low (assessed by dad-lacZ) (Fig. 3) and proliferation is less in SGCs vs GSCs. They present genetic evidence that mutations in BMP pathway receptors and transcription factors suppress some of the non-autonomous effects exhibited by SGCs within bam-mutant tumors (Fig. 4). They show data that bam-mutant cells secrete Dpp, but this data is not compelling (see below) (Fig. 5). They provide genetic data that loss of BMP ligands (dpp and gbb) suppresses the appearance of SGCs in bam-mutant tumors (Fig. 6). Taken together, their data support a model in which bam-mutant GSC-like cells produce BMPs that act on non-mutant cells (i.e., SGCs) to prevent their differentiation, similar to what in seen in the ovarian stem cell niche. This preprint from Shaowei Zhao and colleagues presents results that suggest tumorous germline stem cells (GSCs) in the Drosophila ovary mimic the ovarian stem cell niche and inhibit the differentiation of neighboring non-mutant GSC-like cells. The authors use FRT-mediated clonal analysis driven by a germline-specific gene (nos-Gal4, UASp-flp) to induce GSC-like cells mutant for bam or bam's co-factor bgcn. Bam-mutant or bgcn-mutant germ cells produce tumors in the stem cell compartment (the germarium) of the ovary (Fig. 1). These tumors contain non-mutant cells - termed SGC for single-germ cells. 75% of SGCs do not exhibit signs of differentiation (as assessed by bamP-GFP) (Fig. 2). The authors demonstrate that block in differentiation in SGC is a result of suppression of bam expression (Fig. 2). They present data suggesting that in 73% of SGCs BMP signaling is low (assessed by dad-lacZ) (Fig. 3) and proliferation is less in SGCs vs GSCs. They present genetic evidence that mutations in BMP pathway receptors and transcription factors suppress some of the non-autonomous effects exhibited by SGCs within bam-mutant tumors (Fig. 4). They show data that bam-mutant cells secrete Dpp, but this data is not compelling (see below) (Fig. 5). They provide genetic data that loss of BMP ligands (dpp and gbb) suppresses the appearance of SGCs in bam-mutant tumors (Fig. 6). Taken together, their data support a model in which bam-mutant GSC-like cells produce BMPs that act on non-mutant cells (i.e., SGCs) to prevent their differentiation, similar to what in seen in the ovarian stem cell niche.

      Strengths:

      (1) Use of an excellent and established model for tumorous cells in a stem cell microenvironment

      (2) Powerful genetics allow them to test various factors in the tumorous vs non-tumorous cells

      (3) Appropriate use of quantification and statistics

      Thank you for your valuable comments, and we greatly appreciate them.

      Weaknesses:

      (1) What is the frequency of SGCs in nos>flp; bam-mutant tumors? For example, are they seen in every germarium, or in some germaria, etc or in a few germaria.

      This concern was addressed in the rebuttal. The line number is 106, not line 103.

      (2) Does the breakdown in clonality vary when they induce hs-flp clones in adults as opposed to in larvae/pupae?

      This concern was addressed in the rebuttal. However, these statements are no on lines 331-335 but instead starting on line 339. Please be accurate about the line numbers cited in the rebuttal. They need to match the line numbers in the revised manuscript.

      We have rechecked the line numbers and confirmed that the mismatch arose from the Word-to-PDF conversion process on the eLife website. As this issue has recurred and reviewers’ file-format preferences are unknown to us, we have added a clarifying note at the beginning of each response letter: “Please note that the line numbers cited refer to the revised manuscript in the Microsoft Word format”.

      (3) Approximately 20-25% of SGCs are bam+, dad-LacZ+. Firstly, how do the authors explain this? Secondly, of the 70-75% of SGCs that have no/low BMP signaling, the authors should perform additional characterization using markers that are expressed in GSCs (i.e., Sex lethal and nanos).

      The authors did not perform additional staining for GSC-enriched protein like Sex lethal and nanos.

      The 70-75% of SGCs that have low BMP signaling display the following characteristics: 1) dot-like spectrosomes, 2) positivity for Dad-lacZ, and 3) absence of bamP-GFP expression. This combination of traits is sufficient to classify them as GSC-like cells. Neither Sex lethal nor Nanos is expressed exclusively in GSCs (Chau et al., 2009; Li et al., 2009), rendering them unsuitable for distinguishing GSC-like from cystoblast-like cells.

      (4) All experiments except Fig. 1I (where a single germarium with no quantification) were performed with nos-Gal4, UASp-flp. Have the authors performed any of the phenotypic characterizations (i.e., figures other than figure 1) with hs-flp?

      In the rebuttal, the authors stated that they used nos>flp for all figures except for Fig. 1I. It would be more convincing for them to prove in Fig. 1 than there is not phenoytpic difference between the two methods and then switch to the nos>FLP method for the rest of the paper.

      We appreciate this suggestion. These data are included in Figure 1-figure supplement 3 in the revised manuscript.

      (5) Does the number of SGCs change with the age of the female? The experiments were all performed in 14-day old adult females. What happens when they look at young female (like 2-day old). I assume that the nos>flp is working in larval and pupal stages and so the phenotype should be present in young females. Why did the authors choose this later age? For example, is the phenotype more robust in older females? or do you see more SGCs at later time points?

      The authors did not supply any data to prove that the clones were larger in 14-day-old flies than in younger flies. Additionally, the age of "younger" flies was not specified. Therefore, the authors did not satisfactorily answer my concern.

      We appreciate this critical comment. Figure 1J includes the SGC phenotype data from 1-, 7-, and 14-day-old flies. Both 1- and 7-day-old flies are younger flies in our analyses. The evidence that germline clones were larger in 14-day-old flies than in younger flies was provided in Figure 1-figure supplement 2 in the revised manuscript.

      (6) Can the authors distinguish one copy of GFP versus 2 copies of GFP in germ cells of the ovary? This is not possible in the Drosophila testis. I ask because this could impact on the clonal analyses diagrammed in Fig. 4A and 4G and in 6A and B. Additionally, in most of the figures, the GFP is saturated so it is not possible to discern one vs two copies of GFP.

      In the rebuttal, the authors stated that they cannot differential one vs two copies of GFP. They used other clone labeling methods in Fig. 4 and 6. I think that the authors should make a statement in the manuscript that they cannot distinguish one vs two copies of GFP for the record.

      Thank you for this suggestion. Such statement has been added in the revised manuscript (Lines 177-178).

      (7) More evidence is needed to support the claim of elevated Dpp levels in bam or bgcn mutant tumors. The current results with dpp-lacZ enhancer trap in Fig 5A,B are not convincing. First, why is the dpp-lacZ so much brighter in the mosaic analysis (A) than in the no-clone analysis (B); it is expected that the level of dpp-lacZ in cap cells should be invariant between ovaries and yet LacZ is very faint in Fig. 5B. I think that if the settings in A matched those in B, the apparent expression of dpp-lacZ in the tumor would be much lower and likely not statistically significantly. Second, they should use RNA in situ hybridization with a sensitive technique like hybridization chain reactions (HCR) - an approach that has worked well in numerous Drosophila tissues including the ovary.

      The HCR FISH in Fig.5 of the revised manuscript needs an explanation for how the mRNA puncta were quantified. Currently, there is no information in the methods. What is meant but relative dpp levels. I think that the authors should report in and unbiased manner "number" of dpp or gbb puncta in TFs. For the germaria, I think that they should report the number of puncta of dpp or gbb divide by the total area in square pixels counted. Additionally, the background fluorescence is noticeably much higher in bamBG/delta86 germaria, which would (falsely) increase the relative intensity of dpp and gbb in bam mutants. Although, I commend the authors for performing HCR FISH, these data are still not convincing to me.

      We appreciate these critical comments. Due to variable puncta sizes and frequent clustering in TF and cap cells (see Figure 5A, C), direct quantification of puncta number was unreliable. Therefore, we quantified mean fluorescence intensity instead, as described in the revised figure legend of Figure 5 (Lines 603-604). In Author response image 1 1A, B (modified from Figure 5A, C) , magenta ovals indicate empty background fluorescence areas, which appear similar between w<sup>1118</sup> (wild-type control) and bam<sup>-/-</sup> germaria. In Author response image 1, the yellow oval outlines a neighboring germarium, not an empty area (see the DAPI channel).

      Author response image 1.

      In situ-HCR results of dpp and gbb in wild-type and bam mutant germaria. Magenta ovals indicate empty areas displaying only background fluorescence. In panel (B), the yellow oval outlines a neighboring germarium, not an empty area (see the DAPI channel below).

      (8) In Fig 6, the authors report results obtained with the bamBG allele. Do they obtain similar data with another bam allele (i.e., bamdelta86)?

      The authors did not try any experiments with the bamdelta86 allele, despite this allele being molecularly defined, where the bamBG allele is not defined.

      While we agree that repeating the experiments in Figure 6 with bam<sup>Δ86</sup> would be helpful, our mosaic analysis strategy for two genes on different chromosome arms is technically complex (see genotypes in Source data 1). Switching from bam<sup>BG</sup> to bam<sup>Δ86</sup> would necessitate extensive and time-consuming genetic recombination. Given that both alleles induce the SGC phenotype indistinguishably (Figure 1J), we believe that repeating these experiments with bam<sup>Δ86</sup> would not alter our key conclusion. We appreciate your understanding regarding this technical complexity.

      Reviewer #2 (Public review):

      In the current version, Zhang et al. have made substantial improvements to the manuscript. It is now easier to read, and the data are more solid compared with the previous version, supporting their conclusion that tumor GSCs secrete stemness factors (BMPs and Dpp) to suppress the differentiation of neighboring wild-type GSCs. This study should benefit a broad readership across developmental biology, germ cell biology, stem cell biology, and cancer biology.

      Thank you for your valuable comments, and we greatly appreciate them.

      However, the following suggestions may further improve the clarity and rigor of the research content:

      (1) Clarification of sample size (n).

      Each germarium can contain highly variable numbers of SGCs, sometimes reaching 50-100. When reporting "n" values, the authors are encouraged to also indicate the number of germaria analyzed. For example, in lines 126-128:

      "Notably, 74% of SGCs (n = 132) were GFP-negative, while the remaining 26% were GFP-positive (Figure 2B, C). This suggests that SGCs can be categorized into two distinct groups: those resembling GSCs (GSC-like) and those resembling cystoblasts (cystoblast-like)." Please clarify how many germaria were examined to obtain n = 132.

      We appreciate this comment. In 14-day-old fly ovaries, each germarium that met our criterion for quantifying the SGC phenotype contains approximately 1.5 SGCs (see Figure 1K). For the specific analysis of the “132” SGCs presented in Figure 2C, we did not record the number of germaria from which they originated.

      In addition, it is unclear whether the authors intend to suggest that the GFP-negative SGCs are GSC-like or cystoblast-like; this point should be clarified.

      Thank you for this suggestion. We intend to suggest that the bamP-GFP-negative SGCs are GSC-like, which information has been added in the revised manuscript (Line 129).

      (2) Improvement of Fig. 6 in situ hybridization images.

      The in situ hybridization images in Fig. 6 are not fully convincing. The control images, in particular, would benefit from higher resolution and enlarged views of the germarium region.

      Thank you for this valuable suggestion. The enlarged views of both the control and bam<sup>-/-</sup> germarium regions were included in Figure 5A, C in the revised manuscript.

      In panel C, abundant signals are also present outside the germarium, which may complicate interpretation and should be clarified or controlled for.

      In the right panel of Figure 5C, the abundant signals noted by the reviewer originate from neighboring germaria (see the DAPI channel), not from empty areas, which would be expected to show only background fluorescence. For more details, please refer to our response to Question (7) raised by Reviewer #1.

      Alternatively, the authors could strengthen the in situ analysis by using bam mutants or bam dpp / bam gbb double mutants as controls to better define signal specificity.

      We appreciate this comment. Homozygous dpp or gbb mutants are lethal, precluding the generation of dpp bam or gbb bam double-mutant flies. Additionally, the GFP signal was drastically reduced during our HCR processing, preventing mosaic clone analysis.

      Reviewer #3 (Public review):

      Zhang et al. investigated how germline tumors influence the development of neighboring wild-type (WT) germline stem cells (GSC) in the Drosophila ovary. They report that germline tumors generated by differentiation-arrested mutations (bam and bgcn) inhibit the differentiation of neighboring WT GSCs by arresting them in an undifferentiated state, resulting from reduced expression of the differentiation-promoting factor Bam. They find that these tumor cells produce low levels of the niche-associated signaling molecules Dpp and Gbb, which suppress bam expression and consequently inhibit the differentiation of neighboring WT GSCs non-cell-autonomously. Based on these findings, the authors propose that germline tumors mimic the niche to suppress the differentiation of the neighboring wild-type germline stem cells.

      Strengths:

      The study uses a well-established in vivo model to address an important biological question concerning the interaction between germline tumor cells and wild-type (WT) germline stem cells in the Drosophila ovary. If the findings are substantiated, this study could provide valuable insights that are applicable to other stem cell systems.

      Thank you for your valuable comments, and we greatly appreciate them.

      Weaknesses:

      The authors have addressed some of my concerns in the revised submission. However, the data presented do not allow the authors to distinguish whether the failed differentiation of WT stem cells/germline cells results from "arrested differentiation due to the loss of the differentiation niche" or from "direct inhibition by tumor-derived expression of niche-associated molecules Dpp and Gbb".

      Blocking Dpp or Gbb secretion specifically from germline tumor cells promoted differentiation of neighboring wild-type germ cells (Figure 6). This indicates that BMP ligands secreted by germline tumors are required to inhibit this differentiation. However, we cannot rule out the possibility that disruption of the differentiation niche also contributes to the SGC phenotype, a point highlighted in the manuscript (Line 204).

      The critical supporting data, HCR in situ results, are not sufficiently convincing.

      Below, we provide a point-by-point reply addressing each of your specific recommendations.

      Recommendations for the authors:

      Reviewer #3 (Recommendations for the authors):

      It's a surprising that the authors failed to induce germline tumors at the adult stage, as this has been reported by many labs and would allow for time course analysis of SGC phenotype. As a result, the data in this manuscript address only events occurring after the germline tumor formation (with clonal induction at larval stage) and and focus on the already presene "arrested wild-type germ cells", without providing insight into the process of by which these arrested germ cells are formed.

      In our hands, inducing germline clones by the hs-FLP method at the adult stage was efficient in males but not in females, despite subjecting adult flies to intensive heat-shock at 37°C.

      The HCR in situ data exhibit a high background.

      Regarding the background issue, please see our response to Reviewer #1’s Question (7).

      First, the signal appears stronger in TF cells than in cap cells.

      As demonstrated by Li et al. (Li et al., 2016), dpp-lacZ (P4-lacZ) signals are also stronger in TF cells than in cap cells (see their Figure 4D').

      Second, both dpp and gbb are detected broadly in somatic cells including escort cells. These observations are inconsistent with published data.

      As shown in Figure 5A and C, dpp and gbb were detected broadly in somatic cells of bam<sup>-/-</sup> germaria, but not in those of w<sup>1118</sup> (wild-type) controls. To our knowledge, no previous study has reported the expression pattern of these ligands in a bam mutant background.

      To demonstrate the tumor-derived dpp and gbb, the HCR in situ analysis could be performed in the germarium with mosaic clones. If these niche-associated molecules are indeed expressed in tumor cells, the authors should observe a mosaic expression pattern of these molecules, with signal "ON" in tumor cells and "OFF" in neighbouring arrested germ cells.

      This is a great idea and was indeed our original approach. However, GFP signal was drastically reduced during our HCR processing, ultimately precluding mosaic clone analysis.

      References

      Chau, J., Kulnane, L.S., and Salz, H.K. (2009). Sex-lethal facilitates the transition from germline stem cell to committed daughter cell in the Drosophila ovary. Genetics 182, 121-132.

      Li, X., Yang, F., Chen, H., Deng, B., Li, X., and Xi, R. (2016). Control of germline stem cell differentiation by Polycomb and Trithorax group genes in the niche microenvironment. Development 143, 3449-3458.

      Li, Y., Minor, N.T., Park, J.K., McKearin, D.M., and Maines, J.Z. (2009). Bam and Bgcn antagonize Nanos-dependent germ-line stem cell maintenance. Proc Natl Acad Sci U S A 106, 9304-9309.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      The authors Hall et al. establish a purification method for snake venom metalloproteinases (SVMPs). By generating a generic approach to purify this divergent class of recombinant proteins, they enhance the field's accessibility to larger quantities of SVMPs with confirmed activity and, for some, characterized kinetics. In some cases, the recombinant protein displayed comparable substrate specificity and substrate recognition compared to the native enzyme, providing convincing evidence of the authors' successful recombinant expression strategy. Beyond describing their route towards protein purification, they further provide evidence for self-activation upon Zn2+ incubation. They further provide insights on how to design high-throughput screening (HTS) methods for drug discovery and outline future perspectives for the in-depth characterization of these enzyme classes to enable the development of novel biomedical applications.

      Strengths:

      The study is well-presented and structured in a compelling way. The purification strategy results in highly pure protein products, well characterized by size exclusion chromatography, SDS page as well as confirmed by mass spectrometry analysis. Further, a significant portion of the manuscript focuses on enzyme activity, thereby validating function. Particularly convincing is the comparability between recombinant vs. native enzymes; this is successfully exemplified by insulin B digestion. By testing the fluorogenic substrate, the authors provide evidence that their production method of recombinant protein can open up possibilities in HTS. Since their purification method can be applied to three structurally variable SVMP classes, this demonstrates the robust nature of the approach.

      We thank the reviewer for their positive assessment of our work.

      Weaknesses:

      The universal applicability of the approach could be emphasized more clearly. The potential for this generic protocol for recombinant SVMP zymogen production to be adapted to other SVMPs is somewhat obscured by the detailed optimization steps. A general schematic overview would strengthen the manuscript, presented as a final model, to illustrate how this strategy can be extended to other targets with similar features. Such a schematic might, for example, outline the propeptide fusion design, including its tags, relevant optimizations during expression, lysis, purification (e.g., strategies for metal ion removal and maintenance of protease inactivity), as well as the controllable auto-activation.

      In the revised version of the manuscript, we moved the detailed description of the optimisation of SVMP expression, including mature SVMP expression, Marimastat addition, active site mutations and fusion of propeptides, into the supplement as supplementary text. We hope this improves the clarity and flow. As suggested, we now include a new figure outlining the SVMP production strategy and optimisation steps in the revised manuscript (new Figure S1).

      The product obtained from the purification protocol appears to be a heterogeneous mixture of selfactivated and intact protein species. The protocol would benefit from improved control over the selfactivation process. The Methods section does not indicate whether residual metal ions were attempted to be removed during the purification, which could influence premature activation.

      We agree that improved control of self-activation would be desirable. However, there is an issue: Previous studies reported that (1) SVMP zymogens are processed within secretory cells of the venom gland (Portes-Junior et al., 2014), and (2) mature SVMPs accumulate in secretory vesicles during venom production (Carneiro et al., 2002). Accordingly, preventing the auto-processing of SVMP zymogens is difficult to achieve because this would require Zn<sup>2+</sup> depletion within the insect cells during production which would result in cytotoxicity. We have included this information in the updated Discussion section of the revised manuscript.

      Additionally, it has not been discussed whether the shift to pH 8 in the purification process is necessary from the initial steps onwards, given that a lower pH would be expected to maintain enzyme latency.

      The shift to pH 8 is required for the affinity purification of the SVMP zymogens from the medium, involving the poly-histidine-tag and immobilized metal affinity chromatography (IMAC). At lower pH, the histidines would become protonated, preventing binding of the His-tag to the column. Thus, with the His-tag the shift to pH 7.5 or pH 8 is necessary.

      The characterization of PIII activity using the fluorogenic peptide effectively links the project to its broader implications for drug design. However, the absence of comparable solutions for PI and PII classes limits the overall scope and impact of the finding.

      We agree that such assays would be extremely useful. However, the development of fluorescence based high-throughput assays to test for PI and PII SVMP activity is beyond the scope of this study. Here, our overarching objective is to report a broadly applicable production method for PI, PII and PIII SVMPs.

      Overall, the authors successfully purified active SVMP proteins of all three structurally diverse classes in high quality and provided convincing evidence throughout the manuscript to support their claims. The described method will be of use for a broader community working with self-activating and cytotoxic proteases.

      Thank you.

      Reviewer #2 (Public review):

      Summary:

      The aim of the study by Hall et al. was to establish a generic method for the production of Snake Venom Metalloproteases (SVMPs). These have been difficult to purify in the mg quantities required for mechanistic, biochemical, and structural studies.

      Strengths:

      The authors have successfully applied the MultiBac system and describe with a high level of detail the downstream purification methods applied to purify the SVMP PI, PII, and PIII. The paper carefully presents the non-successful approaches taken (such as expression of mature proteins, the use of protease inhibitors, prodomain segments, and co-expression of disulfide-isomerases) before establishing the construct and expression conditions required. The authors finally convincingly describe various activity assays to demonstrate the activity of the purified enzymes in a variety of established SVMP assays.

      We thank the reviewer for their positive assessment of our work.

      Weaknesses:

      The manuscript suffers from a lack of bottoming out and stringent scientific procedures in the methodology and the characterization of the generated enzymes.

      As an example, a further characterization of the generated protein fragments in Figure 3 by intact mass spectroscopy would have aided in accurate mass determination rather than relying on SEC elution volumes against a standard. Protein shape and charge can affect migration in SEC.

      We agree that intact MS would be useful to determine the mass of the produced SVMPs. In this manuscript, we performed SEC as a purification step, removing aggregates. Furthermore, SEC allowed determining if the SVMPs form monomers or dimers. MS characterisation of intact SVMPs (and their PTMs) is not trivial and beyond the scope of this manuscript (see below).

      Also, the analysis of N-linked glycosylation demonstrates some reactivity of PIII to PNGase F, but fails to conclude whether one or more sites are occupied, or whether other types of glycosylation is present. Again, intact mass experiments would have resolved such issues.

      We concur that glycosylation of SVMPs is an important question. However, analysing the glycosylation of the SVMPs is beyond the scope of this manuscript; it is actually a project on its own: Intact MS can indeed provide information on glycosylation but is not very precise. Unambiguous assignment of the number and occupancy of glycosylation sites is more challenging, especially for large, glycosylated proteins such as our PIII SVMP zymogen. In practice, confident mapping of glycosylation sites would require peptide-level mass spectrometry following enzymatic digestion (Trypsin and Multi-Enzymatic Limited Digestion, ideally). Sample preparation, method optimization, MS acquisition, and data analysis together would require a significant investment. Moreover, we do not have access to the native PIII SVMP from Echis carinatus sochureki venom - this is the main point of our manuscript: we describe a protocol to produce SVMPs which could not be purified from venom. Therefore, a comparison of the glycosylation of the recombinant SVMP and the native SVMP cannot be performed unfortunately (see below).

      The activity assays in Figure 4 are not performed consistently with kinetic assays and degradation assays performed for some, but not all, enzymes, and there is no Echis ocellatus comparison in Figure 4h.

      This is correct. The suggested control experiment is not possible for the PII SVMP and PIII SVMP because we cannot purify the native PII and PIII SVMPs from Echis venom. We have highlighted this information in the revised manuscript in the insulin B degradation section.

      Overall, whilst not affecting the main conclusion, this leaves the reader with an impression of preliminary data being presented. For consistency, application of the same assays to all enzymes (high-grade purified) would have provided the reader with a fuller picture.

      In the revised manuscript, we included new data showing the requested characterisations of all three SVMPs.

      We have included the respective assays in Figure 5 and Supplementary Figure S11. In the original manuscript, we had omitted these assays as the data show no enzymatic activity in the respective assays. Specifically, we show that (1) PII does not cause insulin B degradation (Fig. S11b), (2) that the PI and PII SVMPs do not degrade the fluorogenic peptide which is prototypic for PIII SVMPs and MMPs (Fig. S11a), (3) PI and PIII do not cause platelet aggregation because they lack the entire disintegrin domain (PI) or the RGD motif (PIII) (Fig. 5a), and (4) that the PI and PII SVMPs, like the PIII SVMP, are not pro-coagulant and do not cause blood clotting (Fig. 5d,5e and Fig. S11c). We also included this new information in the main text of our revised manuscript.

      Overall, the data presented demonstrates a very credible path for the production of active SVMP for further downstream characterization. The generality of the approach to all SVMP from different snakes remains to be demonstrated by the community, but if generally applicable, the method will enable numerous studies with the aim of either utilizing SVMPS as therapeutic agents or to enable the generation of specific anti-venom reagents, such as antibodies or small molecule inhibitors.

      Thank you.

      Reviewer #3 (Public review):

      Summary:

      The presented study describes the long journey towards the expression of members' SVMP toxins from snake venom, which are toxins of major importance in a snakebite scenario. As in the past, their functional analysis relied on challenging isolation; the toxins' heterologous expression offers a potential solution to some major obstacles hindering a better understanding of toxin pathophysiology. Through a series of laborious and elegantly crafted experiments, including the reporting of various failed attempts, the authors establish the expression of all three SVMP subtypes and prove their activity in bioassays. The expression is carried out as naturally occurring zymogens that autocleave upon exposure to zinc, which is a novel modus operandi for yielding fusion proteins and sheds also some new light on the potential mechanism that snakes use to activate enzymatic toxins from zymogenic preforms.

      Strengths:

      The manuscript draws from an extensive portfolio of well-reasoned and hypothesis-driven experiments that lead to a stepwise solution. The wetlands data generated is outstanding, although not all experiments along this rocky road to victory were successful. A major strength of the paper is that, translationally speaking, it opens up novel routes for biodiscovery since a first reliable platform for expression of an understudied, yet potent toxin class is established. The discovered strategy to pursue expression as zymogens could see broad application in venom biotechnology, where several toxin types are pending successful expression. The work further provides better insights into how snake toxins are processed.

      We thank the reviewer for their positive assessment of our work.

      Weaknesses:

      The manuscript contains several chapters reporting failed experiments, which makes it difficult to follow in places.

      Based on a similar comment of Reviewer 1, we now moved the ‘failed’ experiments reporting on SVMP expression optimisation to the supplement as new supplementary text. We hope that the revisions have improved the clarity and overall readability of our manuscript.

      The reporting of experimental details, especially sample sizes and replicates, could be optimised.

      The number of replicates has now been added to the figure legends in the revised manuscript. Detailed experimental information is found in the revised Methods part.

      At the time of writing, it remains unclear whether the glycosilations detected at a pIII SVMP could have an impact on the bioactivities measured, which is a major aspect, and future follow-ups should clarify this.

      A detailed analysis of glycosylation of the PIII SVMP is beyond the scope of our manuscript (see above, response to Reviewer 2). Our manuscript describes a generic protocol to produce active SVMPs. Importantly, we cannot purify the native PIII SVMP from Echis carinatus sochureki venom. Therefore, it is not possible to compare our PIII SVMP with the native PIII SVMP.

      We agree that this is an important question, and we will aim in the future to perform such a comparison of a different insect cell-produced PIII with a native PIII SVMP that can be readily purified from venom.

      Finally, the work, albeit of critical importance, would benefit from a more down-to-earth evaluation of its findings, as still various persistent obstacles that need to be overcome.

      We consider cytotoxicity to be the principal bottleneck in SVMP production. In this study, we present a strategy to overcome this bottleneck.

      Major comments to the manuscript:

      (1) Lines 148-149: "indicating that expressing inactivated SVMPs could be a viable, although inefficient, approach". I think this text serves a good purpose to express some thoughts on the nature of how the current draft is set up. It is quite established that various proteases cause extreme viability losses to their expression host (whether due to toxicity, but surely also because of metabolic burden), which is why their expression as inactive fusion proteins is the default strategy in all cases I have thus far seen. I believe that, especially in venom studies, this is of importance given the increased toxicity often targeting cellular integrity, and especially here, because Echis are known to feed on arthropods at younger life history stages, making it very likely that some venom components are especially active against insects and other invertebrates. With that in mind, I would argue that exploring their production in inactive form is the obvious strategy one would come up with and not really the conclusion of a series of (well-conducted and scientifically sound!) experiments. For me, the insight of inactive expression is largely confirmatory of what is established, unless I miss something in the authors' rationale. If yes, it would be important to clarify that in the online version.

      We agree that producing zymogens represents a straightforward strategy and now, in hindsight, would have wished we had tested this first thing, it would have saved us and apparently many others significant effort. However, realising this, and implementing this approach took us considerable time and insight as we described in this manuscript. The alternative strategies we describe in the manuscript, in particular the use of inhibitors and active-site mutation, have been successfully applied for recombinant production of diverse enzymes before, including enzymes that are toxic to host cells.

      We have revised the manuscript as requested and moved the optimisation of SVMP expression to the Supplement. We hope this improved the clarity, overall readability of the text and thus addressed the reviewer’s comment.

      (2) Line 173: Here, Alphafold 3 was used, whereas in previous sections (e.g., line 153, line 210), it was Alphafold 2. I suggest using one release across the manuscript.

      Thank you for bringing this to our attention. In the revised version of the manuscript, we clarified that all models were generated using AlphaFold 3.

      (3) Line 252-254: I fully agree, the PIII SVMP is glycosylated. Glycosylation is an important mediator of snake venom activity, and several works have described their importance in the field. This raises the question, which glycosylations have been introduced here in the SVMP, and to verify that these are glycosylations that belong to those found in snakes. This is important as insects facilitate thousands of N- and O- O-glycosylations to modulate the activity of their proteome, of which many are specific to insects. If some of these were integrated into the SVMP, this could have an impact on downstream produced bioassays and also antigenicity (the surface would be somewhat different from natural toxins, causing different selection).

      We agree that glycosylation is important and warrants a follow-up in the future.

      However, most publications we found reported that de-glycosylation has a negative effect on stability and solubility of SVMPs, which is expected to have a knock-on effect on toxin activity (e.g. AndradeSilva et al., 2025; DOI: 10.1021/acs.jproteome.5c00249). It will be difficult to separate the two effects from each other. We found only a few examples where SVMP glycosylation (sialylation and Nglycosylation) modulated proteolytic and haemorrhagic functions, including interaction with substrates such as e.g. fibrinogen (Schluga et al., 2024; https://doi.org/10.3390/toxins16110486; Chen et al., 2008; 10.1111/j.1742-4658.2008.06540.x; Nikai et al., 2000; DOI: 10.1006/abbi.2000.1795. PMID: 10871038). In our manuscript, we show that our PIII SVMP is very cytotoxic and highly active in casein, fibrinogen and ESO10 degradation assays, with a K<sub>M</sub> and k<sub>cat</sub>/K<sub>M</sub> comparing favourably with other SVMPs and MMPs. We are not aware of a specific substrate for this particular PIII SVMP that depends on a distinct glycosylation pattern. Recombinant production of such SVMPs with specific glycosylation pattern requirement would be a challenge in all commonly used expression systems (yeast, plant, insect cells and mammalian cells). In fact, insect cell expression systems could be advantageous in this respect because the Sf21 and High Five (Hi5) lepidopteran cell lines we utilised are well-characterized for their ability to perform posttranslational modifications on complex secreted proteins:

      (1) N-Glycan conservation: Both Sf21 and Hi5 cells typically produce N-glycans that are trimmed to a core 'paucimannose' structure (Man3GlcNAc2), often with an alpha1,6-fucosylation. While snakes can produce more complex, sialylated N-glycans, glycomic studies of native venoms (e.g., Bothrops venom) have demonstrated that high-mannose and paucimannose structures are also prevalent in native SVMPs. Therefore, the recombinant glycoforms produced in our system are not 'unnatural' in the snake venom context but rather represent a subset of the native glycan microheterogeneity.

      (2) Occupancy vs structure: The critical function of glycosylation in PIII SVMPs is thought to be often structural, facilitating correct folding and protecting the large metalloprotease and disintegrin-like domains from proteolytic degradation. Because Sf21 and Hi5 cells recognize the same Nglycosylation sequon (Asn-X-Ser/Thr) as reptilian cells, the site-occupancy remains consistent with the native protein, preserving the overall topography of the toxin.

      (3) Activity and authentic self-processing: We acknowledge that insect-specific alpha1,3-fucosylation can occur in Hi5 cells and is potentially antigenic. As the recombinant SVMPs will be used for binder selections and for testing in silico designed binders, useful binders will be selected based on neutralising activity against venom toxins. Here, our assays focused on auto-activation and proteolytic activity, which is primarily driven by the catalytic Zn<sup>2+</sup>-site and the protein backbone.

      As stated above, analysis of glycosylation pattern of the PIII SVMP is a project on its own and beyond the scope of this manuscript.

      We have incorporated some of the above information into the discussion section of the revised manuscript to clarify that insect cell glycosylation does not recapitulate the full diversity of SVMP glycosylation observed in native venoms.

      (4) General comment for the bioassays: It would be good to specify the replicates again and report the data, including standard deviations.

      We included this information in the figure legends.

      Discussion:

      I think the data generated in the study is very valuable and will be instrumental for pushing the frontiers in SVMP research, but still I would like to see a bit of modesty in their discussion. As I have pointed out above, it is unclear which effect the glycosilations may have (i.e., are the glycosilations found reminiscent of natural ones?), despite their being functionally important. Also, yes, isolation of SVMPs is challenging, but the reality is that their expression is equally challenging, as evidenced by the heaps of presented negative data (with which I have no problems, I think reporting such is actually important). So far, the "generic" protocol has been used to express one member per structural class of Echis SVMP, but no evidence is provided that it would work equally well on other members from taxonomically more distant snakes (e.g., the pIII known from Naja oxiana). It is very likely, but at the time of writing, purely speculative.

      We have expressed additional PIII SVMPs from Echis and Daboia species and will report their production and characterisation in due course.

      Lastly, the reality is also that the expression in insect cells can only be carried out by highly specialized labs (even in the expression world, as most laboratories work with bacterial or fungal hosts), whereas the isolation can be attempted in most venom labs. That said, production in insect cells also has economic repercussions as it will be very challenging to generate yields that are economically viable versus other systems, which is pivotal because the authors talk about bioprospecting and the toxins used in snakebite agent research.

      We thank the reviewer for this perspective on the practicalities of protein expression. However, we respectfully disagree with the characterization of insect cell expression as an inaccessible or economically non-viable platform for toxin research. We offer the following points:

      (1) Prevalence and accessibility: Contrary to the suggestion that insect cell expression is restricted to highly specialized labs, the Baculovirus Expression Vector System (BEVS) has become a cornerstone of modern biologics production, structural biology and biochemistry. For instance, our MultiBac system (which is but one of several systems currently widely in use) is utilised by over 1,000 laboratories and institutions, academic and pharma/biotech, worldwide. The maturation of commercially available kits, automated platforms, and standardized protocols has moved this technology into the mainstream, making it a standard tool for any lab requiring high-quality eukaryotic proteins.

      (2) Biological necessity: Bacterial (E. coli) and fungal (P. pastoris) systems are widely accessible, however, they appear to be fundamentally incapable of producing functional SVMPs. SVMPs require complex disulfide-bond formation, intricate folding, and N-glycosylation for stability and solubility. Bacterial systems have been widely tried by us and others but typically result in very low expression or misfolded inclusion bodies. Of note, originally, we had invested significant effort to adapt P. pastoris to the production of eukaryotic proteins we are interested in, without success, before moving on to the MultiBac system. The SVMPs that we analysed here are highly cytotoxic, rendering the baculovirus/insect cell system in a way a logical choice given that the cells are no longer 'living' after infection with the baculovirus (but more akin membrane-enveloped bioreactors). Thus, one can make the argument that insect cells represent the most accessible middle ground that provides folding apparatus and necessary post-translational modifications (PTMs) required for biological relevance, and it is possible to produce mg amounts of SVMP proteins per litre cell culture as reported here in our manuscript.

      (3) Economic viability and bioprospecting: Regarding the economic argument, we contend that viability in bioprospecting is defined by functional yield rather than simple volume. Producing large quantities of non-functional or misfolded protein in a cheaper system is economically inefficient. Furthermore, for snakebite research, the ability to produce specific, pure isoforms recombinantly without the contamination of other toxic venom components found in native isolations is essential for high-throughput screening and drug design.

      (4) Scalability: Historically, insect cell production was seen as expensive, but current bioreactor technology and reduction in consumables and media costs allow for significant scaling. Many therapeutic reagents (vaccines, viral vectors, protein biologics) are produced routinely in baculovirus/insect cells. For the purposes of bioprospecting and lead identification, the yields provided by our Hi5/Sf21 system are sufficient for rigorous downstream bioassays and structural characterization.

      Again, I believe the paper is highly important and excellently crafted, but I think especially the discussion should see some refinement to address the drawbacks and to evaluate the paper's findings with more modesty.

      Thank you. We included the discussion about glycosylation patterns.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) It is not entirely clear to me if the final constructs are indeed "fusion-proteins" (line 172, 974), in the sense of chimeric proteins. From the current description, it appears that the prodomain is encoded in the same gene rather than fused as a separate domain. Thus, referring to these constructs as fusion proteins may overstate the degree of protein engineering involved in the study.

      This is correct. In the revised manuscript, ‘fusion protein’ is only used in the context of the propeptide SVMP fusion construct to avoid confusion.

      (2) Figure 2J: It is difficult to assess how much protein is secreted relative to the intracellular amounts. The blot is surely misleading, as the effective protein dilution differs substantially between intracellularly vs. extracellularly. Providing an estimate of the relative dilution of extracellular protein would help clarify the extent of secretion.

      We estimate that the SNP and SN fractions are at least 10-times more concentrated than the media fraction. The blot is analytical and not quantitative.

      (3) The manuscript appears to use both alphafold 2 and alphafold 3 for structural predictions. Clarification on the choice of the version and its impact on results would improve consistency.

      In the revised version of the manuscript, we clarify that all structural models were generated using AlphaFold 3.

      (4) Figure S3b and others: a clear description of the antibodies used in the Western blots would be appreciated (including in the methods).

      We included this information in the figure legends and a paragraph in the methods section for Western blots in the revised manuscript.

      (5) MTT cytotoxicity testing would be more convincing if done in a concentration-dependent manner.

      We repeated this assay using different concentrations of SVMPs and show the results as a new Figure 5f in the revised manuscript.

      (6) Figure S3c: It could be interesting to show the sequence coverage to get an impression of what part of the protein is there.

      We have included this information as Supplementary Figure S4d in the revised manuscript.

      Reviewer #2 (Recommendations for the authors):

      Overall, the study is presented in a step-by-step manner, and its conclusions are valid.

      (1) As suggested in the public review, further characterization of the purified material would be good, for example, by intact mass-spectroscopy to characterize the enzymes in further detail.

      Preliminary MALDI-MS analysis (performed in Loic Quinton’s laboratory) of our PIII SVMP revealed a broad and heterogeneous mass distribution, consistent with heterogeneity caused by the presence of multiple glycoforms (which is not unlike the microheterogeneity in native snake venom). However, owing to the inherent limitations of MALDI-MS for the analysis of glycoproteins, our data do not allow determination of the number of occupied N-glycosylation sites or the identification of additional types of glycosylation.

      Moreover, the relatively large molecular mass of these proteins (zymogen 70.2 kDa protein only, mature PIII 50.6 kDa protein only) makes analysis by electrospray ionisation mass spectrometry technically challenging.

      An MS-based deep analysis of the glycosylation patterns would therefore be a project on its own, and beyond the scope of the present manuscript.

      (2) The studies involving PII appear challenging due to low yields and stability of the enzyme and the mentioned self-degradation. Some studies, such as the casein-degradation, would benefit from working with a well-characterized batch of enzymes to ensure, it is not auto-degrading during the experiment.

      We believe that the finding that the PII SVMP degrades itself after incubation with Zn<sup>2+</sup> is an important observation. It is novel to the best of our knowledge. Moreover, the key message of our manuscript is that we can produce and characterise novel SVMPs that cannot be readily purified from venom (and thus are not well characterised).

      Besides, there are very few intact PII SVMPs in venom (e.g. Suntravat et al. BMC Molecular Biol 2016); the vast majority cleaves itself into a PI and a disintegrin.

      (3) Figure 4h. Degradation of insulin is only shown for recombinant PIII, not the native enzyme, and therefore doesn't convey any information with respect to how well they compare.

      We do not have available any native PII and PIII SVMPs for a comparison with the recombinant SVMPs (in our manuscript we show expression of new, uncharacterised SVMPs). We have included the PIII SVMP in the original manuscript to show that the enzyme is active and has a different specificity compared to PI SVMP. In the revised manuscript, we also included the PII SVMP insulin B degradation assay in Supplementary Figure S11b.

      (4) Figure 5a. Inconsistent use of enzymes - data for PII is presented (both as mature protein and Zymogen) and compared to PIII, but not PI, as both zymogen and mature protein. The current data presentation is confusing and gives the idea of the manuscript assembled with figures produced during the exploratory phase of the study, and not from subsequent experiments systematically conducted for the purposes of clarity and completeness.

      In the revised manuscript, we included the missing enzymatic characterisations in Figure 5 (panel a and e) and Supplementary Figure S11a-c. These data were initially not included because the respective enzymes are inactive in these assays.

      (5) The manuscript would benefit from editing to make it more concise. For an early-career reader, it is of interest and utility to follow the thought and experimental processes that led to the successful solution, but there is a risk of losing the reader's interest along the way by going through expression experiments that did not "work" in the typical sense of the word. To this reviewer, there is no added value in a full paragraph around co-expression with disulfide isomerase, as it did not improve the protein yield. A single sentence, "co-expression with PDI did not improve yields," with a reference to a supplemental figure would convey that message.

      We have moved the optimisation of SVMP expression to the Supplementary Information, which we hope has improved the clarity and flow of the main text.

      We note that the hypothesis that co-expression of protein disulfide isomerases (PDIs) enhances yields of functional SVMPs, given the high expression of PDIs in snake venom gland cells, is well established in the field. While we consider PDIs (and other chaperones) likely to play an important role in SVMP expression, we were unable to demonstrate this effect using the baculovirus-insect cell expression system and hypothesize that efficient insect and/or baculoviral PDIs are already present.

      (6) Similarly with N-linked glycosylation, the section needs a headline (line 241) and firming up of a sentence like "and possibly not all of the glycosylation..." which is vague and appears to state that it was not really of interest to pursue this further. My view is that either an experiment is done properly with a stated aim and purpose, interpreted, and then, based on whether the results are of interest to the main story or not, they are included. If N-linked glycosylation is to be included in the manuscript, it should be with a purpose (e.g., N-linked glycosylation affects enzyme activity). As it stands, the message is "there is some N-linked glycosylation" without further explanation, and this generates information without justifying the inclusion hereof.

      Please see our reply above regarding an in-depth characterisation of insect cell glycosylation of the recombinant PIII SVMP without access to the native enzyme for comparison. In our revised manuscript, we confirm that the PIII SVMP is glycosylated and that this at least partly accounts for the apparent discrepancy in molecular weight observed in SEC and SDS PAGE. We have modified the text to clarify the purpose of the PNGase deglycosylation experiment.

      (7) The manuscript, in its current form, appears to have been copied from a Thesis with very detailed step-by-step logic and description. While this is useful in a scholarly context, a scientific manuscript should be presented more compactly, assuming the readers know basic biochemistry.

      We trust that this Reviewer finds the revised version of our manuscript more compact and concise. 

      Reviewer #3 (Recommendations for the authors):

      (1) Material and Methods plus Figures:

      Please report the number of replicates per experiment and how data is presented (means/ medians/ standard deviation/ others), and add error bars to the plots where needed.

      In the revised manuscript we have included the number of repeats in the figure legends.

      (2) Abstract

      Line 4: I would not say that SVMPs are the most potent viper toxins. This place is probably taken by some of the highly neurotoxic PLA2, such as Crotoxin. Nevertheless, SVMPs are surely some of the most important toxins responsible for pathophysiological effects stemming from viper envenoming, but I would suggest rephrasing for accuracy.

      In the revised manuscript, we have modified this sentence.

      (3) Introduction

      Lines 27-31: I would like to see a reference supporting the existence of all SVMP types across vipers.

      We have included references supporting the existence of PI, PII and PIII SVMPs in viper venom. We also rewrote the sentence to state that “representatives of all three sub-classes are present in different viper venoms.” This clarifies that we do not say that all classes are present in all venoms.

      Lines 59-60: I am not sure if this should be considered such an important impediment. Essentially, many vipers yield double- to triple-digit mg amounts of crude venom per specimen from only a single milking.

      We have rewritten this text in the revised manuscript.

      Currently, it is not possible to purify any given SVMP of interest from venom; in particular for E. ocellatus SVMP isoform mixtures are typically purified rather than individual enzymes (see also introduction section of our manuscript line 57ff). Also, many SVMPs are not present in sufficient amounts in the venom. Here, we provide an approach to recombinantly produce any SVMP of interest, independent of its abundance in the venom.

      (4) Results

      Line 102: The army-fallworms name is Spodoptera, not Spotoptera. Please correct the typo.

      Done. Apologies for our oversight.

      Line 311: Please provide the data at least as a supplement.

      In the revised manuscript, we have included this experiment in Supplementary Figure S6c.

      Line 432- 433: It would be useful to clarify whether the protein should have a pro-coagulant activity (or not).

      We have changed this sentence as follows in the revised manuscript: This shows that our recombinantly produced SVMPs have no pro-coagulant activity, which was unknown before.

    1. Some recommendation algorithms can be simple such as reverse chronological order, meaning it shows users the latest posts (like how blogs work, or Twitter’s “See latest tweets” option). They can also be very complicated taking into account many factors, such as: Time since posting (e.g., show newer posts, or remind me of posts that were made 5 years ago today) Whether the post was made or liked by my friends or people I’m following How much this post has been liked, interacted with, or hovered over Which other posts I’ve been liking, interacting with, or hovering over What people connected to me or similar to me have been liking, interacting with, or hovering over What people near you have been liking, interacting with, or hovering over (they can find your approximate location, like your city, from your internet IP address, and they may know even more precisely) This perhaps explains why sometimes when you talk about something out loud it gets recommended to you (because someone around you then searched for it). Or maybe they are actually recording what you are saying and recommending based on that.

      I agree and have personally witnessed this happening to me as a prominent social media user myself. The social media algorithms are programmed so that you spend as much time on their app as possible. To do this, they make sure they have our attention on their platform at all times by showing us content they think we like and therefore will watch the most. For example, recently I have been watching a lot of Instagram videos about the upcoming FIFA World Cup, and not only do I get videos now, but also my friends, whom I have sent reels to, and those who are the closest to me.

    2. When social media platforms show users a series of posts, updates, friend suggestions, ads, or anything really, they have to use some method of determining which things to show users. The method of determining what is shown to users is called a recommendation algorithm, which is an algorithm (a series of steps or rules, such as in a computer program) that recommends posts for users to see, people for users to follow, ads for users to view, or reminders for users. Some recommendation algorithms can be simple such as reverse chronological order, meaning it shows users the latest posts (like how blogs work, or Twitter’s “See latest tweets” option). They can also be very complicated taking into account many factors, such as: Time since posting (e.g., show newer posts, or remind me of posts that were made 5 years ago today) Whether the post was made or liked by my friends or people I’m following How much this post has been liked, interacted with, or hovered over Which other posts I’ve been liking, interacting with, or hovering over What people connected to me or similar to me have been liking, interacting with, or hovering over What people near you have been liking, interacting with, or hovering over (they can find your approximate location, like your city, from your internet IP address, and they may know even more precisely) This perhaps explains why sometimes when you talk about something out loud it gets recommended to you (because someone around you then searched for it). Or maybe they are actually recording what you are saying and recommending based on that. Phone numbers or email addresses (sometimes collected deceptively [k1]) can be used to suggest friends or contacts. And probably many more factors as well!

      I think algorithms are the most important thing to creating a social media. Because that collected data from users and show what they want or mentioned before on their account. Like we are using Facebook and can see friend suggestion or people you may know when we just met someone once or talked about them. Just like Facebook is reading your mind, sounds like creepy in a funny way. So algorithm is working, So if you and someone else have some connections in common, Facebook kind of “guesses” that you might know each other. I wonder how much social media really know about us.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Response to Reviewers

      We would like to thank the reviewer for their constructive comments on our manuscript. We have addressed all comments made by the reviewers by additional experimental data, data analyses, and text edits. A detailed point-by-point response to the reviewers is documented below.

      Summary of new/amended data panels

      Fig 2C (Rev 2): Cell-by-cell quantification of the GFP fluorescence intensity as a surrogate measure of wild-type (WT) vs mutant Pfn1 rescue construct expression levels in B16F1 KO-rescue studies.

      Figs 1B, 2A, 3C, 4A, 4C (Rev 1, 3): Inclusion of zoomed images of PIP2 staining of select regions of interests.

      Figs 6B, 6D (Rev 2): Quantification of phospho-PKC substrate antibody immunoblots of MDA-231 and B16F1 cells with or without Pfn1 KO.

      Fig 3E (not requested by the reviewers): Time-lapse images of PIP2 biosensor and F-actin in HEK-293 cells.

      __Fig 3H (Rev 3): __Half-life comparison of LatB-induced PIP2 and F-actin responses

      Fig S1 (Rev 1): F-actin and PIP2 staining of MDA-231 cells with or without treatments of myosin inhibitor blebbistatin.

      Figs 6G-I (Rev 2, 3): Quantification of various parameters from Ca2+ imaging studies.

      Fig 6J-M (Rev 2): __Images and quantification of correlative PIP2 and DAG biosensor studies __in HEK-293 cells.

      Fig 7 (not requested by the reviewers)__: __A schematic model of how Pfn1 loss leads to PIP2 reduction in cells.

      Fig S2 (not requested by the reviewers): Effect of Pfn1 knockdown on PI4P in HEK-293 cells.

      Fig S3B (Rev 2): A list of top 100 (50 up, 50 down) differentially expressed genes in response to Pfn1 KO in MDA-231 cells.

      Point-by-Point response

      __REVIEWER 1: __

      1. "The quantifications of the PIP2 levels were apparently done simply by measuring the fluorescence intensities of wild-type and knockout cells stained with monoclonal actin-PIP2 antibody. However, the knockout cells appear more spread compared to the wild-type cells (Fig. 1B), and this can possibly affect the quantifications (e.g. there may be more plasma membrane ruffles/folds in the wild-type cells). Thus, I recommend that in all critical quantifications the authors would also use a general plasma membrane marker to confirm that the PIP2-density (and not just morphology of the plasma membrane) is indeed affected by Pfn1-depletion". Response: For PM PIP2 analysis, we specifically quantified the total rather than the average PM PIP2 staining intensity (as also previously done in other studies - Hammond et al. J. Cell Science 2006; Biochem. J 2009) for three reasons. First, PIP2 is non-uniformly distributed across the PM, and therefore the average intensity calculation collapses a lot of biologically meaningful spatial information. Second, the average intensity calculation is impacted by significant cell shape and area differences that exist between cells within a group as well as between groups. Third, the integrated PM intensity is a better metric of how much total PIP2 is available for metabolic turnover on a cell-by-cell basis. These justifications are now detailed in the revised manuscript.

      In our previous study (Ricci et al., J. Biol. Chem 2024, PMID 38141770), we utilized orthogonal techniques (immunostaining, lipid dot blot) in multiple cell lines to demonstrate that total PIP2 as well as PIP2 intensity at the plasma membrane (PM) (based on manual tracing of hundreds of cells in immunostaining experiments) are reduced by silencing Pfn1 expression, and conversely, elevated upon Pfn1 overexpression. We would like to clarify here that in our present study we used an automated pipeline in "cell profiler" to detect cell edges and quantify integrated PM intensity of PIP2 in control vs Pfn1 knockout (KO) cells, and our present findings in Pfn1 KO setting recapitulated our previous findings in transient knockdown setting. While our cell-profile pipeline accurately detects the cell edges, we address the reviewer's comment on confirmation of findings with a PM marker by providing new experimental data in HEK-293 cells transfected with fluorescence biosensors of PIP2 and DAG along with a PM marker (iRFP-Lyn11), which also shows reduction of PIP2 fluorescence staining at the Lyn11-positive PM regions in Pfn1 knockdown cells relative to control cells (see new data panels Figs 6J, L).

      "To get a better idea about which cellular actin filament structures are important for regulating the PIP2-levels at the plasma membrane, one could also use a larger repertoire of actin/myosin inhibitors (CK666, cytochalasin-B, blebbistatin). By using these compounds, one may e.g. uncover if the Arp2/3-nucleated branched actin networks and/or contractile actomyosin structures would specifically contribute to regulation of the plasma membrane PIP2 levels".

      Response: We thank the reviewer for this suggestion. We have now evaluated the effect of blebbistatin treatment on PIP2 in MDA-231 cells (now shown supplementary Fig S1). A previous study showed that the major effects of blebbistatin on actin cytoskeleton are disintegration of actin stress fibers, softening of cortical actin, and transformation of lamellipodial actin into loose network of accumulated amorphous actin structures that correspond to membrane ruffles (Shutova et al., 2012). These phenotypes were also recapitulated in our experimental settings. In general, blebbistatin-treated cells exhibited protrusive structures in random directions with PIP2 enrichment in peripheral F-actin-rich regions (consistent with the LatB experimental data) and a higher (p=0.09) overall cell edge PIP2 staining vs vehicle-treated cells further underscoring the impact of actin cytoskeletal perturbation on PM PIP2.

      "The effects of PLCb3 silencing on Pfn1-dependent changes in the PIP2 levels are interesting. To gain better insight into the underlying mechanism, one could also check if the levels of active (phosphorylated) PLCb3 are affected upon Pfn1-depletion".

      Response: We would like to point out that unlike PLCg, PLCb is not activated by phosphorylation. While literature has documented that certain site-specific phosphorylations of PLCb by PKC (in a feedback manner) and PKA, these phosphorylation events, if at all, have inhibitory effect on PLCb activity. Since our data supports the model that Pfn1 loss leads to an increase in PLC-mediated PIP2 hydrolysis and downstream PKC activation, we feel that probing for such inhibitory feedback phosphorylation events will not provide any mechanistic insights.

      "In the 'Discussion', the authors speculate that Pfn1 H119E mutant may have more frequent interactions with PIP2 as compared to wild-type Pfn1. This does not make much sense, because Pfn1 binding to PIP2 is very weak (e.g. ref. 28), and it is unlikely that introducing a negativelycharged glutamate would increase its affinity to negatively charged headgroup of PIP2. Thus, it seems unlikely that Pfn1 would affect the PIP2 content of plasma membrane through direct interactions with PIP2".

      Response: __We did not mean to imply that glutamate substitution of H119 residue would necessarily increase Pfn1's __intrinsic affinity to negatively charged PIP2. While PIP2 binding of WT vs H119E-Pfn1 has never been quantified in biochemical assays, we previously (Bae et al. PNAS 2010; PMID 21115820) showed that H119E substation does not affect the membrane fraction of ectopically overexpressed Pfn1 in cells. Along this line, Pascal-Goldschmit and colleagues (PMID: 7673143) also showed that analogous mutant H119D-Pfn1 inhibits PLCg-mediated PIP2 hydrolysis as efficiently as WT-Pfn1, further underscoring the fact that H119D/E-Pfn1 is not defective in membrane phosphoinositide binding. Our data largely supports a model that Pfn1-dependent PIP2 alteration is predominantly related to its actin-regulatory function. However, since Pfn1's binding to actin and PIP2 are mutually exclusive, we cannot absolutely rule out a minor (possibly insignificant) contribution of Pfn1's ability to block PIP2 hydrolysis by direct PM interaction. We therefore offered a hypothetical scenario where H119E-Pfn1 mutant may have more frequent interaction with PM PIP2 simply because it is not able to interact with actin. We have now better clarified this argument in the "Discussion" section of the revision.

      "The cell images in Fig. 2A are bit difficult to follow due to the large number of cells in the images. One could perhaps show higher resolution images with few knockout and rescue cells in the same field of view and indicate the rescued cells in these images e.g. with arrows".

      Response: As requested by the reviewer, we have now shown zoomed images in Fig 2A in the revision.

      "Please clearly describe in each figure legend what the error bars represent"

      Response: We have now clearly mentioned in the Statistics section of "Materials and Methods" that all error bars represent standard deviation unless explicitly mentioned otherwise.



      REVIEWER 2

      1. "The data show that actin binding-deficient mutants of Pfn1 do not rescue the knockdown. In these experiments, it is critical to quantitate the relative expression levels of the mutants. The model that Pfn1 regulation of PIP2 requires interactions with actin is not really clear - is it due to Pfn1 targeting by actin binding, or Pfn1 regulation of actin itself? Either possibility seems possible, and the experiments do not distinguish them". Response: We thank the reviewer for these comments. First, since GFP and Pfn1 rescue constructs are linked by an IRES, we analyzed GFP fluorescence intensity of cells selected for PIP2 analyses as a surrogate measure for comparing the relative expressions of Pfn1 rescue constructs across the various groups. As per these analyses (based on measurements of hundreds of cells from 3 different experiments), the average GFP expression of cells chosen for PIP2 analyses was found to be comparable between the various Pfn1 KO rescue groups (now shown in Fig 2C). Therefore, we argue that our observed phenotypic differences related to PIP2 are not confounded by the expressions of various Pfn1 rescue constructs.

      Second, it is known that Pfn1 loss leads to pronounced reduction in lamellipodial F-actin content (as shown in Figs 3A-B). Our LatB experimental data (Figs 3E-G) show that actin depolymerization leads to pronounced PM PIP2 reduction within minutes. Based on these findings, taken together additional evidence for increased basal PLC activity signature readouts in Pfn1-deficient cells (i.e. greater baseline PKC activity, greater PM DAG/PIP2 ratio from biosensor studies as recommended by the reviewer (new data - shown in Figs 6J-M)), we postulate (concurring with Reviewer 3) that disruption of cortical cytoskeleton (possibly also accompanied by removal of PIP2-binding adaptor proteins) may enhance PIP2's accessibility to hydrolytic enzymes. In fact, two previous studies (Cho et al., PNAS, 2005 and Andrade et al., Scientific Reports 2015) have demonstrated that actin filament disruption increases PM mobility of PIP2. There is also evidence for actin depolymerization-induced uncaging of PLC from the cortical actin network (Huang et al, Planta, 2009). Therefore, in principle, Pfn1 loss may cause more frequent PLC-PIP2 interaction and enhance baseline PIP2 hydrolysis by either increasing PM diffusion of PIP2 and/or uncaging of PLC. We have now included a schematic working model (Fig 7) to illustrate this concept and added these points in the discussion. However, a direct demonstration of increased PIP2 accessibility of PLC in Pfn1-deficient cells is beyond the scope of the present - this is something we will pursue in the future.

      "The knockdown data on PLCbeta is convincing with regard to its role in PIP2 reductions, but the papers does not explain how actin-Pfn1 interactions regulate PLCbeta".

      Response: Please see our detailed response to the previous comment that specifically addresses how we envision Pfn1 negatively regulates PLC-mediated PIP2 hydrolysis via modulating actin cytoskeleton.

      "The transcriptome data must be provided along with the data in Figure 5 - otherwise it is impossible for the reader to evaluate. The fact that the data is being used in another paper is not an adequate reason for its omission".

      Response: The transcriptomic data is now displayed in Supplementary Figure S3, where we have now listed top 100 (50 up, 50 down) differentially expressed genes in response to Pfn1 KO in MDA-231 cells (see panel B in Fig S2). We are in the process of submitting the FASTA file to GEO database.

      "The PKC substrate data is not convincing. The blots are messy, and there is no quantitation".

      Response: Since phospho-PKC substrate antibody is supposed to recognize all phosphorylated proteins by PKC, we expect to see multiple bands. The intensity of each lane in entirety is approximative of PKC activity by detecting proteins at multiple molecular weights phosphorylated at their serine residues. We have replaced the B16 generated data with a better-quality blot and added quantifications with statistical analysis (Figs 6B, D).

      "The calcium data should include statistical analysis of the differences".

      Response: We have now performed statistical analyses of the calcium data. Specifically, we compared the peak amplitude, integrated Ca2+ signal (area under the curve), and the post-stimulation resting value between control and Pfn1 knockdown groups. As per these analyses, we did not see any significant difference in either the peak amplitude or integrated Ca2+ signal between the control and Pfn1 knockdown groups, further underscoring the fact that Pfn1 loss does not necessarily confer cells an increased ability to respond to agonists (i.e. LPA-induced GPCR activation in this specific case). However, we noted that the post-stimulation resting Ca2+ signal was elevated in Pfn1-deficient cells relative to control cells (p2 hydrolysis and/or reduced re-uptake of cytosolic Ca2+ by endoplasmic reticulum and/or reduced efficiency of Ca2+ export. These analyses are now included in Figs 6G-I in the revision.

      "The discussion of DAG and PA levels is problematic. As the authors are aware, whole cell lipidomics can easily miss small changes in specific compartments. If the authors think that lipid sensor analysis of PM DAG and PA would strengthen the analysis, then this should be included. The large change in PC levels does seem to suggest an alternative source of PA. While the authors present arguments against a role for PLD, this could be directly tested. In any case, the finding of a nearly 100-fold greater change in PC than in PA raises question about what the whole cell PA measurements is really detecting".

      Response: We thank the reviewer for these comments and experimental suggestions__. First__, we completely agree with the reviewer that whole cell lipidomic analyses fail to detect small changes in specific compartment; we mention this point in the revision. In the revision, we have displayed our lipids of interest as individual line plots connecting control and Pfn1 KO group experiment-by-experiment to show the trend of lipid change in each experiment. As per these analyses, in 4 out 5 experiments, the total DAG increased in Pfn1 KO cells. However, the large experiment-to-experiment variability in the absolute content as well as Pfn1-dependent changes in DAG precluded us from achieving statistical significance between the two groups. The large variability in the measured DAG content in our experiments is not totally surprising since cellular DAG level is known to fluctuate with growth and/or impacted by unintended changes in the chemical parameters of culture condition. However, the largest pool of DAG is in ER/golgi, and since whole cell lipidomic measurements fail to reveal PM DAG due to PIP2 hydrolysis, as per reviewer's recommendation, we now include lipid biosensor experimental data (Fig 6J-M) of control vs Pfn1 knockdown HEK-293 cells to demonstrate that PM DAG-to-PIP2 ratio (an indicator of the basal PIP2 hydrolysis efficiency) is increased upon Pfn1 depletion. We believe that these new correlative PIP2/DAG biosensor data further strengthen our conclusion.

      Regarding the reviewer's comment on the orders of change in PC vs PA, we clearly mentioned in the original discussion that it is highly unlikely that PA increase in Pfn1-deficient cells is reflective of increased PLD-mediated conversion of PC for two reasons. First, we saw disproportionate orders of magnitude of changes in the content of PA (~3000 pmol/mg increase) vs PC (>200,000 pmol/mg decrease) in response to Pfn1 KO in MDA-231 cells. Second and more importantly, since monomeric actin directly binds to and inhibits the activity of PLD, the expected increased G-to-F-actin ratio in Pfn1-deficient cells, if at all, would likely result in diminished PLD activity reducing PLD-mediated conversion of PC to PA.

      In our opinion, since DAG is the direct hydrolysis product of PIP2 and we are now able to demonstrate elevated PM DAG-to-PIP2 ratio in Pfn1-deficient cells in biosensor experiments, PA biosensor studies are not necessary.

      REVIEWER #3

      1. "General: Scale bar labels are too small, please also provide time-stamps for time course measurements" Response: These concerns have been addressed in the revision.

      "As with every antibody stain, there is a remaining risk that a change in the cellular context affects an off-target of the antibody (e.g., a protein phosphorylation site). I think that this is not particularly likely, but I'd control for it, which can be done in a straightforward manner: The authors could do a strong-detergent treatment to rule out a potential off-target effect of the antibody (e.g., 0.1% Triton X-100, 1 h). This should remove all (non-amino-) lipids from the sample, including the phosphoinositides. Overall, binding of the antibody should be strongly reduced, fluorescence images should be much dimmer & the effect of the Pfn1 KO should mostly disappear."

      Response: The PIP2 antibody used in the present study is a well-vetted and widely used antibody in literature. Notably, two papers published by Dr. Hammond (one of the co-authors), an expert in phosphoinositide signaling, previously showed selectivity of this antibody by blocking with lipids, neomycin, and PH-domain of PIP2-binding proteins (Hammond et al, J. Cell Sci, 2006; Biochem J. 2009). We cite these papers in the revision.

      "Figure 1: Please show images in a larger zoom, cell details are barely visible (same for Figure 3). I also would not use "PM PIP2 levels" in the legend, as nuclei appear visibly lighter, indicating that some PIP2 is likely present in other membranes. The type of PIP2 staining should be specified in either the Figure itself or in the legend."

      Response: We would like to clarify here that we used an automated pipeline in "cell profiler" to detect cell edges and quantify integrated PM intensity of PIP2 in control vs Pfn1 knockout (KO) cells; so nuclear membrane PM is not accounted for in the analyses. We have zoomed PIP2 images in Figure 1 as the reviewer suggested. These changes are incorporated in the revision.

      "Figure 3: Same comment as for Figure 1, zoomed images would really help, especially for the PM/Cytosol distribution of the PIP2 biosensor"

      Response: Zoomed images of Fig 3 have been provided in the revision.

      "The lag time in the dissociation of the PIP2 sensor is interesting, as is the fact that the kinetic of PIP2 biosensor release is (visually) slower. I recommend to do a couple of simple fits to quantify these effects. If my impression holds, this would be a strong support of the author's interpretation that actin depolymerization actually leads to a loss of PM PIP2 - a simple binding/unbinding kinetic would be much closer to the actin depolymerization kinetic".

      Response: As suggested by the reviewer, we have done curve fitting of these data to calculate the half-life of F-actin and PIP2 (results shown in Fig 3H). As per these calculations, the mean half-life of PIP2 (~ 1min) is significantly longer than that of F-actin (~2.2 min) which further supports our interpretation that actin depolymerization leads to a loss of PM PIP2.

      "Figure 4: Same comment as for Figures 1 and 3, zoomed images would be most helpful."

      Response: Zoomed images have been provided in the revision.

      "Figure 5G: It looks like the two conditions were internally normalized. Given that we're looking at differential levels of PIP2/IP3/DAG, I think it is very possible that baseline Ca levels are also different. I'd either report in au or do a global normalization which would also capture any difference between the two conditions. This should also clarify whether there are differences in post-stimulus steady state Ca levels, as it currently looks like".

      Response: Since we used a transfectable Ca2+ biosensor (GCaMP), to account for cell-to-cell variation in the actual expression of the biosensor, we had to baseline-corrected GCaMP fluorescence by normalizing each kinetic datapoint readout to the average pre-stimulation value on a cell-by-cell basis. However, we have now performed additional analyses. Specifically, we calculated the peak amplitude, integrated Ca2+ signal (area under the curve), and the post-stimulation resting value for each of the two groups. As per these analyses, we did not see any significant difference in either the peak amplitude or integrated Ca2+ signal between the control and Pfn1 knockdown groups, further underscoring the fact that Pfn1 loss does not necessarily confer cells an increased ability to respond to agonists (i.e. LPA-induced GPCR activation in this specific case). However, we noted that the post-stimulation resting Ca2+ signal was elevated in Pfn1-deficient cells relative to control cells (p2 hydrolysis and/or reduced re-uptake of cytosolic Ca2+ by endoplasmic reticulum and/or reduced efficiency of Ca2+ export. These analyses are now included in Figs 6G-I in the revision.

      "Please increase the font size in Figure 6C, this is barely readable".

      Response: We have now replaced that panel with one with bigger font texts.


      "Do the authors think that most PIP2 is actually in lipid-protein complexes and actin depolymerization with the corresponding removal of PIP-binding adaptor proteins exposes previously shielded PIP2 molecules to enzymatic hydrolysis?"

      Response: Yes, we certainly think that is the most likely scenario. Please see our detailed response to Reviewer 2's comment #1. We have now clearly included this in the discussion and added a schematic mechanistic model to better illustrate our thinking (Figure 7).

      "The lipidomic changes are extremely interesting. This could indicate a change in overall cellular architecture which goes beyond PIPs. SM/Chol/PC all go down - I'd interpret that this as a relatively lower content of Plasma membrane and ER. It would be interesting to see if the surface to volume ratio of the cell changes - a comparison with total Cardiolipin as a proxy for mitochondrial membrane size could also be informative. It may very well be that the Pfn1 KO effects on structural membrane lipids are the more important finding - but elucidating that mechanism is beyond the scope of the current manuscript. I look forward to learning about it in the next story".

      Response: We thank the reviewer for this insightful comment. However, this is something we would consider as a scope of future studies.

    1. Cognitive Load Theory tells us that our brains need a certain level of difficulty to process information deeply. If something is too easy – like, say, getting AI to write an essay for you – your brain doesn’t engage enough to form lasting knowledge.

      This is the first time I've heard of this theory, and It makes sense that learning requires a certain level of effort for information to be processed deeply and retained. If something is too easy, such as having AI write an essay for you, your brain may not engage as much, which can limit learning. However, I think this depends on how the tool is used. For example, if AI is used as a tool to support studying, such as explaining concepts or organizing ideas, it can still involve active thinking, help in understanding and retaining information. In contrast letting it write a paper requires no thinking skills and requires less active thinking.

    1. In

      Try something like this maybe:

      In this chapter, we will consider models where the variance also depends on covariates. This leads to the following model specification:

      \begin{gather} Y_i \sim N(\mu_i, \sigma_i^2) \nonumber \ \mu_i = \beta_0 + X_{1i}\beta_1 + X_{2i}\beta_2 + \ldots X_{pi}\beta_p \nonumber \ \sigma^2_i = f(Z_i; \delta) \nonumber \end{gather}

      where \sigma_i^2 is written as a function, f(Z_i; \delta), of predictor variables (Z) and additional variance parameters \delta. The set of predictor variables (Z) may overlap with or be distinct from the predictors used in the mean model (X).

      If you don't go with this version, I think splitting up that long sentence into a few distinct sentences and removing the appositive expressions separated by "," in favor of something more readable that doesn't break up the flow as much.

  4. Apr 2026
    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers


      __Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      __Summary: Overall, this study adds a large amount of data for the scyphozoan Aurelia coerulea by producing several single-cell RNA sequencing libraries that cover the transition from polyp to medusa. The study provides a modern view of cell type diversity and cell-specific transcriptome changes during this period of extreme morphological change in this particular cnidarian lineage, which is understudied. Certain unique cell subtypes, including neural cell subtypes and muscle cell subtypes which are specific to different life stages are discussed in detail providing some new insights.

      My overall assessment is that the manuscript has good potential to be impactful, but in its current form it is somewhat clunky and overly complex to read, the figures were too crowded and difficult to comprehend, and the authors did not provide enough context regarding the current state of knowledge and what this study adds to it. In particular, Figure 1 and the section about striated and smooth muscles sharing partial transcriptomic profiles need the most work. The results were presented in the context of the anthozoan Nematostella but this should be broadened further to include other cnidarian single-cell studies, such as those from Hydra and Clytia which are both medusozoans like Aurelia. The writing throughout could be streamlined and simplified to better highlight the major findings as described in the abstract of the paper. Several figures were not well presented or clear and could be improved or decluttered to better communicate and support important results. In addition, some methods were totally missing, and I was unable to access the github repository associated with the paper which should detail all analyses described in the paper. In its current form, reproducibility of analyses would be quite limited. I did greatly appreciate the inclusion of the data on the UCSC Cell Browser, which allows anyone to access the single cell data matrix for visual exploration.

      Answer: We thank the reviewer for the overall positive assessment and have tried to address all of the comments that follow.

      Major comments: The Introduction section was very short - only three paragraphs. I feel that this section could be expanded to give more context about Aurelia as a research organism, and the current resources available. This includes genomic and transcriptomic resources particularly those focused on the transition between life cycle stages (polyp to medusa). Any other relevant background on cell type diversity or if there is anything known about the molecular profile of specific cell types found in different life stages should also be included here . Do marker genes already exist for some of the important cell types discussed in the manuscript? It would be better to present the current state of knowledge, and context for why this study was done, how it builds upon current knowledge, and what it adds to our current understanding so that the study is properly framed from the beginning.

      Answer: Introduction was expanded and also includes explanations to which extant medusa specific cell-types were investigated so far. This additional information is highlighted in blue typeface in the manuscript.

      In the Results section, I find the sentence on p. 4, "Further, ~70% of these gene models do not have readily identifiable orthologs and thus represent putative orphan genes" to be rather confusing. What analysis was performed to determine this percentage, and which set of organisms were compared? Doesn't this percentage seem rather high for a cnidarian? Or is this referring to orthologs outside of cnidaria? Please comment further on how this percentage was determined and possible explanations for it being this high. Right now, it just feels tacked on to this paragraph with no context or further explanation which leads to the confusion.

      __Answer: __This statement originally referred to a lack of any best-blast-hit nor any protein domain annotation found for the sequence. This number has dropped to only 47% with the most recent mapping tool, which is a value also fairly commonly found in other animal genomes. Nonetheless this statement has been removed from the manuscript.

      Figure 1. There are many issues with this figure that encompass how I felt generally about the figures of the paper. The figure should ideally take up the entire width of the page rather than squishing some text next to the figure.

      __Answer: __The figures are intended to be a full page, they are also included embedded into the text to facilitate review of the manuscript and the full-resolution figures are included for proper review. In the revised version we have kept this comment in mind to ensure the figures are legible.

      Figure 1A: The colors of the different developmental stages from which tissue was samples (e.g. polyp1, polyp2, polyp.clover) do not seem to match between legend and figure. For example, the "polyp.clover" stage is circled in blue in the schematic, but given a green dot in the legend. The "medusa.manubrium" is circled in orange in the schematic, but given a purple dot in the legend. Suggest making the colors match between legend and schematics.

      __Answer: __ The colors correspond to the grouped stages and colour palette used for the life cycle stage divisions. This has been considered in the revised figure

      Figure 1E: In Panel E, the labels showing that the top graph is "polyp" and the bottom graph is "medusa" are much too small. Increase the font size of the labels. The font size for the GO terms themselves are also too small.

      __Answer: __This figure has been removed in the revision; Attention has been paid to font sizes in the revised figures.

      Figure 1F: The bulk of this study centers around the single-cell RNA sequencing data and resulting analyses from these data. As such, I would expect the cellular atlas resulting from these data to be similarly highlighted. In Figure 1F, the annotated cell atlas as presented is much too small, making it impossible to even add the labels for the different clusters directly on the UMAP. Suggest increasing the size substantially to at least half of the page width, so that it is possible to do so.

      __Answer: __This has been removed in the revision; the full distribution of the identified clusters is now figure 2. We do not include all of the population sub-types on the UMAP in this figure as this is simply a visualization tool and the distribution of the sub-types on that map is not necessarily informative. Rather we include the relative proportions of the sub-types/states in the bar plot, and the relationships between these clusters in the tree.

      -There should also be a complimentary figure in the supplement that shows all of the individual clusters, each in different colors and clearly annotated with labels, rather than just showing multiple clusters that were combined into the major cell types. There is an example of this in the Clytia single cell paper (see Chari et al. 2021 Figure 2A vs Fig S9).

      __Answer: __A fully coloured UMAP with all cell states is available in the supplement figure S3

      -The graph on the right of this panel showing the "Distribution of cell types in time and space" is overly complicated with all of the colors and the meaning is quite lost as it is quite difficult to interpret at this very small size. Suggest removing and possibly showing as a supplemental figure so that it's meaning is easier to assess.

      __Answer: __This barplot is now larger and includes both the partitions (major cell populations, as seen in the UMAP) and proportion of individual cell clusters. We feel this is an intuitive way to illustrate the relative distributions of all cell type states across the dataset as a whole and so we keep this in the main figures of the manuscript.

      -In addition, striated muscles are marked on the overall UMAP; however, it is not noted until later that the smooth muscles are part of the "outer epidermis" cluster. Suggest altering the legend or the text of the figure itself to show where the smooth muscles are thought to be in the overall UMAP, especially since they are specifically discussed in depth later in the manuscript. Exactly which "part" of the outer epidermis cluster includes the smooth muscle cells?

      __Answer: __We have added the smooth muscle cluster in the main figure umap.

      Figure 1G: Panel G, for example, is not useful in conveying its point as the text labels are too tiny and the figure is overly complex to be squished into a panel of this figure. Suggest removing and making 1G a supplemental figure by itself or perhaps together with 1C (as they are linked) where it is more legible. The figure legend text for Fig 1G is also confusing as it refers to "scyphozoa" in (C) but there is no "scyphozoa" in 1C, only "medusa".

      __Answer: __This is now Figure 1D and E and is given increased space in the figure. We feel the message that the medusa-specific gene set is not restricted to medusa-specific cell types is an important one and so we have kept this in the main figure. We provide a table with all gene annotations in the supplement so that it is accessible to anyone with further interest (DS1.1a and DS1.1b).

      Text, p. 6: The explanation for how the clusters were annotated in Fig 1 and Fig 2 is much too vague. The text states, 'We identified 9 broadly defined cell populations, for which we assign identities by assessing up-regulated gene lists (Data S1.3)." What does this mean? How exactly were the up-regulated gene lists assessed? This needs to be clarified further. What genes were used to label these clusters or groups as particular cell types? How does the annotation relate to Supplemental Tables S1.3 and S1.3b? Does the previous literature need to be cited to support these annotations based on specific genes? Suggest doing a better job overall and providing more detail and context explaining how the single cell clusters were annotated.

      __Answer: __We have expanded our description of how we assigned identities to the nine principal cell type families as follows:

      (pg. 8) The inner epithelia, or gastrodermis, expresses several collagens that are a characteristic of the inner cell layer of anthozoans (39); the outer cell layer houses the ring musculature and is rich in contractile proteins. The striated muscle cluster is also rich in contractile protein and is the only principal cell population absent from the polyp-derived samples (Fig. 2C). The mucin gland expresses mucin-like-proteins, whereas the digestive gland expresses other digestive enzymes, and the neural cluster expresses synapsin and other conserved known neural regulators such as ashA. The cnidocytes express mini-collagens and are enriched in pathways targeting the endoplasmic reticulum (40).

      Text, starting on p14: "Striated and smooth muscles share partial transcriptomic profiles." This section is highly confusing and could do with some simplification in both text and figures. - The genes for which expression is shown in Fig. 5, 6 and 7 are not properly introduced or given nearly enough context in the text. For example, the text states, "To investigate the dynamics of muscle formation, we further compared phalloidin staining of muscle fields with in situ hybridization detection of specific cluster marker expression in polyps (Fig. 5), strobila (Fig. 6), and ephyra (Fig.7)." However, it is not until the legend of Figure 7 and also much later in the text (in the Discussion, p23) that it is noted what types of muscles each of the genes used in ISH actually mark ("While a small set of genes are shared across the two muscle phenotypes (e.g. stmyhc1 and mrlc2), others are more specific to either phenotype (eg. stmyhc5 in striated muscle; myophilin-like-2 in smooth muscle) (Fig.8A), which were verified by in situ hybridization (Figs.5,6,7)". This needs to be rewritten and improved for flow and clarity purposes.

      Answer: Figure 5,6 and 7 were re-assembled in a different structure according to reviewers suggestion. Specifically, we now present the muscle anatomy together first, followed by molecular validations from the atlas data. Marker genes used for in situ hybridization (ish) were introduced as suggested. Text was re-written according to changes in figures. In general, figures and text were simplified to gain more clarity on the muscle chapter.

      • Suggest that the authors show an overall UMAP of smooth and striated muscle (perhaps the smooth muscle subtypes are part of the large 'outer epidermis' cluster; see the comment for Figure 5B above), and then include featureplots that show the expression of each of the genes used in ISH in these clusters. This might make it clearer as to what type of muscle the genes should be highlighting within each developmental stage. It might look something similar to what is shown in Figure 7P (although it is unclear how the featureplots shown in this figure relate to the UMAP shown in Figure 5B). In addition, the featureplots in Figure 7P only show 3 out of the 4 genes used in ISH which is not helpful. Featureplots should be clearly shown for all genes discussed. This is essential to linking the pattern in the single-cell data to the expression data and is the minimum required to provide clear understanding.

      Answer: We took this suggestion under consideration when re-compiling the figures. Now the feature plots and the insitu’s are found in the same figure (Figure 6).

      • The text reads, "To investigate the dynamics of muscle formation, we further compared phalloidin staining of muscle fields with in situ hybridization detection of specific cluster marker expression in polyps (Fig. 5), strobila (Fig. 6), and ephyra (Fig.7)." However, Figure 6 also contains images of ephyra (Fig6. P-S). Suggest that those panels could be included in Figure 7.

      Answer: This text no longer appears in the manuscript. The relevant section now reads as follows (p15:17):

      “We assessed the anatomic location of the muscle fields by phalloidin staining in Aurelia polyps, strobilae and ephyrae (Fig.5). Polyps have three distinct smooth muscle fields (Fig. 5A,B-G): the radial muscles of the oral disc (Fig. 5D), the longitudinal tentacle muscles (Fig. 5E), and the longitudinal retractor muscles that run along the body column (Fig. 5F,G (35)). During strobilation, fragments of the polyp retractor muscles are retained in the early ephyra (Fig. 5J (35)). Striated muscles appear coronally around the oral disc, oriented radially along the lappets of early detached ephyra (Fig. 5L-N). At the tips of the lappets, the border of the coronal muscle, and at the base of the manubrium, fibres show a mixed organization of smooth and striated myofibrils (Fig. 5O,P). These findings corroborate previous studies that used light- (26) or electron microscopy (24,25).

      We next compared expression patterns expected from our single cell data with the phalloidin-based anatomy of smooth and striated muscles. As expected, several genes were shared between the smooth and striated muscle cluster (Fig.6E), while others were highly specific to either smooth (Fig.6C,D) or striated muscle cluster (Fig.6P; Data S1.11). Different calponin paralogs show distinct expression in the different muscle types (Fig. 7A). For example, calponin1 is specific to the smooth retractor muscle of the polyp and no other subpopulation of the smooth muscle type (Fig. 6A-C). At the strobila stage, expression of calponin1 is still visible in fragmented retractor muscles, consistent with the single cell expression profile (Fig. 6F). By comparison, mrlc2 expression marks the locations of all smooth muscle populations in polyps including tentacle muscles, radial muscles of oral disc and retractor muscles of the body column (Fig. 6D,E).”

      • There are parts of this section text where reference to the Figures is complicated and not easy for the reader to follow. I got particularly confused in trying to follow this part of the manuscript. For example, a sentence on p15 reads, "mrlc2 and stmyhc1 reads are detected in both muscle types (Fig. 7pFig. 5M, Fig 6C,E,G-P, Fig. 7J-L,N-P), and ISH indicates that the expression is localised to the fields of striated muscles in ephyrae (Fig.7J,K,N), as well as the smooth muscle populations in polyps including longitudinal tentacle muscles, radial muscles of oral disc and retractor muscles of the body column (Fig. 5M, Fig.6H,I,L,M), and the muscles of the manubrium in the meta-ephyra (Fig. 7L,O)." It is quite difficult to keep jumping between Figures and panels to look at this. A better organization of the Figures and much clearer text that doesn't jump around could go a long way to making it easier to follow.

      Answer: __ We thank reviewer 1 for the suggested changes. We feel that recombining the results from previous versions of the figures helped to improve the clarity in this section. Single cell data was updated to include an UMAP of the muscle subset and gene expression plots highlighting the differential expression in either smooth- striated or both muscle types corresponding to the in situ hybridization (ish) gene expression profile. The figure (__Fig. 6) is now arranged in a way that allows the reader to easily follow the results for the spatial validation of both muscle types since ish for all life stages is shown in one panel together with the muscle subset UMAP and gene expression plots. Additionally, the two muscle clusters are now labelled also in (Fig. 2A) to provide a better understanding for the reader where muscle clusters are located in the UMAP of the full object.

      The text reads now: (Fig. 6, figure caption): (Q) feature plots of all marker genes on the muscle specific subset (R) reference UMAP of whole dataset (left) subset (right) (S) Distribution plot of muscle types across the different Aurelia life stages (left) and medusa tissues (right).

      Discussion -The authors do try to put their results into context with the two Aurelia genome papers (Gold et al. 2018, and Khalturin et al. 2019) and two additional bulk transcriptome studies (Fuchs et al. 2014, Brekhman et al. 2015), but not until the first part of the Discussion. In principle, this would be fine. However, in practice, their discussion of these studies is somewhat vague and generalized and did not really provide a clear review or analysis of how adding in cell-type specific data is helping our understanding. The argument about how their results fit with previous findings was confusing and unclear. They start by discussing "genome usage" but then switch to talking about cell type diversity across life stages. The connections between "genome usage", "gene representation", and cell types was not easy to follow. Suggest rewriting this section to clearly discuss the findings in this manuscript in the context of previous studies with straightforward and precise language.

      -In the discussion about the neural subtypes, comparisons are only made to Nematostella where there are also two major neural classes. It would be even better to include discussion of single-cell data related to neurons in other cnidarians, such as Hydra, where there is detailed discussion of neuron subtypes in both a published manuscript (Siebert et al. 2019, Science) and a preprint (Primack et al. 2023, biorxiv) and Clytia (Chari et al. 2021, Science Advances). I do see that Clytia and Podocoryna are mentioned in the next section of the Discussion, specifically related to the Otx gene.

      Answer: We thank the reviewer for this oversight. We have incorporated comparative observations from the published Hydra dataset in this regard.

      Pg 21 “ This contrasts with the distribution of n1 and n2 class neurons in the freshwater hydozoan polyp Hydra vulgaris, of which only three of the fifteen sub-types are of the ins-positive n1 type (“ec2”, “en2”, and “en3”: Fig. S8D; (58)). Similarly in the Clytia medusa only one of the three neuron groups (neuron cells “A” (16) have INSM reads and thus could be considered type 1 neurons as defined here.”

      -The section about muscle subtypes in the Discussion would need to be rewritten in accordance to changes suggested above for the Results for this section.

      Answer: Discussion was rewritten according to the changes made in the results section like suggested by reviewer1.

      Materials and Methods -In the section "Comparison with Nematostella" the authors discuss running OMA to generate the set of identified 1:1 orthologs but never go on to mention how many orthologs were identified. Please report this number so it is clear whether this is a small or large subset of the total analyzed. In a recent study of the Hydra AEP strain (Cazet et al. 2023 Genome Research), a similar analysis was done between Hydra and Clytia and they found 5979 genes with 1:1 orthologs between the two species. There should also be a supplemental datasheet that provides a list of these orthologs (See Supplemental Data S17 provided in Cazet et al. 2023 as an example). I am curious to know how many 1:1 orthologs were found between Aurelia and Nematostella. I would expect there to be a smaller overall number than between Hydra and Clytia due to the larger phylogenetic distance between these two taxa. I also strongly suggest that the Cazet et al. 2023 paper should be referenced, as it was the first time an attempt to compare single-cell datasets between two cnidarian species was done. The current manuscript took an alternative approach to comparing Aurelia to Nematostella, so it would be good to acknowledge this and justify the methods used in this manuscript compared to those used in Cazet et al. 2023.

      Answer: We recognize our oversight in not properly referencing the previous study comparing two cnidarian species and have integrated this reference now, and include the requested information regarding our OMA analysis as follows:.

      In total 4311 1:1 gene orthologs between the two species were identified (Data S2.). A similar comparison using OrthoFinder (90) between Hydra and Clytia, both members of the Hydrozoa clade, found 5979 1:1 orthologs (66). OMA was preferred in this study over other available orthology databases because it outputs a high-confidence predicted 1:1 gene orthology list that can be used directly to combine multi-species data.

      -There are missing descriptions of methods throughout the paper. One example is in the section about Transcription Factor families that are over or underrepresented amongst upregulated genes compared to their distribution in the genome - I could not find any description of the methods used to identify these Transcription Factor families in the dataset of Aurelia upregulated genes. How were these families chosen? How were they identified in this dataset?

      Answer: Transcription factors were identified and classified using the Animal Transcription Factor Database version 4. (https://guolab.wchscu.cn/AnimalTFDB4/#/). This information has been added to the manuscript methods.

      -I noticed in the Data and materials availability statement and a few other places in the manuscript, a github repository was mentioned: https://github.com/technau/AureliaAtlas. I tried to access this repository to review what was included, but unfortunately it is not accessible. I found seven repositories within github.com/technau but the AureliaAtlas was not one of them. This repository should include all scripts to generate all figures and other analyses in the paper and should be made available to reviewers to better understand exactly how all analyses were completed. A good example of how this could be done is found in the repository related to Cazet et al. 2023 (https://github.com/cejuliano/brown_hydra_genomes), which is very comprehensive and easy to follow. -When I looked through a similar repository https://github.com/technau/CellReports2022/ from the Steger et al. 2022 Cell Reports Nematostella single-cell paper from this same group, I find it to be rather disappointing. They apparently included all code to generate all figures in a single R file that is not easy to follow and not well commented. If this is the same strategy used for this manuscript, I feel that a much stronger effort could be made to make the analyses of this Aurelia manuscript transparent by producing a github that is more like that of https://github.com/cejuliano/brown_hydra_genomes from the Cazet et al. 2023 paper which organizes each type of analysis in a different github subfolder and within each subfolder they include very detailed information and comments explaining each step of each analysis. Doing this would go a long way to making the analyses in this manuscript more transparent and easier to follow and would certainly put some of my concerns to rest.

      __Answer: __We thank the reviewer for pointing this out. We have ensured that the github page is publicly accessible. We have provided all of the necessary R scripts to generate the analysis and figures. The structure is improved over the Steger paper; separate scripts are provided for each step, including importing and processing the raw data for the Seurat workflow, data processing to assess the life cycle and first clustering, analyses of each subset, and finally calling results from the previous scripts to generate all figures contained in the manuscript.

      Minor comments:

      Figures: Figure 2A: In the legend it says "Colour code as in (B) and (C)" but it's really referencing the colors in Figure 1A, correct? It is confusing to have to look back to Figure 1A to understand the colors here.

      __Answer: __The original figures 1 and 2 have been modified and combined into a single figure in this version.

      Figure 2D: Typo in the word "proteins" in the title of this panel.

      __Answer: __This word no longer appears in the revised figures.

      Figure 3F: The placement of the tree and the two featureplots for myc3 in Nematostella and Aurelia is confusing. Suggest moving the featureplot for Aurelia myc3 so that it is beside Nematostella (to the right of the tree) or move the featureplot for Nematostella myc3 so that it is beside the Aurelia featureplot (to the left of the tree).

      __Answer: __We thank the reviewer for this suggestion and have edited this figure accordingly by moving the myc3 expression plots alongside all of the others.

      Figure 4B: The description of this panel reads, "Distribution-histogram across all samples, medusa-specific cell clusters are highlighted with black outline.", however as a reader, the black outline is not very clear. Suggest making it bolder. In addition, this black outline is a little confusing - it should mark the medusa-specific cell clusters; however, the black outline appears in cell clusters in strobila and ephyra?

      __Answer: __ The black outline is now increased in width for clarity. Medusa-specific cell types are defined by their absence from the polyp samples because already in the strobila stage medusa-specific tissues are being generated and thus these transcriptomic profiles begin to appear. We added a clause in the figure legend to clarify this, as well as within the main text when medusa-specific cell states are first defined.

      Pg.8: “ In total we find 12 cell type states that are not represented (<br /> Figure 5B: It is unclear from where this reference UMAP was derived. Does it come from the overall UMAP, showing the 'outer epidermis' cluster only, with the putative smooth muscle cells in red? Or is it the 'outer epidermis' cluster plus the striated muscle cluster? Suggest making this clearer (see below for larger edits to this section of the manuscript).

      Answer: This has been addressed. Figure 6R now includes both the full dataset inset, as well as the muscle-only subset and is consistent with the rest of the manuscript in this regard.

      Figure 5K/L/M: It is unclear which parts of the polyp in K is used for the images shown in L or M. Both come from the large red box, but it is unclear from which part L and M were made. In addition, the subtraction of the background from the image (to make it look white) is distracting and makes the image itself look artificial.

      Answer: New brightfield images were included to give a better understanding of the region of interest. The images in which the background was subtracted were replaced with the original pictures and contrast was enhanced to brighten the background.

      Figure 6C, G-S: - Not sure what the blue boxes around these panels are meant to highlight? - Also not sure what the image in the left of panel C is. Perhaps an oral view of the strobila? The legend or panel itself should mention this. - Again, subtraction of the background from the image (to make it look white) in panels C, D and E is distracting and makes the image itself look artificial.

      Answer: The figure was redone and the boxes are not present anymore.

