10,000 Matching Annotations
  1. May 2025
    1. Reviewer #3 (Public review):

      NCXs are key Ca2+ transporters located on the plasma membrane, essential for maintaining cellular Ca2+ homeostasis and signaling. The activities of NCX are tightly regulated in response to cellular conditions, ensuring precise control of intracellular Ca2+ levels, with profound physiological implications. Building upon their recent breakthrough in determining the structure of human NCX1, the authors obtained cryo-EM structures of NCX1 in complex with its modulators, including the cellular activator PIP2 and the small molecule inhibitor SEA0400. Structural analyses revealed mechanistically informative conformational changes induced by PIP2 and elucidated the molecular basis of inhibition by SEA0400. These findings underscore the critical role of the interface between the transmembrane and cytosolic domains in NCX regulation and small molecule modulation. Overall, the results provide key insights into NCX regulation, with important implications for cellular Ca2+ homeostasis.

      Comments on revisions:

      The authors have adequately addressed my previous comments.

    2. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public Review):

      (1) This study uses structural and functional approaches to investigate the regulation of the Na/Ca exchanger NCX1 by an activator, PIP2, and an inhibitor, SEA0400.  State-of-the-art methods are employed, and the data are of high quality and presented very clearly. The manuscript combines two rather different studies (one on PIP2; and one on SEA0400) neither of which is explored in the depth one might have hoped to form robust conclusions and significantly extend knowledge in the field.

      We combined the study of PIP2 and SEA0400 in this manuscript because both ligands inhibit or activate NCX1 by affecting the Na<sup>+</sup>-dependent inactivation of the exchanger - SEA0400 promotes inactivation by stabilizing the cytosolic inactivation assembly whereas PIP2 mitigates inactivation by destabilizing the assembly. The current study aims to provide structural insights into these ligand binding. We didn’t perform extensive electrophysiological analysis as the functional effects of both ligands have been extensively characterized over the last thirty years.

      (2) The novel aspect of this work is the study of PIP2. Unfortunately, technical limitations precluded structural data on binding of the native PIP2, so an unnatural short-chained analog, diC8 PIP2, was used instead. This raises the question of whether these two molecules, which have similar but very distinctly different profiles of activation, actually share the same binding pocket and mode of action. In an effort to address this, the authors mutate key residues predicted to be important in forming the binding site for the phosphorylated head group of PIP2. However, none of these mutations prevent PIP2 activation. The only ones that have a significant effect also influence the Na-dependent inactivation process independently of PIP2, thus casting doubt on their role in PIP2 binding, and thus identification of the PIP2 binding site. A more extensive mutagenic study, based on the diC8 PIP2 binding site, would have given more depth to this work and might have been more revealing mechanistically.

      The reviewer raises the important question of whether the short-chain PIP2 diC8 and long-chain native PIP2 share the same binding site. We have performed a pilot experiment to address this question. The data indicate that PIP2 diC8 competes with native brain PIP2 for its binding site (Author response image 1).  We believe that the mild effects of diC8 on the biophysical properties of NCX1 are due to its decreased affinity as compared to the long-chain PIP2. We have included this competition assay in the revised manuscript.

      The acyl-chain length-dependent PIP2 activation is consistent with some previous studies. Before PIP2 was demonstrated to regulate NCX1, some earlier studies showed that negatively charged long-chain lipids such as phosphatidylserine (PS) or phosphatidic acid (PA) could have the same potentiation effects on NCX1 as PIP2 (PMID: 1474504; PMID: 3276350). A later study showed that long-chain acyl-CoAs could also have the same potentiation effects on NCX1 as PIP2 (PMID: 16977318).  All these studies demonstrated that activation of NCX by the anionic lipids depends on their chain length with the short chain being ineffective or less effective. These findings have two implications. First, it is the negative surface charge rather than the specific IP3 head group of the lipid that is important for stimulating NCX1 activity. This would imply non-specific electrostatic interactions between the negatively charged lipids and those positively charged residues at the binding site. Second, a longer acyl chain is required for the high-affinity binding of PIP2 or negatively charged lipids. As further discussed in the revised manuscript (Discussion section), we suspect the tail of the long acyl chain from the native anionic lipids can enter the same binding pocket for SEA0400 thereby rendering higher affinity lipid binding than shorter chain lipids.

      As the interactions between PIP2 and NCX1 are both electrostatic involving multiple charged residues as well as hydrophobic involving the long lipid acyl chain, single amino acid substitutions likely only decrease the affinity of PIP2 rather than completely disrupt its binding. Our data demonstrated that mutants R220A, K225A, and R220A/K225A do show a significantly decreased potentiation effect of PIP2 (Figure 3 in the manuscript). We also conducted an experiment with a mutant exchanger in which all four amino were mutated. This K164A/R167A/R220A/K225A mutant is insensitive to PIP2 and shows no Na<sup>+</sup>-dependent inactivation (Figure 3A). The unresponsiveness to PIP2 and lack of Na<sup>+</sup>-dependent inactivation in this mutant is consistent with previous studies demonstrating that PIP2 activates NCX by tuning the amount of Na<sup>+</sup>-dependent inactivation and any mutation that decreases NCX sensitivity to PIP2 will affect the extent of Na<sup>+</sup>-dependent inactivation (PMID: 10751315). Such studies show that the two processes cannot be dissected from each other, making more extensive mutagenesis investigation unlikely to provide new mechanistic insights. A brief discussion related to this quadruple mutant has been added in the revised manuscript.

      Author response image 1.

      Giant patch recording of the human WT exchanger. Currents were first activated by intracellular application of 10 µM brain PIP2. Afterwards, a solution containing 100 mM Na<sup>+</sup> and 12 µM Ca<sup>2+</sup> was perfused for about 5 min (washout). The PIP2 effects was not reversible during this time. The same patch was then perfused internally with the same solution in presence of 10 µM di-C8. Application of the shorted-chained di-C8, partially decreased the current suggesting that that PIP2 and diC8 compete for the binding site.

      (3) The SEA0400 aspect of the work does not integrate particularly well with the rest of the manuscript. This study confirms the previously reported structure and binding site for SEA0400 but provides no further information. While interesting speculation is presented regarding the connection between SEA0400 inhibition and Na-dependent inactivation, further experiments to test this idea are not included here.

      Our SEA0400-bound NCX structure was determined and deposited in 2023, along with our previous study on the apo NCX published in 2023 (PMID: 37794011). We decided to combine the SEA0400-bound structure with the later study of PIP2 binding because both represent ligand modulation of NCX by affecting the Na<sup>+</sup>-dependent inactivation of the exchanger. The SEA0400 inhibition of NCX1 has been extensively investigated previously, which demonstrated a strong connection between SEA0400 and the Na<sup>+</sup>-dependent inactivation. As discussed in the manuscript, SEA0400 is ineffective in an exchanger lacking Na<sup>+</sup>-dependent inactivation. Conversely, enhancing the extent of Na<sup>+</sup>-dependent inactivation increases the affinity for SEA0400. Our structural analysis provides explanations for these pharmacological features of SEA0400 inhibition.

      Reviewer #2 (Public review):

      (1) The study by Xue et al. reports the structural basis for the regulation of the human cardiac sodium-calcium exchanger, NCX1, by the endogenous activator PIP2 and the small molecule inhibitor SEA400. This well-written study contextualizes the new data within the existing literature on NCX1 and the broader NCX family. This work builds upon the authors' previous study (Xue et al., 2023), which presented the cryo-EM structures of human cardiac NCX1 in both inactivated and activated states. The 2023 study highlighted key structural differences between the active and inactive states and proposed a mechanism where the activity of NCX1 is regulated by the interactions between the ion-transporting transmembrane domain and the cytosolic regulatory domain. Specifically, in the inward-facing state and at low cytosolic calcium levels, the transmembrane (TM) and cytosolic domains form a stable interaction that results in the inactivation of the exchanger. In contrast, calcium binding to the cytosolic domain at high cytosolic calcium levels disrupts the interaction with the TM domain, leading to active ion exchange.

      In the current study, the authors present two mechanisms explaining how both PIP2 stimulates NCX1 activity by destabilizing the protein's inactive state (i.e., by disrupting the interaction between the TM domain and the cytosolic domain) and how SEA400 stabilizes this interaction, thereby acting as a specific inhibitor of the system.

      The first part of the results section addresses the effect of PIP2 and PIP2 diC8 on NCX1 activity. This is pertinent as the authors use the diC8 version of this lipid (which has a shorter acyl chain) in their subsequent cryo-EM structure due to the instability of native PIP2. I am not an electrophysiology expert; however, my main comment would be to ask whether there is sufficient data here to characterise fully the differences between PIP2 and PIP2 diC8 on NCX1 function. It appears from the text that this study is the first to report these differences, so perhaps this data needs to be more robust. The spread of the data points in Figure 1B is possibly a little unconvincing given that only six measurements were taken. Why is there one outlier in Figure 1A? Were these results taken using the same batch of oocytes? Are these technical or biological replicates? Is the convention to use statistical significance for these types of experiments?

      Oocytes were isolated from at least 3 different frogs and each data point shown in Fig. 1 A or 1B of the manuscript represents a recording obtained from a single oocyte. For clarity, we have added this information to the Methods section. We understand that 6 observations (Fig. 1B) are a small sample size but electrophysiological recordings of NCX currents are extremely challenging and technically difficult due to the low transport activity of the exchanger. Because of these circumstances, this type of study relies on a small sample of observations. Nevertheless, our data clearly show that native PIP2 and the short-chain PIP2 diC8 can activate NCX activity although with different affinity. The spread of the steady state current data points is due to the variability in the extent of Na<sup>+</sup>-dependent inactivation within each patch, likely due to slightly different levels of endogenous PIP2 or other regulatory mechanisms that control this allosteric process. As PIP2 acts on the Na<sup>+</sup>-dependent inactivation this will lead to varying levels of potentiation. Because of that, we did occasionally observe some outliers in our recordings. Rather than cherry-picking in data analysis, we presented all the data points from patches with measurable NCX1 currents. Despite this variability, a T-test indicates that the effects of PIP2 are more pronounced on the steady-state current than peak current.  The differences between native PIP2 and PIP2 diC8 on NCX1 function are consistent with previous investigations showing that both PIP2 and anionic lipids enhance NCX current by antagonizing the Na<sup>+</sup>-dependent inactivation and long-chain lipids are more effective in potentiating NCX1 activity (PMID: 1474504; PMID: 3276350; PMID: 16977318). A discussion related to the chain length-dependent lipid activation of NCX1 is added in the Discussion of the revised manuscript. 

      (2) I am also somewhat skeptical about the modelling of the PIP2 diC8 molecule. The authors state, "The density of the IP3 head group from the bound PIP2 diC8 is well-defined in the EM map. The acyl chains, however, are flexible and could not be resolved in the structure (Fig. S2)."

      However, the density appears rather ambiguous to me, and the ligand does not fit well within the density. Specifically, there is a large extension in the volume near the phosphate at the 5' position, with no corresponding volume near the 4' phosphate. Additionally, there is no bifurcation of the volume near the lipid tails. I attempted to model cholesterol hemisuccinate (PDB: Y01) into this density, and it fits reasonably well - at least as well as PIP2 diC8. I am also concerned that if this site is specific for PIP2, then why are there no specific interactions with the lipid phosphates? How can the authors explain the difference between PIP2 and PIP2 diC8 if the acyl chains don't make any direct interactions with the TM domain? In short, the structures do not explain the functional differences presented in Figure 1.

      The side chain densities for Arg167 and Arg220 are also quite weak. While there is some density for the side chain of Lys164, it is also very weak. I would expect that if this site were truly specific for PIP2, it should exhibit greater structural rigidity - otherwise, how is this specific?

      Given this observation, have the authors considered using other PIP2 variants to determine if the specificity lies with PI4,5P<sub>2</sub> as opposed to PI3,5P<sub>2</sub> or PI3,4P<sub>2</sub>? A lack of specificity may explain the observed poor density.

      The map we provided to the editor in the initial submission is the overall map for PIP2-bound NCX1. Due to the relative flexibility between the cytosolic CBD and TM regions, we also performed local refinement on each region in data processing to improve the map quality as illustrated in Fig. S2.  The local-refined map focused on the TM domain provides a much better density for PIP2 diC8 and its surrounding residues than the overall map. The map quality allowed us to unambiguously identify the lipid as PIP2 with the IP3 head group having phosphate groups at the 4,5 positions. Furthermore, no lipid density is observed at the equivalent location in the local-refined map from the apo NCX1 TM region as shown in Fig. S3 in the revision. In the revised manuscript, the density for the bound PIP2 is shown in Fig. 2A. Those local-refined maps for PIP2-bound NCX1 were also deposited as additional maps along with the overall map in the Electron Microscopy Data Bank under accession numbers EMD-60921. The local-refined maps for the apo-NCX1 were deposited in the Electron Microscopy Data Bank under accession numbers EMD-40457 in our previous study (https://www.ebi.ac.uk/emdb/EMD-40457?tab=interpretation).

      As discussed in our response to reviewer #1, the acyl-chain length-dependent PIP2 activation is consistent with some previous studies. Before PIP2 was identified as a physiological regulator of NCX1, some earlier studies showed that negatively charged long-chain lipids such as phosphatidylserine (PS) or phosphatidic acid (PA) could have the same potentiation effects on NCX as PIP2 (PMID: 1474504; PMID: 3276350). A later study also showed that acyl-CoA could also have the same potentiation effects on NCX as PIP2 (PMID: 16977318). All these studies demonstrated that activation of NCX1 by the anionic lipids depends on their chain length with the short chain being ineffective.  These findings have two implications. First, it is the negative surface charge rather than the specific IP3 head group of the lipid that is important for stimulating NCX activity. This would imply non-specific electrostatic interactions between the negatively charged lipids and those positively charged residues at the binding site.  Second, a longer acyl chain is required for the high-affinity binding of PIP2 or negatively charged lipids. As further discussed in the revised manuscript (Discussion section), we suspect the tail of the long acyl chain can enter the same binding pocket for SEA0400 thereby rendering higher affinity lipid binding than shorter chain lipids. In light of the equivalent potentiating effect of various anionic lipids on NCX1, PI(4,5)P2 activation of NCX1 is likely non-specific and PI(3,5)P2 or PI(3,4)P2 may also activate the exchanger. However, as a key player in membrane signaling, PI(4,5)P2 has been demonstrated to be a physiological regulator of NCX1 in many studies.

      (3) I also noticed many lipid-like densities in the maps for this complex. Is it possible that the authors overlooked something? For instance, there is a cholesterol-like density near Val51, as well as something intriguing near Trp763, where I could model PIP2 diC8 (though this leads to a clash with Trp763). I wonder if the authors are working with mixed populations in their dataset. The accompanying description of the structural changes is well-written (assuming it is accurate).

      Densities from endogenous lipids and cholesterols are commonly observed in membrane protein structures. Other than the bound PIP2, those lipid and cholesterol densities are present in both the apo and PIP2-bound structures, including the density around Trp763 and Val53. Whether those bound lipids/cholesterols play any functional roles or just stabilize the protein is beyond the scope of this study.  We have added a supporting figure (Fig. S3) showing a side-by-side comparison of the density at the PIP2 binding site between the PIP2-bound and apo structures.

      I would recommend that the authors update the figures associated with this section, as they are currently somewhat difficult to interpret without prior knowledge of NCX architecture. My suggestions include:

      - Including the density for the PIP2 diC8 in Figure 2A.

      As suggested, we have included the density of PIP2 diC8 in Figure 2A.

      - Adding membrane boundaries (cytosolic vs. extracellular) in Figure 2B.

      - Labeling the cytosolic domains in Figure 2B.

      - Adding hydrogen bond distances in Figure 2A.

      We have added and labeled the boundaries for the TM and cytosolic domains in Figure 2B as suggested. Although we can identify those positively charged residues in the vicinity of the PIP2 head group and observe local structural changes, the poorly defined side-chain densities of these residues won’t allow us to properly determine the hydrogen bond distances.

      - Detailing the domain movements in Figure 2B (what is the significance of the grey vs. blue structures?).

      There is a rigid-body downward swing movement at CBDs between the apo (grey) and PIP2-bound (cyan) structures. The movement at the TM region is subtle. We have added the description in the legend for Figure 2B and also marked the movement at the tip of CBD1 in the figure.

      The section on the mechanism of SEA400-induced inactivation is strong. The maps are of better quality than those for the PIP2 diC8 complex, and the ligand fits well. However, I noticed a density peak below F02 on SEA400 that lies within the hydrogen bonding distance of Asp825. Is this a water molecule? If so, is this significant?

      The structure of SEA0400-bound NCX1 was determined at a higher resolution likely because the drug stabilize the exchanger in the inactivated state.  The mentioned density could be an ordered water molecule. We don’t know if it is functionally significant.

      Furthermore, there are many unmodeled regions that are likely cholesterol hemisuccinate or detergent molecules, which may warrant further investigation.

      We constantly observed partial densities from bound lipids, cholesterols, or detergents in our structures. Most of them are difficult to be unambiguously identified and modeled. Whether they play any functional roles is beyond the scope of this study.  

      The authors introduce SEA400 as a selective inhibitor of NCX1; however, there is little to no comparison between the binding sites of the different NCX proteins. This section could be expanded. Perhaps Fig. 4C could include sequence conservation data.

      SEA0400 is more specific for NCX1 than NCX2 and NCX3 as demonstrated in an early study (PMID: 14660663). The lack of structure information for NCX2 or NCX3 makes it difficult to make a direct comparison to reveal the structural basis of SEA0400 specificity.

      Additionally, is the fenestration in the membrane physiological, or is it merely a hole forced open by the binding of SEA400? I was unclear as to whether the authors were suggesting a physiological role for this feature, similar to those observed in sodium channels.

      The fenestration likely serves as the portal for SEA0400 binding as discussed in the manuscript. As further discussed in the revised manuscript, we suspect this fenestration also allows the tail of a long-chain lipid to enter the same binding pocket for SEA0400 and results in higher affinity binding of a long-chain lipid than a short-chain lipid.

      Reviewer #3 (Public review):

      NCXs are key Ca<sup>2+</sup> transporters located on the plasma membrane, essential for maintaining cellular Ca<sup>2+</sup> homeostasis and signaling. The activities of NCX are tightly regulated in response to cellular conditions, ensuring precise control of intracellular Ca<sup>2+</sup> levels, with profound physiological implications. Building upon their recent breakthrough in determining the structure of human NCX1, the authors obtained cryo-EM structures of NCX1 in complex with its modulators, including the cellular activator PIP2 and the small molecule inhibitor SEA0400. Structural analyses revealed mechanistically informative conformational changes induced by PIP2 and elucidated the molecular basis of inhibition by SEA0400. These findings underscore the critical role of the interface between the transmembrane and cytosolic domains in NCX regulation and small molecule modulation. Overall, the results provide key insights into NCX regulation, with important implications for cellular Ca<sup>2+</sup> homeostasis.

      We appreciate this reviewer’s positive comments.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      The manuscript would be strengthened enormously by a much deeper focus on the novel and very interesting PIP2 work, as noted above, and perhaps the removal of the SEA0400 data.

      If that is beyond the scope of the authors' options, then a more robust discussion of limitations of the current work, perhaps speculation regarding other future experiments, a clearer presentation of how these data on SEA0400 are different from/extend from the previously published work, and a better effort to link the two disparate aspects of the work into a more cohesive manuscript should be attempted.

      As discussed in our response to this reviewer’s public review, we combined the study of PIP2 and SEA0400 in this manuscript because both ligands activate or inhibit NCX1 by affecting the Na<sup>+</sup>-dependent inactivation of the exchanger. The functional effects of both ligands on NCX1 have been extensively characterized over the last thirty years. Thus the current study is focused on providing structural explanations for some unique pharmacological features of these ligands. In the revised manuscript, we have added an extra paragraph of discussion that provides a plausible explanation for chain length-dependent PIP2 activation.

      Reviewer #3 (Recommendations for the authors):

      A few comments to consider:

      (1) The short-chain PIP2 appears to have lower potency, but the mechanism remains unclear. Based on structural analyses, are there potential binding sites for the acyl chains of PIP2 that could contribute to this difference?

      As discussed in our response to other reviewers, long-chain anionic lipids can have the same potentiation effect on NCX1 activity as PIP2, but the short-chain ones are ineffective just like short-chain PIP2 diC8. We suspect the tail of a long acyl chain from the native PIP2 can enter the same binding pocket for SEA0400 thereby rendering higher affinity binding for a long-chain lipid than a short-chain lipid. A discussion related to this point has been added to the revised manuscript.

      (2) It is unclear why mutating residues that interact with the IP3 head group retain PIP2 activation. Would it be possible to assess PIP2 and C8 PIP2 binding to these NCX1 variants? Identifying a mutant that abolishes C8 PIP2 binding would be valuable in interpreting those results.

      As the interactions between PIP2 and NCX1 are both electrostatic involving multiple charged residues and hydrophobic involving the long lipid acyl chain, single amino acid substitutions likely only decrease the affinity of PIP2 rather than completely disrupt its binding.  Individual mutants R220A and K225A show a 5-fold decrease in their response to PIP2 application indicating that their replacement alters the affinity of NCX for PIP2.  We have added a new experiment showing that an exchanger with all four residues mutated is insensitive to PIP2 in the revision.

      (3) What are the functional effects of mutating Y226 and R247, residues that seem to play an important role in PIP2-mediated activation?

      In a previous study, mutation at Y226 (Y226T), which is found within the XIP region of NCX, has been shown to have enhanced Na<sup>+</sup>-dependent inactivation (PMID: 9041455).  To our knowledge, the R247 mutation has not been investigated. Also positioned in the XIP region, we suspect its mutation could directly affect Na<sup>+</sup>-dependent inactivation. This would make it difficult to determine if the function effect of the mutation is caused by changing the stability of the XIP region or by changing the binding of PIP2.

      (4) Is there any overlap between the PIP2 and SEA0400 binding regions? Both appear to involve TM4, TM5, and TMD-beta hub interfaces. It might be interesting to discuss any shared mechanisms and why this region might serve as a hotspot for modulation.

      As mentioned in our previous response, we suspect the tail of a long acyl chain from the native PIP2 can enter the same binding pocket for SEA0400 thereby rendering higher affinity binding for a long-chain lipid than a short-chain lipid. A more detailed discussion related to this point has been included in the revision.

      (5) It would be helpful to show the density at the PIP2-binding site in the apo and PIP2-bound structures side by side

      This figure has been added in the revision as Fig. S3.

    1. eLife Assessment

      This study presents valuable findings with practical and theoretical implications for drug discovery, particularly in the context of repurposing cipargamin CIP for the treatment of Babesia spp. The evidence is solid with the methods, data, and analyses broadly supporting the claims. The paper will be of great interest to scientists in drug discovery, computational biology, and microbiology.

    2. Reviewer #2 (Public review):

      Summary:

      In this manuscript, the authors present the repurposing of cipargamin (CIP), a known drug against plasmodium and toxoplasma against babesia. They proved the efficacy of CIP on babesia in the nanomolar range. In silico analyses revealed the drug resistance mechanism through a single amino acid mutation at amino acid position 921 on the ATP4 gene of babesia. Overall, the conclusions drawn by the authors are well justified by the data presented. I believe this study opens up a novel therapeutic strategy against babesiosis.

      Strengths:

      The authors have carried out a comprehensive study. All the experiments performed were carried out methodically and logically.

    3. Reviewer #3 (Public review):

      Summary:

      The authors aim to establish that cipargamin can be used for the treatment of infection caused by Babesia organisms.

      Strengths:

      The study provides strong evidence that cipargamin is effective against various Babesia species. In vitro growth assays were used to establish that cipargamin is effective against Babesia bovis and Babesia gibsoni. Infection of mice with Babesia microti demonstrated that cipargamin is as effective as the combination of atovaquone plus azithromycin. Cipargamin protected mice from lethal infection with Babesia rodhaini. Mutations that confer resistance to cipargamin were identified in the gene encoding ATP4, a P-type Na ATPase that is found in other apicomplexan parasites, thereby validating ATP4 as the target of cipargamin. A 7-day treatment of cipagarmin, when combined with a single dose of tafenoquine, was sufficient to eradicate Babesia microti in a mouse model of severe babesiosis caused by a lack of adaptive immunity.

      Weaknesses:

      Cipargamin was tested in vivo at a single dose administered daily for 7 days. Despite the prospect of using cipargamin for the treatment of human babesiosis, there was no attempt to identify the lowest dose of cipagarmin that protects mice from Babesia microti infection.

      Comments on revisions:

      The authors have edited the manuscript and, in doing so, have addressed all queries pertaining to experimental design. The authors have decided to keep the discussion unchanged, but have replied to this reviewer regarding comments on interpretation of some data. The reader could have benefited from the authors' explanation. Nonetheless, the manuscript in its present form describes a valuable and significant body of work.

    4. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, authors have tried to repurpose cipargamin (CIP), a known drug against Plasmodium and Toxoplasma against Babesia. They proved the efficacy of CIP on Babesia in nanomolar range. In silico analyses revealed the drug resistance mechanism through a single amino acid mutation at amino acid position 921 on the ATP4 gene of Babesia. Overall, the conclusions drawn by the authors are well justified by their data. I believe this study opens up a novel therapeutic strategy against babesiosis.

      Strengths:

      Authors have carried out a comprehensive study. All the experiments performed were carried out methodically and logically.

      We appreciate your positive feedback. Your acknowledgment reinforces our commitment to rigor and thoroughness in our research.

      Reviewer #3 (Public review):

      Summary:

      The authors aim to establish that cipargamin can be used for the treatment of infection caused by Babesia organisms.

      Strengths:

      The study provides strong evidence that cipargamin is effective against various Babesia species. In vitro growth assays were used to establish that cipargamin is effective against Babesia bovis and Babesia gibsoni. Infection of mice with Babesia microti demonstrated that cipargamin is as effective as the combination of atovaquone plus azithromycin. Cipargamin protected mice from lethal infection with Babesia rodhaini. Mutations that confer resistance to cipargamin were identified in the gene encoding ATP4, a P-type Na+ ATPase that is found in other apicomplexan parasites, thereby validating ATP4 as the target of cipargamin. A 7-day treatment of cipagarmin, when combined with a single dose of tafenoquine, was sufficient to eradicate Babesia microti in a mouse model of severe babesiosis caused by lack of adaptive immunity.

      Thank you for the comments and for your time to review our manuscript.

      Weaknesses:

      Cipargamin was tested in vivo at a single dose administered daily for 7 days. Despite the prospect of using cipargamin for the treatment of human babesiosis, there was no attempt to identify the lowest dose of cipagarmin that protects mice from Babesia microti infection. In the SCID mouse model, cipargamin was tested in combination with tafenoquine but not with atovaquone and/or azithromycin, although the latter combination is often used as first-line therapy for human babesiosis caused by Babesia microti.

      Thank you for your insightful comments. We agree that using a single daily dose over 7 days is one of the limitations in the in vivo trial. Our main goals were to demonstrate cipargamin's efficacy and understand its antibabesial agent mechanism. For future work, we plan to conduct dose‐optimization studies to determine the lowest effective dose in vivo. Regarding the drug combination in the SCID mouse model, although atovaquone and/or azithromycin are frequently used as first-line therapies for human babesiosis, resistance to these traditional drugs is emerging. Based on this challenge, we opted to evaluate a combination with tafenoquine as a novel partner, aiming to overcome resistance issues and improve therapeutic outcomes.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      None other than some minor grammatical mistakes.

      We have corrected the grammatical mistakes.

      Reviewer #3 (Recommendations for the authors):

      The revised manuscript is much improved. I have the following comments.

      Comment 1: Atovaquone plus azithromycin is effective against Babesia microti (Figure 1C) but not against Babesia rodhaini (Figure 1E). It would be valuable to provide a possible explanation.

      Thank you for highlighting this issue. One potential explanation is that B. microti and B. rodhaini might have intrinsic differences in drug sensitivity and susceptibility. A previous study reported that both species possess a unique linear monomeric mitochondrial genome with a dual flip-flop inversion system, which generates four distinct genome structures (Hikosaka et al., 2012). In addition, previous studies have shown that mitochondria-associated energy production is greater in B. microti than in B. rodhaini (Shikano et al., 1998). This suggests that B. microti, whose metabolism is largely driven by mitochondrial function, may be more susceptible to drugs (like atovaquone) that induce parasite death by disrupting mitochondrial targets such as cytochrome b (Wormser et al., 2010). Moreover, B. rodhaini tends to proliferate more rapidly and causes acute infections, which may outpace any drug effects. Further, the rapid proliferation of apicomplexan parasites, as is the case in Plasmodium (Salcedo-Sora et al., 2014), Theileria (Metheni et al., 2015), and B. rodhaini (Rickard, 1970; Shikano et al., 1995), has been ascribed to glycolysis as the primary energy source. This may have contributed to the reduced efficacy of atovaquone and azithromycin in B. rodhaini-infected mice in the current study. Nonetheless, we plan to explore these interspecies differences in our future work.

      Comment 2: The relapse that follows a 7-day treatment with cipargamin is transient in BALB/ mice infected with Babesia rodhaini (Figure 1E) but persistent in SCID mice infected with Babesia microti (Figure 5C). It would be valuable to provide a possible explanation.

      Thank you for your insightful comment. One possible explanation is the difference in immune status between the two mouse models. BALB/c mice have a fully functional immune system that can likely clear residual parasites following a transient relapse after cipargamin treatment. In contrast, SCID mice lack an adaptive immune response, which might allow residual B. microti parasites to persist and cause a sustained relapse. Additionally, intrinsic differences between B. rodhaini and B. microti, such as growth rate or drug susceptibility, could also play a role. We plan to explore these factors in future studies.

      Comment 3: The effect of cipargamin on parasite pH is the greatest when assessed 4 to 8 min after exposure is initiated (Figure 3E). Yet, resistance of parasites that carry a mutation in ATP4, the target of cipargamin, was assessed 20 min after cipargamin addition. At this time point, cipargamin has very little effect (Figure 3E). Accordingly, data reported in Figure 3G are of limited value.

      Thank you for your comment. The initial pH increase we see around 4 to 8 minutes likely reflects the rapid inhibition of ATP4-mediated Na⁺/H⁺ exchange by cipargamin, which quickly alkalinizes the cell. However, after the initial increase, compensatory processes, such as proton influx or metabolic acid production, gradually restored the pH, resulting in a later decline. Although assessing the pH level at 20 minutes may have recorded less dramatic changes, it still allowed us to compare the sustained differences between wild-type and mutant strains. We agree that including earlier time points for the mutants might provide further insight and we will consider this in our future work.

      Comment 4: In Figure 3H, please report the lack of statistical significance between wild-type parasites and parasites that carry the mutation L921V.

      In Figure 3H, the ATPase activity in erythrocytes infected with wild-type parasites (6.31 ± 1.20 nmol Pi/mg protein/min) is higher than that of the L921V mutation (5.11 ± 0.50 nmol Pi/mg protein/min), but the difference is not statistically significant (P = 0.095), so no asterisk was added.

      Comment 5: Tafenoquine was administered as a single 20 mg/kg dose. Please specify whether this dose is for tafenoquine succinate or tafenoquine base.

      Thank you for raising this point. In our study, the single 20 mg/kg dose refers to tafenoquine succinate. We have clarified this detail in the revised manuscript (Line 40).

      Comment 6: A single dose of 20 mg/kg tafenoquine succinate was first tested in the SCID mouse model of severe babesiosis by Mordue et al (JID 2019), not by Liu et al. (JID 2024). Please amend discussion accordingly (line 311). As correctly stated in the discussion, the single 20 mg/kg dose was not sufficient to prevent relapse of Babesia microti in the study by Mordue et al. Please provide a possible explanation for why no parasitemia was detected for 90 days in your SCID model (Figure 5C).

      Thank you for your comment. We have modified the suggested citation (Line 309). As noted by Mordue et al. (JID 2019), a single 20 mg/kg dose of tafenoquine succinate was insufficient to prevent relapse in their SCID mouse model using B. microti (ATCC 30221 Gray strain). In our study, however, no parasitemia was detected for 90 days (Figure 5C) using the B. microti Peabody mjr strain (ATCC PRA-99). Differences in the parasite strain and the timing of treatment relative to infection may have contributed to the extended suppression of parasitemia observed in our study. We plan to explore these aspects in future work.