      Figure 6J, M, N, O: - For someone not accustomed to looking at images of strobilating polyps, it is unclear what part and what orientation these images are taken of. Suggest including some of these details in the figure legend at least. Fig 6O actually looks like an ephyra, but is annotated as an "advanced strobila"?

      Answer: Figure was re-done (fig.6) with appropriate schematics next to the images.

      Figure 7H: - Not sure what the white lines in this panel are meant to indicate?

      __Answer: __The white lines were removed.

      Results: p5 - In this sentence, "Because these four pouches look like a cloverleaf from above, we call this stage the "clover-polyp", suggest changing "clover-polyp" to match the Figure 1A (where it is written as polyp.clover), or change the text in the Figure to match the text in the manuscript.

      __Answer: __ We made sure to match this in the revised figure.

      p8 - In this sentence, "the bZIP protein family are over-represented as terminal cell type markers, while the number of zinc-finger proteins of the N2C2 class are under-represented", the "N2C2" class the authors refer to is not clear. Is there a typo here? In the figure to which this sentence refers (Figure 2D), the proteins referenced are "zf-H2C2" or "zf-C2H2".

      __Answer: __This no longer appears in the current manuscript.

      p9 - Typo - should be "medusozoans" rather than "medusazoans".

      __Answer: __This has been corrected.

      p11+ - Section titled, "Aurelia neural complement reveals two neural classes with similarities to anthozoan neurons" - I found the classification of N1 and N2 to be confusing, since initially they are described as neural clusters, however N1 in particular is shown to consist of primarily secretory, non-neural cell types. For example, when looking at Figure 4A and B, it is evident that N1 contains only a relatively small number of neural cell-types (in shades of orange), while most of the cells are other secretory, but non-neural cell types (in shades of brown). Not sure if the authors should alter the title to reflect this? For example, instead of 'neural' classes, they could be called 'neuro-secretory' or 'mixed neural and secretory classes'?

      __Answer: __We appreciate the confusion and have adjusted the heading accordingly. However we choose to maintain the designation as N1 and N2 class to reflect the distinction between insulinoma-positive and pou4-positive major Cnidarian neuroglandular sub-types present as defined in our earlier Nematostella work (Steger et al., 2018). We also include a comment in the discussion regarding the support for this distinction in other published Cnidarian dataset as follows.

      ”This contrasts with the distribution of n1 and n2 class neurons in the freshwater hydozoan polyp Hydra vulgaris, of which only three of the fifteen sub-types are of the ins-positive n1 type (“ec2”, “en2”, and “en3”: Fig. S8D;(58)).”

      p11 - Text reads, "Class 1 neurons in the medusa are also most prevalent within the gastrodermis and manubrium, and includes one subtype that first appears in the strobila and is found in all medusa tissue samples ("n1.3.medusa"; lower black box Fig. 4F).", however there is no "lower black box" in Figure 4F apparent.

      __Answer: __Re-evaluation of the detectable cell states after updating the mapping tool, which addresses issues associated with an overabundance of isoforms, results in the dissolution of this putative medusa-specific cell state. This profile is also found within the polyp and so the second half of this sentence has been removed.

      p13 - The text reads, "We find that class 2 neurons all express elevated levels of specific alpha- and beta- tubulins (TBA1-like3 and TBB-like-1; Fig. 4D).". Make the capitalization of your gene names (TBA1-like3, etc) consistent between text and figure throughout (in Fig. 4D the gene names are lower case).

      __Answer: __We have taken care to be consistent throughout the manuscript.

      p14 - In the first paragraph of this page, Fig. 4C is referenced twice, however both times the referencing sentence does not match this panel (most likely the authors meant to reference 4E, F or G).

      __Answer: __This has been corrected.

      p14 - The final sentence of this upper paragraph, "Specific tubulin-paralog expression within the class n2 neurons suggest that this is the portion of the nervous system labelled by the β-Tubulin antibody." is confusing. Do you mean that the b-tubulin antibody is most likely labelling the product of the tbb-like-1 gene that is shown in the featureplot in Fig 4D? Suggest rewriting this sentence for clarity.

      __Answer: __This sentence has been re-written as follows: “Specific tubulin-paralog expression within the class n2 neurons suggests that these two genes are translated into proteins recognised by this commercial β-Tubulin antibody. Furthermore, this antibody labelling suggests that the MNN is composed of N2 class neurons.” pg 14

      p14 - on this page and others in the manuscript, there are instances of the word "Aurelia" not being italicized.

      __Answer: __This has been corrected.

      p14 - In this sentence, "In the sea anemone Nematostella, anemone-specific gene duplications of members of the PaTH (Paraxis, Twist Hand-related) bHLH family of protein coding genes was driving the diversification of muscle cell types (29)." the "was driving" part of the sentence is grammatically clunky. Suggest rewording slightly. (e.g. "...protein coding genes drive the diversification of muscle cell type").

      __Answer: __We changed this to ‘drove’.

      -Myophilin-like2 in the text of the manuscript is written as myofilin-like2 in the figure panels (e.g. Fig 5L, Fig. 6D). Make consistent between text and figures.

      Answer: We changed all references to myophilin to calponin, which is the better known name of the vertebrate ortholog.

      p15 - on this page and several instances thereafter, "in situ" is not italicized as it should be.

      __Answer: __This has been corrected

      p19 - In the line, "Taken all together these data suggest that the contractile apparatus in the Scyphozoa, using here Aurelia as a proxy, is similar to the bilaterian smooth muscle contractile complex (Fig. 8C)." this should really reference Fig. 8 B-C

      __Answer: __This has been corrected according to the newest figure.

      Reviewer #1 (Significance (Required)):

      General assessment:

      I believe this manuscript adds a significant amount of useful data and provides some novel insights into scyphozoan cell types across an important life history transition from polyp to medusa in Aurelia. Adding the dataset to the USCS Cell Browser is a strength. I think there is the potential to make this an impactful paper but in its current form, it is pretty messy, and not clearly presented, and lacks some transparency. The greatest weaknesses lie in not framing the work adequately or putting it into enough context with previous work and also not relating it to other medusozoans; in the Figures which are overly crowded, and confusing rather than being clear and supporting the results; and in the lack of explanation for some methods like how cell clusters were annotated, how transcription factor families were determined; and the lack of access to the github data repository, which raises questions of reproducibility. It will take a good amount of restructuring figures and reframing to make the study clear and impactful and the methods and analyses reproducible.

      Advance: If the weaknesses are addressed adequately, this study does contribute new insights in the area of further understanding changes across an important scyphozoan life cycle transition in terms of diversity of cell types and their cell-type transcriptomes, opening up further questions which can now be addressed.

      Audience: The broader cnidarian community will be interested in this study. People studying cell type evolution and cell type novelty across the tree of life will also be interested. Anyone looking for examples of how to use modern approaches to understanding life cycle changes in animals will be interested.

      My expertise is in cnidarian cellular and molecular biology and evolution including working with model cnidarian research organisms and employing techniques and approaches similar to those used in this study.

      We thank this reviewer for their detailed comments and suggestions, and feel the manuscript is much improved in its current form. We hope that we have satisfied all concerns raised here.

      __Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      __This paper is well-written and serves as a valuable resource not only for the cnidarian community but also for researchers studying more broadly cell type identity and evolution. A key cell type enabling the transition from polyp to free-swimming medusa is the cnidarian striated muscle, which has only been morphologically identified in medusozoan jellyfish. While this study does not include functional analyses, it lays the foundation for the Aurelia research community to leverage single-cell atlas data for future investigations.

      Key experiments supporting the paper's main conclusions are missing :

      •At the beginning of the Results section, the authors mention identifying a previously undescribed developmental stage, which they name "clover-polyp" However, they do not later discuss whether this newly identified stage has a distinct gene expression signature. This point should be addressed in the paper or removed.

      __Answer: __We do not find any specific transcriptomic signature specific to this stage. We keep this designation as a morphological indicator of a strobilation-competent polyp, but have re-worded our introduction of this term as follows:

      “The first external sign of strobilation is the expansion of the body column into four pouches that are filled with multiple folds of inner cell layer epithelia (Fig. 1A), and resembles a cloverleaf from above; we call this stage the “clover-polyp”.”

      •A key reference is missing in the following sentences :

      "The anthozoan Nematostella vectensis has two principal neural sub-families that have been described that correspond to those with insulinoma expression (n1) and those with pou4 expression (n2) (13,14)."

      "The class n1 family also includes putatively non-neural secretory cell types ("s"), which are enriched in genes associated with digestion and extracellular matrix production (Data S1.10). These data suggest a close relationship between neurons and gland cells, like what has been suggested in other cnidarians (13,27)."

      "Thus, similar to that described for the anthozoan Nematostella vectensis (13,14), Class 1 neurons and related secretory cells comprise the predominant type of neuroglandular cells in the polyp stage. Further, these are the primary neuroglandular cells within the gastrodermis of the medusa."

      The first functional analysis of NvInsm1+ expressing neurons and secretory cells in Nematostella vectensis was conducted in this study (Tournière, O. et al., 2022), making it essential to cite this work.

      __Answer: __We appreciate the reviewer for drawing this oversight to our attention. This has been corrected in the revised manuscript.

      • To validate the neuronal component of this single-cell data, it is essential to confirm the N1 and N2 populations and demonstrate that they do not overlap. I recommend performing in situ hybridization or antibody staining for Insm1+ and Pou4+ cells (or any other suitable markers for these populations) to show that they are expressed in distinct cells/region in Aurelia.

      __Answer: __We appreciate the reviewers comment, however, there are unfortunately no specific antibodies available for Insm1 or Pou4, or any other n1/n2 specific neuronal marker protein. Moreover, we find in situ hybridization in this system to be very challenging except for highly expressed structural genes. Neurons are particularly difficult, because they are very small cells embedded between many other cell types. We attempted to validate distribution of different neuron populations with colorimetric in situ hybridization, FISH as well as HCR (hybridization chain reaction). However, we were not successful in labelling individual neuron bodies and visualising their cytoplasmic RNA content to distinguish individual cells and therefore individual neuron types. Regardless, to validate at least neuronal cell types, we were able to correlate pan-neuronal tbb-like expression with b-Tubulin antibody staining and of RFamide antibody staining with specific neuronal subpopulations.

      •What is labelled in yellow in Figure 5C? The legend should be updated.

      Answer: Figure 5C does not exist in the current version of the manuscript.

      •Figure 5i, j, and k, are not clear, the paper would benefit with bright field pictures.

      __Answer: __Images were replaced and some bright field photos are incorporated into both new figures.

      •Each figure should connect specific gene expression at a given stage with the corresponding single-cell expression data in a dot plot. For instance, in Figure 6, myofillin-like 2, mhc1, and mhc2 should be accompanied by their respective single-cell expression data at this stage in a dot plot.

      Answer: done!

      • The authors repeatedly refer to the polyp as asexual and the medusa as sexual; however, they do not mention any gonadal cluster nor discuss its absence from their single-cell data.

      __Answer: __We have added the following sentence to the current manuscript to account for this: “Despite its larger size, this animal was still reproductively immature and so no gonadal tissues were collected.”

      •The authors include EdU experiments in Figure S2 but discuss them only briefly in the text. If these experiments provide new insights, they should be elaborated on; otherwise, they could be removed from the manuscript.

      __Answer: __We have removed these data from the manuscript.

      • As this paper is primarily a resource for the cnidarian community, ensuring easy access is crucial for enabling species comparisons. I recommend making the data openly available through a single-cell portal, as done in Juliano et al. (2019).

      __Answer: __We have already released these data on the UCSC cellbrowser platform, as was stated in the manuscript. These data have been updated to reflect the current status of the analyses and is publicly available at www.jellyfish-atlas.cells.ucsc.edu

      Reviewer #2 (Significance (Required)): This well-written paper is a valuable resource for the cnidarian community. A key cell type driving the transition from polyp to free-swimming medusa is the cnidarian striated muscle, which has only been morphologically identified in medusozoan jellyfish. While the study lacks functional analyses, further biological validations, such as in situ hybridizations, are needed to confirm the single-cell data. Nevertheless, it lays a strong foundation for the Aurelia research community to utilize single-cell atlas data in future studies. To maximize its impact, the authors should ensure the data is easily accessible to the broader scientific community.

      We thank this reviewer for their recognition of the importance of this work. We have ensured that the data are available for download through the UCSC cell browser, and all scripts used in the data analysis are available on our github page. We additionally included our new gene models that are associated with the single cell data on the companion UCSC genome browser website, which now hosts the NCBI genome assembly with our gene models.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      The manuscript by Link and collaborators presents a well-executed and thorough analysis (statistically significant) of cell types and developmental trajectories in Aurelia coerulea, a cnidarian with a medusa stage. While previous cnidarian cell atlases have focused on embryo-to-polyp development, this study uniquely incorporates adult medusa-stage cells, providing novel insights into cnidarian biology.

      The authors successfully identify a broad range of cell types and precursors in both polyp and medusa stages. By comparing transcriptional profiles, they demonstrate the presence of new cell types, such as neurons, in the medusa. Notably, they provide compelling evidence for the coexistence of both striated and smooth muscle within cnidarians-a topic they have explored in previous work. Their morphological analysis further suggests that striated and smooth muscle forms can exist within single cells, which is particularly intriguing. Overall, the results are convincing.

      A major strength of this study is the extensive number of cells analyzed and the rigorous classification of cell identities based on transcriptional profiles. Unlike many single-cell studies, the authors complement their findings with morphological, immunochemical, and in situ data, strengthening their conclusions. Conducting such an analysis without a fully annotated genome presents a significant challenge, yet the authors navigate this limitation effectively.

      One relative limitation, common to many single-cell studies, is the lack of detailed spatial information on the identified subtypes. While the authors have made efforts in this direction, a higher-resolution atlas that pinpoints these subtypes within the body would enhance the impact of the study. The absence of transgenic tools with cell-type-specific enhancers makes this difficult, but it remains a valuable avenue for future research. Despite this, the study's novelty and quality-particularly its inclusion of medusa-stage data-make it a strong candidate for publication in any journal associated with Review Commons.

      Minor Comments: • The term "terminal cell type markers" may not be the most appropriate for transcription factors that regulate state or specification. A more precise term, such as "state or specification transcriptional regulators," might be preferable.

      __Answer: __This term does not appear in the revised manuscript.

      • The suggestion that cell-type specification is not governed by a random collection of TFs seems self-evident. If not TFs, what alternative regulatory mechanisms (e.g., post-transcriptional regulation, small RNAs) are being implied?

      __Answer: __In the revised manuscript we have removed focus on the TFs.

      • The rationale behind the observation that "'early' cells separate along three principal trajectories (cnido.1, cnido.2, and cnido.3m), then converge upon a second mature transcriptomic phenotype" could be more clearly explained.

      __Answer: __This is a phenomenon that is now well established for cnidarians from the perspective of single cell transcriptomics (Chari et al, 2021: Clytia; Steger et al, 2022, Cole et al 2024, Plessier and Marlow 2026: Nematostella; Cazet et al 2023: Hydra). This phenomena is also described here in terms of the sequence of transcription factors that are activated sequentially in both Aurelia and Nematostella. We have modified the introductory text to better place these observations in context as follows:

      Recently we reported that within the sea anemone Nematostella vectensis, specification of the distinct cnidocyte types is marked by a diverging transcriptomic profile corresponding to the formation of the different capsule types, which then undergo a molecular switch demarcated by up-regulation of GFI1B and converge upon a secondary neural-like expression profile (11). Notably, we find a similar forked trajectory within the cnidocyte population of Aurelia. (Fig. 3A). A cluster of SoxC expressing ‘early’ cells separate along two principal trajectories (cnido.1, cnido.2), which then converge upon a second mature transcriptomic phenotype upon activation of jun/fos (Fig. 3E).

      • The illustrations of the nervous system in the ephyra and rhopalia are intriguing but lack spatial context for different neuronal populations beyond the positioning of class 2 neurons ("alpha- and beta-tubulin cells").

      Answer: We added a better introduction to gain more understanding of the different neuron populations in contrast to various findings of related publications. The text now reads:

      This rhopalia nervous system develops during polyp-medusa metamorphosis and is composed of specialized light- (pigment cup) and gravity- sensing (lithocyte/statocyst) cells, segregated into individual compartments with different developmental origins (12). Rhopalia development involves the gene expression of otx1, pit1 and brn3 in the pigment-cup (10),.... p4/5

      Further, we used findings from previous studies to add a more elaborate description to our results and we finally discuss it, for example:

      The ins-negative populations in both species express pou4 orthologs, also called brn3 (10), that is expressed also within the cnidocyte lineages and thus further supports claims of a close relationship between cnidocytes and insulinoma-negative/pou4-positive n2 neurons (13,14,52). p22

      • Muscle characterization is well-supported by phalloidin staining and gene markers, but is there a specific marker for smooth muscle? Myophilin-like-2 is mentioned, but is it definitive?

      Answer: Yes, there are many, as tabulated in supplemental Data S1.11. For example myophilin-like-2 [calponin] is a specific marker for smooth muscle cells and this is demonstrated via in situ hybridization in fig.6.

      • The finding that ~40% of genes distinguishing smooth and striated muscle lack homologs in other animals is striking. It may be worth investigating their expression patterns via in situ hybridization, particularly for those that differentiate muscle types. The fact that these genes are of unknown affinity does not mean they are uninformative.

      __Answer: __There are a variety of reasons that lead to a lack of orthology information amongst the gene models, including fragmented gene models, inclusion of unidentified lncRNAs, amongst others. However, due to this ambiguity and the lack of identification of these rationals we have removed this observation from the current manuscript. In fact, with the updated mapping tool and current gene annotations this number has fallen to only ~28% of the identified muscle-specific gene models, from a total ~38.7% unannotated gene models in the entire transcriptome. This is similar to other cells types in the dataset (between ~20%-35%), and also similar to the number of unannotated genes in the sea anemone Nematostella vectensis (36.5% overall)

      • The incompleteness of Aurelia genomes is acknowledged as a limitation. However, since the San Diego strain genome appears to be the most complete, is there a reason it was not used in this study? Was it not possible to recover the same strain?

      __Answer: __We have a standing culture in the lab that was used for these collections. While we considered generating a genomic assembly for this laboratory strain, we have concluded that this is not an effective use of resources at this time. We have now updated the reference for mapping however, from a re-analysis of the available Aurelia coerulea isolate AC-2021 genome (NCBI: GCA_039566865.1) annotated with the Gnomon 9.0 automated annotation pipeline, and supplemented with our in-house transcriptome to recover ~5000 additional gene model coordinates on the genome. These are available now via the UCSC genome browser website.

      We further thank this reviewer for the overall positive assessment of our work, and hope that the revised version further strengthens the data analysis and contribution to the community as a whole.

      __ **Referees cross-commenting**__

      Referees, I generally agree with their assessments. Below, I outline my main concerns and suggestions for improvement.

      Figures and Data Presentation

      I concur with Referee 1 that the figures are overcrowded, making it difficult to interpret individual panels. The excessive number of panels within a single figure creates unnecessary complexity. Some of these could be moved to the supplementary materials to improve readability. It seems that the authors aim to present every possible data analysis, but this is not necessary within the main text. As Referee 1 also noted, the key findings should be clearly visible, allowing the reader to follow the story without getting lost in excessive detail.

      __Answer: __We have re-structured most of the figures with this in mind and hope that we have achieved better clarity. Many of the data analyses in the previous versions have been removed if not directly related to the observations highlighted in the current version.

      Additionally, the annotation of clusters remains unclear, a concern also raised by other referees. The manuscript would benefit from a more explicit description of how these clusters were assigned.

      __Answer: __We have expanded our description of how we assigned identities to the nine principal cell type families as follows:

      (pg. 8) The inner epithelia, or gastrodermis, expresses several collagens that is a characteristic of the inner cell layer of anthozoans (39); the outer cell layer houses the ring musculature and is rich in contractile proteins. The striated muscle cluster is also rich in contractile protein and is the only principal cell population absent from the polyp-derived samples (Fig. 2C). The mucin gland expresses mucins, whereas the digestive gland expresses other digestive enzymes, whereas the neural cluster expresses synapsin and other conserved known neural regulators such as ashA. The cnidocytes express mini-collagens and are enriched in pathways targeting the endoplasmic reticulum (40).

      Writing and Discussion

      While I do not have major concerns with the writing, I suggest expanding the discussion, particularly regarding the relationship between muscle cell types and the diversification of paralogs. If the figures are streamlined, the text can also be made more concise, avoiding exhaustive references to every individual data point.

      Clarifications on the Muscle Section

      Several aspects of the muscle analysis require clarification: • The differences between muscle cell types are based on a set of differentially expressed genes, 40% of which (in each set) are of unknown affinities. However, it is surprising that the regulatory genes shared between both muscle profiles are expressed in bilaterian smooth muscles. The manuscript does not address whether bilaterian striated muscles share regulatory genes with the Aurelia striated muscle set. This comparison would be valuable.

      Answer: __With the latest mapping tool the percentage of muscle-specific genes of unknown affinities has dropped to ~28% and we no longer highlight this observation in the manuscript. Regarding the regulatory genes shared with smooth muscles of bilaterians, we feel this may be a misunderstanding. In Fig. 7 we clarify that these are __structural proteins regulating the contraction of the muscle (e.g. Myosin light chain kinase and calponin). With respect to the developmental regulators, e.g. muscle cell type determining transcription factors, we list several in Data S1.3b, S1.4b. A broader phylogenetic and also functional analysis of these transcription factors in different jellyfish species is the focus of another collaborative study and therefore we do not include an in depth discussion of this topic in the current manuscript.__ __

      • The high proportion of unknown genes is concerning. Is this due to issues with the transcriptome assembly, or is it a consequence of insufficient comparative analyses? The statement that "Mapping to this final transcriptome increased confidently mapped genes to 60%" raises questions-does this mean that 40% of differentially expressed genes remain unmapped? This point should be clarified.

      __Answer: __With the latest mapping tool, we now recover a confident alignment for ~80% of the sequences (See supplementary data S2.1). With the previous tool this value was only 60%, which means that 40% of the sequence data could not be used at all to generate the expression matrix. This is a different feature of the data analysis than the identity of the gene models. However, the statement mentioned here no longer appears in the current version of the manuscript.

      • Given the large number of differentially expressed genes with unknown function, could the authors perform in situ hybridization assays on a subset of these genes? This could provide insights into their spatial expression patterns and potential functional relevance.

      Answer: This is an intriguing suggestion, however, given that in situ hybridization for medium and low expressed genes are extremely difficult in this organism, we feel that this is beyond the scope of this study.

      • Both muscle types appear to rely on a similar contractile apparatus but exhibit differential usage of paralogs. This finding is intriguing but is not sufficiently discussed. Are other cell types associated with the differential use of paralogs? Expanding this discussion would add depth to the manuscript.

      Answer: We thank the reviewer for this insightful comment. Indeed, there is circumstantial evidence that differential usage of paralogs is also found among other cell types, e.g. neurons. We indeed discuss the example of a few other genes, e.g. ATOH-like transcription factors and myc. However, the diversity of neuronal populations is very large, which makes the picture quite complex. We are currently working on a phylogenetic framework of cell type families and also between species to address this point, but this requires more theoretical and methodological work. In this paper, we therefore restricted the analyses to the structural proteins of the two types of muscles, which facilitates the assignment of paralogs to either muscle. We point out that this is reminiscent of the differential expression of paralogs in the fast and slow contracting muscle cell types in Nematostella, suggesting that such a subfunctionalization may generally drive also the physiological diversification of muscle cell types in cnidarians (and of animals in general). Future work is aiming to address this on a broader scale, as suggested by the reviewer.

      Neuronal Subtypes

      I reiterate my previous comment regarding neuronal types: • The enrichment of neural subtypes in the medusa stage is an interesting, albeit expected, finding. However, the manuscript lacks details regarding their specific spatial distribution within the body. Providing this information would enhance the biological relevance of the findings.

      Answer: in situ hybridization for neurons is a challenge in all cnidarians, because the small neurons with very thin neurites are embedded and intermingled between many other cell types. In Aurelia, this has proven to be particularly difficult. At the very best, one might see small cell bodies stained, however, it fails to visualize neurites. We also tried HCR (hybridization chain reaction) in combination with antibody staining (b-Tubulin) to get to single cell resolution. However, the results were not conclusive and we therefore refrain from showing them in the paper. As an alternative we connected the findings of previous studies (Nakanishi et al., 2009, 2010) in terms of certain types of neurons located in different compartments of the rhopalia and corresponding marker genes with our single cell data (introduction/discussion). We acknowledge that more work needs to be done, best by generating specific antibodies against neuronal antigens. However, this is beyond the scope of this paper.

      References

      I also agree with Referee 2 that some statements require further substantiation with appropriate references. Strengthening these points with supporting literature would improve the rigor of the manuscript.

      Answer: We added appropriate references at all places indicated, as detailed above.

      Final Remarks

      Overall, while the study presents interesting findings, the manuscript would benefit from a clearer organization of figures, a more explicit explanation of muscle and neural subtype findings, and a deeper discussion on the significance of unknown genes and paralog usage. Addressing these concerns will enhance the clarity and impact of the paper.

      Reviewer #3 (Significance (Required)):

      Overall, this is a significant and well-supported study that advances our understanding of cnidarian cell diversity and muscle evolution. By examining how cell types change across the polyp and medusa stages, this study provides valuable insights not only into cnidarian development but also into broader evolutionary questions regarding the emergence of new body plans and tissue types. As a developmental biologist specializing in invertebrates, I find the results of this work particularly remarkable. It provides valuable insights into the developmental processes occurring in pre-bilaterian animals, shedding light on how cell types emerge and diversify in early-diverging metazoans

      Answer: We thank reviewer 3 for this positive evaluation.

      __Reviewer #4 (Evidence, reproducibility and clarity (Required)):

      __Link et al. have studied cell type diversity in the scyphozoan Aurelia coerulea. More specifically, they compared several stages in the animal's life cycle using single-cell RNA-seq. Many members of the cnidarian clade Medusuzoa (scyphozoans included) have a metagenetic lifecycle that includes a sessile, clonally reproducing polyp and a free swimming, sexually reproducing medusa (jellyfish). The two phases are fundamentally different in their functional morphology, but the cellular basis of this difference has been unknown. The authors generated single cell RNA-seq libraries from eight life-cycle stages of the animal to include polyps, and medusae. Their main finding is that different cell types underlie polyp-medusa transition in this animal. Although expected intuitively, this finding has never been demonstrated experimentally. Moreover, a recent study on a colonial hydrozoan (Salamanca-Diaz et al. 2025) has shown that colony parts, as opposed to different life stages, use largely the same cellular components. Therefore, the current study is of broad interest to developmental and evolutionary biologists. Overall, the experiments and data analyses have been performed to a high standard, the figures are of good quality, and the manuscript is well written. Below are a few minor points to be addressed.

      The Aurelia strain used in the study is somewhat ambiguous (suggested to be A. coerulea). The authors' statements on pp. 24, 25 are somewhat confusing--they first say they got over 90% alignment to the San Diego strain genome assembly but then state (in the 'Transcriptome mapping' section) that they got only 40% of their reads aligned, forcing them to use Trinity de novo transcriptome assembly. Please clarify.

      __Answer: __Alignment to the genome is different from assignment of the alignment to a gene model. Ambiguous alignment cannot be assigned, and missing gene models would not have an assignment. However, we have switched the mapping tool used for this dataset for one that fits both genome sequence alignment AND gene model assignment better than the previously available choices. We now have ~80% of all sequences unambiguously aligned to the genome.

      1. 7--the authors state that some transcription factor families are over/underrepresented as terminal type marker. How do they know which cells are terminally differentiated.

      __Answer: __We have removed our focus on transcription factor families in this work and recognize that the definition of a terminally differentiated cell state from single cell transcriptomics has not been clearly defined.

      The homeobox gene Tlx has been reported to be associated with medusa development, being absent in taxa without medusae (Travert et al. 2023). Is it expressed in the Aurelia medusa (I couldn't find it in the data), and if so, where?

      __Answer: __This is indeed a good point that we were also interested in. However, Tlx is detected ONLY in the ephyra libraries and at very low levels which is why we chose to avoid discussing it as the low detection prevents accurate reporting of the expression and could reflect rather a mapping problem for this gene (mis-annotated 3’ end). As information for this reviewer, the gene model shows some spurious reads specifically in a few neuron subtypes, and outside the ephyra is lowly detected ONLY in the medusa library for medusa neuron n.7 (n2.7m).

      I do not quite understand the authors' arguments for independent striated muscle evolution in cnidarians and bilaterians. Key striated muscle genes (e.g., titin) are present in hydrozoan and anthozoan genomes; furthermore, the expression patterns of Otx is not indicative because its function in medusozoans is unknown. What are the arguments against an alternative scenario in which striated muscles evolved before the cnidarian-bilaterian split, but lost in anthozoans?

      Answer: This is indeed a complex question, which requires a more thorough and targeted comparative analysis. We note that a BLAST hit for Titin can be misleading due to the many domain repeats of this Titin, which are also found in other proteins. To be more prudent, we removed this part from the manuscript. This will be subject of a future, thorough study.

      1. 27, the link https://github.com/technau/AureliaAtlas is broken.

      __Answer: __We appreciate this comment and have ensured that the github archive is publicly available with all relevant scripts associated with all versions of the BioRxiV record.

      p. 24 (limitations of the study section), the authors refer to "cosmopolitan species"; they probably mean "genus".

      __Answer: __We changed to “taxon” and dropped cosmopolitan.

      p. 24-25 on two occasions in the M&M sections, the authors put the abbreviation first and the initials in brackets (ASW and BSA).

      __Answer: __This has been corrected.

      "Metagenic" should be "metagenetic"

      __Answer: __This has been corrected.

      Reviewer #4 (Significance (Required)):

      The study is of broad interest to developmental and evolutionary biologists. It addresses an important question, not dealt with directly in previous studies.

      Answer: We thank reviewer 4 for this positive and encouraging assessment.

    1. Reviewer #2 (Public review):

      Summary

      Previous studies by some of the same authors of the actual manuscript showed that healthy human newborns memorize recently learned nonsense words. They exposed neonates to a familiarization period (several minutes) when multiple repetitions of a bisyllabic word were presented, uttered by the same speaker. Then they exposed neonates to an "interference period" when newborns listened to music or the same speaker uttering a different pseudoword. Finally, neonates were exposed to a test period when infants hear the familiarized word again. Interestingly, when the interference was music, the recognition of the word remained. The word recognition of the word was measured by using the NIRS technique, which estimates the regional brain oxygenation at the scalp level. Specifically, the brain response to the word in the test was reduced, unveiling a familiarity effect, while an increase in regional brain oxygenation corresponds to the detection of a "new word" due to a novelty effect. In previous studies, music does not erase the memory traces for a word (familiarity effect), while a different word uttered by the same speaker does.

      The current study aims at exploring whether and how word memory is interfered with by other speech properties, specifically the changes in the speaker, while young children can distinguish speakers by processing the speech. The author's main hypothesis anticipates that new speaker recognition would produce less interference in the familiarized word because somehow neonates "separate" the processing of both words (familiarized uttered by one speaker, and interfering word, uttered by a different speaker), memorizing both words as different auditory events.

      From my point of view, this hypothesis is interesting since the results would contribute to estimate the role of the speaker in word learning and speech processing early in life.

      Major strengths:

      (1) New data from neonates. Exploring neonates' cognitive abilities is a big challenge, and we need more data to enrich the knowledge of the early steps of language acquisition.

      (2) The study contributes new data showing the role of speaker (recognition) on word learning (word memory), a quite unexplored factor. The idea that neonates include speakers in speech processing is not new, but its role in word memory has not been evaluated before. The possible interpretation is that neonates integrate the process of the linguistic and communicative aspects of speech at this early age.

      (3) The study proposes a quite novel analytic approach. The new mixed models allow exploring the brain response considering an unbalanced design. More than the loss of data, which is frequent in infants' studies, the familiarization, interference and learning processes may take place at different moments of the experiment (e.g. related to changes in behavioural states along the experiment) or expressed in different regions (e.g. related to individual variations in optodes' locations and brain anatomy).

      Main weaknesses:

      I did not find major weaknesses. However, I would like to have more discussion or explanation in the following points.

      (1) It would be fine to report the contribution of each infant to the analysis, i.e. how many good blocks, 1 to 5 in sequence 1 and 2, were provided by each infant.

      (2) Why did the factor "blocknumber" range from 0 to 4? The authors should explain what block zero means and why not 1 to 5.

      (3) I may suggest intending to integrate the changes in brain activity across the 3 phases. That is, whether changes in familiarization relate to changes in the test and interference phases. For instance, in Figure 2, the brain response distinguishes between same and novel words that occurred over IFG and STG in both hemispheres. However, in the right STG there was no initial increase in the brain response, and the response for the same was higher than the one for novels in the 5th block.

      (4) Similarly, it is quite amazing that the brain did not increase the activity with respect to the familiarization during the interference phase, mainly over the left hemisphere, even if both the word and speaker changed. Although the discussion considers these findings, an integrated discussion of the detection of novel words and the detection of a novel speaker over time may benefit from a greater integration of the results.

      Appraisal

      The authors achieved their aims, because the design and analytic approaches showed significant differences. The conclusions are based on these results. Specifically, the hypothesis that neonates would memorize words after interference, when interfered speech is pronounced by a different speaker was supported by the data, in block 2 and 5 and discussed the potential mechanisms underlying these findings, such as separate processing for different speakers, likely related to the recognition of speaker identity.

      I think the discussion is well structured, although I may suggest integrating the changes into the three phases of the study. Maybe comparing with other regions, not related to speech processing.

      Evaluating neonates is a challenge. Because physiology is constantly changing. For instance, in 9 minutes newborns may transit from different behavioral states and experience different physiological needs.

      This study offers the opportunity to inspire looking for commonalities and individual differences when investigating early memory capacities of newborns.

      Comments on revisions:

      The authors provided satisfactory answers to my concerns.

      I recognize that, because of technical and ethical reasons, the studies with neonates are particularly challenging, however, with a well-balanced design as the one the authors applied, even with small samples the data constitute valuable sources to advance in the field.

      Neonate brain works in a particularly state of intense metabolic, functional and structural changes, which we are far to understand. Current data contribute to fill this gap in knowledge.

    2. Author response:

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

      Reviewer #1 (Public review)

      Summary:

      This manuscript investigates whether newborns can use speaker identity to separate verbal memories, aiming to shed light on the earliest mechanisms of language learning and memory formation. The authors employ a well-designed experimental paradigm using functional nearinfrared spectroscopy (fNIRS) to measure neural responses in newborns exposed to familiar and novel words, with careful counterbalancing and acoustic controls. Their main finding is that newborns show differential neural activation to novel versus familiar words, particularly when speaker identity changes, suggesting that even at birth, infants can use indexical cues to support memory.

      Strengths:

      Major strengths of the work include its innovative approach to a longstanding question in developmental science, the use of appropriate and state-of-the-art neuroimaging methods for this age group, and a thoughtful experimental design that attempts to control for order and acoustic confounds. The study addresses a significant gap in our understanding of how infants process and remember speech, and the data are presented transparently, with clear reporting of both significant and non-significant results.

      Weaknesses:

      However, there are notable weaknesses that limit the strength of the conclusions. The main recognition effect is restricted to a specific subgroup of participants and emerges only during a particular testing window, raising questions about the robustness and generalizability of the findings. The sample size, while typical for infant neuroimaging, is modest, and the statistical power is further reduced by missing data and group-dependent effects. Additionally, the claims regarding episodic memory and evolutionary implications are somewhat overstated, as the paradigm primarily demonstrates memory retention over a few minutes without evidence of the rich, contextually bound recall characteristic of fully developed episodic memory.

      Overall, the authors have achieved their primary aim of demonstrating that speaker identity can facilitate memory separation in newborns, providing valuable preliminary evidence for early indexical processing in language learning. The results are intriguing and likely to stimulate further research, but the limitations in effect robustness and theoretical interpretation mean that the findings should be viewed as an important step forward rather than a definitive answer. The methods and data will be of interest to researchers studying infant cognition, memory, and language, and the study highlights both the promise and the challenges of probing complex cognitive processes in the earliest stages of life.

      We thank the reviewer for their thoughtful and positive assessment of our work, and for giving us the opportunity to clarify points that may have been unclear in the original manuscript.

      First, considering that the recognition response was quite consistent in previous studies, we expected the effect to emerge within a specific testing window, in either the first or the second block, depending on task difficulty. Accordingly, our analytical approach was designed to reflect this expectation, which was subsequently confirmed by the results. Second, the main recognition effect is not restricted to a specific subgroup of participants. Recognition responses were observed in both groups in the left IFG and bilateral STG. The only group-specific modulation was found in the right IFG, where the effect was primarily driven by Group A. This suggests that activity in this specific region may be influenced by contextual factors such as the nature and amount of recently processed stimuli. We have clarified these points in the revised manuscript to avoid the impression that the core effect is limited to a subset of participants or not generalizable across studies. 

      Regarding the sample size, a formal calculation was initially attempted based on the effect size reported in a closely related ANOVA-based study (Benavides-Varela et al., 2011; Study 2: Word recognition after intervening melodies, main effect for the comparison same vs novel word [F(1,26) = 19.318; p<0.0001 effect size f =.87). However, inputting this information into a dedicated software (G*power; α = 0.05; number of groups =1; number of measurements = 2) leads to an estimated sample size of N = 5 to 7 (depending on the desired power, range = 0.800.95). This sample size is unrealistically small and not representative of current research standards in the field. A proper formal power analysis for the LMM is otherwise hard to perform, as we lack information about the expected variance and random-effects structure. We therefore aligned our sample size with prior newborn studies using similar stimuli and experimental designs, and with fNIRS studies in newborns and infants (for recent metanalysis see De Roever et al., 2018; Boek et al., 2023; Gemignani et al., 2023; which examined studies with mean N =24; N range= 186 and sample sizes often including various conditions and groups). Note also that our design includes a within-subject comparison, our analytical approach models subject-level variance and handles unbalanced datasets and missing data (which are common in infant studies), thereby improving statistical sensitivity. We have now explicitly clarified this choice in the Introduction.

      Finally, we revised the discussion to ensure that interpretations are aligned with our findings, by including a limitations section and a more explicit note regarding theories of memory.

      Episodic memory is a multifaceted construct that matures over time through the integration of the what–who-where–when information. The present study does not aim to demonstrate the presence of a fully developed episodic memory system at birth; rather, it shows that specific features of episodic-like processing (i.e., what–who) are already bound from the first days of life. Future studies may track the progressive integration of additional episodic-related components leading to a mature episodic memory system.

      Reviewer #1 (Recommendations for the authors):

      (1) I wonder why a control condition with same-speaker interference was not included. Adding such a control would allow you to directly test whether the observed effects are truly due to speaker changes, rather than other acoustic or procedural factors. If it is not feasible to add this condition, please discuss its absence explicitly and clarify how it impacts the interpretation of your findings.

      We thank the reviewer for raising the issue of a same-speaker interference control. A similar control has been tested previously using a closely related paradigm, showing that recognition does not persist when neonates hear another word produced by the same speaker during the retention period (Benavides-Varela et al., 2011). As noted in the manuscript, there were some methodological differences between that study and the current one. Most importantly, in the present study familiarization was reduced (from ten to five blocks) and the retention interval increased (two to three minutes), making the current paradigm more demanding. We reasoned that, if newborns forgot the word under the prior (less challenging) study, they would also forget it here if a same-speaker interference control would have been implemented. With the current manipulation, despite the difficulty of the paradigm, the recognition response was observed. This pattern suggests that speaker change, rather than general procedural factors, is central to the observed effect. Given these prior findings and the ethical constraints of testing newborns, we believe that adding a new same-speaker control is not essential. We have now made this rationale more explicit in the manuscript (discussion section, limitations, p. 16), hoping that this clarification will make our methodological choices clearer.

      (2) It wasn't clear if Group A and Group B have the same number of infants, and whether they were randomly assigned. Please specify.

      Participants were initially assigned to Group A or Group B in a counterbalanced way to maintain comparable group sizes. Due to attrition and subsequent exclusion for various reasons (e.g., low signal quality, fussiness, technical issues), the final sample consisted of 17 infants in Group A and 15 infants in Group B. We have now specified this information in the revised manuscript (p. 20).

      (3) Please specify the exact number of fNIRS channels assigned to each region of interest (ROI), as it is currently difficult to map the channel numbers in Supplementary Table 2 to the optode montage shown in Figure 2. Additionally, report the percentage of usable channels after quality control.

      The inferior frontal gyrus left and right ROIs comprised 4 channels each, the superior temporal gyrus left and right ROIs 5 channels each, and the parietal lobe left and right ROIs 7 channels each. This information has been added to the methods section, along with the average number of channels contributing to each ROI after data rejection and the percentage of channels rejected throughout the recording (p. 23).

      (4) Also, a formal power analysis to justify your sample size would be helpful for evaluating the reliability of your findings and is increasingly expected in developmental neuroimaging research.

      Thanks for this suggestion. As stated in the public response, we agree that power analyses constitute an important component of methodological rigor in the field. In our case, a formal calculation was initially attempted based on the effect size reported in a closely related ANOVAbased study (Benavides-Varela et al., 2011; Study. 2: Word recognition after intervening melodies, main effect for the comparison same vs novel word [F(1,26) = 19.318; p<0.0001 effect size f =.87).

      However, inputting this information into a dedicated software (G’power; α = 0.05; power range = 0.80-0.95; number of groups =1; number of measurements = 2) leads to an estimated sample size of N = 5 to 7, which is unrealistically small and not representative of current research standards in the field. A proper formal power analysis for the LMM is otherwise hard to perform, as we lack information about the expected variance and random-effects structure. We therefore aligned our sample size with prior newborn studies using similar stimuli and experimental designs, and with fNIRS studies in newborns and infants (for recent metanalysis see De Roever et al., 2018; Boek et al., 2023; Gemignani et al., 2023; which examined studies with mean N =24; N range= 1-86 and sample sizes often including various conditions and groups. Note also that our design includes a within-subject comparison, and our analytical approach models subject-level variance and handles unbalanced datasets and missing data (which are common in infant studies), thereby improving statistical sensitivity.

      (5) The manuscript references episodic memory explicitly in the abstract and introduction, emphasizing the role of speaker identity in enabling episodic-like memory from birth. However, this concept is not sufficiently addressed or delineated in the discussion. Episodic memory is generally understood as recalling events with contextual details, involving complex integrative processes that extend beyond simple recognition of auditory stimuli. Your paradigm demonstrates memory retention over a few minutes but does not provide strong evidence for the hallmark features of episodic memory, such as contextual binding or autobiographical recollection. Moreover, infant speech recognition and memory formation in early life are influenced by the immediacy and complexity of sensory input, which may not necessarily engage fully developed episodic systems. Clarifying these distinctions and making sure your interpretations and claims are consistent with them would enhance the conceptual clarity of the manuscript.

      We agree that episodic memory is a multifaceted construct that, in its mature form, entails the ability to retrieve past events with contextual detail, typically involving autobiographical recollection and the integration of what–-who-where–when information (Tulving, 1993). Our study does not aim to demonstrate the presence of a fully developed episodic memory system at birth, nor do we claim that newborns’ performance satisfies all hallmark criteria of mature episodic memory. 

      Here, we focused on sensitivity to speaker identity as a contextual dimension relevant to memory formation. Within this narrower sense, both, the patterns of activation and the localization of the response provide evidence for early source–content binding (i.e., what–who), which can be considered a foundational aspect of episodic-like processing. Following up on this foundational step, future studies may track the gradual integration of additional aspects (where-when), ultimately leading to the maturation of a fully functional human episodic memory system.

      We have now clarified this point in the revised manuscript (p. 17)

      (6) Please add a dedicated limitations section. This should address the group-dependent nature of your main effects, the timing-specific recognition response, and any other methodological constraints that may impact the generalizability of your results.

      We thank the reviewer for this comment. We have made our best to expose the limitations of our study in the text (p.16), specifically regarding the reasons for the lack of a control condition and the effects of frequent changes in sleeping states in newborns. 

      (7) Consider revising sections where claims may be overstated, particularly regarding episodic memory and evolutionary implications.

      These sections have now been revised in the abstract and throughout the manuscript to ensure that interpretations remain proportionate to the data and consistent with current theoretical frameworks.

      Reviewer #2 (Public review):

      Summary:

      Previous studies by some of the same authors of the actual manuscript showed that healthy human newborns memorize recently learned nonsense words. They exposed neonates to a familiarization period (several minutes) when multiple repetitions of a bisyllabic word were presented, uttered by the same speaker. Then they exposed neonates to an "interference period" when newborns listened to music or the same speaker uttering a different pseudoword. Finally, neonates were exposed to a test period when infants hear the familiarized word again. Interestingly, when the interference was music, the recognition of the word remained. The word recognition of the word was measured by using the NIRS technique, which estimates the regional brain oxygenation at the scalp level. Specifically, the brain response to the word in the test was reduced, unveiling a familiarity effect, while an increase in regional brain oxygenation corresponds to the detection of a "new word" due to a novelty effect. In previous studies, music does not erase the memory traces for a word (familiarity effect), while a different word uttered by the same speaker does.

      The current study aims at exploring whether and how word memory is interfered with by other speech properties, specifically the changes in the speaker, while young children can distinguish speakers by processing the speech. The author's main hypothesis anticipates that new speaker recognition would produce less interference in the familiarized word because somehow neonates "separate" the processing of both words (familiarized uttered by one speaker, and interfering word, uttered by a different speaker), memorizing both words as different auditory events.

      From my point of view, this hypothesis is interesting, since the results would contribute to estimating the role of the speaker in word learning and speech processing early in life.

      Strengths:

      (1) New data from neonates. Exploring neonates' cognitive abilities is a big challenge, and we need more data to enrich the knowledge of the early steps of language acquisition.

      (2) The study contributes new data showing the role of speaker (recognition) on word learning (word memory), a quite unexplored factor. The idea that neonates include speakers in speech processing is not new, but its role in word memory has not been evaluated before. The possible interpretation is that neonates integrate the process of the linguistic and communicative aspects of speech at this early age.

      (3) The study proposes a quite novel analytic approach. The new mixed models allow exploring the brain response considering an unbalanced design. More than the loss of data, which is frequent in infants' studies, the familiarization, interference and learning processes may take place at different moments of the experiment (e.g. related to changes in behavioural states along the experiment) or expressed in different regions (e.g. related to individual variations in optodes' locations and brain anatomy).

      Weaknesses:

      I did not find major weaknesses. However, I would like to have more discussion or explanation on the following points.

      (1) It would be fine to report the contribution of each infant to the analysis, i.e. how many good blocks, 1 to 5 in sequence 1 and 2, were provided by each infant.

      (2) Why did the factor "blocknumber" range from 0 to 4? The authors should explain what block zero means and why not 1 to 5.

      (3) I may suggest intending to integrate the changes in brain activity across the 3 phases. That is, whether changes in familiarization relate to changes in the test and interference phases. For instance, in Figure 2, the brain response distinguishes between same and novel words that occurred over IFG and STG in both hemispheres. However, in the right STG there was no initial increase in the brain response, and the response for the same was higher than the one for novels in the 5th block.

      (4) Similarly, it is quite amazing that the brain did not increase the activity with respect to the familiarization during the interference phase, mainly over the left hemisphere, even if both the word and speaker changed. Although the discussion considers these findings, an integrated discussion of the detection of novel words and the detection of a novel speaker over time may benefit from a greater integration of the results.

      Appraisal:

      The authors achieved their aims because the design and analytic approaches showed significant differences. The conclusions are based on these results. Specifically, the hypothesis that neonates would memorize words after interference, when interfered speech is pronounced by a different speaker, was supported by the data in blocks 2 and 5, and the potential mechanisms underlying these findings were discussed, such as separate processing for different speakers, likely related to the recognition of speaker identity.

      I think the discussion is well-structured, although I may suggest integrating the changes into the three phases of the study. Maybe comparing with other regions, not related to speech processing.

      Evaluating neonates is a challenge. Because physiology is constantly changing. For instance, in 9 minutes, newborns may transit from different behavioral states and experience different physiological needs.

      We thank the reviewer for their constructive and positive appraisal of our work and for drawing attention to points that benefited from further clarification or discussion in the manuscript.

      In the following, we address each point in turn, using the numbering of the reviewer’s identified concerns.

      (1) In the Methods section (“Data Processing and Analysis”, p. 22), we have added detailed information about the number of data points contributed by each infant to the analyses.

      (2) The factor “blocknumber” ranged from 0 to 4 for statistical purposes, allowing Block 0 to serve as the reference (intercept) in the model. This coding facilitated the interpretation of parameter estimates. We now clarify this in the revised manuscript (p. 7).

      (3) Thanks for this relevant suggestion. In the Discussion, we now explicitly discuss the relationship across phases. We also acknowledged that a thorough examination of these issues lies beyond the scope of the present study as it will require future work based on multivariate and connectivity analyses.

      (4) We thank the reviewer for this comment. In the revised manuscript, we have expanded the Discussion to clarify the absence of a strong novelty response during interference. The discussion highlights how the temporal properties of the hemodynamic response and the functional demands of each phase jointly shape the observable fNIRS signal in newborns, with purely sensory novelty effects likely increasing with maturation.

      Finally, we agree that evaluating the transitions of sleeping states can further strengthen and clarify the results obtained in the present study. This has now been added as one of the limitations of this study.

    1. Author response:

      [These author responses are to reviews from another journal.]

      Reviewer #1:

      This manuscript investigates the behaviour of a variety of clock proteins in cultured cells when epitope tagged and transiently expressed and try to draw general implications for endogenous function of circadian clock proteins.

      Clock proteins are expressed at low levels in most cells, and so the clock interacting proteins (other kinases, phosphatases, ubiquitin-conjugated enzymes, etc.) are likewise probably at low abundance. Over-expression of one or two or even three components of a multicomponent system is going to produce odd and obscure non-physiological imbalances. The authors do not extend detailed study of these imbalances to more physiologic levels so the importance of their observations to clock function is not clear, and importantly, they are not tested in more biologically relevant models.

      To study the function of components within a system, the steady state must be perturbed in one way or another. This can be achieved through pharmacological treatment, mutagenesis, downregulation, or overexpression. Such interventions are inherently non-physiological, and the relevance of the resulting observations must therefore be carefully validated.

      In our study, the purpose of PER2 overexpression was to investigate its subcellular dynamics in the absence and presence of CRYs, specifically CRY1. This is far less trivial than it might appear at first glance, because our data clearly show that PER2 overexpression triggers, within 24 h, the accumulation of endogenous CRY1 (Fig. 1A), due to PER2-mediated stabilization of CRY1 (Fig. 4). PER2 overexpression also induces the accumulation of endogenous PER1, CK1, and BMAL1 (Fig. 2).

      This effect was not considered in previous studies, such as Yagita et al. (2002), in which PER2 subcellular localization was assessed at a single time point following transient transfection. Yagita et al. found roughly equal proportions of cells with PER2 exclusively in the nucleus, exclusively in the cytoplasm, or distributed between both compartments. Such extreme cell-to-cell variability cannot be explained solely by PER2’s shuttling dynamics, as that would imply synchronous export in one cell and synchronous import in another.

      Our time-resolved analysis of DOX-induced PER2 expression strongly suggests that the variability reported by Yagita et al. reflects a heterogeneous population of unsynchronized cells at different temporal stages along a trajectory from cytoplasmic PER2 (unbound) to nuclear PER2 fully saturated with CRYs (bound), owing to stabilization of endogenous CRYs. Similarly, Öllinger et al. (2014) analyzed PER2 nuclear export in cells constitutively expressing PER2-Dendra. Under such steady-state conditions, PER2-Dendra is already in complex with endogenous CRYs. The slow export rate and lack of dependence on additional CRY1 expression therefore likely reflect export of the complex, which is intrinsically slow.

      Thus, prior to our work, no data on the true shuttling dynamics of PER2 were available.

      Importantly, our results show not only that CRY1 promotes nuclear accumulation of PER2 (as reported by Öllinger et al.) but also that, conversely, PER2 promotes cytosolic accumulation of CRY1, depending on their expression ratio. Since CRY1 is predominantly nuclear and PER2 predominantly cytosolic, and because a PER2 dimer can bind one or two CRY1 molecules, our data suggest that the shuttling equilibrium depends on PER2 saturation state: a PER2 dimer bound to one CRY1 remains cytosolic, whereas a dimer bound to two CRY1 is nuclear.

      These observations are novel and have not been reported previously. They were only possible through time-resolved analysis of overexpressed proteins.

      A number of the findings are confirmatory rather than novel - the phosphorylation-regulated nuclear-cytoplasmic shuttling of CK1 and PER proteins is long known, and it's not clearly stated what is novel here. 

      We acknowledge prior work by Milne et al. (2001), who showed that kinase-dead CK1 is predominantly nuclear and that prolonged treatment with leptomycin B (16 h) enhances its nuclear localization. We cite this study at the beginning of the relevant paragraph. While we confirm these earlier observations, our work extends them in several important and novel ways:

      (1) Rapid dynamics of CK1 localization – We show that pharmacological inhibition of CK1 with PF670 induces rapid (within 1 h) depletion of CK1δ from the centrosome, accompanied by nuclear accumulation and elevated CK1δ levels. These kinetics have not previously been reported. We also show that proteasome inhibition with MG132 enhance centrosomal staining, indicating that centrosomal binding sites are not saturated. Together, the data show that CK1δ equilibrates rapidly between its binding partners. 

      (2) Integration of localization with protein stability – We relate the known localization patterns of WT CK1 and the kinase-dead mutant K38R to CK1 degradation dynamics and further compare them to the tau-like kinase mutant CK1δ-R1178Q. This integration of subcellular localization data with turnover mechanisms provides new mechanistic insight.

      (3) Comprehensive regulatory model – In the revised manuscript, we now include a schematic summarizing how CK1δ is posttranslationally regulated via subcellular shuttling, nuclear degradation, and dynamic interactions with binding partners (Figure EV5C). To our knowledge, such a comprehensive view of CK1δ regulation, linking localization, stability, and partner association, has not been presented before.

      We believe these additions clearly distinguish our findings from prior reports and highlight the novel aspects of our study.

      The formation of PER and CRY and CK1 complexes likewise is well established. The finding that formation of multiprotein complexes stabilize otherwise unstable over-expressed proteins is interesting but not novel.

      We fully agree that the existence of PER–CRY–CK1 complexes is well established. It is also known that PER2 stabilizes CRY1 by occupying the FBXL3 binding site and that CRY1 promotes the nuclear accumulation of PER2. We do not present these established interactions as novel findings.

      Our novel contribution, as outlined above, is the discovery that the shuttling and subcellular localization of PER2 and CRY1 are mutually dependent on their expression ratio. Specifically, we show for the first time that the steady-state shuttling distribution PER2 alone is cytosolic due to its rapid nuclear export wherease CRY1 is predominantly nuclear (known). Given that CRY1 facilitates the nuclear import of PER2 (known) and that a PER2 dimer can bind either one or two CRY1 molecules, our data showing that cytoplasmic PER2-CRY1 foci contain less CRY1 than nuclear foci lead us to conclude that cytoplasmic PER2 complexes contain one CRY1 molecule, while nuclear complexes contain two.

      This model provides a mechanistic explanation for the distribution of PER2 between the cytosol and nucleus and for the relatively lower cytosolic CRY1 levels. Moost importantly, we further show (for the first time) that CK1-mediated phosphorylation of PER2 displaces CRY1. This phosphorylation event would produce PER2 dimers with one or no CRY1 bound, promoting their export to the cytosol. We believe this represents a novel and potentially important mechanism for regulating circadian clock function.

      The results from many of the imaging assays are not quantitated, and the figures often show single cells. It's hard to draw statistical significance from these.

      The phenotypes we report here are result of multiple technical and biological replicates (n >3). Image analysis and statistical analysis was performed when required. We show additional examples in the EVs.

      There are a number of phenomena seen whose physiological relevance is unclear. In figure 1, forced over-expression of CRY1 and PER2 leads to formation of nuclear foci. It is unlikely these foci form at non-overexpressed levels, and so the general interest and relevance is not high nor investigated. This reduces the impact of the finding.

      It has been shown that PERs and CRYs do not form thermodynamically stable, large (detectable) foci under physiological conditions, as we have stated in the manuscript. Whether these proteins have the propensity to form smaller, more dynamic structures of physiological relevance is an interesting question that could be explored elsewhere, but it is not relevant to our study. In our work, these foci are simply convenient markers for analyzing the interaction and subcellular (co)localization of clock proteins under investigation. In the revised version, we have kept the analysis of these foci and the discussion of their potential relevance to a minimum in order to avoid confusion and unnecessary discussions.

      The finding that CK1δ is keep in the dephosphorylated state by binding to PER has been established previously by Johnson and colleagues and should perhaps be mentioned (Qin JBR 2015 (doi: 10.1177/0748730415582127).

      There is clearly a misunderstanding here. Qin et al.’s data show that, in a cell-free system, CK1ε phosphorylates PER2 and also autophosphorylates its C-terminal tail (autoradiograph, Fig. 1E).  

      However, because PER2 phosphorylation is carried out by CK1ε that is tightly anchored to PER2, there is competition between PER2 phosphorylation and tail autophosphorylation. As a result, the kinetics of tail phosphorylation are slower (Fig. 3B and quantification in C) than those observed with free CK1ε (as seen in the presence of the p53 substrate, Fig. 3A,C). We believe that his is also happening in the cell.

      Author response image 1.

      Our data, in contrast, address a different point. It has been known from the Virshup lab for decades that CK1δ/ε undergo futile cycles of (auto)phosphorylation and dephosphorylation, resulting in an active, dephosphorylated kinase in cells because cellular phosphatases are more efficient than CK1 autophosphorylation. We now show that CK1δ is also efficiently dephosphorylated when bound to PER2 (Fig. 3). Nevertheless, despite dephosphorylation of PER2-bound CK1δ, PER2 itself becomes hyperphosphorylated, indicating that cellular phosphatases act differently on these two substrates. To clarify this point, we inhibited phosphatases with calyculin A (CalA). Under these conditions, both PER2 and PER2-bound CK1δ became efficiently hyperphosphorylated (new Fig. 3).

      The degradation of kinase-active but not inactive CK1 is only shown here with 50-fold overexpressed protein so it's interesting, but the relevance to circadian biology is not made clear. The fact that over-expressed CK1 is degraded primarily in the nucleus is interesting, but needs further characterization - is this affected by the epitope tag? Is it true of endogenous CK1 or only over-expressed CK1? Is this not seen with e.g. other forms of CK1, e.g. lacking the C-terminus?

      The observation that unassembled kinase is rapidly degraded is most clearly demonstrated by overexpression experiments. However, Fig. 3 shows that overexpression of CRY1 and PER2 leads to the accumulation of elevated levels of endogenous CK1δ (untagged), indicating that endogenous kinase is likewise degraded in the absence of a stabilizing binding partner. In addition, we present data showing that overexpression of tagged CK1δ reduces the levels of endogenous, untagged CK1δ, further supporting the conclusion that unassembled endogenous CK1δ is unstable and subject to degradation.

      Further characterization of the CK1 degradation pathway is of considerable interest and could form the basis of a separate study, particularly to identify the components that mediate activity-dependent nuclear export and activity-dependent nuclear degradation. The Δ-tail kinase is expressed at very low levels, although interpretation is complicated by the possibility that this reflects pleiotropic effects.

      The final figure, showing that nuclear CK1 is the form responsible for shortening rhythms, is interesting. Is this because massive increases in nuclear CK1 alter PER, or BMAL/CLOCK, or proteasome activity?  

      Our data show that cells expressing either nuclear or cytosolic CK1 are viable, proliferate normally, and maintain a functional circadian clock. Therefore, overexpression of the kinase does not produce pleiotropic effects.

      To assume it's due to PER phosphorylation is in disagreement with the studies of Meng et al. Neuron 2008 DOI 10.1016/j.neuron.2008.01.019.

      The data are not in disagreement with Meng et al.; in fact, they align quite well. Meng et al. showed that CK1ε-tau shortens the circadian period, which we had also previously reported for CK1δ-tau-like (Marzoll et al., 2022). We now demonstrate that CK1δtau-like is enriched in the nucleus, contributing to its period-shortening phenotype. Furthermore, we show that active CK1δ (but not CK1δ-K38R) promotes cytoplasmic accumulation of PER:CRY complexes, consistent with PER2 degradation in the cytosol as described by Meng et al.

      Taken together, these findings suggest that PER proteins acquire their CK1 in the nucleus, and this interaction determines the circadian period length. Following a time delay—set by the kinetics of PER2 phosphorylation—PER2:CRY complexes are exported to the cytosol along with their bound CK1, where they are subsequently degraded.

      Reviewer #2:

      Interactions between the circadian clock proteins PER1/2 with CK1d/e and CRY1/2 influence each of their stability, subcellular localization, and activity, as countless studies over the last two decades have shown. However, many questions still remain, especially in light of newer models of the transcription-translation feedback loop (TTFL) in which the repression phase relies on two distinct mechanisms, a phosphorylation-dependent displacement of the transcription factor by CK1-PER-CRY complexes from DNA early in repression, and a CRY1dependent sequestration of the transcription factor activation domain later in repression. In particular, questions remain about mechanisms triggering nuclear entry/export and activity of these proteins in the cytoplasm and nucleus. 

      Here, the authors utilize a system of induced and/or transient overexpression of proteins with or without with fluorophores to track subcellular localization, stability, and interactions. As the authors point out throughout the manuscript, the overexpression of these clock proteins often causes them to behave differently from the endogenous proteins. It looks as though the authors have done their best to account for these changes, and they have certainly been rigorous in pointing them out, but there is concern that some of the conclusions may be influenced by this overexpression. For example, the relevance of work related to the overexpression-dependent foci is unclear. 

      Same answer as to Reviewer 1: It has been shown that PERs and CRYs do not form thermodynamically stable, large (detectable) foci under physiological conditions, as we have stated in the manuscript. Whether these proteins have the propensity to form smaller, more dynamic structures of physiological relevance is an interesting question that could be explored elsewhere, but it is not relevant to our study. In our work, these foci are simply convenient markers for analyzing the interaction and subcellular (co)localization of the clock proteins under investigation. In the revised version, we have kept the analysis of these foci and the discussion of their potential relevance to a minimum in order to avoid confusion.

      The findings that the stability of the kinase depend on localization, its intrinsic activity, and interaction with PER2 are interesting and important. Use of the CKBD deletion to show that CK1 stabilization depends on its anchoring interaction with PER2 is a nice touch. The authors bring up an excellent point that most of the potential phosphorylation sites on PER1 and PER2 have not been functionally characterized aside from the phosphoswitch mechanism. Their observation that CK1 eventually induces cytoplasmic localization of the CK1-PER-CRY1 complex and the release of CRY1 is intriguing. In particular, the finding that pretreatment of PER2 with CK1 in vitro blocked its ability to interact with CRY1 is very interesting. However, the absence of mechanistic data to explore this in more detail limits the impact of this conclusion. Using the system they have established here to identify the site(s) on PER2 and/or CRY1 that lead to this would help to solidify this work and increase the impact of this work. Overall, there are some interesting findings here but the inclusion of some competing viewpoints and mechanistic data would strengthen the impact of the work.

      Major

      (1) The characterization of the tau-like CK1 mutant R178C as less active than the wild type enzyme is not entirely correct-it is less active on the FASP region as described, but it has increased activity on S478 in the phosphodegron that is independent of inhibition from the FASP region (Gallego et al. PNAS, 2007 and Philpott et al. eLife, 2020). It is still possible that some of the period shortening effects of the mutant could arise from enhanced nuclear accumulation, but the oversimplified description of the mutant as less active should be corrected.  

      In the revised version, we discuss that the enhanced nuclear localization of the Tau-like kinase may contribute, at least in part, to period shortening, similar to how forced nuclear overexpression of wild-type kinase also shortens the period. We emphasize, however, that CK1 Tau is compromised in its priming-dependent activity, whereas its priming-independent activity is context-specific and enhanced toward the β-TrCP site.

      (2) One of main conclusions from the paper, that CK1 induces cytoplasmic localization of the CK1-PER2-CRY1 complex and subsequent release of CRY1 would be strengthened significantly by identifying the phosphorylation site(s) responsible for the cytoplasmic localization of the complex and the release of CRY1. The system they have developed here seems ideal to identify these sites.

      We fully agree with the reviewer. We substituted the known phosphorylation sites in PER2 surrounding the CRY-binding domain, but this had no effect on the phosphorylationdependent release of CRY1. Therefore, a more systematic analysis will be required, including the possibility that phosphorylations in CRY1 itself may contribute. To this end, we are generating PER2 and CRY1 variants in which all Ser/Thr residues are replaced by Ala. Using these constructs alongside the wild-type versions, we will by PCR systematically create hybrids in which specific regions containing phosphorylation sites are exchanged.

      Nevertheless, this will require considerable time and effort, and we believe this investigation exceeds the scope of the present manuscript and will address it in future work.

      (3) The concept of delayed release of CRY1 presented here is an interesting one. It's unclear why the authors have also not incorporated prior findings (Ukai-Tadenuma et al. Cell, 2012, Koike et al. Science, 2012) that peak levels of CRY1 are expressed in a later phase than CRY2, PER1, and PER2. It seems like figure EV6 should reflect the observation that CRY2 is the predominant cryptochrome present during early repression (Koike et al. Science, 2012).

      The reviewer is absolutely right: the expression phases of CRY1, CRY2, PER1, and PER2 are important. I have recently discussed these issues in detail in a News & Views article in The EMBO Journal, commenting on a paper by Smyllie et al. In this News & Views article, I discuss that the presently available data suggest that CRY1 is always present throughout the circadian cycle and keeps circadian transcription partially repressed even at peak phases of expression. In the revised version, I refer to these publications, including those mentioned by the reviewer. However, I would like to keep the model presented in the supplementary figure as simple as possible and specifically focused on the work presented in this manuscript, rather than presenting a comprehensive conceptual model of the circadian clock.

      (4) The model presented in figure EV6 and described throughout the text shows that PER-CRY complexes interact with CK1 in the nucleus, and not in the cytoplasm prior to nuclear entry. Prior work on endogenous protein complexes has shown that CK1-PER-CRY complexes exist in the cytoplasm very early on in the repression phase (Aryal et al. Mol Cell, 2017-ref. 14 in the manuscript). Work by Sancar and colleagues (Cao et al. PNAS, 2020) also shows with endogenous proteins that CK1d has a circadian pattern of nuclear entry (or possibly retention) concomitant with PER2 that is dependent on the presence of PERs and CRYs. Together, these data seem to be inconsistent with your model. 

      We think the data are not inconsistent. The recent Smyllie et al. paper in EMBO Journal shows that PER2 is present in both the cytosol and the nucleus at all times when it is expressed, but cytosolic PER2 is not saturated with CRY, which is more nuclear. Our data demonstrate that PER2 shuttles between the cytosol and the nucleus depending on its occupancy with CRYs (see schematic Fig. 1). Occupancy, in turn, depends on expression levels and binding affinities, including those of CRY2 and PER1. Consequently, PER2 complexes could shuttle continuously throughout the circadian cycle—either because they are not saturated with CRYs due to the balance between expression levels, freely available CRY, and binding affinity, or later in the cycle because CRYs are displaced by phosphorylation. If PER2 acquires casein kinase in the nucleus early in the cycle, it will shuttle out to the cytosol together with the bound CK1. We believe this does occur, but early in the circadian cycle the saturation of PER2 with casein kinase is likely to be very low due to the limited availability of CK1 in the nucleus. I am aware that not everyone will share this interpretation point by point, but discussing it in greater length and detail exceeds the scope of the present manuscript.

      Reviewer #3:

      This manuscript by Serrano and co-workers is a tight body of work that provides much needed insights into the regulation of clock proteins by CK1D, and into the regulation of CK1D itself. While the whole paper relies on artificial overexpression of chimeric/tagged proteins that may have significant differences in the function, the stability and subcellular distribution of the endogenous proteins they are suppose to model, this limitation was been clearly stated by the authors, and nevertheless their study still provides important insights. 

      While the authors have specified which Ck1d isoform (Ck1d1) they are overexpressing in their model cell lines, they may have thought to consider that the overexpression of one Ck1 homologue may affect the endogenous expression of the other homologues and their isoforms, e.g. ck1d1 overexpression may cause an increase in Ck1d2 or Ck1e, which would in turn affect the conclusions. 

      We show in revised Fig. 3 that overexpression of CK1δ1 reduces the expression of endogenous CK1δ1/2. This is consistent with our prediction that overexpressed and endogenous CK1 (including CK1ε) compete for the same stabilizing binding partners, leading to rapid degradation of unassembled kinases.

      Moreover, the antibody they used for endogenous Ck1d (which is ab85320, also mentioned as AF12G4 but that is the clone number, not the catalogue number) is discontinued and its specificity against Ck1d1, Ck1d2 or even the highly identical Ck1e, has not been clearly demonstrated. We know from Fig 3 that it can detect Ck1d1 but it would be great if the authors would provide additional evidence for the specificity of this antibody, for example by overexpressing Ck1d1/Ck1d2/Ck1e to see really which "endogenous" Ck1 we are seeing.

      Are the three bands for example seen in Fig 4A corresponding to the different isoforms? This simple experiment would reinforce the conclusions. 

      We show in the revised figure that the antibody recognizes CK1δ1 and CK1δ2, but not CK1ε. In U2OS cells, the antibody detects a single band (Figure); we do not know whether this represents predominantly one splice isoform or both, which are not resolved. However, this distinction is not relevant for our interpretation, because overexpression of tagged CK1δ1 reduces the expression of whichever endogenous kinase is present.

      There are no minor comments, as the figures, the figure legends and main text are all of good quality and ready for publication.

      Reviewers’ Responses to Point-by-Point Response to Peer Review 

      Referee #1:

      I appreciated the additional efforts by the authors to improve the manuscript. Unfortunately, the underlying approach of forced over-expression remains artifact-prone, and has been largely supplanted by readily available knockin and targeted mutagenesis methods. Over-expression may give clues, but I think more rigorous mechanistic validation is needed to make this compelling. I cannot support publication of this manuscript.

      Referee #2:

      In their response to reviewers, the authors make the valid point that the steady state of a system is usually perturbed to study it. In this study, they have used overexpression of the clock proteins PER2, CRY1 and CK1 to study their effects on subcellular dynamics and stability. In justifying this choice, they refer to several papers that similarly overexpressed at least one of these components, stating that their time-resolved approach brings novel insights. However, there is a missed opportunity here to translate any lessons learned from overexpression studies to a system where the proteins are expressed at physiological levels and stoichiometry.

      The authors reply to reviewer 1 stating that they conclude PER proteins acquire CK1 in the nucleus, but this does not account for other studies showing an apparent PER-CK1 complex in the cytoplasm during the early phases of repression and/or a pattern of PER-dependent nuclear entry of CK1 (Lee et al. 2001, Cell; Aryal et al. 2017 Mol Cell; Cao et al. 2021 PNAS). Given that all 3 of these studies were done with native expression levels, it seems incumbent upon the authors to demonstrate that their conclusions from the overexpression study are physiologically relevant by translating them in some way to a more native system. This also addresses a point made by reviewer 2, major concern 4 that was not satisfactorily addressed by the authors. Perhaps they could validate their hypothesis of PER shuttling and interactions with CK1 or CRY1 that alter this in a native system similar to Aryal or Cao et al. with the use of nuclear export inhibitors?

      The response to reviewer 2, major concern 1 is thoughtful and much appreciated. However, simplifying the effects of the tau mutation on CK1 as having a decreased rate on priming-dependent phosphorylation but not priming-independent is not quite true-the tau mutation also decreases the rate of priming-independent phosphorylation of S662 (in humans) (Philpott et al. 2020, eLife).

      Other papers appearing in this journal seem to all include at least one major new mechanistic insight. Although the authors do a diligent job in characterizing the overexpressed proteins in this system, some of their conclusions are at odds with prior studies of the system in more native conditions, so the potential impact of this work is unclear. To verify these conclusions or test new ones (ie, that CK1 disrupts PER-CRY1 interactions), they should use their insights to generate mutations or make perturbations in a native system and demonstrate that they still hold.

      Referee #3:

      The authors have adequately addressed the reviewers' comments, and it is my opinion that the manuscript is ready for publication. It is true, as previously mentioned by other reviewers, that the evidence presented rely on overexpression, which for the other reviewers seem to preclude publication. However, I find this to be a too strict opinion.

      If the authors had indeed provided evidence using crispr-cas9-mediated genetic manipulation and tagging/mutating endogenous genes for all their experiments, thereby providing more physiological evidence of how clock proteins interact, they would probably have submitted their manuscript to an alternative journal with a higher impact.

      As it stands, it is my opinion that, considering the evidence and limitations of the study, this manuscript is a good match for the journal.

      Author Rebuttal:

      Apologies for the delayed reply regarding our manuscript. In the meantime, we have added several new experiments which address the comments of the reviewers and more. These are now included as Figures 1C, EV3, 4D, 6E, 6F, EV6D, and EV7.

      Figure 1C reinforces our observations from Figure 1B showing that induction of stably-integrated PER2 also results in accumulation of endogenous CRY1 at a timescale that is compatible with the gradual localization of overexpressed PER2 into the nucleus.

      Figure EV3 addresses several technical comments from Reviewers #3 and #1, respectively: Figure EV3A shows that our CK1δ antibody recognizes CK1δ1 and CK1δ2, but not CK1ε. Figures EV 3B and C clearly show how overexpression of our transgenic CK1δ results in decreased endogenous CK1δ which further demonstrates the rapid turnover of active kinase.

      Figure 4D addresses the comment from Reviewer #2. We clearly show that CK1δ is not kept in a dephosphorylated state by binding to PER. In addition to our direct comment to this point, Figure 4D shows that CK1δ regardless if it is expressed alone or in complex with PER2 is phosphorylated to a similar extent when the cells are treated with the phosphatase inhibitor CalA. As indicated in our direct response, we are rather more interested in the observation that cellular phosphatases act differently on PER2 compared to CK1δ despite being in the same PER:CK1δ complex (as shown by the clear stabilization of overexpressed CK1δ by co-expression of PER2).

      Figures 6E, 6F, and EV6D demonstrate that our observations from overexpression systems are also observed in a more physiological context, addressing comments from Reviewers #1 and #2. Figure 6E shows that dephosphorylation of PER2 leads to its relocalization from the cytosol to the nucleus, while Figure 6F analyzes the subcellular localization of PER2 in the context of a functional circadian clock in U2OS cells. The latter demonstrates that PER2 is predominantly nuclear early in the circadian cycle, but redistributes to the cytosol at later time points. We included these experiments in response to the reviewer’s request for a more physiological context. Since we are not a mouse lab, this cell-based system represents the most physiological model we can provide. Figure 6F show the dynamics of endogenous PER2 from DEX-synchronized cells. At early timepoints, PER2 is predominantly nuclear likely due to the incorporation of CRY1 forming the PER:CRY complex. At later timepoints PER2 is redistributed between the cytoplasm and nucleus due to PER2 phosphorylation. Importantly, these results are consistent with and recontextualize the results from Liu et al. (Xie et al., PNAS, 2023) showing the hypophosphorylated PER2 at early timepoints post-DEX is predominantly nuclear and hyperphosphoryated PER2, that appear later post-DEX is predominantly cytoplasmic.

      Finally, Figure EV7 provides a model how the subcellular distribution of CK1δ affects its assembly into the PER:CRY complex emphasizing how nuclear kinase enacts its role in the circadian clock.

      Response to Reviewers:

      We were disappointed by the categorical rejection of overexpression experiments. Without a specific discussion of why they would be inappropriate or not sufficient in the context of the work presented here, the blanket assertion that overexpression inevitably produces artifacts functions more as a rhetorical device than as a substantiated scientific argument. The fact that the term ‘physiological’ generally carries a positive connotation, whereas ‘overexpression’ is often perceived negatively, does not in itself justify the categorical rejection of experiments.

      While we appreciate that some reviewers may personally prefer alternative strategies, we believe that the suitability of any approach must be evaluated in light of the specific biological questions being addressed. I cannot see a single specific point in the reviewers’ responses indicating that any of our experiments yielded artificial results. It is true that targeted knock-in and mutagenesis methods are available, however, these approaches are simply not suited to the questions raised in this manuscript. We also fully agree that, whenever possible, insights from overexpression studies should be validated in systems with a functional clock where proteins are expressed at physiological levels, which we did using U2OS cells, and noting the compatibility of our results with those in the literature using endogenously-tagged constructs. We have cited several recent studies that have investigated the subcellular distribution and circadian dynamics of endogenous or endogenously-tagged clock proteins in mice (Cao et al, 2021; Smyllie et al, 2022, 2016, 2025) and U2OS cells (Öllinger et al, 2014; Gabriel et al, 2021; Xie et al, 2023). While we cannot substantially expand on these previous observations, we confirm them in the revised version by demonstrating the nuclear-to-cytoplasmic relocalization of PER2 in U2OS cells over the course of a circadian cycle. In addition, we show that this process is, in principle, reversible: when CK1 is inhibited with PF670, overexpressed hyperphosphorylated cytosolic PER2 becomes dephosphorylated and accumulates in the nucleus.

      Overall, we consider our approach not only complementary but also essential, as it enables us to address two key questions that would otherwise be difficult or even impossible to resolve:

      (1) Mutual impact of PER2 and CRY1 on subcellular dynamics and the role of PER2 phosphorylation

      Evidence from mouse liver (Cao et al, 2021), mouse SCN (Smyllie et al, 2022, 2025), and U2OS cells (Xie et al, 2023) indicates that a substantial fraction of PER2 remains cytoplasmic throughout its expression cycle, even in the presence of CRY1, which promotes PER’s nuclear import. The mechanisms underlying this cytoplasmic retention remain unclear, and no circadian function has yet been attributed to the cytosolic PER2 pool. Our study addresses how PER2 abundance, phosphorylation state, and stoichiometry relative to CRY1 govern their interaction and subcellular dynamics. This is physiologically relevant because PER1/2 and CRY1/2 proteins oscillate in expression and degradation out of phase, such that their concentrations, stoichiometry, and phosphorylation state vary systematically over the circadian cycle. Transient transfection and inducible overexpression combined with time-lapse microscopy are essential here, as they uniquely allow modulation of protein ratios and CK1δ levels and to resolve their dynamics.

      Previous work established that CRY1 is nuclear and promotes PER2 nuclear accumulation (Smyllie et al, 2022). Our data extend this by showing that subcellular distribution is determined by the CRY1:PER2 ratio. While CRY1 alone is nuclear we show that PER2 alone is cytoplasmic due to rapid nuclear export. Mixed conditions reveal ratio-dependent shifts: at low CRY1-to-PER2 ratios, CRY1 relocalizes to the cytoplasm, whereas at high ratios, PER2 is retained in the nucleus. We explain this behavior by PER2 dimerization: dimers bound to two CRY1 molecules remain nuclear, while dimers bound to a single CRY1 localize to the cytosol. Such species can be expected to form in a physiological context depending on binding affinities and rhythmic expression levels and ratios across circadian time. Importantly, we show that CK1δ-mediated phosphorylation destabilizes PER2 and CRY1 interactions. From this, we infer that PER2 dimers with only a single bound CRY1 transiently form and accumulate in the cytosol, consistent with the lower CRY1-to-PER2 ratio we observe in the cytosol and that has also been reported in the SCN (Smyllie et al, 2025). With continued phosphorylation, PER2 dimers lose CRY1 altogether, while the released CRY1 accumulates in the nucleus. We suggest that this mechanism supports and extends the late repressive phase of the circadian cycle. Recent data show that hypophosphorylated PER2 is predominantly nuclear, whereas hyperphosphorylated PER2 is largely cytoplasmic in mouse liver (Cao et al, 2021; Xie et al, 2023), linking our data to a physiological context.

      Taken together, these findings suggest a mechanism whereby stoichiometry, subunit composition, and CK1δ phosphorylation determine PER:CRY complex composition and localization. Crucially, these complexes and their dynamic relocalization could only be observed using inducible overexpression; knock-in strategies at endogenous levels would not be able to capture such states.

      (2) Posttranslational regulation and subcellular homeostasis of CK1δ and impact on the clock

      Previous work has shown that nuclear export of CK1δ depends on its kinase activity (Milne et al, 2001). Here, we further demonstrate that unassembled CK1δ is subject to degradation, with nuclear turnover accelerated by its catalytic activity. Thus, when evaluating the impact of CK1δ mutants on the circadian clock, one must consider not only kinase activity but also protein stability and subcellular distribution. We find that CK1δ availability for PER2 differs between cytosol and nucleus. In particular, nuclear CK1δ is limiting, and its abundance directly determines circadian period length. This is significant because subcellular CK1δ availability and posttranslational regulation have not previously been examined or incorporated into circadian clock models, as the kinase has been assumed to be non-limiting given its constant expression throughout the circadian cycle. Complex formation between CK1δ and PER is a well-established determinant of circadian timing, with CK1δ overexpression known to shorten period length. Our data explain why: the binding equilibrium between CK1δ and PER must be finely tuned. Previous studies suggested that PER associates with CK1δ in the cytosol and enters the nucleus as a PER:CRY:CK1δ complex (Lee et al, 2001; Aryal et al, 2017). Our data suggest that nuclear PER is not saturated with CK1δ. This is because levels of free, active CK1δ in the nucleus are low, owing to its rapid export or degradation by the nuclear proteasome, which limits its availability for PER binding.

      Our overexpression studies support this mechanism. NES-tagged CK1δ overexpression does not alter circadian period length, because it fails to increase nuclear CK1δ levels: Each PER molecule can coimport only one kinase, a process already occurring in wild-type cells, and the few co-imported molecules rapidly equilibrate with the nuclear pool, where they are subject to export or degradation. In contrast, NLS-tagged CK1δ overexpression directly increases nuclear kinase abundance by antagonizing export, thereby enhancing PER binding and shortening circadian period. This multilayered regulation of CK1δ stability and localization and its consequences for PER2 availability would not have been revealed without targeted overexpression. Our findings therefore fill a key knowledge gap and remain fully consistent with previous studies (Lee et al, 2001; Aryal et al, 2017; Cao et al, 2021).

      Conclusion: In sum, our findings are novel and physiologically relevant, aligning with data from mouse liver and SCN. While studies at strictly endogenous protein levels are important and necessary, perturbation of steady state is a standard strategy to uncover and observe novel mechanisms. Endogenous-level experiments would demand technically unrealistic systems (for example, even the simplest case, analyzing the subcellular dynamics of PER2 alone, would require cells lacking PER1, CRY1/2, and CK1δ/ε). Moreover, adjustment of PER2-to-CRY1 ratios cannot be achieved with stably integrated genes and of course not at physiological expression levels. Thus, inducible overexpression is not merely practical but currently the most feasible approach to dissect these dynamics. We complement our findings with data from U2OS cells with a functional clock, showing that the availability of nuclear CK1δ directly determines circadian period length. Although specific aspects of our extended model require further experimental validation, no published evidence contradicts it to date. Mechanistic discussions of the circadian clock have so far focused primarily on PER protein degradation. Our model broadens this perspective by incorporating CK1δ homeostasis, PER:CRY complex composition, subcellular localization, and their regulation by phosphorylation. In doing so, it provides a detailed framework to be critically tested and refined in future studies.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      The manuscript presents a compelling new in vitro system based on isogenic co-cultures of human iPSC-derived hepatocytes and macrophages, enabling the modelling of hepatic immune responses with unprecedented physiological relevance. The authors show that co-culture leads to enhanced maturation of hepatocytes and tissue-resident macrophage identity, which cannot be achieved through conditioned media alone. Using this system, they functionally validate immune-driven hepatotoxic responses to a panel of drugs and compare the system's predictive power to that of monocyte-derived macrophages. The results underscore the necessity of macrophage-hepatocyte crosstalk for accurate modelling of liver inflammation and drug toxicity in vitro.

      The manuscript is clearly written and addresses a key limitation in liver organoid systems: the lack of immune complexity and tissue-specific macrophage imprinting. Nevertheless, several conclusions would benefit from a more careful interpretation of the data, and some important controls or explanations are missing, particularly in the flow cytometry gating strategies, stress marker validation, and cluster interpretations.

      Strengths:

      (1) Novelty and Relevance: The study presents a highly innovative co-culture system based on isogenic human iPSCs, addressing an unmet need in modelling immune-mediated hepatotoxicity.

      (2) Mechanistic Insight: The reciprocal reprogramming between iHeps and iMacs, including induction of KC-specific pathways and hepatocyte maturation markers, is convincingly demonstrated.

      (3) Functional Readouts: The application of the model to detect IL-6 responses to hepatotoxic compounds enhances its translational relevance.

      Weaknesses:

      (1) Several key claims, particularly those derived from PCA plots and DEG analyses, are overinterpreted and require more conservative language or further validation.

      We agree that PCA does not allow for maturation trajectories and mentioned that it was a hypothesis that the co-culture was promoting maturation, which we later validated by looking at the expression of key hepatocyte markers as well as by pearson correlation comparison with fetal hepatocytes.

      (2) The purity of sorted hepatocytes and macrophages is not convincingly demonstrated; contamination across gates may confound transcriptomic readouts.

      We agree and have highlighted and addressed this limitation in our discussion. Unfortunately, this is a limitation of bulk sequencing that a small amount of contamination might be present, however the TPM values of ALB for example in the iMacs is extremely low especially when compared to the hepatocytes, indicating that the level of contamination is likely to be very low. Likewise, the expression of CSF1R in the co-cultured iHeps is also extremely low. This has been included in Supp Fig 1F and G.

      (3) Stress response genes and ER stress/apoptosis signatures are not properly assessed, despite being potentially activated in the system.

      This has been included in Supp Fig 2C, where we’ve included the expression of ATF4, CASP3 and CASP9. Although there’s a significant difference in ATF4 expression between Day 0 and Day 7 iHep only/Co-culture, there is no significant difference between the Day 7 iHep only and Day 7 iHep Co-culture. There are no significant differences in CASP3 and CASP9 expression across all the samples.

      (4) Some figure panels and legends lack statistical annotations, and microscopy validation of morphological changes is missing.

      Although we agree that the morphology changes would be interesting, we think that this question is unfortunately outside of the scope of our question. Although Kupffer cells are in direct contact with hepatocytes, they migrate from the liver parenchyma into the sinusoidal spaces where they primarily reside. We do not think that the morphology would add much to the paper, especially given that this is a 2D model as well.

      (5) The co-culture model with monocyte-derived macrophages is not fully characterised, making comparisons less informative.

      Although we agree that it would be interesting to look more closely at the monocyte-derived macrophage co-cultures as well, we think that this would be more suited to a future study as the transcriptomic analysis would likely include confounding effects of patient specific transcriptomic changes, and our primary focus was on developing an isogenic co-culture system.

      Reviewer #2 (Public review):

      Summary:

      This study builds on work by Glass and Guilliams showing that mouse Kupffer cells depend on the surrounding cells, including endothelium, hepatocytes, and stellate cells, for their identity. Herein, the authors extend the work to human systems. It nicely highlights why taking monocyte-derived macrophages and pretending they are Kupffer cells is simply misleading.

      Strengths:

      Many, including human cells, difficult culture assays, and important new data.

      Weaknesses:

      This reviewer identified minor queries only, rather than 'weaknesses' as such.

      Reviewer #3 (Public review):

      Summary:

      In this study, the authors establish a human in vitro liver model by co-culturing induced hepatocyte-like cells (iHEPs) with induced macrophages (iMACs). Through flow cytometry-based sorting of cell populations at days 3 and 7 of co-culture, followed by bulk RNA sequencing, they demonstrate that bidirectional interactions between these two cell types drive functional maturation. Specifically, the presence of iMACs accelerates the hepatic maturation program of iHEPs, while contact-dependent cues from iHEPs enhance the acquisition of Kupffer cell identity in iMACs, indicating that direct cell-cell interactions are critical for establishing tissue-resident macrophage characteristics.

      Functionally, the authors show that iMAC-derived Kupffer-like cells respond to pathological stimuli by producing interleukin-6 (IL-6), a hallmark cytokine of hepatic immune activation. When exposed to a panel of clinically relevant hepatotoxic drugs, the co-culture system exhibited concentration-dependent modulation of IL-6 secretion consistent with reported drug-induced liver injury (DILI) phenotypes. Notably, this response was absent when hepatocytes were co-cultured with monocyte-derived macrophages from peripheral blood, underscoring the liver-specific phenotype and functional relevance of the iMAC-derived Kupffer-like cells. Collectively, the study proposes this co-culture platform as a more physiologically relevant model for interrogating macrophage-hepatocyte crosstalk and assessing immune-mediated hepatotoxicity in vitro.

      Strengths:

      A major strength of this study lies in its systematic dissection of cell-cell interactions within the co-culture system. By isolating each cell type following co-culture and performing comprehensive transcriptomic analyses, the authors provide direct evidence of bidirectional crosstalk between iMACs and iHEPs. The comparison with single-culture controls is particularly valuable, as it clearly demonstrates how co-culture enhances functional maturation and lineage-specific gene expression in both cell types. This approach allows for a more mechanistic understanding of how hepatocyte-macrophage interactions contribute to the acquisition of tissue-specific phenotypes.

      Weaknesses:

      (1) Overreliance on bulk RNA-seq data:

      The primary evidence supporting cell maturation is derived from bulk RNA sequencing, which has inherent limitations in resolving heterogeneous cellular states and functional maturation. The conclusions regarding hepatocyte maturation are based largely on increased expression of a subset of CYP genes and decreased AFP levels - markers that, while suggestive, are insufficient on their own to substantiate functional maturation. Additional phenotypic or functional assays (e.g., metabolic activity, protein-level validation) would significantly strengthen these claims.

      We have added a discussion on the limitations of our study.

      (2) Insufficient characterization of input cell populations:

      The manuscript lacks adequate validation of the cellular identities prior to co-culture. Although the authors reference previously published protocols for generating iHEPs and iMACs, it remains unclear whether the cells used in this study faithfully retain expected lineage characteristics. For example, hepatocyte preparations should be characterized by flow cytometry for ALB and AFP expression, while iMACs should be assessed for canonical macrophage markers such as CD45, CD11b, and CD14 before co-culture. Without these baseline data, it is difficult to interpret the magnitude or significance of any co-culture-induced changes.

      We apologise for this oversight, some of the markers were used in determining the purity of the iMacs before co-culture, and we did not end up including these plots for brevity. We have added the purity plots in Supp Fig 2E now, showing that the iMacs were more than 90% pure before co-culture. We acknowledge the concern about cross-contamination for bulk sequencing, and have added in Supp Fig 2G and H the expression of ALB in the iMac fraction, as well as the expression of CSF1R in the iHep fraction, showing minimal contamination with our gating strategy.

      (3) Quantitative assessment of IL-6 production is insufficient:

      The analysis of drug-induced IL-6 responses is based primarily on relative changes compared to control conditions. However, percentage changes alone are inadequate to capture the biological relevance of these responses. Absolute cytokine production levels - particularly in response to LPS stimulation - should be reported and directly compared to PBMC-derived macrophages to determine whether iMAC-derived Kupffer-like cells exhibit enhanced cytokine output. Moreover, the Methods section should clearly describe how ELISA results were normalized or corrected to account for potential differences in cell number, viability, or culture conditions.

      We apologise if this was unclear. The cytokine production from dosed cells was normalized based on the viability of cells measured from the same well.

      (4) Unclear mechanistic interpretation of IL-6 modulation:

      The observed changes in IL-6 production upon drug treatment cannot be interpreted solely as evidence of Kupffer cell-specific functionality. For instance, IL-6 suppression by NSAIDs such as diclofenac is well known to result from altered prostaglandin synthesis due to COX inhibition, while leflunomide's effects are linked to metabolite-induced modulation of immune cell proliferation and broader cytokine networks. These mechanisms are distinct from Kupffer cell identity and may not directly reflect liver-specific macrophage function. Consequently, changes in IL-6 secretion alone - particularly without additional mechanistic evidence or analysis of other cytokines - are insufficient to conclude that co-culture with hepatocytes drives the acquisition of bona fide Kupffer cell maturity.

      We fully agree with the reviewer and have highlighted this in our discussion.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) GSE ID for RNA-seq data has not been provided.

      This has been included.

      (2) Line 291: Can the authors specify what they mean by "state-of-the-art"?

      What we mean here is what others in the field have also recently described. We have rewritten this to be clearer.

      (3) Lines 299-300: check sentence for grammar mistakes.

      We have rewritten and clarified this.