      Comment 7: Real-time PCR was used to confirm eradication of Babesia microti infection (Figure 5D). Please specify the blood volume from which genomic DNA was extracted for each mouse. Please specify the amount of genomic DNA (i.e., not the volume) used in each reaction. Please explain how/why the cut-off was set at 35 cycles. What were the Ct values when blood was obtained from uninfected mice? For infected mice treated with cipargamin plus tafenoquine, there was no amplification. Was each reaction subjected to a maximum of 40 cycles (as suggested by Figure 5D)?

      In our qPCR assay, genomic DNA was extracted from 200 µL of blood per mouse (Line 458). In each reaction, we used 100 ng of genomic DNA (Line 464), and the thermocycling conditions were set at 40 cycles. We set the cut-off at 35 cycles based on our optimization experiments: samples with Ct values ≤ 35 consistently indicated the presence of parasite DNA, while samples without parasite DNA (distilled water and DNA from uninfected mice) had CT values > 35 cycles or undetectable. Although each reaction was run for 40 cycles, for our analysis, we defined samples as negative if no signal was observed beyond cycle 35. In mice treated with cipargamin plus tafenoquine, no signal was detected until 40 cycles, indicating the absence of parasite DNA in the samples.

      Comment 8:  Persistence of parasite DNA in blood of tafenoquine treated mice highlights the limitation of PCR to assess persistence of infection. That is, PCR cannot distinguish between viable parasites and non-viable (or dead) parasites. An adoptive transfer of blood to immunocompromised mice can help determine whether persistence of DNA is due to persistence of viable parasites. Because the experiment was carried out in SCID mice, no adoptive transfer is needed. Few parasites are required for a successful infection of immunocompromised mice (SCID mice included). Given that parasitemia never rose following treatment of SCID mice with a single dose of tafenoquine, it is highly likely that parasite DNA detected on day 90 post-infection in these tafenoquine treated mice came from persistent non-viable/dead parasites.

      We appreciate your comment and acknowledge that the use of PCR has limitations in differentiating between live and dead parasites. It is possible that the residual DNA may represent a small population of dormant parasites that are not actively replicating and thus remain below the detection threshold of parasitemia. Even in highly immunocompromised SCID mice, such dormant parasites might persist without causing overt infection under our experimental conditions. An adoptive transfer experiment in SCID mice, although not strictly necessary, could validate whether the detection of low levels of DNA comes from viable parasites capable of reactivating under different circumstances. Future studies using more sensitive viability assays or adoptive transfer approaches could provide further insights into this possibility.

    1. eLife Assessment

      This study provides important insights as to how interacting brain areas produce movement during the execution of a skilled multi-directional reaching task. Using a combination of single neuron and neural population analysis, optogenetic stimulation, and computational models, the authors provide convincing evidence of an asymmetrical influence between mouse premotor and motor cortex during the execution of a well-practiced behaviour. This asymmetry can only be captured by some but not all population analysis methods, which is a key lesson to the field in and of itself. Analyzing how activity that is shared and private to these areas relates to different aspects of movements, and why different methods provide different outcomes regarding the nature of inter-area interactions would further strengthen this work.

    2. Reviewer #1 (Public review):

      This study examined the interaction between two key cortical regions in the mouse brain involved in goal-directed movements, the rostral forelimb area (RFA) - considered a premotor region involved in movement planning, and the caudal forelimb area (CFA) - considered a primary motor region that more directly influences movement execution. The authors ask whether there exists a hierarchical interaction between these regions, as previously hypothesized, and focus on a specific definition of hierarchy - examining whether the neural activity in the premotor region exerts a larger functional influence on the activity in the primary motor area, than vice versa. They examine this question using advanced experimental and analytical methods, including localized optogenetic manipulation of neural activity in either region while measuring both the neural activity in the other region and EMG signals from several muscles involved in the reaching movement, as well as simultaneous electrophysiology recordings from both regions in a separate cohort of animals.

      The findings presented show that localized optogenetic manipulation of neural activity in either RFA or CFA resulted in similarly short-latency changes of the muscle output and in firing rate changes in the other region. However, perturbation of RFA led to a larger absolute change in the neural activity of CFA neurons. The authors interpret these findings as evidence for reciprocal, but asymmetrical, influence between the regions, suggesting some degree of hierarchy in which RFA has a greater effect on the neural activity in CFA. They go on to examine whether this asymmetry can also be observed in simultaneously recorded neural activity patterns from both regions. They use multiple advanced analysis methods that either identify latent components in the population level or measure the predictability of firing rates of single neurons in one region using firing rates of single neurons in the other region. Interestingly, the main finding across these analyses seems to be that both regions share highly similar components that capture a high degree of the variability of the neural activity patterns in each region. Single units' activity from either region could be predicted to a similar degree from the activity of single units in the other region, without a clear division into a leading area and a lagging area, as one might expect to find in a simple hierarchical interaction. However, the authors find some evidence showing a slight bias towards leading activity in RFA. Using a two-region neural network model that is fit to the summed neural activity recorded in the different experiments and to the summed muscle output, the authors show that a network with constrained (balanced) weights between the regions can still output the observed measured activities and the observed asymmetrical effects of the optogenetic manipulations, by having different within-region local weights. These results emphasize the challenges in studying interactions between brain regions with reciprocal interactions, multiple external inputs, and recurrent within-region connections.

      Strengths:

      The experiments and analyses performed in this study are comprehensive and provide a detailed examination and comparison of neural activity recorded simultaneously using dense electrophysiology probes from two main motor regions that have been the focus of studies examining goal-directed movements. The findings showing reciprocal effects from each region to the other, similar short-latency modulation of muscle output by both regions, and similarity of neural activity patterns, are convincing and add to the growing body of evidence that highlight the complexity of the interactions between multiple regions in the motor system and go against a simple feedforward-like hierarchy.

      The neural network model complements these findings and adds an important demonstration that the observed asymmetry can, in theory, also arise from differences in local recurrent connections and not necessarily from different input projections from one region to the other. This sheds an important light on the multiple factors that should be considered when studying the interaction between any two brain regions, with a specific emphasis on the role of local recurrent connections, that should be of interest to the general neuroscience community.

      Weaknesses:

      While the reciprocal interaction and similarity in neural activity across RFA and CFA is an important observation that is supported by the authors' findings, the evidence for a hierarchical interaction between the two regions appears to be weaker. The primary evidence for a hierarchical interaction comes from a causal optogenetic manipulation, carried out at the onset of the reaching movement and conducted with n = 3 in each experimental group, which shows an effect in both regions, yet the effect is greater when silencing the activity in RFA and examining the resulting change in CFA, than vice versa. Analysis of the simultaneously recorded neural activity, on the other hand, reveals mostly no clear hierarchy with leading or lagging dynamics between the regions. The findings of the optogenetic manipulation might be more compelling if similar effects were observed when the same manipulation was applied at different stages of movement preparation and execution, indicating a consistent interaction that is independent from the movement phase.

      The methods used to investigate hierarchical interactions through analysis of simultaneously recorded activity yielded inconsistent results. For instance, CCA and PLS showed no clear lead-lag relationship, while DLAG provided some evidence suggesting RFA leads CFA. Overall, these methods largely failed to demonstrate a clear hierarchical interaction. Assuming a partial hierarchy exists, this inconsistency may indicate that the hierarchy is not reflected in the activity patterns or that these analytical methods are inadequate for detecting such interactions within complex neural networks that are influenced by multiple external inputs, reciprocal inter-regional connections, and dominant intra-regional recurrent activity.

      As is also argued by the authors, these inconsistent findings underscore the need for caution when interpreting results from similar analyses used to infer inter-regional interactions from neural activity patterns alone. However, the study lacks sufficient explanation for why different methods yielded different results and more elaborate clarification is needed for the findings presented. For example, in the population-level analyses using CCA and PLS, the authors show that both techniques reveal components that are highly similar across regions and explain a substantial portion of each region's variance. Yet, shifting the activity of one region relative to the other to explore potential lead-lag relationships does not alter the results of these analyses. If the regions' activities were better aligned at some unknown true lead-lag time (or aligned at zero), one would expect a peak in alignment within the tested range, as is observed when these same analyses are applied to activity within a single region. It is thus unclear why shifting one region's activity relative to the other does not change the outcome. The interpretation of these results therefore, remains ambiguous and would benefit from further clarification.

    3. Reviewer #2 (Public review):

      Summary:

      While technical advances have enabled large-scale, multi-site neural recordings, characterizing inter-regional communication and its behavioral relevance remains challenging due to intrinsic properties of the brain such as shared inputs, network complexity, and external noise. This work by Saiki-Ishkawa et al. examines the functional hierarchy between premotor (PM) and primary motor (M1) cortices in mice during a directional reaching task. The authors find some evidence consistent with an asymmetric reciprocal influence between the regions, but overall, activity patterns were highly similar and equally predictive of one another. These results suggest that motor cortical hierarchy, though present, is not fully reflected in firing patterns alone.

      Strengths:

      Inferring functional hierarchies between brain regions, given the complexity of reciprocal and local connectivity, dynamic interactions, and the influence of both shared and independent external inputs, is a challenging task. It requires careful analysis of simultaneous recording data, combined with cross-validation across multiple metrics, to accurately assess the functional relationships between regions. The authors have generated a valuable dataset simultaneously recording from both regions at scale from mice performing a cortex-dependent directional reaching task.

      Using electrophysiological and silencing data, the authors found evidence supporting the traditionally assumed asymmetric influence from PM to M1. While earlier studies inferred a functional hierarchy based on partial temporal relationships in firing patterns, the authors applied a series of complementary analyses to rigorously test this hierarchy at both individual neuron and population levels, with robust statistical validation of significance.

      In addition, recording combined with brief optogenetic silencing of the other region allowed authors to infer the asymmetric functional influence in a more causal manner. This experiment is well designed to focus on the effect of inactivation manifesting through oligosynaptic connections to support the existence of a premotor to primary motor functional hierarchy.

      Subsequent analyses revealed a more complex picture. CCA, PLS, and three measures of predictivity (Granger causality, transfer entropy, and convergent cross mapping) emphasized similarities in firing patterns and cross-region predictability. However, DLAG suggested an imbalance, with RFA capturing CFA variance at a negative time lag, indicating that RFA 'leads' CFA. Taken together these results provide useful insights for current studies of functional hierarchy about potential limitations in inferring hierarchy solely based on firing rates.

      While I would detail some questions and issues on specifics of data analyses and modeling below, I appreciate the authors' effort in training RNNs that match some behavioral and recorded neural activity patterns including the inactivation result. The authors point out two components that can determine the across-region influence - 1) the amount of inputs received and 2) the dependence on across-region input, i.e., relative importance of local dynamics, providing useful insights in inferring functional relationships across regions.

      Weaknesses:

      (1) Trial-averaging was applied in CCA and PLS analyses. While trial-averaging can be appropriate in certain cases, it leads to the loss of trial-to-trial variance, potentially inflating the perceived similarities between the activity in the two regions (Figure 4). Do authors observe comparable degrees of similarity, e.g., variance explained by canonical variables? Also, the authors report conflicting findings regarding the temporal relationship between RFA and CFA when using CCA/PLS versus DLAG. Could this discrepancy be due to the use of trial-averaging in former analyses but not in the latter?

      (2) A key strength of the current study is the precise tracking of forelimb muscle activity during a complex motor task involving reaching for four different targets. This rich behavioral data is rarely collected in mice and offers a valuable opportunity to investigate the behavioral relevance of the PM-M1 functional interaction, yet little has been done to explore this aspect in depth. For example, single-trial time courses of inter-regional latent variables acquired from DLAG analysis can be correlated with single-trial muscle activity and/or reach trajectories to examine the behavioral relevance of inter-regional dynamics. Namely, can trial-by-trial change in inter-regional dynamics explain behavioral variability across trials and/or targets? Does the inter-areal interaction change in error trials? Furthermore, the authors could quantify the relative contribution of across-area versus within area dynamics to behavioral variability. It would also be interesting to assess the degree to which across-area and within-area dynamics are correlated. Specifically, can across-area dynamics vary independently from within-area dynamics across trials, potentially operating through a distinct communication subspace?

      (3) While network modeling of RFA and CFA activity captured some aspects of behavioral and neural data, I wonder if certain findings such as the connection weight distribution (Figure 7C), across-region input (Figure 7F), and the within-region weights (Figure 7G), primarily resulted from fitting the different overall firing rates between the two regions with CFA exhibiting higher average firing rates. Did the authors account for this firing rate disparity when training the RNNs?

      (4) Another way to assess the functional hierarchy is by comparing the time courses of movement representation between the two regions. For example, a linear decoder could be used to compare the amount of information about muscle activity and/or target location as well as time courses thereof between the two regions. This approach is advantageous because it incorporates behavior rather than focusing solely on neural activity. Since one of the main claims of this study is the limitation of inferring functional hierarchy from firing rate data alone, the authors should use the behavior as a lens for examining inter-areal interactions.

      Comments on revisions:

      I appreciate the authors' thoughtful revisions in response to prior reviews, which I believe have substantially improved the manuscript. In particular, I found the addition of the new section "Manifestations of hierarchy in firing patterns" to be valuable, as it begins to address some of the more complex and potentially conflicting observations

    4. Reviewer #3 (Public review):

      This study investigates how two cortical regions which are central to the study of rodent motor control (rostral forelimb area, RFA, and caudal forelimb area, CFA) interact during directional forelimb reaching in mice. The authors investigate this interaction using (1) optogenetic manipulations in one area while recording extracellularly from the other, (2) statistical analyses of simultaneous CFA/RFA extracellular recordings, and (3) network modeling. The authors provide solid evidence that asymmetry between RFA and CFA can be observed, although such asymmetry is only observed in certain experimental and analytical contexts.

      The authors find asymmetry when applying optogenetic perturbations, reporting a greater impact of RFA inactivation on CFA activity than vice-versa. The authors then investigate asymmetry in endogenous activity during forelimb movements and find asymmetry with some analytical methods but not others. Asymmetry was observed in the onset timing of movement-related deviations of local latent components with RFA leading CFA (computed with PCA) and in a relatively higher proportion and importance of cross-area latent components with RFA leading than CFA leading (computed with DLAG). However, no asymmetry was observed using several other methods that compute cross-area latent dynamics, nor with methods computed on individual neuron pairs across regions. The authors follow up this experimental work by developing a two-area model with asymmetric dependence on cross-area input. This model is used to show that differences in local connectivity can drive asymmetry between two areas with equal amounts of across-region input.

      Overall, this work provides a useful demonstration that different cross-area analysis methods result in different conclusions regarding asymmetric interactions between brain areas and suggests careful consideration of methods when analyzing such networks is critical. A deeper examination of why different analytical methods result in observed asymmetry or no asymmetry, analyses that specifically examine neural dynamics informative about details of the movement, or a biological investigation of the hypothesis provided by the model would provide greater clarity regarding the interaction between RFA and CFA.

      Strengths:

      The authors are rigorous in their experimental and analytical methods, carefully monitoring the impact of their perturbations with simultaneous recordings and providing valid controls for their analytical methods. They cite relevant previous literature that largely agrees with the current work, highlighting the continued ambiguity regarding the extent to which there exists an asymmetry in endogenous activity between RFA and CFA.

      A strength of the paper is the evidence for asymmetry provided by optogenetic manipulation. They show that RFA inactivation causes a greater absolute difference in muscle activity than CFA interaction (deviations begin 25-50 ms after laser onset, Figure 1) and that RFA inactivation causes a relatively larger decrease in CFA firing rate than CFA inactivation causes in RFA (deviations begin <25ms after laser onset, Figure 3). The timescales of these changes provide solid evidence for an asymmetry in impact of inactivating RFA/CFA on the other region that could not be driven by differences in feedback from disrupted movement (which would appear with a ~50ms delay).

      The authors also utilize a range of different analytical methods, showing an interesting difference between some population-based methods (PCA, DLAG) that observe asymmetry, and single neuron pair methods (granger causality, transfer entropy, and convergent cross mapping) that do not. Moreover, the modeling work presents an interesting potential cause of "hierarchy" or "asymmetry" between brain areas: local connectivity that impacts dependence on across-region input, rather than the amount of across-region input actually present.

      Weaknesses:

      There is no attempt to examine neural dynamics that are specifically relevant/informative about the details of the ongoing forelimb movement (e.g., kinematics, reach direction). Thus, it may be preemptive to claim that firing patterns alone do not reflect functional influence between RFA/CFA. For example, given evidence that the largest component of motor cortical activity doesn't reflect details of ongoing movement (reach direction or path; Kaufman, et al. PMID: 27761519) and that the analytical tools the authors use likely include this component (PCA, CCA), it may not be surprising that CFA and RFA do not show asymmetry if such asymmetry is related to control of movement details. An asymmetry may still exist in the components of neural activity that encode information about movement details, and thus it may be necessary to isolate and examine the interaction of behaviorally-relevant dynamics (e.g., Sani, et al. PMID: 33169030).

      The idea that local circuit dynamics play a central role in determining the asymmetry between RFA and CFA is not supported by experimental data in this paper. The plausibility of this hypothesis is supported by the model but is not explored in any analyses of the experimental data collected. Further experimental investigation is needed to separate this hypothesis from other possibilities.

      Comments on revisions:

      The authors have improved the manuscript by reviewing several aspects of the text and the addition of supplemental materials. I believe these revisions have clarified some important aspects of the results.

    5. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      This study examined the interaction between two key cortical regions in the mouse brain involved in goal-directed movements, the rostral forelimb area (RFA) - considered a premotor region involved in movement planning, and the caudal forelimb area (CFA) - considered a primary motor region that more directly influences movement execution. The authors ask whether there exists a hierarchical interaction between these regions, as previously hypothesized, and focus on a specific definition of hierarchy - examining whether the neural activity in the premotor region exerts a larger functional influence on the activity in the primary motor area than vice versa. They examine this question using advanced experimental and analytical methods, including localized optogenetic manipulation of neural activity in either region while measuring both the neural activity in the other region and EMG signals from several muscles involved in the reaching movement, as well as simultaneous electrophysiology recordings from both regions in a separate cohort of animals.

      The findings presented show that localized optogenetic manipulation of neural activity in either RFA or CFA resulted in similarly short-latency changes in the muscle output and in firing rate changes in the other region. However, perturbation of RFA led to a larger absolute change in the neural activity of CFA neurons. The authors interpret these findings as evidence for reciprocal, but asymmetrical, influence between the regions, suggesting some degree of hierarchy in which RFA has a greater effect on the neural activity in CFA. They go on to examine whether this asymmetry can also be observed in simultaneously recorded neural activity patterns from both regions. They use multiple advanced analysis methods that either identify latent components at the population level or measure the predictability of firing rates of single neurons in one region using firing rates of single neurons in the other region. Interestingly, the main finding across these analyses seems to be that both regions share highly similar components that capture a high degree of variability of the neural activity patterns in each region. Single units' activity from either region could be predicted to a similar degree from the activity of single units in the other region, without a clear division into a leading area and a lagging area, as one might expect to find in a simple hierarchical interaction. However, the authors find some evidence showing a slight bias towards leading activity in RFA. Using a two-region neural network model that is fit to the summed neural activity recorded in the different experiments and to the summed muscle output, the authors show that a network with constrained (balanced) weights between the regions can still output the observed measured activities and the observed asymmetrical effects of the optogenetic manipulations, by having different within-region local weights. These results put into question whether previous and current findings that demonstrate asymmetry in the output of regions can be interpreted as evidence for asymmetrical (and thus hierarchical) inputs between regions, emphasizing the challenges in studying interactions between any brain regions.

      Strengths:

      The experiments and analyses performed in this study are comprehensive and provide a detailed examination and comparison of neural activity recorded simultaneously using dense electrophysiology probes from two main motor regions that have been the focus of studies examining goal-directed movements. The findings showing reciprocal effects from each region to the other, similar short-latency modulation of muscle output by both regions, and similarity of neural activity patterns without a clear lead/lag interaction, are convincing and add to the growing body of evidence that highlight the complexity of the interactions between multiple regions in the motor system and go against a simple feedforward-like network and dynamics. The neural network model complements these findings and adds an important demonstration that the observed asymmetry can, in theory, also arise from differences in local recurrent connections and not necessarily from different input projections from one region to the other. This sheds an important light on the multiple factors that should be considered when studying the interaction between any two brain regions, with a specific emphasis on the role of local recurrent connections, that should be of interest to the general neuroscience community.

      Weaknesses:

      While the similarity of the activity patterns across regions and lack of a clear leading/lagging interaction are interesting observations that are mostly supported by the findings presented (however, see comment below for lack of clarity in CCA/PLS analyses), the main question posed by the authors - whether there exists an endogenous hierarchical interaction between RFA and CFA - seems to be left largely open. 

      The authors note that there is currently no clear evidence of asymmetrical reciprocal influence between naturally occurring neural activity patterns of the two regions, as previous attempts have used non-natural electrical stimulation, lesions, or pharmacological inactivation. The use of acute optogenetic perturbations does not seem to be vastly different in that aspect, as it is a non-natural stimulation of inhibitory interneurons that abruptly perturbs the ongoing dynamics.

      We do believe that our optogenetic inactivation identifies a causal interaction between the endogenous activity patterns in the excitatory projection neurons, which we have largely silenced, and the downstream endogenous activity that is perturbed. The effect in the downstream region results directly from the silencing of activity in the excitatory projection neurons that mediate each region’s interaction with other regions. Here we have performed a causal intervention common in biology: a loss-of-function experiment. Such experiments generally reveal that a causal interaction of some sort is present, but often do not clarify much about the nature of the interaction, as is true in our case. By showing that a silencing of endogenous activity in one motor cortical region causes a significant change to the endogenous activity in another, we establish a causal relationship between these activity patterns. This is analogous to knocking out the gene for a transcription factor and observing causal effects on the expression of other genes that depend on it. 

      Moreover, our experiments are, to our knowledge, the first that localize a causal relationship to endogenous activity in motor cortex at a particular point during a motor behavior. Lesion and pharmacological or chemogenetic inactivation have long-lasting effects, and so their consequences on firing in other regions cannot be attributed to a short-latency influence of activity at a particular point during movement. Moreover, the involvement of motor cortex in motor learning and movement preparation/initiation complicates the interpretation of these consequences in relation to movement execution, as disturbance to processes on which execution depends can impede execution itself. Stimulation experiments generate spiking in excitatory projection neurons that is not endogenous.

      That said, we would agree that the form of the causal interaction between RFA and CFA remains unaddressed by our results. These results do not expose how the silenced activity patterns affect activity in the downstream region, just as knocking out a transcription factor gene does not expose how the transcription factor influences the expression of other genes. To show evidence for a specific type of interaction dynamics between RFA and CFA, a different sort of experiment would be necessary. See Jazayeri and Afraz, Neuron, 2017 for more on this issue.

      Furthermore, the main finding that supports a hierarchical interaction is a difference in the absolute change of firing rates as a result of the optogenetic perturbation, a finding that is based on a small number of animals (N = 3 in each experimental group), and one which may be difficult to interpret. 

      Though N = 3, we do show statistical significance. Moreover, using three replicates is not uncommon in biological experiments that require a large technical investment.

      As the authors nicely demonstrate in their neural network model, the two regions may differ in the strength of local within-region inhibitory connections. Could this theoretically also lead to a difference in the effect of the artificial light stimulation of the inhibitory interneurons on the local population of excitatory projection neurons, driving an asymmetrical effect on the downstream region? 

      We (Miri et al., Neuron, 2017) and others (Guo et al., Neuron, 2014) have shown that the effect of this inactivation on excitatory neurons in CFA is a near-complete silencing (90-95% within 20 ms). There thus is not much room for the effects on projection neurons in RFA to be much larger. We have measured these local effects in RFA as part of other work (Kristl et al., biorxiv, 2025), verifying that the effects on RFA projection neuron firing are not larger.

      Moreover, the manipulation was performed upon the beginning of the reaching movement, while the premotor region is often hypothesized to exert its main control during movement preparation, and thus possibly show greater modulation during that movement epoch. It is not clear if the observed difference in absolute change is dependent on the chosen time of optogenetic stimulation and if this effect is a general effect that will hold if the stimulation is delivered during different movement epochs, such as during movement preparation.

      We agree that the dependence of RFA-CFA interactions on movement phase would be interesting to address in subsequent experiments. While a strong interpretation of lesion results might lead to a hypothesis that premotor influence on primary motor cortex is local to, or stronger during, movement preparation as opposed to execution, at present there is to our knowledge no empirical support from interventional experiments for this hypothesis. Moreover, existing results from analysis of activity in these two regions have produced conflicting results on the strength of interaction between these regions during preparation. Compare for example BachschmidRomano et al., eLife, 2023 to Kaufman et al., Nature Neuroscience, 2014.

      That said, this lesion interpretation would predict the same asymmetry we have observed from perturbations at the beginning of a reach - a larger effect of RFA on CFA than vice versa.

      Another finding that is not clearly interpretable is in the analysis of the population activity using CCA and PLS. The authors show that shifting the activity of one region compared to the other, in an attempt to find the optimal leading/lagging interaction, does not affect the results of these analyses. Assuming the activities of both regions are better aligned at some unknown groundtruth lead/lag time, I would expect to see a peak somewhere in the range examined, as is nicely shown when running the same analyses on a single region's activity. If the activities are indeed aligned at zero, without a clear leading/lagging interaction, but the results remain similar when shifting the activities of one region compared to the other, the interpretation of these analyses is not clear.

      Our results in this case were definitely surprising. Many share the intuition that there should be a lag at which the correlations in activity between regions may be strongest. The similarity in alignment across lags we observed might be expected if communication between regions occurs over a range of latencies as a result of dependence on a broad diversity of synaptic paths that connect neurons. In the Discussion, we offer an explanation of how to reconcile these findings with the seemingly different picture presented by DLAG.

      Reviewer #2 (Public review):

      Summary:

      While technical advances have enabled large-scale, multi-site neural recordings, characterizing inter-regional communication and its behavioral relevance remains challenging due to intrinsic properties of the brain such as shared inputs, network complexity, and external noise. This work by Saiki-Ishkawa et al. examines the functional hierarchy between premotor (PM) and primary motor (M1) cortices in mice during a directional reaching task. The authors find some evidence consistent with an asymmetric reciprocal influence between the regions, but overall, activity patterns were highly similar and equally predictive of one another. These results suggest that motor cortical hierarchy, though present, is not fully reflected in firing patterns alone.

      Strengths:

      Inferring functional hierarchies between brain regions, given the complexity of reciprocal and local connectivity, dynamic interactions, and the influence of both shared and independent external inputs, is a challenging task. It requires careful analysis of simultaneous recording data, combined with cross-validation across multiple metrics, to accurately assess the functional relationships between regions. The authors have generated a valuable dataset simultaneously recording from both regions at scale from mice performing a cortex-dependent directional reaching task.

      Using electrophysiological and silencing data, the authors found evidence supporting the traditionally assumed asymmetric influence from PM to M1. While earlier studies inferred a functional hierarchy based on partial temporal relationships in firing patterns, the authors applied a series of complementary analyses to rigorously test this hierarchy at both individual neuron and population levels, with robust statistical validation of significance.

      In addition, recording combined with brief optogenetic silencing of the other region allowed authors to infer the asymmetric functional influence in a more causal manner. This experiment is well designed to focus on the effect of inactivation manifesting through oligosynaptic connections to support the existence of a premotor to primary motor functional hierarchy.

      Subsequent analyses revealed a more complex picture. CCA, PLS, and three measures of predictivity (Granger causality, transfer entropy, and convergent cross-mapping) emphasized similarities in firing patterns and cross-region predictability. However, DLAG suggested an imbalance, with RFA capturing CFA variance at a negative time lag, indicating that RFA 'leads' CFA. Taken together these results provide useful insights for current studies of functional hierarchy about potential limitations in inferring hierarchy solely based on firing rates.

      While I would detail some questions and issues on specifics of data analyses and modeling below, I appreciate the authors' effort in training RNNs that match some behavioral and recorded neural activity patterns including the inactivation result. The authors point out two components that can determine the across-region influence - 1) the amount of inputs received and 2) the dependence on across-region input, i.e., the relative importance of local dynamics, providing useful insights in inferring functional relationships across regions.

      Weaknesses:

      (1) Trial-averaging was applied in CCA and PLS analyses. While trial-averaging can be appropriate in certain cases, it leads to the loss of trial-to-trial variance, potentially inflating the perceived similarities between the activity in the two regions (Figure 4). Do authors observe comparable degrees of similarity, e.g., variance explained by canonical variables? Also, the authors report conflicting findings regarding the temporal relationship between RFA and CFA when using CCA/PLS versus DLAG. Could this discrepancy be due to the use of trial-averaging in former analyses but not in the latter?

      We certainly agree that the similarity in firing patterns is higher in trial averages than on single trials, given the variation in single-neuron firing patterns across trials. Here, we were trying to examine the similarity of activity variance that is clearly movement dependent, as trial averages are, and to use an approach aligned with those applied in the existing literature. We would also agree that there is more that can be learned about interactions from trial-by-trial analysis. It is possible that the activity components identified by DLAG as being asymmetric somehow are not reflected strongly in trial averages. In our Discussion we offer another potential explanation that is based on other differences in what is calculated by DLAG and CCA/PLS.

      We also note here that all of the firing pattern predictivity analysis we report (Figure 6) was done on single trial data, and in all cases the predictivity was symmetric. Thus, our results in aggregate are not consistent with symmetry purely being an artifact of trial averaging.

      (2) A key strength of the current study is the precise tracking of forelimb muscle activity during a complex motor task involving reaching for four different targets. This rich behavioral data is rarely collected in mice and offers a valuable opportunity to investigate the behavioral relevance of the PM-M1 functional interaction, yet little has been done to explore this aspect in depth. For example, single-trial time courses of inter-regional latent variables acquired from DLAG analysis can be correlated with single-trial muscle activity and/or reach trajectories to examine the behavioral relevance of inter-regional dynamics. Namely, can trial-by-trial change in inter-regional dynamics explain behavioral variability across trials and/or targets? Does the inter-areal interaction change in error trials? Furthermore, the authors could quantify the relative contribution of across-area versus within-area dynamics to behavioral variability. It would also be interesting to assess the degree to which across-area and within-area dynamics are correlated. Specifically, can acrossarea dynamics vary independently from within-area dynamics across trials, potentially operating through a distinct communication subspace?

      These are all very interesting questions. Our study does not attempt to parse activity into components predictive of muscle activity and others that may reflect other functions. Distinct components of RFA and CFA activity may very well rely on distinct interactions between them.

      (3) While network modeling of RFA and CFA activity captured some aspects of behavioral and neural data, I wonder if certain findings such as the connection weight distribution (Figure 7C), across-region input (Figure 7F), and the within-region weights (Figure 7G), primarily resulted from fitting the different overall firing rates between the two regions with CFA exhibiting higher average firing rates. Did the authors account for this firing rate disparity when training the RNNs?

      The key comparison in Figure 7 is shown in 7F, where the firing rates are accounted for in calculating the across-region input strength. Equalizing the firing rates in RFA and CFA would effectively increase RFA rates. If the mean firing rates in each region were appreciably dependent on across-region inputs, we would then expect an off-setting change in the RFA→CFA weights, such that the RFA→CFA distributions in 7F would stay the same. We would also expect the CFA→RFA weights would increase, since RFA neurons would need more input. This would shift the CFA→RFA (blue) distributions up. Thus, if anything, the key difference in this panel would only get larger. 

      We also generally feel that it is a better approach to fit the actual firing rates, rather than normalizing, since normalizing the firing rates would take us further from the actual biology, not closer.

      (4) Another way to assess the functional hierarchy is by comparing the time courses of movement representation between the two regions. For example, a linear decoder could be used to compare the amount of information about muscle activity and/or target location as well as time courses thereof between the two regions. This approach is advantageous because it incorporates behavior rather than focusing solely on neural activity. Since one of the main claims of this study is the limitation of inferring functional hierarchy from firing rate data alone, the authors should use the behavior as a lens for examining inter-areal interactions.