      (4) Figure 1B: The PCA does not really allow for following maturation trajectories. Also, all samples (day 3 Co-iHep, day 7 Co-iHep, day 7 iHep) look as if they cluster more or less together. Therefore, the conclusion drawn in lines 303-305 does not hold. Why is day 3 iHep not also shown here?

      We agree that PCA does not allow for maturation trajectories and mentioned that it was a hypothesis that the co-culture was promoting maturation, which we later validated by looking at the expression of key hepatocyte markers as well as by pearson correlation comparison with fetal hepatocytes.

      (5) Can the authors show that the cells that they are sorting in the double negative gate are indeed hepatocytes? Typically, these cells are big in cell size; therefore, showing the FSC/SSC gate would also be important.

      We have added the FSC/SSC gate in supp fig. 1E to show that the populations have different sizes.

      (6) Can the authors provide microscopy pictures of iHeps, iMacs, and the co-cultured cells for the reader to appreciate whether the morphology of cells already changes during the co-culture experiments?

      Although we agree that the morphology changes would be interesting, we think that this question is unfortunately outside of the scope of our question. Although Kupffer cells are in direct contact with hepatocytes, they migrate from the liver parenchyma into the sinusoidal spaces where they primarily reside. We do not think that the morphology would add much to the paper, especially given that this is a 2D model as well.

      (7) Please show expression of apoptotic and ER stress genes comparing Day7 iHeps and Co-iHeps, since genes such as c-Fos and Ppp2r3b can also be associated with cellular stress.

      This has been included in Supp Fig 2C, where we’ve included the expression of ATF4, CASP3 and CASP9. Although there’s a significant difference in ATF4 expression between Day 0 and Day 7 iHep only/Co-culture, there is no significant difference between the Day 7 iHep only and Day 7 iHep Co-culture. There are no significant differences in CASP3 and CASP9 expression across all the samples.

      (8) In addition to the genes shown in Figure 1E, could the authors extract a longer gene list of maturing hepatocytes and display them all in bar graphs or heatmaps, or similar? E.g., Albumin expression is shown later, but why not show it already here?

      There are not many differences in the canonical hepatocyte markers, which is why we chose only to show the interesting genes that were different, as seen in the later ALB expression plot where there wasn’t a difference in ALB expression after 7 days of co-culture. Instead, we have included a new heatmap in Supp Fig 2B showing the top 40 genes that are contributing to the similarity by pearson correlation.

      (9) Along these lines, how do the authors ensure that they are culturing only hepatocytes and do not have a mixture of cells that may "dilute" the hepatocyte signature?

      Unfortunately, this is an limitation of our methodology, although the expression of key hepatic markers are routinely confirmed by qPCR to ensure that the majority of the cells are hepatocyte-like.

      (10) Lines 347-350: similar to the interpretation of the PCA for hepatocytes, this is a completely random interpretation. The expression of ALB in the co-cultured iMacs indicates that there are some hepatocytes that ended up in the macrophage gate.

      We agree and have highlighted and addressed this limitation in our discussion. Unfortunately, this is a limitation of bulk sequencing that a small amount of contamination might be present, however the TPM values of ALB for example in the iMacs is extremely low especially when compared to the hepatocytes, indicating that the level of contamination is likely to be very low. Likewise, the expression of CSF1R in the co-cultured iHeps is also extremely low. This has been included in Supp Fig 1F and G.

      (11) Figure 2D: Among the pathways shown, there are also stress pathways (acute phase response, HMGB1). Also for these cells, control of apoptotic and ER stress signatures is necessary.

      As mentioned, we have included some stress genes in Supp Fig 2C to address this.

      (12) Lines 385-386: Why would FCGRA3 indicate tissue residency? Is there literature to support this statement?

      CD16 is a marker often used to distinguish Kupffer cells from the surrounding cells, although it also expressed by non-classical monocytes, we have clarified the text here (Lines 356-357).

      (13) Figure 3E: ALB and other genes were at the same or even lower levels expressed in D7 compared to D3. Why is that? Are the cells starting to de-differentiate after 7 days? Please discuss.

      This is a very interesting question that we were wondering ourselves as well, although sadly we do not have an answer yet. We hypothesized that this might be due to the activation of cell proliferation/developmental programmes as the cells are kept longer together, as shown by the expression of morphogens like OSM and IGF-2 after co-culture. We have added some discussion for this (Lines 532-540)

      (14) Line 459: Word "in" is double

      We thank the reviewer for catching this, this has been corrected

      (15) Figure 5: The findings are interesting, but the co-culture model remains somewhat unclear. Can the authors show, e.g., using qRT-PCR, how hepatocytes are developing in this culture system? If the development with monocyte-derived macrophages is altered, then one would expect that also the cellular response is different.

      We agree with the reviewer, but we think that this question would be better answered in a follow-up study. We were looking to answer if the addition of isogenic iMacs would change the drug response of iHeps, and were using the PBMC-derived macrophages here as a control. A more complete study taking into account the genetic background of the donor PBMC-derived macrophages would be much more informative, but sadly outside of the scope of our present study.

      (16) Lines 482-484: The authors talk about LPS-treated cultures and refer to Figure 4. However, there is no graph shown for LPS.

      We apologise for being unclear here, but the co-cultures were co-treated with LPS during the drug stimulation assays, as it had been shown that LPS increases the sensitivity of the liver toward hepatotoxic drugs. We have clarified this in the main text (Lines 435-437).

      Reviewer #2 (Recommendations for the authors):

      (1) It would be nice to add some protein production by the hepatocytes. For example, can they produce albumin or some other protein that can be measured? Perhaps I missed this.

      The protein expression of Albumin and Urea were assessed in the hepatocytes prior to co-culture in Supp Fig 1C; however we did not measure the protein level changes after co-culture as the co-culture would have a significant number of macrophages as well which we thought might affect the readout. Instead, after co-culture the primary analysis was done on the RNA levels of ALB and other cytochrome genes after sorting in Fig 3.

      (2) Was there an increase in hepatocyte number? Did one cell outgrow the other, or did they maintain numbers?

      The relative proportion of the iHeps remained the same, although we did see an expansion in the iMac population after 7 days by flow cytometry in Fig 1D.

      (3) What happens if the iMACs and the iHeps are grown in Costar chambers with pore sizes too small to allow for cell contact, but allowing supernatant to be continuously exposed to both cell types?

      We were primarily focused on the acquisition of KC-like phenotype in the iMacs with regards the question of direct contact, which was why we chose to use conditioned iHep media as part of the iMac experimental set up. However, it would be very interesting to see if the converse is also true, and whether secreted factors from the iMacs alone would be sufficient to drive the changes we observed in the iHeps after co-culture in a follow-up study.

      (4) The discussion could use a brief paragraph on some limitations and what could be added to the co-culture system. For example, could stellate cells and sinusoidal endothelium also impart KC identity? Would growing KCs on endothelium provide a more natural substratum?

      Once again, these are very interesting questions which are unfortunately outside of the scope of our study. However, we have included a short section discussing this in the paper, as we do think that it would be interesting to look at iMacs educated by hepatocyte vs stellate cells for example (Lines 530-536).

      (5) The axonal guidance pathway in early iMACs is interesting. A recent report in vivo showed that macrophages migrate from the liver parenchyma into the sinusoids in neonates when they are still immature. The process could be chemotaxis, or it could be repulsion by parenchyma. Numerous axonal guidance molecules are repulsive, pushing axons away (robo/slit, etc). The migration of Kupffer cells into sinusoids could be a repulsive rather than a chemoattractant pathway. Did the RNA seq data provide any interesting molecules in this regard?

      Reviewer #3 (Recommendations for the authors):

      This manuscript presents a conceptually well-designed approach to modeling hepatocyte-macrophage crosstalk in vitro. The authors develop a co-culture system aimed at recapitulating key aspects of Kupffer cell (KC) identity and hepatocyte maturation. The data convincingly show that macrophages acquire KC-like features under co-culture conditions. However, several major issues limit the strength of the conclusions, the depth of mechanistic insight, and the translational impact of the work.

      First, the study relies heavily on bulk RNA-seq data with minimal functional or protein-level validation - particularly for hepatocyte maturation. To substantiate claims of functional maturation, additional assays measuring albumin secretion, urea production, and CYP activity are essential. Furthermore, the omission of zonation-associated markers (e.g., GLUL, CPS1, CYP2E1) leaves a critical gap in assessing whether the iHEPs achieve physiologically relevant functional states.

      Second, statistical interpretation and reporting are inconsistent. Significant and non-significant findings are frequently conflated, which risks overinterpretation. For instance, the reported reduction in HNF4A expression is not statistically significant, and AFP expression is only significantly reduced in Day 7 co-iHEPs - yet these distinctions are not clearly stated.

      Third, although the authors emphasize the role of cell-cell contact in promoting KC identity, no experiments (e.g., transwell separation, adhesion-blocking assays) directly test this claim. As a result, the mechanistic basis for this conclusion remains speculative.

      Finally, while the data support enhanced macrophage differentiation toward a KC-like phenotype, the evidence that co-culture significantly promotes hepatocyte maturation is far less convincing and requires additional functional, mechanistic, and statistical validation before firm conclusions can be drawn.

      Minor comments:

      (1) Methodology: The choice of a 2.5:1 iHEP:iMAC ratio is not justified. This proportion does not reflect physiological hepatocyte-to-KC ratios in vivo and should be either rationalized or benchmarked against native liver composition.

      We admit that the ratio here is on the higher side of things, but it has been previously reported that there can be between 20 to 40 macrophages per 100 hepatocytes (1:5 to 1:2.5) in the adult mouse liver (Baratta et al., 2009), while admittedly in the developing mouse liver the ratio is closer to 1:4 (Lopez et al., 2011). We chose 1:2.5 as we anticipated that not all of the macrophages would be able to attach, and would thus be lost during media change, as evident by the flow cytometry of the co-culture on Day 3 of the co-culture, where only 20% of the cells had clear CD45 and CD14 expression. We have clarified our methodology in paper (Lines 141-143).

      (2) Effect of iMAC on iHEP (Section 3.2, Supplementary Figure 1E):

      (2.1) The authors should explain why Day 3 co-cultured iHEPs show stronger transcriptomic similarity to primary hepatocytes than Day 7 cells. Possible biological mechanisms (e.g., transient paracrine signaling or temporal changes in maturation dynamics) should be discussed.

      We have added some discussion for this (Lines 309-311, 536-540).

      (2.2) The figure legend refers to "fetal hepatocytes," while the correlation map states "hepatocytes." This discrepancy must be clarified. Moreover, if fetal hepatocytes are used as the reference, and the goal is to assess maturation, comparisons to adult hepatocytes are necessary. 

      The comparison was done against fetal hepatocytes, and has been clarified in the figure. We chose to use fetal hepatocytes here as it would be unfair to compare iPSC-derived cells that are less than 3 weeks old to adult human tissue, and any similarity or differences between the mono/co-cultures to the adult tissue might be due to the shifting transcriptomic landscape during development. However, we do recognise the nuanced nature of using “maturation” here, and what we mean is that the iPSC-derived cells become more similar to their in-vivo counterparts.

      (2.3) Baseline characterization of both cell types before co-culture is insufficient. For iHEPs, flow cytometry data on ALB and AFP positivity rates should be presented, along with post-co-culture changes. For iMACs, marker expression (CD45, CD11b, CD14) should be shown before and after co-culture. The methods mention CD163, CX3CR1, and CD11b, but these data are absent from the results. Additionally, the gating strategy for cell sorting prior to bulk RNA-seq must be clearly described - including how potential cross-contamination of cell fractions (e.g., macrophages in the hepatocyte population) was excluded.

      We apologise for this oversight, some of the markers were used in determining the purity of the iMacs before co-culture, and we did not end up including these plots for brevity. We have added the purity plots in Supp Fig 2E now, showing that the iMacs were more than 90% pure before co-culture. We acknowledge the concern about cross-contamination for bulk sequencing, and have added in Supp Fig 2G and H the expression of ALB in the iMac fraction, as well as the expression of CSF1R in the iHep fraction, showing minimal contamination with our gating strategy.

      (3) IGF2 Expression: The observed upregulation of IGF2, a fetal marker, contradicts the conclusion that co-culture promotes hepatocyte maturation. This inconsistency should be addressed, and possible explanations (e.g., transient fetal-like activation driven by macrophage-derived signals) discussed. The lack of statistical significance for this finding must also be explicitly noted.

      We thank the reviewer for pointing this out. The expression of IGF2 was actually significantly different when comparing the Day 0 Hepatocyte only and Day 7 Hepatocyte only to the Day 3 Co-cultured Hepatocytes, but the significance is lost with the Day 7 co-cultured Hepatocytes. One possible explanation is as the reviewer suggested, that there is a transient program that is activated upon co-culture that is subsequently downregulated. We have updated the figure and text, and added some discussion to reflect this (Lines 309-311, 536-540).

      (4) Effect of iHEP on iMAC: The reported upregulation of KC-related genes is overstated. Changes in LYVE1 and ID1 are not statistically significant (Figure 2G), yet they are presented as meaningful. Clear separation of statistically significant results from non-significant trends is critical to avoid overinterpretation.

      We apologise for this, as it was never our intention to present these markers as significant, but rather we presented these markers because we thought that these markers would be of interest to the audience. We have clarified the text to reflect that these are trends and non-significant (Lines 367-369).

      (5) Mimicking In Vivo Clinical Responses:

      (5.1) The authors' conclusion that IL-6 responses are not recapitulated when iMACs are replaced by monocyte-derived macrophages (MoMs) is not fully supported by the data presented. In fact, the MoM co-cultures exhibit a noticeable trend toward increased IL-6 production (e.g., approximately 150% with LTG at 66.6 µM and 400 µM), suggesting that some degree of responsiveness is retained. To substantiate the claim that the observed cytokine modulation is unique to iKC-containing co-cultures, the authors should perform direct statistical comparisons of absolute IL-6 secretion levels between iKC and MoM co-cultures at each drug concentration. Such analyses are essential to determine whether the differences are statistically significant and biologically meaningful, and to clarify whether the observed effects truly reflect KC-specific functionality rather than general macrophage activation.

      (5.2) The effects of drug exposure on hepatocytes themselves are not addressed. It is important to evaluate whether the co-culture remains viable under treatment, whether it recovers after drug withdrawal, and whether there is evidence of cytotoxicity or irreversible phenotypic loss.

      (6) Interpretation of IL-6 Modulation and Model Specificity:

      The authors show that IL-6 secretion in their co-culture system varies in response to multiple hepatotoxic drugs and parallels some reported clinical trends - notably, a concentration-dependent decrease with diclofenac (DIC) and leflunomide (LFM). They further report that this pattern is not observed in hepatocyte-PBMC-derived macrophage co-cultures, and they conclude that iMAC/iKC-like cells are essential for capturing immune-mediated hepatotoxic responses. However, the data presented do not fully justify such a conclusion. Several key mechanistic issues weaken the interpretation:

      (6.1) Mechanistic ambiguity in the DIC response: The decrease in IL-6 following DIC exposure is most likely attributable to reduced prostaglandin E₂ (PGE₂) production via COX inhibition, which secondarily suppresses IL-6 signaling. This effect is a general pharmacological property of NSAIDs and is not necessarily reflective of Kupffer cell-specific pathways. Direct evidence - such as prostanoid quantification or PGE₂ rescue experiments - is required to establish that the observed effects are liver-specific rather than nonspecific NSAID responses.

      (6.2) Pharmacogenetic complexity in the LFM response: LFM-induced hepatotoxicity is highly variable and largely dependent on CYP2C9 polymorphisms, which determine conversion to the active metabolite teriflunomide. Because hepatotoxicity and the associated cytokine responses are not universal among patients, a simplified co-culture model lacking metabolic diversity cannot be assumed to faithfully reproduce patient-specific immune responses. The observed IL-6 suppression could arise from differences in metabolic activation, intracellular exposure, or indirect signaling changes rather than from intrinsic KC-specific mechanisms.

      These points significantly undermine the authors' claim that IL-6 modulation provides definitive evidence of model specificity or predictive value. At minimum, the manuscript should (i) explicitly acknowledge these mechanistic limitations, (ii) include supporting data such as prostanoid profiling, CYP2C9 modulation, or teriflunomide quantification, and (iii) temper its claims regarding the model's capacity to recapitulate immune-mediated hepatotoxicity. Without such evidence, the current interpretation risks overstating the functional significance and translational relevance of the co-culture system.

      We fully agree with the reviewer and have highlighted this in our discussion (Lines 540 – 551).

    1. Author response:

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

      eLife Assessment

      The analysis of neural morphology across Heliconiini butterfly species revealed brain area specific changes associated with new foraging behaviours. While the volume of the centre for learning and memory, the mushroom bodies, was known to vary widely across species, new, valuable results show conservation of the volume of a center for navigation, the central complex. The presented evidence is convincing for both volumetric conservation in the central complex and fine neuroanatomical differences associated with pollen feeding, delivered by experimental approaches that are applicable to other insect species. This work will be of interest to evolutionary biologists, entomologists, and neuroscientists.

      Many thanks for your assessment and time handling this manuscript. We value the constructive input of both reviewers and believe that the result is an improved publication.

      Public Reviews:

      Reviewer #1 (Public review):

      The authors previously reported that Heliconius, one genus of the Heliconiini butterflies, evolved to be efficient foragers to feed pollen of specific plants and have massively expanded mushroom bodies. Using the same image dataset, the authors segmented the central complex and associated brain regions and found that the volume of the central complex relative to the rest of the brain is largely conserved across the Heliconiini butterflies. By performing immunostaining to label a specific subset of neurons, the authors found several potential sites of evolutionary divergence in the central complex neural circuits, including the number of GABAergic ellipsoid body ring neurons and the innervation patterns of Allatostatin A expressing neurons in the noduli. These neuroanatomical data will be helpful to guide future studies to understand the evolution of the neural circuits for vector-based navigation.

      We thank Reviewer 1 for the constructive feedback and criticism, which will have strengthened this publication.

      Strengths:

      The authors used a sufficiently large scale of dataset from 307 individuals of 41 species of Heliconiini butterflies to solidify the quantitative conclusions and present new microscopy data for fine neuroanatomical comparison of the central complex.

      Weaknesses:

      (1) Although the figures display a concise summary of anatomical findings, it would be difficult for non-experts to learn from this manuscript to identify the same neuronal processes in the raw confocal stacks. It would be helpful to have instructive movies to show a step-by-step guide for identification of neurons of interest, segmentations, and 3D visualizations (rotation) for several examples, including ER neurons (to supplement texts in line 347-353) and Allatostatin A neurons.

      We approached this with the following logic:

      All 3D segmentations were animated, to illustrate how they are generated from raw imaging data. This means we are providing a video file for each major species group (Heliconius/outgroup-Heliconiini) for Figure 4 (general CX anatomy), Figure 7 (ER neuron projections), Figure S5 (ER neuron/bulb anatomy). This visual connection should help the reader relate 3D segmentations to image stacks. We have also added a reference to these videos in the relevant Figure captions.

      We also annotated image stacks, but did so selectively. We annotated key stacks of Figure 4 (general CX anatomy), Figure 7 (ER neuron projections), Figure S5 (ER neuron/bulb anatomy) and include a reference in figure caption to them.

      We refrained from annotating stacks of Figures 5, 6, 8 and S4. This is because we believe that the annotations we have performed in the figure panels will be sufficient for readers interested in the finer detail of these anatomies who are familiar with general CX anatomy.

      We believe that our approach will help the reader to gain a visual illustration of those parts of the manuscript which report key results and novel insights, such as ER neuronal variation, and that the data and figures collectively provide accessible information sufficient for this purpose.

      Text changes in Figure captions 4, 7 and S5: “See animated 3D segmentations and annotated stacks in file repository.”

      (2) Related to (1), it was difficult for me to assess if the data in Figure 7 support the author's conclusions that ER neuron number increased in Heliconius Melpomene. By my understanding, the resolution of this dataset isn't high enough to trace individual axons and therefore authors do not rule out that the portion of "ER ring neurons" in Heliconius may not innervate the ER, as stated in Line 635 "Importantly, we also found that some ER neurons bypass the ellipsoid body and give rise to dense branches within distinct layers in the fan-shaped body (ER-FB)". If they don't innervate the ellipsoid body, why are they named as "ER neurons"?

      Thanks for pointing to this. We believe this is primarily a nomenclature issue but have tried to specify in the text.

      Ultimately, neurons from this group that project to the EB forming the actual ring neurons and those that project to the FB with unclear function, thus far, emerge through the same lineage, DALv2 (as determined by Kandimalla et al 2023) and therefore have common developmental origin (also noted by Homberg et al 2018). To acknowledge their common developmental origin and to simplify nomenclature, and therefore also provide easier comprehension by non-experts, we specify which DALv2 progeny project to which areas, but refer to both adult neuron populations to “ER neurons”. We have changed the following text to acknowledge our definition specifically, which we hope mitigates the understandable confusion.

      Lines 354-357: “Here, we refer to these neurons, as well as those neurons projecting to the fan-shaped body (GU neurons in [66]), as ER neurons due to their common developmental origin [45,66] and to simplify anatomical descriptions.”

      Lines 386-387: “Whether these ER neurons solely branch in the fan-shaped body, as shown for GU neurons elsewhere [66] or have additional side branches entering the ellipsoid body is not clear.”

      (3) Discussions around the lines 577-584 require the assumption that each ellipsoid body (EB) ring neuron typically arborises in a single microglomerulus to form a largely one-to-one connection with TuBu neurons within the bulb (BU), and therefore, the number of BU microglomeruli should provide an estimation of the number of ER neurons. Explain this key assumption or provide an alternative explanation.

      Thanks for this. We do not think that our hypothesis necessarily requires any specific assumptions regarding the ratio of microglomerulus to ER or TuBu neurons. Even in Drosophila the ratio of ER to MG is only approximately 1:1, as some microglomeruli seem to combine into one. In other species this relationship might be very different. Indeed, our data suggests that in outgroup-Heliconiini the ratio is 4.4 microglomeruli to 1 ER neuron, and in Heliconius it is 3.4. However, as these MG numbers are extrapolated and cannot be precisely counted, they may be too imprecise to come to a definite conclusion, hence why we do not mention this in the text. Importantly, extrapolation in the current form is a valid additional way for us to describe overall bulb anatomy (next to bulb volume, average microglomerulus size).

      In any case, the inference we make here is that a conserved bulb anatomy in volume, MG numbers and size supports our assumption that the additional neurons in the ER neuron group/DALv2 progeny do not arborize in the bulb, but do so in the SMP/SLP region and in the fanshaped body. We believe we have described this inference accurately in the current manuscript.

      An additional point, not mentioned in the manuscript, but emerging through lineage annotations of connectome data, is that some DALv2 progeny have been identified as MBONs as well as being GABA-ergic, which could potentially be the ER-FB neurons that we describe (Schlegel et al 2024 Nature). We refrain from mentioning this here, as its too speculatory, but we thought the reviewer may be interested in this observation.

      (4) The details of antibody information are missing in the Key resource table. Instead of citing papers, list the catalogue numbers and identifier for commercially available antibodies, and describe the antigen, and whether they are monoclonal or polyclonal. Are antigens conserved across species?

      We have now added substantial information to Table 2, including research resource identifiers (RRIDs) and antigen descriptions, as well as information about specificity and conservation. In the text itself, in line 757, we already provide publications that have illustrated conservation very extensively.

      We believe that with the additional information provided in Table 2, all necessary information is now provided.

      (5) I did not understand why authors assume that foraging to feed on pollens is a more difficult cognitive task than foraging to feed on nectar. Would it be possible that they are equally demanding tasks, but pollen feeding allows Heliconius to pass more proteins and nucleic acids to their offspring and therefore they can develop larger mushroom bodies?

      This is an excellent point. Our current understanding is that pollen feeding is a cognitively more demanding task, because, a) the density of pollen resources is lower than nectar resources, and b) the competition for pollen is higher (pollen is depleted quickly, and Heliconius compete with each other, and other taxa including hummingbirds). There is therefore a benefit to high foraging efficiency, which favours the evolution of learning. This is likely reinforced by the long lives of Heliconius which live up to a year, compared to ~4 weeks for most outgroups and the temporal stability of major pollen resources, resulting in a memorised location providing benefit for the long periods of time (Young and Montgomery 2020 Proc B).

      We now refer to an additional publication (Young and Montgomery 2020 Proc B) in lines 103-104 for a fuller description of the ecology of pollen feeding, and in the current manuscript simply focus on the impact of mushroom body expansion on the CX.

      Reviewer #2 (Public review):

      Summary:

      In this study, Farnsworth et al. ask whether the previously established expansion of mushroom bodies in the pollen foraging Heliconius genus of Heliconiini butterflies co-evolved with adaptations in the central complex. Heliconius trap line foraging strategies to acquire pollen as a novel resource require advanced spatial memory mediated by larger mushroom bodies, but the authors show that related navigation circuits in the central complex are highly conserved across the Heliconiini tribe, with a few interesting exceptions. Using general immunohistochemical stains and 3D reconstruction, the authors compared volumes of central complex regions, and unlike the mushroom bodies, there was no evidence of expansion associated with pollen feeding. However, a second dataset of neuromodulator and neuropeptide antibody labeling reveals more subtle differences between pollen and non-pollen foragers and highlights sub-circuits that may mediate species-specific differences in behavior. Specifically, the authors found an expansion of GABAergic ER neurons projecting to the fanshaped body in Heliconius, which may enhance their ability to path-integrate. They also found differences in Allatostatin A immunoreactivity, particularly increased expression in the noduli associated with pollen feeding. These differences warrant closer examination in future studies to determine their functional implication on navigation and foraging behaviors.

      We thank Reviewer 2 for the constructive and thorough review. We believe that addressing these criticisms will have improved this publication.

      Strengths:

      The authors leveraged a large morphological data set from the Heliconiini to achieve excellent phylogenetic coverage across the tribe with 41 species represented. Their high-quality histology resolves anatomical details to the level of specific, identifiable tracts and cell body clusters. They revealed differences at a circuit level, which would not be obvious from a volumetric comparison. The discussion of these adaptations in the context of central complex models is useful for generating new hypotheses for future studies on the function of ER-FB neurons and the role of Allatostatin A modulation in navigation.

      The conclusions drawn in this paper are measured and supported by rigorous statistics and evidence from micrographs.

      Weaknesses:

      The majority of results in this study do not reveal adaptations in the central complex associated with pollen foraging. However, reporting conserved traits is useful and illustrates where developmental or functional constraints may be acting. The implied hypothesis in the introduction is that expansion of mushroom bodies in Heliconius co-evolved with central complex adaptations, so it may be helpful to set up the alternate hypotheses in the beginning.

      Thank you for this relevant comment. We have added to the text in lines 124-128, as follows

      “Indeed, these circumstances permit us to test the hypotheses that modifications in the mushroom bodies either occurred in isolation from other integrative centres, or that they occurred in concert with specific changes in centres, such as the central complex. This provides insights into the functional flexibility of two interacting, integrative centres across evolutionary time.”

      In the main text, the authors describe differences in GABAergic neurons "across several species" but only one Heliconius and one outgroup species seem to be represented in the figures. ER numbers in Figure 7H are only compared for these two species. If this data is available for other species, it would strengthen the paper to add them to the analysis, since this was one of the most intriguing findings in the study. I would want to know if the increased ER number is a trend in Heliconius or specific to H. melpomene.

      This points to imprecise phrasing. We indeed have additional data in other species, but unfortunately not to an extent that would permit quantification of cell numbers, which is why we chose to put these data into the supplement, Fig. S4.

      We modified the text to more directly point at the additional data in Fig S4, now reading in lines 362-368

      “…, we noticed a pronounced difference in a portion of projections leading into the fan-shaped body and a strong difference in signal inside layer III in our two focal species H. Melpomene and D. iulia, as well as other representatives of the Heliconiini tribe (Figure S4A-B, Figure 7). To understand how these differences could have occurred, we quantified ER neuron numbers in our focal species, and identified a significant difference, reflecting a 35% increase in Heliconius (t = 4.221, P = 0.004; Figure 7H).”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Add a detailed description about each of the tiff files that were deposited at https://doi.org/10.5281/zenodo.15304965. It was hard for me to relate these raw images with the Figure panels. For instance, "Melp_GAD_26-F_detailed_conc.tif" in the Figure 7 folder seems to be used to make Figure 7L and N, but that information is cryptic.

      We agree with the reviewer. We added further descriptions, and have created a detailed readme file which explains which original file refers to which figure. Together with the efforts for Reviewer 1’s first comment, we hope that this updated version of our repository is easier to understand.

      In addition, we made additional changes in image orientation in some of the files supplied, and which were originally incorrect.

      (2) Add descriptions about the dataset for large-scale volumetric analysis. With the current methods and texts, it is hard to understand what kinds of staining and microscopes were used. I initially thought that they could be micro-CT data.

      We have made two improvements:

      We have added an additional readme file to explain the different datasets, and which datasets were used for each figure, to relate them to the original data deposited at zenodo.org (see your previous comment).

      We have added descriptions in several places in the manuscript file, i.e.

      Lines 133-135, now reading “To assess evidence of volumetric changes in the central complex and associated neuropils, we drew data from a large dataset of immunostained brains from 307 individuals of 41 species, …”

      Lines 144-149, now reading “We used a combination of phylogenetic comparative analysis across a large dataset of brains immunostained against the structural marker synapsin in 41 species and 307 individuals, and more targeted sampling of species that represent the behavioural and neuroanatomical diversity of Heliconiini for more fine-scale assessments of patterns of divergence in substructures of the CX with various antibodies (Figure 1A-B).”

      (3) Line 275: Non-expert readers would need an explanation about what the gamma lobe is.

      Agreed and added in line 273

      “Some of the ventral projections seemed to directly originate from the γ lobe, a portion of the mushroom body, thus potentially labelling projections of mushroom body output neurons into the fan-shaped body (Figure 5a-c) [12,21].”

      (4) Figures 4 I-L are missing.

      We modified the figure caption accordingly, and address annotated differences more directly. This section now reads

      “G/H: Labelling reveals two distinguishable layers in the fan-shaped body while additional staining elsewhere reveals further detail (arrows in G/H-2/3). Thicker tract conflations indicate the columnar architecture determined through the four columnar neuron bundles (arrowheads in G/H-3). Labelling in the EB reveals two pronounced layers (arrows in G/H-1/2), while obvious columns could not be indicated. PB protocerebral bridge, FB fan-shaped body, EB ellipsoid body. A anterior, P posterior. Scale bars are 50 μm.”

      (5) In the current version of Figure 1B, AOTU is displayed with the mushroom body. The authors can emphasize its relation to the central complex by showing it on the right side of panels together with the central complex.

      Great suggestion. We have done this now. We have kept the AOTU at the scale of the MB, indicated by the different scale bars of the bottom of the figure, as we’re showing the CX at a slightly larger scale.

      (6) Figure 1C: What do the colors of the lines represent?

      We now changed these colours so that they correspond to the colours chosen in Figures 2 and S2 as well as in a previous publication of the lab, added an asterisk next to Heliconius aoede, and added text to the figure legend:

      “Colour indicates focal groups here and elsewhere [29]. The asterisk at the branch of H. aoede indicates a secondary loss of pollen feeding.”

      (7) Figures 2A and B: What does the size of the circles represent? I guess that small ones are individuals, and larger ones are species averages. Plots with only species averages would be easier to see. It is difficult to distinguish Heliconius and Helicononius aoede in these panels. It would be easier if Heliconius circles were outlined with thin black lines. 

      Thanks for this. We wanted to keep both the averages and individual data points in one figure, as to not overcrowd the manuscript with additional figures. We still hope that the changes we made address the confusion sufficiently. We made the following modifications to Figure 2 and S1 and S2:

      (1) Added text in the figure legend clarifying what solid and transparent circles indicate (“Solid data points indicate species averages, while opaque circles indicate individual data points.”)

      (2) Added, as suggested, additional contours, to all Heliconius data points, and added corresponding text to the legend (“Black contours indicate Heliconius sp. data points.”)

      (3) Changed opacity settings of individual data points.

      Reviewer #2 (Recommendations for the authors):

      (1) Line 391 and Methods. It was unclear how the extrapolated microglomeruli numbers were calculated. Please clarify this in the methods.

      Agreed. We substantially modified the text to address this.

      Lines 392-396: “We generated high resolution images of the bulb to determine its size (Figure S5 C-F), and 3D segmented seven microglomeruli per individual with which we generated an extrapolated approximation of total microglomeruli number by dividing bulb volume with average microglomerulus volume. This was necessary as most microglomeruli were not discernible from each other (Figure S5 G-H).”

      Lines 862-873: “To segment the bulb, we created high resolution images and were particularly careful to only segment the area of the bulb that comprised large synapses/glomeruli, excluding parts of the LEa/IT projection. This was essential, because we relied on extrapolating the total number of microglomeruli from a subset of segmented microglomeruli and the total volume that contained microglomeruli, which means any section containing tracts and not glomerular structures would skew the estimated total number of microglomeruli. Extrapolation was necessary, as not all microglomeruli were visually discernible. We achieved an unskewed bulb volume by leaving out dense pieces of tubulin-positive tract material. We segmented seven microglomeruli per individual from the posterior section of the bulb, where they were most clearly visible, to get the most comparable impression across individuals and species. We then calculated average microglomerulus size and divided this by bulb volume to determine an approximation of microglomeruli number.”

      (2) Line 439. It would be helpful to add that Kaiser et al. studied honeybees.

      Agreed! Now reads in lines 443-444

      “Moreover, Kaiser et al. [75] identified Allatostatin A expression in three fan-shaped and two ellipsoid body layers in the honey bee brain, …”

      (3) Line 492. "outcome" should be "outcomes".

      We believe that this refers to original line 481. Corrected. Thank you.

      (4) Figure 3B. If there is significance to the colors and triangle directions, please include a key/legend.

      We have added:

      “Cell type depictions are examples with localisation inside each neuropil being purely visual (as well as their colour), while triangles indicate approximate output sites.”

      We also corrected the following issues that were noted during our revisions:

      line 587, wrong reference.

      We updated references 37 and 44, which are now respectively

      Hodge, E. A. et al. Modality-specific long-term memory enhancement in Heliconius butterflies. Philos Trans R Soc Lond B Biol Sci 380, 20240119 (2025).

      Hodge, E. A. et al. Conservation of sensory pathways implies a localised change in the mushroom bodies is associated with cognitive evolution in Heliconius butterflies. Evol qpag005 (2026) doi:10.1093/evolut/qpag005.

      Figure S5 had an error in panels C and D, where the pictures in C were actually for H. Melpomene in D and the reverse; the other panels were correct. We have corrected this.

      In the data submitted on Zenodo: we corrected a few inconsistencies in channel colours and orientation in the .tiff files for Fig 6, 8 and S4.

      We added important bulb 3D segmentation files to the repository on Zenodo.

    1. Author response:

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

      eLife Assessment

      This is an important paper that reports in vivo physiological abnormalities in the hippocampus of a rat model of traumatic brain injury (TBI). In this study, authors focused on changes in theta-gamma phase coupling and action potential entrainment to theta, phenomena hypothesized to be critical for cognition. While the authors provide solid evidence of deficits in both features post-TBI, the study would have been stronger with a more hypothesis-driven approach and consideration of alterations of the animal's behavioral state or sensorimotor deficits beyond memory processes.

      We would like to thank the reviewers for their comments on our manuscript. By incorporating their feedback, we were able to make our hypotheses more clear, expand our analyses to compare physiological processes across similar behavioral states, and address extra hippocampal input and potential sensorimotor confounds in our data.

      Specifically, we have added new data in Figure 5 showing how theta amplitude correlates with theta-gamma PAC and entrainment strength. We have also added supplementary Figure 1 demonstrating that there are no differences in exploration or movement velocity in injured animals compared to shams. Supplementary Figures 2, 3, and 4 were added to compare oscillatory power while animals were still, moving at a higher velocity, and following a broadband power shift correction respectively. We also added Supplementary Figure 7 demonstrating that there were no differences in firing rates between sham and injured animals while they were still or moving and Supplementary Figure 8 showing no changes in pyramidal cell bursting. Finally, we added Supplementary Figure 10 showing that there was no difference in velocity or distance traveled during testing in the MWM between sham and injured animals and that learning curves were similar across groups before sham/injury surgery. We believe that the addition of this data significantly improves our manuscript by more strongly controlling for the animal’s behavioral state in our analyses and provides strong evidence that significant sensory/motor deficits were not present in injured animals at this injury level and time point post injury. Below we address specific points raised by the reviewers.

      Reviewer #1 (Public review):

      Summary:

      This study investigated how traumatic brain injury affects oscillatory and single-unit hippocampal activity in awake-behaving rats.

      Strengths:

      The use of high-density laminar electrodes enabled precise localization of recording sites. To ensure an unbiased, rigorous approach, single-unit analysis was performed by a reviewer who was blind to experimental conditions. A proof of concept study was undertaken to characterize the pathology that resulted from the specific TBI model used in the main study. There was an effort to link abnormalities in hippocampal activity to memory disruption by running a cohort of rats on the Morris Water Maze task.

      Weaknesses:

      The paper is written as if the experiment was exploratory and not hypothesis-driven despite the fact that there is a wealth of experimental evidence about this TBI model that could have informed very specific predictions to test a hypothesis that is only hinted at in the discussion. The number of rats used for the spatial working memory experiment is not reported. Some of the statistics are not completely reported. It is also unclear what the rationale was for recording single units in a novel and familiar environment. Furthermore, this analysis comparing single-unit activity between familiar and novel environments is quite rudimentary. There are much more rigorous analyses to answer the question of how hippocampal single-unit firing patterns differ across changes in environments. There are details lacking about the number of units recorded per session and per rat, all of which are usually reported in studies that record single units. Spatial working memory assessment is delegated to a single panel of a supplementary figure. More importantly, there is no effort to dissociate between spatial working memory deficits and other motor, motivational, or sensory deficits that could have been driving the lower "memory score" in the experimental group.

      In order to address these important concerns, we have made the following changes:

      (1) We have updated the results section to include more rationale for the recordings and analyses used to clarify our hypotheses. In addition, we hope that our extensive characterization will lay the groundwork to inform future studies investigating circuit-specific disruptions following TBI and neuromodulatory therapies.

      (2) The number of rats used for the spatial working memory experiment is reported in the text and figure legend.

      (3) We have added supplemental Table 2 to include the requested statistical information (t-statistic, degrees of freedom, and 1 vs 2-tailed analyses).

      (4) Unfortunately, we did not have adequate occupancy to robustly extract and compare place cell properties across groups and environments which obscured the rationale of our study design and limited us to more rudimentary analyses. While animals did actively explore the two environments, the relatively short recording time limited the spatial sampling of the two-dimensional environment. We were able to extract putative place cells and found some evidence that place cells in TBI rats had lower spatial information content than in shams (as has previously been described). However, we did not feel that place cell analyses were rigorous enough to include in this manuscript due to the limited spatial sampling. Future studies in the lab will assess how TBI affects place cell information content, stability, and phase precession with better occupancy.

      (5) We have added Supplemental Table 1 that includes the total number of units recorded for each animal.

      (6) The spatial working memory deficit we report in the MWM is not a novel finding in this model of TBI. However, we wanted to ensure that <sub>L</sub>FPI in our hands at this injury level reproduced this known deficit. Importantly, the swim speed and distance traveled during testing did not differ between groups, suggesting that differences were not due to motor deficits. Additionally, the learning curves before sham/<sub>L</sub>FPI surgery were the same across groups. This data has been added to the manuscript in Supplementary Figure 10. While we did not test animals in a version of the task where the platform was visibly marked, previous studies have demonstrated that sham and injured rats perform comparably in a version of the MWM where the platform is visible or when a constant start location is used. These citations have been added to the manuscript.

      Reviewer #1 (Recommendations for the authors):

      For a more rigorous way of analyzing changes in hippocampal firing patterns across environments, see Wills et al 2005 for example.

      Addressed in point 4 above

      Spatial working memory tasks should always be compared with a control task to rule out confounding performance variables. Examples would be to use a variant of the MWM task that does not require the hippocampus such as using a visible escape platform.

      Addressed in point 6 above

      Statistics are typically reported including a t-statistic and degrees of freedom, not just the p-value. In addition, the authors should indicate whether the t-test is one or two-tailed.

      Addressed in point 3 above

      Reviewer #2 (Public review):

      Summary:

      The authors investigate changes in theta-gamma phase amplitude coupling, and action potential entrainment to theta following traumatic brain injury (TBI). Both phenomena are widely hypothesized to be important for cognition, and the authors report deficits in both after TBI. The manuscript is well-written, the figures are well-constructed, and the author's use of high-level analysis methods for TBI EEG data collected from awake, behaving animals is welcome.

      Major Comments:

      The animal n's are small (4 sham and 5 injured). In Figure 3, for instance, one wonders if panels D and E might have shown significant differences if more animals had been recorded.

      There are conflicting reports regarding the effect of <sub>L</sub>FPI on single cell firing rates. This is likely due to differential task demands and variations in <sub>L</sub>FPI severity across studies. We agree that the firing rates do appear to be trending; however, overall firing rate changes can be difficult to interpret. Because firing rates are influenced by behavior and brain state, we further separated firing rates into epochs when animals were moving or still and found similar trends that did not reach significance (data added in Supplementary Figure 7). We also assessed bursting in pyramidal cells to investigate whether potential changes in bursting influenced overall firing rates, and we found no differences between sham and injured animals across conditions (data added in Supplementary Figure 8). While the n’s are small when considered by animal, the number of units is actually fairly large, so if there were robust effects (as there were for the entrainment analyses), we would expect to see significant differences.

      The text focuses on deficits in the theta and gamma bands, but the reduction in power appears to be broadband (see Figure 1F, especially Pyramidal cell layer panel). Therefore, the overall decrease in broadband (in the injured population) must be normalized between sham and injured animals before a selective comparison between sham and injured animals can be conducted. That is the only way that selective narrow bands i.e., theta and low gamma can be compared between the two cohorts. A brief discussion of the significance of a broadband decrease would be appreciated.

      This is an excellent point that has now been addressed with the addition of Supplementary Figure 4. We used a well-established method (Donoghue et al 2020) to flatten power spectra in order to compare specific frequency bands in the context of a broadband shift. After applying this correction, we show that theta power is still reduced in injured rats compared to shams. While there is no difference in gamma power between groups in the corrected power spectra, this result should be interpreted with caution especially since there is not a large distinct peak in the gamma frequency range in the power spectrum of either sham or injured animals. However, if this is interpreted to mean that gamma power is not different between sham and injured animals, it makes the PAC data even more compelling. While there is clearly a broadband shift, the frequency range of this shift is still limited in the frequency domain to ~4-90Hz which contains physiologically relevant frequencies associated with synaptic currents. Importantly, the power spectra of sham and injured animals converge at low (<4Hz) and high (>100Hz) frequencies. This suggests that slow oscillations which could include delta and respiration-associated oscillations are not affected by TBI (though sleep recordings would be needed to properly address this). High-frequency activity can include ripples and HFOs which need to be separately extracted when comparing between groups due to their transient nature. However, overall spiking activity including the depolarizing spike and the after hyperpolarization significantly contribute to power in the high frequency range. Because this general high-frequency power is not different between groups, it suggests that the limited range of the broadband power reduction still contains important physiological signals. This broadband shift may result from a global reduction in or desynchronization of synaptic input to CA1. The specific mechanisms behind this broadband shift and the consequences it has on coding information in the hippocampus are fascinating questions that we hope will be specifically investigated in future studies. This point is now addressed in the Discussion.

      Reviewer #2 (Recommendations for the authors):

      Minor Comments:

      Please define your reference waveform for theta - is it theta recorded on the channel containing the cell? Average theta for all electrodes in SP? SP + SO? Theta for the nominal "St. pyr." channel? Please define.

      For all entrainment analyses, entrainment was measured referenced to the theta oscillation recorded from st. pyr. on the specific shank where the unit was detected. We added clarification in the results and methods sections regarding this point.

      Similarly, even though the peak of the theta wave appears from the figures to be taken as 0 degrees, please explicitly state this in the text.

      This has been added to the results and methods.

      Did the authors check for any difference between interneurons in SP and interneurons in SO?

      This is an excellent suggestion that we had hoped to investigate as it could inform whether specific interneuron populations were affected. However, we did not record enough units in st. ori to make this comparison.

      On page 8, Figures 3E and 3F are incorrectly labeled 4E and 4F.

      This has been fixed.

      Figure 1, panel C: please add a numerical scale to the colored scale bar.

      This has been added

      Figure 1, panel F: how was the significance between the frequency bands calculated?

      Statistics were done using a t-test at each frequency point with significance set at α=0.01 for multiple comparisons. This has been clarified in the figure legend and methods.

      Figure 3, panel A legend: Please add "Spike at 0 ms omitted for clarity.”

      This has been added

      Figure 4, panel A, right side: please provide the MVL for this cell, so that readers have a benchmark for evaluating the MVL as a parameter. A sample poorly entrained cell, with MVL, would also be informative.

      We added the MVL for this cell. We were unable to add a poorly entrained cell without making the figure more confusing.

      Raw data must be provided for the Morris Water Maze experiments described in Supplementary Figure 3.

      We added data showing no difference in the swim velocity or distance traveled between the sham and injured groups during memory testing as well as data showing that the two groups had similar learning curves during training before sham/injury surgery. See Supplementary Figure 10.

      Antibody 22C11 for APP has been shown to be non-specific when used for immunocytochemistry (it may be fine for Westerns). In addition, using a biotinylated secondary with an ABC kit for visualization risks contamination by post-injury changes in biotin. Reviewed in Xiong et al., 2023, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10580020/.

      As is standard practice in neuropathology, negative controls were run for all of these experiments (identical preparations minus the primary antibody.) No non-specific staining was present that could be mis-interpreted as APP-positive axonal profiles in either sham or injured tissue. While beyond the scope of this response, there are many reasons the authors of the cited paper may have had non-specific staining, including a concentration 450X that of the one utilized here and the absence of an antigen-retrieval technique in their protocol.

      Tummala et al. used in vivo calcium-imaging after TBI and also investigated single-cell activity in familiar and novel environments, and when moving or still. The authors could consider discussing their work.

      We have added a citation for this paper

      Reviewer #3 (Public review):

      Summary:

      In this study, the authors studied the effects of traumatic brain injury created by LFPI procedure on the CA1 at the network level. The major findings in this study seem to be that the TBI reduces theta and gamma powers in CA1, reduces phase-amplitude coupling in between theta and gamma bands as well as disrupts the gamma entrainment of interneurons. I think the authors have made some important discoveries that could help advance the understanding of TBI effects at the physiological level, however, more investigations into deciphering the relationship of the behavioral and brain states to the observed effects would help clarify the interpretations for the readers.

      Strengths:

      The authors in this study were able to combine behavioral verification of the TBI model with the laminar electrophysiological recordings of the CA1 region to bring forward network-level anomalies such as the temporal coordination of network-level oscillations as well as in the firing of the interneurons. Indeed, it seems that the findings may serve future studies to functionally better understand and/or refine the therapies for the TBI.

      Weaknesses:

      Discoveries made in the paper and their broad interpretations can be helped with further characterization and comparison among the brain and behavioral states both during immobility and movement. The impact of brain injury in several parts of the brain can alter brain-wide LFP and/or behavior. The altered behavior and/or LFP patterns might then lead to reduced spiking and unreliable LFP oscillations in the hippocampus. Hence, claims made in the abstract such as "These results reveal deficits in information encoding and retrieval schemes essential to cognition that likely underlie TBI-associated learning and memory impairments, and elucidate potential targets for future neuromodulation therapies" do not have enough evidence to test whether the disruptions were information encoding and retrieval related or due to sensorymotor and/or behavioral deficits that could also occur during TBI.

      Movement velocity is already known to be correlated to the entrainment of spikes with the theta rhythm and also in some cases with the gamma oscillations. So, it is important to disentangle the differences in behavioral variables and the observed effects. As an example, the author's claims of disrupted temporal coding (as shown in the graphical abstract) might have suffered from these confounds. The observed results of reduced entrainment might, on one hand, be due to the decreased LFP power (induced by injury in different brain areas) resulting in altered behavior and/or the unreliable oscillations of the LFP bands such as theta and gamma, rather than memory encoding and retrieval related disruption of spikes synchrony to the rhythms, while on the other hand, they may simply be due to reduced excitability in the neurons particularly in the behavioral and brain state in which the effects were observed, rather than disrupted temporal code. Hence, further investigations into dissociating these factors could help readers mechanistically understand the interesting results observed by the authors.

      We appreciate the Reviewer’s insights into disentangling the complex interactions between power, entrainment, and excitability, and have attempted to dissociate these further in our analyses. Regarding the broad effects of TBI, we agree that TBI affects many brain regions outside of the hippocampus as well as white matter pathways containing axons from areas where pathology is not visible, which likely results in widespread changes to LFPs across regions and altered behavior. Here we report disrupted network activity in the hippocampus which is likely a consequence of numerous pathologies across multiple brain regions. In the discussion, we speculate that disrupted power and coupling comes from desynchronization of inputs (especially those from the mEC and MS) as well as changes to local circuits within the hippocampus which combine to disrupt temporal coding. While the disrupted processes we report in the hippocampus are implicated in computational processes thought to support learning and memory, we acknowledge that results from this study do not causally reveal a specific mechanism that is directly responsible for cognitive impairments. We have changed the language of the quoted sentence from the abstract to make our claim less causal as we agree that the direct effects of these results on cognition are difficult to quantify due to the fact that animals were not performing a spatial navigation task with measurable outcomes during recordings. We have also removed the graphical abstract as we believe it is an oversimplification of the results given new analyses.

      Regarding the possible contribution of sensory and motor deficits or differences in behavioral states to the observed changes, we agree that it is essential to consider potential sensorimotor deficits as well as the animal’s behavioral state when comparing oscillations and single unit activity in the hippocampus, especially since these phenomena have been extensively liked to movement velocity and exploration. To address this, we have added Supplementary Figure 1 showing that there are no differences in movement velocity or exploration time between sham and injured animals. Because animals were simply foraging during electrophysiological experiments we do not expect there to be any major additional behavioral differences that would influence oscillations or spiking once locomotion is controlled for, though differences in attention or arousal cannot be ruled out. Additionally, analyses throughout the manuscript are performed independently during periods when animals were moving or still. Data in Figures 1 and 2 also only include data from the familiar environment to rule out any effects of novelty on hippocampal oscillations. Supplementary Figures 2 and 3 were added to demonstrate that TBI-associated reductions in power were consistent when animals were still and when a higher threshold for movement (>20 cm/sec) was used. Finally, supplementary Figure 10 was added showing no differences in swim velocity or distance traveled in the MWM between sham and injured animals, further suggesting that there are no significant sensorimotor deficits at this injury level and timepoint. Additionally, previous studies have demonstrated that sham and injured rats perform comparably in a version of the MWM where the platform is visible or when a constant start location is used, which provides further support that sensorimotor deficits are not responsible for memory deficits in this task (see above).

      Regarding the contribution of neuronal excitability to the reported changes, we agree that changes in the excitability of neurons could have a strong effect on entrainment. Importantly, we show that the disrupted oscillations recorded in the injured hippocampus do not coincide with significant changes in neuronal firing rates between sham and injured animals. We have added Supplementary Figure 7 demonstrating this holds true both when animals are still and when they are moving. Additionally, we have added Supplementary Figure 8 showing no differences in pyramidal cell bursting between sham and injured animals. While this suggests that there are not major changes in excitability, homeostatic plasticity mechanisms may impact firing rates and bursting, and the extent of these effects and their role on entrainment are unclear. This point was added to the Discussion.

      To address the effects of LFP power on entrainment strength, Figure 5 has been updated to show theta and gamma entrainment strength as well as theta-gamma PAC as a function of theta amplitude. We found that, during periods of comparable theta power, interneurons from sham and injured animals are similarly entrained to theta, but pyramidal cells from injured animals become significantly more entrained to theta than in shams. We address the potential implications of these results in the Discussion.

      Reviewer #3 (Recommendations for the authors):

      The authors have stated on page 7 and Figure 2E, "Taken together, injured rats show a decrease in the strength of theta-gamma PAC that is specific to st. pyr, and a shift in peak gamma amplitude to a later phase of theta in both st. pyr and st. rad". Is the shift in the peak position greater than expected by chance?

      We are unaware of a rigorous method that would allow us to compare this shift statistically. We have reported the observed shift and avoided calling the shift significant for that reason.

      The authors state on page 9 "cells (sham familiar=1.63{plus minus}0.23 Hz, n=51, injured familiar=2.11{plus minus}0.20 Hz, n=141, p=0.446; sham novel=1.84{plus minus}0.18 Hz, n=55, injured novel=2.23{plus minus}0.21 Hz, n=134, p=0.170; mean{plus minus}SEM; ks-test; Fig 4E) between sham and injured groups, but a higher percentage of pyramidal cells were active (firing rate >0.1Hz) in both the familiar and novel environment in injured rats compared to shams (sham=74%, injured=87%, p=0.025, Fisher's exact test; Fig 4F)." Do the authors mean Figures 3E and 3F respectively in place of Figures 4E and 4F?

      This has been fixed.

      Regarding the finding of similar firing rates and differences in the overlap of the neurons that were active in between injured and control animals, it is imperative to study the differences in behaviors of the animals. First of all, it seems appropriate to quantify and compare the immobility and mobile periods as well as the movement velocity of the animals in both groups. Then, it would be interesting to see if any behavioral variables correlate with the firing characteristics of the cells in both the sham and the injured animals. Since hippocampal cells have been known to have different levels of recruitment and firing rates according to different behavioral states such as movement velocity, some of the similarities or differences in neural findings might as well be attributed to the differences in behaviors in between the groups. However, some differences may be observed in the injured rats despite similar behavior and the LFP powers. In other words, studying the effects of injury during similar behavioral (e.g. firing rate as a function of movement velocity) and brain states (e.g. categorical effects of awake theta state, type two theta, and ripple states on firing rates and the entrainment) might help dissociate some effects that might only be due to difference in the behavior caused by the injury throughout the brain and might as well have less to do with specific injury induced local circuits level deficits in the hippocampus. The results in Figures 4, 5, and 6 reveal such interesting differences and hence, it becomes even more important to quantify and correlate behavioral states (movement velocity and theta/ripple) to the neuronal characteristics (LFP power, PAC, firing rates, and entrainment) presented in Figure 3.

      These are excellent points, and we have addressed them in the following ways:

      We added Supplementary Figure 1 demonstrating that there were no differences in movement velocity between sham and injured animals during electrophysiological recordings.

      Power and PAC analyses were done exclusively when the animal was moving to compare across similar behavioral states. Additionally, these analyses were constrained to recordings from the familiar environment to rule out any effects of novelty. Because animals were simply foraging during recordings we do not expect other behavioral factors besides movement velocity to play a major role in these processes. We have also added Supplementary Figures 2 and 3 which demonstrate that TBI-associated differences in oscillatory power follow similar trends when animals are still (Sup. Fig 2) or when a higher movement threshold (>20cm/sec) is used (Sup Fig 3). We also added Supplementary Figures 7 and 8 showing that there were no significant differences in firing rates or bursting while animals were still or while they were moving.

      The Discussion was expanded to discuss how TBI may disrupt circuits outside the hippocampus which may contribute to our findings. Additionally, we acknowledge the limitation that these recordings were not obtained while animals were doing a quantitatively measurable spatial navigation task which limits our ability to assess whether changes are truly behaviorally relevant.

      We have also updated Figure 5 to show entrainment across different levels of theta power.

      Elaborating on the abovementioned point, Figures 4B and 4E depict a finding that mean entrainment is reduced in the injured during immobility. The following factors may contribute to the results:

      (1) Reduction in theta power during immobility (reduced attention and/or LFP profile due to brain-wide injury), which makes theta cycles unreliable, which can contribute to the results.

      (2) Changes in neural firing properties during immobility, such as reduced burst rates or firing rates during immobility.

      (3) As the authors claimed in the graphical abstract, there might be an actual disruption of temporal code associated with the memory encoding. It would be awesome if the temporal disruption could be investigated during the comparable theta power and behavioral states. This analysis would test whether there is an unconfounded disruption in the temporal code in the hippocampus due to the injury. In any case, it would be ideal to isolate the epochs during sleep in which animals were in theta state and exclude ripple states to make a definitive assessment of the aforementioned factors. These further investigations would also help the interpretations made by authors in the discussion section such as "This can disrupt type II theta which occurs when animals are not actively moving and exploring the environment. We found that single unit entrainment to theta was substantially decreased in injured rats when they were not moving, a phenomenon not seen in shams, which suggests a disruption in type II theta. This provides further evidence that cholinergic signaling may be dysfunctional following TBI."

      (1) While theta power is reduced in injured animals, it can still be reliably detected even at rest. We added Supplementary Figure 2 showing power spectra while animals were not moving, and a distinct peak can be seen in the theta frequency range. Additionally, clear peaks in entrainment can be seen in the theta frequency band in Fig 4B while animals were still. This suggests that theta can still be reliably detected in injured animals even when they are not moving. However, we agree that reduced attention or arousal could contribute to these changes, and this point has been added to the Discussion.

      (2) We added Supplementary Figures 7 and 8 showing no differences in firing rates or bursting parameters between groups during periods of immobility.

      (3) We updated Figure 5 which now shows entrainment strength as a function of theta amplitude. We found that the theta entrainment strength of both pyramidal cells and interneurons increased with increasing theta amplitudes. We address potential implications of these changes in the Discussion.

      On page 10 the authors state, "theta entrainment strength drastically increased when rats began moving in injured but not sham animals." It is unclear if the effect was confined to the periods when rats started movement. Also, it would be of interest to investigate whether movement epochs and velocity were affected in the periods when the effects were observed.

      This was not confined to the exact points when the rats started moving. We removed the word “began” for clarity. See point regarding velocity above.

      On page 12 the authors state, "On test day, injured rats had a lower memory score than shams (sham=114.8 {plus minus} 21.8, n=9; injured=51.5{plus minus}6.8, n=14; p=0.020; mean {plus minus} SEM; Welch's t-test) indicating poor spatial memory (Sup Fig 3A)." The result is the validation of the TBI injury on a hippocampal-dependent Morris water maze task. However, it would be nice to see the quantification of the movement velocity in the water maze and the trajectory length in each group to further dissect whether animals were constrained in the movement and hence, they could not get to the platform or they forgot where it was located. Also, it would help to compare the rats' performance after sham or TBI surgeries to their performance during the training before the surgeries (assuming the data during the training periods were recorded as well).

      We have added Supplemental Figure 10 to include all of this information. Importantly, movement velocity and distance traveled were not different between groups on testing day, and the learning curves of both groups were the same before sham/injury surgery.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study utilises fNIRS to investigate the effects of undernutrition on functional connectivity patterns in infants from a rural population in Gambia. fNIRS resting-state data recording spanned ages 5 to 24 months, while growth measures were collected from birth to 24 months. Additionally, executive functioning tasks were administered at 3 or 5 years of age. The results show an increase in left and right frontal-middle and right frontal-posterior connections with age and, contrary to previous findings in high-income countries, a decrease in frontal interhemispheric connectivity. Restricted growth during the first months of life was associated with stronger frontal interhemispheric connectivity and weaker right frontal-posterior connectivity at 24 months of age. Additionally, the study describes some connectivity patterns, including stronger frontal interhemispheric connectivity, which is associated with better cognitive flexibility at preschool age.

      Strengths:

      The study analyses longitudinal data from a large cohort (n = 204) of infants living in a rural area of Gambia. This already represents a large sample for most infant studies, and it is impressive, considering it was collected outside the lab in a population that is underrepresented in the literature. The research question regarding the effect of early nutritional deficiency on brain development is highly relevant and may highlight the importance of early interventions. The study may also encourage further research on different underrepresented infant populations (i.e., infants not residing in Western high-income countries) or in settings where fMRI is not feasible.

      The preprocessing and analysis steps are carefully described, which is very welcome in the fNIRS field, where well-defined standards for preprocessing and analysis are still lacking.

      We thank the reviewer for highlighting the strengths of this work.

      Weaknesses:

      While the study provides a solid description of the functional connectivity changes in the first two years of life at the group level and investigates how restricted growth influences connectivity patterns at 24 months, it does not explore the links between adverse situations and developmental trajectories for functional connectivity. Considering the longitudinal nature of the dataset, it would have been interesting to apply more sophisticated analytical tools to link undernutrition to specific developmental trajectories in functional connectivity. The authors mention that they lack the statistical power to separate infants into groups according to their growing profiles. However, I wonder if this aspect could not have been better explored using other modelling strategies and dimensional reduction techniques. I can think about methods such as partial least squares correlation, with age included as a numerical variable and measures of undernutrition.

      We agree with the reviewer that this complex and rich longitudinal dataset would benefit from more sophisticated analytical approaches to characterise developmental trajectories in functional connectivity and to more directly link them to measures of undernutrition. However, conducting such analyses would require substantial additional methodological development, model validation, and careful interpretation, which fall beyond the scope and timeline of the present manuscript. Our aim here was to provide a clear and robust characterisation of functional connectivity changes during the first two years of life and to examine associations with growth outcomes at a specific developmental stage, while ensuring methodological transparency and statistical reliability. Importantly, these more advanced trajectory-based analyses are currently being pursued in the final phase of the BRIGHT project (BRIGHT IMPACT), in collaboration with expert statisticians and data scientists. This ongoing work aims specifically to leverage the longitudinal richness of the dataset to model developmental trajectories and their associations with early-life adversity and nutritional factors. We therefore see the present study as an important foundation for these forthcoming analyses.

      Connectivity was assessed in 6 big ROIs. While the authors justify this choice to reduce variability due to head size and optodes placement, this also implies a significant reduction in spatial resolution. Individual digitalisation and co-registration of the optodes to the head model, followed by image reconstruction, could have provided better spatial resolution. This is not a weakness specific to this study but rather a limitation common to most fNIRS studies, which typically analyse data at the channel level since digitalisation and co-registration can be challenging, especially in complex setups like this. However, the BRIGHT project has demonstrated that it is possible and that differences in placement affect activation patterns, which become more localised when data is co-registered at the subject level (Collins-Jones et al., 2021). Could the co-registration of individual data have increased sensitivity, particularly given that longitudinal effects are being investigated?

      We agree with the reviewer that the fNIRS community should work toward more precise methods for spatial registration of optodes, not only at the group level but also at the subject level, in order to make more precise inferences about the locations of activations. However, we followed a very thorough offline procedure to model headgear placement based on each participant’s photographs, which we believe complements the coregistration work performed by Collins-Jones in 2021. As reported in the fNIRS data acquisition section “Infants were excluded from further analysis if the band was excessively high over the front above the eyebrows” (line 409, methods section). Moreover channels displacement was measured from the photos, and if it was “equal or greater than 1.6 cm were renumbered, so that each channel was shifted either backward or forward one full channel location in space” (line 413, methods section). While these practices are thoroughly followed in the BRIGHT project, we are aware that they are not part of the standard procedure in many infant fNIRS studies. We hope that this work provides guidance for other researchers on how to coregister infant fNIRS data.

      Considering the spatial resolution of fNIRS, which is on the order of centimetres, and the thorough procedure combining fNIRS–MRI coregistration with channel displacement assessment based on photographs, we do not think that individual-level coregistration would have significantly increased the sensitivity of the results.

      I believe that a further discussion in the manuscript on the application of global signal regression and its effects could have been beneficial for future research and for readers to better understand the negative correlations described in the results. Since systemic physiological changes affect HbO/HbR concentrations, resulting in an overestimation of functional connectivity, regressing the global signal before connectivity computation is a common strategy in fNIRS and fMRI studies. However, the recommendation for this step remains controversial, likely depending on the case (Murphy & Fox, 2017). I understand that different reasons justify its application in the current study. In addition to systemic physiological changes originating from brain tissue, fNIRS recordings are contaminated by changes occurring in superficial layers (i.e., the scalp and skull). While having short-distance channels could have helped to quantify extracerebral changes, challenges exist in using them in infant populations, especially in a longitudinal study such as the one presented here. The optimal source-detector distance that minimises sensitivity to changes originating from the brain would increase with head size, and very young participants would require significantly shorter source-detector distances (Brigadoi & Cooper, 2015). Thus, having them would have been challenging. Under these circumstances (i.e., lack of short channels and external physiological measures), and considering that the amount the signal is affected by physiological noise (either coming from the brain or superficial tissue) might change through development, the choice of applying global signal regression is justified. Nevertheless, since the method introduces negative correlations in the data by forcing connectivity to average to zero, I believe a further discussion of these points would have enriched the interpretation of the results.

      We added a paragraph discussing the choice of using GSR in our pipeline in the discussion of the manuscript as follows: “Importantly, these results remained significant even without GSR, indicating that our findings are not solely driven by preprocessing choices. While the use of GSR in FC studies remains debated (Murphy & Fox, 2017), in the absence of short channels (which are difficult to use reliably with infants (Emberson et al., 2016)) and external physiological measures, applying GSR represented the most appropriate preprocessing option. In fact, failure to correct for systemic physiological fluctuations can, in fact, lead to artificially elevated connectivity estimates in fNIRS data (Abdalmalak et al., 2022)” (line 250, discussion section).

      Reviewer #2 (Public review):

      Strengths:

      The article addresses a topic of significant importance, focusing on early life growth faltering in low-income countries-a key marker of undernutrition-and its impact on brain functional connectivity (FC) and cognitive development. The study's strengths include the laborious data collection process, as well as the rigorous data preprocessing methods employed to ensure high data quality. The use of cutting-edge preprocessing techniques further enhances the reliability and validity of the findings, making this a valuable contribution to the field of developmental neuroscience and global health.

      We thank the reviewer for highlighting the strengths of this work.

      Weaknesses:

      The study fails to fully leverage its longitudinal design to explore neurodevelopmental changes or trajectories, as highlighted by all three reviewers. The revised manuscript still primarily focuses on FC values at a single age stage (i.e., 24 months) rather than utilizing the longitudinal data to investigate how FC evolves over time or predicts cognitive development. Although the authors acknowledge that analyzing changes in FC (ΔFC) would reduce degrees of freedom (to ~30) and risk interpretability, they do not report or discuss these results, even as exploratory findings.

      As suggested, we added the table reporting the results of the associations between changes in functional connectivity (DFC) between 5 and 24 months and cognitive flexibility in the supplementary materials (Table SI3). We additionally explored the relationship between changes in growth and cognitive flexibility as suggested by Reviewer #3 and we reported these additional analyses in the text as follows: “We also explored whether changes in growth and changes in functional connectivity between 5 and 24 months were associated with cognitive flexibility at preschool age, but we did not find any significant association (Table SI3 and Table SI4).” (line 213, results section).

      Furthermore, the study lacks specificity in identifying which specific brain networks are affected by growth faltering, as the current exploratory analyses mainly provide an overall conclusion that infant brain network development is impacted without pinpointing the precise neural mechanisms or networks involved.

      We added this limitation in the discussion as follows: “While the impact of undernutrition on brain development has been documented in LMICs (46), herein, we provided empirical evidence that growth faltering specifically in infants younger than five months of age impacts observable development of functional brain networks in the second year of life. Future studies may be needed to pinpoint which specific brain networks are impacted” (line 279, discussion section).

      Reviewer #3 (Public review):

      Summary

      This study aimed to investigate whether the development of functional connectivity (FC) is modulated by early physical growth, and whether these might impact cognitive development in childhood. This question was investigated by studying a large group of infants (N=204) assessed in Gambia with fNIRS at 5 visits between 5 and 24 months of age. Given the complexity of data acquisition at these ages and following data processing, data could be analyzed for 53 to 97 infants per age group. FC was analyzed considering 6 ensembles of brain regions and thus 21 types of connections. Results suggested that: i) compared to previously studied groups, this group of Gambian infants have different FC trajectory, in particular with a change in frontal inter-hemispheric FC with age from positive to null values; ii) early physical growth, measured through weight-for-length z-scores from birth on, is associated with FC at 24 months. Some relationships were further observed between FC during the first two years and cognitive flexibility, in different ways between 4- and 5-year-old preschoolers, but results did not survive corrections for multiple comparisons.

      Strengths

      The question investigated in this article is important for understanding the role of early growth and undernutrition on brain and behavioral development in infants and children. The longitudinal approach considered is highly relevant to investigate neurodevelopmental trajectories. Furthermore, this study targets a little studied population from a low-/middle-income country, which was made possible by the use of fNIRS outside the lab environment. The collected dataset is thus impressive and it opens up a wide range of analytical possibilities.

      We thank the reviewer for highlighting the strengths of this work.

      Weaknesses

      Data analyses were constrained by the limited number of children with longitudinal data on NIRS functional connectivity. Nevertheless, considering more advanced statistical modelling approaches would be relevant to further explore neurodevelopmental trajectories as well as relationships with early growth and later cognitive development.

      While in this study we selected specific FC and outcome variables based on our hypothesis, the final phase of the BRIGHT project, known as BRIGHT IMPACT, aims to apply advanced statistical models to integrate a range of project variables into a single comprehensive analysis. We have acknowledged this in the discussion as follows: “Applying more advanced statistical modelling methods and structural equation modelling analyses may provide greater insight with further investigations in contexts of adversity and, in turn, establish which outcomes are predicted by FC” (line 309, discussion section).

      The abstract and end of the discussion should make it clearer that the associations between FC and cognitive flexibility are results that need to be confirmed, insofar as they did not survive correction for multiple comparisons.

      We have acknowledged this in the abstract as follows: “Our results highlight the measurable effects that poor growth in early infancy has on brain development and the possible subsequent impact on pre-school age cognitive development, underscoring the need for early life interventions throughout global settings of adversity”.

      We have acknowledged this in the discussion as follows: “While our results are consistent with previous studies, we acknowledge that the significant associations between early FC and later cognitive flexibility do not withstand multiple comparisons. Therefore, we encourage future studies that may replicate these findings with a larger sample” (line 300, discussion section).

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In Figure 1 B and C the authors should indicate that the results refer to HbO.

      We have added the suggested specification in the caption of the figure as suggested.

      (2) Figure SI2. Please indicate in the caption that these are the results when pre-processing did not include global signal regression.

      We have added the suggested specification in the caption of the figure as suggested.

      Reviewer #3 (Recommendations for the authors):

      (1) The sentence l529-531 ("To investigate whether FC early in life predicted...") should be more explicit as it is not clear which of the two variables is regressed by the other: is it the measure of cognitive flexibility that is regressed by FC, as the hypothesis suggests? Were other variables considered in the regression model? (For linear regression with only one "prediction" variable, the square root of the coefficient of determination 𝑅2 is equal to the correlation between the two variables.)

      Yes, it is the measure of cognitive flexibility that is regressed by FC. We have rephrased it in the text as follows: “we regressed later cognitive flexibility against FC that showed a significant change across the first two years of life”. There were no other variables in the regression model.

      (2) A summary table of the statistical results for FC-cognitive flexibility associations should be included as for other analyses, in addition to Figure 3B.

      We added a table of the results for the association between FC and cognitive flexibility in the supplementary materials (Table SI2, page 10), matching the same colours of Table 2. We referenced the table in the text in the main manuscript (line 211, result section).

      (3) Figure 3B: The legend should precise that these results did not survive corrections for multiple comparisons.

      We have specified this in the legend of Figure 3 as suggested.

      (4) For the young pre-schooler group, it seems that the age is around 4 years (age mean +/- SD=47.96 +/- 2.77 months) and not 3 years as indicated at several places in the manuscript.

      We found only once instance in which we erroneously said that the younger preschoolers were around 3 years. We replaced “Gambian infants from BRIGHT were cross-sectionally assessed at the age of 3 or 5 years for cognitive flexibility” with Gambian infants from BRIGHT were cross-sectionally assessed between the age of 3 and 5 years for cognitive flexibility (line 489, method section).

      (5) The authors use the term "intra-hemispheric" connections for the ones within each of the 6 sections. This might be misleading since fronto-posterior connections are also intra-hemispheric ones. Specifying "short-range" or "within-section" connections might be clearer.

      As suggested by the reviewer, we replaced “intra-hemispheric” with “intra-hemispheric within section” where appropriate through the whole manuscript.

      (6) Abstract: what is the justification for using the term "optimal" for describing developmental trajectories of FC?

      The term “optimal” refers to knowledge about typical developmental trajectories, coming especially from fMRI studies, as mentioned in the introduction: “Based on data from fMRI, current models hypothesize that FC patterns mature throughout early development (23–27), where in typically developing brains, adult-like networks emerge over the first years of life as long-range functional connections between pre-frontal, parietal, temporal, and occipital regions become stronger and more selective (28–31). [...]. Importantly, normative developmental patterns may be disrupted and even reversed in clinical conditions that impact development; e.g., increased short-range and reduced long-range FC have been observed in preterm infants (36) and in children with autism spectrum disorder (37, 38)” (line 93-106, introduction).

      (7) The confidence interval should be added in Figure SI3.

      As suggested, confidence intervals have been added in Figure SI3.

      (8) Other scatterplot examples of associations might be added as supplementary information.

      As suggested, we added several additional scatterplots to Figure SI3 (with confidence intervals as noted in the comment above) to show other associations between changes in growth and FC at 24 months.

      (9) Figure SI6: % in x-axis is still indicated.

      We apology for the oversight, all the percentage signs have now been removed from the x-axis tick labels.

      (10) The authors might show the (even not significant) results of the associations between changes in growth and cognitive flexibility in supplementary information.

      As suggested, we added the table reporting the results of the associations between changes in growth (DWLZ) and cognitive flexibility in the supplementary materials (Table SI3). We additionally explored the relationship between changes in functional connectivity and cognitive flexibility as suggested by Reviewer #2 and we reported these additional analyses in the text as follows: “We also explored whether changes in growth and changes in functional connectivity between 5 and 24 months were associated with cognitive flexibility at preschool age, but we did not find any significant association (Table SI3 and Table SI4).” (line 213, results section).

    1. In the past, in the field of education, we often referred to this concept as “parent involvement” rather than “family engagement.” We use the term “family” instead of “parent” to recognize that MLs may live with and have strong relationships with family members instead of or in addition to parents. These family members may play a crucial role in the student’s education and should be included by schools and communities (Staehr Fenner, 2014). The use of the word “engagement” rather than “involvement” indicates an active partnership and shared responsibility between families and educators.

      I can see why the concept of "parent involvement" was changed to "family engagement" and I think the term is all the better for the word change. Because its true that there are some ML students who may be living with extended family rather than with their parents, they could be living with an aunt and uncle or their house could involve both their parents and their extended family all under one roof. And having the ML students family "engaged" instead of "involved" sends a more positive message of wanting to give the family a chance to not only be included in their own child's education but also the class as a whole. An ML student's family sharing their experiences can benefit the non-ML students as well and help them understand the culture their ML students come from.

    1. Author response:

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

      Reviewer #1 (Public review):

      Weaknesses:

      In my view, the presentation of the data is in some cases not ideal. The phrasing of some conclusions (e.g., group-attacks and wolf-pack-hunting by the bacteria) is in my opinion too strong based on the herein provided data.

      We agree with your comment and have replaced the terms “Group-attacks” and “wolf-pack-hunting by “attacks” throughout the manuscript.

      Reviewer #1 (Recommendations for the authors):

      (1) Figure 2AB, please add the name of the statistical test and the number of replicates that the data is based on to the figure legend.

      We thank Reviewer#1 for highlighting the need for more detail. We have revised the manuscript accordingly. The captions of figures 2, 3, 4 and S1 were revised to include the name of the statistical test and the number of replicates. Asterisks indicate significant differences in a multiple comparison test (One -way ANOVA with post hoc Tukey test),* P ≤ 0.05, ** P≤0.01, *** P≤ 0.001

      (2) Figure 2C is this figure referred to in the text?

      We apologize for this oversight. Figure 2C was replaced by new figures 2C and 2D and the old figure 2C is now referenced in the manuscript as Fig 3B1.

      (3) Movie 1, could the movie please also be provided as .mp4? I suggest including individual images across time in the main figure so that readers do not rely on opening a supplementary file for this key finding of the study.

      In the revised manuscript, all the videos were converted to mp4 format and individual images across time were included in Figure 2C and 2D (Chronological snapshots of one attack) and in figure 3B1 (Chronological snapshots of the complete event), thereby improving the readability of the manuscript.

      (4) Figure 3A2 (text l. 355), I am afraid I do not find this figure.

      Fig. 3A2 which previously corresponded to Fig. 3B1, correspond now to Fig. 2C and Fig. 2D. This has been corrected in the revised version of the manuscript.

      (5) Lines 356ff, I am afraid that I find it hard to follow what the authors refer to as the right cell or the left cell. I suggest either adding labels to the movies or providing individual images across multiple timepoints into the main figure that can be labelled and bring across the point.

      Arrows have been added to videos 3–5 to clearly indicate the cells referred to in the text and facilitate tracking across time.

      (6) In general, for all the microscopy, on how many cells have these phenomena been observed? What is n=x? Has this been quantified?

      We thank the reviewer for pointing this out.

      In caption of Fig. 3, the sentence “(A) Percentage of motile A. pacificum ACT03. (B) A. pacificum ACT03 attacked by V. atlanticus LGP32 and (C) A. pacificum ACT03 lysis after 0, 15, 30, 45 and 60 min of interaction. “was replaced by “(A) Cumulative percentage of motile A. pacificum ACT03 cells. (B) Cumulative number of cells attacked by V. atlanticus LGP32 and (C) Cumulative cell lysis after 0, 15, 30, 45 and 60 minutes of interaction.”. In Fig. 3 caption, the sentence “All percentages were determined based on a minimum of 2,000 cells of A. pacificum ACT03.” was also added.

      In Fig. 4 caption, the sentence “All percentages were determined based on a minimum of 2,000 cells of A. pacificum ACT03.” was added.

      In Fig. S1 caption, the sentence “All percentages were determined based on a minimum of 2,000 cells of A. pacificum ACT03.” was added.

      (7) Figure S1A, does this figure show means plus/minus standard deviation? If yes, please add this to the figure legends.

      In Fig. S1 caption, the sentence “Error bars represent the standard deviation of the mean of three independent experiments” was added.

      How do the authors explain the big variation in the test condition and not in the control?

      Regarding the higher variation observed in the test condition compared to the control, this may, on the one hand, reflect biological variability between independent batches of 60-h V. atlanticus cultures used to prepare the supernatants, and, on the other hand, a heterogeneity in the physiological status of independent algal batches (N = 3 ; 2 × 10^4 cells ; see Materials and Methods, Co-culture assay), which may not be perfectly synchronized . In contrast, the control condition consists of A. pacificum cultures incubated in fresh medium without bacterial supernatant, for which algal motility is highly reproducible and thus shows very little variation.

      (8) Line 375, "The lysis phase corresponded to initial vesicle formation followed by the bursting of A. pacificum ACT03 cells (Movie 5) and was induced by the old-starved culture supernatant of V. atlanticus LGP32 (Fig. S1)." Is this reference to Figure S1 correct? S1 shows motility, doesn't it? I don't see how this data supports the statement made in this sentence.

      We apologize for this unclear message.

      "The lysis phase corresponded to initial vesicle formation followed by the bursting of A. pacificum ACT03 cells (Video 5) and was induced by the old-starved culture supernatant of V. atlanticus LGP32 (Fig. S1)." was replaced by "The lysis phase corresponded to initial vesicle formation followed by the bursting of A. pacificum ACT03 cells (Fig. 3C and 3C1).

      And “We next tested whether this lytic effect was mediated by thermostable molecule (s) secreted by Vibrio. “was replaced by “We next tested whether this lytic effect was linked to Vibrio culture supernatant and mediated by thermostable molecule (s) secreted by Vibrio.

      (9) Line 388ff, "Group attacks were observed on non-degraded A. pacificum ACT03 cells, but not on previously lysed cells." No reference to a figure is provided. I am afraid I don't see the data that this statement is based on.

      As it is impossible to show a lack of attack, we just clarified the basis of our experiment.

      “To this end, A. pacificum ACT03 in exponential growth phase was first exposed for 30 minutes to the supernatant of a 60-hour culture of V. atlanticus LGP32, which induced 25% lysis of A. pacificum ACT03 cells. Next, the corresponding V. atlanticus LGP32 cells were added. During exposure, attacks were observed only on undegraded A. pacificum ACT03 cells, but not on previously lysed cells” was replaced by “To this end, A. pacificum ACT03 in exponential growth phase was first exposed for 30 minutes to the supernatant of a 126-hour culture of V. atlanticus LGP32, which induced lysis of 70% of the A. pacificum ACT03 cells (Figures 3C and 3C1, arrow 2 and video 4). Next, cells of V. atlanticus LGP32 from a 60-hour culture, capable of attacking A. pacificum ACT03 cells (Fig. 3B), were added. For 1 hour of exposure, no attack was observed on the previously lysed algae.”

      (10) Figure 4a, Based on the labeling of the figure, in particular the x-axis, it is not fully clear to me what I am looking at.

      Figure 4A has been reworked and its legend modified. We hope that this graph is clearer now.

      (11) Line 428, did the authors consider complementing the pvuD deletion mutant and testing for gain of function when providing the gene in trans?

      We did not investigate pvuD in this study and did not construct a pvuD deletion mutant. We therefore assume that the recommendation refers to pvuB, which was the focus of our work. Unfortunately, we did not perform this experiment. However, several lines of evidence support the implication of PvuB and the vibrioferrin uptake system in this process: (i) the loss of attack behaviour is specific to the mutant in the vibrioferrin uptake pathway and (ii) our expression and proteomic data show a strong induction of vibrioferrin uptake components under starvation and iron-manipulated conditions, which correlate with the attack phenotype.

      (12) Use of the term "group attack" in parentheses in the text, but in the section header and title. Is there really sufficient actual data to say that this is a "group attack"? What exactly are the indications for this being a behaviour of a group?

      We agree with you. The terms “group attacks” and “wolf-pack hunting” were replaced by the more neutral term “attacks” throughout the manuscript.

      (13) Table S1 and S2, those tables give a nice overview. Do the authors provide the raw data based on which they make a claim on "+" and "-" in the individual categories? I would prefer to see the actual data or at least have the possibility to look into this.

      In the revised versions of Tables 1 and 2, we have improved the captions and clarified the meaning of each column in order to avoid any ambiguity between the results of this study and the bibliographic information.

      Specifically regarding Table 2 :

      We do not present any visuals of the interaction between Vibrio and Alexandrium because these species all look alike. Regarding the other algae species tested in interaction with Vibrio, phenomena other than lysis or cell attack have been observed and are the subject of specific laboratory studies.

      (14) Line 456 "first study", line 40f "first evidence of a new mechanism". I suggest toning this down a bit and being clearer in the abstract about this being a working model that can be suggested based on individual bits of data.

      We thank Reviewer #1 for this helpful suggestion.

      In the summary:

      “This is the first evidence of a new mechanism that could to be involved in regulating Alexandrium spp. blooms and giving Vibrio a competitive advantage in obtaining nutrients from the environment.” was replaced by “The interaction model we propose here suggests that Vibrio could play a role in regulating the proliferation of Alexandrium spp., giving it a competitive advantage in obtaining nutrients from the environment.”

      In the discussion:

      Considering predator as a free organism that feeds at the expense of another, this study is the first evidence of the capacity of some Vibrio to develop a predatory strategy against an alga. This behaviour differs from parasitism, because the survival of Vibrio is not exclusively dependent on algae in environment” was replaced by “Consider a predator as a free-living organism that kills its prey and feeds on it, this study provides data suggesting the ability of Vibrios to develop an original predator-like behaviour to kill and feed on algae.”

      (15) Line 469 "Overall, these observations show that V. atlanticus LGP32 is able of wolf-pack hunting behaviour." I see the similarities. I feel that the term "show" is a bit too strong here, or I suggest referring to "wolf-pack-like behaviour".

      The sentence “Overall, these observations show that V. atlanticus LGP32 is able of wolf-pack hunting attack behaviour” was replaced by “Overall, these observations suggest that V. atlanticus LGP32 can exhibit a predator-like behaviour”

      Reviewer #2 (Public review):

      As Weaknesses Reviewer #2 include:

      (1) A lack of early, clear definitions for several important terms used in the paper, including 'predation', 'coordination' and 'coordinated action', 'group attack', and 'wolf-pack hunting', along with a corresponding lack of criteria for what evidence would warrant use of some of these labels. (For example, does mere simultaneity of attacks of an A. pacificum cell by many V. atlanticus cells constitute "coordination"? Or, as it seems to us, does coordination require some form of signalling between predator cells?)

      The term “Coordinate” was replaced by “simultaneous” throughout the manuscript

      The terms “Group attack” and “wolf pack hunting” were replaced by “attack” throughout the manuscript

      (2) Absence of controls for cell density in the test for starvation effects on predatory behaviour; unclear how the length of incubation affects the density of V. atlanticus cells.

      We thank the reviewer for pointing this out.

      Cells density experiment was already performed (cf. Fig. 4A).

      The sentence. ”All percentages were determined based on a minimum of 2,000 cells of A. pacificum ACT03.“ was added in captions of Fig. 3, Fig. 4 and Fig S1

      (3) Lack of clarity in some of the methodological descriptions

      The Methodology has been checked and some improvements have been made.

      Reviewer #2 (Recommendations for the authors):

      (A) Title

      (1) Could 'induces' be better than 'promotes'?

      We agree with Reviewer #2. The initial title, “Starvation of the bacterium Vibrio atlanticus promotes lightning group-attacks on the dinoflagellate Alexandrium pacificum”, was replaced by “Starvation of the bacterium Vibrio atlanticus induces simultaneous attacks on the dinoflagellate Alexandrium pacificum”.

      (B) Abstract

      (1) Perhaps define pycosphere in the abstract - many readers might not know this word.

      We have revised the abstract to define the term phycosphere and added the sentence “This occurs in the microenvironment surrounding phytoplankton cells, the phycosphere. An interface rich in nutrients and organic molecules exuded by the cell.”

      (2) Perhaps "on dinoflagellates".

      We thank Reviewer #2 for this suggestion. We have revised the abstract by replacing “on the dinoflagellates species” with “on dinoflagellates”.

      (3) Line 33 - The word 'prey' is used without a claim of predation having yet been made; only killing has been claimed so far.

      We agree and have replaced the word “prey” by “algae” in the abstract.

      (4) Line 34 - It is unclear whether the description refers to the 'attack stage' or to 'wolf-pack attack' in general. The sentence is written in such a way that it seems to refer to 'wolf-pack attack'. However, this would seem to be incorrect, with the description being specific to V. atlanticus.

      To avoid this ambiguity, we have removed the sentence “resembles the ‘wolf-pack attack’ strategy” from the abstract.

      (5) Line 35 - Should there be a 'consumption phase'?

      We agree with the reviewer #2, “degradation” was replaced by “consumption”.

      (6) If predation is claimed later in the manuscript (which it is), it should be explicitly claimed in the abstract.

      We thank Reviewer #2 for this helpful suggestion.

      We have revised the abstract. The sentence “Results showed that Vibrio atlanticus was able to coordinate lightning group attacks then kill the dinoflagellate Alexandrium pacificum ACT03” was replaced by “The results showed that Vibrio atlanticus was capable of attacking and killing the dinoflagellate Alexandrium pacificum ACT03”.

      (C) Main text

      (1) Line 54 - Perhaps "Among HAB-causing organisms...".

      We agree with the reviewer’s suggestion and have revised the wording.

      (2) Line 56 - "that, together with..., form the "Alexandrium tamarense" complex".

      We agree with the reviewer’s suggestion and have revised the sentence.

      (3) Line 57 - What this "complex" is and its significance should be explained.

      “Among them, Alexandrium pacificum is a flagellated eukaryotic unicellular organism that together with Alexandrium tamarense and Alexandrium fundyense form the "Alexandrium tamarense" complex (Hadjadji et al., 2020)” was replaced by

      “Among them, Alexandrium pacificum is a flagellated eukaryotic unicellular organism that together with Alexandrium tamarense and Alexandrium fundyense form the "Alexandrium tamarense" complex, responsible for paralytic shellfish poisoning worldwide (Hadjadji et al., 2020)”

      (4) Line 58 - What is a Rephy survey?

      We clarified this point, “by rephy survey” was replaced by “by the French phytoplankton observation and monitoring network (Rephy)”

      (5) Line 59 - 'resulting in' instead of 'resulting of'.

      We agree with the reviewer and have replaced “resulting of” with “resulting in”.

      (6) Line 65 - It seems that ', influencing the time of appearance of blooms' would be more correct than the current phrasing. The current phrasing is unclear regarding the relation between species, tolerance range, and the time of appearance of blooms.

      To address this point, “Depending on the phytoplankton species, the tolerance range of physicochemical parameters is different and influences the time of appearance of blooms” was replaced by “Depending on the species of phytoplankton, tolerance to physicochemical parameters varies, which influences when blooms occur.”

      (7) Line 76 - Run-on sentence which should probably be split after the reference to Wang et al., 2020.

      We agree with the reviewer and have split the sentence.

      (8) Line 89 - What are these observations?

      This sentence was reformulated.

      “Based on observations from the natural environment showing a potent relationship between Vibrio and Alexandrium algae bloom events, this study aim to determine in vitro, the main factors implicated in this relationship” was replaced by ”This study aims to describe observations made in the natural environment between Vibrio bacteria and Alexandrium algal blooms, and to determine in vitro the main factors involved in this relationship.”

      (9) Line 94 - This is the first clear reference to a predator-prey interaction, and it is stated as if it's established. Is it not a central goal of the study to demonstrate that predation is even happening?

      Based on the title and abstract, I would have expected the major claims of the paper highlighted in the abstract to be:

      (i) that predation of algae by bacteria occurs in this system,

      (ii) there is a social component of predation,

      (iii) claims about what induces this predatory behaviour.

      The summary has been amended accordingly, and the term “predation” has been removed, along with all sentences referring to it.

      (10) Line 99 - What does n.d. mean?

      This point was addressed in the revised version.

      (11) Line 97 section - specify qPCR.

      This point was clarified in the revised version.

      (12) Line 139 - Mentioning the oligonucleotides in this part of the methods seems out of place. Would this not fit better in the section on Gene expression analysis?

      This sentence was discarded from this paragraph.

      (13) Line 147 - Where did the co-cultured phytoplankton species come from?

      To answer this point, reference to Table 2 was added

      (14) Line 149 - Is it known if the phytoplankton strains had all grown to the same density after 24 hours?

      The doubling time of dinoflagellates in laboratory culture is between 5 and 7 days. During the duration of the experiments, the dinoflagellate concentration did not change significantly.

      The sentence “(doubling time between 5 and 7 days)” was added

      (15) Line 150 - Was the density of the Vibrio cultures at the different incubation times measured? Density might play an important role in predation, and so it would be important to control for density in these assays.

      The concentrations of live vibrio in each individual culture were not actually measured. However, the role of vibrio density in attacks was measured and is shown in Figure 4A and observed in Fig 2B.

      (16) Line 153 - How long was the co-incubation?

      The incubation times were added in the revised version.

      (17) Line 158 - What is mean by "independent experiments", more exactly?

      To clarify this point, “Data are the means of three independent experiments” was replaced by “The data come from three independent experiments using independent phytoplankton cultures and independent bacterial cultures.”

      (18) Line 161 - Perhaps give the source information about the Vibrio strain at its first mention.

      A reference has been added in the revised preprint.

      (19) Line 163 - line 141 refer to multiple non-axenic species, whereas here "the algal strain" is referred to.

      And

      (20) Line 164 - language phrasing throughout the manuscript could use some polishing, e.g., "this means that additional bacteria...".

      To address this comment, “As the algal strain used in the study is not axenic, means that additional bacteria, other than the V. atlanticus LGP32, are potentially present in the experiments.” was replaced by “As the A. pacificum ACT03 strain (table 2) used in the study is not axenic, there is potential for bacteria other than V. atlanticus LGP32 to be present in the experiments.”

      (21) Line 208 - Why were both magnitude and p-value criteria used rather than just p-values?

      In the present proteomic approach each experimental condition was measured six times, and the average (mean) value was used to reduce random noise. Then we selected differences that had to be large enough to matter biologically, this is a central criterion and at least a 2-fold change was considered to focus exclusively on biologically relevant differences, which allowed us to control for the effect size. However, the differences also had to be statistically significant, we applied a statistical confidence at P < 0.01, to be sure that there is less than a 1% chance the result happened randomly. In the present proteomic approach each experimental condition was measured six times, and the average (mean) value was used to reduce random noise.

      Then we selected differences that had to be large enough to matter biologically, this is a central criteria and at least a 2-fold change was considered to focus exclusively on biologically relevant differences, which allowed us to control for the effect size. However, the differences also had to be statistically significant, we applied a statistical confidence at P < 0.01, to be sure that there is less than a 1% chance the result happened randomly. We considered that using both criteria makes the results meaningful and trustworthy, not just a small or random fluctuation.

      (22) Line 270 - Were these three replicate experiments also "independent"; if yes, in what sense?

      “All experiments were conducted in triplicate” was replaced by “The experiments were performed using biological triplicates, each of which was analyzed in triplicate.”

      (23) Line 296 - Perhaps "the temperature-sensitivity (or resistance) of" rather than "the nature of".

      The modification was made in the new manuscript.

      (24) Line 307 - The sentence mentions only one influential period that was removed from the dataset, but the word 'whenever' suggests multiple occurrences.

      We agree, “whenever” was replaced by “because”.

      (25) Line 325 - line 327 - The rationale behind the first part of the following sentence isn't clear to me, and what is meant by the second part is also not clear.

      To clarify this point, “This result is consistent with the difficulty that Vibrio has in growing at temperatures below 20°C and with the complex interacting factors driving bloom dynamics (Laanaia et al., 2013)” was replaced by “This result is consistent with the difficulty Vibrio has in growing at temperatures below 20°C and with the many environmental factors that influence the dynamics of algae proliferation (Laanaia et al., 2013)."

      (26) Line 327 - line 328 - Hard to interpret; does this refer to living algal cells, or all algal cells, living and degraded?

      To improve clarity, “Interestingly, in spring 2015, the mean densities of all Alexandrium cells and of free-living Vibrio were positively correlated” was replaced by “Interestingly, in spring 2015, the mean densities of Alexandrium cells (living and degraded) and of free-living Vibrio were positively correlated”

      (27) Figure 2 - These results strongly point to predation, but why the Vibrio population would already be elevated in the co-culture treatment relative to the control immediately after inoculation (0 hrs) is not clear.

      The experiments were not conducted at the same time, and the first value on the graphs corresponds to the concentration of vibrio determined after 1 hour of exposure/incubation and not at time 0. Figures 2A and 2B have been modified accordingly, and substantial changes have been made to the relevant section of the results.

      (28) Line 348 - There's no mention of Figure 2C in the main text, or of the statistical test associated with it in the Figure 2 legend.

      To address this comment, Figure 2C has now been cited in the main text, and the statistical analysis method has been added to the Figure 2 caption.

      (29) Line 352 - Text descriptions of videos are not easy to connect with the video content. Label the file names the same as how they are referred to in the text.

      We agree with you, the sentence “Epifluorescence microscopy observation of GFP-labelled V. atlanticus LGP32 (previously grown in Zobell medium) in interaction showed that A. pacificum ACT03 cells that had lost their motility were attacked individually by V. atlanticus LGP32 before being lysed (Fig, 2C and Video 1). “was rephrased and replaced by “Epifluorescence microscopy observation of GFP-labelled V. atlanticus LGP32 (previously grow in Zobell medium) in interaction showed that V. atlanticus LGP32 simultaneously attacks A. pacificum ACT03 cells (Fig, 2C and Video 1).”

      (30) Movie 1 could be cut to remove uninteresting footage at the start. What indicates lysis? Is the deformation of the cells an indication of lysis?

      To respond to this comment, Video 1 has been shortened and in the caption, “degraded” was replaced by “lysed”

      (31) Line 353 - Video could be zoomed in more on a few typical attacks to remove visual noise.

      A chronological overview of an attack has been added to Figure 2 corresponding to Figure 2D, and a chronological overview of the overall event has been added to Figure 3 corresponding to Figure 3B1.

      (32) Line 355 - There does not seem to be a Figure 3A2.

      To address this point, the Fig. 2 and Fig. 3 has been revised for more clarity. See above

      (33) Figure 3 - Can the authors fully exclude an effect of bacterial density as distinct from an effect of growth/starvation phase? It would be helpful to determine bacterial viable population densities at 12, 36, 60, and 126 hrs of incubation in Zobell medium, and to control for density in testing for effects on algae.

      Information on Vibrio densities incubated in Zobell medium for 12, 36, 60, and 126 hours has been now included in the results section “Attack of A. pacificum ACT03 is activated by V. atlanticus LGP32 starvation.”

      (34) Line 363 - It is unclear how the degradation of the flagella is apparent from movie 3. It would be helpful to have a comparison with healthy flagella.

      Alexandrium cells with intact flagella move so quickly that it is impossible for us to follow them and film their flagella with the tools at our disposal.

      For greater clarity, arrows have been added to videos 3, 4 and 5.

      (35) Line 364 - Sudden change from referring to the recording as 'video' instead of movie. What is meant by erratic swimming? The cell does not seem to move much.

      To address this comment, “Movie” was replaced by “Video” throughout the manuscript and “erratic swimming” was replaced by “irregular swimming”

      (36) Line 365 - How did you observe the detachment of the flagellum?

      The detachment of the flagellum can be observed using a confocal microscope. This process was filmed and presented in Video 3. Arrows have been added to the video to clearly indicate the flagellum detachment.

      (37) Line 368 - Perhaps this is due to it not being clear regarding which movie is meant, but there is no clear attack visible in movie 4.

      To make this clearer, arrows have been added to the video 4 to indicate attached cells.

      And the sentence in the caption of the video 4 “Vibrio, filmed under a confocal microscope, attacks in groups one immobilized Alexandrium cell then moves on to attack — still as a group — another cell without touching the other whole cells, suggesting active communication between Vibrio cells” was rewritten and replaced by “This video, recorded under a confocal microscope, shows Vibrios simultaneously attacking a first immobilized Alexandrium cell, then moving on to attack a second cell without ever targeting the other cells present, suggesting active communication between the Vibrio bacteria.”

      (38) Line 369 - It seems the peak attach % was reached at 45 minutes, not 15-30 minutes.

      Sorry for the confusion. In fig. 3 for more clarity, the sentence “(A) Percentage of A. pacificum ACT03 motile cells. (B) cells attacked by V. atlanticus LGP32 and (C) cells lysis after 0, 15, 30, 45 and 60 min of interaction” was replaced by “(A) Cumulative percentage of motile A. pacificum ACT03 cells. (B) Cumulative number of cells attacked by V. atlanticus LGP32 and (C) Cumulative cell lysis after 0, 15, 30, 45 and 60 minutes of interaction.”

      (39) Line 382 - "clearly show role of nutrient limitation", see comment re controlling for any role of bacterial density.

      To address this point, information’s on Vibrio densities were added in the manuscript. See cf comment 33.

      (40) Line 385 - line 386 - Phrasing unclear.

      We have revised the text accordingly, “To this aim, A. pacificum ACT03 in exponential growth phase was first exposed for 30 min to supernatant from 60 hours starved V. atlanticus LGP32 Zobell media that induced 25% lysis of A. pacificum ACT03 cells and next to the corresponding V. atlanticus LGP32 cells. Group attacks were observed on non-degraded A. pacificum ACT03 cells, but not on lysed cells.“ was replaced by “To this end, A. pacificum ACT03 in exponential growth phase was first exposed for 30 minutes to the supernatant of a 126-hour culture of V. atlanticus LGP32, which induced lysis of 70% of the A. pacificum ACT03 cells (Figures 3C and 3C1, arrow 2 and video 4). Next, cells of V. atlanticus LGP32 from a 60-hour culture, capable of attacking A. pacificum ACT03 cells (Fig. 3B), were added. For 1 hour of exposure, no attack was observed on the previously lysed algae.”

      (41) Line 413 - Is this the only pathway for quorum sensing in V. atlanticus?

      Indeed, the last two sentences of this paragraph are unclear.

      To address this point:

      “By targeted mutagenesis of key genes involved in QS pathways ΔluxM (HAI-1 production), ΔluxS (AI-2 production) and ΔluxR (high-density QS master regulator) did not lead to any change in the attack behaviour of V. atlanticus LGP32 (Fig. 4C).” was replaced by “Targeted mutagenesis of key genes involved in two of the three known QS pathways in vibrios (Fig. S3), ΔluxM (HAI-1 production), ΔluxS (AI-2 production), and ΔluxR (main high-density QS regulator), did not result in any changes in the attack behavior of V. atlanticus LGP32 (Fig. 4C).”

      And “Taken together these results showed that attack by V. atlanticus LGP32 is not link to QS.” was replaced by. “Combined with the absence of overexpression of the CqsS gene (inducible by CAI-1) involved in the last known QS pathway in Vibrio (Fig. S3), these results indicated that the attack by V. atlanticus LGP32 is most likely unrelated to QS.”

      (42) The references to tropism aren't clear.

      You're right, there's no reason to use the term tropism here. We have removed it.

      (43) Line 439 - Why was H3BO4 used as a control for the addition of FeCl3?

      For clarity, the sentence “Boron being known to be a regulator or capable of being transported by vibrioferrin (Romano et al., 2013; Weerasinghe et al., 2013), we tested its potential involvement in the interaction but no effect was evidenced here.” was replaced by “Given that boron is known for its role in regulating a global bacterial cellular response to phytoplankton and to bind to vibrioferrin (Romano et al., 2013; Weerasinghe et al., 2013), we tested its potential involvement in simultaneous vibrio attacks. Compared to the Zobell control, no effect on the number of attacks was observed”

      (44) Line 441 - line 449 - Should explicitly say in text that no attacks were observed for any species other than the Alexandrium and Gymnodinium species.

      We agree and have explicitly stated in the text that no attacks were observed for any species other than Alexandrium and Gymnodinium.

      (45) Line 454 - line 455 - The last part of this sentence seems a strange statement, since

      (i) it has long been know that predatory bacteria can eat a wide range of eukaryotes, ii) one of the cited papers (Perez et al) actually highlights a case of bacterial predation on algae, and iii) in the next paragraph the authors themselves highlight Streptomyces predation of algae.

      To make this clearer, « Among predators, predatory bacteria are found in a wide variety of environments, and like bacteriophages and predatory protists, they have been reported to prey exclusively on other bacteria » was replaced by “Among predators, predatory bacteria are found in a wide variety of environments and, like bacteriophages and predatory protists, feed primarily on other bacteria, although a few cases of predation on microbial eukaryotes have also been reported.”

      (46) Line 455 - Better to clarify the authors' definition of a predator at the start of the paper. The offered definition seems more like a definition of 'consumer' than 'predator', as the latter normally involves both the killing and consumption of other organisms, not just consumption with some kind of "expense".

      To address this comment:

      - “predator behaviour” was replaced by “predator-like behaviour”

      - and “Considering predator as a free organism that feeds at the expense of another, this study is the first evidence of the capacity of some Vibrio to develop a predatory strategy against an alga. This behaviour differs from parasitism, because the survival of Vibrio is not exclusively dependent on algae in environment” was replaced by “Consider a predator as a free-living organism that kills its prey and feeds on it, this study provides data suggesting the ability of Vibrios to develop an original predator-like behaviour to kill and feed on algae.”

      (47) Line 457 - Don't see the benefit of trying to distinguish from parasitism here, especially since parasitism can be facultative, whereas the authors' phrasing suggests that it is always obligate.

      You are right, this sentence has been deleted.

      (48) Line 463 - line 464 - The authors should clearly explain exactly what detailed aspects of Myxococcus and Lysobacter predation they think the "attack stage" of V. atlanticus resembles.

      Accordingly, “The second stage, the ‘attack stage’ corresponding to physical contact between Vibrio and Alexandrium resembles the ‘wolf-pack attack’ strategy described for Myxococcus xanthus and Lysobacter regardless of the prey species used, M. xanthus must be in close proximity to prey cells in order to induce their lysis and to benefit from their biomass (Martin, 2002; Perez et al., 2014)” was replaced by “The second stage, the ‘attack stage’ corresponding to the physical contact between Vibrios and Alexandrium, is similar to the strategy used by Myxococcus xanthus and Lysobacter. These bacteria must be in close proximity to their prey in order to cause lysis and utilize their biomass, regardless of the prey's species (Martin, 2002; Genovesi et al., 2013; Perez et al., 2016; Zhang et al., 2020)”

      (49) Line 466 - line 467 - The comparison to bacteria clustering around lysed cells is surprising since the authors show that V. atlanticus does not attack already lysed cells.

      The sentence was rephrased, “This phenomenon is comparable to that of bacteria clustering around lysed ciliate cells “was replaced by “Visually, this phenomenon resembles bacteria clustering around lysed ciliate cells.”

      (50) Line 469 - Missing is a statement of exactly what criteria constitute "wolf-pack hunting behaviour" and exactly how V. atlanticus meets those criteria.

      To address this point, “wolf-pack hunting behaviour” was replaced by “predator-like behaviour”

      'Able of' should be corrected to 'Capable of'.

      We agree and have reworded the sentence.

      (51) Line 470 - Consider starting a new paragraph for the material on quorum sensing.

      Accordingly, we have separated the section concerning QS pathway from the section concerning iron pathway.

      (52) As part of their discussion on the role of iron uptake, can the authors comment on any relationship between starvation and iron uptake, and in particular the observations that, while general nutrient deprivation induces attacks, supplementation with a specific nutrient (iron) also induces attacks (Figure 4D)? Do bacteria starved for general growth substrates take up more iron than growing bacteria?

      To respond to this comment, “Future study could demonstrate further the role of vibrioferrin in group attack, by adding iron-saturated vibrioferrin to algae-Vibrio co-cultures.” was replaced by “Interestingly, if a general nutrient deficiency causes attacks, iron supplementation increases the number of attacks (Figure 4D), suggesting the importance of iron absorption in the attack behavior. Future studies should determine whether nutrient deficiency increases the iron absorption capacity of Vibrios and whether this plays a major role in the attack mechanism.”

      (53) Line 486 - Of what is boron known to be a regulator?

      To respond to this comment, “Given that boron is known for its regulatory properties and for being transportable by vibrioferrin“ was replaced by “Given that boron is known for its role in regulating a global bacterial cellular response to phytoplankton and to bind to vibrioferrin”.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      This paper describes the localisation of DNA repair proteins, which carry out their DNA repair function in the nucleus, to the cytoplasmic Golgi apparatus. Using the Human Protein Atlas to identify candidates, the authors use antibody localisation to show that a significant number of DNA repair proteins also localise at the Golgi. It appears that proteins involved in common DNA repair pathways localise to common regions of the Golgi. The Golgi-nucleus distribution of the DNA repairs proteins changes upon DNA damage, indicating a dynamic relationship. The authors focus on the DNA repair protein RAD51C and show that its loss from the Golgi and translocation to the nucleus upon DNA damage is mediated by the ATM kinase. Anchoring at the Golgi is shown to be mediated by the golgin giantin. A functional role for giantin in DNA repair is shown in knockdown studies, supporting a mechanism whereby Golgi anchoring of RAD51C, and possibly other DNA repair proteins, by giantin, is required to maintain proper control of DNA repair. The data are clear and support the authors' conclusions. The data are carefully quantified throughout. I found the text easy to read.

      • Major points:*

      • 1.) To validate the Golgi localisation, KD using siRNA was used. It was deemed that a signal reduction of 25% was enough to indicate specific antibody labelling. This seems like a low number, and not very stringent. For some of the hits, expressing tagged versions of the proteins would greatly strengthen the Golgi assignment. This may not be possible for all, but for RAD51C would seem an important experiment. *

      Response: We thank the reviewer for raising the important issue of antibody validation stringency. We agree that for a single-candidate study, a larger reduction after knockdown would generally be preferable. In our case, the 25% cutoff was used only in the primary high-content screening step as part of an intentionally inclusive two-stage workflow, for the following reasons:

      First, because this dataset is generated in a screening format across hundreds of targets, knockdown-efficiency, protein turnover, and the relative size of the Golgi associated pool are unknown and highly variable between genes. For many proteins the Golgi pool represents a small fraction of total cellular signal, and a modest change in total abundance can translate into a smaller absolute change in the Golgi ROI after segmentation, background subtraction, and imaging noise. We therefore selected a permissive cutoff to reduce false negatives and ensure we did not systematically miss candidates with slower turnover, partial knockdown, or small Golgi pools. This strategy is consistent with large scale subcellular mapping efforts, including the Human Protein Atlas, where genetic depletion by siRNA is used as a key validation pillar for immunofluorescence localization and is combined with additional validation strategies when deeper confidence is required (Stadler et al, 2012). Furthermore, it is important to note that this validation was performed in a high-content screening format in which fixation, permeabilisation, antibody concentration, and blocking conditions were kept uniform across all candidates rather than optimised for each individual antibody. In standard single-target immunofluorescence experiments, these parameters would be titrated to maximise signal-to-noise for the specific antibody and antigen in question. Under non-optimised screening conditions, the absolute magnitude of signal change upon knockdown is inherently attenuated compared to what would be expected from a purpose-optimised assay. We therefore consider a 25% reduction threshold under these uniform, non-optimised screening conditions to be a meaningful and appropriately calibrated criterion.

      Second, we wish to clarify that the primary intent of our screen was not to validate the Golgi-nuclear localisation of any single protein in isolation, but rather to identify whether entire functional pathways are represented at the two organelles. This is precisely why the bioinformatic network analysis was performed as an integral part of the workflow, and not as an afterthought. The finding that the validated hit list is significantly enriched for coherent functional clusters, most notably a network spanning multiple core DNA repair pathways (HR, MMR, BER, MMEJ) serves as an in silico validation of the dataset as a whole. The emergence of pathway-level organisation, with proteins from the same repair pathways co-associating, localising to the same Golgi sub-compartments, and redistributing in the same direction upon genotoxic stimuli, provides biological coherence that goes beyond what individual antibody validation can offer, and substantially reduces the likelihood that the Golgi signal represents a collection of unrelated false positives.

      Third, our mechanistic conclusions do not rely on the 25% screening threshold. For RAD51C, we used multiple orthogonal validation approaches, including independent antibodies recognizing distinct RAD51C epitopes and genetic depletion, supported by biochemical evidence.

      In response to this comment, we have provided the full screening validation dataset as source data (Supplementary____Table S1), including intensity changes for the candidates, so that readers can inspect the distributions and apply their own thresholds. We have also clarified in the Results section the rationale behind our screening strategy (lines 128-139) and the role of the bioinformatic network analysis as an integral validation step (lines 141-156).

      Turning to the specific suggestion of tagged RAD51C, we fully agree that tagged proteins can provide valuable orthogonal validation. We attempted endogenous tagging using CRISPR-mediated homologous recombination but were unable to obtain viable colonies following editing, consistent with the essential role of RAD51C in homologous recombination. We also attempted ectopic expression of tagged RAD51C but were unable to obtain constructs that preserved physiological expression levels, maintained robust cell viability or produced interpretable localization. This difficulty is not unique to our laboratory: colleagues working on RAD51 paralog complexes have reported that tagging or overexpression of RAD51C perturbs both its localisation and its ability to form functional paralog complexes (Greenhough et al, 2023; Rawal et al, 2023; Somyajit et al, 2015; Berti et al, 2020) all use purified complexes or untagged proteins for functional assays. We discussed these challenges extensively with experts in the DNA damage repair field at several international meetings (EMBO Sounio, Keystone Symposia, German DNA Repair Society). For these reasons, we relied on orthogonal approaches that do not require tagging (genetic depletion plus independent antibodies, and biochemical fractionation) to support the Golgi localization claim. We agree with the reviewer that this represents a limitation of this study, and we addressed these concerns in the discussion of our revised manuscript (lines 630-641).

      *2.) The total signal should be quantified for each DNA repair protein upon genotoxic stress, in addition to the Golgi to nucleus ratio. For many of the proteins it looks like the total signal goes down, which could influence interpretation. *

      Response: __We thank the reviewer for this important point. We wish to clarify that our imaging pipeline uses marker-based segmentation throughout, the Golgi compartment is segmented using GM130 and the nucleus using Hoechst, as unsegmented whole-cell masks without organelle markers yield unreliable intensity measurements in this experimental setup. True total cellular signal is therefore not directly accessible in this dataset. In the revised manuscript we provide the absolute fluorescence intensities for both the Golgi and nuclear compartments separately. In addition, we now include total (Golgi + nuclear) intensity measurements for each protein (__Supplementary Figures 3D, 4D, __and 5E__) as the most reliable proxy for overall protein distribution. These data are presented alongside the redistribution ratio to enable comprehensive interpretation.

      As the reviewer correctly notes, a subset of proteins shows a reduction in total signal after treatment, particularly with doxorubicin. This is consistent with known effects of doxorubicin-induced DNA damage on cellular proteostasis, including widespread ubiquitination and suppression of protein translation (Halim et al, 2018). Several DDR regulators are subject to ubiquitin-dependent turnover following genotoxic stress, such as CHK1 (Zhang et al, 2005). More broadly, ubiquitin and proteasome mediated regulation is an integral component of the DNA damage response and can affect the abundance and detectability of DDR factors (Brinkmann et al, 2015). Changes in abundance are therefore an expected biological feature of the response. For this reason, we used the Golgi-to-nucleus ratio as the primary redistribution readout, as it captures relative compartmental partitioning independently of changes in total protein levels.

      *3.) The study would benefit from live imaging of the Golgi to nucleus translocation of RAD51C. This would give a better indication of dynamics. *

      __Response: __We agree that live imaging would directly visualize the dynamics of RAD51C redistribution between the Golgi and the nucleus. This was indeed one of our initial goals following the identification of the Golgi-associated RAD51C pool. However, as described above in our response to Major Comment 1, live imaging requires a fluorescently tagged RAD51C construct, and all tagging strategies we attempted, both endogenous CRISPR-mediated tagging and ectopic expression, failed to yield cell lines with robust signal while preserving physiological behaviour. This appears to be a broader challenge for highly conserved and functionally constrained DNA repair proteins, and is not unique to our laboratory.

      Given these constraints, we focused on tag-independent approaches: multiple independent RAD51C antibodies combined with genetic depletion controls, quantitative fixed-cell time courses, and biochemical fractionation. These orthogonal datasets together support compartment-specific changes over time in a manner consistent with redistribution. We have clarified this limitation explicitly in the manuscript and avoided any wording that could be interpreted as implying direct single-molecule tracking in live cells. We present this as an important avenue for future work, contingent on the development of viable RAD51C-expressing cell lines (lines 630-641).

      *4.) The double depletion experiments suggest a functional relationship between giantin and RAD51C. But they do not formally show it. Experiments to more directly address the functional role of the interaction between these two proteins would strengthen the study. *

      Response: We agree with the reviewer that double depletion alone cannot formally prove that the physical Giantin-RAD51C interaction is the sole determinant of the observed DDR phenotypes. However, we would like to highlight the breadth of evidence we have assembled in support of this functional relationship:

      • Physical interaction between endogenous Giantin and RAD51C demonstrated by colocalisation (Figure 4F-G) and co-immunoprecipitation (Figure 4H-I).
      • Damage-induced dissociation of the Giantin-RAD51C complex that is prevented by ATM inhibition or Importazole treatment, directly linking the interaction to the DDR signalling axis (Figure 3K-P)
      • Premature nuclear accumulation of RAD51C upon Giantin depletion, producing aberrant nuclear foci lacking canonical HR markers and impaired ATM signalling (Figure 4B-E & J-M)
      • DR-GFP reporter assay confirming that Giantin depletion reduces HR efficiency to approximately 60% of control, consistent with the reduction previously reported in the genome-wide HR screen (Adamson et al. 2012) and validating the functional significance of Giantin in HR (Figure 5L).
      • Partial rescue of ATM phosphorylation, genomic instability and proliferation phenotypes by RAD51C co-depletion, arguing for RAD51C as a functionally relevant conduit of the Giantin-dependent phenotype (Figures 5M-5P). These observations are further supported by the established literature on RAD51C function, its roles in CHK2 phosphorylation, replication fork stabilisation, and RAD51 filament formation (Badie et al, 2009; Somyajit et al, 2015; Prakash et al, 2022) providing a mechanistically coherent framework in which mislocalisation of RAD51C, whether directly or indirectly through Giantin, leads to dysregulation of DDR signalling and repair capacity, as we directly demonstrate with the HR efficiency assay.

      Nonetheless, we fully agree that the most direct proof of the functional relevance of the physical Giantin-RAD51C interaction would come from separation-of-function experiments, ideally using an interaction-deficient Giantin mutant or an RAD51C variant unable to bind Giantin. We wish to be transparent that both approaches face substantial technical barriers in this system. RAD51C tagging consistently compromised cell viability and protein function, precluding the generation of interaction-deficient variants at physiological expression levels. Engineering an interaction-deficient Giantin mutant presents an independent challenge: Giantin is one of the largest Golgi matrix proteins (~376 kDa), composed almost entirely of extended coiled-coil domains that are resistant to structural prediction, and identifying a discrete RAD51C interaction interface without disrupting broader scaffolding function would require a dedicated structural and biochemical programme. We have framed these explicitly as the most important future priorities in the Discussion (lines 555-564), rather than over-interpreting the current data.

      *5.) The Kaplan-Meier plots in Fig S9 seems to be quite selective in that only breast cancer is shown. Does giantin reduction correlate with poor prognosis in other cancers? *

      __Response: __We thank the reviewer for this suggestion. We initially focused on breast cancer because RAD51C is a clinically established hereditary breast and ovarian cancer susceptibility gene (Meindl et al, 2010; Ghannoum et al, 2023), providing direct clinical context for a study centred on RAD51C dynamics and genome stability. We agree however that restricting the survival analysis to a single cancer type can appear selective.

      To address this directly, we expanded the in-silico survival analysis of Giantin (GOLGB1) using GEPIA2 (Tang et al, 2019) across all available TCGA cohorts (overall survival, median cutoff, FDR correction). In the pooled pan-cancer analysis, higher GOLGB1 expression is significantly associated with improved overall survival (HR(high) = 0.75, p = 6.6 × 10⁻¹⁵). When stratified by tumour type, the majority of individual associations do not reach statistical significance. The two most robust statistically significant associations are kidney renal clear cell carcinoma (KIRC; HR(high) = 0.57, p = 3.4 × 10⁻⁴), where high GOLGB1 expression is associated with improved survival, and lower-grade glioma (LGG; HR(high) = 1.5, p = 0.036), where the association is in the opposite direction. A significant association is also observed in thymoma (THYM; HR(high) = 7.3, p = 0.031), though this should be interpreted with caution given the small cohort size (n = 59). Notably, the breast cancer association observed in the KM Plotter analysis (HR = 0.71, p = 1.8 × 10⁻¹¹; n = 4,929) does not reach significance in the TCGA BRCA cohort (HR = 1.1, p = 0.68; n = 1,070), most likely reflecting the substantially smaller sample size of the TCGA cohort, which is approximately 4.6-fold smaller and therefore underpowered to detect a modest effect. These context-dependent associations are consistent with the tumour-type-specific roles of Golgi scaffolding proteins and are discussed accordingly in the revised manuscript.

      In the revised manuscript we have retained the original breast cancer Kaplan-Meier plots and supplemented them with a pan-cancer survival map across all TCGA cohorts (lines 611-625; Figure S9G) and a summary table (Supplementary Table 3) reporting hazard ratios, sample sizes, and p-values for each tumour type, allowing readers to assess the clinical relevance of GOLGB1 expression.

      *Minor points: There are a few grammatical errors here and there. The figures do not appear in the correct order in the text, which makes the early parts of the paper a bit difficult to follow. Some of the figures don't seem to clearly match the text. For example, it is mentioned that RAD51C labelling was done with 3 different antibodies. I could not find this data. *

      Response: __We thank the reviewer for these helpful observations. In the revised manuscript we have (i) carefully proofread the text and corrected grammatical errors throughout; (ii) revised the Results section to ensure that figures and supplementary figures are cited in sequential order and that each panel is explicitly introduced before being discussed, improving readability in the early sections. and (iii) corrected figure callouts to ensure they match the text. In particular, the statement that RAD51C labeling was performed with three different antibodies has been linked to the corresponding figure panels in the Results section. Antibody identifiers, sources, and dilutions are clearly reported in the Methods and in the table in __Supplementary Table S1.

      __ Reviewer #1 (Significance (Required)):__

      *This paper is novel and should be of significant interest to the field. It has important implications for how we think about the Golgi apparatus, and for how DNA repair pathways may be controlled. The pattern is clearly complex, with many DNA repair proteins localising to the Golgi, and some showing opposite dynamics. However, by focussing on RAD51C and giantin, the paper nicely demonstrates a novel mechanism for controlling DNA repair by these proteins. *

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      Background - Eukaryotic cells rely on tightly regulated DNA repair pathways to preserve genome stability under the constant threat of both endogenous and exogenous genotoxic stress. While the nucleus, and to a lesser extent the mitochondria, is the primary site where DNA damage is detected and repaired, accumulating evidence indicates that extranuclear organelles, particularly the Golgi apparatus, play a surprisingly important role in modulating stress signaling, proteostasis, and the trafficking/activation of key DNA repair factors.

      • Emerging evidence has shown that genotoxic stress can result in a major remodeling of the Golgi apparatus; however, the crosstalk between the Golgi and the nucleus, and its contribution to the DNA damage response, remains poorly defined. The present study offers timely insight by examining the spatiotemporal behavior of DNA repair proteins that shuttle between the Golgi and the nucleus, and how this trafficking contributes to the maintenance of genomic stability.*

      Main findings - The authors employed the Human Protein Atlas (HPA) project to shortlist proteins that might link Golgi-nuclear function and validated each candidate using an siRNA-mediated antibody-validation pipeline, thereby identifying 163 proteins that localize to both the Golgi and the nucleus. Bioinformatic analysis of these candidates revealed a significant enrichment for DNA damage response (DDR) regulators, including multiple factors from core DNA repair pathways, suggesting that a portion of the DDR machinery may reside in the Golgi at steady state. Interestingly, the authors observed that dual-localizing DDR proteins undergo lesion-specific redistribution between the Golgi and the nucleus in response to specific types of DNA injuries. For instance, BER and MMEJ proteins shifted from nucleus to Golgi in response to doxorubicin, whereas MMR and HR proteins redistributed from Golgi to nucleus. This trend was reversed with H2O2 or KBrO3 treatments.

      • To gain further insight into the link between the DDR and Golgi-nuclear communication, the authors focused on the HR factor RAD51C, which also plays a key role during the replicative stress response. The authors noticed that RAD51 is significantly associated with the Golgi, in addition to its known nuclear pool. Interestingly, they demonstrated that doxorubicin triggers the ATM-dependent release of this Golgi-tethered RAD51C pool and its Importin-β-mediated import into the nucleus, where it forms repair-associated foci. They further identified Giantin as the Golgi scaffold that anchors RAD51C at steady state in this subcellular compartment and showed that its depletion leads to premature nuclear accumulation of RAD51C, formation of aberrant RAD51C foci lacking canonical HR markers, reduced ATM activation, elevated genomic instability, and increased cell proliferation. *

      Together, this study revealed an underappreciated and functionally meaningful spatiotemporal level of regulation within the DDR, suggesting that the Golgi, rather than functioning solely as a trafficking organelle, acts as a platform that anchors, releases, and temporally controls the availability of key DNA repair factors in response to genotoxic stress. In particular, the authors demonstrated that the timely and regulated release of RAD51C from the Golgi is essential for maintaining genome stability and is dependent on canonical DDR signaling pathways, including ATM activation and Importin-β-mediated nuclear import.

      • Overall Critique - This manuscript offers a novel and compelling perspective on the regulation of the DDR by positioning the Golgi as an active participant in the spatiotemporal control of DNA repair factors. By integrating multiple experimental layers, including a systematic localization screening, a sub-Golgi mapping, several dynamic redistribution assays, and functional perturbation read-outs, the authors built a strong and coherent case for a biologically meaningful Golgi-nucleus communication axis during the DDR. Therefore, the study is timely and highly relevant for the DNA repair field, with broader implications for our understanding of how subcellular organelles coordinate genome maintenance and cellular homeostasis.

      While the manuscript is clearly written and the figures are coherent and supportive of the main findings of the study, several issues should be addressed to ensure full interpretability and reproducibility.

      Major Comments*

      *1. Limited use of agents causing genotoxic stress - The authors report intriguing lesion-specific shifts in Golgi-nuclear redistribution, yet much of the mechanistic work relies heavily on doxorubicin, a pleiotropic drug that induces diverse forms of DNA damage beyond DSBs. Expanding the core analysis of the study to include a broader panel of mechanistically defined genotoxins (e.g., etoposide, camptothecin, neocarzinostatin, or ionizing radiation) would substantially strengthen the conclusion that the trafficking patterns reflect damage-type specificity rather than drug-specific off-target effects. Such broader analysis would also clarify whether Golgi-nucleus communication responds differentially to replication-associated breaks, Topo II-dependent lesions, oxidative stress, or crosslinks. *

      __Response: __We thank the reviewer for this important point. We would first note that while doxorubicin is indeed pleiotropic, its primary and best-established mechanism of action is the poisoning of Topoisomerase II, leading to DNA double-strand breaks, a mechanism it shares with etoposide (van der Zanden et al, 2021; Thorn et al, 2011). The additional effects of doxorubicin, including reactive oxygen species generation and chromatin remodelling, are well-documented but secondary to this DSB-inducing activity, as we note in the revised manuscript. Nonetheless the goal of this study was not to comprehensively map lesion-specific trafficking for every DDR protein, but rather to establish the existence of a dynamic Golgi-nucleus redistribution axis and then focus mechanistically on the validated targets, in this case RAD51C. The lesion-dependent redistribution patterns are therefore presented as an initial, hypothesis-generating observation emerging from our screening and characterisation framework. A systematic, lesion-by-lesion dissection of redistribution kinetics across the broader DDR network would represent a substantial additional study and is beyond the scope of the present work.

      Importantly, our key mechanistic observations for RAD51C are not restricted to doxorubicin. We tested a panel of genotoxic agents covering mechanistically distinct lesion classes: camptothecin (CPT; Topoisomerase I-associated replication breaks), etoposide (ETO; Topoisomerase II-dependent DSBs), and mitomycin C (MMC; interstrand crosslinks) (Figures S8A-S8I). Across all DSB-inducing agents, RAD51C consistently redistributed from the Golgi to the nucleus, demonstrating that this response is not a doxorubicin-specific off-target effect. Notably, RAD51C did not redistribute in response to oxidative lesions induced by hydrogen peroxide or potassium bromate, consistent with its established role in homologous recombination and DSB repair rather than oxidative damage pathways, as discussed in the manuscript. This lesion-type selectivity provides additional evidence that the Golgi-nuclear redistribution we observe is a biologically specific response rather than a non-selective stress effect.

      *2. Functional implications of RAD51C redistribution for HR efficiency - Although the study convincingly demonstrates a release of RAD51C from the Golgi and its subsequent nuclear foci formation, it remains unclear how this redistribution influences HR efficiency. Incorporating a functional HR assay (e.g., DR-GFP reporter, RAD51 filament assembly, or fork protection assays) would help determine whether Golgi-anchored RAD51C release is directly required for HR or instead primarily modulates upstream DDR signaling. *

      Response: __We thank the reviewer for this important suggestion. We have performed DR-GFP reporter assays to directly assess HR efficiency following Giantin and RAD51C depletion. Depletion of Giantin reduced HR efficiency to approximately 60% of control levels, and RAD51C depletion to approximately 40%, consistent with the HR reduction previously reported in the genome-wide HR screen (Adamson et al, 2012). Co-depletion of Giantin and RAD51C reduced HR to levels comparable to RAD51C depletion alone, suggesting that the effect of Giantin on HR is mediated primarily through RAD51C, consistent with RAD51C being the key effector of the Giantin-dependent spatial regulatory mechanism we describe. These data are included in the revised manuscript (__lines 455-465; Figure 5L).

      *In addition, the manuscript does not fully reconcile how Golgi-tethering of RAD51C fits with its well-established nuclear roles during replication stress, where timely availability of RAD51C is essential for fork stabilization and restart. *

      Response: __We agree that the nuclear function of RAD51C during replication stress is well established and important to reconcile with our findings. Our imaging data consistently show a detectable nuclear RAD51C population at steady state across all cell lines examined, and we do not propose that RAD51C is exclusively Golgi-localised. We suggest that the two pools serve distinct functional purposes: the constitutive nuclear pool supports ongoing replication fork stabilisation and restart, processes that require RAD51C availability independently of acute DNA damage, while the Golgi-tethered fraction represents a damage-responsive reserve that is released acutely upon DSB induction in an ATM-dependent manner. We wish to be transparent that this two-pool model is speculative at present, formally distinguishing the contributions of each pool would require direct labelling of the Golgi-anchored fraction, which was not technically feasible in this system as discussed above. Nonetheless, this model is consistent with established principles of signal-responsive protein sequestration in cell biology, and is directly supported by our Giantin depletion data: premature release of the Golgi pool leads to aberrant nuclear RAD51C foci lacking canonical HR markers and impaired ATM signalling, demonstrating that unscheduled nuclear accumulation is actively detrimental rather than simply redundant. We have added a paragraph to the revised Discussion explicitly framing the two-pool distinction as a working model and identifying direct pool-identity tracking as an important future direction (__lines 566-587).

      *3. Specificity of Giantin-related phenotypes - The phenotypes observed upon Giantin depletion (e.g., increased micronuclei, comet tail moments, impaired ATM signaling, and elevated proliferation) could partially reflect a global dysfunction of the Golgi rather than RAD51C-specific tethering defects. Although co-depletion of RAD51C provides partial rescue, additional controls examining Golgi integrity, trafficking competence, or rescue with siRNA-resistant Giantin would help confirm specificity and distinguish direct from indirect effects. *

      __Response: __We thank the reviewer for raising this important concern, which was a central consideration throughout our investigation. We address it through three complementary lines of evidence.

      First, regarding Golgi structural integrity and trafficking competence: as previously reported, Giantin depletion has not been associated with strong Golgi fragmentation or major morphological alterations (Koreishi et al, 2013; Bergen et al, 2017; Stevenson et al, 2021), and we observed no significant Golgi fragmentation upon Giantin knockdown in our system. Consistent with the literature, Giantin has been implicated in specific cargo trafficking, most notably collagen secretion, rather than general secretory pathway function (Stevenson et al, 2021). To directly confirm that general Golgi trafficking competence was preserved in our experimental system, we performed the VSV-G-YFP trafficking assay (Presley et al, 1997), a well-established functional readout of general secretory trafficking. Giantin depletion did not result in a significant change in trafficking efficiency compared to control siRNA (Rebuttal Figure 1), consistent with the literature and arguing against a general collapse of Golgi function as the basis for the phenotypes observed.

      Rebuttal ____Figure 1. VSV-G-YFP trafficking assay.

      (A) Representative images of cells treated with control siRNA or giantin siRNA. Nuclei are stained with Hoechst. Total VSV-G-YFP (YFP-tsO45G) signal is shown together with antibody staining against VSV-G in non-permeabilized cells to assess cell surface levels. Scale bars, 10 μm.

      (B) Quantification of VSV-G trafficking from two independent biological replicates.

      Second, the phenotypes are RAD51C-dependent and not a generic Golgi dysfunction: the genomic instability and DDR signalling defects we observe upon Giantin depletion are not phenocopied by GMAP210 depletion, another Golgin family member, indicating that the phenotypes are not a generic consequence of Golgin loss. Critically, we now directly demonstrate using the DR-GFP reporter assay that Giantin depletion reduces HR efficiency to approximately 60% of control, and that co-depletion of RAD51C produces no further reduction beyond RAD51C depletion alone, consistent with RAD51C epistasis over Giantin for HR capacity (Figure 5L). This functional epistasis, together with the physical interaction between Giantin and RAD51C by co-immunoprecipitation, their co-localisation within the same Golgi sub-compartment, and the partial rescue of ATM phosphorylation, micronuclei formation and proliferation phenotypes upon RAD51C co-depletion, provides a coherent mechanistic chain linking Giantin specifically to RAD51C-dependent DDR outcomes. While we cannot formally exclude indirect contributions from other Giantin-associated factors, none of our observations are consistent with the phenotype arising from non-specific Golgi perturbation.

      Third, Giantin may play a broader role in connecting DDR signalling to cytoplasmic and Golgi-resident processes, beyond RAD51C tethering alone: we consider this a feature of the biology rather than a confound. Golgins are well established as multi-cargo scaffolding platforms, and Giantin in particular occupies a strategic position where several processes converge: the tethering of DDR factors, the regulation of damage-induced signalling cascades, and the directional trafficking of repair factors between compartments. This would explain why Giantin depletion produces a phenotype that extends beyond what RAD51C co-depletion alone can fully rescue, and is consistent with the pathway-level coherence we observe across our screen. Understanding the full complement of Giantin-associated DDR interactions represents one of the most compelling directions emerging from this work.

      In response to this comment, we have expanded the Discussion (lines 545-565) to explicitly propose that Giantin functions as a broader organisational node coordinating multiple DDR factors, while our data specifically and consistently implicate RAD51C as a primary conduit.

      *4. Positioning of ATM in the Golgi-nuclear signaling - While ATM inhibition prevents RAD51C release, its spatial and mechanistic basis of this regulation remains obscure. It is not clear whether ATM acts locally at the Golgi, through cytoplasmic pools, or indirectly via nuclear feedback signaling. Clarifying or discussing this point in more depth would improve the mechanistic coherence of the proposed model. *

      __Response: __We thank the reviewer for raising this important mechanistic question. The spatial basis of ATM action at the Golgi is indeed an emerging and exciting area of cell biology. A growing body of evidence demonstrates that ATM associates with the Golgi membrane through binding to phosphatidylinositol-4-phosphate (PI4P), and that this Golgi-resident pool modulates the magnitude and kinetics of the nuclear DDR (Ovejero et al, 2023). Importantly, the most recent work in this area demonstrates that Golgi-associated ATM is not merely a passive reservoir but is enzymatically active and capable of phosphorylating Golgi-resident substrates (Soulet et al, 2026), providing a compelling mechanistic basis for how damage-induced ATM signalling could reach the Golgi to license RAD51C release.

      To directly examine whether ATM localises to the Golgi in our system and whether its activation state changes upon DNA damage, we performed a biochemical Golgi enrichment assay using the Minute{trade mark, serif} Golgi Apparatus EnrichmentKit (Cat #: GO-037) to examine ATM distribution across cis- and trans-Golgi fractions. Fraction purity was validated using GM130 (cis-Golgi), TGN46 (trans-Golgi), and HSP60 (membrane fraction) (Rebuttal Figure 2A). This analysis revealed that ATM is detectable in the total membrane fraction and enriched in the cis-Golgi fraction under basal conditions (Rebuttal Figure 2A). Under normal physiological conditions, activated ATM (pATM) was absent from Golgi-enriched fractions (Rebuttal Figure 2B), but was detectable in the cis-Golgi fraction following doxorubicin-induced genotoxic stress (Rebuttal Figure 2C). While these observations are preliminary and require further validation, they are consistent with the emerging literature and raise the intriguing possibility that ATM is recruited to and activated at the Golgi in a damage-dependent manner, where it could act locally to license RAD51C release.

      Rebuttal Figure 2. Biochemical Golgi fractionation confirms ATM enrichment in cis-Golgi compartments.

      *Western blot of HeLa-K fractions enriched for cis- and trans-Golgi membranes, probing for (A) ATM under basal conditions, and (B and C) pATM under basal conditions and (B) pATM (C) after treatment with DOX (40 μM) (markers: GM130 for cis-Golgi, TGN46 for trans-Golgi, HSP60 for membrane fraction (MEM). *

      We consider the precise spatial and mechanistic dissection of ATM signalling at the Golgi and its relationship to nuclear feedback, one of the most exciting directions to emerge from this work, and one that we hope our study has helped to open. We have expanded the Discussion (lines 525-543) accordingly to place our findings in the context of the emerging Golgi-ATM literature and to frame this as an important unresolved question for future investigation.

      *5. RAD51C is examined in silo, without consideration for the BCDX2 complex - RAD51C is exclusively analyzed in isolation, despite its well-established function as part of the BCDX2 paralog complex (RAD51B-RAD51C-RAD51D-XRCC2). Because RAD51C does not normally operate as a standalone factor, it is unclear why only RAD51C, among all paralogs, would be subjected to Golgi tethering, ATM-dependent release, and Importin-β-driven nuclear import. This raises important mechanistic questions: Are other BCDX2 members also Golgi-associated? Do they undergo similar trafficking dynamics? Does Golgi tethering selectively regulate RAD51C, or does the complex translocate together? Addressing these points would greatly strengthen the biological plausibility and mechanistic coherence of the proposed model. *

      Response: We thank the reviewer for raising this important point. We fully agree that RAD51C functions as a core component of the BCDX2 (RAD51B-RAD51C-RAD51D-XRCC2) and CX3 (RAD51C-XRCC3) paralog complexes, and that its canonical roles in HR and replication fork protection occur within these assemblies. Our decision to focus on RAD51C was driven by the screening data: of the DDR proteins identified, RAD51C displayed the most robust Golgi-associated pool, the clearest damage-induced redistribution dynamics, and a tractable anchoring interaction with Giantin that could be interrogated biochemically.

      We would also note that extending this analysis to other RAD51 paralogs is not straightforward with current tools. The available commercial antibodies against RAD51B, RAD51D and XRCC2 perform poorly in immunofluorescence applications, and most localisation studies for these proteins have relied on overexpression of tagged constructs, a strategy that, as discussed above, risks perturbing both localisation and complex assembly. The lack of reliable antibodies for endogenous paralog detection at the resolution required for Golgi localisation analysis represents a genuine technical barrier that we encountered directly during this study.

      Whether Golgi association and ATM-dependent release involve RAD51C alone or extend to other BCDX2 or CX3 members is therefore a genuinely open and important question. We note that our co-immunoprecipitation data were performed on total cell lysate and cannot distinguish whether the Golgi-associated RAD51C is complexed with other paralogs or represents a monomeric subpopulation. Golgins are well established as multi-cargo scaffolding platforms, and it is entirely plausible that Giantin organises a broader paralog module rather than tethering RAD51C as an isolated subunit. A systematic analysis of RAD51 paralogs for Golgi localisation and lesion-dependent trafficking enabled by improved reagents such as proximity labelling or endogenous tagging approaches compatible with essential proteins would determine whether the BCDX2 complex translocates as a unit or whether individual subunits are differentially regulated, with potentially distinct consequences for HR fidelity. We have revised the manuscript accordingly and identify this as an explicit priority for future work in the revised Discussion (lines 583-602).

      Minor Comments

      1. Pathway-specific sub-Golgi localization patterns - The finding that DDR proteins map to distinct cis/trans Golgi subdomains is an interesting and potentially important observation. However, the dataset is limited to 15 proteins, making the proposed pathway-level trends (e.g., HR factors enriched in cis-Golgi; BER/MMEJ factors enriched in trans-Golgi) preliminary. Strengthening this conclusion by increasing the number of DDR proteins analyzed would help determine whether sub-Golgi compartmentalization contributes meaningfully to DNA repair pathway regulation.

      Response: We thank the reviewer for this constructive suggestion. We agree that extending sub-Golgi mapping to a larger number of DDR proteins would be valuable, and we present the current dataset explicitly as a first, hypothesis-generating map rather than a definitive pathway atlas.

      We would like to highlight, however, that the value of this observation lies not simply in the number of proteins mapped, but in the biological coherence of the patterns that emerge. The finding that proteins from the same repair pathway tend to occupy the same Golgi sub-compartment: BER and MMEJ factors enriching in the trans-Golgi, HR factors in the medial/cis-Golgi, and that this sub-compartmental positioning correlates with the direction of their redistribution upon genotoxic stress, is a pattern that would be unlikely to arise by chance across 15 independently validated proteins. This internal consistency argues that the sub-Golgi organisation reflects genuine pathway-level biology rather than noise, even if the dataset is not yet exhaustive. Together with the bioinformatic network analysis, which independently supports pathway-level clustering across the broader validated hit list, these observations reinforce each other as complementary layers of evidence.

      2. Is the Golgi-released RAD51C indeed the pool that enters the nucleus? The major assumption of the study is that the RAD51C population released from the Golgi upon DNA damage is the same pool that subsequently accumulates in the nucleus to form repair foci. While the imaging and fractionation data are consistent with this model, the study does not directly track or distinguish Golgi-derived RAD51C from cytoplasmic or pre-existing nuclear pools. Without a method to specifically label, pulse-chase, or track the Golgi-anchored fraction, it remains formally possible that nuclear RAD51C originates from other subcellular reservoirs.

      __Response: __We thank the reviewer for highlighting this important mechanistic point, which we agree cannot be fully resolved with the current dataset. Several independent lines of evidence are nonetheless consistent with a model in which the Golgi-associated pool contributes directly to damage-induced nuclear accumulation.

      • Our time-resolved imaging demonstrates a reciprocal decrease at the Golgi and a concurrent increase in the nucleus following genotoxic stress, consistent with redistribution rather than independent compartment-specific changes (Figures 3E-3I).
      • Biochemical fractionation provides an orthogonal readout of the same reciprocal shift under identical conditions (Figures 3J and S6D).
      • ATM inhibition simultaneously prevents Golgi loss and blunts nuclear accumulation, while Importin-β perturbation blocks nuclear entry, together supporting an active and regulated translocation route (Figures 3K-3P).
      • Giantin depletion, which releases the Golgi-tethered RAD51C pool prematurely, leads to aberrant nuclear RAD51C foci lacking canonical HR markers and impaired ATM signalling, strongly supporting that the Golgi-tethered fraction has functional consequences in the nucleus consistent with it being the relevant pool (Figures 4B-4E and 4J-4M).
      • In the revised manuscript we have included cytoplasmic RAD51C signal quantification across the doxorubicin time course (Figure 3H). The cytoplasmic signal shows only a moderate and gradual reduction that is kinetically distinct from the sharp Golgi decrease and does not precede the nuclear increase. This pattern is inconsistent with a large pre-existing cytoplasmic reservoir driving the nuclear accumulation; if the cytoplasmic pool were the primary source, one would expect a rapid and prominent cytoplasmic decrease coinciding with or preceding nuclear accumulation, which we do not observe. Instead, the data are more consistent with rapid transit of Golgi-released RAD51C through the cytoplasm rather than stable cytoplasmic accumulation prior to nuclear entry. We acknowledge that definitive pool-identity tracking would require spatially restricted labelling approaches such as Giantin-proximal TurboID or photoactivatable tagging strategies, which are precluded by the technical constraints on RAD51C tagging described above. We have revised the manuscript to avoid overstatement on this point and identify these approaches as important future directions (lines 297-305 & lines 715-719).

      Reviewer #2 (Significance (Required)):

      General assessment - This study presents a novel and conceptually compelling view of the DNA damage response (DDR) by positioning the Golgi apparatus as an active regulator of the spatiotemporal availability of DNA repair factors. The strongest aspects of the work include its integration of a systematic immune-localization screening, a sub-Golgi compartment mapping, dynamic redistribution assays, and functional perturbations to build a coherent model of Golgi-nucleus communication during genotoxic stress. The mechanistic focus on RAD51C provides a clear case study linking organelle-level regulation to genome stability.

      • Advance - To my knowledge, this is the first comprehensive demonstration that the Golgi can serve as a spatiotemporal coordination node for DDR proteins, including those involved in HR. The identification of a substantial pool of RAD51C, and reportedly other DDR factors, anchored within specific Golgi subdomains represents a significant conceptual advance. The demonstration that Golgi-tethered RAD51C is released in an ATM-dependent manner and subsequently participates in nuclear foci formation suggests a previously unrecognized organelle-level regulatory checkpoint in genome maintenance. This work therefore extends current models of the DDR by revealing a layer of intracellular coordination that bridges classical nuclear pathways with cytoplasmic organelle function.*

      • Audience - This study will be of strong interest to a specialized audience in the fields of DNA repair, genome stability, and cell biology, particularly those studying the spatial organization of repair pathways and intracellular stress signaling. It will also appeal to researchers investigating organelle biology, intracellular trafficking, and the broader coordination of cytoplasmic and nuclear responses to stress. Beyond these communities, the work may be relevant to cancer, as it suggests new mechanisms by which organelle perturbations or Golgi-associated scaffolding proteins could influence therapeutic responses or genomic instability.

      Reviewer expertise - Field of expertise: DNA repair, genome stability, organelle biology, cancer cell biology.*

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      *This study investigates the communication between the Golgi complex and the nucleus of the cell, which remains a largely unexplored field. The authors used publicly available siRNA and antibody data from the Human Protein Atlas as a basis for finding overlap between the proteomes of the two cellular compartments. In validating the data from the HPA, the study finds a novel cluster of DNA repair proteins present in the Golgi, which they validate and resolve to sub-compartmental localization. To do so they use immunofluorescence (IF) localization on ¬cis- and trans-Golgi cisternae marked by GM130 and TGN46, respectively. The authors find that many of the fully validated proteins present in both the nucleus and Golgi redistribute between the Golgi and the nucleus dependent on the protein and the type of DNA lesion. They focused on RAD51C, a recombination factor. They show that RAD51C resides in both the ¬cis- and trans- subsections prior to damage and responds to DNA damage in an ATM-dependent manner via release of a Golgi-based pool bound to Giantin, which is then imported into the nucleus via Importin-β. Knockdown experiments showed that Giantin regulates RAD51C spatially and temporally. The work reveals a dynamic interchange of proteins between the Golgi and nucleus that controls cell functions beyond the classic secretory, membrane trafficking, and PTM roles of the Golgi. The authors build on prior work on Golgi impacts on DDR, offering an alternative cellular compartment for storage of DDR factors prior to damage. Overall, the data is timely and relevant, as it finds new roles for the Golgi in DNA damage response (DDR) regulation. The data is largely convincing and well controlled. The IF data is presented in black and white single channels and merged in color, which allows good comparison of the different protein stains. The scope of the initial screen of HPA antibodies and Golgi/Nuclear dual proteomes is impressive, and the overlap of DDR proteins is characterized for fifteen different proteins at a sub-compartmental level. The focus on RAD51C as a member of the HR pathway was a strong choice, and the study presents interesting information on its regulation by Golgi complex members, as well as a feedback look with pATM. The possibility of the Golgi storing specific DDR factors in specific compartments is well-supported and intriguing. There are a few major and minor points that should strengthen the paper and improve clarity prior to publication. *

      Major Comments:

      *1. Much of the strength of the IF data is lost in the choice of scale for presentation of the data. In almost all cases, enlarged sections should be shown of the areas currently indicated by arrow, in all channels. This is done well in Figure 3A, where an area of the Golgi is enlarged and the overlap of RAD51C in the GM130-marked Golgi is clearly visible in the merged channel, even when printed out. I would highly recommend including the white box and enlarged in all images and channels, while keeping the representative fields as is (e.g. if the image is 40mm, draw a 7mm box around representative cells/Golgi, and enlarge to 15mm in the bottom left). This change should be made to F1E, F2F, F3E, F3J, and F3M, as well as having enlarged figures in the corners in all supplementary data IF figures. Where possible, a fully enlarged image of the bounding box could also be included. Some of the IF data would be strengthened by using the nuclei stain to draw a masking outline to include in the black and white channels, to clearly delaminate what is Golgi-localized and what is nuclear. *

      Response: We thank the reviewer for this helpful suggestion and fully agree that enlarged insets substantially improve the visibility of Golgi-localised signal, particularly when figures are printed. We share the reviewer's view that alternative display formats with larger insets would be preferable, and we have implemented enlarged boxed regions wherever space constraints permitted.

      Specifically, we have added boxed regions with enlarged insets to Figure 1E, all panels of Figure 3. For Figure 2, the number of conditions and proteins displayed simultaneously within the constraints of standard journal figure dimensions made it impractical to include enlarged insets for all panels without reducing the overall field size to the point of losing contextual information. We have nonetheless improved the visibility of the Golgi signal in Figure 2 as much as possible within these constraints, and note that the final figure layout will be further optimised in line with the journal's specific formatting guidelines. In addition, all figures have been provided as high-resolution image files to allow electronic magnification, enabling readers to inspect the Golgi-localised signal in detail beyond what is visible in the printed version.

      Regarding the use of nuclear outline masks in single-channel images, we tested this approach but found that given the number of structures present within each field, including Golgi stacks, nuclear foci, and cytoplasmic signal, overlaying nuclear outlines on individual channels added visual complexity that made the images harder rather than easier to interpret. As an alternative, we have included a full-colour merged panel, when possible, which we consider a cleaner way to delineate nuclear versus Golgi-localised signal and allows the reader to directly compare compartment-specific distributions across channels.

        1. *There is a lack of consistency in the representative images shown by IF. For example, Figure 1 gives the impression of very little RAD51C in the nucleus but this is rightly shown to not be the case in Supp. Fig 2A. The same is true of the various images of LIG1. The authors should use representative data that better reflects the distribution of the proteins being studied and maintain consistency across images. If there is a lot of variation in staining patterns, the authors should show images and percentages corresponding to the variations especially for the key gene studied, RAD51C.

      Response: We agree and have replaced the representative IF panels for RAD51C and LIG1 with images that better reflect the quantified distributions across biological replicates. The revised panels were selected to match the quantified compartment intensities shown in the accompanying graphs rather than representing outlier cells. We would also note that the apparent discrepancy between Figure 1E and Supplementary Figure S2A partly reflects a difference in imaging conditions: Supplementary Figure S2A __and __Figure 2F were acquired directly from the high-content screening pipeline under uniform, non-optimised antibody and fixation conditions at widefield resolution, whereas Figure 1E shows representative single optical section confocal images acquired after candidate identification with antibody conditions optimised for each individual protein. The improved signal-to-noise in the optimised confocal images more faithfully captures the dual Golgi and nuclear localisation of RAD51C, and the apparent difference between the two image sets is therefore expected rather than inconsistent. We have updated the figure legends to clarify the imaging modality and conditions for each panel. Furthermore, the quantified distribution of RAD51C across Golgi, nuclear and cytoplasmic compartments across multiple cell lines is shown in Figure 3B and 3D, providing a population-level representation of the dual localisation that complements the representative images shown in Figure 1E.

        1. *The initial screening by siRNA-mediated knockdown pipeline that validated and confirmed dual Golgi and nuclear localization of 163 of the 329 dual-localization HPA proteins does not have any data included. This seems like a very large amount of data to gloss over and not include even as supplementary data. This should be included as source data, and discussion of the in-text information should be strengthened. The data included with the networking of these validated proteins is strong, but the process of elimination and validation has not been shown. In addition, the antibody information included in the supplementary data does not include dilution factors or blocking factors is not included, which would be beneficial to future studies to include.

      Response: We agree and have addressed this in full. We note that the HPA antibody validation data, including immunofluorescence images and siRNA knockdown results, are publicly available for inspection on the Human Protein Atlas website (www.proteinatlas.org) for the majority of candidates, providing an independent layer of verification. In the revised submission, we additionally provide the complete siRNA-mediated validation dataset generated in our laboratory as source data (Table S1; lines 1025-1041), including for each candidate the HPA antibody identifier, gene symbol, Ensembl ID, antibody staining pattern, siRNA identifier, cell number per replicate, and normalised Golgi and nuclear signal ratios for both experimental replicates. This allows readers to inspect the validation metrics directly and apply alternative thresholds if desired. We have also expanded the antibody information to include diluent conditions (4% FBS in 0.1% Triton-X100 for all HPA antibodies used at 2 μg/ml in the screening pipeline), enabling reproducibility and reuse of the dataset by the community.

        1. *The authors should expand upon the paragraph lines 155-162 to include more discussion on Figure S2A and S2B. The expanse of this data is some of the strongest in the paper, and it should be further discussed in-text. Also, the rationale behind the choice in the specific proteins that are included in these analysis / figures is not always clear in -text, and more attention should be spent on the narrowing down of the analysis to the final proteins. This is also especially important as many of the DDR proteins chosen are not the most common DDR proteins. Also note in text that the Golgi marker GM130 (presumably) was used for the screening, which means that some proteins which are only localizing to the TGN46 trans Golgi might have been lost in the validation step (or, explain why this is not the case).

      Response: __We expanded the Results text (__lines 141-163) to discuss Figures S2A and S2B in more depth and clarified the rationale for selecting the final set of DDR proteins taken forward, including considerations of pathway representation, bioinformatic annotations, literature-described roles in DNA repair. We would also note that the identity of the DDR proteins identified in this screen was determined by the HPA dataset and the unbiased validation pipeline rather than by prior assumptions about which repair factors would be present at the Golgi. The presence of less commonly studied DDR factors is therefore a direct reflection of the screen output, and we consider this one of the strengths of the approach.

      We would also like to address the reviewer's concern about potential GM130-based bias directly: at the widefield or confocal resolution used in the high-content screening pipeline, the Golgi apparatus appears as a single perinuclear structure and cis- and trans-Golgi subdomains cannot be resolved. GM130 was therefore used purely as a segmentation marker to define the Golgi compartment as a whole rather than to selectively label the cis-Golgi cisternae. The resulting Golgi mask captures signals from the entire Golgi ribbon, including trans-Golgi regions, meaning that proteins with exclusively trans-Golgi localisation would not have been systematically excluded at the screening stage. Sub-compartmental resolution of cis versus trans localisation was only possible in subsequent analyses using nocodazole-dispersed mini-stacks imaged by confocal microscopy with co-staining for both GM130 and TGN46.

      *5. The relationship between Giantin loss, increased cell proliferation, and elevated endogenous DNA damage as it relates to RAD51C remains insufficiently resolved and requires further clarification. Several of the proliferation assays used are not optimal for addressing changes in cell growth. For example, Figure 5O appears to quantify cell numbers by counting fields from IF images, which is an unconventional approach. This should be done by growth curves, luminescent viability or colony formation assays. In addition, this point will be greatly strengthened by performing rescue experiments for Giantin directly (instead of co-depletion as a means of rescue) and/or using a mutant of RAD51C that does not bind to Giantin. If these additional experiments are beyond the current scope, the conclusions should be softened in the discussion. *

      Response: We thank the reviewer for raising these important points, which we address in turn:

      Giantin-RAD51C relationship and mechanistic interpretation. __We acknowledge that establishing the full causal chain between Giantin loss, RAD51C mislocalisation, elevated endogenous DNA damage and increased cell proliferation is challenging within the scope of a single study, and we discuss this openly in the Discussion (__lines 555-564). Our evidence collectively includes: physical interaction between endogenous Giantin and RAD51C by co-immunoprecipitation (Figures 4H and 4I), premature nuclear accumulation of RAD51C upon Giantin depletion (Figures 4B-4E and 4J-4M), new additional experiment showing direct reduction of HR efficiency in the DR-GFP assay (Figure 5L), impaired ATM signalling (Figures 5J and 5M), elevated genomic instability (Figures 5A-5E), and epistatic rescue by RAD51C co-depletion (Figures 5M-5P). These observations are further contextualised by the established literature on RAD51C function: RAD51C is known to regulate CHK2 phosphorylation and cell cycle checkpoint signalling (Badie et al, 2009), stabilise replication forks (Somyajit et al, 2015), and promote RAD51 filament formation required for DSB repair (Prakash et al, 2015). Dysregulation of these functions through Giantin-dependent mislocalisation provides a mechanistically coherent explanation for the elevated genomic instability and altered proliferation we observe, and is entirely consistent with our model. Together, the experimental evidence and the published biology of RAD51C support a model in which Giantin spatially regulates RAD51C to maintain proper DDR signalling and HR capacity.

      We agree that separation-of-function tools would further strengthen this model and identify these as important future priorities. We wish to note however that both approaches face substantial technical barriers in this system. As described in our response to Reviewer 1 Major Comment 1, RAD51C tagging, whether by CRISPR-mediated endogenous editing or ectopic expression, consistently compromised cell viability and protein function, precluding the generation of interaction-deficient variants at physiological expression levels. Engineering an interaction-deficient Giantin mutant presents an independent and considerable challenge: Giantin is one of the largest Golgi matrix proteins (~376 kDa), composed almost entirely of extended coiled-coil domains that are intrinsically difficult to model structurally, and identifying a discrete interaction interface with RAD51C without disrupting the broader scaffolding function of the protein would require a dedicated structural and biochemical programme. We therefore consider these important but substantial future directions rather than straightforward experimental additions to the current study.

      Proliferation assays. Colony formation assays provide a rigorous readout of long-term proliferative capacity, and these data are presented for single knockdown conditions in Figures 5F-5I. The cell number quantification in Figure 5P was specifically included to assess the double knockdown of Giantin and RAD51C simultaneously, a condition not covered by the colony formation assay. We respectfully note that automated fluorescence microscopy-based nuclear counting is a well-established approach for measuring cell proliferation in siRNA screening contexts. Nuclear counting from high-content imaging has been used as a direct readout of cell growth and proliferation in RNAi screens (Boutros et al, 2004; Martin et al, 2014; Garvey et al, 2016; Mikheeva et al, 2024), and has been shown to produce results comparable to or superior to conventional viability assays including MTT and flow cytometry-based methods (Mikheeva et al, 2024). We have nonetheless clarified in the revised figure legend that Figure 5P reports relative cell number quantified by automated nuclear counting from high-content imaging fields as a secondary concordant measure alongside the colony formation data, rather than a standalone proliferation assay.

      *6. It is unclear from the discussion and from presented data whether proteins are directly transported between the Golgi and the nucleus, or whether they go into the cytoplasm for a transient period, presumably when they could interact with Importin β. There is also some data where cytoplasm signal could be quantified to address this (Figure 3E-I). *

      Response: We thank the reviewer for this mechanistic point. In the revised manuscript we have included cytoplasmic RAD51C signal quantification alongside Golgi and nuclear measurements for the doxorubicin time course (lines 297-305; Figure 3H). The cytoplasmic signal shows a moderate and gradual reduction distinct in both magnitude and kinetics from the sharp Golgi decrease, consistent with a transient cytoplasmic intermediate rather than a stable pool. Regarding the identity of the translocating pool, two observations directly support a Golgi origin. First, Importazole treatment prevents RAD51C release from the Golgi following genotoxic stress and simultaneously reduces nuclear RAD51C foci formation, demonstrating that Importin-β-mediated import is required both for Golgi clearance and for productive nuclear accumulation. Second, Giantin depletion which prematurely releases the Golgi-tethered pool, leads to aberrant nuclear RAD51C foci, directly linking the Golgi-anchored fraction to nuclear accumulation. Together these data support a model in which Golgi-resident RAD51C transits through the cytoplasm for Importin-β-mediated nuclear import. We acknowledge that without direct labelling of the Golgi-anchored fraction, the precise contribution of each subcellular pool to the nuclear accumulation cannot be fully resolved with the current dataset. We discuss the development of appropriate tagging strategies as an important future direction to dissect the dynamics of this process in further detail.

      *7. Statistical analysis on experiments with more than two samples need to be performed with ANOVA and a follow up post-hoc test, not with two-tailed unpaired Student's t-test, which only compares the control and each individual sample. This type of analysis inflates the Type 1 error rates (false positives) in your datasets. For example, the two-tailed unpaired Student's t-test is appropriate in Figure 2F-H, but not in Figure 3 when the samples are timepoints. In this case, a One-way ANOVA with Tukey's post-hoc test (if you want to show all coparisons), or Bonferroni/Sidak if you only need to compare several samples). *

      Response: We agree with the reviewer and thank them for highlighting this important statistical issue. We have revised the statistical analysis for all experiments involving more than two groups to avoid inflation of Type I error rates caused by multiple pairwise Student's t tests. Specifically, for Figures 3F-I, 4C-E, and Figure 5, the data were reanalysed using one way ANOVA followed by the appropriate multiple comparisons post hoc test. The Methods section and corresponding figure legends have been updated to clearly state the statistical tests used for each dataset.

      Minor Comments: General 1. Throughout the text, the reference to many figures and supplementary figures in the same sentence, with little discussion of the data therein makes it hard to follow. In-text referencing is particularly confusing in the section "Dual-localising DDR proteins dynamically redistribute between the Golgi and nucleus in response to specific types of DNA injuries," where the reader is switching between multiple figures and supplementary figures.

      __Response: __We thank the reviewer for this helpful comment. In the revised manuscript, we have improved the readability of the text and revised the figure references to make them clearer. We hope these revisions make the manuscript easier to follow and allow readers to better inspect the figures.

      1. In figures that display technical replicates as individual data points, consider distinguishing each replicate by using different marker shapes (e.g., repeat 1 = upright triangle; repeat 2 = inverted triangle; repeat 3 = diamond). This would provide additional clarity regarding the consistency and repeatability of each technical repeat.

      __Response: __We thank the reviewer for this suggestion. We have updated the data presentation to distinguish biological replicates using different marker shapes in datasets where replicate tracking is of particular relevance to the interpretation. For datasets where individual replicate values are already clearly separable, we have maintained the existing presentation to avoid unnecessary visual complexity.

      1. Make sure all western blot data includes the marker size (F3C and F5L has none, F4H/I have size of proteins not size of markers).

      __Response: __We added missing marker sizes to our western blot data in the revised manuscript.

      1. Be consistent with use of capitalization in figure legends and graph/figure labels.

      __Response: __We made sure that the capitalisation is consistent in figure legends, graph and figure legends in the revised manuscript.

      Figure 2

      In Figure 2A, please include in the figure itself that GM130 is the cis Golgi, and TGN46 is the trans Golgi (Figures should not be dependent on the text for full understanding).

      __Response: __We revised Figure 2A and 2C to label GM130 as cis-Golgi and TGN46 as trans-Golgi within the figure, making it self-explanatory.

      1. Why are LRIG2 and LRRIQ3 not included in the 2E cis vs trans Golgi data, when all other proteins from F1D are included? Include, or comment on in-text.

      __Response: __Both LRIG2 and LRRIQ3 are included in 2E in both the original and revised manuscript.

      1. Be sure to include scale bar data in each figure legend (F2A-E is currently missing it), and include updated scales included in the enlarged data.

      __Response: __Scale bar data is now included in each figure legend in the revised manuscript.

      1. In Figure 2F, make sure that the merged green channel is presented at the same intensity as it is in the single black and white channel, as the green looks very overexposed in several of the merged (CCAR1 DMSO merged is the most noticeable).

      __Response: __We agree and thank you for pointing this out. We have now revised the images and corrected the issue by updating all image panels in the figure.

      1. In Figure 2G, include the grey label in the figure legend.

      __Response: __We thank the reviewer for this comment. The grey label has now been included in the figure legend in the revised manuscript.

      1. In Figure 2G-H, the method of data presentation in the graphs coupled with the statistical analysis is confusing and should be expanded upon in the legend.

      __Response: __We agree that the amount of data presented may appear overwhelming. In the revised figure, we have adjusted the placement of the statistical annotations to improve clarity. Also, we improved the figure legend, to make the figure easier to read and interpret.

      Figure 3

      Figure E/F/G: Is there cytoplasmic quantification as well? Your rationale is that the Golgi RAD51C goes into the nucleus, but via the cytoplasm (due to Importin β import); do you see the cytoplasmic levels increase? Or is it too dilute to notice a difference? At least, this omission needs to be mentioned in-text.

      Figure H/I also include the quantification of the cytoplasmic fraction. It is mentioned in-text on line 272, but not quantified. This comes up as a big question: Do the proteins go directly between the Golgi and nucleus, or do they go through the cytoplasm?

      __Response: __We thank the reviewer for both of these related points. As described in our response to Major Comment 6 above, we have added cytoplasmic RAD51C signal quantification to the doxorubicin time course in the revised manuscript (Figure 3H) and discuss the implications for the proposed translocation route.

      Figure 3A, 3E, and if the data is present for 3J and 3M, could all benefit from using the nuclei staining as a mask to draw an outline around the nucleus in the other channels, and then show a merge in full color instead of a nuclei-only channel. Also note from the major comments, that this data especially is so small to see without enlarged images.

      __Response: __We thank the reviewer for this suggestion. Regarding nuclear outline masks, we tested this approach but found that the number of structures present in each field, including Golgi stacks, nuclear foci and cytoplasmic signal, made overlaid outlines visually confusing rather than clarifying. We have instead included a full-colour merged panel in Figure 3E, which we consider a cleaner way to distinguish nuclear from Golgi-localised signal while preserving the spatial context of the data.

      Regarding image size, we have added enlarged insets to Figures 3E, 3J and 3M in the revised manuscript. We have chosen to display multiple cells per panel rather than a single enlarged cell in order to capture the heterogeneity of the cell population, which we consider important for an accurate representation of the data. All figures have been provided as high-resolution image files to allow electronic magnification, enabling detailed inspection of the signal beyond what is visible in the printed version. We acknowledge that the constraints of standard journal figure dimensions limit how large individual panels can be, and the final layout will be optimised in line with the journal's formatting guidelines.

      *In-text discussion of the results from Figure 3 has an in-depth discussion of the NLS and NES in RAD51C, but this is not followed up on with site-directed mutagenesis or any data; perhaps move this to the discussion instead of results section. *

      __Response: __We have removed the discussion of the NLS and NES from the Results section.

      Figure 4

      Comments from earlier figures hold, with size of enlarged events and using the nuclei as an outline in the single channels. E.g. Figure 4F arrows appear to point to nothing at the chosen scale. The zoom in 4G is insufficient, as the chosen feature is so small it is not even visible in full fields.

      __Response: __We thank the reviewer for this comment. The arrows in Figure 4F indicate individual nocodazole-dispersed Golgi mini-stacks, which are displayed at higher magnification in Figure 4G. The full field in Figure 4F is intentionally shown to illustrate the degree of Golgi dispersion achieved by nocodazole treatment, a context that may be unfamiliar to readers outside the Golgi field, before zooming into a single representative mini-stack in Figure 4G for the cisternal localisation analysis.

      • Figure 4H and 4I need to show the size of the markers *

      __Response: __The size of the markers are now included in the revised manuscript.

      *The representative image in 4L for siGiantin pATM has no pATM foci, while the quantification in 4M has a reduction from ~50% to ~25%, so this image is not representative of this data, or the data quantification is not as strong as the actual data. *

      __Response: __We thank the reviewer for this observation. We wish to clarify that the quantification in Figure 4M reports the mean percentage of RAD51C foci co-localising with pATM across the entire cell population from three independent biological replicates. A reduction from ~50% to ~25% therefore reflects a population-level shift in co-localisation frequency, not that every individual cell shows exactly 25% co-localisation. Given the inherent cell-to-cell variability in foci number and co-localisation, individual cells will span a range of values around this mean, and the representative image shown in Figure 4L reflects one such cell.

      Figure 5

      *Figure 5A has overexposure of the nuclei stain in order to visualize micronuclei. Readjust the levels, and enlarge the images for better visualization. (is this DAPI-stained? Please label). *

      __Response: __The display levels of the nuclear stain in Figure 5A are intentionally set to allow visualisation of micronuclei, which are significantly dimmer than the main nucleus and would not be detectable at display settings optimised for the primary nuclear signal. This is standard practice in micronuclei quantification studies and is necessary to accurately identify and score these structures. The nuclear stain is Hoechst 33342, and this has been explicitly labelled in the revised figure legend.

      *Figure 5A-C: Figure 5A does not show siRAD51, but it is included in the DMSO only graph. Please either show RAD51 data in 5A and 5C, or do not include in 5B. If the DMSO and ETO experiments were performed separately and that accounts for this discrepancy, then show separately. *

      __Response: __We thank the reviewer for this observation. The siRAD51C condition is included in Figure 5B as an internal positive control, consistent with its well-established role in genome stability. RAD51C depletion combined with etoposide treatment resulted in severe cellular toxicity and insufficient cell numbers for reliable quantification, and this condition was therefore excluded from Figure 5C. This has been clarified in the revised figure legend.

      *Figure 5M the white label is difficult to see in the green box. *

      __Response: __We have updated the label colour in Figure 5M to improve visibility against the green background in the revised manuscript.

      * Supplementary Figures*

      Consider reordering/ subdividing supplementary figures for ease of reference during reading.

      Response: We thank the reviewer for this suggestion. The current supplementary figure structure was intentionally designed to minimise the total number of supplementary figures and maintain a logical correspondence with the main figures, avoiding a situation where readers need to navigate an extensive supplementary section, a concern the reviewer raised regarding figure presentation. We believe the current organisation achieves a reasonable balance between completeness and accessibility.

      SF1 and SF2A: Include enlarged boxes or full images so that data is visible.

      __Response: __As described in our response to Major Comment 1, all figures have been provided as high-resolution image files to allow electronic magnification. Space constraints within standard journal figure dimensions preclude the addition of enlarged insets to all supplementary panels without substantially reducing the contextual field of view.

      *SF3A, SF4A, and SF5A: Include enlarged images, include nuclei marker if possible (otherwise, the nuclear intensity is not proven nuclear). *

      Response: We appreciate the suggestion, but adding enlarged insets and nuclei markers to all panels in Figures S3A, S4A and S5A would disproportionately increase the length and complexity of the supplementary section, making it harder rather than easier to navigate. The nuclear intensity measurements are derived from automated segmentation of the Hoechst channel using CellProfiler, which reliably defines nuclear boundaries independently of the antibody channel, and are therefore not dependent on visual confirmation of nuclear localisation in each representative image.

      *SF3B-C, SF4B-C, and SF5 B-D: Change the data presentation in the same method as changed for F2G-H. *

      Response: We have updated the figure legends for Figures S3B-C, S4B-C and S5B-D to improve readability.

      SF3D: List proteins in the same order as in B and C.

      Response: The proteins in Figure S3D are listed in the same order as in Figures S3B and S3C.

      SF6D: Label M N and C more clearly. Include size labels.

      Response: We have added clearer labels for the membrane (M), nuclear (N) and cytoplasmic (C) fractions and included molecular weight size markers in the revised Figure S6D.

      *SF7A-B: Include enlarged. *

      Response: We respectfully note that the purpose of Figures S7A-B is to display the overall cellular response to inhibitor treatments across the cell population, rather than to highlight specific subcellular structures. Enlarged insets would reduce the number of cells visible per panel and would not add scientific value in this context. The Golgi and nuclear signals are clearly visible at the chosen magnification.

      *SF8: Include arrows as in previous experiments, include enlarge. *

      Response: Arrows have been added to Figure S8 to indicate Golgi and nuclear RAD51C signal, consistent with the annotation style used in the main figures. The images already show two representative cells per condition to maximise the visible detail at the chosen scale.

      *SF9G: G is labelled, but not included. *

      Response: Figure S9G has been added in the revised manuscript, showing the pan-cancer overall survival map for GOLGB1 expression across all TCGA cohorts generated using GEPIA2. The figure legend has been updated accordingly.

      *Reviewer #3 (Significance (Required)): *

      * The work finds new roles for the Golgi in regulation of DNA damage responses and the screen could be an important dataset (but results need to be made available) for the DNA repair community. The scope of the initial screen of HPA antibodies and Golgi/Nuclear dual proteomes is impressive, and the overlap of DDR proteins is characterized for fifteen different proteins at a sub-compartmental level. The work provides important insights into RAD51C regulation, however, there are key mechanistic insights and control experiments missing from the studies involving RAD51C and Giantin, dampening its impact. The idea of an alternative cellular compartment for storage of DDR factors prior to damage is interesting, and suggests the spatial regulation of specific lesion responses are stored in specific sub-compartments of the Golgi, which could contribute to repair regulation.*

      References:

      Adamson B, Smogorzewska A, Sigoillot FD, King RW & Elledge SJ (2012) A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nat Cell Biol 14: 318-328

      Badie S, Liao C, Thanasoula M, Barber P, Hill MA & Tarsounas M (2009) RAD51C facilitates checkpoint signaling by promoting CHK2 phosphorylation. J Cell Biol 185: 587-600

      Bergen DJM, Stevenson NL, Skinner REH, Stephens DJ & Hammond CL (2017) The Golgi matrix protein giantin is required for normal cilia function in zebrafish. Biol Open 6: 1180-1189

      Berti M, Teloni F, Mijic S, Ursich S, Fuchs J, Palumbieri MD, Krietsch J, Schmid JA, Garcin EB, Gon S, et al (2020) Sequential role of RAD51 paralog complexes in replication fork remodeling and restart. Nat Commun 11: 3531

      Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, Koch B, Haas SA, Paro R, Perrimon N & Heidelberg Fly Array Consortium (2004) Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303: 832-835

      Brinkmann K, Schell M, Hoppe T & Kashkar H (2015) Regulation of the DNA damage response by ubiquitin conjugation. Front Genet 6: 98

      Garvey CM, Spiller E, Lindsay D, Chiang C-T, Choi NC, Agus DB, Mallick P, Foo J & Mumenthaler SM (2016) A high-content image-based method for quantitatively studying context-dependent cell population dynamics. Sci Rep 6: 29752

      Ghannoum S, Fantini D, Zahoor M, Reiterer V, Phuyal S, Leoncio Netto W, Sørensen Ø, Iyer A, Sengupta D, Prasmickaite L, et al (2023) A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression. PLoS Comput Biol 19: e1010995

      Greenhough LA, Liang C-C, Belan O, Kunzelmann S, Maslen S, Rodrigo-Brenni MC, Anand R, Skehel M, Boulton SJ & West SC (2023) Structure and function of the RAD51B-RAD51C-RAD51D-XRCC2 tumour suppressor. Nature619: 650-657

      Halim VA, García-Santisteban I, Warmerdam DO, van den Broek B, Heck AJR, Mohammed S & Medema RH (2018) Doxorubicin-induced DNA damage causes extensive ubiquitination of ribosomal proteins associated with a decrease in protein translation. Mol Cell Proteomics 17: 2297-2308

      Koreishi M, Gniadek TJ, Yu S, Masuda J, Honjo Y & Satoh A (2013) The golgin tether giantin regulates the secretory pathway by controlling stack organization within Golgi apparatus. PLoS One 8: e59821

      Martin HL, Adams M, Higgins J, Bond J, Morrison EE, Bell SM, Warriner S, Nelson A & Tomlinson DC (2014) High-content, high-throughput screening for the identification of cytotoxic compounds based on cell morphology and cell proliferation markers. PLoS One 9: e88338

      Meindl A, Hellebrand H, Wiek C, Erven V, Wappenschmidt B, Niederacher D, Freund M, Lichtner P, Hartmann L, Schaal H, et al (2010) Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene. Nat Genet 42: 410-414

      Mikheeva AM, Bogomolov MA, Gasca VA, Sementsov MV, Spirin PV, Prassolov VS & Lebedev TD (2024) Improving the power of drug toxicity measurements by quantitative nuclei imaging. Cell Death Discov 10: 181

      Ovejero S, Kumanski S, Soulet C, Azarli J, Pardo B, Santt O, Constantinou A, Pasero P & Moriel-Carretero M (2023) A sterol-PI(4)P exchanger modulates the Tel1/ATM axis of the DNA damage response. EMBO J 42: e112684

      Prakash R, Rawal Y, Sullivan MR, Grundy MK, Bret H, Mihalevic MJ, Rein HL, Baird JM, Darrah K, Zhang F, et al(2022) Homologous recombination-deficient mutation cluster in tumor suppressor RAD51C identified by comprehensive analysis of cancer variants. Proc Natl Acad Sci U S A 119: e2202727119

      Prakash R, Zhang Y, Feng W & Jasin M (2015) Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins. Cold Spring Harb Perspect Biol 7: a016600

      Presley JF, Cole NB, Schroer TA, Hirschberg K, Zaal KJM & Lippincott-Schwartz J (1997) ER-to-Golgi transport visualized in living cells. Nature 389: 81-85

      Rawal Y, Jia L, Meir A, Zhou S, Kaur H, Ruben EA, Kwon Y, Bernstein KA, Jasin M, Taylor AB, et al (2023) Structural insights into BCDX2 complex function in homologous recombination. Nature 619: 640-649

      Somyajit K, Saxena S, Babu S, Mishra A & Nagaraju G (2015) Mammalian RAD51 paralogs protect nascent DNA at stalled forks and mediate replication restart. Nucleic Acids Res 43: 9835-9855

      Soulet C, Catalan J & Moriel-Carretero M (2026) The DNA Damage Response kinase ATM restricts Golgi extension. bioRxiv

      Stadler C, Hjelmare M, Neumann B, Jonasson K, Pepperkok R, Uhlén M & Lundberg E (2012) Systematic validation of antibody binding and protein subcellular localization using siRNA and confocal microscopy. J Proteomics 75: 2236-2251

      Stevenson NL, Bergen DJM, Lu Y, Prada-Sanchez ME, Kadler KE, Hammond CL & Stephens DJ (2021) Correction: Giantin is required for intracellular N-terminal processing of type I procollagen. J Cell Biol 220

      Tang Z, Kang B, Li C, Chen T & Zhang Z (2019) GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis. Nucleic Acids Res 47: W556-W560

      Thorn CF, Oshiro C, Marsh S, Hernandez-Boussard T, McLeod H, Klein TE & Altman RB (2011) Doxorubicin pathways: pharmacodynamics and adverse effects. Pharmacogenet Genomics 21: 440-446

      van der Zanden SY, Qiao X & Neefjes J (2021) New insights into the activities and toxicities of the old anticancer drug doxorubicin. FEBS J 288: 6095-6111

      Zhang Y-W, Otterness DM, Chiang GG, Xie W, Liu Y-C, Mercurio F & Abraham RT (2005) Genotoxic stress targets human Chk1 for degradation by the ubiquitin-proteasome pathway. Mol Cell 19: 607-618

    1. I deal with two kinds of writingblocks. One occurs when we cannot write in fluent, timely fashion. Thisfirst sort of block is a familiar pressure for many of us (and for our stu-dents). The second kind of writing block refers to the paradoxical reluc-tance evidenced by academicians who could but do not offer help tostymied colleagues or students as writers.

      This is interesting and makes me think of other instances outside of writing where I may experience that paradoxical reluctance.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      This work demonstrates that MORC2 undergoes phase separation (PS) in cells to form nuclear condensates, and the authors demonstrate convincingly the interactions responsible for this phase separation. Specifically, the authors make good use of crystallography and NMR to identify multiple protein: protein interactions and use EMSA to confirm protein: DNA interactions. These interactions work together to promote in vitro and in cell phase separation and boost ATPase activity by the catalytic domain of MORC2.

      However, the authors have very weak evidence supporting their potentially valuable claim that MORC2 PS is important for the appropriate gene regulatory role of MORC2 in cells. Exploring causal links between PS and function is an important need in the phase separation field, particularly as regards the role of condensates in gene regulation, and is a non-trivial matter. Any study with convincing data on this matter will be very important. For this reason, it is crucial to properly explore the alternative possibility that soluble complexes, existing in the same conditions as phase-separated condensates, are the functional species. It is also critical to keep in mind that, while a specific protein domain may be essential for PS, this does not mean its only important function pertains to PS.

      In this study, the authors do not sufficiently explore the role that soluble MORC2 complexes may play alongside MORC2 condensates. Neither do they include enough data to solidly show that domain deletion leads to phenotypes via a loss of phase separation per se, rather than the loss of phase separation being a microscopically visible result, not cause, of an underlying shift in protein function. For these reasons, the authors' conclusions regarding the functional role of MORC2 condensates are based on incomplete data. This also dampens the utility of this work as a whole, since the very nice work detailing the mechanism of MORC2 PS is not paired with strong data showing the importance of this observation.

      We thank the reviewer for this thoughtful and constructive critique. We agree that establishing a causal link between phase separation (PS) and biological function—particularly in transcriptional regulation—is a central and non-trivial challenge in the condensate field. We also appreciate the reviewer’s emphasis on two critical alternative interpretations: (i) that soluble MORC2 complexes, rather than condensates, may represent the primary functional species, and (ii) that loss of phase separation upon domain deletion could reflect a downstream consequence of altered protein function rather than its cause.

      To address these concerns, we have performed a series of new experiments specifically designed to decouple condensate formation, and condensate dynamics, thereby allowing us to more rigorously interrogate the functional relevance of MORC2 condensates.

      First, to overcome the limitation of domain deletions which may affect MORC2 function beyond phase separation we introduced a micropeptide-based kill switch (KS) to the C terminus of MORC2. This strategy has recently emerged as a powerful approach to selectively reduce condensate dynamics without disrupting protein expression, folding, or domain architecture [1]. Importantly, unlike CC3 or IDRa deletions, MORC2+KS robustly form nuclear condensates but exhibits markedly reduced internal dynamics, as demonstrated by FRAP analyses showing minimal fluorescence recovery after photo bleaching (Fig. 6a-c). This strategy therefore allows us to perturb condensate material properties independently of MORC2 domain integrity.

      Second, we systematically compared the transcriptional consequences of rescuing MORC2-knockout HeLa cells with MORC2FL, condensation-deficient mutants (ΔCC3 and ΔIDRa), and the dynamics-defective MORC2+KS (Fig. 6d). Despite being expressed at substantially higher levels than MORC2FL (Fig. 6e), all three mutants showed a striking and consistent failure to restore MORC2-dependent transcriptional regulation (Fig. 6f-h). This effect was particularly pronounced for transcriptionally repressed genes, including two sets of high-confidence MORC2 targets reported in prior studies (Fig. 6i and Fig.S10). These findings demonstrate that neither increased protein abundance nor the mere presence of condensate-like structures alone is sufficient to restore MORC2 function.

      Third, our data instead support a model in which both soluble MORC2 complexes and dynamic MORC2 condensates are required for full transcriptional regulation activity. While soluble MORC2 is likely involved in target recognition and complex assembly, our results indicate that proper condensate formation—and critically, condensate dynamics—are essential for effective transcriptional repression and activation. The inability of the MORC2+KS mutant to rescue transcriptional defects, despite intact condensate formation, points away from a model in which MORC2 condensates represent only microscopically visible byproducts of MORC2 activity.

      We believe these new data strengthen the manuscript by pairing the detailed mechanistic dissection of MORC2 phase separation with direct functional evidence, enhancing the conceptual impact and biological significance of the study.

      Strengths:

      Static light scattering and crystallography are nicely used to demonstrate the dimerization of MORC2FL and to discover the structure of the CC3 domain dimer, presumably responsible for the dimerization of MORC2FL (Figure 1).

      Extensive use of deletion mutants in multiple cell lines is used to identify regions of MORC2 that are important for forming condensates in the nucleus: the IBD, IDR, and CC3 domains are found to be essential for condensate formation, while the CW domain plays an unknown role in condensate morphology (Figure 3). The authors use NMR to further identify that the IBD domain seems to interact with the first third of the centrally located IDR, termed IDRa, but not with the latter two-thirds of the IDR domain (Figure 4). This leads them to propose that phase separation is the product of IDB:IDRa interaction, CC3 dimerization, and an unknown but important role for the CW domain.

      Based on the observation that removal of the NLS resulted in diffuse cytoplasmic localization, they hypothesized that DNA may play an important role in MORC2 PS. EMSA was used to demonstrate interaction between DNA and several MORC2 domains: CC1, CC2, IDR, and TCD-CC3-IBD. Further in vitro microscopy with purified MORC2 showed that DNA addition significantly reduces MORC2 saturation concentration (Figure 5).

      These assays convincingly demonstrate that MORC2 phase separates in cells, and identify the protein domains and interactions responsible for this phenomenon, with the notable caveat that the role of the CW domain here is left unexplored.

      We appreciate the reviewer for their positive and detailed assessment of the strengths of our study. Our understanding of the CW domain’s function remains preliminary. Although we observed that the CW domain can influence condensate size, the IDR, IBD, and CC3 domains constitute the core structural elements driving phase separation. Consequently, the CW domain was not a primary focus of the current study. Nonetheless, investigating its functional contributions represents an interesting avenue for future work.

      Weaknesses:

      Although the authors demonstrated phase separation of MORC2FL, their evidence that this plays a functional role in the cell is incomplete.

      Firstly, looking at differentially upregulated genes under MORC2FL overexpression, the authors acknowledge that only 10% are shared with differentially regulated genes identified in other MORC2FL overexpression studies (Figure 6c, d). No explanation is given for why this overlap is so low, making it difficult to trust conclusions from this data set.

      We thank the reviewer for raising this important concern. In response, we have improved the quality and robustness of our RNA-seq analysis by repeating the experiments with optimized sample handling and increased sequencing depth. Using this updated dataset, we identified a considerably higher overlap between MORC2-regulated genes in our study and those reported previously.

      Specifically, we observed 84 overlapping genes with the study by Nikole L. Fendler et al. [2], corresponding to approximately 32% of the MORC2-regulated genes reported in that work (Fig. 6i). In addition, we identified 102 overlapping genes with the dataset reported by Iva A. Tchasovnikarova et al. [3], representing approximately 22% of the genes identified in that study (Fig. S10b).

      We note that complete concordance with previous reports is not expected, given substantial differences in experimental design. For example, Fendler et al. employed a doxycycline-inducible MORC2 expression system [2], whereas our study relies on transient overexpression in MORC2-knockout HeLa cells. In contrast, Tchasovnikarova et al. compared transcriptomes between MORC2 knockout and wild-type cells [3], rather than MORC2 rescue conditions. Moreover, RNA-seq results are inherently influenced by cell line batch variability, sequencing depth, and analysis pipelines, all of which differ across studies.