      As we state above, we agree that examining interactions specific to movement-related activity components could reveal interesting structure in interregional interactions. Since it remains a challenge to rigorously identify a subset of neural activity patterns specifically related to driving muscle activity, any such analysis would involve an additional assumption. It remains unclear how well the activity that decoders use for predicting muscle activity matches the activity that actually drives muscle activity in situ.

      To address this issue, which related to one raised by Reviewer #3 below, we have added an additional paragraph to the Discussion (see “Manifestations of hierarchy in firing patterns”).

      Reviewer #3 (Public review):

      This study investigates how two cortical regions that are central to the study of rodent motor control (rostral forelimb area, RFA, and caudal forelimb area, CFA) interact during directional forelimb reaching in mice. The authors investigate this interaction using

      (1) optogenetic manipulations in one area while recording extracellularly from the other, (2) statistical analyses of simultaneous CFA/RFA extracellular recordings, and (3) network modeling.

      The authors provide solid evidence that asymmetry between RFA and CFA can be observed, although such asymmetry is only observed in certain experimental and analytical contexts.

      The authors find asymmetry when applying optogenetic perturbations, reporting a greater impact of RFA inactivation on CFA activity than vice-versa. The authors then investigate asymmetry in endogenous activity during forelimb movements and find asymmetry with some analytical methods but not others. Asymmetry was observed in the onset timing of movement-related deviations of local latent components with RFA leading CFA (computed with PCA) and in a relatively higher proportion and importance of cross-area latent components with RFA leading than CFA leading (computed with DLAG). However, no asymmetry was observed using several other methods that compute cross-area latent dynamics, nor with methods computed on individual neuron pairs across regions. The authors follow up this experimental work by developing a twoarea model with asymmetric dependence on cross-area input. This model is used to show that differences in local connectivity can drive asymmetry between two areas with equal amounts of across-region input.

      Overall, this work provides a useful demonstration that different cross-area analysis methods result in different conclusions regarding asymmetric interactions between brain areas and suggests careful consideration of methods when analyzing such networks is critical. A deeper examination of why different analytical methods result in observed asymmetry or no asymmetry, analyses that specifically examine neural dynamics informative about details of the movement, or a biological investigation of the hypothesis provided by the model would provide greater clarity regarding the interaction between RFA and CFA.

      Strengths:

      The authors are rigorous in their experimental and analytical methods, carefully monitoring the impact of their perturbations with simultaneous recordings, and providing valid controls for their analytical methods. They cite relevant previous literature that largely agrees with the current work, highlighting the continued ambiguity regarding the extent to which there exists an asymmetry in endogenous activity between RFA and CFA.

      A strength of the paper is the evidence for asymmetry provided by optogenetic manipulation. They show that RFA inactivation causes a greater absolute difference in muscle activity than CFA interaction (deviations begin 25-50 ms after laser onset, Figure 1) and that RFA inactivation causes a relatively larger decrease in CFA firing rate than CFA inactivation causes in RFA (deviations begin <25ms after laser onset, Figure 3). The timescales of these changes provide solid evidence for an asymmetry in the impact of inactivating RFA/CFA on the other region that could not be driven by differences in feedback from disrupted movement (which would appear with a ~50ms delay).

      The authors also utilize a range of different analytical methods, showing an interesting difference between some population-based methods (PCA, DLAG) that observe asymmetry, and single neuron pair methods (granger causality, transfer entropy, and convergent cross mapping) that do not. Moreover, the modeling work presents an interesting potential cause of "hierarchy" or "asymmetry" between brain areas: local connectivity that impacts dependence on across-region input, rather than the amount of across-region input actually present.

      Weaknesses:

      There is no attempt to examine neural dynamics that are specifically relevant/informative about the details of the ongoing forelimb movement (e.g., kinematics, reach direction). Thus, it may be preemptive to claim that firing patterns alone do not reflect functional influence between RFA/CFA. For example, given evidence that the largest component of motor cortical activity doesn't reflect details of ongoing movement (reach direction or path; Kaufman, et al. PMID: 27761519) and that the analytical tools the authors use likely isolate this component (PCA, CCA), it may not be surprising that CFA and RFA do not show asymmetry if such asymmetry is related to the control of movement details. 

      An asymmetry may still exist in the components of neural activity that encode information about movement details, and thus it may be necessary to isolate and examine the interaction of behaviorally-relevant dynamics (e.g., Sani, et al. PMID: 33169030).

      To clarify, we are not claiming that firing patterns in no way reflect the asymmetric functional influence that we demonstrate with optogenetic inactivation. Instead, we show that certain types of analysis that we might expect to reflect such influence, in fact, do not. Indeed, DLAG did exhibit asymmetries that matched those seen in functional influence (at least qualitatively), though other methods we applied did not.

      As we state above, we do think that there is more that can be gleaned by looking at influence specifically in terms of activity related to movement. However, if we did find that movement-related activity exhibited an asymmetry following functional influence, our results imply that the remaining activity components would exhibit an opposite asymmetry, such that the overall balance is symmetric. This would itself be surprising. We also note that the components identified by CCA and PLS do show substantial variation across reach targets, indicating that they are not only reflecting condition-invariant components. These analyses were performed on components accounting for well over 90% of the total activity variance, suggesting that both conditiondependent and condition-invariant components should be included.

      To address the concern about condition-dependent and condition-invariant components, we have added a sentence to the Results section reporting our CCA and PLS results: “Because our results here involve the vast majority of trial-averaged activity variance, we expect that they encompass both components of activity that vary for different movement conditions (condition-dependent), and those that do not (condition-invariant).” To address the general concerns about potential differences in activity components specifically related to muscle activity, we have also added an additional paragraph to the Discussion (see “Manifestations of hierarchy in firing patterns”).

      The idea that local circuit dynamics play a central role in determining the asymmetry between RFA and CFA is not supported by experimental data in this paper. The plausibility of this hypothesis is supported by the model but is not explored in any analyses of the experimental data collected. Given the focus on this idea in the discussion, further experimental investigation is warranted.

      While we do not provide experimental support for this hypothesis, the data we present also do not contradict this hypothesis. Here we used modeling as it is often used - to capture experimental results and generate hypotheses about potential explanation. We do feel that our Discussion makes clear where the hypothesis derives from and does not misrepresent the lack of experimental support. We expect readers will take our engagement with this hypothesis with the appropriate grain of salt. The imaginable experiments to support such a hypothesis would constitute another substantial study, requiring numerous controls - a whole other paper in itself.

      Recommendations for the authors:  

      Reviewer #1 (Recommendations for the authors):

      (1) There are a few small text/figure caption modifications that can be made for clarity of reading:

      (2) Unclear sentence in the second paragraph of the introduction: "For example, stimulation applied in PM has been shown to alter the effects on muscles of stimulation in M1 under anesthesia, both in monkeys and rodents."

      This sentence has been rephrased for clarity: “For example, in anesthetized monkeys34 and rodents35, stimulation in PM alters the effects of stimulation in M1 on muscles.”

      (3) The first section of the results presents the optogenetic manipulation. However, the critical control that tests whether this was strictly a local manipulation that did not affect cells in the other region is introduced only much later. It may be helpful to add a comment in this section noting that such a control was performed, even if it is explained in detail later when introducing the recordings.

      We have added the following to the first Results section: “we show below that direct optogenetic effects were only seen in the targeted forelimb area and not the other.”

      (4) Figure 1D - I imagine these averages are from a single animal, but this is not stated in the figure caption.

      “For one example mouse,” has been added to the beginning of the Figure 1D legend.

      (5) Figure 2F - N=6 is not stated in the panel's caption (though it can make it clearer), while it is stated in the caption of 2H.

      “n = 6 mice” has been added to the Figure 2F legend.

      (6) There's some inconsistency with the order of RFA/CFA in the figures, sometimes RFA is presented first (e.g., Figure 1D and 1F), and sometimes CFA is presented first (e.g., panels of Figure 2).

      We do not foresee this leading to confusion.

      (7) "As expected, the majority of recorded neurons in each region exhibited an elevated average firing rate during movement as compared to periods when forelimb muscles were quiescent (Figure 2D,E; Figure S1A,B)" - Figure S1A,B show histograms of narrow vs. wide waveforms, is this the relevant figure here?

      We apologize for the cryptic reference. The waveform width histograms were referred to here because they enabled the separation of narrow- and wide-waveform cells shown in Figure 2D,E. We have added the following clause to the referenced sentence to make this explicit:  “, both for narrow-waveform, putative interneurons and wide-waveform putative pyramidal neurons.”

      (8) Figure 2I caption - "The fraction of activity variance from 150 ms before reach onset to 150 ms after it that occurs before reach onset" - this sentence is not clear.

      The Figure 2I legend has been updated to “The activity variance in the 150 ms before muscle activity onset, defined as a fraction of the total activity variance from 150 ms before to 150 ms after muscle activity onset, for each animal (circles) and the mean across animals (black bars, n = 6 mice).”

      (9) Figure 4B-G - is this showing results across the 6 animals? Not stated clearly.

      Yes - the 21 sessions we had referred to are drawn from all six mice. We have updated the legend here to make this explicit.

      (10) DLAG analysis - is there any particular reasoning behind choosing four across-region and four within-region components?

      In actuality, we completed this analysis for a broad range of component numbers and obtained similar results in all cases. Four fell in the center of our range, and so we focused the illustrations shown in the figure on this value. In general, the number of components is arbitrary. The original paper from Gokcen et al. describes a method for identifying a lower bound on the number of distinct components the method can identify. However, this method yields different results for each individual recording session. For the comparisons we performed, we needed to use the same range of values for each session.

      (11) Figure 5A seems to show 11 across-session components, it's unclear from the caption but I imagine this should show 12 (4 components times 3 sessions?)

      As we state in the Methods, any across-region latent variable with a lag that failed to converge between the boundary values of ±200 ms was removed from the analysis. In the case illustrated in this panel, the lag for one of the components failed to converge and is not shown. We have now clarified this both in the relevant Results paragraph and in the figure legend.

      (12) Figure 5B - is each marker here the average variance explained by all across/within components that were within the specified lag criteria across sessions per mouse? In other words, what does a single marker here stand for?

      We apologize for the lack of clarity here. These values reflect the average across sessions for each mouse. We have updated the legend to make this explicit.

      Reviewer #2 (Recommendations for the authors):

      As I have addressed most of my major recommendations in the public review, I will use this section to include relatively minor points for the authors to consider.

      (1) The EMG data in Figure 1C shows distinct patterns across spouts, both in the magnitude and complexity of muscle activations. It would be interesting to investigate whether these differences in muscle activity lead to behavioral variations (e.g., reaction time, reach duration) and how they relate to the relative involvement of the two areas.

      We agree that it would be interesting to examine how the interactions between areas vary as behavior varies. While the differences between reaches here are limited, we have addressed this question for two substantially different motor behaviors (reaching and climbing) in a follow-up study that was recently preprinted (Kristl et al., biorxiv, 2025).

      (2) How do the authors account for the lingering impact of RFA inactivation on muscle activity, which persists for tens of milliseconds after laser offset? Could this effect be due to compensatory motor activity following the perturbation? A further illustration of how the raw limb trajectories and/or muscle activity are perturbed and recovered would help readers better understand the impact of motor cortical inactivation.

      To clarify the effects of inactivation on a longer timescale, we have added a new supplemental figure showing the plots from Figure 1D over a longer time window extending to 500 ms after trial onset (new Figure S1). Lingering effects do persist, at least in certain cases. In general, we find it hard to ascertain the source of optogenetic effects on longer timescales like this. On the shortest timescales, effects will be mediated by relatively direct connections between regions. However, on these longer timescales, effects could be due to broader changes in brain and behavioral state that can influence muscle activity. For example, attempts to compensate for the initial disturbance to muscle activity could cause divergence from controls on these longer timescales. Muscle tissue itself is also known to have long timescale relaxation dynamics, and it would not be surprising if the relevant control circuits here also had long timescales dynamics, such that we would not expect an immediate return to control when the light pulse ends. Because of this ambiguity, we generally avoid interpretation of optogenetic effects on these longer timescales.

      Reviewer #3 (Recommendations for the authors):

      (1) Page 9: ". We measured the time at which the activity state deviated from baseline preceding reach onset," - I cannot find how this deviation was defined (neither the baseline nor the threshold).

      We have added text to the Figure 2G legend that explicitly states how the baseline and activity onset time were defined.

      (2) Given the shape of the curves in Figure 2G, the significance of this result seems susceptible to slight modifications of what defines a baseline or a deviation threshold. For example, it looks like the circle for CFA has a higher y-axis value, suggesting the baseline deviance is higher, but it is unclear why that would be from the plot. If the threshold for deviation in neural activity state were held uniform between CFA and RFA is the difference still significant across animals?

      We have repeated the analysis using the same absolute threshold for each region. We used the higher of the two thresholds from each region. The difference remains significant. This is now described in the last paragraph of the Results section for Figure 2.

      (3) Since summed deviation of the top 3 PCs is used to show a difference in activity onset between CFA/RFA, but only a small proportion of variance is explained pre-movement (<2% in most animals), it seems relevant to understand what percentage of CFA/RFA neuron activity actually is modulated and deviates from baseline prior to movement and to show the distribution of activity onsets at the single neuron level in CFA/RFA. Can an onset difference only be observed using PCA? 

      Because many neurons have low firing rates, estimating the time at which their firing rate begins to rise near reach onset is difficult to do reliably. It is also true that not all neurons show an increase around onset - some show a decrease and others show no discernible change. Using PCs to measure onset avoids both of these problems, since they capture both increases and decreases in individual neuron firing rates and are much less noisy than individual neuron firing rates. 

      However, based on this comment, we have repeated this analysis on a single-neuron level using only neurons with relatively high average firing rates. Specifically, we analyzed neurons with mean firing rates above the 90th percentile across all sessions within an animal. Neurons whose activity never crossed threshold were excluded. Results matched those using PCs, with RFA neurons showing an earlier average activity onset time. This is now described in the last paragraph of the Results section for Figure 2.

      (4) It is stated that to study the impact of inactivation on CFA/RFA activity, only the 50 highest average firing rate neurons were used (and maybe elsewhere too, e.g., convergent cross mapping). It is unclear why this subselection is necessary. It is justified by stating that higher firing rate neurons have better firing rate estimates. This may be supportable for very low firing rate units that spike sorting tools have a hard time tracking, but I don't think this is supported by data for most of the distribution of firing rates. It therefore seems like the results might be biased by a subselection of certain high firing rate neuron populations. It would be useful to also compute and mention if the results for all neurons/neuron pairs are the same. If there is worry about low-quality units being those with low firing rates, a threshold for firing rate as used elsewhere in the paper (at least 1 spike / 2 trials) seems justified.

      The issue here is that as firing rates decrease and firing rate estimates get noisier, estimates of the change in firing rate get more variable. Here we are trying to estimate the fraction of neurons for which firing rates decreased upon inactivation of the other region. Variability in estimates of the firing rate change will bias this estimate toward 50%, since in the limit when the change estimates are entirely based on noise, we expect 50% to be decreases. As expected, when we use increasingly liberal thresholds for this analysis, the fraction of decreases trends closer to 50%. 

      As a consequence of this, we cannot easily distinguish whether higher firing rate neurons might for some reason have a greater tendency to exhibit decreases in firing compared to lower firing rate neurons. However, we see no positive reason to expect such a difference. We have added a sentence noting this caveat in interpreting our findings to the relevant paragraph of the Results.

      The lack of min/max axis values in Figure 3B-F makes it hard to interpret - are these neurons almost silent when near the bottom of the plot or are they still firing a substantial # of spikes?

      To aid interpretation of the relative magnitude of firing rate changes, we have added minimum firing rates for the averages depicted in Figure 3B,C,E and F to the legend. Our original thinking was that the plots in Figure 3G and H would provide an indication of the relative changes in firing.

      It would be interesting to know if the impact of optogenetic stimulation changed with exposure to the manipulation. Are all results presented only from the first X number of sessions in each animal? Or is the effect robust over time and (within the same animal) you can get the same results of optogenetic inactivation over time? This information seems critical for reproducibility.

      We have now performed brief optogenetic inactivations in several brain areas in several different behavioral paradigms, and have found that inactivation effects are stable both within and across sessions, almost surprisingly so. This includes cases where the inactivations were more frequent (every ~1.25 s on average) and more numerous (>15,000 trials per animal) than in the present manuscript. Thus we did not restrict our analysis here to the first X sessions or trials within a session. We have added additional plots as Figure S3T-AA showing the stability of optogenetic effects both within and across sessions.

      Given that it can be difficult to record from interneurons (as the proportion of putative interneurons in Figure S1 attests), the SALT analyses would be more convincing if a few recordings had been performed in the same region as optogenetic stimulation to show a "positive control" of what direct interneuron stimulation looks like. Could also use this to validate the narrow/wide waveform classification.

      We have verified that using SALT as we have in the present manuscript does detect vGAT+ interneurons directly responding to light. This is included in a recent preprint from the lab (Kristl et al., biorxiv, 2025). We (Warriner et al., Cell Reports, 2022) and others (Guo et al., Neuron, 2014) have previously used direct ChR2 activation to validate waveform-based classification.

      Simultaneous CFA/RFA recordings during optogenetic perturbation would also allow for time courses of inhibition to be compared in RFA/CFA. Does it take 25ms to inhibit locally, and the cross-area impact is fast, or does it inactivate very fast locally and takes ~25ms to impact the other region?

      Latencies of this sort are difficult to precisely measure given the statistical limits of this sort of data, but there does appear to be some degree of delay between local and downstream effects. We do not have a statistical foundation as of yet for concluding that this is the case. It will be interesting to examine this issue more rigorously in the future.

      Given the difference in the analytical methods, the authors should share data in a relatively unprocessed format (e.g., spike times from sorted units relative to video tracking + behavioral data), along with analysis code, to allow others to investigate these differences.

      We plan to post the data and code to our lab’s Github site once the Version of Record is online.

    1. eLife Assessment

      This study provides valuable findings that MK2 inhibitor CMPD1 can inhibit the growth, migration and invasion of breast cancer cells both in vitro and in vivo. The evidence supporting the claims of the authors is solid, although the detailed molecular mechanism and additional animal experiments would strengthen the paper. This study will be of interest to the breast cancer field.

    2. Reviewer #1 (Public review):

      In this paper, the authors reveal that the MK2 inhibitor CMPD1 can inhibit the growth, migration and invasion of breast cancer cells both in vitro and in vivo by inducing microtubule depolymerization, preferentially at the microtubule plus-end, leading to cell division arrest, mitotic defects, and apoptotic cell death. They also showed that CMPD1 treatment upregulates genes associated with cell migration and cell death, and downregulates genes related to mitosis and chromosome segregation in breast cancer cells, suggesting a potential mechanism of CMPD1 inhibition in breast cancer. Besides, they used the combination of an MK2-specific inhibitor, MK2-IN-3, with the microtubule depolymerizer vinblastine to simultaneously disrupt both the MK2 signaling pathway and microtubule dynamics, and they claim that inhibiting the p38-MK2 pathway may help to enhance the efficacy of MTAs in the treatment of breast cancer.

    3. Reviewer #2 (Public review):

      Summary:

      This study explores the potential of inhibiting the p38-MK2 signaling pathway to enhance the efficacy of microtubule-targeting agents (MTAs) in breast cancer treatment using a dual-target inhibitor.

      Strengths:

      The study identifies the p38-MK2 pathway as a promising target to enhance the efficacy of microtubule-targeting agents (MTAs), offering a novel therapeutic strategy for breast cancer treatment. The study also employs a wide range of techniques, especially live-cell imaging, to assess the microtubule dynamics in TNBC cells. The revised manuscript added new in vitro and in vivo evidence that furtherly supported the conclusions.

      Comments on revisions:

      The authors have appropriately addressed all of my comments and concerns. Specifically, they performed additional in vitro experiments using MCF10A cells and p53 knockout cells to determine the IC50 of CMPD1. They also repeated the in vivo treatment experiment and evaluated the toxicity of the drug treatment in the CAL-51 model. Furthermore, they provided genetic evidence for the combination treatment. I'm satisfied with the revision and have no further major comments. Minor comment: make sure the name of the chemo drug shown in Fig. 3 is consistent.

    4. Reviewer #3 (Public review):

      Summary:

      The authors demonstrated MK2i could enhance the therapeutic efficacy of MTAs. With the tumour xenograft and migration assay, the author suggested that the p38-MK2 pathway may serve as a promising therapeutic target in combination with MTAs in cancer treatment.

      Strengths:

      The authors provided a potential treatment for breast cancer.

      Comments on revisions:

      A xenograft experiment should be included to evaluate the synergistic effect of MK2i and vinblastine.

    5. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      In this paper, the authors reveal that the MK2 inhibitor CMPD1 can inhibit the growth, migration, and invasion of breast cancer cells both in vitro and in vivo by inducing microtubule depolymerization, preferentially at the microtubule plus-end, leading to cell division arrest, mitotic defects, and apoptotic cell death. They also showed that CMPD1 treatment upregulates genes associated with cell migration and cell death, and downregulates genes related to mitosis and chromosome segregation in breast cancer cells, suggesting a potential mechanism of CMPD1 inhibition in breast cancer. Besides, they used the combination of an MK2-specific inhibitor, MK2-IN-3, with the microtubule depolymerizer vinblastine to simultaneously disrupt both the MK2 signaling pathway and microtubule dynamics, and they claim that inhibiting the p38-MK2 pathway may help to enhance the efficacy of MTAs in the treatment of breast cancer. However, there are a few concerns, including:

      (1) What is the effect of CMPD1 on breast cancer metastasis?

      In this study, we hypothesized that the MK2 signaling pathway could synergize with microtubule-targeting agents (MTAs) to enhance anti-cancer efficacy. We utilized CMPD1 as a potent dual-function inhibitor, targeting both MK2 and microtubule dynamics. By simultaneously inhibiting these pathways, CMPD1 not only shows the therapeutic impact of MTAs, but also significantly suppresses breast cancer cell migration and invasion. Therefore, we propose that CMPD1, through its dual inhibition of MK2 activity and microtubule dynamics, may offer enhanced specificity and efficacy in preventing breast cancer metastasis and limiting tumor progression.

      (2) The mechanism is lacking as to how MK2 inhibitors enhance the efficacy of MTAs.

      Thank you for the valuable suggestion. We agree that our current findings do not fully elucidate the underlying mechanism by which MK2 inhibition synergistically enhances the efficacy of MTAs. We recognize this as an important area for further investigation and are committed to exploring the molecular interplay between MK2 signaling and microtubule dynamics in future studies. A deeper mechanistic understanding will be critical to establishing a strong rationale for the potential co-treatment of MK2 inhibitors and MTAs in clinical breast cancer therapy.

      Reviewer #2 (Public review):

      Summary:

      This study explores the potential of inhibiting the p38-MK2 signaling pathway to enhance the efficacy of microtubule-targeting agents (MTAs) in breast cancer treatment using a dual-target inhibitor.

      Strengths:

      The study identifies the p38-MK2 pathway as a promising target to enhance the efficacy of microtubule-targeting agents (MTAs), offering a novel therapeutic strategy for breast cancer treatment. In addition, the study employs a wide range of techniques, especially live-cell imaging, to assess the microtubule dynamics in TNBC cells.

      We sincerely appreciate your recognition of the significance and impact of our work.

      Weaknesses:

      The study primarily uses RPE1 cells as the control for normal cells, which may not fully capture the response of normal mammary epithelial cells. While CMPD1 is shown to be effective in suppressing tumor growth in MDA-MB-231 xenograft, the study lacks detailed toxicity data to confirm its safety profile in vivo.

      Thank you for your valuable suggestions. In the revised manuscript, we have included CMPD1 treatment in MCF10A cells, a more appropriate non-transformed control line commonly used in breast cancer research. Notably, MCF10A cells exhibited results similar to those observed in RPE1 cells, further reinforcing our conclusion that breast cancer cells display increased sensitivity to CMPD1 treatment. These new findings are presented in Figure 2-Supplement 1A-C. Additionally, we performed further xenograft experiments using CAL-51 and MDA-MB-231 cells. We collected data on tumor growth, mouse body weight, survival rates, and other relevant parameters to comprehensively assess toxicity. The newly obtained results are presented in Figure 3F-G and Figure 3-Supplement 1-3.

      Reviewer #3 (Public review):

      Summary:

      The authors demonstrated MK2i could enhance the therapeutic efficacy of MTAs. With Tumor xenograft and migration assay, the author suggested that the p38-MK2 pathway may serve as a promising therapeutic target in combination with MTAs in cancer treatment.

      Strengths:

      The authors provided a potential treatment for breast cancer.

      Thank you for recognizing the importance and significance of our work.

      Weaknesses:

      (1) In Figure 2, the authors used a human retinal pigment epithelial-1 (RPE1) cell line to show that breast cancer cells are more sensitive to CMPD1 treatment. MCF10A cells would be suggested here as a suitable control. Besides, to compare the sensitivity, IC50 indifferent cell lines should be measured.

      In the revised manuscript, we have addressed these points by determining the IC50 values for CMPD1 in MDA-MB-231, CAL-51, MCF10A, and CAL-51 p53 knockout cells. These new results are presented in Figure 2-Supplement Figure 3.

      (2) The data of MDA-MB-231 in Figure 1D is not consistent with CAL-51 and T47D, also not consistent with the data in Figures 2B-C.

      In the revised manuscript, we have included all relevant statistical analyses in Figure 1D. In MDA-MB-231 cells, there are no statistically significant differences in mitotic duration between 1 µM and 5 µM, 5 µM and 10 µM, or 1 µM and 10 µM CMPD1 treatments. Similarly, no significant differences are observed between 1 µM and 5 µM or 5 µM and 10 µM CMPD1 treatments in CAL-51 cells, and between 5 µM and 10 µM in T-47D cells. These results suggest that mitotic duration does not exhibit a clear dose-dependent relationship within the 1–10 µM range, likely because mitotic arrest has reached a near-plateau effect at these concentrations.

      It is also important to note that the experimental conditions in Figures 1 and 2 are fundamentally different. Figure 1 investigates the effects of higher concentrations of CMPD1 (≥1 µM), which severely disrupt microtubule organization and result in robust mitotic arrest, with cells arrested in mitosis for over 8 hours. In contrast, the conditions in Figure 2 utilize much lower concentrations of CMPD1 (10–50 nM), which are insufficient to cause complete microtubule depolymerization, but are capable of inducing a subtle yet statistically significant mitotic delay, particularly in breast cancer cell lines. These lower concentrations were chosen to mimic clinically relevant intratumoral drug levels. Previous studies have reported that paclitaxel (PTX) concentrations in patient tumors approximate ~50 nM when modeled in vitro. At these physiologically relevant levels, PTX does not induce strong mitotic arrest but instead causes moderate delays that result in division errors and chromosomal instability, ultimately contributing to cancer cell death. In this study, the conditions used in Figure 2 emulate these clinically relevant concentrations for CMPD1. We found that, similar to PTX, low-dose CMPD1 induces a slight but significant mitotic delay without triggering a full mitotic arrest. Notably, unlike PTX, CMPD1 appears to exert this effect selectively in breast cancer cells, contributing to mitotic errors and potentially enhancing therapeutic efficacy through targeted chromosomal instability.

      (3) To support the authors' conclusion in Figure 5, an additional animal experiment performed by tail vein injection would be helpful.

      While current technical limitations have precluded us from conducting this suggested experiment in this study, we have performed complementary xenograft studies using CAL-51 cells treated with CMPD1. These experiments included a comprehensive toxicity analysis. Furthermore, we carried out an in vitro migration assay using CAL-51 cells under combined treatment with the MK2 inhibitor and vinblastine. These additional findings are presented in Figure 3–Supplement 1–3 and Figure 6–Supplement 3. We recognize the importance of the suggested tail vein injection approach and are actively pursuing further mechanistic studies, including this experiment, in our ongoing and future work.

      (4) Page 14, to evaluate the combination result of MK2i and vinblastine, an in vivo animal assay must be performed.

      We appreciate the reviewer’s valuable suggestion. We are actively investigating the synergistic mechanisms between the MK2 inhibitor and microtubule-targeting agents (MTAs). In future studies, we plan to extend our findings by conducting xenograft experiments to further evaluate their therapeutic potential in vivo.

      (5) The authors used RNA-seq to show some pathways affected by CMPD1. What are the key/top genes that were affected? How about the mechanism?

      In the revised manuscript, we have included the top 20 upregulated and downregulated genes identified from RNA-seq analysis using MDA-MB-231 cells. This new data is presented in Figure 6-Supplement Figure 4. Gene Ontology (GO) Biological Process (BP) pathway enrichment analysis revealed that the most significantly enriched pathways among upregulated genes are associated with cell migration, whereas the downregulated genes are primarily involved in mitosis and chromosome segregation. These transcriptional changes are consistent with the phenotypic outcomes observed in our experiments, supporting the functional relevance of CMPD1 treatment. However, further investigation will be necessary to elucidate the detailed molecular mechanisms underlying these effects.

      (6) Line 127, more experiments should be involved to support the conclusion.

      In the revised manuscript, we have addressed this point by performing additional experiments, including determination of the IC₅₀ values of CMPD1 in MDA-MB-231, CAL-51, MCF10A, and CAL-51 p53 knockout cells. We also conducted live-cell imaging analyses using MCF10A cells. These new results further reinforce our conclusion that breast cancer cells are more sensitive to CMPD1 treatment than normal breast epithelial cells, and that this sensitivity is independent of p53 status. The new data are presented in Figure 2-Supplement Figures 1 and 3.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Figure 1D: As the concentration of CMPD1 increased, the mitotic duration of MDA-MB-231 cells decreased, why was that?

      Although there appears to be a slight decrease in mitotic duration with increasing concentrations of CMPD1, our quantitative analysis reveals no statistically significant differences among the 1 to 10 µM treatment groups in MDA-MB-231 cells. In the revised manuscript, we have included all relevant statistical analyses in Figure 1D for clarity. Importantly, all CMPD1-treated groups exhibit a pronounced and statistically significant prolongation of mitosis compared to the DMSO-treated control. While the average mitotic duration in control cells is approximately 30 minutes, cells exposed to 1–10 µM CMPD1 consistently display mitotic durations exceeding 8 hours, indicating a strong and sustained mitotic arrest across this concentration range.

      Reviewer #2 (Recommendations for the authors):

      (1) The rationale for using RPE1 as normal cell control instead of normal mammary epithelial cells as control is unclear. Using normal mammary epithelial cells such as MCF10A for the study is recommended.

      Thank you for this valuable suggestion. In the revised manuscript, we have included additional experiments using non-transformed mammary epithelial MCF10A cells. The new data, presented in Figure 2-Supplement Figures 1 and 3, include both IC50 measurements and live-cell imaging analyses. These results further support our conclusion that breast cancer cells are significantly more sensitive to CMPD1 treatment compared to normal mammary epithelial cells.

      (2) It is intriguing that CAL-51 cells are more sensitive to CMPD1 than MDA-MB-231 cells; examining how p53 signaling changes in these cells would be worthwhile.

      We appreciate this insightful comment. In the revised manuscript, we have measured the IC₅₀ values for both CAL-51 and CAL-51 p53 knockout (p53KO) cells. The results show no significant difference in CMPD1 sensitivity between the two, suggesting that the enhanced sensitivity of CAL-51 cells is independent of p53 status. These new findings are presented in Figure 2—Supplement Figure 3.

      (3) Figures S1A and B are not described and cited in the main text.

      We apologize for this oversight. In the revised manuscript, we have correctly cited and described Figures S1A and B (Figure 2-Supplement Figure 2 A-B in revised manuscript) in the main text.

      (4) I'm not that convinced by the conclusion made from Lines 201-204. First, Figure S2C, which is the growth of tumor volume, does not reflect the toxicity of the drug treatment. No additional data evaluating the toxicity (such as body weight change) under the regimen was shown. Second, although the tumor weight by the endpoint indicated some anti-tumor effect in the MDA-MB-231 xenograft model, the tumor volume does not show the same pattern (the dot lines do not well distinguish which group from which). I would suggest repeating the in vivo experiment using CAL-51 cells since it is more sensitive to CMPD1 according to the previous data.