      Taken together, we consider an overlap in the range of ~20–30% to be reasonable and biologically meaningful in the context of these experimental differences, and we believe that the revised RNA-seq data provide a more reliable foundation for our conclusions regarding MORC2-dependent transcriptional regulation.

      Secondly, of the 21 genes shared in this study and in earlier studies, the authors note that the differential regulation is less pronounced when a phase-separation-deficient MORC2 mutant is overexpressed, rather than MORC2FL (Figure 6e). This is taken as evidence that phase separation is important for the proper function of MORC2. However, no consideration is made for the alternative possibility that the mutant, lacking the CC3 dimerization domain, may result in non-functional complexes involving MORC2, eliminating the need for a PS-centric conclusion. To take the overexpression data as solid evidence for a functional role of MORC2 PS, the authors would need to test the alternative, soluble complex hypothesis. Furthermore, there seems to be low replicate consistency for the MORC2 mutant condition (Figure S6a), with replicate 3 being markedly upregulated when compared to replicates 1 and 2.

      We thank the reviewer for raising these important concerns. In the revised manuscript, we have substantially strengthened both the experimental evidence and the data presentation to directly address the alternative “soluble complex” interpretation as well as the issue of replicate consistency. Specifically, we now provide data that clarify the functional impact of phase-separation-deficient MORC2 mutants and explicitly show replicate-level RNA-seq analyses. The Fig. 6 and Fig. S10support these improvements and enhance both the robustness and transparency of our transcriptional analyses. Collectively, these revisions directly address the reviewer’s concerns regarding the functional interpretation of MORC2 phase separation.

      Thirdly, the authors close by examining the in-cell PS capabilities and ATPase activity of several disease-associated mutants of MORC2 (Figure 7). However, the relevance of these mutants to the past 6 figures is unclear. None of these mutations is in regions identified as important for PS. Two of the mutations result in a higher percentage of the cell population being condensate-positive, but this is not seemingly connected to ATPase activity, as only one of these two mutants has increased ATPase activity. Figure 7 does not add any support to the main hypotheses in the paper, and nowhere in the paper do the authors investigate the protein regions where the mutations in Figure 7 are found.

      We thank the reviewer for raising this point regarding Fig. 7. At the current stage, the results for disease-associated mutations are primarily descriptive. While we observed that certain mutations clustered at the N-terminus can affect MORC2 condensate formation, ATPase activity, and DNA binding, we did not identify a mechanistic explanation for these correlations. Notably, the T424R mutation, previously reported to significantly enhance ATPase activity [4], also increased both intracellular condensate formation and in vitro DNA binding in our experiments. In contrast, other mutations did not show such consistent effects. Previous studies have established that MORC2’s ATP-binding and DNA-binding activities are independent [4]. Our results further suggest that MORC2’s phase separation behavior is independent of both ATP and DNA binding affinity, although existing evidence hints at potential cross-regulatory interactions among these three functions.

      We would also like to emphasize an additional observation that may help contextualize the relevance of N-terminal mutations. Although deletion of the MORC2 N-terminus does not prevent the remaining C-terminal region from forming nuclear condensates, these C-terminal condensates exhibit a marked loss of fluorescence recovery in FRAP assays (Fig. S11). This finding suggests that while the N-terminus is not strictly required for condensate assembly, it plays an important role in regulating condensate fluidity. Accordingly, disease-associated mutations distributed across the N-terminal region may influence MORC2 function by modulating condensate material properties rather than condensate formation per se. Based on this hypothesis, we evaluated the fluidity of condensates formed by the E236G and T424R mutants. FRAP measurements indicated substantially reduced fluorescence recovery in E236G, whereas T424R exerted minimal effects (Fig. 7e, f).

      Overall, our interpretation of the results in Fig. 7 is still at a preliminary stage. Nevertheless, the role of the MORC2 N-terminus in modulating condensate fluidity, together with the observed impairment caused by the E236G mutation, appears to be robust, although the underlying mechanism remains to be elucidated. We have incorporated additional discussion on this point and consider it an important direction for future study.

      Reviewer #1 (Recommendations for the authors):

      (1) Why does MORC2 overexpression lead to changes in gene regulation that are so different from past MORC2 overexpression studies? This is unsettling to me.

      (2) Likewise, why is replicate 3 for the MORC2ΔCC3 variant so different from replicates 1 and 2? Perhaps repeating this experiment would be helpful, both for showing better repeatability and perhaps as regards pulling out a stronger phenotype.

      We have repeated the experiments and obtained improved data quality.

      (3) A better explanation of the relevance of Figure 7 to the story of the rest of the paper, especially the phase-separation of MORC2, would be important to improving this paper.

      We thank the reviewer for this suggestion. We have performed additional experiments and expanded the discussion.

      (4) Are expression levels of mutant proteins in Figure 7 uniform between mutants? If not, is it possible that expression levels might account for the difference in condensate-positive cells between mutants?

      We cannot fully exclude the possibility that differences in expression levels may contribute to the observed differences among mutants. In our experiments, equal amounts of plasmid DNA were used for transfection across all conditions. Although we did not directly quantify post-transfection protein expression levels by immunoblotting or similar approaches, even if certain mutations were to affect protein expression, it would be technically challenging to further optimize the strategy to fully normalize expression levels across mutants.

      Importantly, we note that MORC2 does not form condensates in all transfected cells, even when EGFP fluorescence indicates robust expression levels that are comparable to, or even exceed, those observed in condensate-positive cells. This observation suggests that high expression alone is not sufficient to drive MORC2 phase separation in cells. Therefore, we do not favor the interpretation that the E236K and T424R mutations enhance MORC2 condensation simply by increasing MORC2 protein expression levels.

      Minor:

      (1) I would suggest considering using the term "dynamic" rather than "liquid-like", as FRAP is technically a measurement of the dynamicity of a protein within a volume, rather than a measurement of the actual fluidity of that volume.

      We thank the reviewer for this helpful suggestion. We agree that FRAP measurements primarily report protein mobility and condensate dynamics rather than the physical fluidity of the condensates. We have therefore revised the manuscript to replace “liquid-like” with “dynamic” where conclusions are based on FRAP analyses.

      (2) A further investigation of the role of the CW domain would be very interesting, since it clearly has a major role in condensate morphology. Perhaps CW confers important heterotypic interactions which contribute to compositional control of the MORC2 condensates, and thus function and morphology? However, due to the complexity of this specific question and the potentially marginal improvement offered by this paper, I do not think this is a critical addition.

      We thank the reviewer for this insightful suggestion. We have noted this possibility in the Discussion as an important avenue for future investigation.

      (3) Why is TCD not tested alone by EMSA for affinity to DNA in Figure 5?

      Our inference regarding the DNA-binding capacity of the TCD domain was based on comparative EMSA analyses. Specifically, we found that the TCD–CC3–IBD fragment was able to bind DNA, whereas the CC3–IBD fragment alone showed no detectable DNA binding. From this comparison, we inferred that the TCD domain is responsible for the observed DNA-binding activity.

      Because the TCD domain does not affect MORC2 condensate formation, it was not a central focus of the present study, which primarily aims to elucidate the mechanisms underlying MORC2 phase separation and its functional relevance. For this reason, we did not further test TCD alone by EMSA in Figure 5.

      Reviewer #2 (Public review):

      Summary:

      The study by Zhang et al. focuses on how phase separation of a chromatin-associated protein MORC2, could regulate gene expression. Their study shows that MORC2 forms dynamic nuclear condensates in cells. In vitro, MORC2 phase separation is driven by dimerization and multivalent interactions involving the C-terminal domain. A key finding is that the intrinsically disordered region (IDR) of MORC2 exhibits strong DNA binding. They report that DNA binding enhances MORC2's phase separation and its ATPase activity, offering new insights into how MORC2 contributes to chromatin organization and gene regulation. The authors try to correlate MORC2's condensate-forming ability with its gene silencing function, but this warrants additional controls and validation. Moreover, they investigate the effect of disease-linked mutations in the N-terminal domain of MORC2 on its ability to form cellular condensates, ATPase activity, and DNA-binding, though the findings appear inconclusive in the manuscript's current form.

      Thank you for your thorough and constructive review of our manuscript. In response to the concerns raised regarding the functional relevance of MORC2 condensate formation, we have redesigned and expanded the experiments presented in Fig. 6 and Fig. S6 to directly link MORC2’s condensate-forming capacity with its transcriptional regulatory function. These new experiments provide additional controls and validation, strengthening the causal relationship between MORC2 condensate dynamics and gene regulation.

      At the current stage, the results for disease-associated mutations are descriptive. While we observed that certain mutations clustered at the N-terminus can affect MORC2 condensate formation, ATPase activity, and DNA binding, we did not identify a mechanistic explanation for these correlations. Notably, the T424R mutation, previously reported to significantly enhance ATPase activity [4], also increased both intracellular condensate formation and in vitro DNA binding in our experiments. In contrast, other mutations did not show such consistent effects. Previous studies have established that MORC2’s ATP-binding and DNA-binding activities are independent [4]. Our results further suggest that MORC2’s phase separation behavior is also independent of both ATP and DNA binding, although existing evidence hints at potential cross-regulatory interactions among these three functions.

      Strengths:

      The authors determined a 3.1 Å resolution crystal structure of the dimeric coiled-coil 3 (CC3) domain of MORC2, revealing a hydrophobic interface that stabilizes dimer formation. They present extensive evidence that MORC2 undergoes liquid-liquid phase separation (LLPS) across multiple contexts, including in vitro, in cellulo, and in vivo. Through systematic cellular screening, they identified the C-terminal domain of MORC2 as a key driver of condensate formation. Biophysical and biochemical analyses further show that the IDR within the C-terminal domain interacts with the C-terminal end region (IBD) and also exhibits strong DNA-binding capacity, both of which promote MORC2 phase separation. Together, this study emphasizes that interactions mediated by multiple domains-CC3, IDR, and IBD- drives MORC2 phase separation. Finally, the authors quantified the effect of removing the CC3 on the upregulation and downregulation of target gene expression.

      We thank the reviewer for their appreciation of the key findings presented in this manuscript.

      Weaknesses:

      Though the findings appear compelling in isolation, the study lacks discussion on how its findings compare with previous studies. Particularly in the context of MORC2-DNA binding, there are previous studies extensively exploring MORC2-DNA binding (Tan, W., Park, J., Venugopal, H. et al. Nat Commun 2025), and its effect on ATPase activity (ref 22). The contradictory results in ref 22 about the impact of DNA-binding on ATPase activity, and ATPase activity on transcriptional repression, warrant proper discussion. The authors performed extensive in-cellulo screening for the investigation of domain contribution in MORC2 condensate formation, but the study does not consider/discuss the possibility of some indirect contributions from the complex cellular environment. Alternatively, the domain-specific contributions could be quantified in vitro by comparing phase diagrams for their variants. While the basis of this study is to investigate the mechanism of MORC2 condensate-mediated gene silencing, the findings in Figure 6 appear incomplete because the CC3 deletion not only affects phase separation of MORC2 but also dimerization. Furthermore, their investigation on disease-linked MORC2 mutations appears very preliminary and inconclusive because there are no obvious trends from the data. Overall, the discussion appears weak as it is missing references to previous studies and, most importantly, how their findings compare to others'.

      We thank the reviewer for their careful assessment of MORC2’s DNA-binding properties and its relationship with ATPase and transcriptional activities. We would like to offer the following clarifications to address these concerns, which will also be incorporated into the Discussion section of the revised manuscript.

      First, recent work by Tan et al. [5] similarly identified multiple DNA-binding sites in MORC2, consistent with our findings, though there are discrepancies in the precise binding regions. In particular, they reported that isolated CC1 and CC2 domains do not bind 60 bp dsDNA, which contrasts with our observations. We attribute this difference to the types of DNA used in the assays. In our study, we employed 601 DNA, a defined nucleosome-positioning sequence, which differs substantially from randomly designed short dsDNA. For instance, prior work by Christopher H. Douse et al. [54] also confirmed that MORC2’s CC1 domain can bind 601 DNA.

      Second, in the study by Fendler et al. [2], DNA binding was reported to reduce MORC2’s ATPase activity—an observation that appears inconsistent with the results presented in our Fig. 5j. A critical distinction between the two studies lies in the experimental systems used: Fendler et al. [2] employed MORC2 constructs and 35 bp double-stranded DNA (dsDNA), whereas our experiments utilized full-length MORC2 and 601 bp DNA (a sequence with high nucleosome assembly potential). These differences including the absence of potentially regulatory C-terminal regions in the truncated construct and the varying length/structural properties of the DNA substrates introduce variables that substantially complicate direct comparative analysis of ATPase activity outcomes.

      Separately, Douse et al. [4] demonstrated that the efficiency of HUSH complex-dependent epigenetic silencing decreases as MORC2’s ATP hydrolysis rate increases, implying an inverse relationship between ATPase activity and silencing function. Notably, our current work has not established a direct mechanistic link between MORC2 phase separation and its ATPase activity. Thus, we refrain from inferring that the effect of MORC2 phase separation on transcriptional repression is mediated through modulation of its ATPase function this remains an important question to address in future studies.

      Finally, we have redesigned and expanded the experiments presented in Fig. 6 and Fig. S6 to directly link MORC2’s condensate-forming capacity with its transcriptional regulatory function.

      Reviewer #2 (Recommendations for the authors):

      Major concerns:

      (1) Unaddressed discrepancies with the previous study:

      (a) Inadequate discussion of Reference 22 and apparent contradictions. Notably, Reference 22 provides evidence for reduced ATPase activity upon DNA binding, in contrast to the current study's observations. Moreover, Reference 22 demonstrates that ATP hydrolysis (ATPase activity) is inversely associated with MORC2-mediated gene silencing, whereas this study concludes that 'the silencing function of MORC2 requires its ATPase activity'. These apparent contradictions warrant a more thorough discussion to reconcile the differences, including potential mechanistic explanations and experimental context that could account for the discrepancies. Additionally, the authors should discuss potential reasons why Ref. 22 may not have observed phase separation during MORC2 biophysical analysis. For instance, in Ref. 22, SEC-MALS was performed at 2 mg/mL (~16 µM) MORC2 FL in the presence of 150 mM NaCl, conditions that could influence phase behavior based on the current manuscript's results. Addressing whether differences in protein construct, buffer composition, or experimental design might account for this discrepancy would strengthen the discussion.

      We thank the reviewer for pointing out the apparent discrepancies between our results and those reported in Ref. 22. We agree that these differences warrant explicit discussion, and we have revised the Discussion accordingly to clarify the experimental and conceptual distinctions between the two studies.

      First, regarding the effect of DNA binding on ATPase activity, Ref. 22 examined MORC2 ATPase activity under conditions where MORC2 does not undergo detectable phase separation, whereas our ATPase assays were performed under conditions in which MORC2 readily forms condensates in the presence of DNA. We therefore propose that the observed increase in ATPase activity in our study may reflect a distinct biochemical regime in which phase separation and/or high local protein concentration modulates enzymatic activity. Importantly, our data do not exclude the possibility that DNA binding per se can inhibit ATPase activity under non-condensing conditions, as reported in Ref. 22.

      Second, with respect to transcriptional repression, Ref. 22 reported an inverse correlation between ATP hydrolysis and MORC2-mediated silencing, whereas our study finds that ATPase activity is required for efficient repression. We suggest that these observations are not necessarily contradictory but may reflect different regulatory layers of MORC2 function. Specifically, ATP binding and hydrolysis may be required for MORC2 structural remodeling and chromatin engagement, while excessive or dysregulated ATP hydrolysis could impair stable silencing complexes, as suggested previously [4]. We now explicitly discuss this possibility in the revised manuscript.

      Finally, we appreciate the reviewer’s suggestion regarding the absence of phase separation in Ref. 22. Indeed, SEC-MALS experiments in Ref. 22 were conducted at ~16 µM MORC2 in the presence of 150 mM NaCl (the purification condition is 500 mM NaCl, 10% glycerol), conditions that based on our phase diagrams—are close to or above the saturation concentration but also strongly influenced by ionic strength. This combination of factors explains why the UV peak from SEC-MALS is not indicative of a homogeneous sample [3].

      (b) The DNA binding capacity of individual MORC2 domains was tested in Fig. 5. IDR appears to be the strongest DNA binder among others. Is this the effect of IDR being isolated from the rest of the protein? A recent paper (Tan, W., Park, J., Venugopal, H. et al. Nat Commun 2025) also investigated DNA binding capacity of different regions of MORC2 using hydrogen-deuterium exchange experiments and EMSA. Interestingly, it can be seen in Figure S9 that the DNA binding capacity of different regions changes when compared together to when in isolation (MORC2 1-603 vs 1-265; 1-495; 496-603). In line with the above, MORC2 IDR's interaction with DNA warrants additional investigation, taking the system as a whole to avoid misinterpretation arising from non-specific interactions.

      We appreciate the reviewer’s insightful comments regarding domain-specific DNA binding and the potential caveats of studying isolated regions. In Figure 5, our EMSA analyses show that the isolated IDR exhibits the strongest DNA-binding signal among the tested fragments. We agree that this observation may, at least in part, reflect the removal of structural or regulatory constraints imposed by the full-length protein.

      Consistent with the reviewer’s point, Tan et al. [5] demonstrated that DNA-binding behavior of MORC2 regions differs when analyzed in isolation versus in the context of larger constructs. We have now incorporated this comparison into the Discussion and explicitly note that DNA binding by the IDR should be interpreted as a contextual and potentially cooperative property rather than an autonomous function.

      Importantly, our conclusions do not rely on the IDR acting as an independent DNA-binding module in vivo. Rather, we propose that the IDR contributes to DNA engagement and phase behavior within the architectural framework of full-length MORC2. We now emphasize this limitation and highlight the need for future studies that probe DNA binding in the context of intact MORC2 or minimally perturbed constructs.

      (2) MORC2 DNA binding impacting phase separation and ATPase activity:

      While it is clear that MORC2: DNA interaction facilitates MORC2 phase separation, the impact on ATPase activity is not conclusive. First, they observe an opposite trend (compared to ref. 22) for DNA binding on MORC2's ATPase activity. Secondly, it is not clear if the increase in ATPase activity is mediated by DNA binding or phase separation. The ATPase activity was measured at 1 µM MORC2 protein concentration in the presence of DNA, where MORC2 appears to phase separate. To draw more definitive conclusions, additional controls are necessary. Specifically, a phase separation-deficient mutant (from this study) and a DNA-binding-deficient mutant (see ref. 22) should be included to disentangle the contributions of DNA binding and phase separation to ATPase activity. The choice of ATP-binding-deficient mutant N39A as a negative control seems inconclusive in this regard. Additionally, why is there an increase in ATP hydrolysis rate for the ATP-binding-deficient mutant in the presence of DNA, resulting in ATP hydrolysis rates similar to WT MORC2? This raises further questions about the underlying mechanism.

      We agree with the reviewer that disentangling the contributions of DNA binding and phase separation to ATPase activity is challenging and that our current data do not fully resolve this issue. As noted, ATPase assays were performed at protein concentrations (1 µM) where MORC2 undergoes DNA-induced phase separation, making it difficult to distinguish whether enhanced ATP hydrolysis arises directly from DNA binding or indirectly from condensate formation.

      We acknowledge that inclusion of additional mutants such as phase separation deficient or DNA-binding deficient variants would provide a more definitive mechanistic separation of these effects. However, generating and validating such mutants in a manner that preserves overall protein integrity is beyond the scope of the current study. Accordingly, we have revised the text to present our findings more cautiously and to frame the observed ATPase enhancement as a correlation rather than a causal mechanism.

      Regarding the ATP-binding–deficient N39A mutant, we agree that its behavior in the presence of DNA raises interesting mechanistic questions. We now explicitly note this unexpected observation and discuss possible explanations, including partial ATP binding, altered oligomeric states, or indirect effects mediated by condensate formation.

      (3) Dissecting the domain-specific contribution in MORC2 phase separation:

      (a) While in cellulo data indicate that the presence of IDR, NLS, CC3, and IBD is all essential for MORC2 condensate formation, it is not clear if this is the effect of the complex cellular environment or whether it is intrinsic for MORC2 phase separation ability. In lines 256-259, the authors suggest IDRa interaction with IBD may serve as a nucleation mechanism for LLPS. In other places, it has been mentioned that CC3 dimerization acts as a scaffold for condensate formation. It is not clear if all of these are essential for MORC2 phase separation, or one of them is essential while the other domain(s) facilitates the phase separation. Though Figure 3 provides a qualitative overview of the contribution of different regions in MORC2 phase separation in cellulo-influenced by the complex cellular environment and substrate interactions, the absolute domain contribution in phase separation would be better studied in vitro by quantitatively comparing phase diagrams (for example, c-sat vs temperature) of different domain deletion constructs.

      We thank the reviewer for highlighting the distinction between intrinsic phase separation propensity and cellular context dependent effects. Our in cellular screening was designed to identify regions required for condensate formation under physiological conditions, where chromatin, binding partners, and macromolecular crowding are present. We agree that this approach does not directly quantify the intrinsic phase separation contribution of individual domains.

      While CC3 dimerization, IDR–IBD interactions, and nuclear localization all contribute to condensate formation, our data do not imply that these elements are mechanistically equivalent. Rather, we propose that CC3 provides a structural scaffold, while IDR-mediated interactions lower the energetic barrier for condensation. We have revised the manuscript to clarify this hierarchical model and to avoid implying that all domains contribute equally or independently.

      We agree that quantitative in vitro phase diagrams would provide valuable insight into intrinsic domain contributions. Whereas the MORC2ΔCC3-IBD (1–900) and CC3-IBD (900-1032) fragment fails to induce phase separation, the IDR mix CC3–IBD fragment drives robust phase separation; additionally, phase separation is entirely abrogated in the absence of domain–domain interactions. These observations collectively verify that phase separation is contingent on specific domain combinations and their interactions.

      (b) Similarly, for line 228-231: 'Notably, condensates formed exclusively in the nucleus and not in the cytoplasm of transfected HeLa cells, suggesting that chromatin-associated nuclear factors, such as DNA, may contribute to the nucleation or stabilization of MORC2 condensates.' This is an important observation made by the authors. Since MORC2 readily phase separates in vitro under physiological conditions, it is important to discuss why MORC2 does not make condensates in the cytoplasm (in the case of MORC2deltaNLS). In this regard, how does the concentration of overexpressed EGFP-MORC2 constructs compare with in vitro tested droplets of MORC2?

      We thank the reviewer for highlighting this important conceptual point. Although MORC2 readily undergoes phase separation in vitro under physiological buffer conditions, the absence of condensate formation in the cytoplasm of cells expressing MORC2ΔNLS underscores the importance of the nuclear environment in promoting MORC2 assembly.

      The cytoplasm differs fundamentally from the nucleus not only in overall molecular composition but also in the availability of high-valency scaffolds such as chromatin. We propose that chromatin-associated components, particularly DNA, provide a platform that locally concentrates MORC2 and increases its effective valency, thereby facilitating nucleation or stabilization of condensates in the nucleus. In contrast, the cytoplasm lacks such scaffolds, even when MORC2 is expressed at appreciable levels. In cultured cells, MORC2 is seldom observed in the cytoplasm. While specific experimental contexts may facilitate its cytoplasmic localization, such observations are rarely reported [6]. In transfection-based systems, MORC2 predominantly displays droplet-like behavior in the nucleus. Notably, in endogenous EGFP–MORC2 chimeric mice, we detected punctate MORC2 structures in the neuronal cytoplasm of the brain and spinal cord. The functional significance and biophysical state of cytoplasmic MORC2 remain largely unexplored.

      With respect to protein concentration, while EGFP-MORC2 is robustly expressed in cells, direct comparison between cellular expression levels and the protein concentrations used in vitro is inherently challenging. Importantly, in vitro phase separation is driven by bulk protein concentration under defined conditions, whereas in cells, effective local concentration and interaction valency are strongly shaped by spatial confinement and chromatin association. We have revised the manuscript text to emphasize this distinction and to avoid interpreting nuclear specificity as a purely concentration-dependent phenomenon.

      (c) Lines 227-228: '... CW domain restricts condensate overgrowth or fusion', this inference is based on CTDdeltaCW puncta being larger in size (Figure 3a). However, in Figure 4h MORC2deltaIDRb and MORC2deltaIDRc also result in larger puncta. Making a final conclusion that the CW domain restricts condensate overgrowth or fusion warrants additional investigation.

      We thank the reviewer for pointing out the limitation of our original conclusion. We agree that the enlarged puncta in both CTDΔCW (Figure 3a) indicate that condensate size regulation involves the CW domain was insufficiently rigorous.

      Re-analysis of existing data identifies clear phenotypic disparities between the mutants: MORC2ΔIDRb/ΔIDRc mutants show two distinct phenotypes (reduced puncta number with enlarged size, or unchanged puncta number with uniform enlargement), and their total puncta area per cell is comparable to the WT. By contrast, CTDΔCW mutants display markedly larger puncta relative to the WT. Based on this distinction, we have revised our conclusion to a more cautious formulation: "These observations suggest that the CW domain may participate in regulating initial nucleation size and the exact molecular mechanisms require further investigation."

      (4) MORC2 condensate-mediated gene silencing:

      This is one of the key investigations of this study where the authors evaluate the ability of MORC2 condensates to regulate gene silencing (transcriptional repression). The major concern here is that the authors are drawing their conclusion based on a CC3 domain deletion mutant of MORC2 and comparing it with wild-type MORC2. Notably, the CC3 domain is responsible for MORC2 dimerization, and as the authors quote, 'The dimeric assembly of CC3 is essential for maintaining the structural integrity of the protein', the absence of CC3 would have a direct impact on its function (such as ATPase activity). With these considerations, it is not clear whether the effect of CC3 domain deletion on gene regulation is an effect of no phase separation or a consequence of loss of function. This necessitates additional validation by including other controls, such as IBD domain deletion mutant, IDRa domain deletion mutant, where the phase separation is impeded without affecting dimerization.

      We appreciate the reviewer’s concern regarding the interpretation of CC3 deletion experiments. We agree that CC3 deletion affects both dimerization and phase separation, complicating attribution of gene regulatory effects solely to condensate formation. Our intention was not to claim that loss of repression arises exclusively from impaired phase separation, but rather to demonstrate that disrupting condensate-dynamic capacity correlates with impaired silencing.

      To directly address these concerns, we have performed a series of new experiments specifically designed to decouple condensate formation, condensate dynamics, and protein abundance, thereby allowing us to more rigorously interrogate the functional relevance of MORC2 condensates.

      First, to overcome the limitation of domain deletions which may affect MORC2 function beyond phase separation we introduced a micropeptide-based kill switch (KS) to the C terminus of MORC2. This strategy has recently emerged as a powerful approach to selectively reduce condensate dynamics without disrupting protein expression, folding, or domain architecture [1]. Importantly, unlike CC3 or IDRa deletions, MORC2+KS robustly form nuclear condensates but exhibits markedly reduced internal dynamics, as demonstrated by FRAP analyses showing minimal fluorescence recovery after photo bleaching (Fig. 6a-c). This strategy therefore allows us to perturb condensate material properties independently of MORC2 domain integrity.

      Second, we systematically compared the transcriptional consequences of rescuing MORC2-knockout HeLa cells with MORC2FL, condensation-deficient mutants (ΔCC3 and ΔIDRa), and the dynamics-defective MORC2+KS (Fig. 6d). Despite being expressed at substantially higher levels than MORC2FL (Fig. 6e), all three mutants showed a striking and consistent failure to restore MORC2-dependent transcriptional regulation (Fig. 6f-h). This effect was particularly pronounced for transcriptionally repressed genes, including two sets of high-confidence MORC2 targets reported in prior studies (Fig. 6i and Fig. S10). These findings demonstrate that neither increased protein abundance nor the mere presence of condensate-like structures alone is sufficient to restore MORC2 function.

      Third, our data instead support a model in which both soluble MORC2 complexes and dynamic MORC2 condensates are required for full transcriptional activity. While soluble MORC2 is likely involved in target recognition and complex assembly, our results indicate that proper condensate formation and critically, condensate dynamics are essential for effective transcriptional repression and activation. The inability of the MORC2+KS mutant to rescue transcriptional defects, despite intact condensate formation, points away from a model in which MORC2 condensates represent only microscopically visible byproducts of MORC2 activity.

      We believe these new data strengthen the manuscript by pairing the detailed mechanistic dissection of MORC2 phase separation with direct functional evidence, enhancing the conceptual impact and biological significance of the study.

      (5) Uncertain impact of pathogenic MORC2 mutations:

      Line 356-365: While the statements such as "disease-associated mutations primarily affect enzymatic and phase behaviors rather than DNA affinity" and "these findings provide mechanistic insight into how specific mutations may contribute to distinct pathological outcomes" are conceptually compelling, the data presented in Figure 7b-d do not appear to fully support these conclusions. For many of the mutants, the differences from WT across key parameters-condensation, ATPase activity, and DNA binding-are either modest or statistically insignificant. As such, drawing a unified mechanistic conclusion from these datasets may overstate what the data actually support.

      We agree that the effects of disease-associated MORC2 mutations described in Fig. 7 are modest and, in some cases, statistically insignificant. Our intention was to document observable trends rather than to propose a unified mechanistic framework. We have revised the manuscript to temper these conclusions and to emphasize the descriptive nature of these data.

      (6) Important conceptual clarifications:

      (a) Intrinsically disordered regions (IDRs) are not synonymous with phase separation. As the authors show, it is a combination of IDR-mediated interactions and CC3 dimerization that contributes towards the phase separation of MORC2. While IDRs can act as scaffolds for multivalent weak interactions that may promote biomolecular condensate formation, many IDRs serve other roles-such as mediating transient interactions, signaling, or regulatory functions-without undergoing phase separation. Researchers should avoid generalizing the assumption that the mere presence of IDRs in a protein implies its ability for phase separation. In this regard, authors should consider restructuring some of their generalized statements: Line 87-88: 'Recent studies suggest that intrinsically disordered regions (IDRs) can drive liquid-liquid phase separation (LLPS)' and Line 159-161: 'we noticed a long unstructured region at its C-terminus (Fig. S1b), a characteristic often associated with proteins capable of phase separation'.

      We agree that IDRs are not synonymous with phase separation and have revised the Introduction to avoid generalized statements. The revised text now emphasizes that IDRs can contribute to phase separation in a context-dependent manner and act in concert with structured oligomerization domains such as CC3-IBD.

      (b) Liquid-liquid phase separation: I would suggest switching the phrase to just phase separation. The rationale is that the in vitro studies of MORC2 (FRAP, droplet imaging) do not show liquid-like behavior, but perhaps liquid-solid. The FRAP studies suggest liquid-like behavior for some of the constructs. Given the differences in viscoelastic properties across the in vitro and in cellulo studies, it is better to generalize to "phase separation". Movies for droplet fusion and FRAP, wherever applicable, would be much appreciated. As the nature of in vitro MORC2 droplets appears different than in cells, movie representations of the above would enable readers to better assess the viscoelastic nature of the droplets (whether liquid, gel, etc).

      We appreciate the reviewer’s insight regarding the viscoelastic properties of MORC2. Our experimental data indeed show a disparity in dynamics between the two environments: while in vitro MORC2-FL condensates exhibit relatively low internal mobility, the in cellulo MORC2-FL puncta display high dynamics, characterized by rapid internal recovery in FRAP assays and droplet fusion events (Fig. S2f).

      This contrast suggests that the intracellular microenvironment plays a critical role in regulating the material state of MORC2 condensates. Consequently, we have focused on providing in vivo fusion data, as we believe in vitro characterizations (such as fusion or FRAP under various artificial conditions) may not faithfully represent the physiological behavior of MORC2. We have revised the manuscript to use the more general term “phase separation” or “condensation” and have added a discussion on these limitations to avoid overinterpreting the material properties observed in vitro.

      (7) Methods:

      (a) Figure 6 S2b: If phase separation occurs at, say, 1.8 µM protein concentration, this indicates that the protein has reached its saturation concentration (c-sat). Beyond c-sat, any additional protein should partition into the dense phase, while the concentration of the dilute phase remains constant. However, in this figure, the dilute phase concentration appears to increase with increasing total protein concentration, which is inconsistent with expected phase separation behavior. As the methods section does not have any sub-section for the sedimentation assay, it becomes difficult to understand how this experiment was performed, whether there is any technical discrepancy in the way soluble and pellet fractions were handled and processed for loading onto the gels. This is also the case with Figure 3d.

      We thank the reviewer for carefully examining the sedimentation assay and for raising this important conceptual point. We agree that, for an ideal two-phase system at thermodynamic equilibrium, the concentration of the dilute phase is expected to remain constant once the saturation concentration (c-sat) is reached.

      In our study, the sedimentation assay was used as an operational readout to assess concentration-dependent partitioning rather than to quantitatively define equilibrium phase boundaries. The assay involves centrifugation-based separation of supernatant and pellet fractions followed by SDS–PAGE analysis, and therefore does not necessarily report the equilibrium concentrations of coexisting dilute and dense phases. In particular, this approach can be influenced by incomplete physical separation of phases, kinetic trapping, and redistribution of material during handling, especially in systems where condensate maturation or internal reorganization occurs on longer timescales.

      Consequently, the apparent increase in the supernatant fraction with increasing total protein concentration likely stems from kinetic limitations and inherent technical constraints of the sedimentation assay, rather than a genuine deviation from classical phase separation behavior. These caveats are now explicitly clarified in the Methods section, with similar limitations of centrifugation-based assays for defining equilibrium phase behavior of biomolecular condensates reported previously.

      (b) Figure 4: The NMR comparisons appear to be primarily qualitative, lacking quantitative analyses such as chemical shift perturbation (CSP) and intensity ratio plots, which would offer deeper mechanistic insights. The NMR spectra detailing interactions among the IDR domains need to be quantified.

      We thank the reviewer for the suggestion. We have now performed quantitative CSP analyses for the NMR data shown in Fig. 4, and the corresponding CSP plots have been added to the revised manuscript (Fig. S7).

      As expected for interactions mediated by intrinsically disordered regions involved in phase separation, the observed CSPs are generally small. Notably, the CSP profile of IDRa closely matches that observed for the full-length IDR, whereas IDRb and IDRc show minimal perturbations. These results indicate that the interaction is primarily mediated by IDRa, with little contribution from the remaining regions.

      Peak intensity analyses were also examined but did not reveal additional residue-specific trends. Together, the quantitative CSP data support our conclusion that the interaction is weak, dynamic, and region-specific, consistent with an IDR-driven, phase-separation-related mechanism. We add this statement in method: CSPs were calculated in Hz at 600 MHz using the following equation:

      Minor comments:

      (1) Line 59-60: The Authors mention the HUSH-complex and then the MORC protein family, but do not discuss the relation between the two.

      We thank the reviewer for this comment. We have revised the Introduction to explicitly state that MORC2 may serve as a component of the HUSH complex and to clarify the functional relationship between MORC family proteins and HUSH-mediated transcriptional repression.

      (2) Line 74: 'Despite their structural similarities...', similarities between what all?

      We agree that this statement was ambiguous. We have revised the text to explicitly specify that the comparison refers to structural similarities among MORC family members.

      (3) Line 75: 'MORC-mediated repression remains...', this is the first time the word 'repression' is mentioned in the text and directly as an outstanding question.

      We have revised the Introduction to introduce the concept of transcriptional repression earlier and to provide appropriate context before posing it as an outstanding question.

      (4) The third paragraph does address issues in comments 1 and 3 to some extent, but the introduction needs some restructuring to provide a proper flow of information.

      We agree that the Introduction required restructuring. We have revised this section to improve logical flow, better integrate prior studies, and more clearly articulate the motivation and scope of the present work.

      (5) Line 83-85: How does the presence of IDRs suggest potential regulatory mechanisms?

      We have revised this sentence to clarify that IDRs may contribute to regulatory mechanisms by enabling multivalent and dynamic interactions, rather than implying that IDRs inherently confer regulatory function or phase separation capability.

      (6) Line 106-107: 'To determine whether MORC2 has N- and C-terminal dimerization interfaces similar to those...', reference 14 has already established that CC3 (denoted as CC4 in ref 14) is responsible for dimerization. Consider acknowledging their work in this regard?

      We thank the reviewer for this reminder. We have now explicitly acknowledged Ref. 14, which previously established the role of CC3 (denoted CC4 in that study) in MORC2 dimerization.

      (7) Lines 117-122: Are the authors comparing morphology from negative stain EM with AlphaFold predicted structure (Figure S1a and S1b)? If so, providing a zoomed-in inset from Figure S1a would be helpful.

      Yes, the comparison was intended to relate the negative-stain EM morphology to the AlphaFold-predicted architecture. We have added a zoomed-in inset in Fig. S1a to facilitate clearer comparison.

      (8) Line 152-153: '...even under varying physiological conditions', what are these varying conditions? Are the authors trying to point towards any of their specific results?

      We have revised this phrase to explicitly refer to variations in salt concentration and protein concentration tested in our in vitro assays.

      (9) Line 154-155: 'The dimeric assembly of CC3 is essential for maintaining the structural integrity of the protein', if it has been established, then please provide a reference.

      We thank the reviewer for this suggestion. For MORC family proteins, C-terminal coiled-coil–mediated dimerization is necessary for correct homodimer formation and functional stability (Xie et al., 2019, Cell Commun Signal. 17:160, Ref 14 in the revised manuscript).

      (10) Line 159-161: 'we noticed a long unstructured region at its C-terminus (Figure S1b), a characteristic often associated with proteins capable of phase separation25.', again authors are generalizing a statement which is, in most cases, context-dependent. For example, ref 25 mentions that unstructured regions or IDRs serve as a scaffold for multivalent interactions.

      We agree with the reviewer and have revised this sentence to avoid generalization. The revised text now emphasizes that IDRs may facilitate multivalent interactions in a context-dependent manner, rather than being intrinsically indicative of phase separation. Additionally, we have explicitly cited the mechanistic insight from Reference 25 that IDRs serve as scaffolds for multivalent interactions, to strengthen the logical link between the structural feature and its potential functional relevance.

      (11) Methods section for NMR (Line 665-667) mentions that nucleotides were added to a final concentration of 10 mM. There is no figure or section for MORC2 NMR with added nucleotides/DNA.

      We thank the reviewer for pointing this out. The nucleotide (ATP) addition was part of preliminary NMR trials and is not directly associated with the figures presented. We have deleted this in the Methods section to avoid confusion.

      (12) Line 285-294: Authors compare the effect of DNA binding on the phase separation of both MORC2FL and MORC2 CTDdeltaCW and conclude that DNA-induced condensation is primarily mediated through interactions with the IDR-NLS region. This appears not to be backed by proper control experiments. The authors do not show whether DNA binding mediates any phase separation for the isolated NTD or not? Similarly, what is the effect of DNA binding on MORC2 deltaIDR?

      We thank the reviewer for this insightful comment and agree that additional controls are essential for rigorously dissecting the contribution of DNA binding to MORC2 phase separation. Our interpretation that DNA-enhanced condensation is primarily mediated through the IDR–NLS region was based on comparative analyses of MORC2FL and MORC2 CTDΔCW, together with EMSA results demonstrating that DNA binding activity is conferred by the IDR–NLS–containing region. We acknowledge, however, that DNA binding alone is not sufficient to infer phase separation behavior.

      To address this point, we have performed additional analyses using the isolated NTD’ (residues 1–536) and MORC2 ΔIDR–NLS mutants (Fig. S6). The isolated NTD’ exhibited detectable DNA binding [4] but did not undergo DNA-induced condensation under conditions while MORC2FL or MORC2 CTDΔCW (residues 537-1032) readily formed condensates, indicating that DNA binding by itself is insufficient to drive phase separation. In parallel, MORC2 ΔIDR–NLS mutants showed severely compromised solubility and stability in vitro, which limited their quantitative characterization in phase separation assays. Nevertheless, under the conditions tested, these mutants did not display DNA-enhanced condensation comparable to MORC2FL.

      Taken together, these observations support a model in which the IDR–NLS region plays a critical role in coupling DNA binding to condensation, while additional domains are required to sustain robust phase separation. We have revised the manuscript text to clarify the experimental scope and to avoid overinterpreting the contribution of DNA binding in the absence of fully reconstituted control systems.

      (13) How did the authors assign the backbone amide NMR chemical shifts for MORC2?

      Backbone assignments of MORC2 IBD (1004-1032) were obtained using SOFAST versions of standard triple-resonance experiments, including HNCACB and CBCACONH, recorded at 298 K. Residual assignment ambiguities were resolved using [15] N-edited HMQC-NOESY-HMQC spectra.

      (14) Line 256: 'The partial compaction of IDRa...', what does the author mean here with 'partial compaction'? How did they measure compaction here?

      Regarding the term “partial compaction” mentioned previously, we apologize for the typographical error this phrase was erroneously used in place of “key component”.

      (15) Line 312-315: Why is there even a MORC2 readout for MORC2 KO cells with only EGFP? Also, the authors suggest that IDR deletion may impair mRNA stability or transcription; however, the expression levels of MORC2 deltaIDR and MORC2 deltaCC3 do not appear drastically different in Figure 3a.

      We thank the reviewer for raising these points. The apparent MORC2 signal in MORC2 knockout cells transfected with EGFP alone is due to the presence of residual MORC2 mRNA. Although CRISPR–Cas9–mediated knockout introduces a frameshift that prevents MORC2 protein expression, the mRNA can still be detected by RNA-seq. This is because nonsense-mediated decay (NMD), which targets transcripts with premature stop codons for degradation, is not always 100% efficient. Therefore, some MORC2 transcripts remain and produce detectable RNA-seq reads, even though no functional protein is expressed.

      Regarding the apparent discrepancy in expression levels, Fig. 3a displays only EGFP-positive cells, within which the fluorescence intensity of MORC2ΔIDR and MORC2ΔCC3 appears comparable to that of WT MORC2. However, the overall fraction of EGFP-positive cells is markedly reduced for these mutants compared to WT. Thus, while expression levels among successfully transfected cells are similar, fewer cells express detectable levels of the ΔIDR or ΔCC3 constructs across the total population. We therefore interpret this reduction in EGFP-positive cell fraction as reflecting impaired expression efficiency of these mutants, potentially arising from altered transcriptional output, mRNA stability, or protein stability. We have revised the manuscript text to clarify this distinction and to avoid overinterpreting the underlying mechanism in the absence of direct measurements.

      Author response image 1.

      EGFP, EGFP–MORC2 (FL), EGFP–MORC2 (ΔCC3), and EGFP–MORC2 (ΔIDR) were re-expressed in MORC2-knockout HeLa cells. Confocal imaging revealed that full-length MORC2 formed condensates in the nucleus, whereas mutants lacking either the CC3 or IDR domain failed to exhibit such behavior. Notably, under identical experimental conditions, we observed a marked reduction in the transfection efficiency of the EGFP-MORC2 (ΔIDR) construct. In contrast to the other variants, EGFP signals for ΔIDR were detectable in only a small fraction of the total cell population, despite consistent DNA loading and protocol synchronization. This observation suggests that the IDR might be required not only for biomolecular condensation but also for maintaining the steady-state levels of the MORC2 mRNA/protein or overall cellular fitness.

      (16) Line 330: 'MORC2 deltaCC3 failed to repress any of the 18 downregulated targets...'. This does not appear to be entirely true as repression of some targets (LBH, TGFB2, GADD45A) are closer to MORC2 FL than the EGFP control.

      We thank the reviewer for pointing out this inconsistency and for highlighting the need for precise wording. We have updated the dataset and revised the text to describe the results more accurately. We now describe that the mutants impair MORC2FL-mediated transcriptional regulation, consistent with the overall trend observed across these target genes.

      (17) Line 347-350: Based on the percent of cells with condensates, the authors conclude that CMT2Z-linked E236G and SMA-linked T424R mutants promote MORC2 phase separation. Again, the effect of these mutations on MORC2 condensation in cells may be direct or indirect. This can be investigated by comparing the in vitro effect of these mutations on MORC2 phase separation.

      We thank the reviewer for raising this important point and fully agree that the effects of disease-associated MORC2 mutations on condensate formation in cells may arise from either direct alteration in intrinsic phase separation propensity or indirect influences mediated by the cellular environment.

      In our study, disease-associated MORC2 mutants were assessed for condensate formation in HEK293F cells. Attempts were made to characterize these mutants in vitro; however, the E236G mutant exhibited markedly reduced solubility and stability upon purification, which precluded reliable in vitro phase separation analysis. We therefore evaluated the impact of E236G in cells and found that this mutation significantly impaired the dynamics of nuclear MORC2 condensates. For the T424R mutant, we note that its intracellular condensates displayed FRAP recovery kinetics comparable to those of WT MORC2, suggesting broadly similar dynamic properties of the assemblies formed in cells, but not necessarily implying a direct enhancement of intrinsic phase separation.

      In light of these considerations, we have revised the text in Lines 347–350 to avoid attributing a direct causal role of these mutations in promoting MORC2 phase separation. Instead, we now describe the observed increase in the fraction of cells containing condensates as a descriptive cellular correlation. We further emphasize that systematic in vitro characterization of disease-associated MORC2 mutants will be required to distinguish direct from indirect effects and represents an important direction for future investigation.

      (18) The discussion section lacks referencing to individual figures in the results section as well as previous literature.

      We agree with the reviewer that the Discussion would benefit from clearer integration with both the Results figures and prior literature. In the revised manuscript, we have substantially restructured the Discussion to explicitly reference key figures when interpreting experimental findings and to more clearly distinguish conclusions drawn from specific datasets. In addition, we have expanded citations to previous studies where relevant, particularly in the context of MORC2 DNA binding, ATPase regulation, chromatin association, and disease-linked mutations. These revisions aim to better situate our findings within the existing literature and to guide readers more clearly between experimental observations and their interpretation.

      Reviewer #3 (Public review):

      Summary:

      The manuscript by Zhang et al. demonstrates that MORC2 undergoes liquid-liquid phase separation (LLPS) to form nuclear condensates critical for transcriptional repression. Using a combination of in vitro LLPS assays, cellular studies, NMR spectroscopy, and crystallography, the authors show that a dimeric scaffold formed by CC3 drives phase separation, while multivalent interactions between an intrinsically disordered region (IDR) and a newly defined IDR-binding domain (IBD) further promote condensate formation. Notably, LLPS enhances MORC2 ATPase activity in a DNA-dependent manner and contributes to transcriptional regulation, establishing a functional link between phase separation, DNA binding, and transcriptional control. Overall, the manuscript is well-organized and logically structured, offering mechanistic insights into MORC2 function, and most conclusions are supported by the presented data. Nevertheless, some of the claims are not sufficiently supported by the current data and would benefit from additional evidence to strengthen the conclusions.

      Thank you for your insightful review and constructive suggestions, which have been invaluable in refining our manuscript.

      The following suggestions may help strengthen the manuscript:

      Major comments:

      (1) The central model proposes that multivalent interactions between the IDR and IBD promote MORC2 LLPS. However, the characterization of these interactions is currently limited. It is recommended that the authors perform more systematic analyses to investigate the contribution of these interactions to LLPS, for example, by in vitro assays assessing how the IDR or IBD individually influence MORC2 phase separation.

      We appreciate the reviewer’s insightful comment regarding the characterization of IDR–IBD interactions. In this study, we combined NMR spectroscopy, domain deletion analysis (in vivo), and in vitro phase separation assays to demonstrate that interactions between the IDR and IBD contribute to MORC2 condensate formation. To systematically assess the individual contributions of the IDR and IBD to MORC2 phase separation, we performed in vitro reconstitution assays using purified domain constructs (Fig. S6). Neither the isolated IDR nor the IBD alone exhibited phase separation under buffer conditions approximating the physiological environment, indicating that each domain is individually insufficient to drive condensation. Upon the addition of 10% PEG8000, phase separation was selectively observed for the IDR but not for the IBD, suggesting that the IDR possesses an intrinsic propensity for phase separation that can be enhanced by crowding molecular. Importantly, when the IDR and IBD were mixed, phase separation was robustly induced, supporting a model in which cooperative inter-domain interactions between the IDR and IBD promote MORC2 condensation. In the absence of PEG, no phase separation was observed for the IDR–IBD mixture. These observations imply that IDR–IBD interactions cannot drive phase separation on their own, but require cooperation with CC3-mediated dimerization to achieve this process, which is the central point we wish to emphasize.

      (2) The authors mention that DNA binding can promote MORC2 LLPS. It is recommended that they generate a phase diagram to systematically assess how DNA influences phase separation.

      We agree that constructing a full phase diagram would provide a more systematic evaluation of the effect of DNA on MORC2 phase separation. In the current study, we assessed DNA-dependent condensation across multiple protein and DNA concentrations, which consistently showed that DNA enhances MORC2 phase separation. At low protein concentration (0.5 µM), phase separation requires sufficient DNA, whereas increasing either DNA or protein concentration promotes liquid droplet formation. At high DNA and protein concentrations, amorphous structures dominate, indicating a transition away from dynamic assemblies. We have clarified this point in the Results and Discussion sections and now note that a comprehensive phase diagram analysis represents an important direction for future work.

      (3) The authors use the N39A mutant as a negative control to study the effect of DNA binding on ATP hydrolysis. Given that N39A is defective in DNA binding, it could also be employed to directly test whether DNA binding influences MORC2 phase separation.

      We thank you for your constructive suggestions. The purified wild-type MORC2(1–603) exhibited weak but detectable ATPase activity, whereas the N39A mutant was completely inactive [5]. Based on this characteristic, the N39A mutant was used as a negative control for the ATP-binding-deficient mutant in this study [3]. However, no evidence has been provided to demonstrate that the N39A mutant is defective in DNA binding. Importantly, both our results and previous studies [5-6] indicate that MORC2 engages DNA via multiple domains, suggesting that a single-point mutation is unlikely to significantly compromise its overall DNA-binding capacity.

      (4) Many of the cellular and in vitro LLPS experiments employ EGFP fusions. The authors should evaluate whether the EGFP tag influences MORC2 phase separation behavior.

      We appreciate the reviewer’s concern regarding the potential influence of the EGFP tag. The use of EGFP fusions in our study was primarily to maintain consistency with the in-cell experiments. Importantly, we confirmed that EGFP alone does not undergo phase separation in cells, and this observation is consistent with previous studies [7]. Additionally, in vitro phase separation of MORC2 was independently validated using Cy3–labeled CTD (Fig. S5), which recapitulated the condensate formation seen with EGFP-fused protein. Together, these results indicate that the EGFP tag does not significantly influence MORC2 phase separation, supporting the validity of our conclusions.

      Reviewer #3 (Recommendations for the authors):

      (1) The authors claim to have obtained nucleic acid-free protein, but no data are provided to support this assertion. It is recommended that they include appropriate validation to confirm the absence of nucleic acids.

      We thank the reviewer for highlighting this point. To validate that the purified MORC2 protein is indeed free of nucleic acid contamination, we have additional experimental evidence (e.g., A260/280 measurements, agarose gel analysis, or EMSA in Fig. 5), which has been added to the Methods section and Table S2.

      Note: Agarose gel analysis for MORC2 constructs to confirm the absence of nucleic acids. The pET32 vector as the positive control, the protein preparation for analysis is 0.05 mg. E means E. coli and H means HEK293F.

      (2) The FRAP recovery curves are not normalized to 0, making comparison difficult. The authors should normalize the post-bleach intensity to 0 and re-plot the curves to allow a more standard interpretation of mobile fractions.

      We agree with the reviewer and have now normalized the FRAP recovery curves by setting the post-bleach intensity to 0. The revised plots are presented in the Figures (2f, j, l; 6c, 7f), allowing for more direct comparison of mobile fractions across different conditions.

      (3) The HSQC spectra for IBD appear inconsistent: the peak positions in Fig. 4C do not align with those shown in panels D-F. The authors should verify the spectral assignments and ensure consistency across figures.

      We thank the reviewer for pointing this out. The apparent inconsistency arose from the fact that different spectral regions were displayed in Fig. 4c versus Fig. 4d-f for visualization purposes, which may have given the impression of mismatched peak positions. The spectral assignments themselves are consistent across all panels.

      To avoid confusion, we have now adjusted the spectral window shown in Fig. 4c to match that used in Fig. 4d-f. The revised figure ensures consistent presentation of the same spectral region across all panels.

      Reference:

      (1) Zhang, Y., Stöppelkamp, I., Fernandez-Pernas, P. et al. Probing condensate microenvironments with a micropeptide killswitch. Nature 643, 1107–1116 (2025).

      (2) Fendler NL, Ly J, Welp L, et al. Identification and characterization of a human MORC2 DNA binding region that is required for gene silencing. Nucleic Acids Res.53(4):gkae1273 (2025).

      (3) Tchasovnikarova, I., Timms, R., Douse, C. et al. Hyperactivation of HUSH complex function by Charcot–Marie–Tooth disease mutation in MORC2. Nat Genet 49, 1035–1044 (2017).

      (4) Douse, C. H. et al. Neuropathic MORC2 mutations perturb GHKL ATPase dimerization dynamics and epigenetic silencing by multiple structural mechanisms. Nat Commun 9, 651 (2018).

      (5) Tan, W., Park, J., Venugopal, H. et al. MORC2 is a phosphorylation-dependent DNA compaction machine. Nat Commun 16, 5606 (2025).

      (6) Sánchez-Solana B, Li DQ, Kumar R. Cytosolic functions of MORC2 in lipogenesis and adipogenesis. Biochim Biophys Acta. 1843(2):316-326 (2014).

      (7) Li, C.H., Coffey, E.L., Dall’Agnese, A. et al. MeCP2 links heterochromatin condensates and neurodevelopmental disease. Nature 586, 440–444 (2020).

    1. Reviewer #4 (Public review):

      Summary:

      In this manuscript, the authors present data describing the development of a model of ALS in rhesus macaques. They use a viral intersectional model to overexpress TDP-43 in a population of motor neurons and then study the spread of the pathology about 7 months later. They demonstrate that both the cervical spinal cord and motor cortex (new and old M1) are full of TDP-43, suggesting that the pathology spreads from the single motor pool to presumably related neurons.

      Strengths:

      This is a super-important study in two main ways:

      (1) This could be the birth of a really important model, one that is really needed for making progress in understanding ALS and the development of therapeutics. There are shortfalls with all the rodent models. Models dependent on cell cultures are superb for understanding cell-autonomous processes, but miss out on connectivity, particularly the long-range connectivity. Organoids may ultimately prove to be beneficial, but they would need cortex, spinal cord, and muscle, and translatability from them is not assured. So a NHP model is needed, and this may be it. Furthermore, the Methods are meticulously described and will undoubtedly facilitate reproducibility.

      (2) The concept of the spread of pathology has been proposed for some time, I think, based initially on the detailed clinical observations of Ravits and colleagues. The authors have looked at this directly and provide supporting evidence for this interesting hypothesis. They show spread locally and contralaterally in the spinal cord (although a figure would be nice) and to the motor cortex.

      Taking only these 2 points into account is more than sufficient for me to be enthusiastic about this work.

      Weaknesses:

      I'd like to make a couple of points that if addressed, could, in my view, help the authors strengthen this work.

      (1) We don't know how many MNs were transduced by the rAAV. There was no tdTom expression, for whatever reason. The authors show an image of a control experiment with a single MN transduced, but there should be a red motor pool, at least in the control experiments. The impression that I get is that very few were transduced, and, in my mind, this makes the findings even more interesting - maybe you don't need many "starter" MNs.

      (2) Continuing on this point, this leads the authors to conclude that all BR MNs have died. They support this by the reduced MN count (see point 3). Firstly, do we know how many BR MNs there are in the rhesus macaque, and does the reduction seen correspond to this number? Secondly, and more importantly, the muscle looks normal on MRI at 28 weeks - it does not look like a denervated muscle. The authors state that it has maybe been reinnervated, but by what, if all the BR MNs are dead? This does not seem like a plausible explanation to me. Muscle histology, NMJs, and fibre typing would have been useful to understand what's going on with the MNs. (And electrophysiology would have been wonderful, but beyond the scope of this study.)

      (3) Some MN biologists, like me, fuss a lot about how to count MNs, which is almost as difficult as counting the number of angels on the head of a pin. Every method has its problems. Focusing on the two methods here: (a) ChAT immunohistochemistry is pretty good in healthy states, but we don't know what happens to ChAT expression in different diseases, particularly when you have a new model. If its expression is decreased, then it is not a good marker for MNs; (b) Identifying MNs based on the size and morphology of neurons in the ventral horn is also insufficient. For example, ~30% of neurons in a typical pool are small gamma MNs, and a significant proportion (depending on the muscle) of the remainder will be small alpha MNs. So what one is counting is, at best, the large alpha MNs, not all the MNs in a pool. And in ALS, it's these largest MNs that are affected at the earliest stages. The small ones might be fine. So results will be skewed. (Hence, it would be interesting to see if the muscle had a higher proportion of Type I fibres after being reinnervated by S-type MNs.)

      (4) Statistics. These are complex experiments looking at the spread of a disease. The experimental unit is therefore the monkey, n=2. In each monkey, multiple sections are analysed, which are key technical replicates and often summative. For example, do we care about the average cell number in Figures 4D, E, 5 I, J or 6G, H, or rather the total cell number? Do the error bars mean anything? To be clear, I am by no means minimising the importance of the overall convincing findings. But I do not think this statistical analysis is particularly meaningful.

    2. Author response:

      Public Reviews:

      Reviewer #1 (Public review): 

      Summary: 

      The authors have used a macaque (two animals only) to follow the migration of 'seeded' TDP43 protein in neuronal pathways - thus mimicking the spread of ALS in the human CNS. Previous experiments in rodents failed to demonstrate this, posing interesting and important biological differences, possibly related to the UMN-LMN system in higher order apes and humans. 

      Strengths: 

      An important step forward. 

      Weaknesses: 

      No weaknesses were identified by this reviewer. Only 2 animals were used, but that is appropriate given the sensate status of the macaque. In the opinion of this reviewer, the results are entirely convincing. 

      Reviewer #2 (Public review): 

      Summary: 

      There are astonishingly few papers trying to reproduce the process of initiation and spreading that Braaks studies have suggested and postulated. The authors should be applauded for pioneering such a difficult experiment. They overexpressed the TDP-43 protein in the motor neuron pool of the brachioradialis muscle and showed that by this technique, motor neurons in this pool died, and the muscle got denervated. They had evidence of a spreading process from the spinal cord to the cortex, demonstrated by showing widespread deposits of phosphorylated TDP-43 bilaterally in the cervical cord and the motor cortex. By their experiment, they created a dying-backwards model, not a model of corticofugal spread, like that shown by Braak. No muscle weakness was observed, not even in the brachioradialis. 

      Strengths: 

      The strength of this innovative study is the fact that this spreading experiment uses the phylogenetically young connectome of primates (macaques). They also made the thought-provoking observation of spreading from the cord to the motor cortex, not the corticofugal spread model observed by Heiko Braak. This is thought-provoking because this enables the observer to compare their model with the findings in humans. 

      Weaknesses: 

      The following aspects are not a weakness but need to be better explained for the interested reader - and potentially improved in future studies for which the authors laid the foundation: 

      (1) Why do the authors use the brachioradialis motor neuron pool to overexpress TDP-43? More is known about other muscles and how they are embedded in the motor connectome of primates. Why not the biceps brachii or the hand extensors or - even better - the small muscles of the hand? These are known to be strongly monosynaptically connected with the motor cortex. The authors should explain this. I am unclear if there was a specific reason which I did not see or understand. In my view, the brachioradialis is not the best representative of the primate connectome, for example, to examine this model and compare it with the corticofugal spread. 

      The brachioradialis muscle was chosen primarily for reasons of animal welfare; our concern when designing the experiments was that the muscle we chose for injection might become very wasted and weak before the experiment had been completed. If we had injected a hand muscle, this would have affected manipulation, feeding and grooming behaviours, whereas had we injected biceps brachii or forearm extensors, this would have affected more important behaviours requiring strength for body support in the home cage (e.g. climbing, swinging, etc.). The advantage of choosing brachioradialis is that there is some functional redundancy; in macaques, compared to biceps brachii, brachioradialis has a relatively minor role in elbow flexion and supination of the forearm. We therefore reasoned that there should be physiological compensation for any weakness in brachioradialis, and thus minimal effects on normal behaviour.

      A secondary practical consideration was the importance of good quality MR imaging of the injected muscle and the positioning of the focussing coil; because of the physical constraints related to the monkey sitting in our narrow-bore scanner, the forearm muscles were the optimal choice. 

      With reference to the ‘primate connectome’, whilst hand muscles are known to have strong cortico-motoneuronal connections, we have shown previously that monosynaptic corticomotoneuronal connections are as strong in muscles innervated by the deep radial nerve (like brachioradialis) as in intrinsic hand muscles (Witham et al, 2016).

      Finally, for the purposes of these experiments, all we required was a method for inoculating TDP-43 into a motor neuron pool within the spinal cord, without direct surgical trauma to the spinal cord. Our aim was to test the hypothesis that extracellular TDP-43 is sufficient to cause spreading neuronal changes in macaque, similar to those observed in human ALS/MND; our aim was not to replicate the actual pattern of human MND observed clinically.

      These points will be addressed in a revised version of the manuscript. 

      (2) In the Braaks experiment, only (seemingly soluble) non-phoshorylated TDP-43 "crossed" synapses. Phosphorylated TDP-43 did not do this. The authors of this study saw phosphorylated TDP43 in motor neurons and the cortex. Is there any potential explanation for how it crosses synapses? If it really does, there is an obvious difference to the human situation which needs to be emphasized and explained (in the future). 

      To clarify, there was no evidence of phosphorylated TDP-43 crossing synapses. It is more likely that excess non-phosphorylated TDP-43 crossed synapses, and that this then subsequently led to TDP-43 phosphorylation.  

      (3) There were significant deposits of phosphorylated TDP-43 in oligodendrocytes in humans. Whilst I understand that one experiment cannot solve every question - I am curious about whether the authors saw anything in oligodendrocytes? 

      We have not looked at this.

      (4) Which was the pattern of damage? Of course, this pattern is not likely to have a monosynaptic pattern - like in humans........but was there a pattern? Did it have a physiologically meaningful basis? Was there any relation to the corticofugal monosynaptic pattern? What are the differences? The authors speak of "multiple waves". Does this mean that if this were a corticofugal model, for example, oculomotor neurons would also degenerate? 

      The description of ‘multiple waves’ in paragraph 2 of the discussion section is entirely hypothetical, based on the assumption that there are different mechanisms by which TDP-43 spreads through the nervous system, from slow local spread by diffusion to more rapid long-range axonal spread to widely separated regions. For the neuropathological staging analysis, we therefore looked at different brain regions (hypoglossal nuclei, reticular formation, inferior olives, frontal cortex, temporal cortex and hippocampal formation). This analysis only showed loss of motor neurons in the spinal cord ipsilateral to the side of the muscle injections, in segments consistent with the location of brachioradialis motoneurons. We did not demonstrate a ‘pattern of damage’ as described in humans in our experiments because this is a pre-symptomatic pre-clinical model, with no established ‘damage’ from each wave. We speculate that this is because animals were terminated too early in the disease process.

      However, whilst there was no established neuronal degeneration outside the cervical spinal cord, the observation that there were more pTDP-43 positive Betz cells in left (contralateral to the brachioradialis injection) New M1 than Old M1 (see Figure 6I and J) would support spread via monosynaptic connections to motoneurons; New M1 is where most monosynaptic cortico-motoneuronal connections originate.

      Reviewer #3 (Public review): 

      Summary: 

      In this paper by Jones and colleagues, a non-human primate model is described in which wild-type TDP-43 is expressed in the cervical spinal cord. This gave rise to loss of motor neurons in the ventral horn at that level in the cervical spinal cord. MRI of the muscles allowed to see increased intensity in the mostly affected brachioradialis muscle, suggesting this muscle becomes denervated. At the neuropathological level, TDP-43 and pTDP-43 staining in the cytoplasm is increased, not only at the specific level of the cervical spinal cord, but also at a distance. 

      Strengths: 

      A clear strength is the state-of-the art focal expression of the TDP-43 transgene at a focal site in the cervical spinal cord. This is achieved by combining a general expression of a flipped loxP flanked TDP-43 vector using AAV9 intrathecal administration, followed by an intramuscular AAV2 hSyn CRE-TdTomato vector in the brachioradialis muscle in order to induce focal recombination and expression of TDP-43 in motor neurons innervating this muscle on one side. 

      Another strength is the non-human primate background, which is much closer to the human situation. 

      Weaknesses: 

      Given the complexity and cost of the model, the n is very low. 

      As is common in most studies in non-human primates, we have carried out all statistical analysis within one animal (e.g. the comparison of motoneuron numbers between left and right cord). We then show that results are reproducible in two animals. Although the number of animals is lower than in a typical rodent study, we see this as an advantage of the model, adhering to the 3Rs principle of ‘reduction’.

      The design of the experiments and the results shown about the toxicity induced by this focal TDP-43 expression do not allow us to conclude that it is a good model for ALS for several reasons. It is not clear that the TDP-43 overexpression results in spreading weakness or in spreading motor neuron loss. The neuropathological changes described suggest that there is a kind of stress response, which extends to regions away from the site of primary damage, but more is needed to provide convincing evidence that there is spreading of disease pathology reminiscent of human ALS. 

      As already noted in our response to Reviewer 2 (point 1), animal welfare is an important consideration when designing these complex experiments in primates. We could not therefore justify allowing the animals to survive until extensive wasting and weakness were evident, recapitulating the human disease. 

      The model developed in these experiments is therefore a pre-symptomatic pre-clinical model, in which animals are terminated before pathology leading to widespread motor neuron loss is evident. At post mortem we do have evidence of motor neuron loss in the segments supplying brachioradialis (C4-C8).

      Stress of various forms, including blunt trauma (e.g. Anderson et al, 2021), stab/electrode insertion injury (e.g. Zambusi et al, 2022), chemical (e.g. arsenite) exposure (e.g. Huang et al, 2024), or hypoxia (Marcus et al, 2021) can result in pathological nucleocytoplasmic translocation of TDP-43. In our model, there was no direct trauma to the brain or spinal cord ante mortem, excluding one major cause of tissue stress. Hypoxia during the process of euthanasia is possible, but we would expect there would not be enough time before death for this to manifest as TDP-43 translocation. In the literature TDP-43 translocation due to stress is diffuse; we have demonstrated that in our model the TDP-43 pathology is not diffuse but selective. For example, there was no evidence of disease in the oculomotor nuclei; in the primary motor cortex (M1) there are significantly more pathological changes in the evolutionarily younger ‘NewM1’ compared to the neighbouring ‘OldM1’.

      It is therefore improbable that our findings could be explained by ‘a kind of stress response’. Our findings are better explained by spread of the TDP-43 protein.

      Reviewer #4 (Public review): 

      Summary: 

      In this manuscript, the authors present data describing the development of a model of ALS in rhesus macaques. They use a viral intersectional model to overexpress TDP-43 in a population of motor neurons and then study the spread of the pathology about 7 months later. They demonstrate that both the cervical spinal cord and motor cortex (new and old M1) are full of TDP-43, suggesting that the pathology spreads from the single motor pool to presumably related neurons. 

      Strengths: 

      This is a super-important study in two main ways: 

      (1) This could be the birth of a really important model, one that is really needed for making progress in understanding ALS and the development of therapeutics. There are shortfalls with all the rodent models. Models dependent on cell cultures are superb for understanding cell-autonomous processes, but miss out on connectivity, particularly the long-range connectivity. Organoids may ultimately prove to be beneficial, but they would need cortex, spinal cord, and muscle, and translatability from them is not assured. So a NHP model is needed, and this may be it.

      Furthermore, the Methods are meticulously described and will undoubtedly facilitate reproducibility. 

      (2) The concept of the spread of pathology has been proposed for some time, I think, based initially on the detailed clinical observations of Ravits and colleagues. The authors have looked at this directly and provide supporting evidence for this interesting hypothesis. They show spread locally and contralaterally in the spinal cord (although a figure would be nice) and to the motor cortex. 

      Taking only these 2 points into account is more than sufficient for me to be enthusiastic about this work. 

      Weaknesses: 

      I'd like to make a couple of points that if addressed, could, in my view, help the authors strengthen this work. 

      (1) We don't know how many MNs were transduced by the rAAV. There was no tdTom expression, for whatever reason. The authors show an image of a control experiment with a single MN transduced, but there should be a red motor pool, at least in the control experiments. The impression that I get is that very few were transduced, and, in my mind, this makes the findings even more interesting - maybe you don't need many "starter" MNs. 

      Unfortunately, we cannot know how many motoneurons were transduced.

      However, the reviewer may be correct, that it is actually only a small fraction of the brachioradialis pool. This is supported by the evidence for rather focal denervation seen on MRI.

      (2) Continuing on this point, this leads the authors to conclude that all BR MNs have died. They support this by the reduced MN count (see point 3). Firstly, do we know how many BR MNs there are in the rhesus macaque, and does the reduction seen correspond to this number? Secondly, and more importantly, the muscle looks normal on MRI at 28 weeks - it does not look like a denervated muscle. The authors state that it has maybe been reinnervated, but by what, if all the BR MNs are dead? This does not seem like a plausible explanation to me. Muscle histology, NMJs, and fibre typing would have been useful to understand what's going on with the MNs. (And electrophysiology would have been wonderful, but beyond the scope of this study.) 

      To clarify, we did not conclude that all brachioradialis motor neurons had died, rather that all transfected brachioradialis motor neurons pool had died. As noted above, when these cells die and the muscle is denervated, the MRI signal changes occupy only a small volume of the muscle and are transient. We would not expect to see long-term MRI changes in muscle anatomy after this limited denervation-reinnervation event. 

      Analysis of muscle histology, including fibre typing, is outwith the scope of this initial paper reporting the model; we hope that this will form the basis of a future publication.

      (3) Some MN biologists, like me, fuss a lot about how to count MNs, which is almost as difficult as counting the number of angels on the head of a pin. Every method has its problems. Focusing on the two methods here: (a) ChAT immunohistochemistry is pretty good in healthy states, but we don't know what happens to ChAT expression in different diseases, particularly when you have a new model. If its expression is decreased, then it is not a good marker for MNs; (b) Identifying MNs based on the size and morphology of neurons in the ventral horn is also insufficient. For example, ~30% of neurons in a typical pool are small gamma MNs, and a significant proportion (depending on the muscle) of the remainder will be small alpha MNs. So what one is counting is, at best, the large alpha MNs, not all the MNs in a pool. And in ALS, it's these largest MNs that are affected at the earliest stages. The small ones might be fine. So results will be skewed. (Hence, it would be interesting to see if the muscle had a higher proportion of Type I fibres after being reinnervated by S-type MNs.) 

      This is an interesting point, and we agree that each method used to quantify MN number carries its own limitations. The problem of MN identification is heightened in a MND-like pathological state, especially when considering evidence of reduced ChAT activity in spinal motoneurons in end-stage disease in post mortem human samples (Oda et al, 1995), and more recent evidence from Casas et al. (2013), who demonstrated early presymptomatic reduction in ChAT expression in SOD1G93A mice. It is important to note that this was a modest reduction, not complete abolition of signal (76% of control levels). ChAT immunoreactivity was still present and motor neurons were still identifiable as ChAT-positive at this pre-clinical stage of disease. As counts in our study were performed based on detecting ChAT in cells, it seems unlikely that we would miss cells. However, we cannot rule this out. If indeed this did occur, it would mean that the reduced motoneuron counts which we observed reflect not only cell death, but also profound motoneuron dysfunction which is presumably the proximal precursor to cell death.

      We acknowledge that size-based criteria applied to ChAT-positive neurons will preferentially capture large alpha motor neurons, and that gamma motor neurons and small alpha motor neurons are likely underrepresented in our counts. Our counts therefore reflect the large alpha motor neuron population rather than the total motor neuron pool. We believe that this is not a critical limitation in the context of the present study. Large alpha motor neurons are the population of primary pathological interest in ALS and related MND, being the earliest and most severely affected subtype. The selective vulnerability of fast-fatigable large alpha motor neurons in ALS is well established, and their preferential loss is the defining feature of disease progression in both human post mortem tissue and rodent models (Lalancette-Hébert et al., 2016). In this respect, our size threshold selects for precisely the population whose degeneration is most relevant to the disease phenotype we are modelling. 

      We intend to include comments on these important points in the revised version of the manuscript.

      In response to the final point regarding muscle histology and proportions of Type I fibres, as stated above, reporting of muscle histology, including fibre typing, is planned for a separate publication.

      (4) Statistics. These are complex experiments looking at the spread of a disease. The experimental unit is therefore the monkey, n=2. In each monkey, multiple sections are analysed, which are key technical replicates and often summative. For example, do we care about the average cell number in Figures 4D, E, 5 I, J or 6G, H, or rather the total cell number? Do the error bars mean anything? To be clear, I am by no means minimising the importance of the overall convincing findings. But I do not think this statistical analysis is particularly meaningful. 

      Here, the experimental unit is the tissue slice, mounted on a slide for histological analysis, and not the monkey. All statistical comparisons are made within a single animal. We then show that the findings can be replicated in two animals, both of which show significant results. This is standard approach taken in primate neuroscience, given the need to reduce animal numbers to the minimum consistent with producing convincing results.

    1. On 2026-04-09 21:38:21, user Alizée Malnoë wrote:

      The manuscript by Fridman et al. explores the unexpected finding that Aeromonas jandaei antagonistically employs a Type VI secretion system (T6SS) in a liquid environment. While researching the effector protein Awe1, which forms part of the T6SS apparatus, the authors observed T6SS-dependent intoxication of susceptible bacteria. Using a novel fluorescence-based screening method (named LiQuoR for liquid quantification of rivalry), the authors further determine that this intoxication is contact-dependent, and that contact between kin and non-kin Aeromonas bacteria in liquid is mediated by specific adhesins. Fridman et al. also identify additional marine bacteria capable of inflicting T6SS-mediated intoxication in liquid media, suggesting a mechanism for specific and contact-dependent bacterial competition and positing that such competition in liquid media may be more common in marine bacteria than previously documented. These findings have exciting implications for bacterial antagonism, potentially shifting the paradigm of how we view bacterial interactions in marine environments. We found this study to be well-written, containing high-quality data. Overall, the data presented in this manuscript are done well and support the claims made by the authors. We outline some major and minor adjustments aimed at aiding the clarity of reporting and presentation, strengthening the findings, as well as providing additional context for a broader audience.

      Major Comments<br /> - We are interested in the broader implications of the LiQuoR assay, particularly pertaining to this workflow’s application to different bacteria. The observation that the amount of prey luminescence in WT on solid media grew/increased after 4 h seemed counterintuitive to us (Figure 1E). It seems as if this result could make the workflow less sensitive for experiments done solely on solid media, further explanation of this finding would clarify on the workflows applicability to other solid surface experiments. Is this related to surface area? While this does not change the findings that inhibition is occurring in both liquid and in solid, it would enhance the clarity of these results to provide speculation on why this was seen.<br /> - We are curious about your perspective on the observation that kin-kin aggregation facilitated by CaCl2 supplementation does not increase kin intoxication but does increase non-kin intoxication (Figure 2A). Please speculate on this result in the discussion. Is the concentration used physiological? <br /> - While the images shown in Figure 2B make it clear that aggregates are forming in liquid media, we have a suggestion to improve the strength of these results and account for the images not shown. For instance, quantification of the % of prey cells displaying Sytox staining would more strongly demonstrate the presence of permeabilized E. coli in multiple aggregates. This quantification could substitute Figure 2C (which can be moved into the supplemental): it was not totally clear to us why an orthogonal view was included here. If this is significant for the findings, it would increase clarity to include an explanation for an audience less familiar with this system.<br /> -Lines 192-214: From a genomics perspective, we think further explaining how potential adhesins were identified would be helpful to increase the clarity and reproducibility of the experimental design. Please explain how you narrowed down these adhesins and located them in the genome, and why adhesins were targeted for this analysis over other proteins that could facilitate a physical interaction between predator and prey species. Define the acronyms and provide rationale for naming. <br /> -Figure 6B nicely demonstrates that intoxication takes place in liquid between certain marine bacteria but not in Vpara. However, please include a control showing that V. para does intoxicate prey in solid media to strengthen these findings and confirm that this strain of V. para is capable of intoxicating prey under typical conditions.<br /> -Given the significance of the TssB deletion for the core message of this work that type VI intoxication occurs in liquid media, please consider including data that confirm the TssB deletion e.g. sanger sequencing in supplemental or as source data. A complementation assay of TssB to show that regaining TssB restores the awe1 toxicity would be valuable.<br /> - Lines 224-225/Figure 5: We are curious and excited about the implications of the balance between kin-aggregation and non-kin aggregation and how this may aid our understanding of bacterial interactions in marine environments. Based on our understanding of these results, the observation that deletion of CraAj (responsible for kin-kin aggregation) increased non-kin intoxication (mediated by LapAj) could suggest that aggregation between two kin cells, who both contain the needed immunity proteins, could dampen the intoxication of nearby non-kin cells. This result is implied by the data but not specifically speculated on or addressed. Though it may not be within the scope of this experimental design, our group was intrigued by these findings. Given your expertise in this area, consider discussing how these bacterial interactions may play out and/or include these observations as part of Figure 5.

      Minor Comments<br /> -All figures: In the legends, it is stated “these experiments were repeated three times with similar results”. Please define what is meant by an experiment e.g. technical or biological replicate.<br /> -All figures: We felt that having the exact p-values indicating statistical significance is not necessary. For instance, in Figure 3B and 3D, we found it distracting that all of the values were significant by a factor of <1E-4, even when they appear different from each other. If this is simply a cutoff value, it would be helpful to keep that consistent between figures. Also, Figure 6A/B: The p-values presented, specifically the comparison between WT and T6SS – supplemented with 1 mM CaCl2 (6A) and the two left hand panels of 6B, do not appear to match the differences shown between the experimental groups. By eye, these groups do not appear different from one another but are shown to be either highly statistically significant or not statistically significant at all.<br /> - Figure 1A: To increase readability, we suggest that the colors could be more intuitive here- put WT in grey and then mix colors for double mutants. Bringing the light pink line (Δawei1 ΔtssB + pAwe1) to the front of the graph would further increase clarity.<br /> -Figure 1B/F: Making color scheme consistent between 1B and 1F would increase clarity.<br /> -LiQuoR assay: As there is often some level of variation in expression levels when working with a transformed population, confirmation that all prey strains luminesce to a similar level would provide further validation of this novel assay (similarly to what is done in FigS3B). <br /> -Figure 2A: The colored box legends showing whether CaCl2 is present or absent are inverted relative to one another, which we found to be confusing. To increase readability, please make them on the same side.<br /> -Figure 3B,C,D,E: To help guide the eye on the graphs, we suggest adding dashed lines between each new mutation group (+/- TssB).<br /> - Figure S1: Please include a loading control to verify assay input. <br /> - Table S1: Clarify the gene and strain for each mutation.<br /> - Line 112-113: It serves as an excellent control that the action of the T6SS apparatus is required for intoxication, however, since the T6SS apparatus is contained within the bacterium, would spent media contain free-floating T6SS proteins, or are these proteins only ejected from the bacterium in the presence of prey species? Please clarify. Direct evidence, such as immunoblotting, that effectors are present in the spent media from WT would make this claim more compelling.<br /> - Line 35: While this part of the introduction provides excellent background regarding the role of T6SS in interactions with eukaryotic cells, it would be helpful to also specifically mention the role of T6SS in prokaryotic communities, as much of the later work focuses on competition between bacteria.<br /> -Lines 70-71: A more thorough background on Aeromonas (lifestyle, importance, etc) is warranted.<br /> -Line 84: Please provide the exact genotype when first introducing this mutant, it would improve clarity for the reader to explicitly state that this is a double mutant.<br /> -Line 97: Clarify here that “Aj prey” in this paragraph refers to Aj which do not possess the cognate immunity protein, as the current phrasing could be interpreted to mean “prey of Aj”.<br /> -Line 138: “Desired conditions for competition” is vague. Is solid media also incubated with shaking or is it static?<br /> -Lines 156-157: The statement that all three effectors are injected into prey cells is broad and not necessarily supported within these findings. The injection of one effector could be favored, but other effectors could compensate in its absence.<br /> -Line 189: Describes Aj as stably binding to other competing bacteria. To this point, imaged aggregates have been fixed so stability of aggregates may not be known.<br /> -Line 248: Here, it is mentioned that there was a switch from using the Lux operon to using the RFP mCherry for improved cell detection. It might be helpful to clarify which fluorescent tag was used for each assay, as multiple different fluorescent tags are used.<br /> -Line 317: As the choice to test CaCl2 and the biological relevance of calcium for Aeromonas hosts is explained earlier in the manuscript, it would be interesting to include a brief explanation about the choice to include sodium chloride when assessing Vibrio intoxication rates. Presumably, sodium chloride was picked because Vibrio is commonly found in brackish water, but someone from outside the field may not be familiar with this biology. Additionally, since Aeromonas can be found in both fresh and brackish water, an interesting follow-up experiment would be to test the Aeromonas strains under different salinities.<br /> -Line 375-377: Needs citation.<br /> -Line 385: Clarify “under specific conditions not addressed within the scope of this study”.

      Carter Collins and Lily Pumphrey (Indiana University Bloomington) - not prompted by a journal; this review was written within a Peer Review in Life Sciences graduate course led by Alizée Malnoë with input from group discussion including Camy Guenther, Josy Joseph and Tahreem Zaheer. We are part of the Dept. of Biology where Julia Van Kessel’s group is located, Julia is a collaborator of the corresponding author and did not influence the choice of this preprint for our class.

    1. On 2025-12-19 20:20:10, user Michael Ailion wrote:

      This manuscript documents careful genetic analysis to better understand where and how Rho signaling acts in the C. elegans egg laying circuit. The authors demonstrate that Rho functions in mature neurons to promote egg laying, as well as in vulval muscle. By using calcium imaging, the authors were able to demonstrate how Rho signaling (specifically in the HSN neurons) regulates cell excitability presynaptically (HSN) and postsynaptically (vulval muscles). We found the experiments to be well designed and the data to be robust, with the major conclusions to be supported by the data.

      Minor comments:

      1) The introduction included a detailed analysis of the Gq signaling pathway and the candidate targets that regulate neuronal activity (i.e. DAG-regulated effectors and ion channels), but the scope of the paper does not include testing or identifying the targets downstream of TrioRhoGEF/Rho. On the other hand, the focus of this manuscript is neurotransmission in the egg laying circuit, and little detail is provided about how and what neurotransmitters are released by HSN. Only in the results section is NLP-3 mentioned, but it is known that both serotonin and NLP-3 released from HSN each contribute significantly to egg laying. <br /> 2) The authors conclude that Rho promotes synaptic transmission, and this is on the whole correct, but the authors could be more careful/precise with their wording and interpretations. As noted in comment 1, both serotonin and NLP-3 contribute to synaptic transmission in the egg laying circuit, but it is not known how directly these two components act in synaptic transmission. For example, NLP-3 is a neuropeptide that is released from dense core vesicles (DCVs), and it is possible that serotonin is also incorporated into DCVs as well as synaptic vesicles. In addition, serotonin and NLP-3 are known to act extrasynaptically as well as synaptically, and it is possible that Rho contributes to extrasynaptic release of serotonin and NLP-3. <br /> 3) When analyzing their data, the authors bin calcium imaging measurements in the active vs inactive state. The active and inactive egg laying states are characteristic for wildtype worms, but as the authors show, altering the activity of the HSN affects egg laying. Another interpretation of their data is that when Rho is activated (HSN::Rho-1(G14V)) the worm is always in the active egg laying state, and when Rho is inhibited (HSN C3 Transferase) the worm never enters the active egg laying state. While we don’t think they need to change how they analyze the data, the authors could just add this interpretation to the discussion. <br /> 4) We feel like the authors should include a more detailed discussion of why they see a difference in the effect of expressing dominant negative Rho (T19N) vs the C3 transferase in HSN. Why did Rho-1(T19N) expressed in HSN not show such a clear inhibition of calcium activity and egg laying as the C3 transferase expressed in HSN?<br /> 5) In general, gain-of-function experiments are hard to interpret. Activated Rho could increase cell excitability, but that does not necessarily mean that is the function of Rho normally. The loss-of-function experiments are more convincing, aside from the discrepancy we noted in comment 4. This could be noted in the discussion. <br /> 6) Lines 148 & 179: provide more detail or a reference for how extrachromosomal arrays were integrated.<br /> 7) Lines 195 & 214: it is unclear how GCaMP arrays were confirmed by mCherry fluorescence (nlp-3p::mCherry) given that these strains also have arrays carrying tph-1p::mCherry and both nlp-3p::mCherry and tph-1p::mCherry should express in the HSNs.<br /> 8) Line 339: the authors conclude that Rho acts “downstream of Trio RhoGEF.” However, the data show that a Trio mutant is only partially bypassed by expression of activated Rho – i.e. # of eggs is intermediate between the Trio mutant alone and activated Rho alone. These data are consistent with Rho acting downstream of Trio, but with RhoGEF activity still contributing to full activation of the “activated” Rho(G14V). The data would also be consistent with Trio and Rho acting at least partially in parallel, which could occur within the same cell or in different cells. A further complication to the interpretation of these data is that different activated Rho arrays are used in the WT and Trio mutant backgrounds. These different arrays could have different expression levels, which is a big caveat to making these comparisons. Ideally, one would use the same array in the WT and Trio mutant backgrounds.<br /> 9) p. 16, lines 348-459: many of the Fig 2 callouts on this page refer to the wrong panel.<br /> 10) Line 347: says 70%, but the data in the figure show >80%.<br /> 11) Line 348: says 3 +/- 1 eggs, but Fig 2B says 3 +/- 0.2 eggs for same strain.<br /> 12) Line 363: we were confused by this. Are the authors suggesting that you can’t quantitatively compare the effects of the HSN vs. muscle specific expression of activated Rho(G14V) because the arrays are mosaic? While it is true that the arrays may be mosaic, they also carry an mCherry marker expressed in the same cells, so they should know whether the array is expressing activated Rho as intended in the worms assayed, and it is unclear why mosaicism is an issue. A bigger issue to quantitatively comparing these strains is that they probably have different expression levels of activated Rho.<br /> 13) Line 396: “outside of egg-laying active states (Figure 3A).” However, the data in Fig 3A shows HSN activity “during an egg-laying active state” according to the figure legend. Data showing activity outside egg-laying active states are not shown, but should be presented.<br /> 14) Line 423: it is unclear how “instantaneous” transient frequency is defined. This should be added to the methods or figure legend.<br /> 15) Line 428: says “more than 5 transients per minute” but the data in Fig 3C show it to be just under 4 transients per minute.<br /> 16) Line 561-562. “This difference largely resulted from a lack of twitch transients around egg-laying events in C3T-expressing animals.” This argument doesn’t make sense to us. How could a lack of twitch transients affect the amplitude of the transients that are seen?<br /> 17) Line 648: “we do not see dramatic effects on HSN morphology and presynaptic structure upon Rho inactivation.” Presynaptic structure was not assayed, so this should be cut.

      Reviewed (and signed) by Amy Clippinger and Michael Ailion

    1. On 2025-11-19 21:19:50, user Daniel Vásquez-Restrepo wrote:

      This preprint already received a “major revision” decision. Unfortunately, the original reviewers were not available to evaluate it again, and the process stalled. Despite sending 15 additional peer-review invitations, no one agreed to take it on. Although the manuscript has now entered a new review process, I am attaching the previous reviewers’ comments.


      Reviewer 1

      This isn’t a finding as not only is it already available information, the use of the available IUCN maps and statuses was part of the methodology.

      R/ We rephrased the sentence to clarify that it refers to the underlying data itself and not to our results.

      I like the approach they’ve taken, but none of this is novel information or unexpected.

      R/ Although it is well known that mountains promote diversity and endemism at a global macroevolutionary scale, this information has not been explicitly tested in Colombian squamates in conjunction with threat categories. We consider that clearly stating the result of hotspots of diversity and endemism in Colombian squamates can help local environmental policies. Therefore, while our results are consistent with theoretical expectations, this alignment does not diminish the novelty of our findings, as we provide the first quantitative analysis supporting these patterns in the local context.

      This is the main novel finding of the work and I’d recommend reorganising the text to stress this.

      R/ We modified several sections of the text to emphasize the finding highlighted by the reviewer, also in accordance with comments made by the other reviewer.

      Unclear what this means in the context of this paper.<br /> R/ We rephrased the section for clarity.

      This is just the existing EDGE list, so I’m not sure it warrants mentioning as an output here.

      R/ In accordance with a comment from Reviewer 2, we acknowledge that this is a local rather than a global list, and that species rankings may differ between the two. Therefore, we believe it is an output worth highlighting. Nevertheless, we have clarified in the text the differences between the local and global scores and their implications.

      This entire paragraph seems superfluous, and this work has nothing to do with the latitudinal gradient so it’s a strange thing to focus discussion on.

      R/ While we briefly mention the latitudinal gradient, the main purpose of this introductory paragraph is to provide general context on biodiversity, leading into the key argument of the subsequent sections: the need to understand biodiversity and extinction risk as multidimensional phenomena. We have made minor adjustments to better integrate the role of the latitudinal gradient in promoting tropical diversity, thereby reinforcing the importance of prioritizing conservation efforts in regions of exceptionally high biodiversity.

      Suggested added context as this was unclear as worded.

      R/ We accepted the reviewer’s suggestion and revised the text accordingly.

      I’m not sure this follows - more that, as the paragraph goes onto say, it results in a lack of understanding of the impacts and vulnerability of the species.

      R/ We rephrased the idea to make it clearer.

      This seems to be an inappropriate reference, as Paez et al. 2006 focused on turtles rather than squamates. Please check and reword as needed.

      R/ We double-checked the reference and confirmed that it is correct, as it covers not only turtles but all Colombian reptiles (including squamates, crocodiles, and turtles).

      This seems inconsistent with the earlier statement that “a local assessment is lacking” - should this rather say a recent local assessment? Though as the paper goes on to reference a 2015 ‘local assessment’, it’s unclear what this section means.

      R/ We agree with the reviewer and revised the text to clarify that we refer to a recent assessment that also considers different facets of biodiversity, not just species richness (i.e., taxonomic diversity).

      The figure given later is 597, and that was used as the basis for the analysis. This may be a discrepancy due to a later update, but the same Reptile Database update should be cited throughout the paper for consistency.<br /> R/ In the Introduction, we refer to the most recent estimate of 620 reptile species for Colombia, based on the latest update of the Reptile Database (2024). However, the analyses in this study were based on the 2023 version of the database, which listed 597 species at that time. Given that the analyses were conducted using the 2023 data, and a complete reanalysis would be required to incorporate the updated figures, we chose to retain the original dataset to ensure consistency and reproducibility. We have clarified this point in the text to avoid confusion.

      Better to use the term ‘squamates’ rather than ‘reptiles’ if crocs and turtles are to be excluded.

      R/ Done, we have consistently replaced "reptiles" with "squamates" throughout the text where appropriate.

      Once again, this could benefit from clarity. The data in the Reptile Database should be reviewed with reference to available material and literature to be used as a formal checklist, but it should be ‘complete’ - it’s more likely to erroneously list species from a country than to miss ones that actually occur there.

      R/ We agree with the reviewer and rephrased the sentence to make the idea clearer.

      Are the authors able to explain the discrepancy between this figure and the maps (which represented 81% of the dataset)? Most IUCN assessments will have maps, but no IUCN maps will be associated with species that don’t have assessments.

      R/ The figures were validated against the information provided in Table S1. As the reviewer correctly points out, there are more assessments than polygons, consistent with the supplementary material. The figure of 77% corresponds to 461 species (excluding DD and NE categories) out of 597 species in our dataset (461/597 = 0.77). Meanwhile, the figure of 81% refers to 481 species with available geographic information, including species categorized as DD (481/597 = 0.81). The discrepancy arises because DD species were included when considering geographic data but excluded from threat category analyses. We have revised the Methods and Results sections to clarify this distinction explicitly. Also, we updated the previous 77% figure to include DD species too, increasing it to 92%.

      This is not a sufficient way to evaluate whether the assessments are likely to need updating - the Criteria take account of the distribution and extent of threats to each species, not simply its distribution. The ‘needs update’ tag is applied by the Red List only to assessments more than 10 years old, which is all that should be mentioned here.

      R/ We understand the reviewer’s concern and acknowledge that a mismatch between EOO and threat classification is not sufficient by itself to determine if an update is needed. We have separated these ideas in the text: first, we highlight species whose assessments are formally tagged as “needs update” after 10 years; second, we discuss species whose EOO does not align with their current threat classification. We moved the second point to the 3.2 Geographic patterns section, and expanded the Discussion to better explain these observations.

      See above. The authors didn’t ‘show’ this, they interpreted the Criteria incorrectly.

      R/ See previous answer. We further expanded the Discussion section to better frame this point.

      I would consider it suitable for the manuscript to be more fully revised as a shorter paper, as the region-scale analysis within Colombia and the phylogenetic results are of more interest than the well-trodden path of identifying the Andes as an area of greater endemism than Amazonia and the additional analyses included in the paper render its main findings somewhat opaque in places.

      R/ We consider that highlighting the Andes as an area of high endemism is necessary to provide context for interpreting the patterns of phylogenetic diversity. While it may be a well-known topic, not all readers will have the same background. Although the manuscript is extensive because it covers taxonomic, geographic, and phylogenetic patterns, its current length (ca. 6,300 words, excluding references) is well within the 9,000-word limit for Original Research articles in Biodiversity and Conservation and only slightly above the typical 5,000-word range. Nevertheless, we made an effort to shorten unnecessary sections to improve focus and clarity. For example, we removed some analysis related to diversification rates and extinction risk, since as the Reviewer 2 pointed out, some metrics depending on branch lengths may be biased.<br /> <br /> Reviewer 2

      L393-405: it is important to acknowledge the phylogenetic incompleteness of a national-level analysis, and how that might be affecting these results – divergence times are influenced by phylogenetic coverage and structure, removing >90% of squamate species from the phylogeny will give you divergence times between Colombian species, not true lineage age/divergence time information. This could be addressed with sensitivity analyses to explore how lineage age varies between pruned and complete trees, or with stronger discussion of the pitfalls of this approach in the methods and discussion, with clearer wording in the results.

      R/ We appreciate the reviewer’s insightful comment and fully agree. We performed additional calculations to assess sensitivity, and indeed, the age of some lineages can be severely affected, while others remain largely unchanged. Following the reviewer’s recommendation, we revised the Methods and Discussion sections to place greater emphasis on the limitations of using evolutionary metrics derived from pruned trees and on the considerations needed when interpreting these results. As the reviewer also notes, these results are not necessarily incorrect, since global conservation priorities do not always align with local ones. Additionally, we introduced local and global subscripts to our metrics to explicitly distinguish between them.

      407-418: Distinction is needed between EDGE scores and national EDGE scores (literally just saying ‘national EDGE scores’ would suffice). It may also be useful to identify national-specific priorities – i.e. high ranking national EDGE species that are not highly ranked in global context. There are EDGE scores available for all vertebrates at the global level here ( https://www.nature.com/articles/s41467-024-45119-z) . There are endemic Colombian squamates that are high EDGE in this study and also high EDGE at the global scale (e.g. Lepidoblepharis miyatai) but also species that are high EDGE nationally because of the phylogenetic diversity they are solely responsible for in Colombia, but the responsibility for which is shared beyond Colombia’s borders. These key cases can be instrumental in ensuring species that are globally ‘safe’ but locally important do not fall through the cracks.

      R/ Please refer to the previous response. We now explicitly distinguish between national EDGE scores and global EDGE scores throughout the text and highlight cases where species are locally important but not necessarily globally prioritized.

      L41 and throughout: “threatenedness” = “extinction risk” or “level of threat”.

      R/ Done.

      Throughout: It’s the IUCN Red List, not IUCN, particularly when referring to versions of the Red List database.

      R/ Done.

      L145: make it clear you’re referring to national endemics.

      R/ The Resolución 0126/2024 from Colombia’s Ministry of Environment (MADS) covers not only national endemics but all species occurring within the country’s administrative boundaries.

      L167: ensure it’s clear that its imputation based on taxonomy alone.

      R/ Done.

      L182: check references.

      R/ We reviewed the references cited at this point and confirm they are correct.

      L222-224 and throughout: phylogenetic diversity == Faith’s PD – the other measures are indices of phylogenetic distance/relatedness that are calculated in same units as PD, but are not phylogenetic diversity – that should be clarified.

      R/ Done. We clarified that Faith’s PD refers specifically to phylogenetic diversity, while the other metrics represent measures of phylogenetic relatedness or distance.

      L393: extinction risk should not be though of as a trait evolving but as the manifestation of extrinsic and intrinsic factors.

      R/ Agreed. We rewrote the sentence.<br /> L393-397: unclear what the relationships discussed are, and what they infer.

      R/ We have removed this section from both the Methods and Results. Given that the correlations discussed involved metrics dependent on branch length — and, as the reviewer previously pointed out, branch lengths can be affected by pruning the phylogenetic trees — we decided to eliminate this section. Overall, it did not substantially contribute to the text or to the discussion.

      L428-429: This is higher than, or at least comparable to, the global % of DD/NE squamates I think, so might not be considered relatively low for squamates.

      R/ We rewrote the sentence to clarify that it is comparable to or higher than the global percentage, as the reviewer correctly pointed out.

      L429-432: it might be worth highlighting how taxonomists and others can contribute to rapid reassessment of species with basic information in ecological publications see: https://doi.org/10.1016/j.biocon.2018.01.022

      R/ Done. We incorporated the reviewer’s suggestion.

      L442-444: Unclear what is meant here? A species can be assessed as CR with a wide range if its under population decline criteria, and a small-ranged species can be assessed as not-threatened if there is no evidence of decline/ongoing degradation.

      R/ This comment was also raised by Reviewer 1. We addressed it accordingly by revising the text to clarify that species can indeed have wide distributions and still qualify as Critically Endangered if facing significant threats, and vice versa. Please refer to our responses to Reviewer 1.

    1. On 2025-11-03 07:59:20, user Zoya Yefremova wrote:

      Dear colleagues,

      I read with great interest your preprint describing Tamarixia citricola Hansson and Guerrieri sp. nov. (Hymenoptera: Eulophidae), a putative new parasitoid of Diaphorina citri discovered during a classical biological control program in Cyprus. Congratulations on this interesting contribution to the taxonomy and biological control of psyllid pests.<br /> If I may, I would like to respectfully draw your attention to a publication that may be relevant to your study: Burckhardt, D., Yefremova, Z.A., & Yegorenkova, E. (2015). Diaphorina teucrii sp. nov. and its parasitoid Tamarixia dorchinae sp. nov. from the Negev desert, Israel (Zootaxa 3920 (3): 463–473). I apologise for the self-reference, but given the biogeographical proximity and the relevance of the Israeli Tamarixia fauna to the region, it was somewhat surprising not to see it cited.

      In Israel, we have documented five native species of Tamarixia, including T. dorchinae, which shares several morphological characters with what you describe as T. citricola, particularly in forewing and antennal structure across sexes. A comparative discussion of these taxa might offer further insights into whether the specimens from Cyprus are truly distinct species. A discussion comparing the putative new species with other taxa in the region is warranted anyway.<br /> Additionally, I think that host specificity in Tamarixia isgenerally more consistent with psyllid host genus rather than the associated plant. This ecological pattern may be worth emphasizing in your discussion.<br /> We are in the process of barcoding the Tamarixia species of Israel, and a comparison with your material would be most useful.<br /> Thank you again for sharing this work,

    1. On 2025-10-08 14:25:37, user Michal Tal wrote:

      Since I was asked to review this paper several months ago and waived my anonymity on review, I'm sharing my review publicly here as a comment. The TL/DR is that I think this paper is both very informative, and very important. However, it does need to be contextualized as a deep study of a recovery cohort, which is then being compared to public data from cohorts with a significant percentage of people who are not recovering, and that needs to be accounted for. Comparing immune cells from the PBMC fraction of blood of people who all went on to recover to cells from tissue of cohorts including those made up of 40% people who did not go onto recover does not allow for making conclusions about differences between the blood and the tissue without accounting for the differences in immune responses of those on a trajectory to recover and those who are not. Those immune responses could look very different, both in the blood and in the tissue.

      Here is my full review:

      This is an important and comprehensive study by Rostomily et al., "Multiomics Reveals Compartmentalized Immune Responses and Tissue-Vascular Signatures in Lyme Disease," which significantly advances our understanding of the immunopathology of acute Lyme disease (LD). I found it easy to read, and the figures were clear and compelling. By employing a longitudinal, multiomics approach integrating plasma proteomics, metabolomics, and PBMC immunophenotyping, supplemented with a meta-analysis of skin lesion transcriptomics, the authors present a compelling narrative of compartmentalized immunity. They propose that the robust alterations in circulating plasma proteins and metabolites, linked to endothelial barrier stability, metabolic reprogramming, and symptom severity, are predominantly driven by local immune processes within the skin and associated vasculature, while systemic PBMCs remain largely quiescent. It is quite surprising to see the PBMCs and metabolites show such fast resolution, and it feels like this is likely related to the complete recovery seen in this cohort. This work offers novel insights into effective immune responses against Borrelia burgdorferi and the kinetics of recovery from infection, particularly highlighting vascular involvement, and provides a valuable resource for future biomarker discovery and therapeutic development in LD. <br /> A critical aspect for the authors to address, perhaps in the limitations or discussion, is the high recovery rate observed in their patient cohort. The manuscript states, "Following antibiotic treatment, symptoms resolved in most patients, with only a few reporting mild symptoms attributable to LD at 6 months or at 1 year post-treatment". This contrasts with broader literature suggesting that 10-20% of LD patients develop Post-Treatment Lyme Disease Syndrome (PTLDS) with persistent symptoms. It would be beneficial for the authors to discuss why their cohort experienced such a high recovery rate. Were specific exclusion criteria applied that might have inadvertently selected for individuals less prone to PTLDS (e.g., absence of certain co-morbid conditions known to be risk factors, that’s very interesting to speculate)? The methods section details exclusions such as fibromyalgia, chronic fatigue syndrome, traumatic brain injury, prolonged undiagnosed somatic complaints, morbid obesity, sleep apnea, autoimmune disease, uncontrolled cardiopulmonary or endocrine disorders, recent malignancy, liver disease, major psychiatric illness, or substance abuse. While extensive, it's worth considering if these fully account for the low PTLDS rate. Additionally, the cohort demographics (Figure 1B) show a skew towards male patients (27 male vs. 22 female). Given that some infection-associated chronic illnesses, including potentially PTLDS, may skew female, could this gender distribution contribute to the observed recovery outcomes? Clarification on these points would help contextualize the study's findings regarding the typical immune trajectory of acute LD.<br /> Major Points:<br /> 1) Comparability of Meta-Analysis Cohorts: The conclusions regarding skin-derived systemic signals rely heavily on meta-analyses of public datasets (GSE63085, GSE154916, GSE169440). It is crucial to provide a more detailed comparison of the clinical characteristics (symptoms, treatment, PTLDS rates) of these external cohorts with the primary study cohort. For instance, the GSE63085 PBMC dataset is from a cohort with a reported PTLDS-like symptom rate of ~46%, substantially different from the near-complete recovery in the current study's cohort. These differences should be explicitly discussed as they could influence the nature and interpretation of immune responses. I wonder if the major differences seen in the skin vs PBMCs here are driven more by immune differences in people who are on a trajectory to recover vs those who are not. There are public datasets available on PBMCs as well, such as from the SLICE cohort including those on a trajectory to recover and those who are not. These should be compared in the analysis.<br /> 2) The finding of largely quiescent PBMCs in the face of infection and systemic mediator changes is surprising. The authors should expand their discussion to contextualize this observation against other types of infections, or Borrelia infections where people go on to develop borrelia infection-associated chronic illness. For example, how does this compare to PBMC responses in other chronic infections, tissue-localized (versus systemic/blood-borne) infections, or infections caused by slow-growing (like B. burgdorferi) versus fast-growing bacteria? Or, back to point #1, is this more just what PBMCs look like in someone who has been successfully treated with an antibiotic for a bacterial infection, and is this just what being on track to a full recovery looks like? That would explain why this looks so different from PBMC profiles in chronic illnesses like TB/HIV/HCV/ T. cruzi, but would make more sense in the context of a cleared infection and recovery. One additional thing to consider is that most of the immune granulocyte cells will be spun out of the PBMC fraction, but that does not mean those responses aren't circulating in the blood, they just won't be found in the PBMCs.<br /> 3) The T3 timepoint seems to stand out compared to T2 or T4, and it’s not clear why, and this isn’t adequately addressed in the discussion or limitations.<br /> Minor Points (Organized by Figure):<br /> Figure 1: Study overview and clinical manifestations <br /> Panel B: The gender distribution is skewed male. It would be useful to know if any sex-based differences in the measured parameters were analyzed, as this was not apparent throughout the manuscript.<br /> Panel C: The T3 (6 months) timepoint for C6 ELISA is missing; only T1, T2, and T4 are shown. Is that because T3 looks weird throughout, and you didn’t want to show it? <br /> Panel F: It would be helpful to indicate which correlations are statistically significant (e.g., using asterisks or by highlighting significant bubbles).<br /> Figure 2: Differential expression of circulating proteins and their correlation with symptoms <br /> Panel A: The separation into fast- and slow-resolving clusters is a very interesting and insightful presentation. However, the text states PRDX5 remained significantly elevated at T2, but this is not immediately clear from the heatmap's visual representation for PRDX5 in the T1-T2 comparison. Only IL17C is labeled as significant (T2-T3) in the slow responding genes.<br /> Panel B: It is unclear why not all rows are labeled as they appear in A across all pathway comparisons, which makes it harder to assess the full dynamics. Maybe this circles back to the fact that some of them were significant T1-T2, and not T1-3, but then again yes T1-4 so maybe it looked messy to show it that way? But this way you only show the first set it was significant for, and not the dynamics in between…<br /> Panel C and D: The rationale for selecting T1 versus T3 for this heatmap of cardiovascular, metabolism, and organ damage proteins could be clarified, especially as Panel A focuses on pairwise comparisons across all timepoints. And at other times T3 seems to be intentionally excluded. Displaying patient-based trends rather than just row-based averages might also be informative. The asterisks on the left indicating significance are somewhat hard to read on the opposite side from the label.<br /> Panel E: This is a visually appealing figure, though the bundling can make specific correlations slightly challenging to trace.<br /> Figure 3: Integrated community analysis and diagnostic modeling <br /> Panel A: Could the authors add descriptions of any shared features or overarching themes among the analytes within each of the three largest communities beyond endothelial disruption/protection? The rho scale for symptom correlations (-0.4 to 0.6) suggests many correlations are not very strong; indicating that adding statistical significance for these symptom correlations would be beneficial.<br /> Panel B, C, D: These ROC curves are interesting for diagnostic potential. Suggestion: If data are available, showing a baseline ROC curve using standard clinical diagnostic features (e.g., EM presence, basic serology if used for initial classification rather than just inclusion) could provide a useful comparison for the multiomic models.<br /> Figure 5: Minimal peripheral changes in acute LD <br /> Panel A: The highest variance explained by PC1 in the PCA of PBMC abundances is relatively low (18.4% for patients, 16.2% for controls), suggesting considerable heterogeneity not captured by the main principal components.<br /> Panel B: The decrease in plasmablasts over time would possibly be expected if it aligned with the development of memory B cells. But that doesn’t seem to be the case from this data. That might be a fit with what Nicole Baumgarth has described in B6 mice, and definitely warrants further discussion.<br /> Panel C: The UMAP visualization shows minimal separation. Without non-recovered patients, it's difficult to discern disease-specific trends versus inter-individual variability.<br /> Figure 6: Dramatic changes in a case with severe disseminated disease<br /> The boxplots effectively highlight how different the severe outlier patient is. This case underscores the point that systemic activation can occur. I really wonder if compared to publicly available data from people who did and did not recover after their acute infection, if you would see a lot more of this. Replicating this in a dataset with more patients with severe, non-recovering disease would be necessary to draw broader conclusions about this hyperinflammatory state.<br /> Figure 7: Skin immune responses reflect plasma protein and metabolic signatures <br /> Panel A: the source/location of "unaffected skin" biopsies can influence cellular profiles. This should be addressed.<br /> Panel C: The differential expression of CXCL8 (IL-8) across various skin-resident cell types is very interesting as is LILRB4 expression in skin-resident cells which would support the tissue-based regulation hypothesis as long as we had more comparators between the symptoms and inflammatory state of the individuals these cohorts.<br /> I think this paper is both very informative, and very important. However, it does need to be contextualized as a deep study of a recovering cohort, perhaps being compared to cohorts with more people who are not recovering, and that needs to be accounted for.

    1. On 2025-06-02 17:22:57, user Karl Milcik wrote:

      We reviewed this paper as part of our regular journal club. Below is a collection of the comments made by the various group members:<br /> --- 1 ---<br /> It's unclear why asymmetry in the latent embeddings is required.

      No mention of the model predicting trivial results during training due to the symmetric KL? Ablation might reveal that the loss weights require very careful tuning to avoid predictions or that the reference distribution is extremely important.

      There are a number of implicit assumptions being made with the model architecture, primarily that there is sufficient information to align two datasets. It becomes an issue when combining datasets from very different modalities (e.g. scRNA-seq and sc proteomics). Adding multiple modalities is definitely possible, but the overlapping information becomes smaller and lose additional information. It would be good to see where the model stops working. Small datasets will similarly carry little information: is there a minimum number of samples for the model to function as expected (exact number not required, but getting a sense with a few datasets of different modalities would be informative). As-is, we wouldn't expect the model to apply to most single-cell datasets.<br /> Aligning modalities that are of extremely-different dimensionality implies either redundant information in one modality or information loss. This should be discussed.

      Specifics of training, hyperparam optimization, etc. would be better in a supplemental (assuming the targeted venue allows it). The main contribution appears to be the combination of the various losses. The article could be shortened by focusing on that when describing the method.

      Re: training procedure. No mention of balancing the different modalities. "Difficult" modalities would be more difficult to learn. early stopping could be preventing complex modalities from being sufficiently mapped because the simpler modalities are overfit faster than the complex ones are learned.

      Evaluation metrics: NMI is very similar to the symmetric KL that is used to train the model. I'm not sure if it's a reliable metric for this.

      Fig. 2a: the figure amounts to "the model removed information," which is the point of batch correction but doesn't quantify what other information was lost. Fig. 6 suggests that there is quite a bit of biological information is lost.

      Fig. 3: scRNA reconstruction is producing high values for some genes when it shouldn't (purple cluster, top). If one were to use this, we would conclude that those genes are highly differentially expressed when they are not in the original data. This is a fatal problem.

      --- 2 ---<br /> 1. Lack of Evaluation in Downstream Biological Applications<br /> While UniVI shows strong performance in latent space alignment and cross-modality prediction, its utility in downstream biological tasks (e.g., identifying novel cell subtypes, inferring regulatory programs, or reconstructing differentiation trajectories) remains under explored. Demonstrating improvements in real biological discovery would substantially enhance the manuscript's impact.<br /> 2. Insufficient Validation of Generalizability Across Conditions<br /> The datasets used in evaluation are mostly standard and clean (e.g., PBMCs from 10x Genomics). It is unclear whether UniVI generalizes well to more diverse or challenging settings (e.g., different sequencing technologies, species, or tissues).<br /> 3. No Ablation Studies to Justify Model Design<br /> The architecture includes several important design choices (e.g., β-VAE, shared and private latent spaces, MoE layers), but the manuscript lacks ablation experiments to validate the contribution of each component.<br /> 4. Lack of Interpretability for Latent Space Representations<br /> The latent space is central to UniVI’s function, but its biological interpretability is not addressed. It is unclear which features (genes, peaks, proteins) drive the alignment, or how latent dimensions relate to known biology.<br /> 5. Failure Cases and Limitations Are Not Discussed<br /> The manuscript does not address situations where UniVI might fail or yield poor alignments. Understanding when and why the method breaks down would be critical for end users.

      --- 3 ---<br /> 1) They mention that scATAC-seq is not reliable for determining cell type specificity, then why did they necessarily include ATAC-seq?

      2) The dataset they use are reliable but I think it would be good for them to mention why exactly they preferred these dataset and databases, there is not much information about this

      --- 4 ---<br /> Figure 4: recommend labeling panels rather than referring to top left, etc. In the boxplots at the top left, uniVI and totalVI seem really similar in NMI, ARI, ACC but no formal statistical comparison done<br /> usability may be limited if you have to manually fit the model with your own data<br /> is overfitting a problem with very small datasets? is computational time a problem with very large datasets (eg early stopping used)?

      --- 5 ---<br /> -Use of the model to generate new data is stated and referenced throughout, but I felt the true utility of this is underexplored. Why would someone want to do this? The authors mentioned data augmentation, but the authors could be more explicit on any other uses.

      -Did the authors consider using alternative methods to grid search for their training procedure (e.g., neural architecture search)? Also what were the ranges of values searched and with what step sizes?

      -For adding >2 modalities, are there any considerations with computational complexity and training time at a certain point? How would this scale to K>2?

      -In general, the paper is well organized and detailed, but almost to a fault. I suggest moving details less relevant to the average reader into a supplemental section. For example, knowing the function calls and variables probably isn't relevant to most readers. Those that want to know that could look in the code or point the reader to a supplement. These somewhat irrelevant details to the figures were also mixed with critical details such that I felt a little lost on trying to pick out the most important parts of the methods.

      -On the same note, simple details are often over-explained or restated multiple times in the text (e.g., the explanation for subsetting the data to obtain non-overlapping labels is repeated several times), while more complex concepts such as the Beta term, mixture of experts model, etc. are often underexplained in my opinion.

      -For Figure 1, I am still confused on what exactly UniVI provides a benefit over in some panels versus just looking at individual UMAPs and annotating by the labels, since these are already known? More specific explanation on why a shared latent space is usual to find new biology would help.

      -Exploring more on the fringe cases in which data does not align is interesting. For example, the authors mention cell 59 aligning closer to a Dendritic cell than B cell. They mention this could be biological variation or technical error, but exploring more about this 'misalignment' in this and other datasets could be be a key way of identifying unique insights from this model, though would require biological validation. Perhaps the authors could suggest some such experiments as future work to tie in dry and wet lab approaches/experimental designs that would complement this model in the lab.

      --- 6 ---<br /> In the paper authors mention that approximately 1% of the dataset shows inconsistent alignment. Could you elaborate on how this might be interpreted as reflecting dynamic cellular states in continuous development? A deeper discussion of this would be very helpful.

      --- 7 ---<br /> Figure 7: how to prove that the reconstruction retains the biology signal or better illustrate:<br /> It’s weird that the error did not increase significantly with the higher dropout rate.<br /> As well as for the Correlation<br /> When no dropout is applied, the correlation between the raw and reconstructed data is only 0.52. Does this suggest that the pathways have changed significantly? It may be necessary to check which pathways have changed and which have not.

      --- 8 --- <br /> Lack of QC metrics and if there were any filtering involved for the data. Transparency is missing in the QCs.

      --- 9 ---<br /> A limitation is that this must be only used for measurements made from the exact same cells - we cannot apply this framework to cells measured in parallel with different methods

      Figure 2 not sure that they compared to CCA or OT as those were introduced alternatives in the beginning.

      Figure 2 : I like that they show the measurement pairs for each cell - can they quantify this globally somehow?

      The distinction between “imputation” and alternative mode reconstruction is unclear from their description; they mention fitting a gaussian mixture model with their data and then using that for input - does that mean they use the true values from one measurement modality and then use all zeros for the other? Why not simply run a forward pass from the one modality encoder and then use the opposite decoder?

      They comment on higher expression levels having higher reconstruction MSE - this is a common feature of autoencoders that compress the range of predictions so as to minimize error from any large magnitude predictions. The methods claim to have used pp.scale() which should have removed this effect of the measurements original magnitude?

      It would be interesting to know what are the limits in terms of minimum (or maximum) features per modality and minimum measurements for training.

      Based on figure 4, the claim that uniVI “outperforms existing state of the art integration methods does not appear to be statistically supported. It appears to be indistinguishable from TotalVI and perhaps even Seurat. The authors should compute p values using random samples of the data with replacement (I think these experiments used identical samples, which would violate the assumption of independence for t-testing). TotalVI appears to have been published over 4 years ago in Nature Methods. However they claim that TotalVI requires “modality specific priors”. This “prior” appears to be a specific model term that is learned from the data to account for background, so I agree that uniVI is more generalized but not by as much as I thought before seeing this prior work.

      The authors should be careful about statements of distance based on UMAP “The model preserved meaningful cellular distinctions, with closely related populations remaining spatially proximate in the latent space, underscoring UniVI’s ability to harmonize intra-modality variation while retaining biologically relevant structure.”

      Figure 6C is a neat application of this data. Does this scale beyond this data and how can it be less slushy in the representations?

      Can this be fit on very deep single cell omic data and then applied to predict missing depth from more shallow studies?

      It would be interesting to repeat the dropout experiment with multiple random dropouts to get a sense of variance in the genes that are dropped out.

      I’m confused why the pre and post reconstruction heatmaps in figure 7 bear no resemblance even with 0% dropout. Are these hierarchically clustered differently or should we be able to compare the shapes between them.

      Is there overlapping information between true SCP and SCT (beyond cite-seq where the proteomic measurement part is substantially limited based on the number of antibodies)?

      Does this work well beyond measurements from blood cells (what seems like an easy case)?

      --- 10 ---<br /> I was hoping to see more of the unified cell state concept play out in its experiments. I feel like they got sidetracked (or rather, realized they didn’t have enough to really fulfill that ambition), but it would be nice to have that addressed more clearly.

      I was wondering if weights trained for a single modality as paired to a second modality could be transferred to a third modality comparison. Doubtful, but it would be interesting to explore.<br /> Not sure if this is something that you actually want to include in the review. It was more what I was focusing on and was somewhat dissatisfied by.

      The text in the figures is too small to read, generally speaking. I found issues with all figures with the possible exception of the first.<br /> Figure 1b, Cell-Cell Alignment is not intuitive. It goes from a UMAP to decode as a graph figure, and is not consistent with the batch correction element of the same subfigure. It’s an odd inconsistency.

    1. Reviewer #1 (Public review):

      Summary:

      The question of how or whether "extensive memory training affects neocortical memory engrams" (to use the words of the authors) is an interesting question and an area where I think there is room for advancing current knowledge. That said, I do not think the current paper succeeds in meaningfully addressing this question. At a conceptual level, I really struggled with the predictions and interpretations of the findings. There are also several elements of the experimental paradigm and analysis decisions that feel incompatible with the claims that are made. While the manuscript does demonstrate that several measures of neural pattern similarity differ between the various groups of individuals, the issue is that it is difficult to draw clear conclusions from these findings.

      Strengths:

      (1) This is a very unique dataset. Being able to recruit and enroll high-level memory athletes is impressive.

      (2) In principle, comparing memory athletes to control subjects, active control subjects (who received working memory training), and trained subjects (who received method of loci training) is very appealing.

      (3) In several ways, the authors were rigorous in their analyses.

      (4) In principle, the question of how memory training influences neural similarity vs. dissimilarity is of potential interest.

      Weaknesses:

      (1) As far as I can tell, the training manipulation is fully confounded with instructions. That is, subjects were only instructed to use the method of loci if they had completed method of loci training (or if they were the memory athletes). For the training group, in the pre-training session, there was no strategy instruction (subjects could do whatever they wanted), but post-training, they were told to use the method of loci. I understand the argument, of course, that naïve subjects might not be very good at using the method of loci if they had no experience with it. But, it does seem entirely possible that some (or even many) of the observed fMRI results that are attributed to "extensive training" are better explained by strategy use. That is, maybe the effects can be explained by TRYING to use the method of loci as opposed to actual proficiency with the method of loci. It seems impossible to address this, given the design of the experiments. As such, any claims about the effects of memory training, per se, feel inappropriate. It feels equally plausible that the effects are due to the strategy instruction. If the same results could be obtained through a simple strategy manipulation without ANY training at all, that would radically alter the interpretation of the effects. I think the strategy use account is, in fact, quite viable because it is very easy to improve subjects' memories with a method of loci instruction (relative to no strategy instruction) without ANY practice at all. Obviously, practice does improve memory performance with the method of loci, but my point is that even without any meaningful practice, there is likely to be SOME immediate benefit to adopting the method of loci as a strategy. There is also the question of why the effects for the memory athletes weren't obviously stronger than for the trained group, given that the memory athletes have much more experience with the method of loci. Ultimately, the problem with the current design is that I don't see how one can tease apart the role of training, per se, vs. strategy use.

      (2) There is no clear theoretical framework for the predictions or interpretations. The Results section is mostly a list of lots of different permutations of analyses (similarity within a group, between groups, between trials, across trials between subjects, during encoding vs. retrieval, frontal vs. hippocampal vs. parietal ROIs, etc). For each analysis, I did not have an intuition for what the prediction should be (e.g., should athletes have higher or lower pattern similarity?), and even after seeing all the results, I still do not have an intuition for how to interpret them. For the main results related to dissimilarity in prefrontal cortex, I would have, if anything, predicted the opposite: that when individuals are trained to use a common strategy, there would be MORE similarity between them. The Discussion acknowledges a very wide range of possible factors that might contribute to measures of similarity/dissimilarity, but I am ultimately left feeling that I have no idea how to interpret the results because the design and analyses were not structured such that any of these interpretations could be teased apart.

      (3) Same theme: the analyses shift from frontal regions (when looking at encoding) to hippocampus and precuneus (when looking at temporal recency). This shift in ROIs is confusing. The analyses (encoding vs. recognition) are essentially confounded with the ROIs (frontal vs. hippocampal/precuneus), so it's hard to know whether different analyses yielded different patterns or different ROIs yielded different patterns. Why were the frontal regions that were important for encoding ignored for the temporal recency judgments? And the fact that medial temporal lobe regions showed opposite effects to the frontal regions during encoding did not get much attention. Given that there were opposing patterns (dissimilarity vs. similarity) across different brain regions, the framing of the paper (that "the method of loci may bolster uniqueness") feels like a very selective representation of the data.

      (4) One of the more surprising aspects of the analyses (or at least one of the analyses) is that representational similarity analyses (RSA) are used to compare the average activity pattern (averaged across all trials) between different individuals. At a conceptual level, this really just reduces to a univariate analysis. It is not standard (or intuitive) to think about RSA that is essentially blind to the actual representational content. In other words, averaging across trials obviously washes out the content, and what is left are process-level effects. For process-level analyses, univariate analyses are far more common and seem more straightforward. However, these 'RSA' analyses are described as reflecting the "uniqueness of each word-location association" (an account which strongly implies content-level effects). This feels like an inappropriate description of what the analyses actually reflect.

      (5) I think the analysis looking at trial-by-trial similarity during word encoding (showing greater dissimilarity among the experienced individuals) is a somewhat interesting result, but again, I think the interpretation is very difficult. It is hard (or, impossible, I think) to get a clear sense of what is driving those differences. Is it the association of a unique spatial context? Is it somehow a product of better encoding, per se (as opposed to distinct spatial contexts)? These things could be tested by actually manipulating the spatial contexts in a more controlled way. For example, the paper by Liu et al. that is cited several times - and also a just-published paper by Christopher Baldassano (Nature Human Behaviour) - each used a very controlled paradigm where the (imagined) spatial location associated with each item was known/manipulated. However, the design of the current study does not allow for these things to be teased apart.

      (6) Relatedly, the training group seemed to receive instruction on a common spatial route, but, surprisingly, "Participants were free to choose which route and how many they would use to anchor the 72 items." Thus, if I understand correctly, we don't know whether the trained individuals were using common or distinct locations. And the fact that they learned a 50-location route but then studied a 72-word list is also a bit strange. Not having control or knowledge of the location that was associated with each word (sequence position) is a major limitation and also a major difference between the current study and other recent studies. For that matter, the word order was also randomized, so there was no control over whether the words and/or locations matched. These issues really complicate interpretation.

      (7) Again, same theme: for the result showing lower trial-by-trial similarity (within-subject similarity), the question is why, exactly, training/experience is associated with lower trial-by-trial similarity. Does training specifically or preferentially lead to greater differentiation between temporally-adjacent trials (as in Liu et al)? Does it lead to greater differentiation IF subjects associate each word with a unique location? Or maybe there is a more abstract effect of sequence/position that is independent of spatial location? Importantly, each of these three possibilities that I mention here has a precedent in prior studies that were more tightly controlled. But here, there is no way to tease these apart because of the experimental design, limiting the conclusions.

      (8) The ISC analysis described on p. 9 (line 328) is confusing. If I understand correctly, correlations between different trials were not computed (e.g., subject 1 trial 1 was not correlated with subject 2 trial 2). Rather, trial 1 was always correlated with trial 1 (in other subjects). Thus, it is not clear whether trial-level alignment matters at all. Maybe the same results would be obtained if there were no correspondence across subjects in trial number. Or if the trial order was shuffled within the subject. Given this, I simply don't know how to think about the data. And why did memory athletes show higher pattern similarity in this analysis as opposed to lower pattern similarity (as in some other analyses)? And why was this analysis performed by comparing memory athletes to each other as opposed to memory athletes to non-athletes? And, conceptually, why was this selective to the memory athletes or to the precuneus? And why was it selective to the temporal order test and not encoding? I am not asking the authors to answer each of these questions; rather, the point I am trying to make is that this analysis, and many of the analyses, seem to raise more questions than they answer.

      (9) The ISC analyses are interpreted in terms of scene construction and context reinstatement, but these conclusions go (very) far beyond what the data actually shows. Again, I don't see how this analysis lends itself to a meaningful conclusion. And this general critique applies to many of the analyses reported in this paper.

      (10) The fact that words were in random order per subject also makes the ISC analysis even more confusing to think about. The memory athletes had unique spatial routes (that they used for the method of loci) and unique word lists. So, why would it make sense to look at trial-level ISC? At a conceptual level, I simply don't understand what this is intended to capture.

      (11) Differences in the pattern of results between the encoding and temporal memory recognition task are hard to make sense of and are not addressed in much detail. Why would it make more sense to have across-trial similarity during recognition than during encoding? I think any account of this is very speculative.

    1. On 2025-05-06 22:01:39, user Young Cho wrote:

      1. Key Findings: <br /> The researchers conducted a comprehensive comparison of 16S rRNA gene-sequencing (metagenomics) and meta-transcriptomic (RNA-seq) analyses to profile the microbiota of the female reproductive tract (FRT). They revealed that the 16S rRNA sequencing effectively identified the bacterial taxa present; however, the authors did not account for the functional or metabolic activity of the bacteria. The meta-transcriptomic sequencing captured gene expression, identifying which microbes are transcriptionally active. This distinction is interesting, for it became clear that microbial communities inferred from DNA-based methods do not always reflect active nor beneficial contributors to the local ecosystem. The study found profound differences between the DNA and RNA profiles from the same samples, leading to significantly different conclusions to which microbes dominate the FRT environment. <br /> For example, the Lactobacillus species that are traditionally considered beneficial and dominant in healthy FRT were abundant in 16S profiles but exhibited low transcriptional activity in RNA-seq data. In contrast, the potentially pathogenic or dysbiosis-associated genera like Gardnerella and Prevotella were underrepresented in 16S data but demonstrated high transcriptional activity, especially in samples where DNA-based methods did not identify their presence as significant. These findings suggest that the mere presence of Lactobacillus may not be a reliable indicator of vaginal health unless the bacteria are also metabolically active. By exposing the divergence between microbial abundance and activity, the study challenges the assumption that taxonomic dominance equals functional influence, allowing the authors to propose that integrating both DNA and RNA-based molecular profiling is essential to an accurate understanding of the microbial dynamics in the FRT and to improve diagnostics and interventions for female reproductive health.

      2. Results:

      3. Figure 1 effectively supports the paper’s conclusion by demonstrating that integration of both methods of 16S rRNA gene sequencing and <br /> meta-transcriptomic analysis shows the different microbes in the female reproductive tract. This means this approach can detect both live and dead microbes.
      4. Figure 2 shows the abundance of various microbes in the female reproductive tract from utilization of the dual approach and supports the dual method in significantly increasing or improving the detection of microbial composition.
      5. Suggestions for the box plots are to add asterisks to visually see any significances and possibly only show the top 10 most abundance or significant genera to reduce clutter and highlight the meaningful results.
      6. Figure 3 supports the conclusions by showing the microbial diversity in the endometrium by comparing it to the vagina based on the different sample types as well. The significance was shown by asterisks as well.
      7. Figure 4 strongly supports the conclusion by effectively showing both DNA and RNA profiles across the samples, showing limitations of just depending on the RNA-based profiling alone, and the table also shows the support for the importance of quality interpretation of RNA-seq data as seen through the dramatic drops of number from human reads to microbial reads.
      8. Suggestions include grouping or ordering samples on the x-axis by the sample type, so far it appears random. This would help make it easier to compare patterns. For human vs microbial reads, label clearly with commas or decimals.
      9. Figure 5 effectively shows overlapping and unique genera, as well as emphasizing methods and tissue specific differences. They were able to show that the microbiome composition detected varied according to method and the type of sampling.
      10. Figure 6 supports conclusions by showcasing the main genera varied by methods and emphasizing that the microbe activity does not necessarily equal abundance . Suggestions include adding significance asterisks to show the differences.\
      11. Figure 7 reinforces the conclusions of the paper by showing functional activity vs structural presence and that specific genera in the endometrium may be undermined by relying on DNA-based approaches alone.
      12. Figure 8 strongly supports the conclusion that the 16S rRNA and meta-transcriptomic approaches result in different microbial profiles and that both approaches are essential to understand the endometrium microbiome. They directly compared DNA vs RNA endometrial biopsy samples.
      13. Figure 9 is an excellent figure in illustrating the workflow and summary for characterizing the microbiome and microbiota in different samples types. It was clear on their methods, analyses, and objectives on what they wanted to look at.
      14. Discussion: <br /> I liked that the beginning of the discussion section started off reiterating the importance of this study. One area that could have been improved was the first sentence. What diseases or medical conditions can 16S rRNA gene sequencing of the female reproductive microbiota help? Further into the discussion, I liked that the authors explained the importance of each experiment. For example, going into detail about why the Tao Brush and decontamination was a necessary step. Another area of improvement would be discussing the future directions with this novel concept. After these findings, how else can the authors use it to advance their understanding of the female microbiota? Other than that, I thought the discussion summarized the findings of the study well.
      15. Methods: <br /> Overall, the methods were well-written with thorough explanations as to why each experiment was conducted and this section was nicely organized. There are some missing gaps of information that could be elaborated upon to make the paper more digestible. For example, the study cohort consisted of women aged from 27-42 years old. I think the authors could have done a better job at explaining how they were able to define the exclusion criteria for reproductive age range. I noticed that when I google “reproductive age range”, there are a variety of ranges and am curious as to why the authors chose this range. In addition, the study cohort consisted of 44 women and the validation cohort consisted of 5 women. Why is the validation cohort such a smaller number of women? Does this affect any statistical analysis? Another section that could be expanded upon is on page 27, where they discuss 16S rRNA gene sequencing. A bit more of an explanation as to why the V4 hypervariable region was amplified may be helpful. As for Figure 9, while the figure is relatively easy to follow along, I think there were other ways to display the workflow and could have helped the readers more. Other sections such as the DNA and RNA isolation and Bioinformatics methods were easy to follow along and understand.
      16. Strengths and Limitations: <br /> One of the strengths of this study lies in its innovative side-by-side comparison of 16S rRNA gene sequencing and meta-transcriptomic analysis applied to the same clinical samples from the female reproductive tract. This dual approach offers a more nuanced view of the microbiota by distinguishing between microbial presence and metabolic activity, an important distinction that previous studies relying solely on DNA-based techniques have overlooked. The authors implemented a rigorously controlled sample processing pipeline that included steps to minimize host RNA contamination, which increases the reliability of microbial transcript detection. The study is supported by robust bioinformatics workflows with clear visualizations like principal component analysis and<br /> taxonomic heatmaps that effectively illustrate the divergence between DNA and RNA-based microbial profiles. The findings have important implications for clinical diagnostics, for they suggest that relying solely on taxonomic abundance may be insufficient to assess microbial function or pathogenic potential in reproductive health contexts. <br /> There are a few limitations that constrain the broader applicability of the study’s conclusions. The relatively small sample size of only ten women limits the statistical power and restricts the generalizability of the results across diverse populations; moreover, the cross-sectional nature of the study means it captures a snapshot in time and cannot account for dynamic changes in the microbiome across different phases of the menstrual cycle, pregnancy, or infection. While the detection of microbial transcripts adds a valuable functional layer, the study stops short of validating gene expression with proteomic or metabolomic data, leaving open questions about whether detected transcripts translate to actual protein production or metabolic impact. Also, the authors do not account for host physiological factors such as hormone levels, immune activity, or vaginal pH, which could influence microbial transcriptional activity. Addressing these variables in future studies would help refine interpretations and improve the clinical relevance of microbial activity profiles.
      17. Editorial Decision: <br /> Overall, I think the paper is relatively well-written and breaks down each section in a digestible way. I am not often exposed to these types of research but I was able to follow along. There were some minor suggestions I have which just include adding more detail to help the reader understand more. <br /> The overall paper does an excellent job in presenting the results in a way that allows the reader to follow along and understand their methods and the why. They effectively showed the benefits and specificity of the dual method through comparison of certain methods alone to emphasize how significant their dual method approach is. The results show the significance of implementing a dual approach for the potential clinical use to impact gynecological disease Suggestions: <br /> ● Some results could be grouped together such as Figure 2 and 3. It would be neat to show together both the abundance of microbes in the female reproductive tract and the diversity of microbes. As well as combine figures 7 and 8, both figures go over the abundances of the most abundant microbes in endometrial brush vs endometrial biopsy samples and compare DNA vs RNA. Combining these figures together to make one figure would allow the reader to quickly see the pattern or any differences. ● In the methods section, there are a couple spelling/grammatical errors. On page 25, under the sample collection header, the word “gynaecologist” is spelled incorrectly. The proper spelling for this should be gynecologist. On page 26, “two additional aliquot<br /> were…”, it should be aliquots written plurally. Then, on page 27, the sentence reads “a double purification with magnetics beads…”, shouldn’t it be magnetic beads? ● In discussion, they can emphasize more on the interpretation on the discrepancies such as why is there a discordance between DNA and RNA. They could also dig deeper as to why the RNA-based analysis provided higher resolution in detecting certain pathogens, even in the endometrium. <br /> Some minor revisions should be considered to strengthen the manuscript and improve its clarity and reproducibility. First, we recommend expanding the discussion on the clinical relevance of microbial activity profiling. For example, how might the distinction between dormant and transcriptionally active bacteria influence treatment strategies for recurrent bacterial vaginosis or fertility assessments? Second, it would be helpful to include a brief statement on whether sequencing batch effects were assessed or controlled, especially since subtle technical variability can influence community composition in small-sample studies. Clarifying this will reinforce confidence in the strength of the researchers’ findings. Third, the methods section should provide more detail in regards to RNA integrity metrics, for RNA quality is critical in meta-transcriptomic studies where degradation can skew transcriptional profiles. <br /> The paper fills a methodological and conceptual gap in the field and provides a framework for future studies incorporating both taxonomic and functional dimensions of microbiome analysis.
    1. On 2025-04-24 20:51:03, user Alizée Malnoë wrote:

      The manuscript by Peterman et al. investigates the role of microtubule dynamics in Langerhans cell morphology, phagocytosis, and directed migration in the epidermis. Through live imaging in zebrafish explants, the study shows that microtubules originating from a perinuclear microtubule organizing center (MTOC) guide the extension of dendrites for effective debris engulfment and enable precise migration toward tissue damage. When microtubules are disrupted, Langerhans cells become less efficient at phagocytosis and lose directional control during migration. These defects are linked to altered actin cytoskeleton polarity through the RhoA/Rho-associated kinase (ROCK) signaling pathway. The findings highlight how microtubule-dependent cell polarity enables immune cells to respond effectively within complex epithelial microenvironments. We found this study to be well-written and containing high-quality data that advances the fields of microtubule and immune cell biology. Overall, the data presented in this manuscript are done well and support the claims made by the authors. We outline some major and minor adjustments aimed at aiding the clarity of reporting and presentation.

      Major comments<br /> Page 10, Lines 286-289: We felt it was somewhat unsupported that F-actin accumulation in the trailing half of the cell was “consistent with the idea depolymerizing microtubules increases RhoA activity at the rear of the cell.” While the data clearly show a disruption in F-actin distribution with nocodazole treatment, we felt it was not clear that this would increase F-actin in the trailing half rather than evenly throughout the cell. Our lack of expertise in the field may lead to our misinterpretation of this sentence, however we felt additional explanation is needed (e.g. on the Lifeact-mRuby reporter) to clarify the section and support the conclusions drawn. Consider including a schematic of the model to ease interpretation of the data shown in Figure 4.

      Minor comments <br /> Page 2: It may be more effective to explicitly introduce RhoA/ROCK in the introduction rather than first mentioning it on page 10. This could connect your ideas more thoroughly, even if it’s just a brief mention in the introduction.

      Page 3, Line 102: You mention that the mpeg1.1 promoter labels multiple macrophage populations. Is there a concern that you’re labeling more than Langerhans cells in the epidermis, and that cells could be confused due to their altered morphology during the treatment?

      Page 3: The writing may be clearer if all acronyms (i.e. EMTB as ensconsin microtubule binding domain, EB3 as end-binding 3) are defined at their first use.

      Figure 1D: We found this panel somewhat difficult to interpret. Consider showing this panel in two dimensions displaying the percentage of EMTB+ dendrites as a function of the number of dendrites per cell.

      Figure 1K: It appears that the nocodazole treatment has one outlier (value of 100 µm). Does removing this datapoint change the significance of the treatment on maximum dendrite length?

      Figure 2E: It was unclear how the distance between the MTOC and phagosome was determined, i.e. whether the phagosome was measured from the point most distal or proximal to the cell body.

      Figure 2J: We thought your data would be most effective if you showed both the number and percentage of engulfment events for both control and nocodazole-treated cells to demonstrate how many events happened under each condition.

      Figure 3B: It appears that there are fewer Langerhans cells present in nocodazole-treated samples. Is this a significant impact or just coincidence in the images shown? Furthermore, could off-target effects or toxicity be impacting the migration differences seen here?

      Page 10, Line 263-264: There may be a typo here, where it‘s omitted that the “Langerhans cells had a smaller meandering index” were nocodazole-treated.

      Figure 4: A quantification of RhoA activation, e.g., using immunoblot, would be stronger evidence to support the conclusion that disruption of microtubules alters actin polarity through the RhoA/ROCK signaling pathway. This may be technically challenging: can one compare pulled-down microtubules to quantify RhoA binding between treated and non-treated?

      Figure 5: We’re interested to see if nocodazole-treated Langerhans cells would respond similarly to vehicle-treated (5C) or paclitaxel-treated (5D-E), especially considering the impacts of nocodazole on dendrite morphology (decreased cell dendrite number with increased length) you showed in Fig. 1G and Supplemental Video 3. We don't think this is a necessary experiment but may be worth including to provide alternative evidence of the impact of microtubule alteration on cell migration. We also found the placement of Figure 4 to disrupt the line of thinking connecting Figure 3 and 5. Consider moving Figure 5 after Figure 3 for logical flow, as Figure 4 is more mechanistic and addressing the question of the role actin plays in this process.

      Page 14, Line 385: It seems there may be a typo here, where “n=128 cells counted from N=13 scales” should include that these are in paclitaxel conditions.

      Page 14, Line 395: You mention that “acute chemical perturbations” were used in this paper. We thought that the laser ablation and/or scratch injury assays may be more accurately described as a physical or mechanical perturbation rather than chemical, but this may be from a lack of familiarity with writing conventions within the field.

      Page 15: In the second paragraph under “Cell motility,” there’s no name given for the image processing software used, which we think it would be helpful to include.<br /> Methods, Line 522: Could you write the exact percentage of DMSO used for the vehicle controls either here or directly in the figure legends.

      Supplemental Videos: We found your supplemental videos extremely informative. Would it be possible to include these in the main text?

      Madison McReynolds and Mandkhai Molomjamts (Indiana University Bloomington) - not prompted by a journal; this review was written within a Peer Review in Life Sciences graduate course led by Alizée Malnoë with input from group discussion including Sally Abulaila, Kim Kissoon, Michael Kwakye, Madaline McPherson, Habib Ogunyemi, Octavio Origel, and Warren Wilson.

    1. On 2025-03-10 04:21:18, user Young Cho wrote:

      Dear Authors,<br /> Thank you for sharing your insightful work, "In Silico Engineering of Stable siRNA Lipid Nanoparticles: Exploring the Impact of Ionizable Lipid Concentrations for Enhanced Formulation Stability." Your study makes an important contribution to the field of lipid nanoparticle (LNP) research by highlighting the role of ionizable lipid concentrations in siRNA encapsulation and stability. The use of coarse-grained molecular dynamics (MD) simulations and steered molecular dynamics (SMD) provides a detailed molecular-level understanding of LNP formation, which is particularly valuable for optimizing RNA-based drug delivery systems.<br /> Summary<br /> This study examines how neutral and positive ionizable lipids influence LNP stability and siRNA encapsulation efficiency. The findings indicate that LNPs with positive ionizable lipids encapsulate siRNA more effectively than those with neutral lipids, likely due to their integration with phospholipids and the prevention of siRNA escape. Interestingly, low and medium concentrations of both neutral and positive DLKC2 showed better compartment formation and encapsulation efficiency compared to high concentrations. Additionally, neutral lipids exhibited greater aggregation, which could impact LNP stability.<br /> Introduction<br /> Your introduction effectively establishes the relevance of this study by situating it within the broader context of LNP research. The discussion of existing challenges in siRNA delivery and the role of lipid composition is well-articulated. However, further elaboration on how your study builds upon previous experimental findings could help connect computational insights with practical applications.<br /> Results<br /> The figures and data presentation generally support your conclusions. Figure 4, which illustrates LNP compartment formation at different lipid concentrations, is particularly valuable in showing how high concentrations lead to instability. We do think that some quantitative metrics such as bilayer thickness, lipid density, or compartment size would enhance the strength of these findings. Additionally, since water is omitted from the visualizations for clarity, we think it would be beneficial to include a figure that shows water so we can visualize the hydration effects and lipid-water interactions.<br /> Discussion<br /> Your discussion effectively compares findings with prior studies, reinforcing that positive ionizable lipids enhance siRNA encapsulation and that lipid aggregation in neutral systems may reduce stability. While you mention previous molecular dynamics studies (e.g., Paloncýová et al. and Trollmann & Böckmann), we feel a more direct comparison of numerical data and trends from these works would further contextualize your results. Additionally, discussing potential experimental validation techniques (e.g., cryogenic electron microscopy or encapsulation efficiency assays) could provide future directions for integrating simulations with laboratory-based studies. However, that is just our opinion as we do understand that this study takes on a more computational approach and is still very impactful.<br /> Suggestions for Improvement<br /> 1. Expand quantitative analysis in Figure 4 by including measurements of bilayer thickness, lipid density, and compartment size to provide a more rigorous validation of LNP stability.<br /> 2. Clarify the role of hydration in lipid-water interactions since water was omitted in visualizations.<br /> 3. Strengthen comparisons with previous molecular dynamics and experimental studies by integrating direct numerical contrasts.<br /> 4. Discuss potential experimental validation approaches that could complement your computational findings and enhance their real-world applicability.<br /> Final Thoughts<br /> Overall, this paper presents a well-structured and valuable contribution to siRNA delivery research. With minor refinements in quantitative analysis, literature comparisons, and discussion of experimental validation, the study could be even more impactful. Thank you for your efforts in advancing the field of LNP-based RNA therapeutics!<br /> Best regards,<br /> UHM MBBE 602 Graduate Students

    1. On 2024-12-06 17:54:14, user Malte Elson wrote:

      The remarks below are a summary of the points discussed during the Cake Club of the Psychology of Digitalisation lab at University of Bern ( https://www.dig.psy.unibe.ch/studies/cake_club_/index_eng.html ). They do not reflect the opinions of each individual journal club participant. Any responses to these points should be addressed to Malte Elson.

      In their preprint, Spiess et al. (2024) illustrate the impact of influential data points on statistical significance in linear regression analyses. The authors reanalyzed data from three high-impact journals by searching for the term "linear regression” and digitizing graphs of the included papers (due to the absence of raw data). Their findings revealed that excluding influential data points often rendered previously significant results non-significant. The simulations included in the study largely confirmed expected outcomes, supporting the overall argument for incorporating leave-one-out analyses in data analyses practices. The authors ultimately advocate for broader adoption of such methods to enhance the robustness of statistical conclusions.

      We found the paper to be interesting and an illustrative contribution to statistical education, both in terms of the potential fragility of published claims and as an illustration of an intuitive but underused outlier detection method. We identified points that might allow the authors to strengthen future versions of the manuscript, including some critical points about potential weaknesses or absences in the current version of the manuscript.

      1) TERMINOLOGY CONFUSION AND REPORTING ISSUES<br /> * Graphs vs. Papers: There is some confusion regarding the unit of analyses, and probably some reporting errors: On p. 4, l. 115, the paper states that the sample was 24 + 30 + 46 = 100 graphs, whereas on p. 6, l. 170 the authors state they examined 100 publications (going by Table 1, this is a simple clerical error, and should say graphs).

      * Similarly, the description of the columns in Table 1 (p. 11) is confusing, and we think has at least one reporting error:

      * It is unclear what “Hits” represent: Are these unique papers, or do the search engines of Science/Nature/PNAS return the same paper multiple times for each instance of the search term (“linear regression”)?

      * What does "number of graphs that were not shown" mean? We think these are instances of linear regressions that simply were not reported with a corresponding graph in the original publication, but they could also be graphs missing, inaccessible, or excluded <br /> * The “Articles” column is described as “number of Articles in which the analyzable graphs were found” (p. 11, l. 314), but we think these are the 21 articles in which the 29 “influential variables” were found. The number of articles with analyzable graphs is not reported. It thus remains unclear how many papers were included, and how many graphs were analyzed from each paper.

      * On p. 6, the authors report having identified 29 graphs in 21 papers in which the removal of one datapoint changes the result of a linear regression (see also Figure 1). On p. 6, l. 179 the “incidence” (should be prevalence instead) of changes in papers is reported as ~20%. However, this puts papers (21) in the numerator and graphs in the denominator (100), which underestimates the prevalence. On the graph-level, it should be 29/100 = 29%. The paper-level prevalence cannot be calculated because the authors do not report the number of papers with analyzable graphs (see above).

      * We strongly recommend reporting a Prisma flowchart to clarify the inclusion/exclusion of graphs and papers. In the same vein, the paper lacks basic information about the included studies, such as sample sizes or the distribution of p-values. Other information would also help emphasizing the importance of the present study, e.g. citation metrics.

      * The authors refer to “Supplementary Data 1” (p. 4, l. 121) but provide no link.

      2) SAMPLING STRATEGY <br /> * The study focuses on digitizable graphs without overlapping data points, inherently excluding studies with (1) larger samples and (2) homogeneous effects, where overlapping data points should be more frequent. This selection skews the included papers towards studies with smaller samples and p-values near 0.05 (due to lower power and publication bias / p-hacking), which are more susceptible to the illustrated effects. This is not a problem per se, but means the findings (including the prevalence rate) are about a narrower population of studies. Either way, the selection effects should be discussed in the paper.

      * It is not fully clear how it was decided which graphs are analyzable and which are not. Moreover, on p. 4, l. 127-130 the authors state that the obtained regression parameters match those reported in the paper closely, but they do not further explain what exactly this means, or what happened when they did not match

      3) ANALYSES AND CONCLUSIONS <br /> * The analysis does not account for dependencies when multiple graphs from the same paper, which will likely be based on the same data (which are then susceptible to the exclusion effects), are included.

      * In a way, the susceptibility of findings to the removal of a single data point is a restatement of issues related to small samples. Small samples are inherently more fragile, and larger sample sizes are more robust to the influence of removing (or adding) single data points and render p-values (and other estimates) more stable. This is not to say that the findings reported are not interesting; however, we were wondering whether a table of all included studies sorted by observed p-value and sample size would have flagged the same fragile papers. This is also not to say that dfstat is redundant, and we absolutely see the pedagogical value in being able to point at individual data points that “cause” a finding to be significant. Rather, we would be interested to what extent dfstat converges with common heuristics.

      * Relatedly, the authors decry that influence measures such as dfstat are largely ignored, even by statisticians (p. 4, l. 139). This may well be, but of course, statisticians (and non-statisticians) are obviously aware of issues related to low power and small samples, and one of these issues is the problem of spurious findings (e.g. due to few, extreme data points).

      * The authors largely blame frequentist statistics, particularly on p. 10, where e.g. they state that “[a]s long as stating significance or not is still based on the ubiquitous α = 0.05 threshold, these statements can be sensitive to the presence of a single data point.” (l. 282-284). However, it is unclear how this follows from their findings. Any inference (not just α = 0.05) could be susceptible to the influence of single data points when the estimate is close to the criterion. Moreover, particularly when the sample size is low, any metric’s value (e.g. point estimates) will vary as a function of the removal of individual data points, regardless of whether the inference is threshold-based or not. This is simply a property of statistical models fit to a limited amount of data. So again, the issue seems to be with small sample sizes.

      4) RECOMMENDATIONS AND FUTURE DIRECTIONS<br /> Things we would have liked to see:

      * Additional analyses, such as leave-two-out or leave-k-out methods. The leave-one-out analyses are providing a good intuition of how fragile some small-sample study results are. Additional leave-k-out analyses would provide further information about the fragility of the entire sample.

      * So far, the authors are concerned with the fragility of results as an outcome of removing data points. An additional study exploring the reverse scenario would be valuable. Specifically, it could investigate how extreme an additional data point would need to be to alter results, and how adding non-extreme data points could mitigate the relative weight of extreme data points.

      * Discussing dfstat as a robustness metric (“How many individual data points would have to be removed/added to render a significant result nonsignificant or vice versa”)

      * A discussion of how dfstat could be used for p-hacking by showing researchers which data points they would have to remove to turn a nonsignificant study result into a significant one.

      * The authors graciously and immediately shared data and code with one of us who requested it, and we thank them for this. We would like to see this data and code provided in a public repository and linked to in a future version of the manuscript.

      * We note that the authors chose to anonymise their data so that the reader cannot tell which original study’s results are robust or not. Personally, we think that meta-scientific interests are best served by making this information public; that is, we would like this data to not merely be used to illustrate the method but also inform the reader about the fragility or robustness of those publications’ results. Of course, not everyone agrees with this practice - perhaps the authors could comment on their perspective on this issue in a future version of the manuscript.

    1. On 2024-07-15 17:30:04, user priyanka.bajaj3193@gmail.com wrote:

      Reviewed by Priyanka Bajaj and Christian B. Macdonald (UCSF)

      Summary:

      Fusion oncoproteins occurring from genomic rearrangements are commonly observed in cancers and often drive oncogenesis. Although these fusions frequently involve kinases or transcription factors, they are a diverse group at both molecular and functional levels, and a unified description of their oncogenetic properties is lacking. Robust methods for predicting oncogenicity of unknown fusions would be immediately clinically useful, making this an important gap. At a more basic level, this points to a gap in our ability to describe a key biological phenomenon. Some recent work has tackled this problem by examining the physicochemical properties of fusion oncoproteins, notably [1], but this is essentially still an open question.

      In this manuscript, the authors present a language model of fusion oncoproteins, FusOn-pLM, by fine-tuning ESM-2 with two recent databases of human fusion oncoproteins. They compare random masking vs. one using their previous fine-tuned ESM-2 model SaLT&PepPr and benchmark their results on a number of tasks, demonstrating reasonably increased specificity on specific tasks and improvement with non-random masking. The model training and benchmarking are sound and convincingly demonstrate the improvement.

      Despite this, the lack of clarity about what unifies fusion oncogenes is a major challenge. Language models can be powerful ways to learn these sorts of definitions in a less biased way, and in that light this is an important step towards clarifying this basic gap. However, as written, the work uses a working definition of fusion oncogene that is based on physicochemical properties that may or may not be specific to oncogenes. Examining the benchmarking tasks the authors use makes this clearer: they are almost entirely predictions of condensate and IDR properties rather than oncogenetic ones. The one truly cancer-specific benchmark, differentiating carcinoma classes, is fairly narrow and no model performs particularly well here. As a result, we are unsure how strongly this model will perform in discrimination or generalization tasks.

      Another general problem for the field is the lack of negative controls. Gene fusions are relatively common mutations, but bona fide oncogenic fusions are a small fraction of all fusions, making this a class imbalance problem. Even within tumors, the majority of fusions are thought to be passengers rather than driver mutations. Any predictor should be able to discriminate between these, but the lack of good data on non-oncogenetic fusions makes this challenging. This is evident in this work, where the model’s discrimination is not strongly tested.

      In summary, we believe this is technically strong work which addresses a pressing need, and which also presents some general strategies for domain-specific language model fine-tuning, but which is unfortunately hamstrung by defects in the available data and conceptualization of the field that are outside of the authors’ control. As presented, it will be of interest to AI practitioners and oncofusion researchers, but the clinical utility is unclear.

      Major points:

      1) As discussed, we think the concept of an “oncofusion” is somewhat diffuse, as it describes an extremely heterogeneous set of proteins. This makes the prediction task particularly difficult. While the introduction discusses the barriers to prediction of fusion oncoproteins due to their intrinsically disordered regions and large size, we believe a bit more care with the effective definition they are using is warranted. Related to this is the choice of FOdb to train their model, which is essentially a database of condensate properties of oncofusions rather than oncogenetic ones. The implications of this choice also warrant a bit more discussion.

      2) We wonder if there is a class imbalance problem. The databases used to fine-tune their model have a small fraction of possible fusion proteins, and don’t contain large amounts of negative training information. We are thus unsure if FusOn-pLM’s significant improvements over ESM-2 are specific to driver fusion oncogenes.

      3) The method is not contextualized with respect to prior work in computational oncofusion prediction and characterization. Such methods are few ([2],[3],[4],[5],[6] among others) but important to understand FusOn-pLM’s performance.

      4) Several experimental datasets for fusion oncogenes have been published, including [7], [5], and [8]. FusON-pLM’s performance on these would be a compelling way to show its utility, as well as a more specific oncogenetic task.

      Minor points:

      1) Figure 2D: Although FusON-pLM is doing a slightly better job at distinguishing carcinoma prediction into two classes (BRCA vs. STAD), the performance metrics are the worst across the board. What does this mean for the prediction problem overall? Does the fact that IDR and condensate properties are much better predicted mean that the model is actually not learning an oncogenetic task? This seems worthy of more discussion.

      2) Figure 4A: The authors present a FusOn-pLM embedding visualization of fusion oncoproteins, along with the corresponding head and tail protein sequences. It would be beneficial to clarify whether the protein sequences used for the head and tail counterparts are full-length sequences or only up to the exon breakpoint that forms the chimeric fusion protein. This information can be included in the Materials and Methods section.

      3) Figure 4A: The authors demonstrate that FusON-pLM is able to separate out fusions from their head and tail components. To demonstrate that it is learning more specific embeddings for fusion oncoproteins, a comparison of the embeddings with untuned ESM-2 would be appropriate.

      4) Figure 4B: In the main text of results section the authors write “FusOn-pLM largely clusters sequences by key properties such as the fraction of polar, charged, and disordered residues as well as the propensity to form pi-pi and pi-cation interactions and prion-like domains, via the PLAC NLLR score.” From the data shown in Figure 4B, this conclusion seems fine for polar residues and NLLR scores, but not for disordered residues and pi-pi/pi-cation interaction propensity by eye. Without quantification of the clustering, we are not sure this statement is supported.

      References:<br /> 1. Tripathi S, Shirnekhi HK, Gorman SD, Chandra B, Baggett DW, Park C-G, et al. Defining the condensate landscape of fusion oncoproteins. Nat Commun. 2023;14: 6008.<br /> 2. Shugay M, Ortiz de Mendíbil I, Vizmanos JL, Novo FJ. Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions. Bioinformatics. 2013;29: 2539–2546.<br /> 3. Abate F, Zairis S, Ficarra E, Acquaviva A, Wiggins CH, Frattini V, et al. Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. BMC Syst Biol. 2014;8: 97.<br /> 4. Lovino M, Montemurro M, Barrese VS, Ficarra E. Identifying the oncogenic potential of gene fusions exploiting miRNAs. J Biomed Inform. 2022;129: 104057.<br /> 5. Li J, Lu H, Ng PK-S, Pantazi A, Ip CKM, Jeong KJ, et al. A functional genomic approach to actionable gene fusions for precision oncology. Sci Adv. 2022;8: eabm2382.<br /> 6. Liu J, Tokheim C, Lee JD, Gan W, North BJ, Liu XS, et al. Genetic fusions favor tumorigenesis through degron loss in oncogenes. Nat Commun. 2021;12: 6704.<br /> 7. Frenkel M, Hujoel MLA, Morris Z, Raman S. Discovering chromatin dysregulation induced by protein-coding perturbations at scale. bioRxiv. 2023. doi:10.1101/2023.09.20.555752<br /> 8. Kobayashi Y, Oxnard GR, Cohen EF, Mahadevan NR, Alessi JV, Hung YP, et al. Genomic and biological study of fusion genes as resistance mechanisms to EGFR inhibitors. Nat Commun. 2022;13: 5614.

    1. On 2024-06-07 16:53:51, user Reviewer 6 wrote:

      I am a C. elegans researcher with some familiarity with the topics discussed. I do not personally know, nor have I interacted with any of the authors involved. I have read in detail both the preprint and the response in the comments. Below I provide some comments in the hope that they will hone arguments from both sides. For brevity, I refer to the authors of this preprint as “the authors” and Dr. Coleen Murphy as “CM”.

      Summary:<br /> In my view, there are two issues here (1): the technical reproducibility of the choice assay; and (2) the physiological importance of CM’s results in a natural setting given the points raised by the authors. While CM makes some valid arguments on (1) – the authors should really have shown at least a few assays that attempted to follow the protocol exactly as stated by CM – the deviations here are in my view minor enough to raise significant questions about the choice assay and its interpretation. I believe the authors are justified in stating that (2) if the variables discussed here indeed significantly obscure detection of the phenotype, then the ecological significance of the inherited learned avoidance in a natural setting is in question. This is especially important given that, contrary to CM’s response, the authors do in fact see learned avoidance of PA14 as well as daf-7 expression at P0 and F1 in some experiments (indicating that the learning was induced) but not beyond in the F2 progeny of these same worms which displayed learned avoidance. Below is a detailed discussion of these points.

      Specific comments:<br /> - CM states that the lack of naïve PA14 preference seen by the authors is a “serious cause for concern”. In CM’s 2024 paper (Fig 1, https://journals.plos.org/p... , worms are tested for bacterial food choice between OP50 (the lab food) versus bacterial species C. elegans may be exposed to in the wild. However, it seems that worms naively avoid OP50 (i.e. ‘prefer’ test bacteria) in essentially every comparison made by CM. This is contrary to reports by other labs (PMID: 38228683, PMID: 38228683) and in my view potentially a more serious concern with the assay. Contrary to CM’s assertion, while CM’s group and others see *mild* PA14 preference in naïve worms, other groups also do not observe such a preference in naïve worms or report more variable results (e.g., PMID: 21172617, PMID: 28877481, PMID: 31371455). Overall, the authors did replicate P0 and F1 learned avoidance in some runs and had a “learning index” consistent with prior reports in these experiments, so I do not see how the lack of purported naïve PA14 preference (which is quite minor and variable to begin with) is a significant concern here. <br /> - Looking at the authors’ raw data (table S2) for individual experiments, it seems the authors used <200 worms as advised by CM for most of their plates. The “up to 770 on a spot” was from a single plate, so I do not think this would change the conclusions of the authors. The authors compared worm density with choice index and found that there is no correlation within the ranges tested here.<br /> - “no azide or other paralytic used” (CM) – the authors claim to have tested this and state that addition of azide did not affect their results. They also claim that worms make a choice within 15 minutes and do not leave the respective lawn in the first hour of the assay. But none of this data is shown (it should be). <br /> - It seems that CM’s group counts worms in proximity to lawns “if they are within a few millimeters of the bacterial spot.” (STAR protocol). This may introduce systemic bias given the OP50 and PA14 lawns are clearly visibly distinct. Again, this raises questions to me regarding the reliability of this assay for interpreting minute effects and making broad generalizations.<br /> - Aspirating worms for counting would be unlikely to affect results.<br /> - The fact that conditions tested by the authors are varied between experiments is in my view a strength of this study given they did not observe F2 effects in any of their tests (you would normally change parameters rather than keep repeating the same protocol if you were unable to reproduce something, no?). However, testing variables/conditions such as temperature, light/dark etc. are informative only in a context where the authors have first fully followed through on the exact CM protocol with no deviations. So, I do think it is crucial to show a few attempts where the protocol is followed exactly as stated by CM.<br /> - The use of Triton X after bleaching may be a concern as CM points out. Though seemingly low (0.01%), this may hypothetically make bleached (i.e. already somewhat stressed) embryos or newly hatched L1s more vulnerable to pathogenic bacteria or alter their physiology. I do not see a point in including Triton X during or after bleaching, it is not standard nor required and is certainly a confounding variable. However, given the CMC of Triton X is 0.02% and the authors use below this concentration and only during plating, I would be surprised if this led to a dramatic change in the phenotype observed.<br /> - I do not find CM’s critique on daf-7 expression to be substantive. CM asserts that the authors do not see elevated daf-7p::gfp expression. Except they do! Which is especially evident with the single copy (SC) construct Fig 2 under SC at both 20 and 25oC. The magnitude of P0 daf-7 increase with the SC construct (~2 fold) is similar to what other groups observe at this generation (albeit with the multicopy strain, so it is hard to compare). I think the use of a single copy reporter is a strength of this paper, but in the future assays of daf-7 expression should really be done using endogenous CRISPR/Cas9 reporters. That an F2 response is not observed in runs where there is a high upregulation in the F1 generation is consistent with the authors’ interpretation.<br /> - The authors should show representative images of what is being quantified as CM states, as without this we do not know which neurons are being assayed. I do not think averaging both ASI neurons in a worm is a concern – even if there is an increase in one ASI, it would still be reflected in the average (as long as the correct neuron is being quantified). It may even reduce variability or bimodality to average the two, given the brightness of reporters on a confocal image can depend on the depth of the imaging plane as the authors state. <br /> - CM states that chunking is an unusual way to maintain the fluorescent strain. But this is a genomically INTEGRATED multi copy array (ksIs2), no? The point of the authors is that the fluorescence expression and associated Rol marker are unstable in their expression, which is not unusual for such integrated repetitive multicopy arrays. This is not an extrachromosomal array wherein fluorescent worms need to be picked to maintain the array, so CM’s statement that it is “standard accepted practice” to do so is simply wrong. In fact I find it quite concerning if CM’s group picks fluorescent worms to maintain this strain as it biases the worms for an epigenetic state in which the integrant is poised for expression, which may indicate other epigenetic issues in the strain’s background (i.e., lack of silencing of repetitive sequences). The instability of this strain I assume is why the authors obtained a single copy daf-7 reporter, which in any case would supersede any results obtained from a multicopy array. CM says nothing about the single copy integrant results, and I believe that given the authors observe P0 and F1 upregulation with the single copy integrant, I think the case is solid that there is no response observed in F2 worms from F1s showing daf-7 upregulation. An endogenous CRISPR/Cas9 reporter (e.g., transcriptional/SL2::GFP if a translational fusion is not possible) would really push home this point. <br /> - CM states that the authors replicates show poor “consistency”. However, we can only see this because the authors, unlike CM, show each experiment independently! We have no idea whether every experiment CM performed actually displayed learned avoidance behaviour, given the source data for CM’s choice assays is apparently not public. CM’s reports only show all learning experiments in aggregate, and I believe if the authors aggregated all their runs herein to a single plot, they would indeed see a seemingly ‘consistent’ avoidance effect. CM could easily address this by releasing raw/source data for choice/learning assays.<br /> - CM claims that in their hands behaviour from a set of training plates is ‘always’ consistent, but data are not shown. Both sides need to avoid making important claims without showing data.<br /> - CM states that the authors use of the same population to assay and then maintain for the next generation may confound the results. Again, the authors need to do the assay exactly as stated by CM, but if a few extra minutes of suspension in buffer really so obscures the phenotype beyond any detection, then how ecologically relevant can it possibly be? To my knowledge, there is no major phenotype that is completely ablated by a few minutes additional incubation in buffer. By this standard nothing involving washing off worms in a buffer would be interpretable.<br /> - It is interesting that sid-1 and 2 mutants do not show a learned F1 avoidance, but daf-7 expression is still elevated. It may be sufficient to have one SID protein for elevated daf-7 expression in progeny but require both for the behavior. Given both sid-1 and 2 are RNA transport channels, without double mutants and reliable daf-7 readout from an endogenous reporter, it is difficult for either group to infer any epistatic relationships between these genes. <br /> - I read the protocol file with notes from CM. I did not find any changes that are severe enough to cause concern and it seems that these are more clarifications/updates than changes to the fundamental principles of the assay. I also did not find the authors’ statements on this disingenuous, as there were clearly differences between the original STAR protocol and the updates provided. It is important for both parties here to refrain from personal attacks and address the substance of the arguments made.<br /> - I did find that some details in the STAR protocol were excessive, e.g., the height of plate stacks. I appreciate the detail but again, this raises the question that if such artificial variables really influence the phenotype so severely that it is no longer at all detectable, how physiologically relevant or robust can the phenotype be? <br /> - The statistical error in the STAR protocol pointed out by the authors: it seems either CM is misinterpreting a two-way ANOVA or that this was an oversight. I did not find this point too important overall as correcting such a statistical error would not change the conclusion of CM’s papers given the magnitude of effects previously described. <br /> - CM states that expression of P11 is essential for TEI. In CM’s 2020 paper (Kaletsky et al) it is stated that: “moreover, training on a P11 mutant that disrupts the perfect match to maco-1 but conserves P11 secondary structure induced no avoidance (Fig. 4e)”. As written, it seems essential not just for TEI (F2 effect) but also the P0 learning itself (unless CM can clarify that it is only required for the F2+ effect and that in Fig 4e only F2+ are being tested). So as I understand it, if lack of P11 expression is the issue, then there should be no P0 or F1 avoidance at all in any of these runs. Given the authors do not see an F2 effect in worms with robust P0 and F1 responses, it seems that this point is moot. I also do not think the authors can be blamed for any putative lack of P11 expression as it seems that for this portion (PA14 growth) they adhered to the protocol quite closely and explored various PA14 lines including those obtained from CM’s and other labs.

      In summary, I think CM’s response is insufficient to alleviate many of the key concerns raised by the authors herein. I do not believe the lack of naïve PA14 attraction is a major concern, as there are literature examples where (a quite minor) naïve PA14 attraction is not observed. Furthermore, this is also confounded by CM’s recent (2024) paper wherein their worms prefer essentially every bacterium among a panel over OP50 in a naïve test, again contrary to prior reports from other labs. This makes me question the robustness as well as any broad conclusions that can be drawn from this assay.

      The authors do also observe P0/F1 learned avoidance and elevated daf-7 expression contrary to CM’s rebuttal. I agree that the effects shown are not consistent between experiments here, but we cannot say whether this is simply because we are seeing here individual runs of inherently inconsistent assays whereas looking at an aggregate of data in CM’s papers (since the source data for the choice assays are not public). The major concern is that in those populations with P0/F1 responses (meaning the learning has been successfully induced), there is no further inheritance of avoidance beyond F1, and similarly for daf-7 wherein populations expressing high daf-7 at P0 and F1 do not transmit this to progeny. I believe this precludes “basic concerns about [the authors’] bacterial and C. elegans growth conditions, assay conditions, and assay techniques”. Overall, while it is important for the authors to show a few runs where the protocol is followed exactly as described by CM, I believe the deviations here are minor enough that even if they were able to replicate the transgenerational effect successfully, the sensitivity of the effect to such minutia would greatly diminish its physiological relevance to the worms - and its importance as an adaptive paradigm of transgenerational epigenetic inheritance - in a natural setting.

      I also do not find it constructive for any party involved to address anything other than the scientific substance of arguments or engage in personal attacks. Given the attention and broad reach these studies have garnered, as well as the important implications, it is essential – and the normal course of the scientific endeavor – for such claims to be rigorously tested.

      I also very much appreciate that the authors have shared these observations, and find it very commendable that CM has responded in a timely and comprehensive manner (as well as been responsive to the authors in refining their protocol).

    2. On 2024-06-05 18:16:30, user Coleen Murphy wrote:

      Point-by-point critique of Gainey et al. 2024:

      Figure 1: <br /> 1. (A-C) It has been reported by many groups that PA14 is mildly attractive to C. elegans, that is, given a choice between PA14 and OP50, worms choose PA141,2. However, in almost every assay shown in this paper, the worms prefer OP50 over PA14 – that is, they are already avoiding PA14 - prior to training (naïve preference), which is odd. This suggests that the authors are not using conditions that are standard, either in PA14 or OP50 growth or in choice assays (see note about choice assay performance). This is a serious cause for concern that is independent of any training conditions. In fact, as far as we can see, in only one case (Fig. 1C, F1) did their experiments replicate the naïve choice results observed by other groups. <br /> 2. Choice assays: their “choice assays” involve putting 3-4x the recommended number of worms on a plate (up to 770 on a spot!), letting them roam for variable amounts of time (“30-60 minutes”) without trapping them (no azide or other paralytic used), and then putting them in a 4°C incubator (which does not immediately halt worm movement), then counting them. None of this follows our published choice assay protocols, or the standard chemotaxis assay protocol3–6. Putting more than 200 worms on a single plate can lead to altered choice because of crowding. In the absence of a paralytic, worms change their preference due to various factors, including adaptation; therefore, in this case, the worms’ first choice (which is what we measure in all our assays) is not being measured. They also count the worms by “aspirating” the worms off of the plate, which is not standard in any behavioral assays, as far as we know.<br /> 3. Table 2 and Figure 1: There are almost no true replicates, as in each experiment, at least one or more condition is changed. (For example, the authors only tested the PA14 we sent them in one replicate - Exp 3). <br /> 4. daf-7p::GFP imaging experiments (Fig. 1D, F, H) – Hunter and colleagues do not report seeing increased daf-7p::gfp expression in the P0 generation. Increased daf-7p::gfp expression after exposure to PA14 has been reported by multiple groups7, not just ours, and is usually not small or highly variable, as it is due to the combination of bacterial cues and P11 small RNA; if they cannot replicate this basic result, it suggests that something is seriously wrong with their protocols or technique, or their worms are very sick, even before trying to use our protocol to train worms. <br /> 5. Additionally, they do not report the expression of daf-7p::gfp in the ASJ neuron7, which is very strange, since we have been able to reliably replicate Meisel, et al.’s finding in the P0 generation. Therefore, it is not clear from which neuron the authors are quantifying daf-7p::gfp levels. <br /> 6. Instead of imaging and reporting fluorescence levels in individual neurons, the authors averaged fluorescence intensity/worm, which is explicitly not what we did or others have done, because different neurons in each worm can have different intensities – particularly if they are the ASI rather than ASJ neurons. <br /> 7. While we see modest decreases in fertility after PA14 training, the authors report severe decreases in fertility: about one fifth of normal egg production, and a severe developmental delay) in their F1 generation that we do not observe. Both facts indicate that their worms are very sick, even the worms that have not been exposed to PA14. If their worms are extremely sick, it might account for the small number of progeny, poor imaging results, and a developmental delay that shifted the training times. This could be a result of overbleaching, which causes developmental delays; the bleaching protocol described in Gainey et al. deviates from our published protocol. Additionally, they add Triton X100 to their final M9 wash, which is used (although at a higher concentration) to permeabilize embryos in other protocols. We are not aware of any bleaching protocols that include Triton in a wash step, and our lab certainly does not; this addition might also damage the progeny.

      Figure 2 <br /> 1. P0 imaging data suggest that the daf-7p::gfp response to PA14 is not reproducible in their hands; again, this has nothing to do with our paper or protocols, but rather appears that they cannot replicate previous results in the field that precedes our work. <br /> 2. Does “25°C” mean that the worms were grown at or assayed at 25°C, or both? This high temperature is generally hard on the worms. <br /> 3. Technical note: it appears that instead of consistently picking fluorescent daf-7p::gfp animals, the authors “chunked” large groups of worms, resulting in populations of non-fluorescent animals in their experiments. <br /> 4. Scale of P0 and F1 are extremely different (due to sickness of the P0s?).

      Figure 3 <br /> 1. Notes that panels A, C, and D are repeated from Figure 1.<br /> 2. The authors discuss “OP50 aversion” but this does not make sense, since both trained and untrained animals are placed on HGs after bleaching. <br /> 3. Their naïve in F1 is sometimes even lower than in the P0 (Fig. 3D).<br /> 4. There is no consistency in their results across replicates, within experiments, or across figures of the paper – not just the inability to see an F2 effect, but in their naïve chemotaxes, P0 trained choice indices, and F1 results; the authors claim that their F1 assays are reproducible, but only 3 out of the 9 assays in this figure show F1 learned avoidance. <br /> 5. In 3J, data that are not replicates, as they have been performed using different conditions, have been pooled. <br /> 6. Gainey et al. observe substantial variation in behavior between training plates (Figure 3, table 2, S2 annotated protocol), and incorrectly treat each training plate as a biological replicate, rather than a technical replicate. (Each training plate is seeded and grown in the same conditions, and worms from the same bleached population are added onto the plates, therefore these are not biological replicates but rather technical replicates; biological replicates require starting with different worm populations and carrying out the whole experiment independently.) In our hands, behavior from a set of training plates is always consistent. <br /> 7. Additionally, we note that the authors use the same population of worms for the choice assays and subsequently for bleaching, meaning that worms are held in liquid for an extended time before bleaching; this may cause worms additional stress which may interfere with behavior.

      Figure 4 <br /> 1. OP50 growth conditions: this would only matter if the controls and experimentals were grown on different plate types, which is not the case (but if the authors are in fact putting the controls on different plates from experimentals, then the experiment is done incorrectly).

      Figure 5 <br /> 1. We also found that sid-1 and sid-2 are required, but since their controls are inconsistent (Fig. 3) in the first place, it is hard to know how to interpret their data. <br /> 2. Other mutants (rde-1, hrde-1, sid-1, sid-2) – still show increased daf-7p::gfp in F1 – again, these data are hard to interpret since they do not show a wild-type control that worked here. This also has little bearing on our work since other training paradigms (e.g., 4- and 8-hour training that engages small RNA-independent pathways) also induce daf-7p::gfp. It is also unclear which neuron (ASI vs ASJ) they are imaging.

      Discussion <br /> 1. daf-7p::gfp - Picking fluorescent worms or rollers is standard worm husbandry; it is not a “result” to say that they noticed that Rol can be lost – but it does indicate that they should have discarded any results that they obtained before noticing that the array might have been lost in the worms they assayed. The fact that they have brought this up more than once suggests that they are not using standard accepted practices to maintain transgenic lines. <br /> 2. Dennis Kim’s work on phenazine-induced avoidance has been oddly neglected in this work7. Kim’s group found that phenazine-1-carboxamide induces Pdaf-7::gfp expression in the ASJ neuron, which we see quite reliably in our assays as well. No Pdaf-7::gfp imaging of the ASJ neuron is presented in this work, suggesting that either the PA14 they grew also did not make phenazines, or their image analysis is unreliable. <br /> 3. They made a lot of changes to our protocol (temperatures, light/dark, etc). We cannot find in this paper a single example of an experiment that followed our protocol entirely. <br /> 4. The authors make a point of calling OP50 a pathogen, which is odd; C. elegans grown on OP50 typically live for 2-3 weeks. They cite Garigan et al. 20028, which showed that when worms get old (past 15 days) eventually the pharynx stops grinding up bacteria and the gut will start to fill up with OP50, and killing bacteria does slightly extend lifespan - but this is not an effect observed in young (Day 1) animals on the short timescales used in the experiments here. In any case, since both control and trained animals are grown on HG plates with OP50, it cannot explain the behavior of the control animals. <br /> 5. The authors also never replicate the “bias towards Pseudomonas in choice assays ((Ha et al., 2010; Lee et al., 2017; Moore et al., 2019)” – Those papers also used OP50 vs PA14 to demonstrate this bias towards Pseudomonas, so it is unclear how the author think that their failure to replicate this basic finding is somehow supportive of any of their arguments. It is more likely that there is something fundamentally wrong in their initial conditions that have prevented the replication of all other groups’ findings, not just ours. Moreover, in our experiments, other than the 24 hrs of training on PA14 vs OP50, our control and trained animals are always on the same plates. This argument makes no sense, unless the authors have introduced an additional variable of plating control worms on one kind of plate/bacteria and their trained animals on a different plate/bacteria (which we do not do). <br /> 6. It is unclear why the authors grew worms at different temperatures. 20°C is the standard temperature for worm growth and assays. <br /> 7. In our hands, naïve OP50-PA14 choice index is not significantly different between P0 (when NGM plates are used) and the subsequent generations (when HG plates are used). The survival assay correlates well with the idea that their worms are very sick, much sicker than we see in our assays, although the sparse intervals in both assays make it difficult to draw any conclusions – not possible to draw the conclusion that the bacteria are “more lethal” since they are trying to compare two lifespans from different labs etc. - but if they are, it might be due to their PA14 cultivation conditions or the health of their worms. But the fact that they see massive leaving and desiccation of worms, they might indeed be growing PA14 under much more pathogenic conditions. <br /> 8. The authors state: “Near the conclusion of these experiments, we received an updated protocol that included several clarifying edits and additional deviations from the published protocols (C. Murphy, Personal communication).”

      We clarified our protocols, we didn’t “deviate” from them. This is a concerning way to present our email communications in which we tried to correct errors in their protocol and offer constructive advice; we even extended an invitation to Hunter to visit our lab to learn the assay. We are happy to provide these emails if necessary.

      In order to help others, we continuously update our lab’s protocols to make clarifications that will help future users. Any note from the Murphy lab is an example of this type of updating. For example, later we made a new bacterial construct that used a Kan marker and constitutive promoter instead of an Ara inducible promoter and Carb marker to streamline experiments. This is not a deviation, it is a natural progression of the research in our lab and our practice of continuously improving our assays and updating protocols.

      It is disingenuous for the authors to present our updates to our protocols as if we have “deviated” from them – in every instance, we gave the authors all of the information that we had available to us at the time. Our suggestions were made genuinely and in good faith, with the assumption that the authors wanted to get the assay working rather than using it to point out changes in our protocol.

      Moreover, this statement corroborates our assertion that all or most of the data in this paper seem to have been generated using a protocol that differs significantly from our lab’s, as the bulk of their experiments appear to have been done before contacting us: “Incorporating these changes into our procedures did not reliably alter our results.” (no data shown)

      1. “[T]his example of TEI is insufficiently robust for experimental investigation of the mechanisms of multigenerational inheritance” – The authors failed to test the fundamental requirement for transgenerational inheritance, that is, the expression of P11 sRNA by PA14, which only happens on plates at 25°C. Since they cite our subsequent papers where we first identified P11 sRNA as the key to TEI9, then our finding that the Cer1 retrotransposon is also required for P11-mediated TEI10 and then our finding that other Pseudomonas species use a similar small RNA to induce TEI11, they are definitely aware of this fact. Thus, it is not clear to us why they have not attempted to test P11 sRNA levels while searching for conditions that would replicate our findings. As a result, we can never know whether P11 sRNA was produced in any of the conditions that the authors tested in the experiments shown.

      Together, Hunter and colleagues’ failure to replicate the basic naïve attraction to PA14 over OP50 demonstrated by other labs, their failure to replicate the P0 daf-7 expression published by other labs, and their failure to reliably replicate the P0 and F1 behaviors shown by other labs suggests to us that there are more basic concerns about their bacterial and C. elegans growth conditions, assay conditions, and assay techniques independent of any of the attempts to replicate the findings from our work.

      References <br /> 1. Zhang, Y., Lu, H., and Bargmann, C.I. (2005). Pathogenic bacteria induce aversive olfactory learning in Caenorhabditis elegans. Nature 438, 179–184. https://doi.org/10.1038/nat....<br /> 2. Ha, H., Hendricks, M., Shen, Y., Gabel, C.V., Fang-Yen, C., Qin, Y., Colón-Ramos, D., Shen, K., Samuel, A.D.T., and Zhang, Y. (2010). Functional Organization of a Neural Network for Aversive Olfactory Learning in Caenorhabditis elegans. Neuron 68, 1173–1186. https://doi.org/10.1016/j.n....<br /> 3. Moore, R.S., Kaletsky, R., and Murphy, C.T. (2019). Piwi/PRG-1 Argonaute and TGF-β Mediate Transgenerational Learned Pathogenic Avoidance. Cell 177, 1827-1841.e12. https://doi.org/10.1016/j.c....<br /> 4. Moore, R.S., Kaletsky, R., and Murphy, C.T. (2021). Protocol for transgenerational learned pathogen avoidance behavior assays in Caenorhabditis elegans. STAR Protoc. 2, 100384. https://doi.org/10.1016/j.x....<br /> 5. Kauffman, A.L., Ashraf, J.M., Corces-Zimmerman, M.R., Landis, J.N., and Murphy, C.T. (2010). Insulin Signaling and Dietary Restriction Differentially Influence the Decline of Learning and Memory with Age. PLoS Biol. 8, e1000372. https://doi.org/10.1371/jou....<br /> 6. Kauffman, A., Parsons, L., Stein, G., Wills, A., Kaletsky, R., and Murphy, C. (2011). C. elegans Positive Butanone Learning, Short-term, and Long-term Associative Memory Assays. J. Vis. Exp., 2490. https://doi.org/10.3791/2490.<br /> 7. Meisel, J.D., Panda, O., Mahanti, P., Schroeder, F.C., and Kim, D.H. (2014). Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans. Cell 159, 267–280. https://doi.org/10.1016/j.c....<br /> 8. Garigan, D., Hsu, A.-L., Fraser, A.G., Kamath, R.S., Ahringer, J., and Kenyon, C. (2002). Genetic analysis of tissue aging in Caenorhabditis elegans: a role for heat-shock factor and bacterial proliferation. Genetics 161, 1101–1112. https://doi.org/10.1093/gen....<br /> 9. Kaletsky, R., Moore, R.S., Vrla, G.D., Parsons, L.R., Gitai, Z., and Murphy, C.T. (2020). C. elegans interprets bacterial non-coding RNAs to learn pathogenic avoidance. Nature 586, 445–451. https://doi.org/10.1038/s41....<br /> 10. Moore, R.S., Kaletsky, R., Lesnik, C., Cota, V., Blackman, E., Parsons, L.R., Gitai, Z., and Murphy, C.T. (2021). The role of the Cer1 transposon in horizontal transfer of transgenerational memory. Cell 184, 4697-4712.e18. https://doi.org/10.1016/j.c....<br /> 11. Sengupta, T., St. Ange, J., Kaletsky, R., Moore, R.S., Seto, R.J., Marogi, J., Myhrvold, C., Gitai, Z., and Murphy, C.T. (2024). A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance. PLOS Genet. 20, e1011178. https://doi.org/10.1371/jou....

    1. On 2024-01-16 14:43:15, user Reviewer1 wrote:

      This study investigates the distribution of food source partitioning, across major groups of the animal kingdom. The overarching aim is to create a global trophic pyramid of biomass, partitioned by food source. The authors collected a large dataset on diet composition from the literature and other sources, ensuring a broad taxonomic spread. They then estimate diet partitioning for major taxonomic groups (~class) by averaging species-level data, and further estimate partitioned food source biomass by multiplying with class-level biomass estimates. This is taken to be provide a representation of a trophic pyramid, and the findings are discussed in the light of this concept. The major claim of this study is that they find a middle-heavy trophic pyramid, with invertivory more prominent (by biomass) than herbivory.

      The study pursues a very interesting question in studying the trophic pyramid on a global level. The authors have invested a lot of effort in compiling a large dataset on species-level diet partitioning, and such a dataset would certainly be very valuable for species-level comparisons and analyses, such as the taxonomic distribution of feeding styles or the evolutionary history of feeding specialisations. However, such questions are not the focus of the present study. Rather, an attempt is made to convert this species-level dataset into a trophic pyramid of food source biomass. In the process, the authors make several sweeping assumptions and generalisations, resulting in analyses that are not at all well supported by the underlying data.

      First, the conversion of species-level data to class-level partitioning of food sources, by averaging the data from available species, assumes that the compiled species are representative of the group (class) as a whole, and that a simple species average would provide a meaningful group average. Both are highly doubtful and not supported by any data.