      Thank you for this thoughtful and constructive feedback. In the revised manuscript, we have addressed these concerns through several additional experiments. We performed new xenograft studies using CAL-51 TNBC cells, in parallel with further toxicity-focused analyses in the MDA-MB-231 model. Consistent with previous results, CMPD1 treatment significantly suppressed tumor growth in CAL-51 xenografts (Figure 3F-G), further supporting its efficacy in a more sensitive cell line. To evaluate drug-associated toxicity, we measured body weight changes throughout the course of treatment. CMPD1-treated mice maintained a comparable weight gain to the control group, whereas mice treated with paclitaxel (PTX) showed significantly reduced body weight (Figure 3-Supplement Figure 2A). Notably, animal deaths occurred only in the PTX-treated groups in both MDA-MB-231 and CAL-51 models (Figure 3-Supplement Figure 2B). We also assessed organ toxicity, including both anatomical and functional evaluations of the kidney and liver, and observed no significant damage in CMPD1-treated mice (Figure 3-Supplement Figures 3A-B and 3D). Furthermore, white blood cell (WBC) counts remained stable in the CMPD1 group, while PTX treatment led to a significant reduction (Figure 3-Supplement Figures 3C-D). These additional data provide strong evidence for the anti-tumor efficacy and lower toxicity of CMPD1 in vivo.

      (5) While I appreciate the combination effect of treating cells with the MK2 inhibitor with vinblastine. I would consider using genetic knockdown as a complementary approach to demonstrate that inhibiting the p38-MK2 pathway synergized with microtubule depolymerizing agents. In addition, could inhibition of the p38-MK2 pathway alone induce the cell growth inhibition observed with CMPD1 treatment?

      Thank you for these important suggestions. In the revised manuscript, we have incorporated siRNA-mediated knockdown of MK2 in combination with vinblastine treatment. This genetic approach revealed synergistic effects on mitotic index and mitotic errors, closely mirroring the phenotypes observed with pharmacological co-treatment using the MK2 inhibitor and vinblastine (Figure 6-Supplement Figure 2A-C). These results further validate the role of the p38-MK2 pathway in modulating mitotic progression in the presence of MTAs. To address whether MK2 inhibition alone is sufficient to impair cell growth, we performed validation experiments using the MK2 inhibitor at 10 µM. At this concentration, the inhibitor effectively blocked phosphorylation of Hsp27, a major downstream substrate of MK2, under H2O2-induced ROS stress conditions (Figure 6-Supplement Figure 1A-B), confirming MK2 signaling pathway inhibition. However, treatment with the MK2 inhibitor alone did not significantly affect cell proliferation, as shown by a 4-day growth curve analysis in CAL-51 cells (Figure 6-Supplement Figure 1C). These findings suggest that inhibition of the p38-MK2 pathway alone is not sufficient to suppress cancer cell growth, and that its synergistic interaction with MTAs, such as vinblastine, is essential for the observed anti-proliferative effects.

      (6) Phenotypic studies (such as anchorage-independent growth and cell migration and invasion assay) of combining MK2 inhibitor with vinblastine in TNBC cells are recommended.

      Thank you for this valuable suggestion. In the revised manuscript, we have conducted cancer cell migration assays using CAL-51 TNBC cells treated with control, MK2 inhibitor alone, vinblastine alone, or the combination of both. Our results demonstrate that the combination treatment significantly enhances the inhibition of cell migration compared to either agent alone (Figure 6-Supplement Figure 3A-C). These findings provide additional phenotypic evidence supporting the synergistic interaction between MK2 inhibition and microtubule-targeting agents in TNBC cells.

      Reviewer #3 (Recommendations for the authors):

      The authors can utilize diverse experiments to support their conclusions.

      Thank you for this important suggestion. In the revised manuscript, we have conducted a series of additional experiments to robustly support our conclusions.

      These include:

      (1) Xenograft studies using CAL-51 TNBC cells, along with comprehensive toxicity evaluations.

      (2) CMPD1 sensitivity analysis in non-transformed MCF10A mammary epithelial cells.

      (3) IC50 measurements in MDA-MB-231, CAL-51, CAL-51 p53 knockout, and MCF10A cells.

      (4) Cell migration assays assessing the combination effects of MK2 inhibitor and vinblastine

      (5) siRNA-mediated genetic knockdown of MK2 to complement pharmacological findings

      Collectively, these additional data sets substantially strengthen the evidence base for our conclusions and provide a more comprehensive mechanistic understanding.

    1. eLife Assessment

      This manuscript makes a valuable contribution to the field by uncovering a molecular mechanism for miRNA intracellular retention, mediated by the interaction of PCBP2, SYNCRIP, and specific miRNA motifs. Overall, the findings are convincing and advance our understanding of RNA-binding protein-mediated miRNA sorting, providing deeper insights into miRNA dynamics.

    2. Reviewer #1 (Public review):

      In this study, Marocco and colleages perform a deep characterization of the complex molecular mechanism guiding the recognition of a particular CELLmotif previously identified in hepatocytes in another publication. Having miR-155-3p with or without this CELLmotif as initial focus, authors identify 21 proteins differentially binding to these two miRNA versions. From these, they decided to focus on PCBP2. They elegantly demonstrate PCBP2 binding to miR-155-3p WT version but not to CELLmotif-mutated version. miR-155-3p contains a hEXOmotif identified in a different report, whose recognition is largely mediated by another RNA-binding protein called SYNCRIP. Interestingly, mutation of the hEXOmotif contained in miR-155-3p did not only blunt SYNCRIP binding, but also PCBP2 binding despite the maintenance of the CELLmotif. This indicates that somehow SYNCRIP binding is a pre-requisite for PCBP2 binding. EMSA assay confirms that SYNCRIP is necessary for PCBP2 binding to miR-155-3p, while PCBP2 is not needed for SYNCRIP binding. Then authors aim to extend these finding to other miRNAs containing both motifs. For that, they perform a small-RNA-Seq of EVs released from cells knockdown for PCBP2 versus control cells, identifying a subset of miRNAs whose expression either increases or decreases. The assumption is that those miRNAs containing PCBP2-binding CELLmotif should now be less retained in the cell and go more to extracellular vesicles, thus reflecting a higher EV expression. The specific subset of miRNAs having both the CELLmotif and hEXOmotif (9 miRNAs) whose expressions increase in EVs due to PCBP2 reduction is also affected by knocking-down SYNCRIP in the sense that reduction of SYNCRIP leads to lower EV sorting. Further experiments confirm that PCBP2 and SYNCRIP bind to these 9 miRNAs and that knocking down SYNCRIP impairs their EV sorting.

      In the revised manuscript, the authors have addressed most of my concerns and questions. I believe the new experiments provide stronger support for their claims. My only remaining concern is the lack of clarity in the replicates for the EMSA experiment. The one shown in the manuscript is clear; however, the other three replicates hardly show that knocking down SYNCRIP has an effect on PCBP2 binding. Even worse is the fact that these replicates do not support at all that PCBP2 silencing has no effect on SYNCRIP binding, as the bands for those types of samples are, in most of the cases, not visible. I think the authors should work on repeating a couple of times EMSA experiment.

    3. Reviewer #2 (Public review):

      Summary:

      The author of this manuscript aimed to uncover the mechanisms behind miRNA retention within cells. They identified PCBP2 as a crucial factor in this process, revealing a novel role for RNA-binding proteins. Additionally, the study discovered that SYNCRIP is essential for PCBP2's function, demonstrating the cooperative interaction between these two proteins. This research not only sheds light on the intricate dynamics of miRNA retention but also emphasizes the importance of protein interactions in regulating miRNA behavior within cells.

      Strengths:

      This paper makes important progress in understanding how miRNAs are kept inside cells. It identifies PCBP2 as a key player in this process, showing a new role for proteins that bind RNA. The study also finds that SYNCRIP is needed for PCBP2 to work, highlighting how these proteins work together. These discoveries not only improve our knowledge of miRNA behavior but also suggest new ways to develop treatments by controlling miRNA locations to influence cell communication in diseases. The use of liver cell models and thorough experiments ensures the results are reliable and show their potential for RNA-based therapies

      Weaknesses:

      The manuscript is well-structured and presents compelling data, but I noticed a few minor corrections that could further enhance its clarity:

      Figure References: In the response to Reviewer 1, the comment states, "It's not Panel C, it's Panel A of Figure 1"-this should be cross-checked for consistency.<br /> Supplementary Figure 2 is labeled as "Panel A"-please verify if additional panels (B, C, etc.) are intended.

      Western Blot Quality: The Alix WB shows some background noise. A repeat with optimized conditions (or inclusion of a cleaner replicate) would strengthen the data. Adding statistical analysis for all WBs would also reinforce robustness.

      These are relatively small refinements, and the manuscript is already in excellent shape. With these adjustments, it will be even stronger.

    4. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      In this study, Marocco and colleagues perform a deep characterization of the complex molecular mechanism guiding the recognition of a particular CELLmotif previously identified in hepatocytes in another publication. Having miR-155-3p with or without this CELLmotif as the initial focus, the authors identify 21 proteins differentially binding to these two miRNA versions. From there, they decided to focus on PCBP2. They elegantly demonstrate PCBP2 binding to the miR-155-3p WT version but not to the CELLmotif-mutated version. miR-1553p contains a hEXOmotif identified in a different report, whose recognition is largely mediated by another RNA-binding protein called SYNCRIP. Interestingly, mutation of the hEXOmotif contained in miR-155-3p did not only blunt SYNCRIP binding but also PCBP2 binding despite the maintenance of the CELLmotif. This indicates that somehow SYNCRIP binding is a pre-requisite for PCBP2 binding. EMSA assay confirms that SYNCRIP is necessary for PCBP2 binding to miR-155-3p, while PCBP2 is not needed for SYNCRIP binding. The authors aim to extend these findings to other miRNAs containing both motifs. For that, they perform a small-RNA-Seq of EVs released from cells knockdown for PCBP2 versus control cells, identifying a subset of miRNAs whose expression either increases or decreases. The assumption is that those miRNAs containing PCBP2-binding CELLmotif should now be less retained in the cell and go more to extracellular vesicles, thus reflecting a higher EV expression. The specific subset of miRNAs having both the CELLmotif and hEXOmotif (9 miRNAs) whose expressions increase in EVs due to PCBP2 reduction is also affected by knocking-down SYNCRIP in the sense that reduction of SYNCRIP leads to lower EV sorting. Further experiments confirm that PCBP2 and SYNCRIP bind to these 9 miRNAs and that knocking down SYNCRIP impairs their EV sorting.

      We thank this Reviewer for the time spent on our manuscript and for having appreciated our characterization of the present molecular mechanism controlling miRNA export/cellretention in hepatocytes.

      While the process studied in this work is novel and interesting, there are several aspects of this manuscript that should be improved:

      (1) First of all, the nature of the CELLmotif and the hEXOmotif they are studying is extremely confusing. For the CELLmotif, the authors seem to focus on the Core CELLmotif AUU A/G in some experiments and the extended 7-nucleotide version in others. The fact that these CELLmotif and hEXOmotif are not shown anywhere in the figures (I mean with the full nucleotide variability described in the original publications) but only referred to in the text further complicates the identification of the motifs and the understanding of the experiments. Moreover, I am not convinced that the sequences they highlight in grey correspond to the original CELLmotif in all cases. For instance, in the miR-155-3p sequence, GCAUU is highlighted in grey. However, the original CELLmotif is basically 7-nucleotide long: C, A/U, G/A/C, U, U/A, C/G/A, A/U/C or CAGUUCA in its more abundant version. I can only see clearly the presence of the Core CELLmotif AUUA in miR-155-3p; however, the last A is not highlighted in grey. It is true that there is some nucleotide variability in each position in the originally reported CELLmotif by the authors in ref. 5 and the hEXOmotifs in ref. 7; however, not all nucleotides are equally likely to be found in each position. This fact seems to be not to be taken into account by the authors as they took basically any sequence with any length and almost sequence combination as valid CELLmotif. This means that I cannot identify the CELLmotif in many cases among the ones they highlight in grey. Instead, they should really focus on the most predominant CELLmotif sequence or, instead, take a reduced subset of "more abundant" CELLmotif versions from the ones that could fit in the originally described CELLmotif. Altogether, the authors need to explain much better what they have considered as the CELLmotif, what is the Core CELLmotif and what is hEXOmotif in each case and restrict to the most likely versions of the CELLmotif and hEXOmotif.

      We thank the Reviewer for having raised this concern and indeed we must agree with her/him and therefore, we modified the text and the figure accordingly. 

      In brief, as now stated, with respect to the CELL motif, miR 155-3p, miR-155-5p, miR-181d5p, miR-3084-5p, miR-122b-3p, miR-192-5p, miR-26b-3p, miR-31-3p, miR-195a-5p and miR-421-3p have the Core CELL motif (AUUA/G) described by Garcia- Martin and colleagues (ref. 5). 

      Other miRNAs (miR-345-3p, miR-23a-5p and miR-214-3p) share the described CELL motif (ref.5) with the most frequent nucleotides, considering also the reported variability. Also for the hEXO motif described by Santangelo and collaborators (ref.7), the most frequent nucleotides defining the motif sequence have been taken into consideration. The motifs have been better highlighted in the new version of Fig. 1 panel C.

      (2) Validation of EV isolation method: first, a large part of Supplementary Figure 2 is not readable. EV markers seem to be enriched in EV isolates; however, more EV and cell markers should be assayed to fulfill MISEV guidelines.

      We apologize for the low quality of the figure. In order to address this issue, we replaced the Supplementary Figure 2 panel A (now panel B) and we added further EV markers (TSG101, Alix, Flotillin) in Supplementary Figure 2 panel B (now panel A). Notably, in the same Western blot analysis we also addressed the expression of SYNCRIP and PCBP2 (that were found in the cellular end EV compartments or only in the intracellular compartment respectively).

      (3) A key variable is missing in Supplementary Figure 2, which is whether PCBP2 or SYNCRIP knockdowns impair EV secretion rates. A quantification of the nr vesicles released per cell upon knocking down each of these factors would be essential to rule out that any of the effects seen throughout the paper are not due to reduced or enhanced EV production rather than miRNA sorting/retention.

      We addressed this issue by quantifying the number of EVs per cell in shPCBP2 or shSYNCRIP with respect to the shCTR conditions. Data are shown in the new Supplementary Figure 2 panel C and indicate that there are not significant differences on EVs production rate upon PCBP2 or SYNCRIP knockdown.

      (4) The EMSA experiment is important to support their claims. Given the weak bands that are shown, the authors need to show all their replicates to convince the readers that it is reproducible.

      We are aware that the signals appear faint; the experimental replicates showing the robustness of the observation are reported below. 

      Author response image 1.

      (5) Although the bindings of SYNCRIP and PCBP2 to miR-155-3p and other miRNAs having both hEXOmotif and CELLmotif seem clear, the need for SYNCRIP binding to allow for PCBP2-mediated cellular retention is counterintuitive. What happens to those miRNAs that only contain a CELLmotif in terms of cellular retention and SYNCRIP dependence for cellular retention? In this regard, a representative miRNA (miR-31-3p) is analyzed in several experiments, showing that PCBP2 does not bind to it unless a hEXOmotif is introduced (Figure 3). However, this type of experiment should definitely be extended to other miRNAs containing only CELLmotif without hEXOmotif.

      Based on the Reviewer’s suggestion we confirmed previous findings by extending the observation to further two miRNAs embedding the sole CELL-motif (miR-195a-5p and 4213p) whose sequences are reported in Figure 4C. Data relative to qPCR amplification are reported in Figure 4D, Figure 5 panels A-B, Figure 6 and new Supplementary Figure 3. They confirm that miRNAs only containing CELL motif are not EV-exported in dependence of SYNCRIP and are cell-retained independently of PCBP2 silencing. 

      (6) Along the same line, I am missing another important experiment: the artificial incorporation of CELLmotif. For example, miR-365-2-5p lacks a CELLmotif but has a hEXOmotif. Does PCBP2 bind to this miRNA upon incorporation of CELLmotif? Does this lead now to enhanced cellular retention of this miRNA?

      We are grateful for the Reviewer's concern. As suggested, we added RNA pull-down experiments for miR-365-2-5p in wild type form and in mutated form (with the inclusion of CELL motif). As reported in the new Figure 1 panel E, the addition of the CELL motif maintains SYNCRIP binding and allows PCBP2 interaction with this miRNA. 

      (7) What would be the net effect of knocking down both SYNCRIP and PCBP2 at the same time? Would this neutralize each other's effect or would the lack of one impose on the other? That could help in understanding the complex interplay between these two factors for mediating cellular retention and EV sorting.

      SYNCRIP and PCBP2 play opposite roles in the dynamics of miRNA retention/export. SYNCRIP is involved in the loading of miRNAs into EVs through the recognition of hEXO motif. Instead, PCBP2 is involved in cellular retention of miRNAs, acting as a negative regulator of SYNCRIP activity. PCBP2 binding and function requires both CELL-motif and SYNCRIP binding in order to negatively regulate miRNAs export into EVs.

      Being SYNCRIP silencing sufficient to cause miRNA retention (as shown in Supplementary Figure 3), we believe that the contemporary silencing of PCBP2 should not disclose any additional aspect on cellular retention and EV sorting dynamics.

      (8) The authors have here a great opportunity to shed some light on an unclear aspect of miRNA EV sorting and cellular retention: whether the RBPs go together with the miRNA to the EVs or not. While the original paper describing hEXOmotif found SYNCRIP in EVs, another publication (Jeppesen et al, Cell 2019; PMID: 30951670) later found this RBP being very scarce in small EVs compared to cellular bodies or large EVs (Supplementary Tables 3 and 4 in that publication). Can the authors find SYNCRIP and PCBP2 in the EVs? Another important question would be the colocalization of these RBPs in the place where the miRNA selection is supposed to take place: in multivesicular bodies (MVB). Is there a colocalization of these RBPs with MVBs in the cell?

      We are thankful for the Reviewer’s suggestions. As reported in Supplementary Figure 2A SYNCRIP is present in both the intracellular end EV compartment and PCBP2 is detectable only in the intracellular one.

      (9) In Figure 4C, the authors state in the text that CELLmotif and hEXOmotif are present in extra-seed region; however, for miR-181d-5p and miR-122-3p this is not true as their CELLmotifs fall within the seed sequence.

      We apologize for our mistake. While for hEXO motif, it is confirmed that it is present in extraseed region on all analyzed miRNAs (as in ref. 7), the CELL motif on the cited miRNAs is overlapping with the seed sequence. We modified the text accordingly.

      (10) The authors need to describe how they calculate the EV/cell ratio in gene expression in some experiments (for instance, Figures 1H, 4D, etc). Did they use any housekeeping gene for EV RNA content, the same RNA load, or some other alternative method to normalize EV vs cell RNA content?

      We apologize for having not well clarified the calculation of EV/cell ratio in the cited figures. Data are shown as ratio of miRNAs expression in EVs with respect to the intracellular compartment. Expression of miRNAs in both compartments are normalized with respect to the spike-in sequence (cel-miR-39-3p), included in miRNAs sample (EVs and intracellular samples). This is also better clarified in the Materials and Methods section.

      (11) I would suggest that the authors speculate a bit in the discussion section on how the interaction between PCBP2 and SYNCRIP takes place. Do they contain any potential interacting domain? The binding of one to the miRNA would impose a topological interference on the binding of the other?

      We now speculate on the interaction between PCBP2 and SYNCRIP in the discussion section. Briefly, we described that PCBP2 interaction with several proteins have been reported (as in PMID 19881509 and 10772858), indicating the C-terminal domain including also the two KH1 and KH2 regions as the domains with the highest propensity interaction with proteins. Also in the case of SYNCRIP binding, the domains of interaction with proteins have been reported (as in PMID 10734137, 29483512 and 16765914) and we should hypothesize that these domains represent conserved regions responsible for its interaction also with PCBP2. Moreover, we also discussed that upon the interaction between SYNCRIP and the miRNAs a topological switch can occur, impacting the affinity of PCBP2 for the same miRNAs. 

      Reviewer #2 (Public review):

      Summary:

      The author of this manuscript aimed to uncover the mechanisms behind miRNA retention within cells. They identified PCBP2 as a crucial factor in this process, revealing a novel role for RNA-binding proteins. Additionally, the study discovered that SYNCRIP is essential for PCBP2's function, demonstrating the cooperative interaction between these two proteins. This research not only sheds light on the intricate dynamics of miRNA retention but also emphasizes the importance of protein interactions in regulating miRNA behavior within cells.

      We thank this Reviewer for having appreciated our characterization of the molecular dynamics governing miRNA export/cell-retention in hepatocytes.

      Strengths:

      This paper makes important progress in understanding how miRNAs are kept inside cells. It identifies PCBP2 as a key player in this process, showing a new role for proteins that bind RNA. The study also finds that SYNCRIP is needed for PCBP2 to work, highlighting how these proteins work together. These discoveries not only improve our knowledge of miRNA behavior but also suggest new ways to develop treatments by controlling miRNA locations to influence cell communication in diseases. The use of liver cell models and thorough experiments ensures the results are reliable and show their potential for RNA-based therapies

      Weaknesses:

      Despite its strengths, the manuscript has several notable limitations. The study's exclusive focus on hepatocytes limits the applicability of the findings to other cell types and physiological contexts. While the interaction between PCBP2 and SYNCRIP is wellcharacterized, the manuscript lacks detailed insights into the structural basis of this interaction and the dynamic regulation of their binding. The generalization of the findings to a broader spectrum of miRNAs and RNA-binding proteins (RBPs) remains underexplored, leaving gaps in understanding the full scope of miRNA compartmentalization.

      Furthermore, the therapeutic implications of these findings, though promising, are not directly connected to specific disease models or clinical scenarios, reducing their immediate translational impact. The manuscript would also benefit from a deeper discussion of potential upstream regulators of PCBP2 and SYNCRIP and the influence of cellular or environmental factors on their activity. Additionally, it is important to note that SYNCRIP has already been recognized as a major regulator of miRNA loading in extracellular vesicles (EVs). However, the purity of EVs is a concern, as the author only performed crude extraction methods without further purification using an iodixanol density gradient. The study also lacks in vivo evidence of PCBP2's role in exosomal miRNA export.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Improve figure quality in some cases (Figures 1A, 4B, Supplementary Figure 2).

      Figures have been improved accordingly. 

      Reviewer #2 (Recommendations for the authors):

      Questions for the Authors:

      (1) Why was hepatocyte-specific data prioritized, and how generalizable are the findings to other cell types?

      This work is based on our previous publication (Santangelo et al., Cell Reports), concerning the identification of the RBP SYNCRIP as an actor in the loading machinery of miRNAs in Extracellular Vesicles in hepatocytes. Since  both SYNCRIP and  PCBP2 are  expressed in different cell types  (Keerthikumar et al., 2016, PMID: 26434508; https://www.bgee.org/gene/ENSMUSG00000056851), is conceivable  that our  findings can be translated also in other cellular systems. To formally proof this hypothesis seems out of the scope of this manuscript. 

      (2) Can the authors elaborate on the functional impact of PCBP2-mediated miRNA retention? Which biological pathways are directly influenced by miRNAs retained by PCBP2?

      We appreciate the suggestion; in line with this comment, we performed a Gene Ontology enrichment analysis of the targets of the retained miRNAs. In order to be the most exhaustive, we included both validated and predicted targets, respectively obtained from TarBase v9.0 database and DIANA-microT web server. As reported in the new figure 4, panel E, and in the new supplementary figure 4, the analysis highlighted several biological pathways collectively influenced by the PCBP2-dependent cell-retained miRNAs, including establishment of organelle localization, regulation of cell cycle and lymphocyte differentiation. 

      (3) What criteria were used to select the miRNAs (e.g., miR-155-3p) for this study?

      miR-155-3p was selected as initial bait for RNA pulldown based on the reported presence of Core CELL motif in AML12 cell line (PMID: 34937935).

      (4) How do the results using recombinant PCBP2 in RNA pull-down assays compare with those using native PCBP2 in cellular extracts?

      The RNA-pull down with recombinant PCBP2 confirms the evidence obtained by RNA-pull downs with cellular extracts. Indeed, PCBP2 interacts with miR-155-3p in the wild type form and this interaction is lost upon the mutation of the CELL motif. Moreover, this experiment highlights a direct and sequence specific interaction.  

      (5) How much protein was loaded for Western blot analysis?

      We’re sorry for not explaining the experimental procedure in depth. For protein expression analysis, as reported in supplementary figure 1 and 2, we loaded 30 µg of proteins. Half of the amount of the protein obtained upon either RNA pull-down or protein immunoprecipitation experiments performed using 2 mg of protein extract were analyzed. This information has been added to the methods section.

      Suggested experiments to strengthen the manuscript:

      (1) Purify EVs using an iodixanol density gradient to eliminate the possibility of soluble PCBP2 contamination.

      We appreciate this suggestion. In order to avoid the effect of PCBP2 contamination that represents a source of variability in the experiments, we evaluated its presence in the purified extracellular vesicles protein extracts. As reported in the new figure Supplementary 2A, PCBP2 is completely absent in EV extracts as assessed by Western Blot; thus, accordingly with MISEV guideline we followed the differential ultracentrifugation method for EV purification. 

      (2) Perform gain- and loss-of-function assays by overexpressing or silencing PCBP2 in various models to observe downstream changes in miRNA-dependent pathways.

      We chose to silence PCBP2 protein since its high expression in our cellular model. Overexpression of PCBP2 would probably have no other significant readout. We are aware that PCBP2 silencing would perturb miRNA biogenesis and in turn miRNA downstream pathway modulation. Indeed, its association with Dicer has been reported as propaedeutic to miRNA processing (Li, et al 2012, Cell metabolism). However, this aspect is out of the scope of the present manuscript, here we focus exclusively on PCBP2 role in the regulation of miRNA EV export. Moreover, to overcome the effects on miRNA processing we evaluated the expression level of each miRNA as ratio between the extracellular and intracellular compartment. 

      (3) Use a murine model with hepatocyte-specific PCBP2 knockout and track changes in EV miRNA content and their functional effects in target tissues.

      We took advantage of our murine cells silenced for PCBP2 and evaluated miRNA content.

      New functional assays (now included in the new figure 4F) with leukocytes obtained from C57BL/6J mice livers show a higher percentage of IFN-+ T cell, NK and myeloid cells upon shPCBP2 EVs treatment in comparison to the shCTR EVs; this suggests that PCBP2 silencing results into an EV-mediated modulation of the immune response.

      (4) Conduct co-culture experiments to assess EV-mediated intercellular communication between donor and recipient cells.

      We reasoned that co-culture experiments don’t limit the observed effect on EVs since the contribution of soluble factors can have a role on recipient cells. Conversely  the treatments with purified EVs, here performed,  allow the evaluation of the sole EV-mediated downstream effects.

      These experiments would provide insights into the PCBP2-SYNCRIP axis, broaden the applicability of the findings, and enhance their translational relevance.

    1. eLife Assessment

      The manuscript by Hawes et al. provides important findings on how striatal projection neurons regulate spontaneous locomotion speed in the context of implicit motivation and distinct contextual valence. Overall, the evidence for the findings is solid, although evidence for the claim that striatonigral projections from the matrix and patches have functionally opposing roles is incomplete. This work will be of broad interest to neuroscientists in the basal ganglia, movement control, and cognition fields.

    2. Reviewer #1 (Public review):

      Summary:

      This fundamental work employed multidisciplinary approaches and conducted rigorous experiments to study how a specific subset of neurons in the dorsal striatum (i.e., "patchy" striatal neurons) modulates locomotion speed depending on the valence of the naturalistic context.

      Strengths:

      The scientific findings are novel and original and significantly advance our understanding of how the striatal circuit regulates spontaneous movement in various contexts.

      Weaknesses:

      This is extensive research involving various circuit manipulation approaches. Some of these circuit manipulations are not physiological. A balanced discussion of the technical strengths and limitations of the present work would be helpful and beneficial to the field. Minor issues in data presentation were also noted.

    3. Reviewer #2 (Public review):

      Hawes et al. investigated the role of striatal neurons in the patch compartment of the dorsal striatum. Using Sepw1-Cre line, the authors combined a modified version of the light/dark transition box test that allows them to examine locomotor activity in different environmental valence with a variety of approaches, including cell-type-specific ablation, miniscope calcium imaging, fiber photometry, and opto-/chemogenetics. First, they found ablation of patchy striatal neurons resulted in an increase in movement vigor when mice stayed in a safe area or when they moved back from more anxiogenic to safe environments. The following miniscope imaging experiment revealed that a larger fraction of striatal patchy neurons was negatively correlated with movement speed, particularly in an anxiogenic area. Next, the authors investigated differential activity patterns of patchy neurons' axon terminals, focusing on those in GPe, GPi, and SNr, showing that the patchy axons in SNr reflect movement speed/vigor. Chemogenetic and optogenetic activation of these patchy striatal neurons suppressed the locomotor vigor, thus demonstrating their causal role in the modulation of locomotor vigor when exposed to valence differentials. Unlike the activation of striatal patches, such a suppressive effect on locomotion was absent when optogenetically activating matrix neurons by using the Calb1-Cre line, indicating distinctive roles in the control of locomotor vigor by striatal patch and matrix neurons. Together, they have concluded that nigrostriatal neurons within striatal patches negatively regulate movement vigor, dependent on behavioral contexts where motivational valence differs.

      In my view, this study will add to the important literature by demonstrating how patch (striosomal) neurons in the striatum control movement vigor. This study has applied multiple approaches to investigate their functionality in locomotor behavior, and the obtained data largely support their conclusions. Nevertheless I have some suggestions for improvements in the manuscript and figures regarding their data interpretation, accuracy, and efficacy of data presentation.

      (1) The authors found that the activation of the striatonigral pathway in the patch compartment suppresses locomotor speed, which contradicts with canonical roles of the direct pathway. It would be great if the authors could provide mechanistic explanations in the Discussion section. One possibility is that striatal D1R patch neurons directly inhibit dopaminergic cells that regulate movement vigor (Nadal et al., Sci. Rep., 2021; Okunomiya et al., J Neurosci., 2025). Providing plausible explanations will help readers infer possible physiological processes and give them ideas for future follow-up studies.

      (2) On page 14, Line 301, the authors stated that "Cre-dependent mCheery signals were colocalized with the patch marker (MOR1) in the dorsal striatum (Fig. 1B)". But I could not find any mCherry on that panel, so please modify it.

      (3) From data shown in Figure 1, I've got the impression that mice ablated with striatal patch neurons were generally hyperactive, but this is probably not the case, as two separate experiments using LLbox and DDbox showed no difference in locomotor vigor between control and ablated mice. For the sake of better interpretation, it may be good to add a statement in Lines 365-366 that these experiments suggest the absence of hyperactive locomotion in general by ablating these specific neurons.

      (4) In Line 536, where Figure 5A was cited, the author mentioned that they used inhibitory DREADDs (AAV-DIO-hM4Di-mCherrry), but I could not find associated data on Figure 5. Please cite Figure S3, accordingly.

      (5) Personally, the Figure panel labels of "Hi" and "ii" were confusing at first glance. It would be better to have alternatives.

      (6) There is a typo on Figure 4A: tdTomata → tdTomato

    4. Reviewer #3 (Public review):

      Hawes et al. combined behavioral, optical imaging, and activity manipulation techniques to investigate the role of striatal patch SPNs in locomotion regulation. Using Sepw1-Cre transgenic mice, they found that patch SPNs encode locomotion deceleration in a light-dark box procedure through optical imaging techniques. Moreover, genetic ablation of patch SPNs increased locomotion speed, while chemogenetic activation of these neurons decreased it. The authors concluded that a subtype of patch striatonigral neurons modulates locomotion speed based on external environmental cues. Below are some major concerns:

      The study concludes that patch striatonigral neurons regulate locomotion speed. However, unless I missed something, very little evidence is presented to support the idea that it is specifically striatonigral neurons, rather than striatopallidal neurons, that mediate these effects. In fact, the optogenetic experiments shown in Fig. 6 suggest otherwise. What about the behavioral effects of optogenetic stimulation of striatonigral versus striatopallidal neuron somas in Sepw1-Cre mice?