      Second, the assumption is made that the class-level partitioning of food sources can be transformed into a partitioning of diet biomass by a multiplication with that group’s estimated biomass value. However, this will yield the biomass of that specific partition (e.g., the combined bodymass of all vertebrate herbivores) and not the biomass of their diet.

      Third, species groups (and their biomass) are assigned to a trophic level by their food source type, which leads to the three categories “herbivores” (= primary consumers), “invertivores” (= secondary consumers) and “vertivores” (presumably considered as predators including apex predators as they are placed at the top of the pyramid in Fig. 2). This is a strong oversimplification and does not represent a trophic pyramid. Most worryingly, the category “invertivores” will lump many higher-level consumers (third-level, fourth-level…) into the secondary consumer category, which as a result has by far the highest proportion (= biomass in this analysis). Thus, one of the key claims of the study, that the global trophic pyramid is middle-heavy, is likely due to a methodological artifact.

      In summary, the study attempts a methodological shortcut for deriving a trophic biomass dataset from species-level data, without verifying the assumptions. At the current time, there appears to be no ready substitute for species-level abundance or biomass data. Until such data are available for the majority of organisms, analyses of trophic pyramids on a global level may be premature.

      Recommendations for the authors:

      As mentioned in my public review, I commend the authors on compiling such a large and potentially very valuable dataset on species-level diet partitioning. I believe such a dataset can be very informative for species-level analyses, or possible investigations into the evolution of such partitioning. However, such a dataset cannot be transformed into a trophic dataset without corresponding data on species abundances and/or biomass. Your attempts to perform this transformation without such data unfortunately fall short, as it requires a series of sweeping assumptions that are almost entirely unfounded by real-world data.

      I will attempt to explain my views in the sections below:

      Title<br /> The title is misleading: in the current form, the manuscript deals with many more analyses than the number of herbivore and predatory species in each class. Though as I mentioned, this species-level analysis is actually the most relevant (and valid) analysis in your study while the trophic pyramid aspect is not.

      Introduction<br /> You provide a very nice overview of the different concepts of trophic pyramids and their development over time. As you point out, all these variants of the pyramid include a measure of scale for each level, such as ‘abundance’, ‘biomass’, or ‘energy’. It is also implicit in this introduction that this concept considers multiple levels (L42: “…food chains…”, L45: “…and so on up to…”) and not just three as in your following analysis.

      Materials and Methods<br /> The success of the method hinges on the representativeness of selected species. This is highly unlikely, as data on diet composition will be much more readily available for large or well-studied organisms, which are not necessarily the ones that are the most important (by number or biomass) members of their class. The authors themselves acknowledge that for many groups, even with a minimum of ~500 species per group, still only ~0.3 to 1.3% of described species are covered for insecta, arachnida, mollusca and crustacea (L265-267). In addition, I would strongly argue that even with good taxonomic coverage, as is achieved for birds and mammals, calculation of the group average has to consider the highly differing abundance and/or biomass of separate species. To illustrate these points, I would like to highlight the study’s data on the arachnida (Figs. 1 and 4). About 20% of their diet is considered as “parasite vertebrate”, with a considerable biomass. Without knowing the details of the species that were considered, I would assume that the majority of these are ticks, as these feed on (mostly) vertebrate blood. Roughly speaking, we know of maybe 60 000 species of arachnida, of which perhaps 1000 are ticks. On the species level, ticks therefore seem to be highly overrepresented in the dataset, possibly because it is straightforward to infer their food source from their specialized morphology. On the other hand, the group arachnida does not seem to consider very many oribatid mites, of which there are around 12 000 known species that are almost exclusively detritivore. In addition, oribatid mites are known to be extremely abundant in soils, so their biomass is likely many times that of ticks. A similarly obvious over-representation in terms of diet and biomass occurs in the marine dataset with “vertivore crustacea”. Please note that I only picked some obvious examples here, but that the same issues will be prevalent in all animal groups.

      Indeed, I believe that your method “validation” using bird species data shows that your estimate can be very unreliable, even for a well-covered group such as birds. Your Results (L345-347) show that “the respective contribution of invertebrates and vertebrates switched from 56% and 8% in the estimate to 23% and 45% in the species-weighted partitioning”. These are very large differences.

      A further point I would like to raise: using an animal group’s biomass to gauge the biomass of the separate diet partitions seems to oversimplify matters. You are assuming that the body biomass equals the diet biomass. However, foods have very different nutritional content (e.g., carbohydrates/protein/fiber). A Panda and a Polar Bear may have fairly similar body weights, but the panda needs to eat much more plant matter biomass due to the poor nutritional content.

      Overall, the Methods section is a little disjointed, and is difficult to match to the Results section. Also, some of the chosen methods are not well justified or explained. E.g., <br /> - How were Wikipedia sources selected and “confirmed” (L130), or how was the literature searched (L132)? <br /> - How did you incorporate a diet category that only exists for a single class (“plant-derived, L150”)? <br /> - How did you deal with separate diet data for juveniles and adults (L157)?<br /> - L184ff: It remains unclear why you compare your global dataset to two location-specific datasets. What did you aim to achieve? A validation of the global dataset in this manner appears dubious, as local datasets may always remain location-specific.<br /> - What is your justification for collecting a further dataset on dinosaur diet? You mention that you aim “to test if herbivory is related to higher body mass and lower metabolic rate” (L206), but then compile only diet data for these dinosaurs (inferred from dental morphology, adding a further level of uncertainty), and no data on body mass or metabolic rate. In addition, I would think that your dataset on mammal diet composition would be much more suitable for this purpose, as it appears to be quite comprehensive and would include many species with “high” body mass. Also, in extant mammal the diet composition has presumably been directly quantified, and not just inferred from dental morphology.<br /> - L214ff: Why have a specific method for assessing human diet? We are just one more species in your dataset.<br /> - L223ff: The use of reptile biomass data for amphibians is not justified. Your assessment that the differences in average body mass and population density ‘cancel each other out’ cannot be verified. If you do not have a good biomass estimate for amphibians, you cannot include this group in the analysis.<br /> - L265ff: Your statistical “validation” of achieving representative data from poor species coverage is inappropriate. By sampling 0.3% of bird species 10 00 times and calculating an average, you merely verify that you can calculate a good average from ~300 000 (~30 species x 10 000), overall randomly sampled, data points. To “validate” your approach, you need to investigate the variance of your 10 000 repeat samples, which presumably is extremely large.<br /> - L265ff: The Methods appear to be incomplete here, as the Results section describes an analysis that was weighted by bird species biomass and abundance (L340).

      Results<br /> Throughout the manuscript, but particularly noticeable in the Results section, you are using misleading terms to refer to your data and results. I believe this stems from your multiple assumption to derive trophic pyramid data from a species-level dataset. E.g.<br /> - Fig.1: “species in most animal groups”; this figure shows the group average diet composition, not the species proportions.<br /> - L355: “partitioning of diets… expressed as biomass (Fig. 2)”; this figure actually shows the biomass of the trophic group, not their diet.<br /> - Etc.

      L333: “we assumed a homogenous distribution of biomass across trophic levels in each group” – a further example of an unfounded assumption that weakens your analyses and conclusions considerably.

      The data on dinosaur diet is missing from the Results.

      Discussion<br /> As outlined above, I believe that your main conclusion of a middle-heavy global trophic pyramid is not supported by your analyses, as are other conclusions on the trophic pyramid. Your study does not support the conclusion of a “paradigm shift” (cf. L407).

      Finally, some further minor comments:<br /> L173: what is the category “Food I”, and why is it relevant to mention these categories here?<br /> L311: Conservation areas might include some “important species” that are missing elsewhere, but that should not distract from the fact that species lists remain highly biased and incomplete there, as everywhere. Most obviously, Kruger NP is bound to have more than 13 species of insect (Fig. S4). And certainly such species list do not consider the microfauna to a meaningful degree.<br /> L402: It seems very unfair to disparage previous efforts as biased, when your own study is based on highly incomplete datasets and unfounded assumptions.<br /> L476f: I find the definition of a carnivore from Román-Palacios et al. in this context highly misleading. Heterotrophs include fungi, which does not make a fungivore a carnivore.<br /> L494: There might have been larger insects in the prehistoric past (at least we know of one large dragonfly), but that hardly makes them “megafauna”.<br /> L523: “a world without insect would potentially mark the end of complex life on Earth” – there is certainly complex life in marine environments, where insects are not prevalent and their potential decline might not have large impacts.<br /> L676: “more abundant” – you are not considering abundance here.<br /> Fig. S8: Here you are literally comparing a species group with a single species (humans). I presume that your reasoning is that the diet of humans has important impacts on the global food web. This is a nice case in point that you absolutely need species-level information on abundance/biomass to construct trophic pyramids and food webs.

    1. On 2023-11-14 16:49:20, user James Mallet wrote:

      Congratulations on this provocative paper which I read with great interest.

      However, I have some questions about the meaning of the results. Your paper suggests that previously, the prevailing belief has been that there is more hybridization, and therefore more gene flow between species, in plants than in animals. However, your preliminary discussion suggests that this is actually an artefact of “rely[ing] on morphological traits to arbitrarily define species (16),” where ref. 16 is Mallet 2005 in TREE. Although it is true that the data summarized in Mallet 2005 was indeed based largely on morphologically identified species (and their hybrids), it doesn’t rely on a morphological species concept. Anyone who knows taxonomy of any group of organisms knows also that morphology is a rather good, although not foolproof, guide to species status; two sister species, when they co-occur in sympatry, will typically display two modes in multivariate morphospace. Actually, Mallet in 1995 and 2005 argues for a genotypic cluster definition of species, which certainly applies to molecular markers as well as morphology. Two related species, if they co-occur in sympatry, will display a series of genetic differences that enables them to be identified, even if they hybridize. There are two modes in the multivariate genotypic distribution; the relationship with the classical taxonomist’s morphological identification of species is clear.

      Then you argue “the emergence of molecular data ... enables substituting the human-made species concept with genetic clusters that quantitatively vary in their level of genetic distance (18),” where ref. 18 is Galtier 2019 in Evolutionary Applications. Now that is interesting, as I think Galtier proposes “Species are defined as entities sufficiently diverged such that gene flow (arrows) is very rare or inexistent” (his Fig. 1). In other words, he appears to have a species concept such that gene flow between species is zero. Any gene flow, he argues, would render the situation “ambiguous”.

      Later, perhaps recognizing that this is too extreme, Galtier proposes using a reference species based system: “...to identify taxa in which large amounts of data are available, and species boundaries are consensual, or can be agreed on. Species delineation in any other taxon could thus be achieved so as to maximize consistency with the reference [taxa].”

      Now perhaps this dickering about what is a species appears rather unreasonable, since I think we all know (and Nicolas Galtier certainly seems to agree) that there is a continuum between populations that are not species and those that are species. However, in order to disprove the prevailing narrative that plant species hybridize more than animal species, you really must take a stance on what you mean by a species, and what you mean by a population that is not a species. My natural history knowledge of flowering plants and animals such as insects and birds suggests that plant species that co-occur in sympatry really do have a higher rate of hybridization than animal species. Not only is a greater fraction of species involved, but when they do hybridize, there are usually a lot more hybrids.

      But you will say perhaps: “that is not really the question we attempt to answer.” And indeed it is not, so perhaps you should not have complained that that finding about whether species hybridize was an artefact, which you appear to do.

      The question you more attempt, I think, to answer is: “is introgression more common in plants than in animals for a given level of genetic divergence, DA?” Rather than a question about species, it seems to me you are asking a question here that is independent of what your (or the reader’s species) concept is (unless you argue that a species has a certain threshold level of genetic divergence).

      After arguing that “the Tree of Life” is “interrupted by species barriers that are progressively established in their genome as the divergence between evolutionary lineages increases,” you then argue that “The consequences of reproductive isolation can therefore be captured through the long-term effect of barriers on reducing introgressing introgression locally in the genomes, which provides a useful quantitative metric applicable to any organism (4).”

      Ref. 4 is Westram et al. (2022) J. Evol. Biol. “What is reproductive isolation?” Westram show that it’s actually very hard to measure overall reproductive isolation, RI, which they say is determined by the level of “effective migration” at neutral loci, or the fraction of the rate of neutral genes that actually establish (reduced due to species barriers) in the recipient population, me, divided by the rate of “potential gene flow,” m, into the population caused by the potential for hybridization and backcrossing, or RI = 1 - me/m. Effective gene flow depends on where in the genome you measure it; in which direction you measure gene flow; whether populations are parapatric or sympatric; whether you want to measure it using an “organismal” or “genetic” focus (in Westram et al.’s terminology). Furthermore, it depends on who is measuring it and how. Everyone who measures it seems to have somewhat different measures of reproductive isolation (Sobel, J. M., & Chen, G. F. (2014). Unification of methods for estimating the strength of reproductive isolation. Evolution, 68, 1511–1522). It doesn’t provide a very useful comparative measure applicable at the whole species level at all. My colleague from Boston University and I conclude from perusing the lengthy discussions in Sobel & Chen and Westram et al. that measuring overall reproductive isolation is unlikely to be useful, and we would be better off just accepting that it is a vague heuristic which expresses something about species (Mallet, J., & Mullen, S.P. 2022. J. Evol. Biol. 35:1175-1182). In contrast, one can readily measure some of its many components, such as “hybrid inviability”, “assortative mating” and so on, and these remain useful and interesting at the whole species level and as comparative indicators.

      Again, it may seem a distraction that I am discussing what is reproductive isolation, but it seems important here, because you are using a measure of reproductive isolation, and then relating it to genetic distance. In Westram et al., the main concern was to develop an experimental measure of reproductive isolation. Westram et al cautioned against estimating reproductive isolation from sequence data, which is the method you employ here. Their reasoning is that sequence divergence is a consequence only of actual gene flow, me (after taking into account barriers to gene flow), and that there is no way of estimating “potential gene flow” from the same data. In the main part of the paper (e.g. the data points in Fig. 1A), there seems to be a non-continuous measure of reproductive isolation, such that “migration” has a value 1, whereas “isolation” has a value zero. It was not entirely clear to me why this should be so, since, whatever it is, it seems clear to me that reproductive isolation should surely be a continuous parameter. Delving into the supplement, I found that “genetic isolation” was indicated “when our ABC framework yields a posterior probability P(migration) < 0.1304. This threshold was empirically determined by the robustness test conducted in (Ref. 6).” Similarly, the same robustness test yielded “strong statistical support for ongoing migration ... when the posterior probability P(migration) > 0.6419.” Pairs of taxa with intermediate posterior probabilities were considered “ambiguous” and were discarded. Note that P(migration) is not the actual mixing rate of the populations, me, or the fraction of the genome exchanged, but, if I understand it correctly, the posterior probability that any gene flow at all occurs. This is a very different measure of reproductive isolation from that proposed by Sobel et al. or Westram et al., or anyone else.

      I think the reason for your choice of a measure of reproductive isolation is indicated by the second question you ask in the introduction: “At what level of molecular divergence do species become fully isolated?” This is related to a common conception of species as irreversibly independent lineages, and the idea that speciation will be “complete” when gene flow becomes zero. But in fact, the “completion” of speciation in this sense seems rather unlikely. The progressive loss of compatibility between diverging lineages seems likely to follow some sort of continuous probabilistic failure law, similar to the way lightbulbs fail over time. The simplest failure law is log-linear with time, although more complex models such as the accelerating “snowball” model of hybrid incompatibility, or the likely “slowdown” model for selective reinforcement, are also possible (Gourbière, S., & Mallet, J. 2010. Are species real? The shape of the species boundary with exponential failure, reinforcement, and the "missing snowball". Evolution 64:1-24); but all have a long asymptotic tail. You seem to recognize this stretched out right-hand side timescale by plotting genetic divergence on a log scale in Fig. 1 (although why is “net divergence,” Nei’s DA, the correct scale on which to base such an analysis? You do not explain or justify this). Nonetheless, by making an argument for complete isolation as an endpoint, you ignore the asymptotic nature of compatibility decline to zero. Based on the data we analyzed, it is rather hard to estimate the shape of the failure curve, mainly because the accumulation of incompatibilities is so variable, even among closely related species, such as Drosophila fruit-flies, for example. This variability between pairs of species shows up only in the data, and not in the fitted curve in Fig. 1A, but is more evident from Fig. 1B.

      Overall, I remain somewhat unconvinced that plants have a more rapid accumulation of species barriers than animals. I agree it is likely that many plants have “less efficient dispersal modalities” than most mobile animals, and that this might mean that actual gene flow becomes lower for plants at a distance from one another, but this is a little different from what I think one would mean by “species barriers.” Reproductive isolation and species barriers should generally be rather independent of geography; in other words reproductive isolation at close range is what we are primarily interested in. This is the problem of using a measure of reproductive isolation that depends purely on actual gene flow. I therefore remain unconvinced that my natural history observations of many plant hybrids in nature, and very few animal hybrids, are not reliable indicators of lower levels of reproductive isolation among plants than among animal species.

    1. On 2023-10-02 17:42:18, user Neil Greenspan wrote:

      The manuscript by Killian et al. is a valuable contribution to the investigation of both the biological and biophysical aspects of the humoral immune response elicited in the context of allogeneic organ transplantation. I do, however, have some reservations regarding the interpretations of the authors.

      1)<br /> The authors suggest that individual amino acid residues shared between an<br /> allogeneic HLA antigen and a self-HLA antigen should be viewed as “self.” I<br /> view this act of classification as problematic. When a donor HLA antigen<br /> differs by one or more amino acids from a host HLA antigen encoded at the same locus, the entire protein is classified, at least from some perspectives<br /> routinely adopted in transplantation immunology, as non-self.

      One way to rationalize this view, which may conflict with the perspective expressed by the authors in this manuscript, is to suggest that what matters in<br /> antibody-antigen interaction are the thermodynamic roles of the amino acids that constitute HLA antigens, not their identities. The claim is that the relevant biochemical/biophysical properties of a given shared amino acid at a particular position in the primary structures of the self and allogeneic HLA molecules can be altered meaningfully as a consequence of the one to several amino acid differences between these proteins. For example, a lysine or tryptophan that is oriented slightly differently in the self vs. the allogeneic molecules or that is more or less likely to fluctuate in certain directions is not necessarily thermodynamically equivalent in the two proteins.

      2)<br /> If the above assertion is accepted, then the claim that breaches of tolerance<br /> are critical for damage to the allograft is not demonstrated. While it is of<br /> interest to know that self-reactive B cells are generated it is not clear from<br /> this study that the antibodies produced by these B cells cause graft damage in vivo. While I acknowledge the evidence that autoreactive anti-A*24:02 antibodies can bind to allogeneic A*01:01 with potentially meaningful intrinsic affinities, that is a necessary but not sufficient condition for contributing meaningfully to clinical allograft tissue damage, especially in the context of a single patient with an autoimmune disease. Experiments designed to test the hypothesis, in a broader range of transplant patients, that such antibodies do contribute to allograft rejection episodes would be of interest.

      In the context of the potential role of autoantibody responses in allotransplantation, it has been accepted for some years that generation of autoantibodies to a variety of proteins can accompany alloimmune responses to an allograft. Some investigators have offered evidence that the presence of such antibodies is associated with damage to allografts. At present, I do not think we know with certainty the extent to which, if at all, such autoantibodies contribute to allograft damage or whether they can do so in the absence of pathogenic alloantibodies.

    1. On 2023-08-30 08:41:17, user Jose E Perez-Ortin wrote:

      This new model for explaining mRNA<br /> buffering is a very interesting piece of work. We would like to suggest some<br /> possible improvements to be considered by the authors in this preprint stage before<br /> it becomes published in a journal.

      In some parts of the manuscript it is said<br /> that mRNA buffering is perfect as total mRNA concentration and even individual<br /> mRNA concentrations are invariant. We think that this is overblown. For<br /> instance, graphs in Sun et al 2013 (ref. #9; Figure 1),<br /> the variability in total mRNA may be as high as 50%. In fact, in García-Martínez et al 2004 (ref. #15;<br /> Figure 2) we published that during the carbon source change mRNA concentration<br /> changes also by a factor of 2. We wonder if this could be important for the modeling<br /> because it seems that on the advantages of the RS model is that it predicts<br /> robust buffering, contrarily to previous feedback models.

      The manuscript misses citation of some<br /> papers that we consider important for the field of mRNA buffering, such as Mena et al 2017 (doi:<br /> 10.1093/nar/gkx974). This paper is especially relevant because the current<br /> preprint describes in the Introduction section that total mRNA concentration is<br /> constant as the cell volume increases (refs. 19-22) but forgets to mention this<br /> piece of work, which was the first one to show that degradation rate perfectly<br /> balances production rate during cell volume change. Instead of our paper, the<br /> preprint cites ref. #27, which is 4 years older than Mena et al 2017.

      Garcia-Martinez et al<br /> 2023 (doi: 10.1016/j.bbagrm.2023.194910) is also highly relevant. We described in that<br /> article a mathematical model that explains mRNA buffering using a simpler<br /> mechanism consisting only one mRNA binding factor that co-transcriptionally imprints<br /> mRNAs. That model also predicts that synergistic changes in synthesis and<br /> degradation rates will provoke faster and stronger responses, as described in<br /> some experiments. We also previously published a multiagent model in Begley et al 2019 (10.1093/nar/gkz660),<br /> which combines mRNA imprinting and feedback mechanisms. That paper also<br /> demonstrates that Ccr4 and Xrn1 act in parallel with different sets of targets<br /> genes. We also have demonstrated in that paper and in other two (Begley et al 2021 doi:<br /> 10.1080/15476286.2020.1845504; and Medina et al 2014 doi:<br /> 10.3389/fgene.2014.00001) that protein factors, such as Ccr4 and Xrn1 act not<br /> only in transcription initiation level but also in elongation . We think it<br /> would be nice this manuscript to discuss the differences of these models with<br /> the proposed RS model.

      Finally, as for the model in Figure 4c, we do not understand why the<br /> activation of a degron used by Chappleboim et al 2022 (ref. #16) only<br /> degrades cytoplasmic Xrn1 molecules (Xc) and leaves Xp molecules intact. All<br /> Xrn1-degron molecules (Xc, Xp, Xn) will be proteolyzed after Auxin addition.<br /> This can affect the predictions made by the RS model.

    1. On 2023-08-21 17:16:09, user Cristiane Paula Gomes Calixto wrote:

      Revision comments from: <br /> Cristiane Paula Gomes Calixto <br /> Flaviane Lopes Ferreira<br /> João Francisco Canal <br /> João Henrique Servilha<br /> Lucca de Filipe Rebocho Monteiro<br /> Victória de Carvalho

      The manuscript titled “Epigenetic and transcriptional landscape of heat-stress memory in woodland strawberry (Fragaria vesca)” aims to investigate the inheritance of heat-induced epigenetic and transcriptional changes in Fragaria vesca through asexual reproduction. The study analyses genome-wide DNA methylation and differential gene expression in the initial generation (heat-stressed and control) and their three subsequent non-stressed asexual generations. The authors observed a decreasing transfer of the stress-induced molecular memory across the generations. Their work has originality/novelty, and we believe the biological question they seek to answer can be interesting for the plant sciences community.<br /> We would like to provide some suggestions which we believe might enhance the quality of the manuscript. Please be aware that these suggestions are not exhaustive.<br /> Major comments<br /> • Please include additional information so as to allow the research to be replicable and reproducible. For example, saying “9:00-11:00 a.m.” might not be precise enough. Using the specific light zeitgeber would better inform when samples were harvested in the diel cycle (lines 140 and 161). Another example, the description “Illumina paired end read sequencing (150 bp)” appears to omit crucial details concerning the specific options utilised in the NGS experiment. Important information, such as mRNA selection method, library construction kit, sequencing platform, and the strand-specificity of reads, among other factors, should be included. Line 192: Please state which transcriptome was used with Salmon. Line 282: Which clustering method was used to build the heatmaps?<br /> • The claim that “… genes linked to gibberellin pathways may contribute to a short transcriptional memory.” should be discussed with the literature.<br /> • Line 642-644: Kindly review the claim in relation to what is depicted in the figure.

      Minor comments<br /> • We recommend English editing to enhance grammar and clarity. <br /> • Scientific names must always be italicised. In the first appearance of the species, it is also required to list the person (or team) who first made the scientific name of that taxon available. <br /> • Lines 131, 134 and 144: could you please add the light intensity in µmol m-2 s-1?<br /> • Line 135: Is there a specific scientific or practical rationale for maintaining consistent temperatures in stress assays throughout both day and night, while implementing varying diel thermos-cycles for control and recovery conditions?<br /> • Line: 158: We found it a bit difficult to understand what was actually collected.<br /> • Line 166: please, add the reference where we can find more details on the bisulfide method used.<br /> • Line 193: It would make it easier for the reader to understand what the authors mean by DEG if the DESeq2 default parameters were described here. Is it log-fold change, p-value cut-off, etc?<br /> • Lines 205-207: Could you provide information on the duration of the heat-stress treatments?<br /> • Lines 264-267: Do terms like "low," "hypermethylation," and "hypomethylation" refer to a comparison with data from control samples? The comparison between different samples was not really clear to us. The same applies to “significantly different” (line 281).<br /> • Figure 1A: We think this figure could be improved to help the reader understand the temperatures used for CM. Additionally, could you confirm whether the application of 24°C on recovery days precisely occurred for 48 hours? It seems that the temperature might not be exactly 24°C, and we think the figure could provide more precise details.<br /> • Figure 1B: Why are scissors, “2w” and “sampling” shown only on the right-hand side of the figure?<br /> • Figure 1C: Detecting differences among samples based on the y-axis is proving to be challenging for us. The authors might want to contemplate plotting by C contexts on the x-axis, or alternatively, segmenting the y-axis into three distinct regions where resolution could be enhanced around 1-5, 13-17, and 38-42.<br /> • Figure 3B: Is it possible to apply colour shading similar to that seen in a heatmap for this figure?<br /> • Figure 3D: Kindly review the genes mentioned in the figure legend in relation to what is depicted in the figure.<br /> • Line 280-281: The phrase between the brackets seems a bit confusing. We recommend rephrasing it for clarity.<br /> • It might be advisable for the authors to verify whether they are employing a colour-blind-friendly palette.<br /> • Some of the finer details in the figures are quite challenging to discern, making it difficult to interpret the results.<br /> • The expression patterns of several FvHSFs were described previously (López et al., 2022), some also undergoing promoter demethylation. How does the expression patterns of these HSFs change in response to a temperature gradient challenge? We believe the paper would considerably improve if heat-shock proteins and chaperones are also investigated.

    1. On 2023-07-06 11:17:24, user Nick Leigh wrote:

      This is a well written and clear manuscript comparing successful and defective heart regeneration in zebrafish versus medaka, respectively. The experiments are well designed and the interpretation is careful and thorough. These kinds of studies are essential and, now powered by single cell sequencing, can cast wide nets that enable unbiased description and investigation of this process. As clearly stated by the authors, the description provided here undoubtedly provides numerous follow-ups, questions, and hypotheses about regenerative success and failure. The authors should also be commended on creating a webtool to allow others’ to query their dataset.

      “Cross-species data integration was effective as both zebrafish and medaka cells were represented in each major cluster”. Agreed that across the major clusters there is good agreement. I’m more curious about if this is potentially overfitting–are you losing a different cluster only present in one species? From published data, could we expect any different clusters between these two species? (addressed a bit later on with zEP cells). In general, it may be worth exploring a couple other strategies for cross species integration to try and prove this further (point 6 also addresses this). <br /> The scale of the interferon-deficiency in the medaka is striking. It’s mentioned that DAMPs from necrotic cells could be a driver of interferon responses, but building on some of your prior work (Balla et al. 2020 PMID: 32413307), are the zebrafish all harboring some virus at this point and the medaka not? Could a viral/microbiome-related reason result in lack of IFN signaling. Relatedly, it would be interesting to see if medaka have type IV interferons (https://www.nature.com/arti... (and if these are included in this one-to-one comparisons/ if they are even annotated in the current version of the zebrafish genome). Finally, is there evidence of any DAMP response? For example, are there still other chemokines and cytokines (potenitlaly NFkB nuclear translocation) being produced in medaka and just specifically not an IFN signature? This is getting at the question of whether this is specifically lack of IFN signaling or if medaka are hyporesponse to, for example, DAMPs. <br /> Is recruitment responsible for increased macrophages in zebrafish or is it expansion of tissue resident cells? This could affect the conclusion drawn in medaka that they are not recruiting macrophages. <br /> Figure 3H, the proportion of TNFa positive cells is reported, but what about the absolute number? Given the relatively higher numbers of macrophages in the zebrafish it would be interesting to see how these compare. The ratio of pro versus anti-inflammatory macrophages could be an interesting metric to report. Do the zebrafish ever mount a substantial pro-inflammatory response? It’s suggested that highly regenerative animals undergo a quick switch from pro- to anti-inflammatory and this is important for regeneration, but data demonstrating that is sparse at best and the question remains if there is ever robust a pro-inflammatory response in regenerative animals. <br /> Paragraph starting with “We know relatively little about the makeup..” is a bit unclear. What type of cells are you referring to? Are these the fibroblast-like cells or fibroblasts? The concluding sentence leads one to believe fibroblasts are benign studied, but earlier on it’s discussed that “epicardial cells cells expressing collagens”. Do you find collagen expression by macrophages? (https://pubmed.ncbi.nlm.nih.... Are mmp15/16 implicated in regeneration? <br /> Regarding the zEP cells and their potential uniqueness to zebrafish, it would be interesting to explore a samap or other tools and see if they still remain separate (https://github.com/atarasha..., https://www.biorxiv.org/con..., note: this paper integrates zebrafish heart single cell data with 4 other species and could be worth looking at). As noted by the authors, more work is needed here. Whole mount FISH of hearts from both zebrafish and medaka would be quite interesting to see if zEPs can be detected anywhere. <br /> The mammalian studies are interesting and could be worth expanding. It would be insightful to tie back into the first few figures and the major findings there. Can you learn anything new from the mouse dataset with the perspectives gleaned from the fish comparison? For example, what is happening with the ISGs in the mouse? It could also be interesting to compare to salamander heart regeneration to provide another evolutionary intermediate (https://www.nature.com/arti... <br /> Do primordial cardiomyocytes wane with age? Do larval/developing medaka contain these cells and do these young medaka regenerate their hearts? (perhaps not experimentally feasible). <br /> What is the role for the compact myocardium when not in regeneration? Why is there so much diversity in its size across species? <br /> Do you think there is a unifying reason for lack of regeneration in medaka? You uncover quite a few differences.

      Minor stuff: <br /> This is a biased comment, but it would be really interesting to know if there is divergence between replicates. You could pull out each sample with some genotype-based demuxing. Check out: https://www.life-science-al.... This might also aid with DE analysis (https://www.nature.com/arti... <br /> “To investigate the contributions of epicardial-derived cells to the fibrotic response, we re-clustered all cells expressing epicardial-specific markers tcf21 and tbx18, and re-clustered them into four…” a bit confusing with double re-clustering here. <br /> Do medaka lack cortical cardiomyocytes or are they just less abundant? The last line of the figure 6 results section suggests an absence with the use of “lack”. <br /> One could consider side-by-side violins might better illustrate between time point comparisons. <br /> Figure 6E and G with numbers for cluster labels is not super clear. Perhaps these could be labeled with the top markers they express or more info added to figure legend to explain. Including on the figure the species for E-F and G-H could also help orient readers more quickly.

    1. On 2023-06-19 11:25:43, user Adrien Jolly wrote:

      These views are my own only (I did not involve any of my past or present colleagues and collaborators)

      Thank you for this ambitious endeavour, I have some comments.

      Comment on the discussion:

      While I agree with your point on exponential distributions (we make exactly this point ref. 36), the claim that one generally cannot fine-tune the variability of the cycle phase length with ODEs (p 15-16) is misleading. we do exactly that with our sub-steps approach (that you mention) which in fact permits the modulation of the cycle phase length variability from quasi invariable to exponential. <br /> It has actually been shown that mammalian cycle phase durations follow Erlang distributions (as they arise from our sub-steps). In our work, we estimate the coefficients of variations of the cycle phase length when identifiable from the data and discuss the information generally contained in this regard in our thymidine analogue incorporation experiments.

      Comments on the agent-based model:

      Minor comment<br /> (1) EdU/BrdU incorporation. In my hands EdU is not immediately detectable in the thymus following injection (as is often assumed) and it takes more than 30 minutes to label all the cells in S phase (admittedly it was IP injection, and as you perform intravenous injection, labeling should be significantly faster). <br /> Here, if I understand correctly, you assume 0.5% of DNA being labeled is sufficient for detection which would label most cells after a couple of minutes in S phase when the analogue is present. Did you check this was the case (thymus collection 10 min after injection for instance)?<br /> You further assume that labeling stops abruptly after 45 minutes. However it does not seem plausible for incorporation to cease suddenly and a gradual decay of the analogue availability seems more realistic.

      Since you have time course data which can reduce the dependence of the result to the initial labeling phase, the effect of these assumptions might be very limited but it would still be useful to check to what extent these assumptions affect your result.

      (2) I found difficult to identify exactly what data you use for fitting (which is of course essential to judge the results) and how the data is assigned to your model, I think some clarifications would really be beneficial to the readers.<br /> Do you use exclusively EdU/BrdU information or do you combine this information with total DNA content (distribution of cells across the cell cycle)?

      Here is a point of particular concern:

      (3) I understand that you do not allow transition from cycling to "long G1"/”quiescent”, sometimes finding these “long G1” cells represent >90% of a given population. Given the duration of each stage of thymic development (60 h for total DP for instance according to your 2017 review) it seems very unlikely that labeled cells do not contribute significantly to the quiescent subpopulations within 20 hours and in any case, this should certainly not be assumed a priori.

      From my own experience ignoring the cells transiting to quiescence/long G1 after the initial label incorporation might greatly distort your result by affecting the rate of entry in S phase. <br /> I expect the introduction of transition rate should improve your fit when a quiescent population is present (for later time points in particular) although I cannot conclude based on the data you currently present. <br /> In general, I find the exclusion of cells from the dynamics (which sometimes turn out to represent the overwhelming majority of the population) to be an extreme decision and I don’t think this should be made without strong evidence (simulations?) that this does not invalidate your result.

      (4) Along the same line, differentiation and transmission of labeled or unlabeled cells between compartments should be considered carefully. Differentiation can certainly affect percentages of labeled cells in a downstream compartment over time.

      While in some cases, the influx compared to local proliferation can be negligible (given the difference in size between compartments and respective cycling properties), it is a point which should be addressed for each cell compartment.

      If I understand correctly, your model poses that cells leaving a compartment are replaced exclusively by non-labeled cells. This is not neutral and, in some cases, may cast significant doubts on your predictions. For instance DN4 are directly downstream of the highly proliferative DN3b, and DN4 cells will be progressively replaced mostly by labeled cells as time goes on.

      At the very least, it should be discussed compartment by compartment why you think the assumption of exclusive influx of non-labeled cells holds given what is known of T cell development dynamics.

      While you have certainly built an important dataset, the manuscript at its current stage gives the impression that some essential features of the EdU/BrdU dynamics have been overlooked in the agent-based model. hope my comments will prove helpful.

    1. On 2023-05-22 22:45:16, user Fraser Lab wrote:

      Summary:

      In protein engineering projects, it is always desirable to screen as efficiently as possible. Screening a relatively small number of variants becomes especially important when enzyme activity cannot be coupled to a high throughput sequencing readout. The major goal of the paper is to provide a proof of concept scoring and filtering system for selecting among proteins generated using computational methods to meet this challenge of efficient screening. They consider proteins generated using 2 machine learning methods and one phylogenetic method (ancestral reconstruction).

      The end result is a scoring filter combining the language model ESM-1v (which uses only sequence information) and the deep learning method ProteinMPNN (which is trained directly to find the most probable amino acid for a protein backbone predicted by AlphaFold2). After accounting for some simple idiosyncrasies of merging generative models with reality (ensuring starts with Met, removing repetitive sequences, accounting for localization signals) with heuristics, their filtering steps results in an enrichment of active sequences.

      The major success of the paper is a pipeline that actually works for selecting active sequences both in the experiments they conduct and (to some extent) literature examples. The table of potential protein failure modes is particularly useful as a baseline approach and reference for people designing sequences with computational methods. It is especially insightful to see how few deliberate filtering steps in the training process can have a big change in the outcome.

      We expect that a combination of sequence and structure-based filters will be used for prioritizing screening resources in the future. This paper lights the way of how to do that. The next steps will be to take into account structural features beyond stability (which is presumably covered by the AF2/ProteinMPNN), such as catalytic residue positioning, pocket size complementarity to substrate, etc. These are presumably implicitly captured by ESM-1. The next logical step (beyond this paper) is to go beyond statistical combination of these two scoring features to account for such features explicitly or with a new integrated deep learning approach.

      Major points:

      We are a bit confused about the exact value and sequencing of each part of the selection/filtering pipeline. We interpret experiment 3 as:<br /> Apply ESM-1v and Quality Filters and then apply a ProteinMPNN filter on top of that. <br /> Select Negative Controls by selecting sequences that fail the first filter (ESM-1v and Quality Filters) but are within 1% sequence identity to the closest natural sequence for some positive.<br /> The quality checks discussed in the supplementary information seem to have substantial impact. If the selected control sequences failed this quality check, it’s not clear whether the success of the pipeline is due to these heuristic quality checks or due to the computational filtering. These filters are biologically simple such as starting with a methionine, removing long repeats and not having a transmembrane domain - and it is kind of amusing to one of us (JF) that generative models have these pathologies so commonly. More discussion on why these filters were applied and what the distribution of effects were for the quality filters vs the insilico filters would help clarify the impact of each stage.

      This confusion then extends to determining how each of the two computational methods affect the selection. The authors contend that “no single metric would be sufficiently generalizable to screen against multiple sequence failure modes” and hypothesize that ProteinMPNN and ESM-1v “may capture distinct features.” However, because negative controls were selected only after failing the initial ESM + Quality Filters, its impossible to know what effect adding ProteinMPNN on top of ESM had. This is even more relevant given that the structures used to obtain proteinMPNN scores are first generated with Alphafold. Alphafold can be computationally intensive (expensive to run) and therefore it is imperative that we understand how much this part of the pipeline contributes to the overall success of the selection process. The authors themselves contend that “Structure-supported metrics, including Rosetta-based scores, AlphaFold residue-confidence scores, and likelihoods computed by neural network inverse folding models, take into account protein atom coordinates potentially directly capturing protein functionality, however, they can be impractical to compute, especially when evaluating thousands of novel sequences.” This is something that can potentially be teased out. In the case of the paper only 200 proteins were selected using ProteinMPNN, however, if many sequences end up passing the ESM filter and budget allows it would be within reason to expand this random ESM selection.

      In summary, it is a bit hard to tell (without some ablation studies) which different pipeline components and filters drive the results. Additionally, it would have helped if these same quality filters were applied in Round 2 but that doesn’t seem to be the case? A deeper discussion on the selection of quality filters would also point the way forward with combining more “functional” structural features as outlined above.

      Minor points:

      1) The author’s generalize the results with a few literature examples: “similar results were obtained by independently validating COMPSS on previously published datasets of six enzyme families generated by models not considered in the present study.” Looking at the results in more detail reveals that some of these (including one that we generated!) are very small samples and this caveat should be discussed. In 3 out of the 6 studies, only 1 sequence was selected by their pipeline. In another of the 6, 2 were selected. In all 4 of these studies, a number of actives were missed. The limited number of selected sequences makes it hard to know how effective the pipeline really is in these 4 studies. Further, with such a stringent filter is not practical especially when we consider the fact that the authors don’t discuss the level of activity across positive and negative active compounds. It’s entirely possible that you could miss very active sequences and select only moderately active sequences. In one retrospective, the results were truly similar, however in the last other study, the filters worked far from intended.

      Even more, my team has observed in its own work that the sensitivity of machine learning models for scoring can be heavily dependent on the sequences the models have seen before. It would have been useful for the authors to consider how the tested enzymes overlap with the model training data to understand whether these scorers generalize outside the models training distribution.

      2) The authors largely discount natural sequence identity as a metric:<br /> “Surprisingly, neither sequence identity to natural sequences nor AlphaFold2 residue-confidence scores were predictive of enzyme activity.”

      I think it’s important to qualify this with the fact that we are looking at sequences in the 70 to 90% range with very little dynamic range here. In their first experiment they looked at sequences in the 70 to 80 range. in their second they look at sequences in the 80 to 90 range. In their third experiment they looked at sequences in the 50 to 80 range but their filters end up selecting for sequences in the 70-80 range anyways. So it’s possible that locally, identity might not select for select for activity but globally, it could be a first filtering step on its own (which maybe is obvious and hence why it’s not more qualified?). Also to note is that sequence identity seemed to fare as well as or better than other metrics in identifying functional GAN-generated sequences and could be its own generative method:

      More problematic I think is figure 3f and figure 3g:

      It seems like the inactive controls are largely in a separate part of the tree compared to the active sequences passing and control. Does this have anything to do with the fact that these features failed the sequence based quality filters. Second,it suggests an approach where if you have some idea of where to focus on in the tree you could use sequence identity to those natural sequences as a metric for selection . Of course this information may not be readily available but the authors should discuss whether we could have hypothesized that the failing controls would have failed beforehand by considering their phylogenetic origins.

      Technical points:

      1) There is some problem with this sentence:

      “CuSOD training sequences had only a single Sod_Cu domain, while MDH had an Ldh_1_N followed by an Ldh_1_C domain and no other Pfam domains that generally only rarely occur in 6.3% and 1.7% of sequences in both families, respectively.”

      It’s much better captured in the supplementary material:

      “For CuSOD, 1,632 out of 25,701 proteins (6.3%) had aberrant architectures. For MDH, 1,127 out of 65,639 (1.7%) had aberrant architectures.”

      2) It’s not clear where/how they selected the natural test sequences for rounds 1 and 2. We assume it’s from the curated set of data but that’s not necessarily a given, further it seems that in round2, sequences were selected to span the range of esm scores. Was this done for the test natural sequences as well?<br /> “Only 13 test natural sequences were selected, as we had already screened five similar natural sequences in the remediation for Round 1.”

      “Besides the identity range, the experimentally tested sequences were selected to span the entire range of scores on each metric (Supplementary Table 4)”

      3) The authors should be more explicit on the natural sequence identities in each round. If you check the supplement you can find this information if you pay attention to the figures or check the supplement but I think that it should be explicitly stated in the section “Round 2: Calibration data for COMPSS” that sequences are selected in the 80-90 range and in Round3 that the filters resulted in sequences with >69% identity.

      4) The following section is confusing:

      “To further test the hypothesis that poor truncation selection was responsible for the lack of observed activity in the Round 1 CuSOD natural test sequences, we assayed an additional 16 natural SOD proteins (pre-test group)…”

      It should be stated at the beginning that 14 of the 16 test sequences are CuSOD sequences and 2 of the sequences are FeSOD sequences vs letting the reader figure that out later in the paragraph. Additionally, it would help the audience to say explicitly that 3/7 bacterial sequences with clipping also passed or include the table from the supplement up front. 3/7 doesn’t seem clearly distinct from 4/5.

      5) What’s the reason for changing the esm-msa sampling method in round 2? Did they observe some benefit or was this purely a computational choice?

      6) I think the text for a and b are switched in the figure 2 description. a is the AUC figure and b is the correlation figure. Further for figure a If the test sequences are natural sequences, is the identity score meaningless here?

      7) From the supplement: “We skipped the 'starts with M' filter because very few of the sequences in these sets start with M, and did not subset by identity to closest training sequence.” This modification to the pipeline should be mentioned in the discussion of the external validation tests. Or they should speculate what would happen if they just added a M at the beginning of every sequence?

      8) Looking at the figures in the supplement e.g. Fig 30 it seems like they had quantitative activity values. It would have been nice to discuss if there was any correlation between scores and activity for ranking purposes. Was this not included because of variance in the assay?

      Joel Beazer (Profluent) and James Fraser (UCSF)

    1. On 2023-05-11 13:43:40, user ADRIAN TREVES wrote:

      Pre-publication review of "Forecasting dynamics of a recolonizing wolf population under different management strategies" by Petracca et al. https://doi.org/10.1101/202...

      Reviewed by<br /> Adrian Treves, PhD<br /> Professor of Environmental Studies, Founder and Director of the Carnivore Coexistence Lab, University of Wisconsin-Madison<br /> +1-608-890-1450<br /> http://faculty.nelson.wisc.... (which includes full disclosures of potentially competing interests in the CCC.php page)<br /> Direct inquiries to atreves@wisc.edu

      11 May 2023

      I appreciate that Dr. Petracca and colleagues posted their manuscript to a preprint server to facilitate independent review and scientific debate. Such preprints are a healthy step in our field to improve the reliability of science.

      Also I acknowledge the risk posed by preprints, such as policy-makers or the public running with results or inferences before they have been approved by qualified peer scientists. I think two aspects of the preprint process guard against such undesirable outcomes: (a) peer reviews attached to the preprint as a comment should serve to caution against such precipitous use of preprints, and (b) the authors can reinforce the need for caution in subsequent revisions to the preprint, even citing their pre-reviewers. The science-policy interface in which this work lies is fraught with difficulties.

      Also I acknowledge these sorts of models are complex and difficult to parameterize realistically with confidence. None of my comments or criticisms below are meant to undermine the hard work put in, but rather they are meant to improve the final product, improve outcomes for wolves, and improve the policy that may result from applied research. Thanks in advance for reading my comments in that spirit.

      I have chosen not to cite much research below, instead calling the authors’ attentions to our website (above) where peer-reviewed substantiation of all my assertions can be found. I welcome peers’ emails to atreves@wisc.edu if anyone has trouble finding the evidence.

      Most of my comments relate to Tables 1 and 2 and the associated scenarios.<br /> A question about Table 1: the caption includes "Lethal removal rate was calculated directly from state agency records." Please provide those with annual numbers and locations (East or West) to help the reader understand the geographic and spatial context of that assertion.

      The annual lethal removal rate was a single point estimate of 0.04. I don’t understand why this was treated as a constant not bracketed by annual variability? Later, the authors wrote "In scenario 1 (“Baseline”) we simulated all relevant factors, as described below, at levels observed in the data collection period (2009-2020)." All factors include those affecting the human-caused mortality, right? There are numerous studies documenting a variable annual rate of lethal removal. There seem to me to be other issues with assuming a constant annual lethal removal rate in baseline and the scenario for increased removals below.

      The assumptions that seem to be made about constant annual lethal removal in the baseline or the increased removal scenarios might be summed up as "livestock losses will never get better or worse so long as the current rate of removal is applied randomly to wolf packs and entire packs are removed." I don’t mean to caricature the assumption, I mean to make it plainer so it can be scrutinized.

      1. If lethal removal is assumed to be effective in preventing livestock loss as WDFW has implied in the past, then it seems surprising that the model would treat it as ineffective or needing constant renewal. Can this be justified scientifically and by reference to articles that have not themselves been undermined by subsequent work? I call your attention to recent reviews of the literature on lethal removal which indicates unpredictable effects of lethal removal of wolves, resulting in increases, decreases and no change in livestock losses depending on study and site and years (the latter of no effect in the majority of cases, see studies of wolf removal by Grente, Krofel, and Santiago-Ávila.

      2. Is predation on livestock random? If not, how does the imposition of a random scheme affect the model (a sensitivity analysis would be useful); many studies reveal that predation on livestock is not spatially random or uniform. Rather livestock losses are sometimes highly predictable from spatial features and wolf pack demographics. Therefore, I also call your attention to risk models that are analogous to resource selection functions, which have been used to model livestock loss in our region among others (see my lab website and search for "risk" and "forecast" please).

      3 . Has WDFW lethal removal eliminated entire packs and in what percentage of cases? This baseline information might be helpful in interpreting the scenarios. I discuss partial or entire pack removal further below.

      I was confused by the increased removals scenario and the harvest scenario. Given they are differentiated I have to assume increased removals is NOT public hunting, trapping, hounding, etc. It is unclear what conditions might lead to such an increase in lethal removals. The authors wrote "In scenarios 4 and 5 (“Increased removals”), we simulated an increased number of lethal management removals such that 30% of the wolf population[*] would be removed every four years, corresponding to an annual removal rate of 8.5%." Does this replace the baseline removal rate or supplement it? I didn’t see a scientific justification for the value of 30% and I don’t understand where 8.5% came from (30 /4 = 7.5%). Even if I add the baseline it does not reach 8.5%. I’m sure I’m missing something but the calculation could be clarified.

      Another concern about this scenario is that it uses a flat mortality rate (% of population) regardless of conditions. That seems to simulate population reduction (sometimes called culling) but applied randomly to entire packs. Given that is a highly unusual pattern of management, it would help to understand the rationale behind it. See below where other more common scenarios are NOT considered. Therefore, I do not understand the criteria applied when selecting scenarios that deserve modeling and scenarios that do not deserve modeling.

      "Harvest"<br /> See issues with terminology in the section on Minor comments below.<br /> Every 6 months: This is an unusual off-take pattern. Readers may be tempted to assume that the policy-makers among the authors or their superiors in state agencies are planning two seasons of wolf-killing per year. The authors might wish to address why such an unusual wolf-killing system was included in this paper. Also, the method that allows only adults or juveniles yet simulates twice-a-year 'harvest’ assumes the public can avoid killing pups. Is there evidence for that assumption? The assumption seems dubious on its face but regardless it requires some consideration of methods of 'harvest’ and accidental non-target killing.

      Additive: While this is more conservative than any compensatory scenarios, it still does not acknowledge the many sources of evidence for super-additive mortality when the public begins killing wolves: Creel, Vucetich, Chapron, or when wolf-killing is liberalized in general: Santiago-Avila, Louchouarn, Suutarinen, Liberg, Treves. There are now more than ten studies quantifying the super-additive effects on population dynamics or the undocumented losses of wolves when killing is liberalized (I.e., undocumented deaths that can be attributed to policies of liberalized killing).

      The OMISSION of any alternative scenario with super-additive mortality and the OMISSIOn of alternative scenarios with increases in illegal killing triggered by the harvest and increased removals scenarios are problematic. I capitalized the word OMISSION to emphasize that they are not scientific decisions but value-based decisions about which scenarios to publish and which not to publish.

      Value-based decisions are akin to unstated assumptions derived from personal or organizational preferences / beliefs / policies. Assumptions about parameter values or interactions between variables should be transparently stated and usually justified scientifically. Unstated assumptions in a modeling paper seem to me to be scientific missteps because the range of possible parameter values was circumscribed for reasons that are not transparent or justified by peer-reviewed research.

      Also, please note that an attempt to scientifically justify circumscribed parameter values might require an even-handed summary of evidence for and against the assumed constraints on parameter values. For example, the increased removal scenarios (currently unjustified) might be paired with a lowered removal scenario or a scenario that curbs ongoing mortality sources such as poaching or vehicle collisions, hypothetically. To me it seems easier to evaluate alternative scenarios even-handedly than to justify the current ones.

      Furthermore, my concern is that the decisions about which scenarios to publish in the current manuscript leave unanswered 'why these scenarios and not others?' And the authors do not touch upon alternative scenarios for how wolf-human coexistence might play out differently. Instead, the scenarios presented in this paper are a subset of wolf-human coexistence and that subset is slanted towards negative views of wolves (more killing). For example, there is nothing scientific telling us to simulate lethal removal at level x or y. We explored this problem in sustainable use models in Frontiers in Conservation Science in 2021.

      My criticism is meant to be constructive as it is not too late to adapt your models to positive wolf-human coexistence scenarios, such as those involving provisioning to improve wolf reproduction or survival, increasing wild prey bases in regions with low prey, better enforcement against unregulated, human-caused mortality, use of non-lethal methods to protect livestock etc. I understand WDFW might never undertake such actions but that does not constrain scientists seeking approximations of reality. Also, administrations change, private actors / organizations sometimes step in, and background conditions change especially for a simulation run for 50 years. <br /> I hope you see how a subset of scenarios was presented for non-scientific reasons.

      Please remind readers that the selection of scenarios is value-based not science-based. Moreover, the selection of parameters within scenarios may also be value-based. For example, partial pack removals — simulated in your methods when "excess" removals are randomly assigned to another pack short of full pack removal — is NOT suggested to be effective in any study, even Bradley et al. 2015. Moreover, can the latter study even be used to justify the effectiveness of removal of entire wolf packs? I don’t think so. Consider that Santiago-Ávila et al. 2018 showed Bradley et al. 2015 was not reproducible until and unless the methods are clarified. Also, the 2018 article identified a possible statistical bias favoring lethal removal. If the data were to be shared (another hallmark of reproducibility), the bias minimized, and the methods clarified, one might argue that full pack removal has a scientific basis. But we’re not there yet.

      Because I noticed omissions of scenarios and circumscribed parameter values without explicit statement of assumptions and missing literature, I offer a comment on potentially competing interests. T

      The scientific community has changed position on this in recent years and is increasingly recognizing the potentially distorting effects of values and ideology on scientific research. Nothing is necessarily disqualifying but all should be disclosed fully and transparently. Ideological commitments expressed through memberships in civil society and professional societies (e.g., TWS or AFWA), institutional policy positions (e.g., WDFW’s current policies), and personal affiliations or rivalries, might all place pressures on individuals that reflect competing interests. These can affect the unstated assumptions, literature reviews (what is cited and summarized versus omitted) and the methods chosen and analyses used, in addition to the traditional issues relating to financial interests. I am not referring to one or two articles being missed but a pattern of omitting peer-reviewed research in highly ranked international journals as I noted here. I emphasize the issue of potentially competing interests as a way to inspire greater public confidence in the scientific endeavor. Thanks for your kind attention.

      Again I admire your decision to publish preprints so that pre-publication review has an opportunity to influence the future manuscript and perhaps public policy.

      Minor concerns<br /> Terminology: <br /> The term "recovery" has a meaning in US federal and state endangered species law as you all no doubt are aware. Recovery in its legal sense may lead policy-makers to shift regulatory schemes to down- or delist wolves. Therefore it is not a value-neutral scientific term and could be viewed as prejudicial. I see passages in your text where recover(y) is appropriate but others where it was used to refer to recolonization or population growth. There I recommend instead using recolonizing or geographic spread or numerical rebound which do not imply a legal status. This seems especially relevant when scenario outcomes suggest a low likelihood of achieving legal recovery.

      Relatedly, I recommend careful consideration of certain jargon words that may be mainstream in wildlife management but are not commonplace in ecological sciences or policy among all publics – and may have value-based or moral connotations, e.g., harvest and depredation. In place of harvest I suggest "permitted, regulated wolf-killing by the public", because harvest is a euphemism that holds implicit assumptions about the values of wolves and motivations of humans who participate. To see why not to use 'depredation’, look at the first definition in the Oxford English Dictionary. I used it for years but now see the error.

      Finally, the discussion of non-lethal methods might benefit from updating to include studies since 2010 on livestock-guarding dogs, and systematic reviews of effectiveness 2016-2021.

    1. On 2023-04-30 15:24:14, user Gul Zerze wrote:

      I sincerely thank both Emil Thomasen and Kresten Lindorff-Larsen for their time, careful reading, and comments on the manuscript. Below, I attach my responses to each point with reproduction of the comment. Since these commentary is not capable of pasting modified visuals, added/modified visuals can be seen in the published version of the manuscript (doi: 10.1021/acs.jctc.2c01273)

      Comment:<br /> The manuscript by Zerze reports on molecular dynamics simulations of the intrinsically disordered low complexity domain (LCD) of FUS using a beta version of the coarse-grained force field Martini 3. The author performed simulations to study the formation of FUS LCD condensates under varying protein-water interaction strengths (in the Martini force field) and at different NaCl concentrations, and concludes that strengthening protein-water interactions by a factor of 1.03 improves the agreement with experimental transfer free energies between the dilute and dense phases. Additionally, the author concludes that the NaCl concentration affects condensate morphology and protein-protein interactions in the condensate, and that the effect of NaCl concentration on protein-protein interactions in the condensate is sensitive to rescaling of the protein-water interactions. The manuscript provides an interesting and novel benchmark of the (beta) Martini 3 model in predicting phase separation of IDPs, and reveals potential short-comings of the model in predicting protein concentrations in (or volumes of) the condensed and dilute phases. This benchmark will be useful for readers who wish to simulate liquid-liquid phase separation of IDPs with Martini 3, and the work will be interesting to a wider audience interested in the biophysics of IDPs and their condensates.<br /> Below we outline some questions and comments that the author might take into account when revising the manuscript. Our main comment regards a clearer assessment of the convergence of the simulations and correspondingly the lack of error estimates for observables calculated from the simulations. We also suggest a clearer presentation of the experimental data used to validate the simulations. While some of these changes are mostly textual, in other cases we suggest additional simulations. We realize that some of these simulations require substantial resources; if these are beyond what is available, we suggest at least to clarify caveats as per the points below.

      The author’s response: I thank the reviewer for their scrutiny and thoughtful comments that greatly helped substantiating the optimization analysis in the revised version of the manuscript.

      Comment: We have the following suggestions for revisions to the manuscript:<br /> 1)<br /> Fig. 1 and 2: The finding of non-spherical droplets is interesting and intriguing. To examine whether the formation of these shapes in the simulations with higher salt and λ-values represent stable states or perhaps trapped metastable states of the system, we suggest that:<br /> 1a) The author runs simulations with the parameters that give rise to non-spherical morphologies (e.g. λ=1.025 and 50 mM NaCl) starting from the structure of the spherical droplet (for example formed with λ=1.0 and no salt) and observe whether the non-spherical morphology is recovered or the droplet remains stable. If the droplet remains stable, then the effect of salt concentration on the inter-chain contacts (Fig. 6) could be assessed without potentially confounding factors from different dense phase morphologies.

      The author’s response: Following the reviewer’s suggestion, I have performed an additional set of simulations for all λ values (1, 1.01, 1.02, 1.025, 1.03) at 50 mM salt concentration starting from a preformed spherical droplet. The initial condition with the preformed droplet is obtained from the last saved frame of the λ=1 simulation for 0 mM salt. We ran the simulations for 10 microseconds each. Within the given time frame the droplet remained stable for λ values 1, 1.01, 1.02, and 1.025 without a dilute phase concentration. I now added these findings into the supporting information (Figure S5).<br /> I also modified the main text (Page 9 last paragraph and Page 10 first paragraph) as follows:

      “Recent studies from independent groups show that the nonspherical droplet formation might be a kinetic arrest, playing an important role in droplet maturation and aging [51–53]. To test whether the nonspherical morphologies we observed are impacted by the initial conditions, we rerun 50 mM at all λ values starting from a preformed droplet (last saved configuration of 0 mM salt, λ = 1 condition). We simulated each λ for 10 μs and presented the analysis in Figure S5. Within the given simulation time, the initially spherical droplets stayed intact and spherical, except for λ=1.03, which had one copy of the FUS LC protein exchange back and forth between the dense and dilute phases). The enlarged droplet in the case of λ=1.03 also deviated from its initially spherical shape. These findings show that the nonspherical morphology was not reproducible for λ values less than 1.03 when starting from a preformed spherical droplet. We argue that the strength of effective protein-protein interactions at low λ are largely<br /> responsible from the initial spherical droplet staying intact.”

      Since the droplets stayed nearly spherical, I also analyzed the contact formation in these simulations (50 mM added salt, initially starting from a spherical preformed droplet) and presented the findings in Figure S7.

      I also discussed these findings in the main text as follows (Page 19, 20, the last paragraph before Conclusions):

      “Finally, we also examined the contact formation for the case of 50 mM added salt that starts from a preformed droplet (see Identification of condensate formation subsection for the description). As presented in Figure S5, we found that the initially spherical droplet remains largely spherical within the simulation time (never forms rod-like percolated structures) for this case. Therefore, this case helps us assess the effect of salt concentration on the inter-chain contacts without potentially confounding factors from different dense phase morphologies. Figure S7 shows both the contact propensity (A.) and the effect of salt concentration (B.) on the contact propensity. Figure S7A shows that the contact propensity decreases as the λ parameter increases, similar to the findings in Figure 5. Figure S7B shows, however, that the change in contact fraction with respect to 0 mM salt at λ = 1 is weaker (resembling λ = 1.02 at 50 mM salt in Figure 6A) although the salting out effect at high λ (λ = 1.025 and 1.03) are more prominent and stronger compared to those in Figure 6A.”

      Comment: 1b) The author shows time-series or distributions of an observable that reports on the dynamics of the proteins in the non-spherical droplet (e.g. Rg, mean square displacement, residue-residue contacts) and/or of an observable that reports on the dynamics of the droplet shape (e.g. the x-, y-, and z-components of the gyration tensor).

      The author’s response: Following the reviewer’s suggestion, we added the analysis of observables that reports on dynamics of shape fluctuations and size and presented them in Figure S4.

      We also modified the main text (Page 9, second half of the second paragraph) to discuss these findings: <br /> “We also investigated the time dependence of the size and shape of these morphologies by quantifying the radius of gyration (Rg) and the ratio of the smallest and largest eigenvalues of the gyration tensor (Figure S4). The latter offers a measure of sphericity of droplets. We found that low λ cases (λ = 1, 1.01, 1.02) at 0 mM salt have the most spherical morphologies. Beyond λ = 1.025 at no salt, the cluster formation is not tight (as evident from the Rg) so it also loses its sphericity. The condition that shows percolation (λ = 1 at 50 mM salt) has the largest deviation from the sphericity (it is rod-like instead) combined with a large Rg.”

      Comment: 1c) Additionally, independent replicas of droplet formation for each condition and parameter set would be ideal, but we realize that this would be expensive in computational resources and may be infeasible.

      The author’s response: We agree with the reviewer that the molecular simulations presented in this work are highly computationally demanding (e.g., a 10-microsecond simulation of one of these simulations at given salt and given λ takes about 25 days in terms of walk-clock time, occupying 28 CPUs and 4 GPUs) While it certainly is computationally demanding to replicate all λ parameters at all salt concentrations, we now rerun 50 mM salt concentration at all λ parameters where we start from a completely different initial condition (preformed droplet) for each. And we found that the morphology was not reproducible within the given simulation time at low λ, highlighting the initial condition dependence at low λ conditions. We now discussed this in the main text (Page 21, Conclusions).

      “We also note that we observed an initial condition dependence of the morphology at low λ conditions at 50 mM salt. This finding emphasizes the necessity of future work for exploring condensate morphology with proper advanced sampling techniques.”

      Comment: 2)<br /> “As λ increases, the volume of the dense phase increases (and condensed phase concentration decreases accordingly) until the system is not capable of forming a dense phase (λ >1.03)”: From Fig. 1 it seems that the rate of cluster formation decreases as λ increases. Is it not then possible that droplet formation at λ>1.03 is stable at equilibrium, but occurs on time-scales greater than those tested in the simulations? To support the statement that no droplets are stable at λ>1.03, we suggest that the author runs simulations with a higher value of λ starting from the structure of the spherical droplet (formed with λ=1.0 and no salt) to observe whether the droplet is dissolved or remains stable.

      The author’s response: Following the reviewer’s suggestion, we have performed a simulation for λ=1.04 at no salt condition starting from the preformed spherical droplet (last saved configuration of λ=1.0 at 0mM salt) and we found that the droplet quickly dissolves for λ=1.04. This finding is now presented in Figure S3.

      The main text is also modified as follows (Page 9, end of the first paragraph):

      “To further verify that no droplets are stable beyond λ = 1.03, we also ran λ = 1.04 simulations<br /> at no salt conditions starting from a preformed spherical droplet (last saved configuration of<br /> λ = 1 at 0 mM salt). We then analyzed the cluster formation as a function of time (Figure<br /> S3) and found that the initial droplet dissolves quickly (at a timescale shorter than that of<br /> the formation of the droplets).”

      Comment: 3)<br /> Figure 3: The use of the radial distribution does not seem ideal for the droplets that have a non-spherical morphology, as certain distances will report on an average over the dense and dilute phases. This should at a minimum be discussed.

      The author’s response: Following the reviewer’s suggestion, we have added further discussion related radial density distribution to the main text (Page 12, first paragraph):

      “This approach works reasonably well for droplets that have spherical/ellipsoidal shapes. However, since the condensates for the conditions with finite salt concentrations significantly deviate from a sphere (they do not show a clear plateau as the center is approached), we used a surface reconstruction method [54] to estimate the volume and concentration instead of fitting the radial density profiles/using the limiting values.”

      Comment: 4)<br /> Table 1: It seems that the discrepancy between the sigmoidal fit approach and the surface reconstruction approach increases with λ, possibly due to sensitivity to the shape of the droplets, illustrating that there might be significant uncertainty associated with the reported dense phase volumes. We think it would be useful to have an error estimate for the reported dense phase volumes (e.g. an error over volume calculation approaches and/or over different probe sizes).

      The author’s response: The volume obtained by surface reconstruction is definitely highly sensitive to the probe size. To justify the size of the probe that I used, I directly compared the sigmoidal fit protein concentrations and the surface construction protein concentration calculated by different probe sizes (Figure S3 in the old SI, Figure S6 in the revised SI). Based on that comparison, probe radius 10 A was the size that minimized the differences considering all lambda values. That’s how I justified the probe size I used. For the uncertainty/error estimates, I performed block averaging analyses (please also see the response to the point 7).

      Comment: 5)<br /> Table 2 and Fig. 4: We suggest that the author more explicitly states which experimental data was used for comparison with the simulations in Fig. 4. We also suggest a more direct comparison with experimental data points where possible (e.g. by showing the experimental values of csat as a function of NaCl concentration).

      The author’s response: We used two experimental papers to extract the experimental data, one is reference 36. In reference 36, the authors state: “Using incubation on ice to increase the driving force for droplet formation followed by centrifugation to fuse the droplets due to their higher density, our 15 ml samples of 1 mM FUS LC phase-separated to form an ∼400 μl viscous, protein-dense phase stable for weeks at room temperature. FUS LC concentration in the phase is approximately 7 mM (120 mg/ml FUS LC) as determined by spectrophotometry.“

      We note that the salt concentration is not specified in this case (or the authors obtained approximately the same protein concentration in the dense phase regardless of the salt concentration). Also, the thermodynamic conditions defined here does not exactly correspond to those in our simulations. That’s partly the reason why we looked for multiple sources of experimental data. The other experimental work that we used is reference 39. In reference 39, the authors state that “The relative intensity of the glutamine side chain residue NMR resonances in the condensed phase compared to a standard concentration (100 μM) dispersed phase FUS LC suggests a concentration of 27.8 mM = 477 mg/ml in the condensed phase.”

      The salt concentration in the corresponding NMR experiments were carried out at 25 °C in 50 mM MES, 150 mM NaCl pH 5.5. The conditions do not exactly correspond to our thermodynamic conditions, either. Since an exact match is not available in the conditions, we did not prefer to present a direct comparison of dense phase concentrations, instead, we preferred to show a range in Figure 4. We now modified the main text (Page 15, right above the Contact Maps subsection) to more explicitly state the source of the data:

      “The experimental data range is referenced from the work by Fawzi and coworkers; [36,39] where reference [36] measures the FUS LC concentration in the dense phase as approximately 120 mg/mL (spectroscopically) and in reference [39], a 477 mg/mL FUS LC concentration is deduced from the relative intensity of the glutamine side chain residue NMR resonances in the condensed phase (compared to a standard protein concentration in the dispersed phase, which is given as 100 μM, or 1.71 mg/mL). 477 mg/mL FUS LC dense phase has been obtained from 15 ml samples of 1 mM FUS LC solutions [36] (from which we calculated the dilute phase concentration as approximately 14.3 mg/mL). We used these dense phase and their respective dilute phase concentrations to calculate the experimental range of transfer free energy (gray-shaded areas in Figure 4).”

      Comment: 6)<br /> “We used the “tiny” bead type (TQ1) both for Na+ and Cl- ions”: The author should clarify the reason for and possible effects of choosing the TQ1 bead type, as TQ5 is, we think, the standard bead type for Na+ and Cl- ions in Martini 3.

      The author’s response: We would like to clarify that tiny refers to the bead type being Txx. We then also would like to clarify that TQ5 type was not available in the MARTINI version that we used. Ion topology file in the version that we used only had TQ1 types as the ion type. We are pasting the contents of “martini_v3.0_ions.itp” file below:

      ;;; IONS<br /> ;

      ;;;;;; SODIUM ION

      [moleculetype]<br /> ; molname nrexcl<br /> TNA 1

      [atoms]<br /> ;id type resnr residu atom cgnr charge<br /> 1 TQ1 1 ION NA 1 1.0

      ;;;;;; CHLORIDE ION

      [moleculetype]<br /> ; molname nrexcl<br /> TCL 1

      [atoms]<br /> ;id type resnr residu atom cgnr charge<br /> 1 TQ1 1 ION CL 1 -1.0

      ;;;;;; CHOLINE ION

      [moleculetype]<br /> ; molname nrexcl<br /> NC3 1

      [atoms]<br /> ;id type resnr residu atom cgnr charge<br /> 1 Q0 1 ION NC3 1 1.0

      ;;;;;; CALCIUM ION

      [moleculetype]<br /> ; molname nrexcl<br /> SCA 1

      [atoms]<br /> ;id type resnr residu atom cgnr charge<br /> 1 SQ2 1 ION CA 1 2.0

      Since we understand that this is causing a confusion, we modified the sentence as below (Page 6, right above the Simulation Details section):

      “We used the relevant TQ bead types for Na+ and Cl- ions and kept the ion-water and ion-protein interactions unmodified.”

      For further details of the parameters (e.g., epsilon-sigma), we made our topology and run parameter files publicly available (please see the response to the point 10).

      Comment: 7)<br /> We suggest that the author, where possible, reports error estimates for the various observables, for example from block error analysis and/or repeated simulations.

      The author’s response: We performed block averaging analysis (using two block) for volume estimation (accordingly, the protein concentration in the dense phase) and included the error estimates in Table 1 (Page 12). We note that for most ???? parameters, the error was less than 1%. But we now added the errors larger than 1% in Figure 4. We modified the Table 1 caption as:<br /> “…. Statistical errors calculated by block averaging of the data (dividing the equilibrated data into two equal blocks) are less than 1% at low ???? conditions. Errors larger than 1% are reported.”

      Comment: 8)<br /> It would be useful to include a discussion of the effects of simulation convergence and simulation starting configurations on the reported results.

      The author’s response: We added a discussion of the reproducibility issue and the initial condition dependence both to the Results and Discussion section and the Conclusions section (please also see the responses to the point 1a and 1c).

      Comment: 9)<br /> A discussion of the potential differences in the effect of non-bonded cut-offs in the dilute and dense phase would also be useful.

      The author’s response: We used a fairly large cutoff distance (1.1 nm) for short-range treatment of vdW and electrostatics but a potential nonbonded cutoff effect that I can think of is the long-range treatment of electrostatics. While vdW interactions are large power of r in denominator (therefore, negligible contribution to the potential at large r), we may argue that the long-range treatment of electrostatics might be a concern in general. It is well known that the simple cutoff of electrostatic interactions introduces artifacts on phase behavior of anomalous liquids that has two distinct phases [e.g., J. Chem. Phys. 131, 104508 (2009)]. Here, we applied the reaction field method for long-range treatment of electrostatics. In this method, a given particle is assumed to be surrounded by a spherical cavity of finite radius within which the electrostatic interactions are calculated explicitly. Outside the cavity, the system is treated as a dielectric continuum. Any net dipole within the cavity induces a polarization in the dielectric, which in turn interacts with the given molecule. The reaction field method allows the replacement of the infinite Coulomb sum by a finite sum plus the reaction field. One caveat of this approach might be the nonuniform distribution of the particles within the system (i.e., one protein-dense phase and one protein-dilute phase), which may jeopardize the assumption that outside the cavity is a uniform continuum dielectric. While this caveat may make the Ewald summation (or particle mesh Ewald, faster version of Ewald sum) look more preferable, we note that Ewald sum and reaction field techniques yield nearly identical phase behavior for liquid crystals (also nonuniform in nature) (see, Molecular Physics 92(4), 723-734 (1997)). We discussed some of these points in the main text as follows (Page 6, third from the last sentence):

      “Long-range electrostatic interactions were calculated using a generalized reaction field method [45]. We note that a long-range treatment of electrostatic interactions is essential to obtain accurate phase behavior [46].”

      Comment: 10)<br /> It would be very useful if the inputs/settings (including starting configurations) used for simulation and code for analysis were available.

      The author’s response: Following the reviewer’s suggestion, we uploaded the initial configurations and run files for all lambda values for 0 mM salt and 100 mM to GitHub and made it publicly available. We now noted in the availability of the data in the main text by modifying the last paragraph of Modeling subsection as follows:

      “Equilibrated initial conditions, topology files, and run parameter files for all λ values of 0 mM and 100 mM salt are publicly available on GitHub (https://github.com/gzerze/m...

      Comment: We also have the following suggestions for minor revisions to the manuscript:<br /> 1)<br /> “We kept the protein-protein interactions unmodified (and no additional elastic backbone constraints were applied)”: The author should clarify whether this includes assignment of secondary structure and/or side chain angle and dihedral restraints (ss and scfix in Martinize).

      The author’s response: Yes, this would apply for any restraints (i.e., they would remain unmodified). This particular protein, FUS LC, is left fully flexible, without any backbone/side chain structure. We clarified this in the main text by modifying the relevant part in the Modeling subsection:

      “No elastic backbone (or side chain) constraints were applied (i.e., FUS LC is kept fully flexible). We kept the protein-protein interactions unmodified but systematically tested a range of scaled protein-water interactions.”

      Comment: 2)<br /> “All simulations were performed using GROMACS MD engine (version 2016.3).”: Error in references.

      The author’s response: The references are fixed.

      Comment: 3)<br /> In the Cluster Formation Analysis section: We suggest that the author cites the specific package used (e.g. SciPy).

      The author’s response: Following the reviewer’s suggestion, we added the name of the routine related references by modifying the relevant part in Cluster Formation Analysis subsection as follows:

      “Any two protein molecules are considered to be in the same cluster if any two beads of the molecules are within 0.5 nm (or less) distance from each other. Based on this criterion, we built adjacency matrices and then found the connected components by using the compressed sparse graph routines of public Python libraries [50]”

      Comment: 4)<br /> Fig. 2: There are small red dots on the droplets, which should either be explained in the figure text or removed.

      The author’s response: Following the reviewer’s suggestion, we remade the Figure 2 by removing the red dots.

      Comment: 5)<br /> Fig. 3: It would be useful for the reader if the NaCl concentration was labelled at the top of each column. Additionally, the radial distribution of the ion concentration is shown as two separate rows, which we assume corresponds to Na+ and Cl- ions. This should be clearly labelled.

      The author’s response: Following the reviewer’s suggestion, we updated Figure 3 with proper labels.

      Comment: 6)<br /> “We found the largest water fraction For the ionic species…”: Typo?

      The author’s response: We removed that incomplete sentence now.

      Comment: 7)<br /> Fig. 4: Depending on how the plot is updated with more details on the experiments, perhaps the range shown on the y-axis could be made smaller.

      The author’s response: Figure 4 is updated as presented above (please see the response to point 7 above).

      Comment: 8)<br /> Fig. 5: May be clearer with a colourmap with three colours, as in figure 6.

      The author’s response: Figure 5 uses a color scale that changes the colors uniformly from black to white. For contact maps (like Figure 5), since the range of change is sequential growth of fraction, we thought a perceptually uniform sequential color scale fits better as opposed to a divergent color scale (e.g. the color scale in Figure 6).

    2. On 2022-11-27 12:46:31, user Kresten Lindorff-Larsen wrote:

      Review of “Optimizing the Martini 3 force field reveals the effects of the intricate balance between protein-water interaction strength and salt concentration on biomolecular condensate formation” by Gül H. Zerze<br /> Reviewed by F. Emil Thomasen and Kresten Lindorff-Larsen

      Comments:The preprinted manuscript by Zerze reports on molecular dynamics simulations of the intrinsically disordered low complexity domain (LCD) of FUS using a beta version of the coarse-grained force field Martini 3. The author performed simulations to study the formation of FUS LCD condensates under varying protein-water interaction strengths (in the Martini force field) and at different NaCl concentrations, and concludes that strengthening protein-water interactions by a factor of 1.03 improves the agreement with experimental transfer free energies between the dilute and dense phases. Additionally, the author concludes that the NaCl concentration affects condensate morphology and protein-protein interactions in the condensate, and that the effect of NaCl concentration on protein-protein interactions in the condensate is sensitive to rescaling of the protein-water interactions. The preprint provides an interesting and novel benchmark of the (beta) Martini 3 model in predicting phase separation of IDPs, and reveals potential short-comings of the model in predicting protein concentrations in (or volumes of) the condensed and dilute phases. This benchmark will be useful for readers who wish to simulate liquid-liquid phase separation of IDPs with Martini 3, and the work will be interesting to a wider audience interested in the biophysics of IDPs and their condensates.

      Below we outline some questions and comments that the author might take into account when revising the manuscript. Our main comment regards a clearer assessment of the convergence of the simulations and correspondingly the lack of error estimates for observables calculated from the simulations. We also suggest a clearer presentation of the experimental data used to validate the simulations. While some of these changes are mostly textual, in other cases we suggest additional simulations. We realize that some of these simulations require substantial resources; if these are beyond what is available, we suggest at least to clarify caveats as per the points below.

      We have the following suggestions for revisions to the manuscript:

      1)<br /> Fig. 1 and 2: The finding of non-spherical droplets is interesting and intriguing. To examine whether the formation of these shapes in the simulations with higher salt and λ-values represent stable states or perhaps trapped metastable states of the system, we suggest that:

      1a) The author runs simulations with the parameters that give rise to non-spherical morphologies (e.g. λ=1.025 and 50 mM NaCl) starting from the structure of the spherical droplet (for example formed with λ=1.0 and no salt) and observe whether the non-spherical morphology is recovered or the droplet remains stable. If the droplet remains stable, then the effect of salt concentration on the inter-chain contacts (Fig. 6) could be assessed without potentially confounding factors from different dense phase morphologies.

      1b) The author shows time-series or distributions of an observable that reports on the dynamics of the proteins in the non-spherical droplet (e.g. Rg, mean square displacement, residue-residue contacts) and/or of an observable that reports on the dynamics of the droplet shape (e.g. the x-, y-, and z-components of the gyration tensor).

      1c) Additionally, independent replicas of droplet formation for each condition and parameter set would be ideal, but we realize that this would be expensive in computational resources and may be infeasible.

      2)<br /> “As λ increases, the volume of the dense phase increases (and condensed phase concentration decreases accordingly) until the system is not capable of forming a dense phase (λ >1.03)”: From Fig. 1 it seems that the rate of cluster formation decreases as λ increases. Is it not then possible that droplet formation at λ>1.03 is stable at equilibrium, but occurs on time-scales greater than those tested in the simulations? To support the statement that no droplets are stable at λ>1.03, we suggest that the author runs simulations with a higher value of λ starting from the structure of the spherical droplet (formed with λ=1.0 and no salt) to observe whether the droplet is dissolved or remains stable.

      3)<br /> Figure 3: The use of the radial distribution does not seem ideal for the droplets that have a non-spherical morphology, as certain distances will report on an average over the dense and dilute phases. This should at a minimum be discussed.

      4)<br /> Table 1: It seems that the discrepancy between the sigmoidal fit approach and the surface reconstruction approach increases with λ, possibly due to sensitivity to the shape of the droplets, illustrating that there might be significant uncertainty associated with the reported dense phase volumes. We think it would be useful to have an error estimate for the reported dense phase volumes (e.g. an error over volume calculation approaches and/or over different probe sizes).

      5)<br /> Table 2 and Fig. 4: We suggest that the author more explicitly states which experimental data was used for comparison with the simulations in Fig. 4. We also suggest a more direct comparison with experimental data points where possible (e.g. by showing the experimental values of csat as a function of NaCl concentration).

      6)<br /> “We used the “tiny” bead type (TQ1) both for Na+ and Cl- ions”: The author should clarify the reason for and possible effects of choosing the TQ1 bead type, as TQ5 is, we think, the standard bead type for Na+ and Cl- ions in Martini 3.

      7)<br /> We suggest that the author, where possible, reports error estimates for the various observables, for example from block error analysis and/or repeated simulations.

      8)<br /> It would be useful to include a discussion of the effects of simulation convergence and simulation starting configurations on the reported results.

      9)<br /> A discussion of the potential differences in the effect of non-bonded cut-offs in the dilute and dense phase would also be useful.

      10)<br /> It would be very useful if the inputs/settings (including starting configurations) used for simulation and code for analysis were available.

      We also have the following suggestions for minor changes to the manuscript:

      1)<br /> “We kept the protein-protein interactions unmodified (and no additional elastic backbone constraints were applied)”: The author should clarify whether this includes assignment of secondary structure and/or side chain angle and dihedral restraints (ss and scfix in Martinize).

      2)<br /> “All simulations were performed using GROMACS MD engine (version 2016.3).”: Error in references.

      3)<br /> In the Cluster Formation Analysis section: We suggest that the author cites the specific package used (e.g. SciPy).

      4)<br /> Fig. 2: There are small red dots on the droplets, which should either be explained in the figure text or removed.

      5)<br /> Fig. 3: It would be useful for the reader if the NaCl concentration was labelled at the top of each column. Additionally, the radial distribution of the ion concentration is shown as two separate rows, which we assume corresponds to Na+ and Cl- ions. This should be clearly labelled.

      6)<br /> “We found the largest water fraction For the ionic species…”: Typo?

      7)<br /> Fig. 4: Depending on how the plot is updated with more details on the experiments, perhaps the range shown on the y-axis could be made smaller.

      8)<br /> Fig. 5: May be clearer with a colourmap with three colours, as in figure 6.

    1. On 2023-04-01 23:15:29, user Vitaly V. Ganusov wrote:

      Review of the paper by Shin et al. “Lung injury induces a polarized immune response by self antigen-specific FoxP3+ regulatory T cells “ (MICR 603 Immunology JC)

      Summary.

      We know that central tolerance – removal of T cells specific to self antigens – is not 100% efficient and some self-reactive T cells do accumulate in the periphery. This leaky process is likely responsible for some autoimmune reaction observed in humans. However, how such self-reactive T cells are activated remains poorly defined. The authors developed an interesting system where they have T cells recognizing a specific antigen that was engineered to be expressed in lung epithelial cells (OVA + 2W + gp66). By using the antigen with several epitopes this allows to investigate how T cell response to one of these epitopes impacts endogenous immune response to other epitopes. Interestingly, authors found that transfer of T cells specific to gp66 epitope into mice does not result in inflammatory response to 2W epitope by endogenous, 2W-specific CD4 T cells. Instead, the authors observed expansion of 2W-specific Tregs. Response was different in the lymph vs. lung. Interestingly, after primary response, immunization with 2W peptide with an adjuvant did not result in expansion of conventional, 2W-specific T cells indicating induction of tolerance. Expansion of 2W-specific Tregs was also observed by intranasal inoculation of LPS into mice. Overall, this study provides an interesting view on how ongoing immune response may influence response of self-specific CD4 T cells.

      Positive feedback.

      There are a lot of interesting things about this paper. First, the system to have lung-restricted antigen that has several well defined epitopes is highly innovative. The methodology to accurately count the number of naive T cells in the whole mouse (we talk about 10-100 cells per mouse!) is impressive. Looking at endogenous response, without transfer of monoclonal TCR-Tg T cells is really fundamental. The way how authors look at two tissues - lymphoid (lymph nodes) and lung - is important. The use of LPS injection as a model for lung injury is interesting as it also allows to look at actual pathology (mouse weight) as a medically relevant read-out. The text is short (perhaps in some places too short, see below for comments) and figures are relatively clear (see comments). Having an experimental layout for how the mice were treated, along with what was harvested for each experiment was very useful. Finally, having many different lines of mice is very impressive!

      Major Concerns

      I do not understand how transfer of naive T cells results in pathology in the lung (Fig 1 results). Per basics of immunology, 3 signals are needed to activate T cells - i.e., there is a need of inflammation to induce immune response and trafficking to the lung. Perhaps activated T cells were transferred but that was not clear from experimental design in Fig 1. Authors must provide better rationale of how transfer of naive T cells causes IgM in BAL to increase. Tracking immune response of transferred cells (e.g., activation markers, division history by CFSE, cell numbers in LNs/spleen over time) would be needed. Also, it would be very important to perform titration experiments to show how the number of transferred T cells impacts pathology. Similarly, why day 7 was chosen as the point to measure the endogenous response was not clear.

      While measurements of T cells in lymph nodes and spleen are typically efficient (most cells are recovered), isolation of activated T cells from nonlymphoid tissues, especially the lung is highly inefficient and may be biased (some subsets could be better isolated than others, PMID: 25957682). Confirming the results of Treg bias in lung samples must be done with using microscopy. Furthermore, when T cells are isolated from tissues due to contamination with the blood, cells in the circulation may be detected as in the parenchyma (24385150). Experiments must be repeated to include intravascular staining to separate cells in the blood vs. parenchyma to indicate that Tregs in the lung are in fact in the lung.

      I found it weird that the authors claim that 2W-specific Tregs are responsible for suppression of endogenous responses to 2W upon antigen+adjuvant injection and yet, depletion of Tregs did not result in a new response. A simpler interpretation is induction of anergy in endogenous T cells upon exposure to Ag in the absence of strong inflammation. Text must be carefully curated to avoid bias towards one favorite explanation.

      Focus on SLOs and lung is clear but I wonder if using another control peripheral tissue that did not express the antigen could be useful. For example, measuring T cell accumulation in the liver may be a useful control.

      It was not clear if expression of OVA is actually restricted to the lung. Perhaps some more thorough analysis of other tissues would be helpful to verify the absence of leakiness of the gene expression.

      Minor concerns

      Having numbers for lines in the paper could allow for better referencing to specific statements made in the paper.

      While for most immunologists Tregs are FoxP3, some younger researchers may not know this. Mentioning that this is how you define Tregs would be useful. Also, assessing the function of these T cells would be useful.

      Please do not use “ns” or “**” to denote statistical significance. Use actual p values, e.g., p=0.34 or p=0.012. Additionally, indicating fold difference between groups (effect size) could be also useful.

      In introduction: Whether autoimmune responses are driven by naive T cells or by cross-reactive memory T cells is unclear. Cross-reactivity may be a simpler explanation given that memory T cells may require lower thresholds for activation.

      Authors should describe better different epitopes used in the construct, e.g., gp66 is from LCMV.

      Why did authors use gp66-specific CD4 T cells and not OVA-specific OTII cells? Are the results the same is using T cells of a different specificity?

      Are the detected Tregs derived from the thymus or are these “converted” naive T cells to the Treg phenotype? I don’t think that the current data allow to discriminate between these alternatives.

      When indicating difference in expansion in the Results section, please indicate how much (how many fold) is that expansion.

      How is the lung injury by LPS dependent on the LPS dose? Perhaps this needs to be discussed.

      I wonder that measuring kinetics of response, e.g., before day 7 and after, may be useful. We know that exposure to self antigens typically results in deletion of naive CD8 T cells (10843383)

      Which specific LNs were isolated? This probably should be listed in materials and methods section.

      I wonder if plotting some data as paired (e.g., Fig 1 - 2W vs. SMARTA) could reveal some additional information.

      How were Tr1 cells gated? Some flow cytometry graphs may be useful here (Suppl Fig S2)

      Suppl Fig 3 would benefit from experimental design panel.

    1. On 2023-01-05 20:51:34, user Gregory Way wrote:

      Wong et al. present a deep learning approach called MOAProfiler (MP) to specifically predict compound mechanism of action (MOA) from Cell Painting images. They benchmark MP against CellProfiler (the standard image-based profiling approach) and DeepProfiler (an emerging image-based profiling approach also based on deep learning) using two publicly-available datasets (JUMP-pilot and LINCS). They evaluate these approaches using precision, recall, and f1 score at k for held out MOA predictions and by comparing similarity between same-MOA and different-MOA profiles. They report an astounding 1,000% performance increase for MP over CellProfiler and DeepProfiler in grouping like MOAs. We thank the authors for posting their work as a preprint - thank you!

      The primary innovation in MP is the specific training approach. MP uses the same architectural backbone as DeepProfiler (EfficientNet), but trains the model directly to predict compound MOA (instead, DeepProfiler uses EfficientNet to derive representations). Additionally, MP does not perform single-cell segmentation, instead training using full field of views and a series of data augmentations. The authors use the last layer as the per-compound feature embedding in their performance benchmarks. The authors also include several convincing supplementary analyses that further support their claims.

      Overall, the paper presents a very interesting observation and pushes against a commonly held mindset of analyzing Cell Painting data with generalist/universal approaches. Instead, the paper suggests that fine-tuned models for specific applications are vastly superior for specifically tailored tasks.

      However, we have two major concerns and several relatively minor comments that the authors might clarify in order to strengthen their findings and claims.

      Major concerns:

      • Our primary concern involves publicly-available resources. Namely, the github url is not public: https://github.com/pfizer-r.... Because we were unable to access the code, we were not able to perform a detailed code review. Additionally, the authors link to the CellProfiler and DeepProfiler embeddings they used to benchmark. These embeddings were derived from https://github.com/broadins.... These are not the official LINCS and JUMP resources, and at least one of the links pointed to level 3 profiles, which are not normalized. This could at least partially explain the exceptionally poor performance for CellProfiler and DeepProfiler.
      • Second, the authors train two separate MP models for both datasets. Did the authors try applying a trained-MP on the alternative dataset? The authors state: “To simulate the real-world use case of identifying MOAs of unknown held-out compounds, we performed an analysis where we split the dataset by compound instead of by wells (Methods).” We imagine that analyzing future compounds using embeddings of a pre-trained MP is also a common real-world application. This analysis would also reveal the level of overfitting occurring in each independently trained dataset. Would combining datasets improve performance?

      Minor comments and concerns:

      • The authors state: “​​Although traditional computer vision techniques have proved useful, they often require much fine-tuning and require human intelligence and intuition for deciding which phenotypic features and their parameters are important to measure.” We think this is a really good point, and we are glad someone else brought up the parameters and all the fine-tuning that typically needs to happen, even for generalist approaches.

      • The authors state: “In contrast, deep learning has emerged as a tool for learning and encoding meaningful representations (i.e. embeddings) without requiring humans to know beforehand what features may be useful for the task of interest.” We may have missed this, but the authors might decide to mention the deep learning limitation of having unlabeled and difficult-to-interpret features.

      • Figure 1B needs a scale bar

      • The authors state: “We divided the dataset such that 60% of the wells were assigned to training, 10% to validation, and 30% to test (Methods).” What does “class-balanced the training set” mean? Is this during cross validation? The authors should clarify.

      • The authors state: “We also ensured each MOA’s test wells spanned multiple plates (at least seven, Figure 2D, left)”. However, Figure 2D shows that most MOAs in LINCS spanned fewer than 7 plates, what did the authors do with those?

      • The authors state: “We also included the negative DMSO as a class to learn but excluded it from all performance metrics because of its overrepresentation in the dataset”. It would be helpful for the authors to clarify how they handled positive controls. Also related, the authors state: “we performed four analyses to assess how well the embeddings captured MOA-specific features.” How did DMSO perform? It would be interesting to see the distribution of DMSO probabilities across classes, which could point to classes with no effect or how often DMSO features might be influenced by batch effects.

      • For Figure 3A, the authors should clarify that their supervised learning architecture was multi-class. This is not explicitly stated.

      • The authors state: “On the held-out test set, the model achieved an area under the precision recall curve (AUPRC) of 0.46 (random AUPRC = 0.006) for image field classification over 176 MOA classes (Figure 3A)”. How are the authors calculating this random AUPRC? If this is theoretical, the authors should compare performance with a model trained with a randomly shuffled baseline.

      • Additionally, the authors state elsewhere: “it was able to correctly predict MOAs for 10.2-13.6% of the compounds in a space of 176 possible MOAs. Compared to a random baseline of 0.6%, this is a 17.9-23.9x improvement.” This begs another question of how the authors formed the baselines. Also, why did the authors choose to not include DP and CP in this eval?

      • The Figure 4B plate map might be wrong. There are more DMSO and what are the NAs?

      • How did the authors determine the categories “strongly correlated” and “weakly correlated”? At different thresholds did MP still outperform?

      • The authors state: “Performance varied depending upon whether we predicted MOA by the neural network’s classification output or by a compound’s latent similarity to training compound embeddings”. The authors should clarify how they determined these classification outputs and latent similarities as they are introduced.

      • The authors state: “(delta = 0.44 for MP, Figure 3C). For both CP and DP, the difference was smaller (delta = 0.03 for CP, 0.03 for DP).” The authors define delta in the figure legend, but this should also be clearly delineated in the methods.