      In the abstract, the authors state that patch SPNs control speed without affecting valence. This claim seems to lack sufficient data to support it. Additionally, speed, velocity, and acceleration are very distinct qualities. It is necessary to clarify precisely what patch neurons encode and control in the current study.

      One of the major results relies on chemogenetic manipulation (Figure 5). It would be helpful to demonstrate through slice electrophysiology that hM3Dq and hM4Di indeed cause changes in the activity of dorsal striatal SPNs, as intended by the DREADD system. This would support both the positive (Gq) and negative (Gi) findings, where no effects on behavior were observed.

      Finally, could the behavioral effects observed in the current study, resulting from various manipulations of patch SPNs, be due to alterations in nigrostriatal dopamine release within the dorsal striatum?

    1. eLife Assessment

      This manuscript provides fundamental new insight into the mechanisms linking photoperiod, reproduction function, and feeding activity, using medaka, a genetic model that itself exhibits photoperiodic responses. As well as identifying key neuropeptide genes that are regulated by photoperiod and involved in regulating feeding activity, the authors establish a knockout line for agrp1 using CRISPR Cas9 - based approach, profiting from the extensive use and development on this methodology in medaka. The combination of the RNAseq and quantitative in situ hybridization analysis with the knockout results as well as the study of ovariectomized fish provides compelling evidence implicating agrp1 in feeding regulation in response to photoperiod and reproductive status.

    2. Reviewer #1 (Public review):

      Summary:

      The authors use the teleost medaka as an animal model to study the effect of seasonal changes in day-length on feeding behaviour and oocyte production. They report a careful analysis how day-length affects female medakas and a thorough molecular genetic analysis of genes potentially involved in this process. They show a detailed analysis of two genes and include a mutant analysis of one gene to support their conclusions

      Strengths:

      The authors pick their animal model well and exploit the possibilities to examine in this laboratory model the effect of a key environmental influence, namely the seasonal changes of day-length. The phenotypic changes are carefully analysed and well controlled. The mutational analysis of the agrp1 by a ko-mutant provides important evidence to support the conclusions. Thus this report exceeds previous findings on the function of agrp1 and npyb as regulators of food-intake and shows how in medaka these genes are involved in regulating the organismal response to an environmental change. It thus furthers our understanding on how animals react to key exogenous stimuli for adaptation.

      Weaknesses:

      The authors are too modest when it comes to underscoring the importance of their findings. Previous animal models used to study the effect of these neuropeptides on feeding behaviour have either lost or were most likely never sensitive to seasonal changes of day-length. Considering the key importance of this parameter on many aspects of plant and animal life it could be better emphasised that a suitable animal model is at hand that permits this.<br /> The molecular characterization of the agrp1 ko-mutant that the authors have generated lacks some details that would help to appreciate the validity of the mutant phenotype. Additional data would help in this respect.

      Comments on revisions:

      The authors dealt adequately with the comments and suggestions of this reviewer.

    3. Reviewer #2 (Public review):

      Summary:

      The authors investigated the mechanisms behind breeding season-dependent feeding behavior using medaka, a well-known photoperiodic species, as a model. Through a combination of molecular, cellular, and behavioral analyses, including tests with mutants, they concluded that AgRP1 plays a central role in feeding behavior, mediated by ovarian estrogenic signals.

      Strengths:

      This study offers valuable insights into the neuroendocrine mechanisms that govern breeding season-dependent feeding behavior in medaka. The multidisciplinary approach, which includes molecular and physiological analyses, enhances the scientific contribution of the research.

      Comments on revised version:

      My concerns from the first review have been addressed. The manuscript's key points are clearly presented, and the conclusions are readily comprehensible

    4. Reviewer #3 (Public review):

      Summary:

      Understanding the mechanisms whereby animals restrict the timing of their reproduction according to day length is a critical challenge given that many of the most relevant species for agriculture are strongly photoperiodic. However, the principal animal models capable of detailed genetic analysis do not respond to photoperiod so this has inevitably limited progress in this field. The fish model medaka occupies a uniquely powerful position since it's reproduction is strictly restricted to long days and it also offers a wide range of genetic tools for exploring, in depth, various molecular and cellular control mechanisms.

      For these reasons, this manuscript by Tagui and colleagues is particularly valuable. It uses the medaka to explore links bridging photoperiod, feeding behaviour and reproduction. The authors demonstrate that in female, but not male medaka, photoperiod-induced reproduction is associated with an increase in feeding, presumably explained by the high metabolic cost of producing eggs on a daily basis during the reproductive period. Using RNAseq analysis of the brain, they reveal that the expression of the neuropeptides agrp and npy that have been previously implicated in the regulation of feeding behaviour in mice, are upregulated in the medaka brain during exposure to long photoperiod conditions. Unlike the situation in mouse, these two neuropeptides are not coexpressed in medaka neurons and food deprivation in medaka led to increases in agrp but also a decrease in npy expression. Furthermore, the situation in fish may be more complicated than in mouse due to the presence of multiple gene paralogs for each neuropeptide. Exposure to long day conditions increases agrp1 expression in medaka as the result of increases in the number of neurons expressing this neuropeptide, while the increase in npyb levels results from increased levels of expression in the same population of cells. Using ovariectomized medaka and in situ hybridization assays, the authors reveal that the regulation of agrp1 involves estrogen acting via the estrogen receptor esr2a. Finally, a loss of agrp1 function mutant is generated where the female mutants fail to show the characteristic increase in feeding associated with long day enhanced reproduction as well as yielding reduced numbers of eggs during spawning.

      Strengths:

      This manuscript provides important foundational work for future investigations aiming to elucidate the coordination of photoperiod sensing, feeding activity and reproduction function. The authors have used a combination of approaches with a genetic model that is particularly well suited to studying photoperiodic dependent physiology and behaviour. The data are clear and the results are convincing and support the main conclusions drawn. The findings are relevant not only for understanding photopriodic responses but also provide more general insight into links between reproduction and feeding behaviour control.

      The manuscript has been further strengthened by the inclusion of additional information according to my advice: The analysis of ovariectomized female fish and juvenille fish has now been reported in terms of their feeding behaviour and so provide a complete view of the position of this feeding regulatory mechanism in the context of reproduction status. Furthermore, the discussion section has been expanded to speculate on the functional significance of linking feeding behaviour control with reproductive function. Modifications made in order to address technical concerns of the other 2 reviewers have also significantly strengthened the presentation of this work.

      Weaknesses:

      These have now been addressed in the revised version.

    5. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors use the teleost medaka as an animal model to study the effect of seasonal changes in day-length on feeding behaviour and oocyte production. They report a careful analysis of how day-length affects female medakas and a thorough molecular genetic analysis of genes potentially involved in this process. They show a detailed analysis of two genes and include a mutant analysis of one gene to support their conclusions

      Strengths:

      The authors pick their animal model well and exploit the possibilities to examine in this laboratory model the effect of a key environmental influence, namely the seasonal changes of day-length. The phenotypic changes are carefully analysed and well-controlled. The mutational analysis of the agrp1 by a ko-mutant provides important evidence to support the conclusions. Thus this report exceeds previous findings on the function of agrp1 and npyb as regulators of food-intake and shows how in medaka these genes are involved in regulating the organismal response to an environmental change. It thus furthers our understanding of how animals react to key exogenous stimuli for adaptation.

      Weaknesses:

      The authors are too modest when it comes to underscoring the importance of their findings. Previous animal models used to study the effect of these neuropeptides on feeding behaviour have either lost or were most likely never sensitive to seasonal changes of day length. Considering the key importance of this parameter on many aspects of plant and animal life it could be better emphasised that a suitable animal model is at hand that permits this. The molecular characterization of the agrp1 ko-mutant that the authors have generated lacks some details that would help to appreciate the validity of the mutant phenotype. Additional data would help in this respect.

      We would like to thank Reviewer #1 for the really constructive advice. In the revised manuscript, we provided more information on the molecular characterization of the agrp1 KO-mutant and to emphasize the importance of our present animal model that permits the analysis of neuropeptide effects on feeding behavior in response to seasonal changes of day length.

      Reviewer #2 (Public review):

      Summary:

      The authors investigated the mechanisms behind breeding season-dependent feeding behavior using medaka, a well-known photoperiodic species, as a model. Through a combination of molecular, cellular, and behavioral analyses, including tests with mutants, they concluded that AgRP1 plays a central role in feeding behavior, mediated by ovarian estrogenic signals.

      Strengths:

      This study offers valuable insights into the neuroendocrine mechanisms that govern breeding season-dependent feeding behavior in medaka. The multidisciplinary approach, which includes molecular and physiological analyses, enhances the scientific contribution of the research.

      Weaknesses:

      While medaka is an appropriate model for studying seasonal breeding, the results presented are insufficient to fully support the authors' conclusions.

      Specifically, methods and data analyses are incomplete in justifying the primary claims:<br /> - the procedure for the food intake assay is unclear;

      - the sample size is very small;

      - the statistical analysis is not always adequate.

      Additionally, the discussion fails to consider the possible role of other hormones that may be involved in the feeding mechanism.

      We would like to thank Reviewer #2 for the helpful comments. As the reviewer suggested, we revised the paragraph describing the procedure for the food intake assay to make it much easier for the readers to understand in the revised manuscript. In Figure 1-Supplementary figure 2, RNAseq was performed to search for the candidate neuropeptides, and that’s why the sample size was the minimum. On the other hand, each group in the other experiments consist of n ≥ 5 samples, which is usually accepted to be adequate sample size in various studies (cf. Kanda et al., Gen Comp Endocrinol., 2011, Spicer et al., Biol Reprod., 2017). As for the statistical analyses, we revised our manuscript so that the readers may be convinced with the validity of our statistical analyses.

      Reviewer #3 (Public review):

      Summary:

      Understanding the mechanisms whereby animals restrict the timing of their reproduction according to day length is a critical challenge given that many of the most relevant species for agriculture are strongly photoperiodic. However, the principal animal models capable of detailed genetic analysis do not respond to photoperiod so this has inevitably limited progress in this field. The fish model medaka occupies a uniquely powerful position since its reproduction is strictly restricted to long days and it also offers a wide range of genetic tools for exploring, in depth, various molecular and cellular control mechanisms.

      For these reasons, this manuscript by Tagui and colleagues is particularly valuable. It uses the medaka to explore links bridging photoperiod, feeding behaviour, and reproduction. The authors demonstrate that in female, but not male medaka, photoperiod-induced reproduction is associated with an increase in feeding, presumably explained by the high metabolic cost of producing eggs on a daily basis during the reproductive period. Using RNAseq analysis of the brain, they reveal that the expression of the neuropeptides agrp and npy that have been previously implicated in the regulation of feeding behaviour in mice are upregulated in the medaka brain during exposure to long photoperiod conditions. Unlike the situation in mice, these two neuropeptides are not co-expressed in medaka neurons, and food deprivation in medaka led to increases in agrp but also a decrease in npy expression. Furthermore, the situation in fish may be more complicated than in mice due to the presence of multiple gene paralogs for each neuropeptide. Exposure to long-day conditions increases agrp1 expression in medaka as the result of increases in the number of neurons expressing this neuropeptide, while the increase in npyb levels results from increased levels of expression in the same population of cells. Using ovariectomized medaka and in situ hybridization assays, the authors reveal that the regulation of agrp1 involves estrogen acting via the estrogen receptor esr2a. Finally, a loss of agrp1 function mutant is generated where the female mutants fail to show the characteristic increase in feeding associated with long-day enhanced reproduction as well as yielding reduced numbers of eggs during spawning.

      Strengths:

      This manuscript provides important foundational work for future investigations aiming to elucidate the coordination of photoperiod sensing, feeding activity, and reproduction function. The authors have used a combination of approaches with a genetic model that is particularly well suited to studying photoperiodic-dependent physiology and behaviour. The data are clear and the results are convincing and support the main conclusions drawn. The findings are relevant not only for understanding photopriodic responses but also provide more general insight into links between reproduction and feeding behaviour control.

      Weaknesses:

      Some experimental models used in this study, namely ovariectomized female fish and juvenile fish have not been analysed in terms of their feeding behaviour and so do not give a complete view of the position of this feeding regulatory mechanism in the context of reproduction status. Furthermore, the scope of the discussion section should be expanded to speculate on the functional significance of linking feeding behaviour control with reproductive function.

      We would like to thank Reviewer #3 for the insightful advice. We added several pertinent sentences describing the ovariectomized female fish and juvenile fish, and our revised manuscript will give more complete view of their feeding regulatory mechanism in the context of reproduction status. In addition, we revised the discussion section to incorporate the valuable suggestion of the Reviewer #3.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      General: the text could profit from a careful editing of errors, including adjusting singular and plural status of nouns and verbs: examples are line 107 noun, line 96 verb suitable text editing software is available to do this task

      Thank you for your suggestion. We thoroughly read the entire manuscript and corrected such errors in the revised manuscript.

      As medaka is a unique genetic vertebrate model to study seasonal effects, it would be interesting to know whether the authors found novel or rather unexpected genes with a differential expression between LD and SD. It is understandable that the authors focused on argrp1 and npyb, as these have already been well studied in mammalian models although not in this context. Novel insights with genes previously not implicated in feeding regulation could underscore the unique nature of medaka as a model.

      We appreciate your kind comments, which we found really encouraging to us. Since we focused on feeding-related peptides, we did not find any novel genes that have not been reported.

      ISH is unreliable as a methodology to quantify expression levels. Yet the authors use this to compare fed and starved females to compare expression levels of agrp1. They use a temporal staining comparison and compare 90-minute and 300-minute staining reactions. However, they do not explain why they use the 90-minute staining time point and why 300 minutes of staining is the "saturation point of staining". They should provide compelling data for their claim and the selection of time points or else refrain from using these (at best) semi-quantitative ISH and provide more detailed (using serial sections) data to quantify the number of expressing cells.

      Anyhow, the quantification of mRNA expression levels may not be that significant when trying to compare different states of gene function, as translational and post-translational steps can have large effects on gene function. This should be discussed adequately.

      Thank you very much for your comments. We conducted ISH by using medaka under LD or SD, not using those under fed or starved conditions. In addition, our previous study demonstrated that the slopes of the increase in the number of cells stained by ISH are also different if there is a difference in the expression level (Mitani et al., 2010). Although we do not have quantitative data of cell numbers, we confirmed that the number of cells expressing agrp1 was saturated around 300 mins in our preliminary experiments, and therefore we terminated the chemogenic reactions at 300 mins. Based on these, we compared the cell ratio of 90 min (beginning of coloring) /300 min (saturation). However, since this analysis may not be worth discussing in detail, we moved this part to the supplementary figure as the reviewer suggested.

      The molecular characterization of the agrp1 ko mutant is a bit thin.

      Line 221: "We obtained agrp1<sup>−/−</sup> medaka, which has lots of amino acid changes in functional site for AgRP1" is a bit vague as a description for the ko-mutation. It would be really helpful if the authors could provide a scheme showing the wt protein with the relevant functional sites alongside the presumptive mutant protein.

      How did the authors verify the molecular nature of their mutation? They should use suitable antibodies and western-blot analysis (maybe reagents from Shainer et al., 2019 work in medaka); in case this is not possible they could isolate & clone the mutant transcript and use in-vitro translation systems to show that the presumptive mutant protein can actually be translated from this transcript. Another strategy could be to use a second non-allelic and (hopefully) non-complementing mutation (ko1/ko2 heterozygots for example) to show that ko-mutation acts the way the authors presume. The authors mention agrp1 ko medaka lines (plural!) in line 520, thus they may have an additional ko allele at hand.

      Thank you very much for your comments. We explained the mutation site in Figure 6-Supplementary Figure 1 (A: DNA sequences and B: predicted amino acid sequence, of WT and mutants). In addition, we added immunohistochemistry data of WT and mutant using anti-AgRP antibody (Figure 6-Supplementary Figure 1C). While AgRP-immunoreactive signals were observed in WT, those were not in agrp1<sup>−/−</sup>. This result suggests that AgRP1 is not functional in agrp1<sup>−/−</sup>.

      Presumably, the authors analysed heterozygous agrp1<sup>+/−</sup> females and found they are as wt. If so the authors should say so.

      Yes, we analyzed food intake of agrp1<sup>+/−</sup>. We added a supplementary figure (Figure 6-Supplementary Figure 2) and a sentence in L. 233-234.

      How about agrp1<sup>−/−</sup> medaka males: do they show a discernible phenotype?

      We analyzed the phenotypes of agrp1<sup>−/−</sup> males but did not describe the results, since the present paper only focused on female-specific feeding behavior.

      agrp1<sup>−/−</sup> females show no significant sensitivity of food intake to day length (Figure 6C). Does their (reduced) oocyte production react to day length? With other words: how much of the seasonal sensitivity is left in agrp1<sup>−/−</sup> females. The authors suggest that E2 acts upstream of agrp1 and therefore some seasonality may still be left in agrp1<sup>−/−</sup> females.

      Although agrp1<sup>−/−</sup> female is suggested to display abnormal seasonality of food intake, agrp1<sup>−/−</sup> female in LD spawns and that in SD does not, indicating that seasonality of gonadal maturation still remains in agrp1<sup>−/−</sup> female.

      The authors show that fshb and lhb are downregulated in agrp1<sup>−/−</sup> females. Is this also the case in wt females at SD?

      Thank you very much for your comment. As described above, agrp1<sup>−/−</sup> can spawn, which indicates that mechanisms for the downregulation of gonadotropins in agrp1<sup>−/−</sup> may be different from that in SD female.

      Figure 1_Supplementary Figure 2: the trends are visible in B and C, however, there is quite some variance between LD1, 2, and 3; the same for SD 1, 2, and 3. Can the authors give an explanation for this?

      Since the data for LD1, 2, and 3 (SD1, 2, and 3) were obtained from different individual fish, the variance may be reasonable. We conducted expression analyses by using RNA-seq to find candidate genes that show larger differences than individual ones.

      Figure 7E: the ovaries are difficult to see and the size bar in the wt picture is missing.

      Thank you very much for your comments. We added a scale bar in the wt picture.

      509 ff: the authors do not describe what exactly the "sham operation" encompasses: were the females just anesthetised or was there an actual operation without removing the ovaries?

      The sham operation group was anesthetized, received an abdominal incision without removing the ovaries, and received skin suture by using a silk thread. We added this explanation in the Method section.

      519 ff: was the agrp1<sup>−/−</sup> ko induced in the d-rR strain to have the same genetic background as the wt fish?

      Exactly. As the reviewer pointed out, the genetic background of agrp1 -/- was the same as that of WT.

      Minor points (Text edits):

      Line 42: change "when" into "where".

      Line: 54 "under the fixed appropriate ambient temperature" change into "while keeping an appropriate temperature constant".

      Line 55: here it would be good to briefly explain what long-day and short-day is so that the reader has an idea about the changes required without having to scroll down to the M&M section. For example LD 14/10 light-dark cycle, SD 10/14 light-dark cycle.

      Line 88: change "measurement" into "measuring".

      Line 96 change eats -> eat.

      Line 107 change female -> females.

      We deeply appreciate the reviewer’s suggestions described above. We corrected them as the reviewer suggested (L. 42, L. 54, L. 55, L. 89, L. 96, L. 107).

      Line 144-145: the sentence "since hypothalamic npy control..." does not make sense. Please correct.

      Thank you very much for your suggestion. We corrected the sentence so that it makes sense (L. 145-146).

      Line 180 and 185: the term here should be "LD induced sexual activity" rather than maturity. Age is the main determinant of maturity whereas light (LD) determines activity, in other words SD females are sexually mature if they are post-puberty stage.

      Thank you very much for your suggestion. Since the sentence “LD-induced sexual maturity” made the reviewer confused, we corrected the sentence “substance(s) from LD-induced mature ovary” or “ovarian maturity”. Even though SD females are at post-puberty stage, their ovaries are immature and do not possess mature oocytes (L. 181).

      Line 222: the authors should include the relevant information about the females: presumably agrp1.

      In Line 226-228, we explained the phenotypes of agrp1 knockout and added information for AgRP1 protein in Figure 6-Supplementary figure 1C.

      Lines 449 ff: authors should state that the analysis was done in females, instead of just writing "medaka". This is also in line with the preceding paragraph of the M&M section.

      Thank you very much for your suggestions. We corrected the sentence as the reviewer suggested (L.469)

      Line 305: change like other mammals -> like in mammals.

      Thank you very much for your suggestion. We corrected the sentence as the reviewer suggested (L. 320)

      Reviewer #2 (Recommendations for the authors):

      (1) The procedure of the food intake assay is not clear.

      - Habituation Period: Medaka were placed into a white cup containing 100 mL of water and allowed to habituate for 5 minutes. However, is 5 minutes sufficient to reduce stress in the fish? A stressed fish does not exhibit the same feeding behavior as an unstressed one.

      Thank you for your comment. We confirmed that 5 minutes is enough for habituation in medaka, since medaka can swim freely in a few minutes after replacement from the tank and show normal feeding behavior.

      - Feeding Protocol: Medaka were fed with 200 μL aliquots of brine shrimp-containing water. This procedure was repeated multiple times. How many times was this feeding procedure repeated? Was it 3, 10, or 100 times?

      Although there was a small variation in each trial, we usually applied tubes about 5 times or so.

      - Brine Shrimp Counting: You collected 10 mL of the breeding water to count the number of uneaten brine shrimp. Can you confirm that sampling 10% of the total volume is representative? Were any tests conducted to validate this? Given that you developed an automated tool to count the brine shrimp, why didn't you count them in all 100 mL?

      The reason for collecting 10 mL is to collect the leftover shrimp as soon as possible. Ten mins after the start of the experiment, we quickly placed a magnetic bar to stir the breeding water so that the shrimp concentration will be constant. Then we collected 10 mL aliquot from the experimental cup by using a micro pipette. In preliminary trials, we applied shrimps, the amount of which is almost the same as that applied to WT medaka in LD, to a white cup containing 100 mL water, and we divided it into 10 mL and 90 mL aliquots and separately counted the number of shrimps in each aliquot. Here, we confirmed that the variance between the numbers calculated by counting the shrimps in 10 mL aliquot and the total volume of 100 mL falls within the range of the variance of total applied shrimp. Thus, our present counting method can be considered reasonable.

      - Brine Shrimp Aliquot Measurement: You mentioned counting the number of brine shrimp in the 200 μL solution three times before and after the experiments. What does this mean? Did you use this procedure to calculate the mean number of brine shrimp in each 200 μL aliquot?

      Thank you for your comment. As the reviewer commented, to calculate the mean number of brine shrimp in each 200 µL aliquot, we counted the number of brine shrimp in the 200 µL solution three times before and after the experiments.

      - How did you normalize the food intake data? This procedure is not detailed in the methods section.

      Thank you very much for pointing it out. We normalized food intake by subtracting the amount of shrimp by the average of those in LD or WT fish. This explanation was added in the Method section (L. 439).

      (2) Sample Size. Various tests were conducted with a low number of medaka (e.g., 2 brains for RNA-seq, 8 females for ovariectomy). Are these sample sizes sufficient to draw reliable conclusions?

      In Figure 1-Supplementary figure 2, RNAseq was performed to search for the candidate neuropeptides, and that’s why the sample size was the minimum; we pooled two brains as one sample and used three samples per group. On the other hand, each group in the other experiments consist of n ≥ 5 samples, which is usually accepted to be adequate sample size in various studies (cf. Kanda et al., Gen Comp Endocrinol., 2011, Spicer et al., Biol Reprod., 2017).

      (3) Statistical Analysis.

      - The authors used both parametric and non-parametric tests but did not specify how they assessed the normal distribution of the data. For example, if I understood correctly, a t-test was used to compare a small dataset (n=3). In such cases, a U-test would be more appropriate.

      Thank you for your comment. As for Figure 1 -Supplementary Figure 2C, we showed the graphs just to show you candidates. To avoid misunderstanding, we deleted statistical statements in that panel.

      - It is unclear why the Steel-Dwass test was used instead of the Kruskal-Wallis test for comparing agrp1 and npyb expressions in control, OVX, and E2-administered medaka.

      While the authors mentioned using non-parametric tests, they did not specify in which contexts or conditions they were applied.

      Thank you very much for your comment. Kruskal-Wallis test statistically shows whether or not there are differences among any of three groups. To perform multiple comparisons among the three groups, we used Steel-Dwass test.

      - The results section lacks details on the statistical tests used, including the specific test (e.g., Z, U, or W values) and degrees of freedom.

      Thank you for your comment. As the reviewer pointed out, we added such statements in all the figure legends containing statistics.

      (4) Previous studies have shown that photoperiod treatments alter the production of various hormones in medaka (e.g., Lucon-Xiccato et al., 2022; Shimmura et al., 2017), some of which, like growth hormone (GH), have been shown to influence feeding behavior (Canosa et al., 2007).

      In your RNA-seq analysis, did you observe any changes in the expression of genes involved in other hormone synthesis pathways, such as pituitary hormones (GH and TSH), leptin, or ghrelin (e.g., see Volkoff, 2016; Blanco, 2020; Bertolucci et al., 2019)?

      Including such evidence in the discussion would provide a broader perspective on the hormonal regulation of food intake in medaka.

      We appreciate your constructive comments. Unfortunately, since we performed RNA-seq using the whole brain after removal of the pituitary, we could not check such changes in the expression of pituitary hormone-related genes. As additional information about the feeding-related hormones, leptin did not show significant difference in our RNA-seq analysis, and we could not analyze ghrelin because ghrelin has not been annotated in medaka (NCBI and ensembl).

      Reviewer #3 (Recommendations for the authors):

      There are some parts of the study that need to be developed further in order to provide a more comprehensive analysis.

      (1) In the juvenile as well as ovariectomized female fish, the authors should confirm experimentally whether day length influences feeding activity.

      Thank you very much for your suggestion. We analyzed feeding behavior of juvenile (Figure 4-Supplementary Figure 1) and OVX female (Figure 5-Supplementary Figure 1). As shown in these figures, food intake in juvenile and OVX were not significantly different between LD and SD.

      (2) More discussion as to the relevance of increasing feeding activity to support reproductive functions such as sustained egg production would be valuable. One assumes the metabolic costs of producing eggs on a daily basis in this species would inevitably require increased food intake. Is this a reasonable prediction?

      We deeply appreciate your suggestion. We strongly agree with this argument, and we added such discussion in “Discussion” section (L. 406-408).

      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 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.

      We appreciate the editor’s suggestion. We added P-value in the main manuscript, where statistical analyses were performed. In addition, we described test statics in the figure legends. We did not use df values for the statistics used in the present analyses, and therefore did not describe it in the main text.

    1. eLife Assessment

      This valuable work formulates an individual-based model to understand the evolution of division of labor in vertebrates, in particular, to examine the role of indirect versus direct fitness benefits. The evidence supporting the main conclusions is incomplete at this stage, with key details of simulation assumptions not adequately described and exploration of alternative assumptions and parameter space lacking.

    2. Reviewer #1 (Public review):

      This paper presents a computational model of the evolution of two different kinds of helping ("work," presumably denoting provisioning, and defense tasks) in a model inspired by cooperatively breeding vertebrates. The helpers in this model are a mix of previous offspring of the breeder and floaters that might have joined the group, and can either transition between the tasks as they age or not. The two types of help have differential costs: "work" reduces "dominance value," (DV), a measure of competitiveness for breeding spots, which otherwise goes up linearly with age, but defense reduces survival probability. Both eventually might preclude the helper from becoming a breeder and reproducing. How much the helpers help, and which tasks (and whether they transition or not), as well as their propensity to disperse, are all evolving quantities. The authors consider three main scenarios: one where relatedness emerges from the model, but there is no benefit to living in groups, one where there is no relatedness, but living in larger groups gives a survival benefit (group augmentation, GA), and one where both effects operate. The main claim is that evolving defensive help or division of labor requires the group augmentation; it doesn't evolve through kin selection alone in the authors' simulations.

      This is an interesting model, and there is much to like about the complexity that is built in. Individual-based simulations like this can be a valuable tool to explore the complex interaction of life history and social traits. Yet, models like this also have to take care of both being very clear on their construction and exploring how some of the ancillary but potentially consequential assumptions affect the results, including robust exploration of the parameter space. I think the current manuscript falls short in these areas, and therefore, I am not yet convinced of the results. Much of this is a matter of clearer and more complete writing: the Materials and Methods section in particular is incomplete or vague in some important junctions. However, there are also some issues with the assumptions that are described clearly.

      Below, I describe my main issues, mostly having to do with model features that are unclear, poorly motivated (as they stand), or potentially unrealistic or underexplored.

      One of the main issues I have is that there is almost no information on what happens to dispersers in the model. Line 369-67 states dispersers might join another group or remain as floaters, but gives no further information on how this is determined. Poring through the notation table also comes up empty as there is no apparent parameter affecting this consequential life history event. At some point, I convinced myself that dispersers remain floaters until they die or become breeders, but several points in the text contradict this directly (e.g., l 107). Clearly this is a hugely important model feature since it determines fitness cost and benefits of dispersal and group size (which also affects relatedness and/or fitness depending on the model). There just isn't enough information to understand this crucial component of the model, and without it, it is hard to make sense of the model output.

      Related to that, it seems to be implied (but never stated explicitly) that floaters do no work, and therefore their DV increases linearly with age (H_work in eq.2 is zero). That means any floaters that manage to stick around long enough would have higher success in competition for breeding spots relative to existing group members. How realistic is this? I think this might be driving the kin selection-only results that defense doesn't evolve without group augmentation (one of the two main ways). Any subordinates (which are mainly zero in the no GA, according to the SI tables; this assumes N=breeder+subordinates, but this isn't explicit anywhere) would be outcompeted by floaters after a short time (since they evolve high H and floaters don't), which in turn increases the benefit of dispersal, explaining why it is so high. Is this parameter regime reasonable? My understanding is that floaters often aren't usually high resource holding potential individuals (either b/c high RHP ones would get selected out of the floater population by establishing territories or b/c floating isn't typically a thriving strategy, given that many resources are tied to territories). In this case, the assumption seems to bias things towards the floaters and against subordinates to inherit territories. This should be explored either with a higher mortality rate for floaters and/or a lower DV increase, or both.

      When it comes to floaters replacing dead breeders, the authors say a bit more, but again, the actual equation for the scramble competition (which only appears as "scramble context" in the notation table) is not given. Is it simply proportional to R_i/\sum_j R_j ? Or is there some other function used? What are the actual numbers of floaters per breeding territory that emerge under different parameter values? These are all very important quantities that have to be described clearly.

      I also think the asexual reproduction with small mutations assumption is a fairly strong one that also seems to bias the model outcomes in a particular way. I appreciate that the authors actually measured relatedness within groups (though if most groups under KS have no subordinates, that relatedness becomes a bit moot), and also eliminated it with their ingenious swapping-out-subordinates procedure. The fact remains that unless they eliminate relatedness completely, average relatedness, by design, will be very high. (Again, this is also affected by how the fate of the dispersers is determined, but clearly there isn't a lot of joining happening, just judging from mean group sizes under KS only.) This is, of course, why there is so much helping evolving (even if it's not defensive) unless they completely cut out relatedness.

      Finally, the "need for division of labor" section is also unclear, and its construction also would seem to bias things against division of labor evolving. For starters, I don't understand the rationale for the convoluted way the authors create an incentive for division of labor. Why not implement something much simpler, like a law of minimum (i.e., the total effect of helping is whatever the help amount for the lowest value task is) or more intuitively: the fecundity is simply a function of "work" help (draw Poisson number of offspring) and survival of offspring (draw binomial from the fecundity) is a function of the "defense" help. As it is, even though the authors say they require division of labor, in fact, they only make a single type of help marginally less beneficial (basically by half) if it is done more than the other. That's a fairly weak selection for division of labor, and to me it seems hard to justify. I suspect either of the alternative assumptions above would actually impose enough selection to make division of labor evolve even without group augmentation.

      Overall, this is an interesting model, but the simulation is not adequately described or explored to have confidence in the main conclusions yet. Better exposition and more exploration of alternative assumptions and parameter space are needed.

    3. Reviewer #2 (Public review):

      Summary:

      This paper formulates an individual-based model to understand the evolution of division of labor in vertebrates. A main conclusion of the paper is that direct fitness benefits are the primary factor causing the evolution of vertebrate division of labor, rather than indirect fitness benefits.

      Strengths:

      The paper formulates an individual-based model that is inspired by vertebrate life history. The model incorporates numerous biologically realistic details, including the possibility to evolve age polytheism where individuals switch from work to defence tasks as they age or vice versa, as well as the possibility of comparing the action of group augmentation alone with that of kin selection alone.

      Weaknesses:

      The model makes assumptions that restrict the possibility that kin selection leads to the evolution of helping. In particular, the model assumes that in the absence of group augmentation, subordinates can only help breeders but cannot help non-breeders or increase the survival of breeders, whereas with group augmentation, subordinates can help both breeders and non-breeders and increase the survival of breeders. This is unrealistic as subordinates in real organisms can help other subordinates and increase the survival of non-breeders, even in the absence of group augmentation, for instance, with targeted helping to dominants or allies. This restriction artificially limits the ability of kin selection alone to lead to the evolution of helping, and potentially to division of labor. Hence, the conclusion that group augmentation is the primary driving factor driving vertebrate division of labor appears forced by the imposed restrictions on kin selection. The model used is also quite particular, and so the claimed generality across vertebrates is not warranted.

      I describe some suggestions for improving the paper below, more or less in the paper's order.

      First, the introduction goes to great lengths trying to convince the reader that this model is the first in this or another way, particularly in being only for vertebrates, as illustrated in the abstract where it is stated that "we lack a theoretical framework to explore the conditions under which division of labor is likely to evolve" (line 13). However, this is a risky and unnecessary motivation. There are many models of division of labor and some of them are likely to be abstract enough to apply to vertebrates even if they are not tailored to vertebrates, so the claims for being first are not only likely to be wrong but will put many readers in an antagonistic position right from the start, which will make it harder to communicate the results. Instead of claiming to be the first or that there is a lack of theoretical frameworks for vertebrate division of labor, I think it is enough and sufficiently interesting to say that the paper formulates an individual-based model motivated by the life history of vertebrates to understand the evolution of vertebrate division of labor. You could then describe the life history properties that the model incorporates (subordinates can become reproductive, low relatedness, age polyethism, etc.) without saying this has never been done or that it is exclusive to vertebrates; indeed, the paper states that these features do not occur in eusocial insects, which is surprising as some "primitively" eusocial insects show them. So, in short, I think the introduction should be extensively revised to avoid claims of being the first and to make it focused on the question being addressed and how it is addressed. I think this could be done in 2-3 paragraphs without the rather extensive review of the literature in the current introduction.

      Second, the description of the model and results should be clarified substantially. I will give specific suggestions later, but for now, I will just say that it is unclear what the figures show. First, it is unclear what the axes in Figure 2 show, particularly for the vertical one. According to the text in the figure axis, it presumably refers to T, but T is a function of age t, so it is unclear what is being plotted. The legend explaining the triangle and circle symbols is unintelligible (lines 227-230), so again it is unclear what is being plotted; part of the reason for this unintelligibility is that the procedure that presumably underlies it (section starting on line 493) is poorly explained and not understandable (I detail why below). Second, the axes in Figure 3 are similarly unclear. The text in the vertical axis in panel A suggests this is T, however, T is a function of t and gamma_t, so something else must be being done to plot this. Similarly, in panel B, the horizontal axis is presumably R, but R is a function of t and of the helping genotype, so again some explanation is lacking. In all figures, the symbol of what is being plotted should be included.

      Third, the conclusions sound stronger than the results are. A main conclusion of the paper is that "kin selection alone is unlikely to select for the evolution of defensive tasks and division of labor in vertebrates" (lines 194-195). This conclusion is drawn from the left column in Figure 2, where only kin selection is at play, and the helping that evolves only involves work rather than defense tasks. This conclusion follows because the model assumes that without group augmentation (i.e., xn=0, the kin selection scenario), subordinates can only help breeders to reproduce but cannot help breeders or other subordinates to survive, so the only form of help that evolves is the least costly, not the most beneficial as there is no difference in the benefits given among forms of helping. This assumption is unrealistic, particularly for vertebrates where subordinates can help other group members survive even in the absence of group augmentation (e.g., with targeted help to certain group members, because of dominance hierarchies where the helping would go to the breeder, or because of alliances where the helping would go to other subordinates). I go into further details below, but in short, the model forces a narrow scope for the kin selection scenario, and then the paper concludes that kin selection alone is unlikely to be of relevance for the evolution of vertebrate division of labor. This conclusion is particular to the model used, and it is misleading to suggest that this is a general feature of such a particular model.

      Overall, I think the paper should be revised extensively to clarify its aims, model, results, and scope of its conclusions.

    4. Author response:

      We will revise the statements of novelty in the introduction by more clearly emphasizing how our model addresses gaps in the existing literature. In addition, we will clarify the description of the dispersal process. Briefly, we use the same dispersal gene β to represent the likelihood an individual will either leave or join a group, thereby quantifying both dispersal and immigration using the same parameter. Specifically, individuals with higher β are more likely to remain as floaters (i.e., disperse from their natal group to become a breeder elsewhere), whereas those with lower β are either more likely to remain in their natal group as subordinates (i.e., queue in a group for the breeding position) or join another group if they dispersed. Immigrants that join a group as a subordinate help and queue for a breeding position, as does any natal subordinate born into the group. To follow the suggestion of the referee and more fully explore the impact of competition between subordinates born in the group and subordinate immigrants, we will explore extending our model to allow dispersers to leave their natal group and join another as subordinates, by incorporating a reaction norm based on their age or rank (D = 1 / (1 + exp (β<sub>t</sub> * t – β<sub>0</sub>)) . This approach will allow individuals to adjust also their dispersal strategy to their competitiveness and to avoid kin competition by remaining as a subordinate in another group.

      We apologize that there was some confusion with terminology. We use the term “disperser” to describe individuals that disperse from their natal group. Dispersers can assume one of three roles: (1) they can migrate to another group as "subordinates"; (2) they can join another group as "breeders" if they successfully outcompete other candidates; or (3) they can remain as "floaters" if they fail to join a group. "Floaters" are individuals who persist in a transient state without access to a breeding territory, waiting for opportunities to join a group in an established territory. Therefore, dispersers do not work when they are floaters, but they may later help if they immigrate to a group as a subordinate. Consequently, immigrant subordinates have no inherent competitive advantage over natal subordinates (as step 2.2. “Join a group” is followed by step 3. “Help”, which occurs before step 5. “Become a breeder”). Nevertheless, floaters can potentially outcompete subordinates of the same age if they attempt to breed without first queuing as a subordinate (step 5) when subordinates are engaged in work tasks. We believe that this assumption is realistic and constitutes part of the costs associated with work tasks. However, floaters are at a disadvantage for becoming a breeder because: (1) floaters incur higher mortality than individuals within groups (eq. 3); and (2) floaters may only attempt to become breeders in some breeding cycles (versus subordinate groups members, who are automatically candidates for an open breeding position in the group in each cycle). Therefore, due to their higher mortality, floaters are rarely older than individuals within groups, which heavily influences dominance value and competitiveness. Additionally, any competitive advantage that floaters might have over other subordinate group members is unlikely to drive the kin selection-only results because subordinates would preferably choose defense tasks instead of work tasks so as not to be at a competitive disadvantage compared to floaters.

      We note that reviewers also mention that floaters often aren't usually high resource holding potential (RHP) individuals and, therefore, our assumptions might be unrealistic. As we explain above, floaters are not inherently at a competitive advantage in our model. In any case, empirical work in a number of species has shown that dispersers are not necessarily those of lower RHP or of lower quality. In fact, according to the ecological constraints hypothesis, one might predict that high quality individuals are the ones that disperse because only individuals in good condition (e.g., larger body size, better energy reserves) can afford the costs associated with dispersal (Cote et al., 2022). By adding a reaction norm approach to explore the role of age or rank in the revised version, we can also determine whether higher or lower quality individuals are the ones dispersing. We will address the issues of terminology and clarity of the relative competitive advantage of floaters versus subordinates, and also include more information in the Supplementary Tables (e.g., the number of floaters). As a side note, the “scramble context” we mention was an additional implementation that we decided to remove from the final manuscript, but we forgot to remove from Table 1 before submission.

      The reviewers also raised a question about asexual reproduction and relatedness more generally. As we showed in the Supplementary Tables and the section on relatedness in the SI (“Kin selection and the evolution of division of labor"), high relatedness does not appear to explain our results. In evolutionary biology generally and in game theory specifically (with the exception of models on sexual selection or sex-specific traits), asexual reproduction is often modelled because it reduces unnecessary complexity. To further study the effect of relatedness on kin structures more closely resembling those of vertebrates, however, we will create an additional “relatedness structure level”, where we will shuffle half of the philopatric offspring using the same method used to remove relatedness completely. This approach will effectively reduce relatedness structure by half and overcome the concerns with our decision to model asexual reproduction.

      Briefly, we will elaborate on the concept of division of labor and the tasks that cooperative breeders perform. In nature, multiple tasks are often necessary to successfully rear offspring. For example, in many cooperatively breeding birds, the primary reasons that individuals fail to produce offspring are (1) starvation, which is mitigated by the feeding of offspring, and (2) nest depredation, which is countered by defensive behavior. Consequently, both types of tasks are necessary to successfully produce offspring, and focusing solely on one while neglecting the other is likely to result in lower reproductive success than if both tasks are performed by individuals within the group. We simplify this principle in the model by maximizing reproductive output when both tasks are carried out to a similar extent, allowing for some flexibility from the mean. In response to the reviewer suggestion about making fecundity a function of work tasks and offspring survival as a function of defensive tasks, these are actually equivalent in model terms, as it’s the same whether breeders produce three offspring and two die, or if they only produce one. This represents, of course, a simplification of the natural context, where breeding unsuccessfully is more costly (in terms of time and energy investment) than not breeding at all, but this is approach is typically used in models of this sort.

      The scope of this paper was to study division of labor in cooperatively breeding species with fertile workers, in which help is exclusively directed towards breeders to enhance offspring production (i.e., alloparental care). Our focus is in line with previous work in most other social animals, including eusocial insects and humans, which emphasizes how division of labor maximizes group productivity. Other forms of “general” help are not considered in the paper, and such forms of help are rarely considered in cooperatively breeding vertebrates or in the division of labor literature, as they do not result in task partitioning to enhance productivity.

      How do we model help? Help provided is an interaction between H (total effort) and T (proportion of total effort invested in each type of task). We will make this definition clearer in the revised manuscript. Thank you for pointing out an error in Eq. 1. This inequality was indeed written incorrectly in the paper (but is correct in the model code); it is dominance rank instead of age (see code in Individual.cpp lines 99-119). We will correct this mistake in the revision.

      There was also a question about bounded and unbounded helping costs. The difference in costs is inherent to the nature of the different task (work or defense): while survival is naturally bounded, with death as the lower bound, dominance costs are potentially unbounded, as they are influenced by dynamic social contexts and potential competitors. Therefore, we believe that the model’s cost structure is not too different to that in nature.

      Thank you for your comments about the parameter landscape. It is important to point out that variations in the mutation rate do not qualitatively affect our results, as this is something we explored in previous versions of the model (not shown). Briefly, we find that variations in the mutation rates only alter the time required to reach equilibrium. Increasing the step size of mutation diminishes the strength of selection by adding stochasticity and reducing the genetic correlation between offspring and their parents. Population size could, in theory, affect our results, as small populations are more prone to extinction. Since this was not something we planned to explore in the paper directly, we specifically chose a large population size, or better said, a large number of territories (i.e. 5000) that can potentially host a large population.

      During the exploratory phase of the model development, various parameters and values were also assessed. However, the manuscript only details the ranges of values and parameters where changes in the behaviors of interest were observed, enhancing clarity and conciseness. For instance, variation in y<sub>h</sub> (the cost of help on dominance when performing “work tasks”) led to behavioral changes similar to those caused by changes in x<sub>h</sub> (the cost of help in survival when performing “defensive tasks”), as both are proportional to each other. Specifically, since an increase in defense costs raises the proportion of work relative to defense tasks, while an increase in the costs of work task has the opposite effect, only results for the variation of x<sub>h</sub> were included in the manuscript to avoid redundancy. We will make this clearer in the revision.

      Finally, following the advice from the reviewers, we will add the symbols of the variables to the figure axes, and clarify whether the values shown represent a genetic or phenotypic trait. In Figure 2, the x-axis is H and the y-axis is T. In Figure 3A, the subindex t in x-axis is incorrect; it should be subindex R (reaction norm to dominance rank instead of age), the y-axis is T. In Figure 3B, the x-axis is R, and the y-axis is T. All values of T, H and R are phenotypic expressed values (see Table 1). For instance, T values are the phenotypic expressed values from the individuals in the population according to their genetic gamma values and their current dominance rank at a given time point.

      References

      Cote, J., Dahirel, M., Schtickzelle, N., Altermatt, F., Ansart, A., Blanchet, S., Chaine, A. S., De Laender, F., De Raedt, J., & Haegeman, B. (2022). Dispersal syndromes in challenging environments: A cross‐species experiment. Ecology Letters, 25(12), 2675–2687.

    1. eLife Assessment

      This study presents an important practical modification of the orthogonal hybridization chain reaction (HCR) technique, a promising yet underutilized method with broad potential for future applications across various fields. The authors advance this technique by integrating peptide ligation technology and nanobody-based antibody mimetics - cost-effective and scalable alternatives to conventional antibodies - into a DNA-immunoassay framework, which convincingly merges oligonucleotide-based detection with immunoassay methodologies.

    2. Reviewer #1 (Public review):

      Summary:

      This manuscript presents a practical modification of the orthogonal hybridization chain reaction (HCR) technique, a promising yet underutilized method with broad potential for future applications across various fields. The authors advance this technique by integrating peptide ligation technology and nanobody-based antibody mimetics - cost-effective and scalable alternatives to conventional antibodies - into a DNA-immunoassay framework that merges oligonucleotide-based detection with immunoassay methodologies. Notably, they demonstrate that this approach facilitates a modified ELISA platform capable of simultaneously quantifying multiple target protein expression levels within a single protein mixture sample.

      Strengths:

      The hybridization chain reaction (HCR) technique was initially developed to enable the simultaneous detection of multiple mRNA expression levels within the same tissue. This method has since evolved into immuno-HCR, which extends its application to protein detection by utilizing antibodies. A key requirement of immuno-HCR is the coupling of oligonucleotides to antibodies, a process that can be challenging due to the inherent difficulties in expressing and purifying conventional antibodies.

      In this study, the authors present an innovative approach that circumvents these limitations by employing nanobody-based antibody mimetics, which recognize antibodies, instead of directly coupling oligonucleotides to conventional antibodies. This strategy facilitates oligonucleotide conjugation - designed to target the initiator hairpin oligonucleotide of HCR -through peptide ligation and click chemistry.

      Weaknesses:

      The sandwich-format technique presented in this study, which employs a nanobody that recognizes primary IgG antibodies, may have limited scalability compared to existing methods that directly couple oligonucleotides to primary antibodies. This limitation arises because the C-region types of primary antibodies are relatively restricted, meaning that the use of nanobody-based detection may constrain the number of target proteins that can be analyzed simultaneously. In contrast, the conventional approach of directly conjugating oligonucleotides to primary antibodies allows for a broader range of protein targets to be analyzed in parallel.

      Additionally, in the context of HCR-based protein detection, the number of proteins that can be analyzed simultaneously is inherently constrained by fluorescence wavelength overlap in microscopy, which limits its multiplexing capability. By comparison, direct coupling of oligonucleotides to primary antibodies can facilitate the simultaneous measurement of a significantly greater number of protein targets than the sandwich-based nanobody approach in the barcode-ELISA/NGS-based technique.

    3. Author response:

      Reviewer #1 (Public review):

      Summary:

      This manuscript presents a practical modification of the orthogonal hybridization chain reaction (HCR) technique, a promising yet underutilized method with broad potential for future applications across various fields. The authors advance this technique by integrating peptide ligation technology and nanobody-based antibody mimetics - cost-effective and scalable alternatives to conventional antibodies - into a DNA-immunoassay framework that merges oligonucleotide-based detection with immunoassay methodologies. Notably, they demonstrate that this approach facilitates a modified ELISA platform capable of simultaneously quantifying multiple target protein expression levels within a single protein mixture sample.

      Strengths:

      The hybridization chain reaction (HCR) technique was initially developed to enable the simultaneous detection of multiple mRNA expression levels within the same tissue. This method has since evolved into immuno-HCR, which extends its application to protein detection by utilizing antibodies. A key requirement of immuno-HCR is the coupling of oligonucleotides to antibodies, a process that can be challenging due to the inherent difficulties in expressing and purifying conventional antibodies.

      In this study, the authors present an innovative approach that circumvents these limitations by employing nanobody-based antibody mimetics, which recognize antibodies, instead of directly coupling oligonucleotides to conventional antibodies. This strategy facilitates oligonucleotide conjugation - designed to target the initiator hairpin oligonucleotide of HCR -through peptide ligation and click chemistry.

      Weaknesses:

      The sandwich-format technique presented in this study, which employs a nanobody that recognizes primary IgG antibodies, may have limited scalability compared to existing methods that directly couple oligonucleotides to primary antibodies. This limitation arises because the C-region types of primary antibodies are relatively restricted, meaning that the use of nanobody-based detection may constrain the number of target proteins that can be analyzed simultaneously. In contrast, the conventional approach of directly conjugating oligonucleotides to primary antibodies allows for a broader range of protein targets to be analyzed in parallel.

      We would like to clarify that MaMBA was specifically designed to address and overcome the limitations imposed by relying on primary antibodies’ Fc types for multiplexing. MaMBA utilizes DNA oligo-conjugated nanobodies that selectively and monovalently bind to the Fc region of IgG. This key feature allows us to barcode primary IgGs targeting different antigens independently. These barcoded IgGs can then be pooled together after barcoding, effectively minimizing the potential for cross-reactivity or crossover. Therefore, IgGs barcoded using MaMBA are functionally equivalent to those barcoded via conventional direct conjugation approaches with respect to multiplexing capability.

      Additionally, in the context of HCR-based protein detection, the number of proteins that can be analyzed simultaneously is inherently constrained by fluorescence wavelength overlap in microscopy, which limits its multiplexing capability. By comparison, direct coupling of oligonucleotides to primary antibodies can facilitate the simultaneous measurement of a significantly greater number of protein targets than the sandwich-based nanobody approach in the barcode-ELISA/NGS-based technique.

      As we have responded above, MaMBA barcoding of primary IgGs that target various antigens can be conducted separately. Once barcoded, these IgGs can then be combined into a single pool. Therefore, for BLISA (i.e., the barcode-ELISA/NGS-based technique), IgGs barcoded through MaMBA offer the same multiplexing capability as those barcoded using traditional direct conjugation methods.

      In in situ protein imaging, spectral overlap can indeed limit the throughput of multiplexed HCR fluorescent imaging. There are two strategies to address this challenge. As demonstrated in this work with misHCR and misHCRn, removing the HCR amplifiers allows for multiplexed detection using a limited number of fluorescence wavelengths. This is achieved through sequential rounds of HCR amplification and imaging. Alternatively, recent computational approaches offer promising solutions for “one-shot” multiplexed imaging. These include combinatorial multiplexing (PMID: 40133518) and spectral unmixing (PMID: 35513404), which can be applied to misHCR to deconvolute overlapping spectra and increase multiplexing capacity in a single imaging acquisition.

    1. eLife Assessment

      This important study demonstrates that interferon beta stimulation induces WTAP transition from aggregates to liquid droplets, coordinating m6A modification of a subset of mRNAs that encode interferon-stimulated genes and restricting their expression. The evidence presented is solid, supported by microscopy, immunoprecipitations, m6A sequencing, and ChIP, to show that WTAP phosphorylation controls phase transition and its interaction with STAT1 and the methyltransferase complex.

    2. Reviewer #1 (Public review):

      Summary:

      This study puts forth the model that under IFN-B stimulation, liquid-phase WTAP coordinates with the transcription factor STAT1 to recruit MTC to the promoter region of interferon stimulated genes (ISGs), mediating the installation of m6A on newly synthesized ISG mRNAs. This model is supported by strong evidence that the phosphorylation state of WTAP, regulated by PPP4, is regulated by IFN-B stimulation, and that this results in interactions between WTAP, the m6A methyltransferase complex, and STAT1, a transcription factor that mediates activation of ISGs. This was demonstrated via a combination of microscopy, immunoprecipitations, m6A sequencing, and ChIP. These experiments converge on a set of experiments that nicely demonstrate that IFN-B stimulation increases the interaction between WTAP, METTL3, and STAT1, that this interaction is lost with knockdown of WTAP (even in the presence of IFN-B), and that this IFN-B stimulation also induces METTL3-ISG interactions.

      Strengths:

      The evidence for the IFN-B stimulated interaction between METTL3 and STAT1, mediated by WTAP, is quite strong. Removal of WTAP in this system seems to be sufficient to reduce these interactions and the concomitant m6A methylation of ISGs. The conclusion that the phosphorylation state of WTAP is important in this process is also quite well supported. The authors have now also provided substantial evidence that phase separation of WTAP upon interferon stimulation facilitates m6A-methylation of multiple interferon stimulated genes.

    3. Reviewer #2 (Public review):

      In this study, Cai and colleagues investigate how one component of the m6A methyltransferase complex, the WTAP protein, responds to IFNb stimulation. They find that viral infection or IFNb stimulation induces the transition of WTAP from aggregates to liquid droplets through dephosphorylation by PPP4. This process affects the m6A modification levels of ISG mRNAs and modulates their stability. In addition, the WTAP droplets interact with the transcription factor STAT1 to recruit the methyltransferase complex to ISG promoters and enhance m6A modification during transcription. The investigation dives into a previously unexplored area of how viral infection or IFNb stimulation affects m6A modification on ISGs. The observation that WTAP undergoes a phase transition is significant in our understanding of the mechanisms underlying m6A's function in immunity. However, there are still key gaps that should be addressed to fully accept the model presented.

      Major points:<br /> (1) More detailed analyses on the effects of WTAPsgRNA on the m6A modification of ISGs:<br /> a. A comprehensive summary of the ISGs, including the percentage of ISGs that are m6A-modified,<br /> b. The distribution of m6A modification across the ISGs, and<br /> c. A comparison of the m6A modification distribution in ISGs with non-ISGs.<br /> In addition, since the authors propose a novel mechanism where the interaction between phosphorylated STAT1 and WTAP direct the MTC to the promoter regions of ISGs to facilitate co-transcriptional m6A modification, it is critical to analyze whether the m6A modification distribution holds true in the data.

      (2) Since a key part of the model includes the cytosol-localized STAT1 protein undergoing phosphorylation to translocate to the nucleus to mediate gene expression, the authors should focus on the interaction between phosphorylated STAT1 and WTAP in Figure 4, rather than the unphosphorylated STAT1. Only phosphorylated STAT1 localizes to the nucleus, so the presence of pSTAT1 in the immunoprecipitate is critical for establishing a functional link between STAT1 activation and its interaction with WTAP.

      (3) The authors should include pSTAT1 ChIP-seq and WTAP ChIP-seq on IFNb-treated samples in Figure 5 to allow for a comprehensive and unbiased genomic analysis for comparing the overlaps of peaks from both ChIP-seq datasets. These results should further support for their hypothesis that WTAP interacts with pSTAT1 to enhance m6A modifications on ISGs.

      Minor points:<br /> (1) Since IFNb is primarily known for modulating biological processes through gene transcription, it would be informative if the authors discussed the mechanism of how IFNb would induce the interaction between WTAP and PPP4.

      (2) The authors should include mCherry alone controls in Figure 1D to demonstrate that mCherry does not contribute to the phase separation of WTAP. Does mCherry have or lack a PLD?

      (3) The authors should clarify the immunoprecipitation assays in the methods. For example, the labeling in Fig. 2A suggests that antibodies against WTAP and pan-p were used for two immunoprecipitations. Is that accurate?

      (4) The authors should include overall m6A modification levels quantified of GFPsgRNA and WTAPsgRNA cells, either by mass spectrometry (preferably) or dot blot.

      Comments on revisions:

      The authors thoroughly addressed the aforementioned points during the review process.

    4. Reviewer #3 (Public review):

      Summary:

      This study presents a valuable finding on the mechanism used by WTAP to modulate the IFN-β stimulation. It describes the phase transition of WTAP driven by IFN-β-induced dephosphorylation. The evidence supporting the claims of the authors is solid.

      Strength:

      The key finding is the revelation that WTAP undergoes phase separation during virus infection or IFN-β treatment. The authors conducted a series of precise experiments to uncover the mechanism behind WTAP phase separation and identified the regulatory role of 5 phosphorylation sites. They also succeeded in pinpointing the phosphatase involved.

    5. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study puts forth the model that under IFN-B stimulation, liquid-phase WTAP coordinates with the transcription factor STAT1 to recruit MTC to the promoter region of interferon-stimulated genes (ISGs), mediating the installation of m<sup>6</sup>A on newly synthesized ISG mRNAs. This model is supported by strong evidence that the phosphorylation state of WTAP, regulated by PPP4, is regulated by IFN-B stimulation, and that this results in interactions between WTAP, the m<sup>6</sup>A methyltransferase complex, and STAT1, a transcription factor that mediates activation of ISGs. This was demonstrated via a combination of microscopy, immunoprecipitations, m<sup>6</sup>A sequencing, and ChIP. These experiments converge on a set of experiments that nicely demonstrate that IFN-B stimulation increases the interaction between WTAP, METTL3, and STAT1, that this interaction is lost with the knockdown of WTAP (even in the presence of IFN-B), and that this IFN-B stimulation also induces METTL3-ISG interactions.

      Strengths:

      The evidence for the IFN-B stimulated interaction between METTL3 and STAT1, mediated by WTAP, is quite strong. Removal of WTAP in this system seems to be sufficient to reduce these interactions and the concomitant m<sup>6</sup>A methylation of ISGs. The conclusion that the phosphorylation state of WTAP is important in this process is also quite well supported.

      Weaknesses:

      The evidence that the above mechanism is fundamentally driven by different phase-separated pools of WTAP (regulated by its phosphorylation state) is weaker. These experiments rely relatively heavily on the treatment of cells with 1,6-hexanediol, which has been shown to have some off-target effects on phosphatases and kinases (PMID 33814344).

      Given that the model invoked in this study depends on the phosphorylation (or lack thereof) of WTAP, this is a particularly relevant concern.

      We are grateful for the reviewer’s positive comment and constructive feedback. 1,6-hexanediol (hex) was considered an inhibitor of hydrophobic interaction, thereby capable of dissolving protein phase separation condensates. Hex (5%-10% w/v) was still widely used to explore the phase separation characteristic and function on various protein, including some phosphorylated proteins such as pHSF1, or kinases such as NEMO1-3. Since hydrophobic interactions involved in various types of protein-protein interaction, the off-target effects of hex were inevitable. It has been reported that hex impaired RNA polymerase II CTD-specific phosphatase and kinase activity at 5% concentration4, which led to the reviewer’s concern. In response to this concern, we investigated the phosphorylation level of WTAP under hex concentration gradient treatment. Surprisingly, we found that both 2% and 5% hex maintained the PPP4c-mediated dephosphorylation level of WTAP but still led to the dissolution of WTAP LLPS condensates (Figure 5-figure supplement 1H; Author response image 1), indicating that hex dispersed WTAP phase separation in a phosphorylation-independent manner. Consistent with our findings, Ge et al. used 10% hex to dissolve WTAP phase separation condensates5. Additionally, we found the phosphorylation level of STAT1 was not affected by both 2% and 5% hex, revealing the off-target and impairment function of hex on kinases or phosphatases might not be universal (Figure 5-figure supplement 1H). Collectively, since the 5% hex we used did not influence the de-phosphorylation event of WTAP, function of WTAP LLPS mediating interaction between methylation complex and STAT1 revealed by our results was independent from its phosphorylation status.

      Author response image 1.

      mCherry-WTAP-rescued HeLa cells were treated with 10 ng/mL IFN-β together with or without 2% or 5% hex and 20 μg/mL digitonin for 1 hour or left untreated. Phase separation of mCherry-WTAP was observed through confocal microscopy. The number of WTAP condensates that diameter over 0.4 μm of n = 20 cells were counted through ImageJ and shown. Scale bars indicated 10 μm. All error bars, mean values ± SD, P-values were determined by unpaired two-tailed Student’s t-test of n = 20 cells in (B). For (A), similar results were obtained for three independent biological experiments.

      Related to this point, it is also interesting (and potentially concerning for the proposed model) that the initial region of WTAP that was predicted to be disordered is in fact not the region that the authors demonstrate is important for the different phase-separated states.

      A considerable number of proteins undergo phase separation via interactions between intrinsically disordered regions (IDRs). IDR contains more charged and polar amino acids to present multiple weakly interacting elements, while lacking hydrophobic amino acids to show flexible conformations6. In our study, we used PLAAC websites (http://plaac.wi.mit.edu/) to predict IDR domain of WTAP, and a fragment (234-249 amino acids) was predicted as prion-like domain (PLD). However, deletion of this fragment failed to abolish the phase separation properties of WTAP, which might be the main confusion to reviewers. To explain this issue, we checked the WTAP structure (within part of MTC complex) from protein data bank (https://www.rcsb.org/structure/7VF2) and found that the prediction of IDR has been renewed due to the update of different algorithm. IDR of WTAP expanded to 245-396 amino acids, encompassing the entire CTD region. Our results demonstrate that the CTD was critical for WTAP LLPS, as CTD deficiency significantly inhibited the formation of liquid condensates both in vitro and in cells. Also, phosphorylation sites on CTD were important for the phase transition of WTAP. These observations highlight the phosphorylation status on CTD region as a key driving force of phase separation, consistent with the established role of IDR in regulating LLPS. We have revised our description on WTAP IDR in our article following the reviewers’ suggestion.

      Taking all the data together, it is also not clear to me that one has to invoke phase separation in the proposed mechanism.

      In this article, we observed that WTAP underwent phase transition during virus infection and IFN-β treatment, and proposed a novel mechanism whereby post translational modification (PTM)-driven WTAP LLPS was required for the m<sup>6</sup>A modification of ISG mRNAs. To verify the hypothesis, we first demonstrated the relationship between PTM and phase separation of WTAP. We constructed WTAP 5ST-D and 5ST-A mutant to mimic WTAP phosphorylation and dephosphorylation status respectively, and figured out that dephosphorylated WTAP underwent LLPS. We also found that PPP4 was the main phosphatase to regulate WTAP dephosphorylation. To further investigation, we introduced the potent PPP4 inhibitor, fostriecin. Consistent with our findings in PPP4 deficient model, fostriecin treatment significantly inhibited the IFN-β-induced dephosphorylation of WTAP and disrupted its LLPS condensates, indicating that PPP4 was the key phosphatase recruited by IFN-β to regulate WTAP, confirming that PTM governs WTAP LLPS dynamics (Figure 2-figure supplement 1C and H). Furthermore, fostriecin-induced impairment of WTAP phosphorylation and phase separation correlated with reduced m<sup>6</sup>A modification level and elevated ISGs expression level (Figure 4C and Figure 4-figure supplement 1E). These findings together emphasized that dephosphorylation is required for WTAP LLPS.