      • We were confused by the legend in figure 4D - why are each of the models showing a different k? Is this the optimal k? MP doesn’t look optimal at k=4.

      • The authors state: “From a low-dimensional t-distributed stochastic neighbor embedding (TSNE) visualization of embeddings from three example MOAs, we could see that different compounds with the same MOA were clustered together with different MOAs inhabiting different areas in latent space (Figure 3G).” How did the authors choose these three example MOAs? Why not include all of them? It would be nice to visualize all embeddings for both datasets, and the TSNE plots look a bit strange, with highly similar distances between points.

      • The authors state: “However, the model created embeddings that were clustered by MOA despite each MOA being represented by multiple compounds (Supplemental Figure 1).” Supplementary Figure 1 is not a specific enough reference - there are multiple panels and it is unclear which panel the reader should focus on.

      • The authors state: “We found minor differences in classification accuracy (0.54 vs .50) suggesting that the model was not leveraging much confounding edge-specific features for its learning” Given the number of NA’s (especially in LINCS platemap in Figure 4), normalization to remove batch effects or TSNE/UMAP to suggest no batch effects would be more convincing.

      • Figure 6G mentions different shapes in the legend but all look like circles in the image (they are different but it's very hard to tell). The authors also forgot to include the letter g in the figure legend.

      • Does supplementary figure 3 show MP embeddings? This is not explicitly stated.

      • Performance across MOA counts for MP is impressive! Very strong performance at low n

      • In the discussion, the authors state: “Second, all the analyses were performed on compounds with just one known MOA. Understanding drugs that are associated with multiple MOAs is an important task, but our study did not address this question.” The authors seem to avoid explaining this in-depth throughout the article. Why is it an important task and is their justification for not including drugs with multiple MOAs good enough? They mention that they didn’t include compounds with multiple MOAs to simplify the compound space and limit polypharmacology intricacies. Did they try to include compounds with multiple MOAs? If so, I think they should report the results. If the results are bad, then that could give insight into how we can improve performance.

      • In the discussion, the authors state: “Although DP is another deep learning based approach to phenotypic profiling that also uses an EfficientNet backbone architecture, we observed larger performance gains with MP.” What was the authors’ rationale for using EfficientNet? Also, “architecture” here and in other sentences appears to have a broad meaning. Could another word be substituted for greater specificity? We think it would be helpful to include a diagram of their model architecture.

      • The authors state: “We permuted each channel’s brightness and contrast independently by a random factor in the range of 0 to 0.30 (just for the LINCS dataset).” This seems non-traditional, the authors should provide a citation. Why not perform this in the JUMP dataset?

      • The authors state: “As a final training augmentation step, we performed random 90-degree rotations on each image, along with random horizontal flips.” The authors should specify how many augmentations they performed, how did this expand the dataset, were any specific augmentations particularly helpful?

      • The authors state: “We kept only the compound data that had no more than one known MOA according to the CLUE Connectivity Map…” How often does compound data have more than one MOA from the CLUE Connectivity Map? Would it create a significant difference in results if others were included? How was CLUE connectivity data joined with or used as a filter for JUMP1?

      • The authors state: “We trained for 100 epochs and selected the model that had the highest accuracy on the validation set. We used a learning rate of 0.1, a weight decay of 0.0001, a dropout rate of 0.2, a learning momentum of 0.9, a learning rate scheduler with a gamma decay of 0.1 at epoch 50 and 75, and batch size of 56 for training.” Did the authors perform any sort of hyperparameter optimization? How did they select these hyperparameters?

      • For their CellProfiler pipelines, the authors do not explain why they used specific modules. The pipeline utilizes various different modules that I haven’t seen in other pipelines so it would help to know what is being done if there were notes.

      Reviewed by:<br /> Gregory P. Way, PhD<br /> Jenna Tomkinson<br /> Roshan Kern<br /> Dave Bunten<br /> Parker Hicks<br /> Rose Doss<br /> Keenan Manpearl

    1. On 2022-10-13 19:16:01, user BacillusBaRosh wrote:

      Author responses to feedback posted on hypothes.is - cut and paste because could not figure out how to respond there https://hypothes.is/a/5fVcAEaSEe2k4CPVTDZz7Q

      AtanasRadkov<br /> Oct 7<br /> on "Magnesium modulates Bacillus s…"<br /> (www.biorxiv.org)<br /> General comments:

      This study carefully delineates the role of magnesium in cell division versus cell elongation. The results are really important specifically for rod-shaped bacteria and also an important contribution to the broader field of understanding cell shape. Specifically, I love that they are distinguishing between labile and non-labile intracellular magnesium pools, as well as extracellular magnesium! These three pools are really challenging to separate but I commend them on engaging with this topic and using it to provide alternative explanations for their observations!

      A major contribution to prior findings on the effects of magnesium is the author’s ability to visualize the number of septa in the elongating cells in the absence of magnesium. This is novel information and I think the field will benefit from the microscopy data shown here.

      I completely agree with the authors that we need to be more careful when using rich media such as LB. It is particularly sad that we may be missing really interesting biology because of that! It’s worth moving away from such media or at least being more careful about batch to batch variability. Batch to batch variability is not as well appreciated in microbiology as it is for growing other cell types (for example, mammalian cells and insect cells).

      For me, the most exciting finding was that a large part of the cell length changes within the first 10min after adding magnesium. The authors do speculate in the discussion that this is likely happening because of biophysical or enzymatic effects, and I hope they explore this further in the future!

      I love how the paper reads like a novel! Congratulations on a very well-written paper!

      Kudos to the authors for providing many alternative explanations for their results. It demonstrates critical thinking and an open-mind to finding the truth.

      Comment<br /> Figure 2C → please include indication of statistical significance<br /> Figure 3C → please include indication of statistical significance<br /> Figure 6A → please include indication of statistical significance<br /> Figure 8B → please include indication of statistical significance<br /> Figure S1B → please include indication of statistical significance<br /> Figure S3B → please include indication of statistical significance

      Response<br /> Easy to add

      Comment<br /> For your overexpression experiments, do the overexpressed proteins have a tag? It would be helpful to have Western blot data showing that the particular proteins are actually being overexpressed. I think the phenotypes that you observe are very compelling, so I don’t doubt the conclusions. Western blot data would just provide some additional confirmation that you are actually achieving overexpression of UppS, MraY, and BcrC.

      Response<br /> The proteins are untagged. For the UppS and BcrC the cell shortening occurs with addition of inducer, , so strong indication expression is occurring. A western would provide information about degree of overexpression, but we don’t think is necessary to support conclusion drawn. Do you think there is an alternative possibility that needs to be excluded? We note that in another preprint (https://www.biorxiv.org/con... the authors delete the native uppS in their inducible Phy-uppS strain (Fig S4) and at 100 uM IPTG (10X less than what we used in experiment) the cells have wt growth on LB plates, so we at least know the Phy-uppS is functional and made (or they would die!). We are introducing the uppS deletion into our strain to see if we can identify a concentration of IPTG that doesn’t affect cell growth but still induces shortening.

      For MraY, the result is negative, so you are spot on – it is impossible to tell if due to lack of overexpression from data shown. We only know the strain is correctly made from sequencing. We will investigate if there is an antibody or functional fusion available. The reason we were not sure was worth doing is because the MraY reaction is reversible (15131133). This means that without a phenotype, there is no simple way to know the reaction can even be pushed forward even if the overexpression is confirmed (more negative data). We actually overexpressed some other proteins that act downstream (MraY, MurJ, AmJ) and they were also negative for shortening. Probably we should remove the negative data or reword to make the caveats of the negative result clear.

      Question<br /> Based on your data, there are definitely differences in gene expression when you compare cells grown in media with and without magnesium. Because the majority in cell length increase occurs in such a short time though (the first 10min), I was wondering if you think that some or most of it is not due to gene expression?

      Response<br /> The shortening is even faster than 10 min (not only statistically significant, but also obvious qualitatively if we mount immediately after adding Mg2+ ). We did not include the first timepoint because original purpose was to check everything was ready with microscope – did not expect shortening so fast! We can definitely add that data in. When we saw, we tried to capture the transition on pads, but going from culture to pad seems to stress the cells too much in the small window where the cool stuff happens. Since growth rate doesn’t appear to be a big factor in those initial divisions, we might be able to grow at lower temp and shift to pads for adjustment period before adding Mg2+. Did not play with it much due to lack of resources atm, but a flowcell setup would probably be best.<br /> In short, we think rapid divisions right after transition do not require transcription or translation. It really “smells” more like a biophysical thing.

      Question<br /> Do you have any hypotheses what is most likely to be affected by magnesium? Do you think if the membrane may be affected?

      Response<br /> We have a lot of hypotheses – all of which are speculative. There could be an extracytoplasmic enzyme involved in envelope synthesis is sensitive to Mg2+ availability, and that at lower concentrations, it’s activity is affected. There is some old literature with membrane preps that suggests PG synthesis requires higher Mg2+ than teichoic acid synthesis. If Und-P is limiting, higher Mg2+ may shift make the pool more available to make the septum. Tingfeng initially hypothesized there might be a receptor/signal mechanism but has not been able to identify one. Und-P seems to be important, but “availability” is not just pool, but how fast (and where!) the flipping across the membrane occurs. If Und-PP needs to be dephosphorylated to Und-P before being flipped back to cytoplasmic side, anything that effects the PPi equilibrium would be predicted to affect the reaction rate, with lower Pi (in periplasm or pseudoperiplasm in case of G+) favoring the dephosphorylation. Cell wall associated Mg2+ could shift equilibrium to be more favorable for a Und-PP phosphatase more closely associated with the divisome. I could go all day… In short, we don’t know enough!

      Question<br /> Why do you think less magnesium activates this program of less division and more elongation? Additionally why is abundant magnesium activating a program of increased cell division and less elongation? Do you think there is some evolutionary advantage, especially considering how important magnesium is for ATP production?

      Response<br /> In the window we looked at, the elongation rate is constant (not less or more) and only the division frequency changes. Some bacteria (like Caulobacter and to lesser extent E. coli) clearly elongate and divide simultaneously, so there is some competition for substrate (like Lipid II). Septators like Bacillus seem to delineate the two processes more, but we have found conditions where even Bacillus invaginates during division, so it’s not absolute. Like eukaryotic cells, bacterial undoubtedly have mechanisms not only commit to a round of DNA replication when there is some signal that resources are sufficient. Clearly with some bugs, this is not the case with cell division. The alternative possibility is that every cell cycle there is an opportunity to divide if some threshold of *something(s)* is reached. There is a hypothesis from Mtb literature that it may be GTP, but it’s not at all clear that is sufficient. In yeast, size at cell division is affected by perturbing 1-C pool.

      Question<br /> Related to this previous question, I also wonder if this magnesium-dependent phenotype would extend to other unicellular organisms, may be protists or algae? That would be a really exciting direction to explore!

      Response<br /> It’s a great question – lots to do! We didn’t even look at another Gram-positive, but we plan to. It’s trickier to limit Mg2+ in Gram-negatives (see 27471053 – we tried Bsub homolog for those wondering – it’s not responsible for phenotype we see).

      Question<br /> Regarding the zinc and manganese experiments, why do you think they lead to additional phenotypes compared to magnesium? Do you have any hypotheses?

      Response<br /> We have hypotheses, but if my (Jen’s) twitter engagement is any indication, way too speculative for public consumption at present. Need grant to acquire preliminary data to write grant.

      Question<br /> Regarding your results that Lipid I availability may be a major a problem for the cell division in the absence of magnesium, do you think that is due to effects magnesium has on the enzymes directly, or do you think magnesium affects the substrate availability/conformation by coordinating the phosphate groups? Or something else, may be membrane conformation?

      Response<br /> Several proteins involved in envelope synthesis (like UppS) are Mg2+ dependent enzymes. But at least for any intracellular players, levels of Mg2+ should be more than high enough to support enzyme activity even when levels are low (0.8 – 3.0 mM is Bsub range I recall off top of head). Could have impact extracytoplasmically by lowering pool sponged into the cell wall, but intuition (for what that is worth) is that it is not the coordination of an enzyme with a metal that is impacted rather the equilibrium with other ions like Pi and H+ and that this impacts net ATP synthesis. Lots to think about and do, and no simple answers. When Tingfeng started project idea was to find mechanism – didn’t realize we were asking “how does the cell work?” Turned out to be a bit much for a dissertation project :)

      -Jen Herman and Tingfeng Guo

    1. On 2022-10-08 16:37:04, user Michael Ailion wrote:

      This paper aims to understand how toxin-antidote (TA)<br /> elements are spread and maintained in species, especially in species where<br /> outcrossing is infrequent and the selfish gene drive of TA elements is limited.<br /> The paper focuses on the possible fitness costs and benefits of the peel-1/zeel-1 element in the nematode C. elegans. A combination of mathematical modeling and experimental tests of<br /> fitness are presented. The authors make a surprising finding: the toxin gene peel-1<br /> provides a fitness advantage to the host. This is a very interesting<br /> finding that challenges how we think about selfish genetic elements,<br /> demonstrating that they may not be wholly “selfish” in order to spread in a<br /> population.

      This paper is of interest to evolutionary biologists and<br /> population geneticists. It provides empirical evidence that supports a previous<br /> hypothesis of how selfish toxin-antidote elements spread in non-obligate<br /> outcrossing species. While the experiments and data are appropriate for<br /> addressing this hypothesis, one major conclusion is not supported by the data<br /> and one other major conclusion is supported only weakly.

      Strengths

      1. The authors support results found with a zeel-1 peel-1 introgressed strain by using<br /> CRISPR/Cas9 genetic engineering to precisely knock-out the genes of interest.<br /> They were careful to ensure the loss-of-function of these generated alleles by<br /> using genetic crosses.

      2. Similarly, the authors are careful with<br /> controls, ensuring that genetic markers used in the fitness assays did not<br /> affect the fitness of the strain. This ensures that the genes of interest are causative<br /> for any source of fitness differences between strains, therefore making the<br /> data reliable and easily interpretable.

      3. A powerful assay for directly measuring the<br /> relative fitness of two strains is used.

      4. The authors support relative fitness data<br /> with direct measurements of fitness proximal traits such as body size (a proxy<br /> for growth rate) and fecundity, providing further support for the conclusion<br /> that peel-1 increases fitness.

      Weaknesses

      1. One major conclusion is that peel-1 increases<br /> fitness independent of zeel-1, but this claim is not well supported by<br /> the data. The data presented show that the presence of zeel-1 does<br /> not provide a fitness benefit to a peel-1(null) worm. But the experiment<br /> does not test whether zeel-1<br /> is required for the increased<br /> fitness conferred by the presence of peel-1.<br /> Ideally, one would test whether a zeel-1(null);peel-1(+) strain is<br /> as fit as a zeel-1(+);peel-1(+) strain, but this experiment may<br /> be infeasible since a zeel-1(null);peel-1(+) strain is inviable.

      2. The CRISPR-generated peel-1<br /> allele in the N2 background only accounts for 32% of the fitness difference<br /> of the introgressed strain. Thus, the effect of peel-1 alone on fitness appears to be rather small. Additionally, this<br /> effect of peel-1 shows only weak<br /> statistical significance (and see point 5 below). Given that this is the key<br /> experiment in the paper, the major conclusion of the paper that the presence of<br /> peel-1 provides a fitness benefit is<br /> supported only weakly. For example, it is possible that other mutations caused<br /> by off-target effects of CRISPR in this strain may contribute to its decreased<br /> fitness. It would be valuable to point out the caveats to this conclusion, or<br /> back it up more strongly with additional experiments such as rescuing the peel-1(null) fitness defect with a<br /> wild-type peel-1 allele or determining<br /> if introduction of wild-type peel-1 into<br /> the introgressed strain is sufficient to confer a fitness benefit.

      3. The strain that introgresses the zeel-1 peel-1 region from CB4856 into the N2 background was made by<br /> a different lab. Given that N2 strains from different labs can vary<br /> considerably, it is unclear whether this introgressed strain is indeed isogenic<br /> to the N2 strain it is competed against, or whether other background mutations<br /> outside the introgressed region may contribute to the observed<br /> fitness differences.

      4. Though the CRISPR-generated null allele of peel-1 only accounts for 32% of the<br /> fitness difference of the zeel-1 peel-1 introgressed<br /> strain, these two strains have very similar fecundity and growth rates. Thus,<br /> it is unclear why this mutant does not more fully account for the fitness<br /> differences.

      5. Improper statistical tests are used. All comparisons use<br /> a t test, but this test is inappropriate when multiple comparisons are made.<br /> Importantly, correction for multiple comparisons may decrease the already weak<br /> statistical significance of the fitness costs of the peel-1 CRISPR allele (Fig 3E), which is the key result in the<br /> paper.

      6. N2 fecundity and growth rate measurements<br /> from Fig 2B&C are reused in Fig 3C&D. This should be explicitly stated.<br /> It should also be stated whether all three strains (N2, the zeel-1 peel-1 introgressed strain, and<br /> the peel-1 CRISPR mutant) were<br /> assayed in parallel as they should be. If so, a statistical test that corrects<br /> for multiple comparisons should also be used.

      7. It appears that the same data for the<br /> controls for the fitness experiments (i.e. N2 vs. marker & N2 vs.<br /> introgressed npr-1; glb-5) may be<br /> reused in Fig 2A and 3E. If so, this should be stated. It should also be stated<br /> whether all the experiments in these panels were performed in parallel. If so,<br /> this may affect the statistical significance when correcting for multiple<br /> comparisons.

      Minor<br /> points

      1. Though the mathematical modeling is interesting from a<br /> theoretical point of view, we feel that it oversells the rationale behind the<br /> experiments, setting up a “straw man” argument to knock down. Also, the modeling<br /> relies on rather high assumptions of the possible carrying cost of peel-1/zeel-1. For example, the modeling<br /> of the effect of outcrossing rate on peel-1/zeel-1<br /> frequency assumes a selection coefficient of 0.35, which seems rather<br /> arbitrary and high. Where does this number come from? Is there any precedence<br /> for this high carrying cost? In our opinion, the idea that energy expenditure<br /> or leaky toxicity accounts for such a high carrying cost seems unlikely.

      2. The two studies cited for “outcrossing rates typical for<br /> C. elegans” estimated vastly different outcrossing rates (~20% or ~1%).<br /> The model presented in Fig S1 specifically uses the lower estimates (0-2%), so<br /> the Sivasundar & Hey paper is miscited here. It is unclear whether there is<br /> a good rationale to go with the lower rate estimates.

      3. The measurement of body-size is unclear in the main<br /> text. Only when reading methods did we realize that body-size is more of a<br /> proxy for growth rate rather than an end-point measurement of worm size.

      4. What is the temporal distribution of egg laying of the<br /> N2 and N2peel-1(null) strains? Based on how the<br /> data collection is described in the Methods, the authors should already have<br /> these data. Does egg-laying start at the same time in the two strains? The fact<br /> that strains carrying peel-1 grow<br /> faster but also apparently produce more sperm (which might slow them down)<br /> makes an analysis of this worthwhile, especially since fitness depends on when<br /> eggs are laid, not just how many. Some more characterization of this fitness<br /> trait seems appropriate and useful for beginning to understand how peel-1<br /> may be increasing fitness. Given that the number of sperm limits how many eggs<br /> are laid, the presence of peel-1 apparently results in more sperm. It is<br /> surprising that a gene exclusively expressed in developing sperm can lead to<br /> production of more sperm.

      5. Line 65: the statement “similar elements have not been<br /> identified in obligate outcrossing Caenorhabditis nematodes” is somewhat<br /> misleading. TA elements may not have been identified in obligate outcrossing<br /> nematodes because of research bias since genetic experiments are easier to<br /> perform in non-obligate outcrossers and it is unclear that there have been<br /> extensive searches for TA elements in outcrossing nematodes. Furthermore, as<br /> the mathematical models in this study suggest, TA elements will spread quickly<br /> with increasing rate of outcrossing. Since a TA element’s non-fixation within a<br /> species has historically been a prerequisite for its discovery, the rapid TA<br /> element fixation that would generally occur in obligate outcrossers would make<br /> their identification more challenging.

      6. Line 209-210: it is stated that this is the “first<br /> measurement of the fitness cost of a TA element to the host” and “first<br /> demonstration that a TA element can benefit the organism.” These claims may be<br /> overstated. It has been previously shown in several cases that TA elements can<br /> provide fitness benefits in bacteria, such as improved antibiotic resistance<br /> (e.g. Bogati et al. 2022, PMID: 34570627).

      7. More details about the CRISPR protocol would be helpful.<br /> It is unclear whether Cas9/sgRNAs were introduced as RNPs or plasmids (and at<br /> what concentrations). It is unclear how worms were screened for edits. It is<br /> also unclear how many Dpy or Rol worms were screened and how many peel-1 or<br /> zeel-1 edited worms were found (the efficiency of CRISPR). The meaning<br /> of the shaded portion of the repairing oligo sequences in the table is not<br /> explained. Finally, it is not stated whether CRISPR-generated mutant strains<br /> were outcrossed.

      Reviewed (and signed)<br /> by Lews Caro and Michael Ailion

    1. On 2022-09-19 14:09:03, user Gregory Way wrote:

      We reviewed this preprint as a part of Arcadia's preprint review initiative: https://twitter.com/Arcadia...

      Peidli et al. present a data resource (for single-cell perturbations) and apply energy distance (e-distance) to quantify differences in perturbations. For the data resource, the authors focus on curating single-cell RNAseq and ATACseq measurements perturbed with CRISPR, drug treatments, and a few other perturbation types. The authors curate a total of 44 datasets. Overall, the paper is very well written with a sound logical flow. However, many elements of the paper seem incomplete. We provide several specific comments regarding our views on how the paper could improve. We thank the authors for posting their preprint and code publicly.

      Our two primary comments are:

      1. The data are not harmonized from reads. Instead, the authors process (in most cases) already processed read count by gene matrices. The authors also use different versions of scanpy to process different datasets. This is definitely still valuable, but the authors should state these facts earlier and probably decrease the use of “harmonization”. Additionally, there is no evaluation to determine the effect or benefit of this read count harmonization. Calculating e-distance before and after harmonization across datasets might be helpful.

      2. E-distance is not sufficiently benchmarked. The math and intuition are described marvelously, but how does E-distance behave across datasets and common perturbations? How does subsampling read depth impact E-distance calculations? How does drug dose impact e-distance? How does sequencing technology impact e-distance? How does modifying the distance metric within the E-distance calculation impact calculations?

      We also have several general comments on different aspects of the paper and github repository. We hope that the authors can benefit from our deep dive on the paper. Thanks again!

      Introduction

      • Definition of single-cell perturbation data (SCPD)

      Overall, this subsection is more of a “methods/techniques overview” of how to collect SCPD rather than defining what SCPD actually is. What is output from these techniques?<br /> - The authors should define these data in more detail.<br /> - The authors should also further define the techniques as it is helpful to have a general idea of why the data collected from the techniques are “good” and not just “more data are better”.

      Motivation for distance measure of high-dimensional profiles:

      • The authors claim that E-distance can identify strong or weak perturbations. It’s unclear what a strong or weak perturbation is. I was unable to find this information from a quick google search so I think they should define that here (not found in methods either).

      Motivation for unifying datasets

      • Their motivation only seems to be “it doesn’t exist yet because it’s difficult to do” so therefore we should do it. What will/could come of the integrated and standardized datasets? What would we hope to find?

      Web Interface

      • The authors claim, “a web interface for data access, analysis and visualization is available at scperturb.org.” There is data access on that site, but analysis and visualization appear to be absent using Brave and Safari browsers.
      • It seems that one would require a computer with enough memory (500G) to run scPerturb to reproduce the analysis. The authors present solutions for how to overcome these requirements, but it did not seem that they attempted to solve them.
      • The authors state that there are Quality Control plots for each dataset on the website but we could not find.

      Results<br /> - The authors should briefly describe the methods underlying the statement “dense low-dimensional embeddings of the original data (see Methods for details)” in a bit more detail upon introduction.<br /> - It is surprising to me that there are so many cells with 2 perturbations (proportionally to a single perturbation) (sup fig 1). Is this because of an overweighting of a specific study?<br /> - It might be helpful to add targeted sequencing depth to table 1 per study, also helpful to add the sequencing platforms used.<br /> - Data source trust: Zenodo sources appear to be auxiliary data downloads as opposed to direct sources. How might other researchers assume trust in the sources? Are the included metadata implied or entrusted to the authors?<br /> - Are the UMAPs in Figure 3E the same UMAP space or are the spaces fit independently in both panels?<br /> - Need to provide a bit more rationale for why the authors chose E-distance over the other options.<br /> - Did they calculate E-distance for all perturbations? Sup Fig 3 shows this, so maybe? It was not obvious where to find the measurements.<br /> - There are only 11 drug perturbations in common. This is a very interesting observation! How many genes are perturbed in common datasets?

      Methods<br /> - For the scATAC-Seq data, it’s not clear to me if they perform LSI jointly across all samples or not. This would cause non-interoperability across datasets if not done jointly since each LSI dimension may mean something different in each dataset. In addition, they provide peaks x counts matrix -- which is dataset specific. I would suggest aligning jointly using a uniform set of peaks -- Running MACS2 on all datasets would be a huge benefit to the community.<br /> - How do the different versions of scanpy impact data processing? Typically, harmonized data are generated with a single pipeline.<br /> - When performing subsampling to fit PCA, did the authors transform the full data subsequently? In other words, does the PCA fitting step impact cell count for e-distance calculation?<br /> - What distance measure is used in the E-distance calculation for ||x_i - x_J||? L2? For perturbations, comparing L2 to other metrics would help benchmark the method.

      Code/Github<br /> - It seems to us a good idea to spend time improving the existing model / code at https://github.com/theislab.... The authors should justify why they are not contributing to existing open source code.<br /> - I can’t find the script “fragments2outputs.R” in their github. From their paper: “All features described in the overview above were computed with ArchR functions. For details inspect the “fragments2outputs.R” script in our code repository (see Data Availability).”

      Data Repo comments:<br /> - Manual data testing for reproducibility within https://github.com/sanderla... (one must perform the steps, the repo doesn’t provide or outline within the code itself)<br /> - Suggests using “mamba” but does not provide instructions on how to install mamba <br /> - Would suggest a small description for each folder in the directory (README) explaining its contents <br /> - There’s no usage example on how to download the data or use the program<br /> - Would be best to have a notebook (or bash script) that describes the entire workflow. <br /> - The notebooks are not sequentially executed and there are no execution instructions<br /> - What environment (OS/hardware/configuration/etc) is required to run the code?<br /> - Is notebook (.ipynb) output expected within committed code? (should these have been scrubbed with nbconvert/jupytext?)

      Data Availability<br /> - Based on this section, their website only contains the first three bullet points (e.g scRNA-seq data, scATAC-seq data, and details about the datasets). We could not easily find the last three bullet points (Quality control plots for each dataset, Filtering, e.g., by readout or type of perturbation, Commands for direct file download using the Unix command curl)

      This review was produced jointly at The University of Colorado by:

      Gregory P. Way, PhD<br /> Natalie Davidson, PhD<br /> Erik Serrano<br /> Parker Hicks<br /> Jenna Tomkinson<br /> Dave Bunten

    1. On 2022-09-07 14:26:19, user Feng Yang wrote:

      I am the corresponding author of the original study. [Journal name redacted to follow bioRxiv's policy] rejected this Preprint based on our Concerns on their concern. Unfortunately, I do not know how to publish the PDF file of our response (it does not fit BioRxiv since our PDF file does not contain additional experimental data). I am pasting it below. We welcome open discussion based on solid experimental data and are looking forward to more independent studies in this area.<br /> Re: On the therapeutic potential of MAPK4 in triple-negative breast cancer <br /> Feng Yang<br /> Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas<br /> * Corresponding Author: Feng Yang, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030. Phone: 713-798-8022; Fax: 713-790-1275; E-mail: fyang@bcm.edu<br /> Boudghene-Stambouli et al. recently published “On the therapeutic potential of MAPK4 in triple-negative breast cancer” in BioRxiv concerning our Nature Communications publication, “MAPK4 promotes triple negative breast cancer growth and reduces tumor sensitivity to PI3K blockade.”, published 11 January 2022 (1). We want to reply to their comments as follows.<br /> Boudghene-Stambouli et al. essentially detected a similar MAPK4 protein expression pattern (Our report (1) vs. Boudghene-Stambouli et al., Fig. 1c) in the human TNBC cells, when using the same commercially available antibody AP7298b. However, they claimed, “We failed to detect a specific ERK4 band in any of the cell lines, including Hs578T cells transfected with human ERK4 cDNA.” They then used their own “validated custom polyclonal ERK4 antibody that we use routinely in our laboratories” to produce a different MAPK4 expression pattern (Boudghene-Stambouli et al., Fig. 1c). They provided a siRNA knockdown for the “validation” of their antibody. In this case, Boudghene-Stambouli et al. largely ignored our previous publications using the commercially available AP7298b to successfully confirm the overexpression, knockdown (up to five independent shRNAs), and knockout of MAPK4 in many human cancer cell lines and in “normal” cells (1-4). AP7298b can also detect a purified GST-MAPK4 fusion protein in the GST pulldown assays and the purified Flag/His-tagged wild-type and mutated MAPK4 proteins in the in vitro kinase assays (2). It should be noted that instead of our extensive validation of AP7298b using many MAPK4-overexpressing, knockdown (up to five independent shRNAs), and knockout cells as well as purified MAPK4 proteins (overexpressed/purified from both prokaryotic and eukaryotic cells), Boudghene-Stambouli et al. only used a single siRNA to “validate” their un-named custom antibody. Besides, they did not confirm HA-MAPK4/Erk4 overexpression in their Hs578T cells (Boudghene-Stambouli et al., Fig. 1c). Please note, due to the sensitivity of different antibodies, even if an HA-positive western blot is provided, it may not confirm significantly increased ectopically overexpressed MAPK4 expression over the endogenous MAPK4. Finally, their custom antibody detected many non-specific bands compared to AP7298b (Boudghene-Stambouli et al., Suppl. Fig. 1c, which was included in their submission recently rejected by [Journal name redacted to follow bioRxiv's policy] after peer-review). Therefore, we have concerns over Boudghene-Stambouli et al.’s concern on MAPK4 protein expression levels in the MAPK4-high TNBC cell lines that we used in our study (1).<br /> It is well-known that mRNA and protein abundances may not correlate well in biological systems. Therefore, Boudghene-Stambouli et al.’s concern about the variation of MAPK4 mRNA expression across the cell lines will not carry that much weight. We also noticed that Boudghene-Stambouli et al. used our reported 5’ primer but a modified 3’ primer for their qPCR data in Fig. 1a. We wonder whether they have performed qPCR using our reported 5’ and 3’ primers to detect MAPK4 expression (3), and what were the results? Besides, although we have not systematically examined MAPK4 mRNA expression in human TNBC cell lines as we did for human prostate cancer cell lines (3), we did qPCR confirmed MAPK4 expression in MDA-MB-231, SUM159, as well as the non-small cell lung cancer H1299 cells. Besides, Zheng et al. independently showed MAPK4 mRNA and protein expression in HCC1937 and MDA-MB-231 cells (5), two of the TNBC cell lines concerned by Boudghene-Stambouli et al. Without knowing the quality of Boudghene-Stambouli et al.’s RNA-seq data, we could not comment on their Fig. 1b data.<br /> Another concern of Boudghene-Stambouli et al. is their failure to verify our reported MAPK4-AKT signaling axis, a conclusion drawn from their Fig. 2 data. Without providing their data, the corresponding author Dr. Meloche has communicated with me about this issue. At that time, I provided the following answer. “I am not sure if you did a transient transfection in the 293 cells. Unlike MK5, phosphorylation of AKT is subjected to many more direct and indirect regulations in the cells. It is hard to imagine that you can easily detect MAPK4 phosphorylation of cell endogenous AKT in the transiently transfected 293 cells. It can be a hit and miss, especially if you do not carefully monitor cell confluency. I think that we only reported data from the stable 293T cells overexpressing MAPK4 or MAPK4 phosphorylating a co-transfected AKT in 293T cells. In the latter case, we suspect that these ectopically overexpressed AKT are less susceptible to endogenous cellular posttranslational modifications and more susceptible to the regulation of overexpressed MAPK4. Again, unless you can’t repeat our data, such as MAPK4 phosphorylating a co-transfected AKT in 293T cells, I do not see a common ground for our debate here either.” Now I see the experimental data, and Boudghene-Stambouli et al. did perform a transient transfection and tried to detect phosphorylation change of endogenous AKT, which we have already expressed concern about in our previous personal communications. Interestingly, as a positive control for their Fig. 2 data, Boudghene-Stambouli et al. showed MAPK4 enhanced the phosphorylation of an ectopically overexpressed but not endogenous MK5, raising concern about this so-called positive control per se. We are also unsure how much MAPK4 was overexpressed compared to endogenous MAPK4 (Western blots on GFP could not provide that information) nor the nature of the seemingly increased AKT T308 phosphorylation in the MAPK4 transfected 293 cells (Boudghene-Stambouli et al., Fig. 2).<br /> I want to finish this discussion using what I wrote to Dr. Meloche in another email. “Without detailed information from your side, it is hard for me to guess what happened. I want to emphasize several technical details that may help. 1. Please collect cells at about 50%-70% confluency. If your lab collected cells at very high confluency, please try this. 2. We have been using Dox-inducible knockdown and overexpression approaches. We typically maintain the cell culture without Dox induction and do a couple of days (such as three days) induction just before the experiments. 3. If you use a non-induction system as we did in some of our studies, please ensure that you only use the engineered cell lines at early passages. You can do this by freezing down many vials from a very early passage and only using the thawed-out cells for minimal additional passage(s). The cancer cells in culture may adapt to the cellular “stress” from long-term MAPK4 overexpression or knockdown.”<br /> We welcome open discussions based on solid experimental data. We will do our best to help if any group meets technical difficulty in repeating our data under the reported experimental conditions. We have validated our MAPK4-AKT signaling in more than 20 human cancer cell lines (Ref. (1-3), and unpublished data), and additional independent reports also confirmed MAPK4 phosphorylates/activates AKT in human cancer cells (5, 6). We welcome and are looking forward to more independent studies in this area.<br /> References <br /> 1. Wang W, et al. MAPK4 promotes triple negative breast cancer growth and reduces tumor sensitivity to PI3K blockade. Nat Commun. 2022;13(1):245.<br /> 2. Wang W, et al. MAPK4 overexpression promotes tumor progression via noncanonical activation of AKT/mTOR signaling. The Journal of clinical investigation. 2019;129(3):1015-1029.<br /> 3. Shen T, et al. MAPK4 promotes prostate cancer by concerted activation of androgen receptor and AKT. The Journal of clinical investigation. 2021;131(4).<br /> 4. Cai Q, et al. MAPK6-AKT signaling promotes tumor growth and resistance to mTOR kinase blockade. Sci Adv. 2021;7(46):eabi6439.<br /> 5. Zeng X, et al. MAPK4 silencing together with a PARP1 inhibitor as a combination therapy in triplenegative breast cancer cells. Molecular medicine reports. 2021;24(2).<br /> 6. Tian S, et al. MAPK4 deletion enhances radiation effects and triggers synergistic lethality with simultaneous PARP1 inhibition in cervical cancer. J Exp Clin Cancer Res. 2020;39(1):143.

    1. On 2022-08-19 20:54:50, user Stephanie Wankowicz wrote:

      Summary: In this paper the authors set out to develop new methods for refinement of models into cryo–EM density maps. There are three primary interrelated contributions:

      -Assigning “responsibility” for different regions of the map to a model and then fitting GMM as a real space B-factor. This is a new way to model atomic B-factors, since it is done in real space, compared to reciprocal space in most other software.<br /> -Sampling an ensemble based on those B-factors. The major success of this paper was that the authors created a new ensemble method that samples within the B-factors to improve the fit of hundreds of cyro-EM maps, demonstrating that their method is robust and can be done in a high throughput manner.<br /> -Refinement procedures for composite maps based on smoothing of responsibility. The examples all seem to be from individual maps with different levels of resolution across the map, not from true composite maps (calculated from different masking procedures for example). This part was very confusing for us to follow and although there are methodological links to the B-factor assignment/ensemble modeling parts of the paper, it might be better explained in a separate manuscript.

      Major comments:<br /> 1. The introduction only briefly discusses B-factors and doesn’t lay out what is distinct about this method. For a contrast, sampling is discussed with references and contrast:<br /> “ The sampling itself is usually based on either molecular dynamics (MD)4,9, minimisation10, normal mode analysis and/or gradient following techniques11,12, or Fourier-space based methods2.”<br /> Similarly, B-factor refinement should be discussed. The way Phenix and Refmac handle it (real vs. reciprocal space), the limitations that the GMM addresses, etc.

      1. With regard to sampling, there are other methods that are now similar for generating ensembles (the EMMI work from Vendruscolo and Bonomi for example). It would be useful to contrast the limitations of those methods and how this method is distinct. For example, this method seems likely to be much more computationally simple to run. It would also be good to benchmark against examples of those ensemble methods in terms of RMSF/inferred B-factors.

      2. When you refer to the TEMPy-REFF models in each case study are they always ensemble models using segmentation?

      3. How are the weights for each focus map decided for when creating a composite map? Stated in ‘combining focused maps into a single overall composite map, with optimal weights of the focused maps.’ (page 3)<br /> We think that more information on how you are generating ensembles belongs in the results section which will help clarify the paper. Some additional specifics we think would make this section strong include: Are the ensembles being created for different segments of the model (based on map segmentation) or the entire model? When creating an ensemble, what is the input model? Has it already gone through iterations of the map to model fitting? How are ensemble models represented? Please provide examples and discuss how you would like these models interpreted.

      4. Please clarify how b-factors are represented in your ensemble models and input into maps. Furthermore, in the discussion you state ‘We address this challenge using B-factor estimation. We find, as previously shown by us and others, that an ensemble of equally-well fitted models represents this local variability better than a single model.’ (page 16). However, it is unclear how the b-factors integrate with the ensemble model to represent local resolution. Please clarify which part of your model correlates with local resolution.

      5. On average, how many models were included in an ensemble? Please provide a graph of CCC values versus number of models in an ensemble for more examples (ie more than SI Figure 7). How are you thinking about the trade-off between a more complex model versus a small gain in CCC? How deterministic is this procedure? Can you repeat and compare at least one dataset? If you generate multiple ensembles starting from the same structure - do you get the same number of models out and are they similar?

      6. If we understand the calculations correctly, the increase in CCC comes from those models being refined independently, not collectively (which makes the increase all the more impressive). Does this suggest the ensemble captures both precision and accuracy (as discussed here: https://pubmed.ncbi.nlm.nih... and therefore the sampling allows escaping of local minima in a clever way. Are there other examples like the His alternative conformation that can help speak to this?

      7. When assigning responsibility for a part of the map that may be able to similarly explain two parts of the model, how does the method decide which part of the model should fit in that segment of the map?<br /> Please provide more insight on the interpretation of uncertainty of discrete positions of different sidechains as described in the sentence ‘ensemble adopting either (bottom inset), or uncertainty in the exact side chain confirmation (bottom inset) of two residues (Y76 and L78)’. How is uncertainty measured? Is the RMSF similar or comparable to what would be inferred by B-factors? Please compare the numbers you are reporting to other traditional refinement softwares such as REFMAC and Phenix. It’s unclear whether this is capturing anharmonic motions in a really different way or just sampling the B-factor harmonic component.

      Minor comments:<br /> 1. In Figure 1a, please provide more description about what you are representing with the blue and orange circles in the responsibility estimation.<br /> 2. How does your method represent very high resolution structures with low b-factors but high numbers of alternative conformers (specifically looking at PDBs: 7A4M, 7A5V of Apoferritin and GABA receptor).<br /> 3. In Figure 5a, please clarify how you are normalizing the B-factor.<br /> 4. Please deposit output models in Zonodo or some other public repository.<br /> 5. What does SMOCf stand for? Please introduce this briefly in the results.

      Review by Stephanie Wankowicz & James Fraser

    1. On 2022-08-09 15:01:20, user Uri Ben David wrote:

      Response to “Revisiting the effects of Cas9 on p53-inactivating mutations reveals sex-biased genome editing by CRISPR-Cas9”.

      Authors: Oana M. Enache, Veronica Rendo, Rameen Beroukhim, Todd R. Golub and Uri Ben-David

      A couple of years ago we reported Cas9-induced p53 signaling in cancer cell lines (ref 1). Here, Guo and Xiong address the possibility that this finding is affected by cell line sex biases (ref 2). In their preprint, they are trying to make 3 points related to our paper. We will address each of these points separately.

      1) TP53 mutations also shrink and not only expand upon Cas9 introduction.

      To study the trend of p53-inactivating mutations to expand or shrink following Cas9 introduction, we performed an analysis of pre-existing subclonal mutations (Fig. 3d in ref1). As mentioned in our paper several times, we deliberately restricted this analysis to pre-existing mutations with 0.02<af<0.48 or="" 0.52<af<0.98="" in="" the="" parental="" cell="" line.="" the="" reason="" for="" the="" focus="" on="" subclonal="" mutations="" in="" this="" analysis="" is="" that="" the="" tendency="" of="" mutations="" to="" expand="" or="" shrink="" can="" only="" be="" tested="" in="" subclonal="" events,="" as="" clonal="" events="" can="" only="" shrink="" and="" not="" expand,="" whereas="" non-detected="" events="" can="" only="" emerge="" but="" not="" shrink.="" inclusion="" of="" such="" clonal="" mutations="" would="" therefore="" bias="" the="" analysis.="" we="" found="" a="" highly="" significant="" trend="" for="" subclonal="" inactivating="" tp53="" mutations="" to="" expand="" following="" cas9="" introduction="" (fig.="" 3d="" in="" ref1),="" and="" tp53="" ranked="" 1st="" among="" all="" genes="" in="" this="" respect="" (fig.3e="" in="" ref1).="" in="" contrast,="" guo="" and="" xiong="" used="" different="" selection="" criteria="" for="" inclusion="" and="" exclusion="" of="" mutations.="" two="" of="" the="" shrinking="" mutations="" identified="" in="" their="" fig.="" 1a="" (in="" ovk18="" and="" c2bbe1)="" are="" clonal="" mutations="" (with="" af="" of="" ~0.5="" or="" ~1="" in="" the="" parental="" population).="" we="" argue="" that="" it="" is="" improper="" to="" include="" clonal="" mutations="" in="" this="" analysis,="" and="" it="" is="" clearly="" wrong="" to="" report="" them="" as="" “tp53="" inactivating="" subclonal="" mutations”="" (legend="" to="" fig.="" 1a="" in="" ref2).="" the="" third="" mutation="" that="" they="" identified="" as="" shrinking="" (in="" a2780)="" was="" also="" not="" analyzed="" by="" us,="" since="" it="" is="" a="" known="" snp="" that="" is="" pretty="" prevalent="" in="" the="" population="" (="">1% in gnomAD (ref3); see Supplementary Data 3 and our exclusion criteria described in the Methods section of ref1). We therefore think that it is a mistake to consider this mutation as an ‘inactivating TP53 mutation’ as well.<br /> Importantly, if one were to include the clonal inactivating mutations that Guo and Xiong have added to our analysis in their Fig. 1a2, then there is no justification for the exclusion of mutations that were not detected at all (AF~0) in the parental cell line but were present in the Cas9-expressing cell line, such as the mutation observed in the cell line SNU1 (Fig. 3c in ref1). However, this event was excluded in Fig. 1a of ref2. Similarly, if one were to include known SNPs in the analysis, then there is no reason to exclude the one in the cell line JHH7, which emerged from AF=0 to AF=1 (and was excluded both from our original analysis and from Fig. 1a2). In other words, the inclusion criteria for Fig. 1a of ref2 are inconsistent. <br /> Lastly, if we add the clonal mutations to the analysis (but exclude the known SNPs), there is still a significant trend for the expansion of TP53-inactivating mutations (p=0.03 in a one-tailed McNemar test for directionality). Guo and Xiong’s statement that they found “significantly shrinking inactivating subclonal mutations of TP53 in Cas9-cells, which means Cas9 also selects against TP53 inactivating mutations” (Abstract of 2) is therefore misleading. (We note that Guo and Xiong report that “four inactivating mutations from four cell lines were shrinking (P=0.039)”, but their manuscript does not provide any information about the statistical test that was applied to calculate significance.)

      2) There is a potential sex-bias in our results.

      We did not test whether any of our results were affected by a potential sex bias. Given that p53 has an effect on X chromosome inactivation, we cannot rule out the possibility that sex may affect p53 signaling following Cas9 introduction. However, sex representation in our cell line cohort was very balanced, and Cas9-induced p53 activation and selection were found in both male and female lines. Of the 43 TP53-WT lines used for the gene expression analyses, 21 were female, 21 were male, and one was of unknown sex; of the 122 TP53-mutant lines, 62 were female, 59 were male, and one was of unknown sex. Moreover, we used TP53-WT cell lines from both sexes (3 male lines, 2 female lines, 1 of unknown sex) to validate p53 activation following Cas9 introduction, and detected p53 pathway activation in both the male and the female lines (Fig. 2 and Extended Data Fig. 2 in ref1). Of the 10 cell lines in which a TP53 mutation was found to emerge or expand (Fig. 2c,d in ref1), 6 were female and 4 were male. Therefore, there is no evidence for any sex bias in these results.<br /> While Guo and Xiong raise an interesting hypothesis, they do not provide any real evidence that any of our results were indeed affected by sex bias. Instead, they make a few anecdotal statements on the matter:

      a) “The largest fold-change of p53 activation was observed in a female cell line (BT159)”.<br /> This is meaningless, as we tested the mRNA expression in 165 cell lines and protein expression in 9 cell lines. Guo and Xiong do not report any systematic comparison of the expression changes between male and female cell lines (although all of the data necessary for such analysis are available in our original paper).

      b) “There were more DNA damage foci in MCF7, which is a female cell line”. This assay was performed in only 3(!) cell lines, precluding any meaningful interpretation of sex bias. We also note that Cas9-induced p53 activation was actually mild in MCF7, compared to other male and female cell lines (Fig. 2e in 1), further weakening this particular anecdotal claim.

      c) “The largest TP53-inactivating subclonal mutations expanding or shrinking (293T, HCC1419, and OVK18) is seen in female lines”. This claim does not hold true if OVK18 is removed from the analysis. Moreover, according to Fig. 1a of ref2, 2 out 4 shrinking mutations and 4 out of 10 expanding mutations are actually seen in male lines, so the trend of mutations to expand or to shrink seems to be pretty sex-balanced.

      d) In the final paragraph of their manuscript, Guo and Xiong state that “We think the possible sex-biased effects of Cas9 may provide a possible reason for their failure to detect p53 activation in Cas9-expressing HCT116 (male) cells." This is factually wrong. We found significant activation of p53 in HCT116 cells transduced with Cas9, as is clearly shown in Extended Data Fig. 2d and<br /> 2e of ref1.<br /> We note that the majority of the manuscript by Guo and Xiong (Fig. 1b-d, Supplementary Fig. S1-S4, Supplementary Table S1) is an analysis of sex bias in CRISPR screens, which does not directly pertain to our paper. Sex biases in CRISPR screens may have nothing to do with the Cas9-induced p53 signaling that we observed. Moreover, we compared CRISPR to shRNA screens and found significant differences associated with p53 mutation status (Fig. 5 in ref1). Guo and Xiong do not discuss this at all, nor do they provide any evidence that this analysis was affected by cell line sex bias.

      3) TP53 mutation status of some cell lines is inaccurate in our paper.

      The Supplementary Note of 2 reads: "We found that 11 cell lines (RERFLCAI, SISO, SNU761, COV644, COLO684, HS294T, G292CLONEA141B1, D283MED, G401, SJSA1, and SNU1041) used as TP53-WT (Fig. 5a and Supplementary Data 5 in ref.1) by Enache et al. actually have non-silent TP53 mutations (Supplementary Table S2), although this should not affect their conclusions."

      There are 698 cell lines in Supplementary Data 5 and Fig. 5a, and we clearly did not validate the TP53 mutation status of each individually, but rather followed established annotations. There are several ways to classify TP53 mutation status in cell lines, and mutation calling algorithms constantly evolve. As described in our Methods section (ref1), we followed the annotations by Giacomelli et al. (ref4), which are based on the CCLE cell line annotations (ref5), according to which all of the 11 cell lines listed above are TP53-WT. These annotations have since been updated, however, and in the version downloaded by Guo and Xiong (22Q2, https://depmap,org/portal/), these cell lines are now classified as TP53-mutant. Importantly, exclusion of these cell lines has no effect on the outcome of the single analysis in which they were used (Fig. 5a in 1; p=8.8x10-6 instead of the original p=2.7x10-5; one-tailed t-test). Therefore, the slight discrepancy between the annotations used by us and those used by Guo and Xiong is irrelevant to the points that they raise.

      In summary, we thank Guo and Xiong for raising the intriguing possibility that sex may affect the cellular response to Cas9, in particular in the context of p53 pathway activation. However, this question remains open for now, as more research and data analysis are needed to determine whether this speculation is correct.

      References<br /> 1. Enache, O. & Rendo V. et al. Cas9 activates the p53<br /> pathway and selects for p53-inactivating mutations. Nat Genet 52, 662-668 (2020).

      1. Guo M. & Xiong Y. Revisiting the effects of Cas9 on<br /> p53-inactivating mutations reveals sex biased genome editing by CRISPR-Cas9. This preprint.

      2. Karczewski K.J. et al. The mutational constraint spectrum<br /> quantified from variation in 141,456 humans. Nature 581, 434-443 (2020).

      3. Giacomelli, A. O. et al. Mutational processes shape the<br /> landscape of TP53 mutations in human cancer. Nat Genet 50, 1381–1387 (2018).

      4. Barretina, J. et al. The Cancer Cell Line Encyclopedia enables<br /> predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012).
    1. On 2022-06-14 18:49:19, user CJ San Felipe wrote:

      In this paper, the authors analyze an intrinsically disordered region (IDR) of the yeast general recognition factor Abf1 with the aim of identifying functional determinants of Abf1’s IDR. The advantage of the authors’ plasmid shuffle experiments is that it allows the study of many mutations and variations of Abf1. The authors reveal that Abf1 possesses an essential motif (EM) as well as several contextual residues that work together to mediate Abf1’s function. Upon further investigation of compositionally and functionally similar IDR’s, the authors hypothesize that sequence specificity and chemical context in IDRs functionally overlap with each other rather than act independently, and propose a 2D model to describe the contributions of each in IDRs. <br /> The major success of this paper is in developing a model that reconciles two contributors to IDR function: sequence specificity and chemical context. The major weakness of the paper is that the model is not comprehensively backed with control experiments. The 2D landscape model presented argues that modulation of essential motifs and contextual amino acids can produce several binding modes; however, no data is presented to show that these chimeras are viable because they interact with the same factors or function in the same way that IDR2 does. Therefore, we can’t be certain if these are off-target effects or the same interactions that occur with IDR2 as put forward in the model. In addition, we found some aspects of the organization of the paper may require more clarity. Overall, the paper reveals some of the functional determinants for Abf1’s IDR and proposes an intriguing model for the functional determinants of other IDRs, but it could be difficult for these findings to be generalized.

      Major points<br /> p.4: <br /> It is unclear to us why the minimal viable construct IDR2 449-662 is the background reference construct. Is it possible that IDR1 (absent in this construct) could provide unknown benefits in particular situations? For example, given the unknowns of Abf1’s interactome, is it possible that IDR1 helps to activate transcription of other genes that could rescue IDR2 mutants? Perhaps the presence of IDR1 could confer viability for IDR2 mutants that were deemed not viable in later experiments. Plasmid shuffle assays with IDR2 mutants that also have IDR1 present could be control experiments that answer this question.

      p.4 <br /> The constructs generated in this paper are tested for viability via plasmid shuffle assay, but there is no control experiment to ensure that these constructs are still interacting with the same partners or functioning in the same way that wildtype IDR2 does. One possible control experiment to test this could be to choose an Abf1-interacting partner based on proteomic literature on Abf1, and perform a co-immunoprecipitation/Western blot to see if the partner is still present across different IDR2 mutants. This control experiment should be done with full length Abf1, the background reference construct (with no IDR1), as well as a construct without the EM and a shuffled construct to represent the two extremes of the 2D landscape.

      p.5: <br /> The decision to choose the G4 motif does not have a strong justification or explanation. In figure 3F it is shown from the alignment between Abf1 and Gal4 that the region considered to have sub-homology does not overlap with the essential motif of Abf1 nor does it show similarity in its sequence. Therefore, in our view, it does not appear that Gal4 has an EM that is homologous to the EM of Abf1.

      Figure S1 PDF:<br /> By eye, it appears that there is large variation between the strains considered inviable – for example, FUS_1_163_WT clone 3 on page 6 and Shuffle 3 clones 2 and 3 on page 3 are both marked as inviable yet differ in growth. It could be helpful to readers if an explanation about why a binary classification of viable vs inviable was used in this study, as opposed to a sliding scale quantification.

      Minor points<br /> For a future direction, after identifying the essential motif in IDR2 (EM), we think it would be compelling to go back to the orthologs initially tested to see how conserved the essential motif is evolutionarily and to see how divergent the orthologs that we’re inviable were. We also feel that this could be incorporated into the paper’s discussion.

      Figure 3: <br /> Panels G-K were difficult for us to understand due to the sheer number of constructs presented. To us, the contrast between sequence-specific motif and chemical context would be clearer if panels E and K were combined, perhaps with labels “sequence specificity” and “chemical context” below the respective constructs, to underscore the two ends of the spectrum that these panels represent and to emphasize the unexpected viability of the constructs in K.

      p.2-3: <br /> The hypothesis that poorly conserved IDRs may still retain functional conservation is compelling, but the proteome-wide analysis of disorder leading up to this hypothesis could be clarified in the methods section. In particular, it would be helpful to include an explanation of why and how disorder score from metapredict and predicted pLDDT were used in conjunction with each other, as opposed to using the predicted consensus disorder score from metapredict alone.

      We review non-anonymously: Daphne Chen, CJ San Felipe, James Fraser (UCSF).

    1. On 2022-05-16 21:15:23, user Jingyi Jessica Li wrote:

      We thank Dr. Hejblum et al for sending us a draft of this article on May 3 before posting it. Below I'm pasting our reply sent to Dr. Hejblum et al on the same day. We believe that our discussion will be beneficial for the community.

      Dear Dr. Hejblum and all,

      Thank you for sending us your correspondence draft. We appreciate your professionalism.

      The main message of our article is that using popular methods without a sanity check may lead to inflated FDR, and permutation offers an easy sanity check.

      We agree that normalization is a tricky issue, and when samples do not need normalization (as is the case for permuted samples, which all come from the same "condition"), normalization may introduce unwanted bias, violate the null hypothesis, and thus deteriorate the FDR control. Meanwhile, we stand with our fundamental assumption that permuted samples should contain no true DE genes. Since many DE methods include normalization as an internal step and only accept count data as input, the only way to fairly compare them is to apply each method as a whole pipeline, not just its DE statistical test step, to the permuted samples. (That is, the "normalization first" approach in your manuscript is inapplicable to the DE methods that only accept count data, unless we dissect these methods and modify their code, which is beyond the scope of our benchmark study.) As a result, any bias introduced by normalizing the permuted samples (which do not need normalization) would be reflected in the actual FDR inflation. The Wilcoxon test is an exception because it is not a DE analysis pipeline, so we applied it to permuted samples without doing normalization in Figure 2A. This explains why our Figure 2A differs from your Figure 1A.

      We would like to clarify that our study is not a comprehensive benchmark because (1) there are numerous DE methods and (2) we did not want to dilute the cautionary message against using the popular DESeq2 and edgeR without a sanity check. Hence, we did not do a dissection of each method to find out how to fix the inflated FDR issue. Our dearseq results are based on dearseq (asymptotic), not dearseq (permuted), because we deemed dearseq (asymptotic) more appropriate when the sample size is large.

      We appreciate your clarification about the effect of normalization on the dearseq performance, and your results motivated us to think about the problem more clearly. However, we respectfully disagree with your conclusion that dearseq outperforms Wilcoxon in your results. Our reasoning is that only dearseq (asymptotic), not dearseq (permuted) has a slight power advantage over Wilcoxon, but dearseq (asymptotic) does not guarantee to control the FDR when the sample size is under 40; on the other hand, Wilcoxon only sacrifices power but not FDR control when the sample size is small. Nevertheless, we agree that dearseq is advantageous in that it can account for more complex experimental designs.

      We would be happy to publicly respond to your correspondence when needed. We believe that our discussion will be beneficial for the community.

      Best,<br /> Jessica


      Jingyi Jessica Li, Ph.D.

      Associate Professor<br /> Department of Statistics<br /> University of California, Los Angeles

      http://jsb.ucla.edu

    1. On 2022-03-21 04:02:34, user Andrew Bell wrote:

      First, well done on achieving such high resolution, and largely noninvasively. Now we can start to see evidence of what is really going on in the cochlea. Your work raises a whole lot of issues, but I’ll just mention a few key findings. I hope you find these comments helpful.

      1. In the abstract a fairly provocative statement is that the data is not explained by current theories. In my view, I don’t think this is quite right, as the motions you reveal appear to be the result of simple resonance between the rows, an idea first raised in my PhD thesis and then in several associated publications. Perhaps the most germane are Bell & Fletcher (2004), The cochlear amplifier as a standing wave, JASA 116, 1016; https://doi.org/10.1121/1.1766053 and Bell (2012), A resonance approach to cochlear mechanics, PLOS One, https://doi.org/10.1371/journal.pone.0047918. Both papers set out a scheme whereby the three rows of OHCs work together to establish a resonant element which gives rise to a standing wave between the rows. Tuning thus depends largely on the row spacing, not the stiffness of the BM. The OHCs are stimulated virtually instantaneously by the fast pressure wave (OHCs are pressure sensors, for which I’ve made a case elsewhere), not the conventional travelling wave. In this way, I think most of your findings can be accommodated, as set out below.

      2. In your Introduction you say that a special sort of phasing is required in order to amplify the travelling wave. This is not necessary if you look at it in terms of resonance. As Bell (2012) broadly explains, the travelling wave is simply the observed result of what happens in response to a graded bank of highly tuned resonators that are almost simultaneously excited by a fast pressure wave. The delay observed is then simply Q/pi cycles, where Q is the tuning sharpness. In other words, I suggest you may be looking at things back-to-front causally: it is the resonance that gives rise to an apparent TW, not that the TW is a causal entity that, through very careful phasing, is able to amplify BM motion and give rise to a large peak! That is, the OHCs don’t amplify motion at all; instead they are pressure transducers which, via electromotility, vibrate in response to the sound pressure surrounding them (the OHCs contain pressure-sensitive ion channels). I’ve published a number of papers on this, and I’m happy to discuss the idea with you in more detail if you wish. In brief, I am suggesting that, if we look at cochlear mechanics differently, the TW is an epiphenomenon of a tuned bank of active elements. The elements are local oscillators – there doesn’t need to be global coupling in order to propagate a TW.

      3. I am suggesting that each triplet of OHC1, OHC2, and OHC3 act together like a guitar string arranged radially. However, unlike a string, there is a fluid connection between the rows (a squirting wave) so that the wave travels at a particularly low velocity. Applied to your observations, at a BF of 46 kHz the wave traverses OHC1 to OHC3 (a distance of about 30 um) in 1/46000 of a second – that is, a speed of about 1 m/s. As an explanation, so-called squirting waves have such low phase velocities, and anatomically are well suited to act in the space between the TM and reticular lamina, as Bell & Fletcher (2004) describe. Electromotility of the OHCs causes squeezing in that space, generating squirting waves.

      4. At their tuned frequency (BF), the amplitude of vibration is largest, and that is consistent with a resonating element that is tuned to that frequency. Thanks to your high resolution, we can see the activity of each of the three OHCs. In Figure 5c there seems to be a larger amplitude of vibration for RL3 than RL1; another radial profile at a different level (Figure 7c) shows that the amplitudes are about equal. Given the intricate geometry, I think that the findings are generally consistent with a radial standing wave with the OHCs at the antinodes.

      5. Now, about the phases. The 3 OHCs seem to have about the same phase, and this is consistent with a standing wave between them. A standing wave is a wave that oscillates in time but whose profile of peak amplitude does not move in space. My papers suggest that OHC2 acts in antiphase to OHC1 and OHC3, an arrangement which is closer to a xylophone bar than a guitar string. In other words, each OHC sits at an antinode, and the result is a full-wavelength standing wave. Your OCT device sees all the OHCs vibrating at the same amplitude, but doesn’t see the wave moving backwards and forwards between them. Other phase arrangements may be possible, but the full wavelength case is probably the simplest. For a guitar string, there is only 1 antinode and 2 nodes, so if this applied in the cochlea, all the work would be done be OHC2 (we wouldn’t need 3 rows of OHCs).

      6. Taking together all the above, I hope you may appreciate that if we had a ringing xylophone bar between OHC1 and OHC3 then an OCT device would see all the OHCs vibrating at the same amplitude and the same phase. It would require special techniques to detect the standing wave, and I wonder if your device has that capability. This would provide convincing evidence in favour of a resonance model.

      7. Note that in my papers I regard the phase lag at resonance to reflect the group delay of the resonators. For a linear resonator, the group delay amounts to Q/pi cycles. It is interesting to look at the group delays you recorded in Figure 8f-h and Figure 10e,f. At BF (resonance) they show a phase lag of 2–3 cycles. So if one considers these delays to derive from a linear resonator (not strictly true, but perhaps not too far off), then the associated Q values would be pi times 2 or 3, which is about 6–9. Such Q values are roughly the same as those measured otoacoustically for the gerbil.

      In summary, I suggest it is possible to interpret your findings using a different causal chain, the inverse of what you have done. That is, the causal chain may involve the direct electromotility of OHCs in response to sound pressure, and not that OHCs have to very carefully amplify atomic-scale BM motions to create a traveling wave – and this approach simplifies cochlear mechanics enormously. The alternative view is that the BM may just be

      a supporting membrane for an array of tuned elements, which are independently excited by the fast pressure wave. Indeed, it is interesting that the ITER team (Khanna and colleagues) adopted this view more than 30 years ago. They said that “The present observations suggest that the outer hair cells vibrate mechanically along their axes in response to acoustical stimulation.” (p.188) https://doi.org/10.3109/00016488909138336. It is perfectly possible to look at your data in a different, but internally consistent, way.

      I hope this helps us move towards the truth of the matter. Best wishes for your publication. Andrew Bell.

    1. On 2022-02-19 17:21:19, user Charles Warden wrote:

      Hi,

      Thank you very much for posting this preprint.

      I appreciate your interest in COHCAP, but I thought that I should mention a couple things:

      1) You cited the COHCAP corrigendum, not a primary reference for the method or applications.

      This would be OK if you were citing something was specifically said in the corrigendum. Likewise, there are comments that complement the factual errors that were formally corrected.

      However, I think you may have meant to cite the following?

      https://pubmed.ncbi.nlm.nih...

      I apologize that I think this is confusing. PubMed correctly lists the 2019 citation as an "Erratum" if you view the original publication, although the separate listing for the corrigendum might look similar to a regular publication in PubMed among a set of search results.

      2) The default setting for the methylation threshold is 0.7 and the default setting for the unmethylated threshold is 0.3.

      For the patient data, we do offer using 0.3 as a troubleshooting suggestion. This may already be clear to some or most readers, although I wanted to mention again that some testing of various parameters may be needed. I also tend to use COHCAP along with at least 1 other method (such as methylKit) to try and assess the data, even if only 1 method is used in the paper (which may or may not be COHCAP).

      There is a newer location for support questions on GitHub (https://github.com/cwarden4..., but most previous questions are still on SourceForge (https://sourceforge.net/p/c....

      So, I think that is OK, but I am not sure if something like the following helps give additional context for readers of this paper:

      https://sourceforge.net/p/c...

      I believe that you referenced the use of thresholds rather than the method, but I am not saying that a beta value of 0.31 is truly significantly different than a beta value 0.29 by itself. The thresholds are 2 possible criteria out of several parameters considered in COHCAP, with the goal being to look for differential methylation.

      I hope this helps.

      Thank you again!

      Sincerely,<br /> Charles

    1. On 2022-01-28 20:16:36, user corihuel wrote:

      Dear Authors,

      Your work was recently reviewed and discussed by the Bacterial Pathogenesis and Physiology Journal Club here at the University of Alabama at Birmingham (UAB). As part of our review of pre-prints, we compile comments from our discussion that we think may better your publication.

      Overall, our group found the manuscript to be a very interesting read with detailed information on the structure/function of SteD emerging. We can tell that considerable thought that went into each experiment as well as figure production. Your lab has shown an exceptional amount of rigor in your experimental designs that made it difficult to refute your findings. This study was very well done, and we all enjoyed discussing it.

      Below we point out some comments and aspects that we feel could improve on the manuscript.

      1) We felt that the text was a little difficult to follow. Though it is probable that this will be alleviated once the paper has been properly formatted, as the figures help a great deal in understanding the text.

      2) We very much appreciated the short anecdotes in the manuscript explaining the specific actions of the chemicals used for your experiments. None in our journal club work this closely with transport systems and it made understanding your work much easier.

      3) We were curious about your justification for using a melanoma cell line in your studies rather than an APC line like BMDMs? We’ve noticed that it has been used for other Salmonella studies, but we think it necessary that you justify in the text why you use this cell line.

      4) The order of your figures is a little confusing, specifically figures 1-3. We think it would really help if you were to either combine Figures 1 and 3 in some manner or reorder them so that Figure 3 comes just after Figure 1, rather than being interrupted by Figure 2. This would streamline the reading and comprehension of your data greatly.

      5) On the topic of Figure 3, we were curious as to why you found the specificities you did and yet continued to use the region 13 mutation rather than the S68A G69A mutations in your experiments for Figure 4. Especially given the problems you had with region 13 mutation expression and release from Salmonella.

      6) Our group wanted to extend our compliments to your inclusion of the protein diagrams you had throughout your paper. The visualization made it easy to understand the mutations made and really helped with the overall comprehension of the paper and the experiments you were completing. On this note, however, we don’t think it necessary to highlight the F and Y residues in Figure 7. They are discussed in the text but are not tested in the figure. That depiction would be better included in a supplemental figure showing the experimental results from those mutations.

      7) Lastly, we believe Figure 5C should be moved to supplementary since it only confirms that your siRNA worked as intended.

      Sincerely,<br /> UAB Bacterial Pathogenesis and Physiology JC

    1. On 2022-01-21 22:03:41, user Debelouchina Lab wrote:

      Hello! This is the Debelouchina Lab at University of California, San Diego. We have begun doing preprint manuscript reviews during our “journal clubs” as a way to enhance our engagement with current literature and to hopefully assist with the manuscript if possible! Our lab also studies the behaviors of biomolecular liquid-solid transitions – with a focus on protein structure. We selected this manuscript out of curiosity for the spatial origins of solidification in liquid-liquid phase separated systems.<br /> Liquid-liquid phase separation (LLPS) is central to the spatiotemporal organization of biomolecules in the cell. Many of the proteins that are thought to mediate LLPS have also been found in pathological aggregates and fibrils that are associated with neurodegenerative disease. It has been demonstrated that liquid-like phase separated bodies can adopt gel-like or solid morphologies over time, which suggests that LLPS droplets may serve as nucleation points for pathological aggregates. This manuscript interrogates this process by characterizing the spatial characteristics of the liquid-to-solid transition within individual alpha-synuclein condensates using a set of fluorescence and infrared microscopy techniques. The authors found that droplets solidify form a central focal point that can be imaged through associated changes in fluorescence lifetime (via fluorescence lifetime imaging, FLIM) and protein secondary structure (via Fourier transform infra-red microscopy, FTIRM). To emphasize this significance in the text, we think it may be helpful if the authors added more background and discussion of previous literature on the spatial origin of solidification.<br /> These findings are exciting as they add new insight into biomolecular liquid-to-solid transitions, and relevant due to the potential role for liquid-to-solid transitions in neurodegenerative disease. We find that the combination of fluorescence microscopy techniques used here presents a strong model for studying spatiotemporal material properties of biomolecular condensates, which are challenging to characterize from a structural perspective due to their inherent heterogeneity and sensitivity to environmental factors. The power of these techniques is shown in their ability to complement the FLIM data into protein mobility (FRAP), structure (FTIRM), and interaction (FRET) components, providing a comprehensive look into the liquid-to-solid transition. We appreciated the use of small fluorophores rather than fluorescent proteins, as well as the confirmation by fluorophore-free techniques (TEM & cryo-SEM). Overall, we find that the data and the resulting model for the spatiotemporal dynamics of the liquid-solid transition are compelling.<br /> One area we are curious about is the sample handling, keeping a sample hydrated for 20 days is difficult. Would you be able to add a few words about the robustness of this moisture chamber in the main text? These aspects of the experimental design might not be obvious to a reader unfamiliar with the practical considerations of experiments like this, so more discussion would be helpful to anyone trying to reproduce the experiments. In a similar vein, a paragraph about the practical aspects of FLIM in the context of LLPS would be helpful. We also wondered about the necessity of the solidification timeline, how would the microscopy procedures described here work for a system that progresses to solid much faster than 20 days? What are the time limitations of these techniques? Would a faster system be expected to have the same center-growth effect as seen here?<br /> We were surprised that droplets appear to solidify from the exact center of the droplet in every case. If the model for solidification is that it begins from a (random) nucleation point, then why would droplet solidification always begin exactly in the center, as opposed to the inner or outer center regions that are mapped in Figure 1. We were left wanting more information about this, especially since FLIM is capable of resolving changes on these scales. It would be interesting to see if there are any cases where solidification does not begin from the exact center of the droplet. <br /> Some minor comments:<br /> -While the figures are clear and well-organized, a more colorblind-friendly palette could be used.<br /> -Infrared is occasionally hyphenated throughout the text.<br /> -The abstract figure may be clarified if the FLIM images were all of a single droplet, matching the cartoon.<br /> -The schematics describing the planes on the droplet are beautifully done and very helpful to understanding the figures.<br /> -Figure 1: formatting error with (e) placement.<br /> -Figure 2: (c) As we are unfamiliar with FTIRM, we thought it may be useful to have the corresponding secondary structure to each wavenumber (like the supplementary table 1 information) in the figure. Similarly, while supplementary figure 7 has a monomer and fibril control, we would have enjoyed that in the main figure.<br /> -Figure 4: (c) We wonder how consistent these recoveries are for several different droplets at the same time point.<br /> -For the TEM data (Fig 5), the results are a little bit different from other attempts to perform TEM on LLPS systems (for example, here: https://pubs.acs.org/doi/10.... A discussion of precedent would be appreciated in the main text. <br /> -Supplementary Fig. 11: We thought these EM images were fascinating and are curious if such images exist elsewhere for biomolecular condensates.


      We appreciated the chance to read and review this manuscript,<br /> The Debelouchina Lab

    1. On 2022-01-11 20:42:36, user Mina Bizic wrote:

      I would like to congratulate Rachel Szabo and colleagues on their great work and effort put into this manuscript. The goal of analyzing such a high number of particles has been something I have been calling for ever-since my work cited in the comment by Dr. Jacob Cram (Bizic-Ionescu et al., 2018). It’s exciting to see the efforts you have made in this direction.

      It’s equally exciting to see that my conclusion from 2018 that the initial colonization of particles is stochastic, is strongly featured in your paper title and well supported by your results.

      As Dr. Cram has mentioned in his comment, we discussed your study and have come up with several aspects that we feel deserve some attention and most likely to be better addressed in the manuscript. Some of these aspects were raised by Dr. Cram in his comment. However, we felt that our opinions on this manuscript were dissimilar enough to warrant separate comments, with some observations that overlap and some that differ.

      My general query goes to the applicability of the results to the natural environment, given several biases introduced by the chosen experimental system. I will list here my opinion on the source of these biases.

      1) The concentration of seawater is likely to have generated an unrealistic microbial community. This is for three reasons (A) concentration of particle-attached microbes, (B) concentration of large bacteria, and (C) non-concentration of DOM: <br /> (A) Filtering the water through a 63 µm mesh should leave all particles smaller than this size in the water The subsequent step of gentle centrifugation most likely further concentrated these microparticles increasing their abundance above natural concentrations. <br /> (B) The gentle centrifugation likely selected for larger bacteria, as smaller cells may not be concentrated by a 5 min 4000 g run. <br /> (C) Finally, the seawater DOM on which bacteria can feed was not concentrated in this process. <br /> Therefore, the resulting inoculum used for the experiment contains a size-selected microbial community and a microparticle enrichment which in the absence of ambient DOM will rapidly drive the experiments towards consumption of the particulate organic matter at rates not representing the natural environment.

      2) The incubation time and small volumes: While samples have been collected already after 12 h the experiment ran for 166 h in a closed microwell. It has been shown by many as well as by my colleagues and I that after 24 h at the latest, the community in the experiment does not represent the environmental one (for example: Baltar et al., 2012; Ionescu et al., 2015; Herlemann et al., 2019). Therefore, seeing such long experiments conducted in fully closed systems, as in this paper, makes me wonder to what degree the rates of events observed in the lab are similar to rates in nature.

      3) One possible problem with the incubation system used, is the effect of the microwell surface on microbial activity. Ploug and Jorgensen (1999), for example, came up with the net-jet system for measuring microprofiles on organic matter aggregates. However, aside of the effect of direct contact of particles with surfaces on particle properties and the microbial activity on it, a second issue is the formation of biofilms may form on the surfaces of the incubation system. Heterotrophic activity is known to increase in closed incubation systems (e.g. Fogg and Calvario-Martinez, 1989; Ionescu et al., 2015). Though it was shown that these biasing effects will occur regardless of bottle size (Hammes et al., 2010), these will likely have a stronger effect in very small incubation volumes (Herlemann et al., 2019), consuming oxygen and nutrients. I don’t recall reading whether the O2 concentration was monitored? My guess is that the system became anoxic relatively fast, unlike it would be in a natural environment. How does this affect the nature of associated (and active) bacteria?

      Having said that, I support the authors’ overall conclusion and applaud the effort that went into the data collection and analyses I am aware from my own work on the difficulties to obtain and maintain such a large number of particles in open systems, such as the one my colleagues and I designed. However, I think that the biases introduced by an experimental system should be openly discussed in the manuscript and if possible, explain how your results remain valid despite them. This is even more important when you often discuss late-stage particles, that are the most to be affected by aspects mentioned above.

      Sincerely,

      Mina Bizc

      References

      Baltar, F. et al. (2012) Prokaryotic community structure and respiration during long-term incubations. Microbiology open, 1, 214–224.

      Bizic-Ionescu, M. et al. (2018) Organic Particles: heterogeneous hubs for microbial interactions in aquatic ecosystems. Front. Microbiol., 9.

      Fogg, G. E. and Calvario-Martinez, O. (1989) Effects of bottle size in determinations of primary productivity by phytoplankton. Hydrobiologia, 173, 89–94.

      Hammes, F. et al. (2010) Critical evaluation of the volumetric “bottle effect” on microbial batch growth. Appl. Environ. Microbiol., 76, 1278–1281.

      Herlemann, D. P. R. et al. (2019) Individual physiological adaptations enable selected bacterial taxa to prevail during long-term incubations. Appl. Environ. Microbiol., 85.

      Ionescu, D. et al. (2015) A new tool for long-term studies of POM-bacteria interactions: Overcoming the century-old Bottle Effect. Sci. Rep., 5.

      Ploug, H. and Jørgensen, B. B. (1999) A net-jet flow system for mass transfer and microsensor studies of sinking aggregates. Mar. Ecol. Prog. Ser., 176, 279–290.

    1. On 2022-01-07 09:57:20, user David Bhella wrote:

      To help readers understand the process of peer-review, I am adding the peer-reviewer comments and article submission history for all of my preprints. For this article, although I was senior author - I was not corresponding author as the work was largely led by Dr Swetha Vijayakrishnan.

      The article was rejected without review at two journals prior to being sent for review at the journal of record. It underwent two rounds of review before acceptance.

      Reviewer Comments (Round 1):

      Reviewer 1

      In their manuscript Vijayakrishnan use Tokuyashi sections for electron microscopic imaging in the frozen hydrated state (‘cryo’). Tokuyashi sections are commonly used for immuno EM imaging in cell biology and then combined with dehydration. Direct imaging in the frozen-hydrated state results in higher molecular preservation compared to dehydration and resin embedding. The method is broadly applicable and relatively straightforward compared to cryo-FIB milling but does not allow comparable resolution levels.

      It was interesting to see that this manuscript again highlights the possible usefulness of cryo imaging of Tokoyashu sections. However, on the experimental side the reviewer does not see the novelty. In particular, Bos et al (ref. 13) seems to cover all novelty claims of the manuscript (application to cell culture, correlation with light microscopy). The remaining possibly novel aspect is the analysis of viruses by subtomogram averaging, which may shed some light on the quality of sample preparation. Nevertheless, the description of methods and analysis is somewhat superficial at this point. The conclusions on the association of pUL36 remain somewhat vague and do not appear statistically significant. Given the low resolution (~6 nm) indeed not too much can be concluded. Overall, the manuscript appears to touch on many things, but there is little novelty and conclusive results.

      Major points:

      • Page 5: “To our knowledge however, use of this method has thus far been confined to 3D imaging of tissue specimens 10-13.” This claim appears to be incorrect as Bos et al (ref. 13) applied the approach to cell culture – just as in this manuscript. Thus, it should be specifically stated which new contribution this manuscript makes to the field.

      • Page 5: “Here we present a modified strategy that combines correlative light microscopy and cryo-ET to locate regions of interest (ROI) in re-vitrified cell sections”. Again: what specifically is the novelty compared to ref. 13?

      • Page 14: “We successfully implemented this method …”. How do the authors validate their success? There are no quantifications provided. Is the method available?

      • Page 14: “To our knowledge this is the first attempt to implement this method on sub tomograms.” Previous implementations have already been reported in Schmid et al, PLOS Pathogens, possibly also later.

      • Probably the major problem in cryo-sectioning is the resulting compression. Thus, the reviewer would have expected an analysis of the effect of compression on subtomogram averages. Such analysis should be relatively straightforward given the available high-resolution structures of capsids.

      • The resolution of subtomogram averages appears overly low. Have the authors focused alignment and/or resolution measurement on specific parts of the capsids to compensate for compression and/or variable density in the core?

      • In the discussion the authors only compare cryo imaging of Tokuyashi sections to cryo-FIB milling / cryo-ET. A comparison to high-pressure freezing with freeze substitution and resin embedding should also be included.

      Reviewer 2

      In this manuscript, Vijayakrishnan et al. present an approach that allows the visualization of cells that have previously been fixed (cross-linking) prior to imaging using electron cryo-microsocpy. In this case the sample is subsequently vitrified in a state where the macromolecules have been chemically altered but in a way that allows direct imaging as opposed to imaging a counterstain, such as osmium or uranyl compounds. The fixation of material is normally avoided due to the significant chemical alteration of macromolecules within sample, and makes the analysis of additional densities associated with any such macromolecule a potential minefield to study. The reviewer appreciates the need to make the analysis of cellular material using cryoEM easier, but is unconvinced that performing structural biology in a background of chemical fixation is an appropriate route to go and will inevitably lead to structural information that is wrong.

      The attempt to visualize viral capsids is an interesting application and is one that is sensible. The capsids in the nucleus look to have retained much of their native architecture. The argument put forward that the C-capsids in the nucleus have extra densities present seen in mature capsids is strong, but is beset by a lack of control experiments, a lack of analysis in terms of other material found in their preparations, and a lack of appropriate interpretation of secondary analyses.

      1. The use of fixation using this approach results in the material not being in a “native” state as is the case with regular cryoEM methods. This is significant as this alteration to the macromolecular structure means that any subsequent structural analysis will be potentially affected by artefacts of this approach. This reviewer believes therefore that one must be very careful when analyzing the results of any potential structural analysis in this manuscript.

      2. The authors have not presented the proper controls for some of the interpretation of their results.

      A control is needed here to structurally analyse the herpesvirus capsid with the CVSC (positive control) after fixation – this should be relatively easy if you fix the mature virions and do sub-volume averaging on these virions to assess whether deformities in the CVSC structure are introduced. It is a gross misrepresentation to compare this structure in a fixed/unnatural/dead state to one from the EMDB determined in a frozen-hydrated state as has been done in Figure 5.

      These controls also apply to the subsequent analysis to determine the architecture of the capsid pore vertex.

      The capsids found in the cytosol exhibit significant breakage and are distorted when compared to those in found inside the nucleus (see figure 3) and is not commented in the manuscript. This is a significant concern as it would suggest that there is some damage to the structural integrity of potential targets. It also a shame, as the cytosolic capsids would appear to me to be a great target to compare structurally with the nuclear capsids.

      This would also be a concern were anyone wanting to use this approach to target processes occurring in the cytosol, as it seems there is a greater effect on macromolecules in this subcellular compartment.

      1. The cells are initially grown to confluency as a monolayer and then infected with the virus for 12hr. At this time point the cells are fixed which completely kills the cells. The cells are then scraped and pelleted. One assumes that after fixation of cells there is significant disruption to the structural integrity of the cells – a picture or demonstration of the state of the cells after this treatment would help to understand what exactly goes into the subsequent steps. Figure S1 shows widespread DAPI staining illustrating the point that there is significant mixing of compartments making knowing exactly what is being imaged difficult. My concern is that an additional step is needed to ascertain where is being imaged as the DAPI is almost everywhere.

      2. The attempt to classify the capsid 5-fold vertices makes the analysis of the CVSC confusing and brings up further questions about what is really going on as the analysis done here restores the CVSC to the B-capsids.

      The techniques outlined aim to address a curious debate in the herpesvirus field – namely whether the capsid vertex specific component (CVSC) is present on C-capsids on the nucleus, and it is important to frame the conclusions of the paper in this context. The protein component has multiple names that reflects the belief among different members in the herpesvirus community as to its true role or when/where/how it functions in relation to the capsid. The CVSC is made up primarily of pUL17 and pUL25 with a significant contribution of two helices from the C-terminal tail of pUL36. pUL36 is a very large protein, and its presence in the nucleus is unlikely in is full-length state. Debate continues in the field as to whether splice isoforms of pUL36 contribute to binding at the CVSC in the nucleus.

      In the present study, extra density is visible on C-capsids that is not visible on other capsids types (A and B), though in the case of B-capsids this density is visible after classification. These discrepancies need to be cleared up as the resolution limitation on the capsids makes it impossible to say what components are visible on the CVSC at this point – UL17 and UL25? UL17, Ul25 and extra density (UL36?)?

      1. Washing the sections a few times in PBS after infiltration would seem to this reviewer not wholly effective at removing73 the sucrose. Fig3 – halo around the multimembrane.

      2. The sentence “The pentaskelion density in B-capsids is more prominent than C-capsids; likely owing to far greater numbers of B-capsids (526) used during processing than of C-capsids (125). These data support our suggestion that low occupancy of CATC on B-capsids led to weaker density in icosahedrally averaged density maps. They are clearly visible upon asymmetric reconstruction (Figure 6), but not during symmetric reconstruction (Figure 4).” The significance of this analysis is not clearly explained.

      3. Introduction is far too long – I suggest the authors rewrite in order to make it more concise and streamlined i.e. significance of SPA, the play-off between cryoET and classical methods and the need to find more approachable methods. This introduction could be written with the same effect in half the space.

      4. It would really help the reader to have a correlative figure in the supplement (for example in S1) that goes from light microscopy

      Figure 1.<br /> The DAPI stain is present in the field of view of both cytosolic and nuclear regions – why is this?

      It is very hard to discern in this figure how the determination of what is nucleus and what is cytoplasm is made.

      Figure 2.<br /> Why have the authors excluded fluorescence data from this figure? One would assume this would be the most effective use of their correlative approach as it is possible to actually discern cellular features directly through EM here.

      The segmentation in Figure 2b is something of an eyesore. I would redraw or redesign a mean of highlighting the membranes.

      It is not easy to see the different types of capsid with this annotation- an A-capsid is not highlighted (left of field of view) for example, and the box is not immediately obvious. Why box and arrow? Why not all box or all arrow?

      Panel d is completely unannotated. Why is there a halo around the multilamellar vesicle (that is not a CTF effect)?

      Figure 3.<br /> The authors should comment on why the capsids in panels A and B look undamaged, while those in C and D exhibit significant damage/deformation.

      Figure 4.<br /> Why do the densities interface between the capsid coat and the inner regions blur as you move from A to B and C? A myriad of cryoEM structures of viral capsids have been determined and do not exhibit such an artefact.

      Figure 5.<br /> The comparison in this figure is not appropriate at all for a number of reasons: the structures are determined via different means (fixed vs non-fixed), the structures are at completely different resolutions which I consider to be a cynical attempt to improve how the authors’ own data appear - the figure on the right should at least be presented at the same resolution as the authors. The colour scheme is inadequate to show the CVSV, which should be the only thing visible here to help the reader to see what the authors are referring to in its entirety.

      Figure 6. <br /> The data in this figure are in conflict with those shown in Figure 5, and leads to some confusion. Symmetrically-determined 5-fold vertices are classified in an asymmetric manner. Therefore, the number of icosahedrally-related positions for the C-capsids remains the same. The data suggest that if you relax the symmetry then the CVSC density on the C-capsids smears due to low numbers – but this seems completely illogical to me. Why would an ordered density smear? Remember that this structure can be refined to ~3.5Å in cryoEM. If the occupancy in B-capsids is too low to get an effective CVSC in an icohedral reconstruction why would it be better in an asymmetric classification unless the structure of the CVSC is different to that of A-capsids? What happens if you reduce the number of particles from each each virus type to be the same number? Does the B-capsid density also smear?

      Once again, using the EMDB structure as shown in C is inappropriate.

      Figure S1.

      It is almost impossible to know how the authors came to the determination that these are different regions of the cell from this figure. This figure makes it clear that it is hard to determine what parts of the cell belong to where.

      Reviewer Comments (Round 2):

      Reviewer 2

      It is a shame that the current pandemic has resulted in the shutdown of the Authors’ Institute, and the reviewer would like to express their sympathy for this situation. Hopefully, things will change in the coming months.

      The lack of experiments validating either of the method or the major results (putative CVSC density on the capsid surface in the nucleus) is still a major concern, and without such experiments it is not possible for the reviewer to recommend publication.

      1. Publishing a single structural result at low resolution and without further validation either from comparison to other subcellular structures (e.g. ribosome or cytosolic capsids) or using biochemical means (e.g. immunolabelling with nanogold of CVSC components) adds to the confusion in the literature as to whether the CVSC is present, in part, whole or not at all, in the nucleus or not and such a publication would not be beneficial. Should analyses on other components also lead to structures that exhibit no difference to results previously published one can be more confident in novel results – though still not 100%.

      2. It is still unclear to this reviewer how exactly capsids are determined to be nuclear from the analysis of Figures 1, 2, and S1. While it is possible to see regions of membranes, the fact that the cells are disrupted using their methodology combined with the presence of DAPI in multiple regions adds to the confusion as to whether the nuclear capsids are indeed nuclear capsids. In Figure 1, it is possible to make out blue dots and red dots separate from one another and together. Capsids also containing DNA and would likely be stained by DAPI. This is not followed on in Figure 2, which is annotated manually. Is it assumed all capsids away from membranous regions are nuclear?

      3. In Figure S1, the caption says nuclei are stained with DAPI. Everything seems to be stained with DAPI.

      4. Figure 4 separates A-, B- and C-capsids. C-capsids would be more prevalent in the cytosol as this is a sign of maturity. Through following Figure 1 and Figure 2 it is not clear how the isolation of populations from subcellular components is achieved. The authors should think about how to make this process clearer.

      5. In terms of the method itself, the Authors propose this as a relatively easy method for routine examination of macromolecules in situ. This should mean that subcellular structures should not be difficult to determine and well know samples should be examined.

      This reviewer would like to re-assert the point that chemical fixation in a background macromolecular milieu is prone to artifacts. As such, fixation in cellulo vs in vitro is different. This is reflected in a statement that remains in the text of the manuscript:

      “The use of chemical fixative may cause some structural artefacts, possibly contributing to the low resolution of capsid structures in our study (5-6 nm), in comparison to resolutions obtained from subtomogram averaging of proteins from unfixed cryo-ET of for example purified virions (0.8-2 nm).”

      In the Authors’ rebuttal, they make the point that gradient fixation methods have been previously employed to determine structures of macromolecular complexes. However, the objective of these methods is to stabilise complexes of recombinantly expressed and isolated macromolecules that are prone to falling apart under buffer conditions. Furthermore, the complexes are known as they are biochemically characterised. The original grafix paper (Kastner et al., 2008) argues that the potential for the technique to improve structure determination is due to homogeneity, and this is borne out by the citations of that article.

      There is also a contradiction in logic; if chemical fixation is one stated factor potentially limiting the resolution of the capsids in this manuscript, why then are grafix methods elsewhere able to be used to determine high-resolution structures. Is It due to the presence of cross-linked entities or due to lack of particles? Such questions are why I feel the need for more work is required to validate the major finding.

      Finally, a 40-60Å structure is not equivalent to a 3-4Å structure and should not be presented as such.

      Reviewer 3

      In this manuscript, Vijayakrishnan et al describe the in-situ structures of HSV-1 capsids within the nuclei of host cells determined by subtomogram averaging, coupled with correlative light and electron microscopy (CLEM) and cryo-electron tomography (cryo-ET) of re-vitrified cell sections. Although at low resolutions, the reconstructions of the three types of capsids show the major components of penton, hexon and triplex. In addition, the C-capsids within the nucleus have extra densities, contributed by the capsid-vertex specific component (CVSC), are readily observed. The structural work is interesting in that the authors demonstrates an economic, easier and high-throughput approach to determine the in-situ structures of viruses using re-vitrified sections. However, a number of overstatements or concerns have to be corrected or be addressed before the publication.

      1. In the abstract on page 2: “Our reconstructions reveal that the capsid associated tegument complex is present on capsids prior to nuclear egress.” This is an overstatement. Previous single particle cryo-EM works have demonstrated that the CVSC binds to capsid prior to nuclear egress. (Conway at al., JMB 2010; Homa et al., JMB 2013; Dai et al., Science 2018 and Ref 29)

      2. In the introduction on page 6: “Our data reveal the presence of the CVSC pentaskelion on HSV nucleocapsids in the nucleus, suggesting that capsids may bind the tegument protein pUL36 (VP1/2) prior to nuclear egress.” This is again an overstatement. Previous single particle cryo-EM works have already revealed the presence of the CVSC on HSV C capsids purified from the nucleus.

      3. On page 10: “There has been uncertainty in the HSV field of how pUL36 and pUL37 are recruited to the capsid, if this happens within the nucleus or after nuclear egress. To shed light on this question, we carried out cryo-ET on the mutant lacking pUL37 (FRΔUL37).” Given the low resolution of the HSV capsid reconstruction determined by the authors, this work has no help to solve the uncertainty of how pUL36 is recruited to the capsid.

      4. Page 14: “Moreover, our analysis revealed pronounced star-like CVSC density at the penton vertex in the C-capsids, comparable to previously reported high-resolution structures of capsids within purified HSV-1 virions.” The CVSC density of nucleocapsid from virion are obviously better than the counterpart from the C-capsid. While the nucleocapsid shows strong CVSC densities extending from the penton to the triplex Ta, the C-capsid shows a much weaker and smaller tegument densities that only bind to the penton of C-capsid (Fig. 5).

      5. Page 15: “Our method opens the possibility of determining and characterising specific complexes and their interactions at high-resolution within the functional context of the cell or tissue, providing snapshots of important and dynamic events in biology.” Given the poor resolution of the HSV capsid determined in this work, this statement is hard to be justified.

      6. Page 20: “The subvolumes were subjected to 3D classification with a T value of 5, to reconstruct a single 5-fold vertex, without refining orientations and origins. A total of 10 classes were calculated with one of them identified to have apparent pentaskelion density over the 5-fold axis, corresponding to CVSC, in both B-capsids and C-capsids. " It is well established that all the vertices of HSV C-capsid and virion nuelcocapsid are fully occupied by CVSC, why only one of the ten classes has apparent pentaskelion density over the 5-fold axis in the C-capsid?

      7. Legend for Figure 5 on page 22: “high-resolution structure of purified capsids from within the nucleus at an equivalent resolution. " This sentence should be corrected. At first, the structure is from virion nucleocapsid not from nuclear capsid; Second, the structure has already been filtered to low resolution and could not be stated as high-resolution.