      As for the function of WTAP LLPS, we assumed that WTAP might undergo LLPS to sequester STAT1 together with m<sup>6</sup>A methyltransferase complex (MTC) for mediating m<sup>6</sup>A deposition on ISG mRNAs co-transcriptionally under IFN-β stimulation. Given that hex dissolved WTAP LLPS condensates without affecting dephosphorylation status (Figure 5-figure supplement 1H; Author response image 1), various experiments we performed previously actually confirmed the critical role of WTAP LLPS during m<sup>6</sup>A modification (Figure 4A), as well as the mechanism that WTAP phase separation enhanced the interaction between MTC and STAT1 (Figure 5E-F). Subsequent to reviewer’s comments, more experiments were conducted for further validation. We found the WTAP liquid condensates formed by wild type (WT) WTAP or WTAP 5ST-A mutant (which mimics dephosphorylated-WTAP) could be dissembled by hex, which also led to the impairment of the interaction between STAT1, METTL3 and WTAP (Figure 5-figure supplement 1E). In addition, in vitro experiments demonstrated that hex treatment significantly disrupted the interaction between recombinant GFP-STAT1 and mCherry-WTAP which expressed in the E. coli system (Figure 5F and Figure 5-figure supplement 1G). Notably, this prokaryotic expression system lacks endogenous phosphorylation machinery, resulting in non-phosphorylated mCherry-WTAP. For further validation, we performed the interaction of WTAP WT or 5ST-A with the promoter regions of ISG as well as the m<sup>6</sup>A modification of ISG mRNAs were attenuated by WTAP LLPS dissolution (Figure 4E and Figure 6E). These findings together revealed that WTAP LLPS were the critical mediators of the STAT1-MTC interactions, ISG promoter regions binding and the co-transcription m<sup>6</sup>A modification.

      Collectively, our results demonstrated that IFN-β treatment recruited PPP4c to dephosphorylate WTAP, thereby driving the formation of WTAP liquid condensates which were essential for facilitating STAT1-MTC interaction and m<sup>6</sup>A deposition, subsequently mediated ISG expression. Since we revealed a strong association between PTM-regulated WTAP phase transition and its m<sup>6</sup>A modification function, WTAP LLPS was a novel and functionally distinct mechanism that must be reckoned with in this study.

      Author response image 2.

      Wild type (WT) WTAP or 5ST-A mutant-rescued WTAP<sup>sgRNA</sup> THP-1-derived macrophages are stimulated with or without with 10 ng/mL IFN-β together followed with 2% or 5% 1,6-hexanediol (hex) and 20 μg/mL digitonin for 1 hour or left untreated. antibody and imaged using confocal microscope. Scale bars indicated 10 μm.

      Reviewer #2 (Public review):

      In this study, Cai and colleagues investigate how one component of the m<sup>6</sup>A methyltransferase complex, the WTAP protein, responds to IFNb stimulation. They find that viral infection or IFNb stimulation induces the transition of WTAP from aggregates to liquid droplets through dephosphorylation by PPP4. This process affects the m<sup>6</sup>A modification levels of ISG mRNAs and modulates their stability. In addition, the WTAP droplets interact with the transcription factor STAT1 to recruit the methyltransferase complex to ISG promoters and enhance m<sup>6</sup>A modification during transcription. The investigation dives into a previously unexplored area of how viral infection or IFNb stimulation affects m<sup>6</sup>A modification on ISGs. The observation that WTAP undergoes a phase transition is significant in our understanding of the mechanisms underlying m<sup>6</sup>A's function in immunity. However, there are still key gaps that should be addressed to fully accept the model presented.

      Major points:

      (1) More detailed analyses on the effects of WTAP sgRNA on the m<sup>6</sup>A modification of ISGs:

      a. A comprehensive summary of the ISGs, including the percentage of ISGs that are m<sup>6</sup>A-modified. merip-isg percentage

      b. The distribution of m<sup>6</sup>A modification across the ISGs. Topology

      c. A comparison of the m<sup>6</sup>A modification distribution in ISGs with non-ISGs. Topology

      In addition, since the authors propose a novel mechanism where the interaction between phosphorylated STAT1 and WTAP directs the MTC to the promoter regions of ISGs to facilitate co-transcriptional m<sup>6</sup>A modification, it is critical to analyze whether the m<sup>6</sup>A modification distribution holds true in the data.

      We appreciate the reviewer’s summary of our manuscript and the constructive assessment. We have conducted the related analysis accordingly to present the m<sup>6</sup>A modification in ISGs in our model as reviewers suggested. Our results showed that about 64.29% of core ISGs were m<sup>6</sup>A modified under IFN-β stimulation (Figure 3-figure supplement 1B; Figure 3G), which was consistent with the similar percentage in previous studies[7,8]. The m<sup>6</sup>A distribution of the ISGs transcripts including IFIT1, IFIT2, OAS1 and OAS2 was validated (Figure 3-figure supplement 1H).

      Generally, m<sup>6</sup>A deposition preferentially located in the vicinity of stop codon, while m<sup>6</sup>A modification was highly dynamic under different cellular condition. However, we compared the topology of m<sup>6</sup>A deposition of ISGs with non-ISGs, and found that m<sup>6</sup>A modification of ISG mRNAs showed higher preference of coding sequences (CDS) localization compared to global m<sup>6</sup>A deposition (Figure 3H). Similarly, various researches uncovered the m<sup>6</sup>A deposition regulated by co-transcriptionally m<sup>6</sup>A modification preferred to locate in the CDS [9-11]. Since our results of m<sup>6</sup>A modification distribution of ISGs was consistent with the co-transcriptional m<sup>6</sup>A modification characteristics, we believed that our hypothesis and results were correlated and consistent.

      (2) Since a key part of the model includes the cytosol-localized STAT1 protein undergoing phosphorylation to translocate to the nucleus to mediate gene expression, the authors should focus on the interaction between phosphorylated STAT1 and WTAP in Figure 4, rather than the unphosphorylated STAT1. Only phosphorylated STAT1 localizes to the nucleus, so the presence of pSTAT1 in the immunoprecipitate is critical for establishing a functional link between STAT1 activation and its interaction with WTAP.

      Thank you for the constructive comments. As we showed in Figure 4, we found the enhanced interaction between phase-separated WTAP and the nuclear-translocated STAT1 which were phosphorylated under IFN-β stimulation, indicating the importance of phosphorylation of STAT1. We repeated the immunoprecipitation experiments to clarify the function of pSTAT1 in WTAP interaction. Our results showed that IFN-β stimulation induced the interaction of WTAP with both pSTAT1 and STAT1 (Figure 5-figure supplement 1C), indicating that most of the WTAP-associated STAT1 was phosphorylated. Taken together, our data proved that LLPS WTAP bound with nuclear-translocated pSTAT1 under IFN-β stimulation.

      (3) The authors should include pSTAT1 ChIP-seq and WTAP ChIP-seq on IFNb-treated samples in Figure 5 to allow for a comprehensive and unbiased genomic analysis for comparing the overlaps of peaks from both ChIP-seq datasets. These results should further support their hypothesis that WTAP interacts with pSTAT1 to enhance m<sup>6</sup>A modifications on ISGs.

      Thank you for raising this thoughtful comment. In this study, MeRIP-seq and RNA-seq along with immunoprecipitation and immunofluorescence experiments supported that phase transition of WTAP enhanced its interaction to pSTAT1, thus mediating ISGs m<sup>6</sup>A modification and expression by enhancing its interaction with nuclear-translocated pSTAT1 during virus infection and IFN-β stimulation. However, how WTAP-mediated m<sup>6</sup>A modification was related to STAT1-mediated transcription remained unclear. Several researches have revealed the recruitment of m<sup>6</sup>A methyltransferase complex (MTC) to transcription start sites (TSS) of coding genes and R-loop structure by interacting with transcriptional factors STAT5B, SMAD2/3, DNA helicase DDX21, indicating the engagement of MTC mediated m<sup>6</sup>A modification on nascent transcripts at the very beginning of transcription [11-13]. These researches inspired us that phase-separated WTAP could be recruited to the ISG promoter regions via interacting with nuclear-translocated pSTAT1. To validate this mechanism, we have conducted ChIP-qPCR experiments targeting STAT1 and WTAP, revealed that IFN-β induced the comparable recruitment dynamics of both STAT1 and WTAP to ISG promoter regions (Figure 6A-B). Notably, STAT1 deficiency significantly abolished the bindings between WTAP and ISG promoter regions (Figure 6C). These findings established nuclear-translocated STAT1-dependent recruitment of phase separated WTAP and ISG promoter region, substantiated our hypothesis within the current study. We totally agree that ChIP-seq data will be more supportive to explore the mechanism in depth. We will continuously focus on the whole genome chromatin distribution of WTAP and explore more functional effect of transcriptional factor-dependent WTAP-promoter regions interaction in the future.

      Minor points:

      (1) Since IFNb is primarily known for modulating biological processes through gene transcription, it would be informative if the authors discussed the mechanism of how IFNb would induce the interaction between WTAP and PPP4.

      Protein phosphatase 4 (PPP4) is a multi-subunit serine/threonine phosphatase complex that participates in diverse biologic process, including DDR, cell cycle progression, and apoptosis[14]. Several signaling pathway such as NF-κB and mTOR signaling, can be regulated by PPP4. Previous research showed that deficiency of PPP4 enhanced IFN-β downstream signaling and ISGs expression, which was consistent with our findings that knockdown of PPP4C impaired WTAP-mediated m<sup>6</sup>A modification, enhanced the ISGs expression[15,16]. Since there was no significant enhancement in PPP4 expression level during 0-3 hours of IFN-β stimulation in our results, we explored the PTM that may influence the protein-protein interaction, such as ubiquitination. Intriguingly, we found the ubiquitination level of PPP4 was enhanced after IFN-β stimulation, which may affect the interaction between PPP4 and WTAP (Author response image 3). Further investigation between PPP4 and WTAP will be conducted in our future study.

      Author response image 3.

      HEK 293T transfected with HA-ubiquitin (HA-Ub) and Flag-PPP4 were treated with 10 ng/mL IFN-β or left untreated. Whole cell lysate (WCL) was collected and immunoprecipitation (IP) experiment using anti-Flag antibody was performed, followed with immunoblot. Similar results were obtained for three independent biological experiments.

      (2) The authors should include mCherry alone controls in Figure 1D to demonstrate that mCherry does not contribute to the phase separation of WTAP. Does mCherry have or lack a PLD?

      According to the crystal structure of mCherry protein in protein structure database RCSB-PDB, mCherry protein presents as a β-barrel protein, with no IDRs or multivalent interaction domains including PLD, indicating that mCherry protein has no capability to undergo phase separation. This characteristic makes it a suitable protein to tag and trace the localization or expression levels of proteins, and a negative control for protein phase separation studies. As the reviewer suggested, we include mCherry alone controls in the revised version (Figure 1D).

      (3) The authors should clarify the immunoprecipitation assays in the methods. For example, the labeling in Figure 2A suggests that antibodies against WTAP and pan-p were used for two immunoprecipitations. Is that accurate?

      Due to the lack of phosphorylated-WTAP antibody, the detection of phosphorylation of WTAP was conducted by WTAP-antibody-mediated immunoprecipitation. We conducted immunoprecipitation to pull-down WTAP protein by WTAP antibody, then used antibody against phosphoserine/threonine/tyrosine (pan-p) to detect the phosphorylation level of WTAP. To avoid the misunderstanding, we have modified the description from pan-p to pWTAP (pan-p) in figures and revised the figure legends.

      (4) The authors should include overall m<sup>6</sup>A modification levels quantified of GFP<sup>sgRNA</sup> and WTAP<sup>sgRNA</sup> cells, either by mass spectrometry (preferably) or dot blot.

      We thank reviewer for raising these useful suggestions. As we showed in Figure 3F and J-K, the m<sup>6</sup>A modification event and degradation of ISG mRNAs were significantly depleted in WTAP<sup>sgRNA</sup> cell lines, indicating that function of WTAP was deficient. Thus, we used the WTAP<sup>sgRNA</sup> #2 cell line to perform most of our experiment. Furthermore, we also found 46.4% of global m<sup>6</sup>A modification was decreased in WTAP<sup>sgRNA</sup> THP-1 cells than that of control cells with or without IFN-β stimulation (Author response image 4), further validating that level of m<sup>6</sup>A modification was significantly affected in WTAP<sup>sgRNA</sup> cells. Taken together, our data confirmed that m<sup>6</sup>A methyltransferase activity was efficiently inhibited in our WTAP<sup>sgRNA</sup> cells.

      Author response image 4.

      Control (GFP<sup>sgRNA</sup>) and WTAP<sup>sgRNA</sup> #2 THP-1-derived macrophages were treated with 10 ng/mL IFN-β for 4 hours. Global m<sup>6</sup>A level was detected and quantified through ELISA assays. All error bars, mean values ± SEM, P-values were determined by two-way ANOVA test independent biological experiments.

      Reviewer #3 (Public review):

      Summary:

      This study presents a valuable finding on the mechanism used by WTAP to modulate the IFN-β stimulation. It describes the phase transition of WTAP driven by IFN-β-induced dephosphorylation. The evidence supporting the claims of the authors is solid, although major analysis and controls would strengthen the impact of the findings. Additionally, more attention to the figure design and to the text would help the reader to understand the major findings.

      Strength:

      The key finding is the revelation that WTAP undergoes phase separation during virus infection or IFN-β treatment. The authors conducted a series of precise experiments to uncover the mechanism behind WTAP phase separation and identified the regulatory role of 5 phosphorylation sites. They also succeeded in pinpointing the phosphatase involved.

      Weaknesses:

      However, as the authors acknowledge, it is already widely known in the field that IFN and viral infection regulate m<sup>6</sup>A mRNAs and ISGs. Therefore, a more detailed discussion could help the reader interpret the obtained findings in light of previous research.

      We are grateful for the positive comments and the unbiased advice by the reviewer. To interpret our findings in previous research, we have revised the manuscript carefully and added more detailed discussion on ISG mRNAs m<sup>6</sup>A modification during virus infection or IFN stimulation.

      It is well-known that protein concentration drives phase separation events. Similarly, previous studies and some of the figures presented by the authors show an increase in WTAP expression upon IFN treatment. The authors do not discuss the contribution of WTAP expression levels to the phase separation event observed upon IFN treatment. Similarly, METTL3 and METTL14, as well as other proteins of the MTC are upregulated upon IFN treatment. How does the MTC protein concentration contribute to the observed phase separation event?

      We thank reviewer for pointing out the importance of the concentration dependent phase transition. Previously, Ge et al. discovered that expression level of WTAP was up-regulated during LPS stimulation, thereby promoting WTAP phase separation ability and m<sup>6</sup>A modification, indicating that WTAP concentration indeed affects the phase separation event. In our article, we have generated the phase diagram with different concentration of recombinant mCherry-WTAP in vitro (Figure 1-figure supplement 1C). For in cells experiments, we constructed the TRE-mCherry-WTAP HeLa cells in which the expression of mCherry-WTAP was induced by doxycycline (Dox) in a dose-dependent manner (Author response image 5A). We detected the LLPS of mCherry-WTAP at different concentrations by increasing the doses of Dox, and found that WTAP automatically underwent LLPS only in an artificially high expression level (Author response image 5B). However, the cells we used to detect the WTAP phase separation in our article was mCherry-WTAP-rescued HeLa cells, in which mCherry-WTAP was introduced in WTAP<sup>sgRNA</sup> HeLa cells to stably express mCherry-WTAP. We had adjusted and verified the mCherry-WTAP expression level precisely to make the protein abundance similar to endogenous WTAP in wild type (WT) HeLa cells (Author response image 5C). We also repeated the IFN-β stimulation experiments and found no significant increase of WTAP protein level (Figure 5-figure supplement 1A). These findings indicated the phase separation of WTAP in our article was not artificially induced due to the extremely high protein expression level.

      MTC protein expression level was crucial for m<sup>6</sup>A modification during virus infection event. Rubio et al. and Winkler et al. revealed that WTAP, METTL3 and METTL14 were up-regulated after 24 hours of HCMV infection[8,17]. Recently, Ge et al. proposed that WTAP protein was degraded after 12 hours of VSV and HSV stimulation5,18. However, these studies only focused on the virus infection event, how the MTC protein expression change after direct IFN-β stimulation was still unclear. Our study investigated the transition change of WTAP under IFNβ stimulation in a short time, we detected the expression level of MTC proteins within 6 hours of IFN-β treatment, and found no significant enhancement of WTAP, METTL3 or METTL14 protein level and mRNA level (Figure 5-figure supplement 1B and Figure 5-figure supplement 1A;). Our in vitro experiments showed that introducing CFP-METTL3 protein have no significant influence on WTAP phase separation (Figure 4H). Additionally, we performed in cells experiments and found that increased expression of METTL3 had no effect on WTAP phase separation event (Author response image 5D). Taken together, WTAP phase separation can be promoted by dramatically increased concentration of WTAP both in vitro and in cells, but the phase separation of WTAP under IFN-β stimulation in our study was not related with the expression level of MTC proteins.

      Author response image 5.

      (A) Immunoblot analysis of the expression of mCherry-WTAP in TRE-mCherry-WTAP HeLa cells treated with different doses of doxycycline (Dox). Protein level of mCherry-WTAP was quantified and normalized to β-actin of n=3 independent biological experiments. Results were obtained for three independent biological experiments. (B) Phase separation diagram of mCherry-WTAP in TRE-mCherry-WTAP HeLa cells treated with different doses of Dox were observed through confocal microscopy. Representative images for three independent biological experiments were shown in b while number of WTAP condensates that diameter over 0.4 μm of n=80 cells were counted and shown as medium with interquartile range. Dotted white lines indicated the location of nucleus. Scale bars indicated 10 μm. (C) Immunoblot analysis of the expression of endogenous WTAP in wildtype (WT) HeLa cells and mCherry-WTAP-rescued WTAP<sup>sgRNA</sup> HeLa cells. (D) mCherry-WTAP-rescued HeLa cells were transfected with 0, 200 or 400 ng of Flag-METTL3, followed with 10 ng/mL IFN-β for 1 hour or left untreated (UT). Phase separation of mCherry-WTAP was observed through confocal microscopy. The number of WTAP condensates that diameter over 0.4 μm of n = 20 cells were counted through ImageJ and shown. Representative images of n=20 cells were shown. All error bars, mean values ± SD were determined by unpaired two-tailed Student’s t-test of n = 3 independent biological experiments in (A). For (A, C), similar results were obtained for three independent biological experiments.

      How is PP4 related to the IFN signaling cascade?

      Both reviewer #2 and reviewer #3 raised a similar point on the relationship between PPP4 and IFN signaling. In short, protein phosphatase 4 (PPP4) participates in diverse biologic process, including DDR, cell cycle progression and apoptosis14 and several signaling pathway. Previous research showed that deficiency of PPP4 enhanced IFN-β downstream signaling and ISGs expression, which was consistent with our findings that knockdown of PPP4C impaired WTAP-mediated m<sup>6</sup>A modification, and enhanced the ISGs expression[15,16]. Since there was no significant enhancement in PPP4C expression level during 0-3 hours of IFN-β stimulation in our results, we tried to explore the post-translation modification which may influence the protein-protein interaction, such as ubiquitination. Intriguingly, we found the ubiquitination level of PPP4 was enhanced after IFN-β stimulation, which may affect the interaction between PPP4 and WTAP (Author response image 4). Investigation between PPP4 and WTAP will be conducted in our further study (also see minor points 1 of reviewer#2).

      In general, it is very confusing to talk about WTAP KO as WTAPgRNA.

      As we describe above, all WTAP-deficient THP-1 cells were generated using the CRISPR-Cas9 system with WTAP-specific sgRNA, and used bulk cells instead of the monoclonal knockout cell for further experiments. Since monoclonal knockout cells were not obtained, we refer it as WTAP<sup>sgRNA</sup> THP-1 cells rather than WTAP-KO THP-1 cells. We confirmed that WTAP expression was efficiently knocked down in WTAP<sup>sgRNA</sup> THP-1 cells, and the m<sup>6</sup>A modification level was significantly impaired (Figure 3I, Figure 3-figure supplement 1A and Author response image 4), which was suitable for mechanism investigation.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Related to the points raised in 'weaknesses' above, if the authors want to claim that this mechanism is reliant on WTAP phase-separated states, additional controls should be done to demonstrate this. Based on the available data it seems that it is just as likely that the phosphorylation state of WTAP is mediating interactions with other factors and/or altering its subcellular localization, which may or may not be related to phase separation.

      We are grateful for the constructive suggestions. As we showed in , Figure 5-figure supplement 1H; Author response image 1 along with the explanation above, 5% hex dispersed the phase separation condensates of WTAP without affecting its phosphorylation status, proving the interaction between STAT1 and methylation complex impaired by hex was depended on WTAP LLPS but not its phosphorylation status (Figure 5E-H). To further confirmed the recruitment of WTAP LLPS on ISG promoter region, we performed the immunoprecipitation and ChIP-qPCR experiments of wild type (WT) WTAP, 5ST-D and 5ST-A rescued THP-1 cells. Our results uncovered the interaction between de-phosphorylated-mimic WTAP mutant and STAT1, and its binding ability with ISG promoter regions were depleted by hex without affecting its phosphorylation status (Author response image 2, Figure 5-figure supplement 1 F, Figure 6E). Taken together, we identified the de-phosphorylation event that regulated phase transition of WTAP during IFN-β stimulation, and proposed that LLPS of WTAP mediated by dephosphorylation was the key mechanism to bind with STAT1 and mediate the m<sup>6</sup>A modification on ISG mRNAs.

      Reviewer #2 (Recommendations for the authors):

      The author order is different for the main text and the supplementary file.

      Thank you for pointing out this mistake. We have corrected it in our revised version.

      Reviewer #3 (Recommendations for the authors):

      Signaling molecules? Do you mean RNA or protein post-translational modification?

      Thank you for pointing out this problem. In this sentence, we mean the post-translational modification of signaling proteins. We have corrected this mistake in our revised version.

      Line 145: Do you mean Figure 1C?

      We have corrected it in our revised version.

      Line 214: Are the cells KO for WTAP? Do you mean CRISPR KO? In general, it is easier to present WTAPgRNA as WTAPKO.

      Thank you for the constructive suggestion. As we explained above, in this project, all WTAP-deficient THP-1 cells were generated using the CRISPR-Cas9 system with WTAP-specific sgRNA, and used bulk cells instead of the monoclonal knockout cells. We confirmed that WTAP expression was efficiently knocked down in WTAP<sup>sgRNA</sup> THP-1 cells, and the m<sup>6</sup>A modification level was significantly impaired (Figure 3I, Figure3-figure supplement 1A and Author response image 4). Since monoclonal knockout cells were not obtained, we refer it as WTAP<sup>sgRNA</sup> THP-1 cells rather than WTAP-KO THP-1 cells.

      Line 221: WTAP KO has no effect on the expression level of transcription factors?

      Thank you for pointing out the uncritical expression. We have corrected this in our revised version.

      Figure 3C: I would suggest removing the tracks and showing the expression levels in TPMs.

      According to the reviewer’s suggestion, we have analyzed the results and showed the ISGs expression levels in fold change of TPMs (Figure 3D).

      Figure 4C: It seems that the IP efficiency from METTL3 is lower in WTAP KO cells. That may impact the author's conclusions.

      We have repeated the immunoprecipitation experiments of METTL3 and confirmed the immunoprecipitation (IP) efficiency from METTL3 had no difference between WTAP<sup>sgRNA</sup> cells and the control cells (Figure 5C).

      I would suggest performing an IP of WTAP with the 5StoA mutation to confirm the missing interaction with WTAP.

      According to the reviewer’s suggestion, we investigated the interaction between STAT1 and WTAP in WT cells and WTAP 5ST-A-rescued THP-1 cells. Our results showed that interaction between STAT1, METTL3 and WTAP were enhanced with WTAP 5ST-A mutation, which was depleted by hex treatment (Figure 5-figure supplement 1E). Thus, the interaction of WTAP WT or 5ST-A with the promoter regions of ISG were attenuated by WTAP LLPS dissolution (Figure 6E). Taken together, the interaction between STAT1 and MTC were relied on LLPS of WTAP.

      In the graphical abstract, it is confusing to represent WTAP as a line. All other proteins are presented as circles. It is easy to confuse WTAP protein with an RNA. Additionally, m<sup>6</sup>A is too big in size. It should be smaller than a protein.

      We thank the reviewer for raising this suggestion. We have modified the graphical abstract to avoid the confusion in our revised version (Figure 6F).

      References

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      (5) Ge, Y., Chen, R., Ling, T., Liu, B., Huang, J., Cheng, Y., Lin, Y., Chen, H., Xie, X., Xia, G., et al. (2024). Elevated WTAP promotes hyperinflammation by increasing m<sup>6</sup>A modification in inflammatory disease models. J Clin Invest 134. 10.1172/JCI177932.

      (6) Hou, S., Hu, J., Yu, Z., Li, D., Liu, C., and Zhang, Y. (2024). Machine learning predictor PSPire screens for phase-separating proteins lacking intrinsically disordered regions. Nat Commun 15, 2147. 10.1038/s41467-024-46445-y.

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    1. eLife Assessment

      TDP-43 mislocalization is a key feature of some neurodegenerative diseases, but cellular models are lacking. The authors endogenously-tagged TDP-43 with a C-terminal GFP tag in human iPSCs, followed by expression of an intrabody-NES that targeted GFP to the cytosol. They convincingly report physical mislocalization and functional depletion of TDP-43, as measured by microscopy and RNAseq. This method will be valuable to investigators studying the biological consequences of TDP-43 mislocalization and the methodology is in line with the current state-of-the-art.

    2. Reviewer #2 (Public review):

      Summary:

      TDP-43 mislocalization occurs in nearly all of ALS, roughly half of FTD, and as a co-pathology in roughly half of AD cases. Both gain of function and loss of function mechanisms associated with this mislocalization likely contribute to disease pathogeneisis.

      Here, the authors describe a new method to induce TDP-43 mislocalization in cellular models. They endogenously-tagged TDP-43 with a C-terminal GFP tag in human iPSCs. They then expressed an intrabody - fused with a nuclear export signal (NES) - that targeted GFP to the cytosol. Expression of this intrabody-NES in human iPSC derived neurons induced nuclear depletion of homozygous TDP-43-GFP, caused its mislocalization to the cytosol, and at least in some cells appeared to cause cytosolic aggregates. This mislocalization was accompanied by induction of cryptic exons in well characterized transcripts known to be regulated by TDP-43, a hallmark of functional TDP-43 loss and consistent with pathological nuclear TDP-43 depletion. Interestingly, in heterozygous TDP-43-GFP neurons, expression of intrabody-NES appeared to also induce the mislocalization of untagged TDP-43 in roughly half of the neurons, suggesting that this system can also be used to study effects on untagged endogenous TDP-43 as well as TDP-43-GFP fusion protein.

      Strengths:

      A clearer understanding of how TDP-43 mislocalization alters cellular function, as well as pathways that mitigate clearance of TDP-43 aggregates, is critical. But modeling TDP-43 mislocalization in disease-relevant cellular systems has proven to be challenging. High levels of overexpression of TDP-43 lacking an NES can drive endogenous TDP-43 mislocalization, but such overexpression has direct and artificial consequences on certain cellular features (e.g. altered exon skipping) not seen in diseased patients. Toxic small molecules such as MG132 and arsenite can induce TDP-43 mislocalization, but co-induce myriad additional cellular dysfunctions unrelated to TDP-43 or ALS. TDP-43 binding oligonucleotides can cause cytosolic mislocalization as well. Each system has pros and cons, and additional ways to induce TDP-43 mislocalization would be useful for the field. The method described in this manuscript could provide researchers with a powerful way to study the combined biology of cytosolic TDP-43 mislocalization and nuclear TDP-43 depletion, with additional temporal control that is lacking in current method. Indeed, the author see some evidence of differences in RNA splicing caused by pure TDP-43 depletion versus their induced mislocalization model. Finally, their method may be especially useful in determining how TDP-43 aggregates are cleared by cells, potentially revealing new biological pathways that could be therapeutically targeted.

      Weaknesses:

      The method and supporting data have some limitations.

      • Tagging of TDP-43 with a bulky GFP tag may alter its normal physiological functions, for example, phase separation properties and functions within complex ribonucleoprotein complexes. The authors show that normal splicing function of GFP-TDP-43 is maintained, suggesting that physiology is largely preserved, but other functions and properties of TDP-43 that were not directly tested could be altered.

      • Potential differences in splicing and micro RNAs between TDP-43 knockdown and TDP-43 mislocalization are potentially interesting. However, different patterns of dysregulated RNA splicing can occur at different levels of TDP-knockdown and can differ in different batches of experiments, thus it is difficult to asses whether the changes observed in this paper are due to mislocalization per se, or rather just reflect differences in nuclear TDP-43 abundance or batch effects.

    3. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      Nuclear depletion and cytoplasmic mislocalization/aggregation of the DNA and RNA binding protein TDP-43 are pathological hallmarks of multiple neurodegenerative diseases. Prior work has demonstrated that depletion of TDP-43 from the nucleus leads to alterations in transcription and splicing. Conversely, cytoplasmic mislocalization/aggregation can contribute to toxicity by impairing mRNA transport and translation as well as miRNA dysregulation. However, to date, models of TDP-43 proteinopathy rely on artificial knockdown- or overexpression-based systems to evaluate either nuclear loss or cytoplasmic gain of function events independently. Few model systems authentically reproduce both nuclear depletion and cytoplasmic miscloalization/aggregation events. In this manuscript, the authors generate novel iPSC-based reagents to manipulate the localization of endogenous TDP-43. This is a valuable resource for the field to study pathological consequences of TDP-43 proteinopathy in a more endogenous and authentic setting. However, in the current manuscript, there are a number of weaknesses that should be addressed to further validate the ability of this model to replicate human disease pathology and demonstrate utility for future studies.

      Strengths:

      The primary strength of this paper is the development of a novel in vitro tool.

      Weaknesses:

      There are a number of weaknesses detailed below that should be addressed to thoroughly validate these new reagents as more authentic models of TDP-43 proteinopathy and demonstrate their utility for future investigations.

      (1) The authors should include images of their engineered TDP-43-GFP iPSC line to demonstrate TDP-43 localization without the addition of any nanobodies (perhaps immediately prior to addition of nanobodies). Additionally, it is unclear whether simply adding a GFP tag to endogenous TDP-43 impact its normal function (nuclear-cytoplasmic shuttling, regulation of transcription and splicing, mRNA transport etc).

      We have included images of the untransduced day 20 MNs derived from the engineered TDP43-GFP iPSC lines and the unedited line (Supplementary Fig. 1B).

      We acknowledge the reviewer’s concern about the potential impact of the GFP tag on TDP43's normal function. To address this, we have validated the functionality of TDP43 by assessing the inclusion of cryptic exons in highly sensitive targets such as UNC13A and STMN2, both of which are known to be directly regulated by TDP43.

      We compared MNs derived from the unedited parent line with the TDP43-GFP MNs prior to nanobody addition. As measured by qPCR, cryptic exon inclusion in UNC13A and STMN2 was not observed in the unedited or edited TDP43-GFP MNs (Supplementary Fig.1C), confirming that the tagging does not induce splicing defects by itself. The cryptic exon inclusion in UNC13A and STMN2 were only observed in TDP43-GFP MNs expressing the NES nanobody (Supplementary Fig. 2D). These findings were further supported by our next-generation sequencing data, which also showed that cryptic exon inclusion was specific to the TDP43 mislocalization condition (Supplementary Fig.3 and 4).

      Thus, we have strong evidence that the GFP-tagged TDP43 behaves similarly to the wild-type protein and does not interfere with its function in our model.

      (2) Can the authors explain why there is a significant discrepancy in time points selected for nanobody transduction and immunostaining or cell lysis throughout Figure 1 and 2? This makes interpretation and overall assessment of the model challenging.

      For the phenotypic data shown in Fig.1, we added the AAVs at day 18 or 20 and analyzed the cells at day 40. For the phosphorylated TDP43 western blot (revised Fig. 3D), cells were treated with doxycycline at day 20 to induce nanobody expression and samples were harvested at day 40. Thus, cells were harvested between days 20 or 22 after adding the nanobodies. The onset of transgene expression when using AAVs in neurons typically display slow kinetics. We observed TDP43 mislocalization in less than 50% of the neurons after 7 days post-transduction that peaked at 10-12 days after addition of the nanobodies, when more than 80% of the cells displayed TDP43 mislocalization. Hence, we do not believe that a two-day difference significantly alters the interpretation of the data.

      The decision to harvest neurons at day 30 for the qPCR data was taken to investigate whether the splicing changes seen at day 40 from the transcriptomics analysis can be detected well before the phenotypes observed at day 40.

      (3) The authors should further characterize their TDP-43 puncta. TDP-43 immunostaining is typically punctate so it is unclear if the puncta observed are physiologic or pathologic based on the analyses carried out in the current version of this manuscript. Additionally, do these puncta co-localize with stress granule markers or RNA transport granule markers? Are these puncta phosphorylated (which may be more reminiscent of end-stage pathologic observations in humans)?

      We have tried immunostaining neurons for phosphorylated TDP43. However, our immunostaining attempts were unsuccessful. Depending on the antibody, we either saw no signal (antibody from Cosmo Bio, TIP-PTD-M01A) or even the control neurons displayed detectable phosphorylation within the nucleus (antibody from Proteintech 22309-1-AP). Consequently, we performed western blot analysis using an antibody from Cosmo Bio, (TIP-PTD-M01A) that clearly shows hyperphosphorylation of TDP43 in whole cell lysates (Fig. 3D, E). Hence, we have referred to these structures as puncta and not aggregates (Page 4).

      To assess co-localization of the puncta with stress granules, we immunostained for the stress granule marker G3BP1. This was done in MNs that were treated with sodium arsenite (SA) or PBS as a control. In the PBS treated control MN cultures, TDP43 mislocalization alone did not induce stress granule formation. G3BP1+ stress granules were only observed following SA stress (0.5 mM, 60 minutes). Further, only a subset of TDP43 puncta overlapped with these stress granules (Supplementary Fig. 7) (Page 6).

      (4) The authors should include multiple time points in their evaluation of TDP-43 loss of function events and aggregation. Does loss of function get worse over time? Is there a time course by which RNA misprocessing events emerge or does everything happen all at once? Does aggregation get worse over time? Do these neurons die at any point as a result of TDP-43 proteinopathy?

      We agree that a time course to analyze TDP43 mislocalization and its consequences would be ideal. However, the mislocalization of TDP43 across neurons is not a coordinated process. At each given time instance, neurons display varying levels of TDP43 mislocalization. Answering the questions raised by the reviewer would require tracking individual neurons in real time in a controlled environment over weeks. Unfortunately, we currently do not have the hardware to run these experiments. However, we do observe increased levels of cleaved caspase 3 in MNs expressing the NES nanobody, indicating that these neurons indeed undergo apoptosis by day 40 (Fig.1).

      We have, however, analyzed changes in splicing using qPCR for 12 genes over a time course starting as early as 4 hours after inducing mislocalization. We detect time-dependent cryptic splicing events in all genes as early as 8 hours after doxycycline addition, coinciding with the appearance TDP43 mislocalization (Fig. 4A, B).

      (5) Can the authors please comment on whether or not their model is "tunable"? In real human disease, not every neuron displays complete nuclear depletion of TDP-43. Instead there is often a gradient of neurons with differing magnitudes of nuclear TDP-43 loss. Additionally, very few neurons (5-10%) harbor cytoplasmic TDP-43 aggregates at end-stage disease. These are all important considerations when developing a novel authentic and endogenous model of TDP-43 proteinopathy which the current manuscript fails to address.

      As shown in Fig .1, the neurons expressing the NES-nanobody display a wide range of mislocalization as assessed by the % of nuclear TDP43 present. By titrating the amount of AAVs added to the culture, the model can be tuned to achieve a wide gradient of TDP43 mislocalization.

      We calculated the size and percentage of neurons displaying TDP43 puncta. The size and the number of aggregates varies across the neurons that display TDP43 mislocalization. Around 50% of the neurons displayed small (1  um<sup>2</sup>) puncta while large puncta (> 5  um<sup>2</sup>) were observed in <10% of the cells, similar to observations in patient tissue (Fig. 1F).

      Reviewer #2 (Public Review):

      Summary:

      TDP-43 mislocalization occurs in nearly all of ALS, roughly half of FTD, and as a co-pathology in roughly half of AD cases. Both gain-of-function and loss-of-function mechanisms associated with this mislocalization likely contribute to disease pathogeneisis.

      Here, the authors describe a new method to induce TDP-43 mislocalization in cellular models. They endogenously tagged TDP-43 with a C-terminal GFP tag in human iPSCs. They then expressed an intrabody - fused with a nuclear export signal (NES) - that targeted GFP to the cytosol. Expression of this intrabody-NES in human iPSC-derived neurons induced nuclear depletion of homozygous TDP-43-GFP, caused its mislocalization to the cytosol, and at least in some cells appeared to cause cytosolic aggregates. This mislocalization was accompanied by induction of cryptic exons in well characterized transcripts known to be regulated by TDP-43, a hallmark of functional TDP-43 loss and consistent with pathological nuclear TDP-43 depletion. Interestingly, in heterozygous TDP-43-GFP neurons, expression of intrabody-NES appeared to also induce the mislocalization of untagged TDP-43 in roughly half of the neurons, suggesting that this system can also be used to study effects on untagged endogenous TDP-43 as well as TDP-43-GFP fusion protein.

      Strengths:

      A clearer understanding of how TDP-43 mislocalization alters cellular function, as well as pathways that mitigate clearance of TDP-43 aggregates, is critical. But modeling TDP-43 mislocalization in disease-relevant cellular systems has proven to be challenging. High levels of overexpression of TDP-43 lacking an NES can drive endogenous TDP-43 mislocalization, but such overexpression has direct and artificial consequences on certain cellular features (e.g. altered exon skipping) not seen in diseased patients. Toxic small molecules such as MG132 and arsenite can induce TDP-43 mislocalization, but co-induce myriad additional cellular dysfunctions unrelated to TDP-43 or ALS. TDP-43 binding oligonucleotides can cause cytosolic mislocalization as well. Each system has pros and cons, and additional ways to induce TDP-43 mislocalization would be useful for the field. The method described in this manuscript could provide researchers with a powerful way to study the combined biology of cytosolic TDP-43 mislocalization and nuclear TDP-43 depletion, with additional temporal control that is lacking in current method. Indeed, the authors see some evidence of differences in RNA splicing caused by pure TDP-43 depletion versus their induced mislocalization model. Finally, their method may be especially useful in determining how TDP-43 aggregates are cleared by cells, potentially revealing new biological pathways that could be therapeutically targeted.

      Weaknesses:

      The method and supporting data have limitations in its current form, outlined below, and in its current form the findings are rather preliminary.

      (1) Tagging of TDP-43 with a bulky GFP tag may alter its normal physiological functions, for example phase separation properties and functions within complex ribonucleoprotein complexes. In addition, alternative isoforms of TDP-43 (e.g. "short" TDP-43, would not be GFP tagged and therefore these species would not be directly manipulatable or visualizable with the tools currently employed in the manuscript.

      With reference to our answer above, we have confirmed using qPCR and RNA-seq analysis that adding a GFP tag to the C-terminus of TDP43 does not result in an appreciable loss of functionality. We do not observe any cryptic exon inclusion in STMN2 and UNC13A. Cryptic exon inclusion in these genes, especially STMN2, has been recognized as a very sensitive indicator of TDP43 loss of function (Supplementary Fig 1C, Supplementary 2D, Fig. 3, Fig.4)

      We acknowledge that truncated alternatively spliced versions of TDP43 will lose the GFP-tag and cannot be manipulated with our system. Since our GFP tag is positioned on the C-terminus, our system cannot manipulate these truncated fragments as the tag is lost in these isoforms. But these isoforms, if present, should be detectable using the Proteintech antibody against total TDP43, which recognizes N-terminal TDP43 epitopes. However, western blot analysis, even 20 days after inducing TDP43 mislocalization, showed no truncated fragments. This suggests that TDP43 mislocalization alone is insufficient to generate significant levels of truncated isoforms. We have added this section to the Limitations paragraph (page 9).

      (2) The data regarding potential mislocalization of endogenous TDP-43 in the heterozygous TDP-43-GFP lines is especially intriguing and important, yet very little characterization was done. Does untagged TDP-43 co-aggregate with the tagged TDP-43? Is localization of TDP-43 immunostaining the same as the GFP signal in these cells?

      The purpose of the heterozygous experiments was to see whether mislocalized TDP43 could potentially trap the untagged TDP43. If this was not the case, we would have seen a maximum of 50% of the TDP43 signal mislocalized to the cytoplasm. The fact that a sizeable proportion of cells had significantly higher levels of TDP43 loss from the nucleus, indicates that mislocalized TDP43 can indeed trap the untagged protein fraction. We used GFP immunostaining to identify the tagged TDP43 while an antibody against the endogenous TDP43 protein was used to detect total TDP43 levels. In the cells that show near complete loss of nuclear TDP43, the total TDP43 signal coincides with the GFP (tagged TDP43) signal. We are unable to distinguish the untagged fraction selectively as we do not have an antibody that can detect this directly.  

      But we agree with the reviewer that these observations need further detailed follow-up that we are unable to provide currently. Hence, we have removed this figure from the manuscript.

      (3) The experiments in which dox was used to induce the nanobody-NES, then dox withdrawn to study potential longer-lasting or self-perpetuating inductions of aggregation is potentially interesting. However, the nanobody was only measured at the RNA level. We know that protein half lives can be very long in neurons, and therefore residual nanobody could be present at these delayed time points. The key measurement to make would be at the protein level of the nanobody if any conclusions are be made from this experiment.

      The reviewer has highlighted an important point. To address this issue, we tagged the nanobodies with a V5 tag that allowed us to directly measure nanobody levels within cells. After Dox withdrawal, we indeed observed significant expression of the nanobody within cells even after two weeks of Dox withdrawal. Extending the time point to three weeks allowed complete loss of the nanobody in most neurons. However, in contrast to our observations at two weeks, this was accompanied by a reversal of TDP43 mislocalization in these neurons at three weeks (Fig. 5).

      Surprisingly, in less than 10% of the neurons, we observed >80% of the total TDP43 still mislocalized to the cytoplasm, despite nearly undetectable levels of the nanobody. Super-resolution microscopy further revealed persistent cytoplasmic TDP43 in these neurons that did not overlap with residual nanobody signal. This suggests that in these neurons, the nanobody was no longer required to maintain TDP43 mislocalization (Fig. 5, page 7)

      (4) Potential differences in splicing and microRNAs between TDP-43 knockdown and TDP-43 mislocalization are potentially interesting. However, different patterns of dysregulated RNA splicing can occur at different levels of TDP-knockdown, thus it is difficult to assess whether the changes observed in this paper are due to mislocalization per se, or rather just reflect differences in nuclear TDP-43 abundance.

      This a fair point. It is possible that microRNA dysregulation might require a greater loss of nuclear TDP43 and maybe more resilient to TDP43 loss as compared to splicing. We have acknowledged this in the discussion section (page 9).

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) It would be helpful to include nuclear vs cytoplasmic ratios of TDP-43 instead of simply "% nuclear TDP-43"

      We have used % nuclear TDP43 as these values have biologically meaningful upper and lower bounds, which makes it easier to compare across experiments. We found that using a ratio of nuclear vs cytoplasmic TDP43 intensities displayed higher variability and a wider range.

      We have re-labelled the y-axis as “% Nuclear TD43 / soma TDP43” to make our quantification clearer. The conversion from % nuclear TDP43 to N/C is straightforward. If the % nuclear TDP43 is X, then the N/C ratio can be calculated as X / (100-X). For example, a % nuclear TDP43 of 80% would amount to an N/C ratio of 80/20 = 4.

      (2) The axis descriptions in Figure 1D are very unclear. While this is described better in the figure legend, it would be beneficial to have a more descriptive y-axis title in the figure (which may mean increasing the number of graphs).

      Axis descriptions and figures changed as recommended.

      (3) In Figure 1, the time points at which iPSNs were transduced with nanobody and/or fixed for immunostaining is somewhat inconsistent across all panels. This hinders interpretation of the figure as a whole. The authors should use same transduction and immunostaining time points for consistency or demonstrate that the same phenotype is observed regardless of transduction and immunostaining day as long as the time in between (time of nano body expression) is consistent. Subsequently, in Figure 2, a different set of time points is used.

      Please see our response in the public comments above

      (4) In Figure 1, please show individual data points for each independent differentiation to demonstrate the level of reproducibility from batch to batch.

      Data points have been shown per replicate (Supplementary Fig. 2)

      We have refined our approach for phenotypic analysis to improve consistency across different clones. Previously, we set thresholds on % nuclear TDP43 to distinguish MNs with nuclear versus mislocalized TDP43. This was done by ranking all cells based on % nuclear TDP43 and applying quantile-based thresholds—designating the top 25% as control and the bottom 25% as mislocalized, ensuring equal number of cells per category. However, we observed significant variability in thresholds across clones. For instance, the E8 clone had thresholds of 96% and 29%, while the E5 clone had 93% and 40%.

      To address this, we reanalysed the data using a standardized three-bin approach:

      (1) Control: MNs expressing the control nanobody.

      (2) Low-Moderate Mislocalization: MNs expressing the NES nanobody with > 40% nuclear TDP43.

      (3) Severe Mislocalization: MNs expressing the NES nanobody with < 40% nuclear TDP43.

      This approach ensured a more reliable comparison of TDP43 mislocalization effects across experiments. The conclusions remain the same.

      (5) In Figure 2, please show individual data points.

      Data points for all the qPCR analyses in the paper have been included as a supplementary text file.

      (6) In Figure 3, please show individual data points.

      Data points for the western blot data have been included as a supplementary data file.

      All other comments are within the public review.

      Reviewer #2 (Recommendations For The Authors):

      (1) In general more robust quantification of many of the described phenotypes are necessary. In particular, no apparent quantification of cytosolic mislocalization was performed in Figure 1, or quantification of mislocalization of Figure 3F. It is unclear in the western blot in Fig 1G if TDP-43 signal were normalized to total protein, and of note it seems that expression of the intrabody-NES reduced total proteins in the western blots that were shown. No quantification or measurement of the insoluble material was done or shown.

      We have quantified cytosolic mislocalization of TDP43 (Fig. 1C). The y-axis indicates the total TDP43 signal observed in the nucleus as a percentage of the total signal observed in the soma (including the nucleus). This value has the advantage of ranging between 100% (perfectly nuclear) to 0% (complete nuclear loss). The boxplots indicate that expression of the NES-nanobody results in a range of cytosolic mislocalization with a median value around 40% of the TDP43 remaining in the nucleus.

      Western blot data in previous Fig. 1G was normalized to alpha-tubulin. We were unable to get a good signal for the insoluble fraction. From the alpha-tubulin alone, it cannot be concluded that NES-nanobody results in a decrease in total protein levels. In the revised western blot for phosphorylated TDP43 (Fig. 3D, E), we have quantified total and phosphorylated TDP43. Here, we observe a six-fold increase in the levels of phosphorylated TDP43 without a significant change in total TDP43 protein levels.

      To avoid potential mis-interpretation of our results, we have now removed the previous Fig. 1G.

      (2) Additional images of nearly all microscopy data at higher magnifications would be required to better evaluate TDP-43 localization. Ideally including images for each channel in addition to merged images, and especially for key figures such as Figure 1B, 3B, 3F.

      Better images have been provided.

      (3) No control images were shown for Figure 1F and 3F. It is unclear what the bright punctate spots of cytoplasmic TDP-43 GFP signal represent. Are these true aggregates? If so, additional characterization would be required before such conclusions can be made, beyond the relatively superficial western blot analysis that was done in Figure 1.

      Control images have now been provided (Figure 1E). As we mentioned above, immunostaining analysis to characterize whether the aggregates are phosphorylated failed to provide a clear signal. However, we have now confirmed that the mislocalized TDP43 is indeed hyper-phosphorylated (Figure 3D, E). We have acknowledged this in the main text, and have referred to these as puncta reminiscent of aggregates (Page 4, Page 6).

    1. eLife Assessment

      This paper reports on an important study that aims to move beyond current experimental approaches in speech production by (1) investigating speech in the context of a fully interactive task and (2) employing advanced methodology to record intracranial brain activity. Together these allow for examination of the unfolding temporal dynamics of brain-behaviour relationships during interactive speech. This approach and the analyses presented in support of the authors' claims pose convincing evidence.

    2. Reviewer #1 (Public review):

      Summary:

      This paper reports an intracranial SEEG study of speech coordination, where participants synchronize their speech output with a virtual partner that is designed to vary its synchronization behavior. This allows the authors to identify electrodes throughout the left hemisphere of the brain that have activity (both power and phase) that correlates with the degree of synchronization behavior. They find that high-frequency activity in secondary auditory cortex (superior temporal gyrus) is correlated to synchronization, in contrast to primary auditory regions. Furthermore, activity in inferior frontal gyrus shows a significant phase-amplitude coupling relationship that is interpreted as compensation for deviation from synchronized behavior with the virtual partner.

      Strengths:<br /> (1) The development of a virtual partner model trained for each individual participant, which can dynamically vary its synchronization to the participant's behavior in real time, is novel and exciting.<br /> (2) Understanding real-time temporal coordination for behaviors like speech is a critical and understudied area.<br /> (3) The use of SEEG provides the spatial and temporal resolution necessary to address the complex dynamics associated with the behavior.<br /> (4) The paper provides some results that suggest a role for regions like IFG and STG in the dynamic temporal coordination of behavior both within an individual speaker and across speakers performing a coordination task.

      Weaknesses:

      (1) The main weakness of the paper is that the results are presented in a largely descriptive and vague manner. For instance, while the interpretation about predictive coding and error correction is interesting, it is not clear how the experimental design or analyses specifically support such a model, or how they differentiate that model from the alternatives. It's possible that some greater specificity could be achieved by a more detailed examination of this rich dataset, for example by characterizing the specific phase relationships (e.g., positive vs negative lags) in areas that show correlations with synchronization behavior. However, as written, it is difficult to understand what these results tell us about how coordination behavior arises.<br /> (2) In the results section, there's a general lack of quantification. While some of the statistics reported in the figures are helpful, there are also claims that are stated without any statistical test. For example, in the paragraph starting on line 342, it is claimed that there is an inverse relationship between rho-value and frequency band, "possibly due to the reversed desynchronization/synchronization process in low and high frequency bands". Based on Figure 3, the first part of this statement appears to be true qualitatively, but is not quantified, and is therefore impossible to assess in relation to the second part of the claim. Similarly, the next paragraph on line 348 describes optimal clustering, but statistics of the clustering algorithm and silhouette metric are not provided. More importantly, it's not entirely clear what is being clustered - is the point to identify activity patterns that are similar within/across brain regions? Or to interpret the meaning of the specific patterns? If the latter, this is not explained or explored in the paper.<br /> (3) Given the design of the stimuli, it would be useful to know more about how coordination relates to specific speech units. The authors focus on the syllabic level, which is understandable. But as far as the results relate to speech planning (an explicit point in the paper), the claims could be strengthened by determining whether the coordination signal (whether error correction or otherwise) is specifically timed to e.g., the consonant vs the vowel. If the mechanism is a phase reset, does it tend to occur on one part of the syllable?<br /> (4) In the discussion the results are related to a previously described speech-induced suppression effect. However, it's not clear what the current results have to do with SIS, since the speaker's own voice is present and predictable from the forward model on every trial. Statements such as "Moreover, when the two speech signals come close enough in time, the patient possibly perceives them as its own voice" are highly speculative and apparently not supported by the data.<br /> (5) There are some seemingly arbitrary decisions made in the design and analysis that, while likely justified, need to be explained. For example, how were the cutoffs for moderate coupling vs phase-shifted coupling (k ~0.09) determined? This is noted as "rather weak" (line 212), but it's not clear where this comes from. Similarly, the ROI-based analyses are only done on regions "recorded in at least 7 patients" - how was this number chosen? How many electrodes total does this correspond to? Is there heterogeneity within each ROI?

      Comments on revisions:

      The authors have generally responded to the critiques from the first round of review, and have provided additional details that help readers to understand what was done.

      In my opinion, the paper still suffers from a lack of clarity about the interpretation, which is partly due to the fact that the results themselves are not straightforward. For example, the heterogeneity across individual electrodes that is obvious from Fig 3 makes it hard to justify the ROI-based approach. And even the electrode clustering, while more data-driven, does not substantially help the fact that the effects appear to be less spatially-organized than the authors may want to claim.

      I recognize the value of introducing this new mutual adaptation paradigm, which is the main strength of the paper. However, the conclusions that can be drawn from the data presented here seem incomplete at best.

    3. Reviewer #2 (Public review):

      Summary:

      This paper investigates the neural underpinnings of an interactive speech task requiring verbal coordination with another speaker. To achieve this, the authors recorded intracranial brain activity from the left (and to a lesser extent, the right) hemisphere in a group of drug-resistant epilepsy patients while they synchronised their speech with a 'virtual partner'. Crucially, the authors were able to manipulate the degree of success of this synchronisation by programming the virtual partner to either actively synchronise or desynchronise their speech with the participant, or else to not vary its speech in response to the participant (making the synchronisation task purely one-way). Using such a paradigm, the authors identified different brain regions that were either more sensitive to the speech of the virtual partner (primary auditory cortex), or more sensitive to the degree of verbal coordination (i.e. synchronisation success) with the virtual partner (left secondary auditory cortex and bilateral IFG). Such sensitivity was measured by (1) calculating the correlation between the index of verbal coordination and mean power within a range of frequency bands across trials, and (2) calculating the phase-amplitude coupling between the behavioural and brain signals within single trials (using the power of high-frequency neural activity only). Overall, the findings help to elucidate some of the brain areas involved in interactive speaking behaviours, particularly highlighting high-frequency activity of the bilateral IFG as a potential candidate supporting verbal coordination.

      Strengths:

      This study provides the field with a convincing demonstration of how to investigate speaking behaviours in more complex situations that share many features with real-world speaking contexts e.g. simultaneous engagement of speech perception and production processes, the presence of an interlocutor and the need for inter-speaker coordination. The findings thus go beyond previous work that has typically studied solo speech production in isolation, and represent a significant advance in our understanding of speech as a social and communicative behaviour. It is further an impressive feat to develop a paradigm in which the degree of cooperativity of the synchronisation partner can be so tightly controlled; in this way, this study combines the benefits of using pre-recorded stimuli (namely, the high degree of experimental control) with the benefits of using a live synchronisation partner (allowing the task to be truly two-way interactive, an important criticism of other work using pre-recorded stimuli). A further key strength of the study lies in its employment of stereotactic EEG to measure brain responses with both high temporal and spatial resolution, an ideal method for studying the unfolding relationship between neural processing and this dynamic coordination behaviour.

      Weaknesses:

      One limitation of the current study is the relatively sparse coverage of the right hemisphere by the implanted electrodes (91 electrodes in the right compared to 145 in the left). Of course, electrode location is solely clinically motivated, and so the authors did not have control over this. In a previous version of this article, the authors therefore chose not to include data from the right hemisphere in reported analyses. However, after highlighting previous literature suggesting that the right hemisphere likely has high relevance to verbal coordination behaviours such as those under investigation here, the authors have now added analyses of the right hemisphere data to the results. These confirm an involvement of the right hemisphere in this task, largely replicating left hemisphere results. Some hemispheric differences were found in responses within the STG; however, interpretation should be tempered by an awareness of the relatively sparse coverage of the right hemisphere meaning that some regions have very few electrodes, resulting in reduced statistical power.

    4. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:  

      Reviewer #1 (Public Review):

      Summary:

      This paper reports an intracranial SEEG study of speech coordination, where participants synchronize their speech output with a virtual partner that is designed to vary its synchronization behavior. This allows the authors to identify electrodes throughout the left hemisphere of the brain that have activity (both power and phase) that correlates with the degree of synchronization behavior. They find that high-frequency activity in the secondary auditory cortex (superior temporal gyrus) is correlated to synchronization, in contrast to primary auditory regions. Furthermore, activity in the inferior frontal gyrus shows a significant phase-amplitude coupling relationship that is interpreted as compensation for deviation from synchronized behavior with the virtual partner.

      Strengths:

      (1) The development of a virtual partner model trained for each individual participant, which can dynamically vary its synchronization to the participant's behavior in real-time, is novel and exciting.

      (2) Understanding real-time temporal coordination for behaviors like speech is a critical and understudied area.

      (3) The use of SEEG provides the spatial and temporal resolution necessary to address the complex dynamics associated with the behavior.

      (4) The paper provides some results that suggest a role for regions like IFG and STG in the dynamic temporal coordination of behavior both within an individual speaker and across speakers performing a coordination task.

      We thank the Reviewer for their positive comments on our manuscript.

      Weaknesses:

      (1) The main weakness of the paper is that the results are presented in a largely descriptive and vague manner. For instance, while the interpretation of predictive coding and error correction is interesting, it is not clear how the experimental design or analyses specifically support such a model, or how they differentiate that model from the alternatives. It's possible that some greater specificity could be achieved by a more detailed examination of this rich dataset, for example by characterizing the specific phase relationships (e.g., positive vs negative lags) in areas that show correlations with synchronization behavior. However, as written, it is difficult to understand what these results tell us about how coordination behavior arises.

      We understand the reviewer’s comment. It is true that this work, being the first in the field using real-time adapting synchronous speech and intracerebral neural data, is a descriptive work, that hopefully will pave the way for further studies. We have now added more statistical analyses (see point 2) to go beyond a descriptive approach and we have also rewritten the discussion to clarify how this work can possibly contribute to disentangle different models of language interaction. Most importantly we have also run new analyses taking into account the specific phase relationship, as suggested.

      We already had an analysis using instantaneous phase difference in the phase-amplitude coupling approach, that bridges phase of behaviour to neural responses (amplitude in the high-frequency range). However, this analysis, as the reviewer noted, does not distinguish between positive and negative lags, but rather uses the continuous fluctuations of coordinative behaviour. Following the reviewer’s suggestion, we have now run a new analysis estimating the average delay (between virtual partner speech and patient speech) in each trial, using a cross-correlation approach. This gives a distribution of delays across trials that can then be “binned” as positive or negative. We have thus rerun the phase-amplitude coupling analyses on positive and negative trials separately, to assess whether the phase amplitude relationship depends upon the anticipatory (negative lags) or compensatory (positive lags) behaviour. Our new analysis (now in the supplementary, see figure below) does not reveal significant differences between positive and negative lags. This lack of difference, although not easy to interpret, is nonetheless interesting because it seems to show that the IFG does not have a stronger coupling for anticipatory trials. Rather the IFG seems to be strongly involved in adjusting behaviour, minimizing the error, independently of whether this is early or late.

      We have updated the “Coupling behavioural and neurophysiological data” section in Materials and methods as follows:  

      “In the third approach, we assessed whether the phase-amplitude relationship (or coupling) depends upon the anticipatory (negative delays) or compensatory (positive delays) behaviour between the VO and the patients’ speech. We computed the average delay in each trial using a cross-correlation approach on speech signals (between patient and VP) with the MATLAB function xcorr. A median split (patient-specific ; average median split = 0ms, average sd = 24ms) was applied to conserve a sufficient amount of data, classifying trials below the median as “anticipatory behaviour” and trials above the median as “compensatory behaviour”. Then we conducted the phase-amplitude coupling analyses on positive and negative trials separately.”

      We also added a paragraph on this finding in the Discussion:

      “Our results highlight the involvement of the inferior frontal gyrus (IFG) bilaterally, in particular the BA44 region, in speech coordination. First, trials with a weak verbal coordination (VCI) are accompanied by more prominent high frequency activity (HFa, Fig.4; Fig.S4). Second, when considering the within-trial time-resolved dynamics, the phase-amplitude coupling (PAC) reveals a tight relation between the low frequency behavioural dynamics (phase) and the modulation of high-frequency neural activity (amplitude, Fig.5B ; Fig.S5). This relation is strongest when considering the phase adjustments rather than the phase of speech of the VP per se : larger deviations in verbal coordination are accompanied by increase in HFa. Additionally, we also tested for potential effects of different asynchronies (i.e., temporal delay) between the participant's speech and that of the virtual partner but found no significant differences (Fig.S6). While lack of delay-effect does not permit to conclude about the sensitivity of BA44 to absolute timing of the partner’s speech, its neural dynamics are linked to the ongoing process of resolving phase deviations and maintaining synchrony.”

      (2) In the results section, there's a general lack of quantification. While some of the statistics reported in the figures are helpful, there are also claims that are stated without any statistical test. For example, in the paragraph starting on line 342, it is claimed that there is an inverse relationship between rho-value and frequency band, "possibly due to the reversed desynchronization/synchronization process in low and high frequency bands". Based on Figure 3, the first part of this statement appears to be true qualitatively, but is not quantified, and is therefore impossible to assess in relation to the second part of the claim. Similarly, the next paragraph on line 348 describes optimal clustering, but statistics of the clustering algorithm and silhouette metric are not provided. More importantly, it's not entirely clear what is being clustered - is the point to identify activity patterns that are similar within/across brain regions? Or to interpret the meaning of the specific patterns? If the latter, this is not explained or explored in the paper.

      The reviewer is right. We have now added statistical analyses showing that:

      (1) the ratio between synchronization and desynchronization evolves across frequencies (as often reported in the literature).

      (2) the sign of rho values also evolves across frequencies.

      (3) the clustering does indeed differ when taking into account behaviour. We have also clarified the use of clustering and the reasoning behind it.

      We have updated the Materials and methods section as follows:

      “The statistical difference between spatial clustering in global effect and brain-behaviour correlation was estimated with linear model using the R function lm (stat package), post-hoc comparisons were corrected for multiple comparisons using the Tukey test (lsmeans R package ; Lenth, 2016). The statistical difference between clustering in global effect and behaviour correlation across the number of clusters was estimated using permutation tests (N=1000) by computing the silhouette score difference between the two conditions.” We have updated the Results section as follows:

      (1) “This modulation between synchronization and desynchronization across frequencies was significant (F(5) = 6.42, p < .001 ; estimated with linear model using the R function lm).”

      (2) “The first observation is a gradual transition in the direction of correlations as we move up frequency bands, from positive correlations at low frequencies to negative ones at high frequencies (F(5) = 2.68, p = .02). This effect, present in both hemispheres, mimics the reversed desynchronization/synchronization process in low and high frequency bands reported above.”

      (3) “Importantly, compared to the global activity (task vs rest, Fig 3A), the neural spatial profile of the behaviour-related activity (Fig 3B) is more clustered, in the left hemisphere. Indeed, silhouette scores are systematically higher for behaviour-related activity compared to global activity, indicating greater clustering consistency across frequency bands (t(106) = 7.79, p < .001, see Figure S3). Moreover, silhouette scores are maximal, in particular for HFa, for five clusters (p < .001), located in the IFG BA44, the IPL BA 40 and the STG BA 41/42 and BA22 (see Figure S3).”

      (3) Given the design of the stimuli, it would be useful to know more about how coordination relates to specific speech units. The authors focus on the syllabic level, which is understandable. But as far as the results relate to speech planning (an explicit point in the paper), the claims could be strengthened by determining whether the coordination signal (whether error correction or otherwise) is specifically timed to e.g., the consonant vs the vowel. If the mechanism is a phase reset, does it tend to occur on one part of the syllable?

      Thank you for this thoughtful feedback. We agree that the relationship between speech coordination and specific speech units, such as consonants versus vowels, is an intriguing question. However, in our study, both interlocutors (the participant and the virtual partner) are adapting their speech production in real-time. This interactive coordination makes it difficult to isolate neural signatures corresponding to precise segments like consonants or vowels, as the adjustments occur in a continuous and dynamic context.

      The VP's ability to adapt depends on its sensitivity to spectral cues, such as the transition from one phonetic element to another. This is likely influenced by the type of articulation, with certain transitions being more salient (e.g., between a stop consonant like "p" and a vowel like "a") and others being less distinct (e.g., between nasal consonants like "m" and a vowel). Thus, the VP’s spectral adaptation tends to occur at these transitions, which are more prominent in some cases than in others.

      For the participants, previous studies have shown a greater sensitivity during the production of stressed vowels (Oschkinat & Hoole, 2022; Li & Lancia, 2024), which may reflect a heightened attentional or motor adjustment to stressed syllables.

      Here, we did not specifically address the question of coordination at the level of individual linguistic units. Moreover, even if we attempted to focus on this level, it would be challenging to relate neural dynamics directly to specific speech segments. The question of how synchronization at the level of individual linguistic units might relate to neural data is complex. The lack of clear, unit-specific predictions makes it difficult to parse out distinct neural signatures tied to individual segments, particularly when both interlocutors are continuously adjusting their speech in relation to one another.

      Therefore, while we recognize the potential importance of examining synchronization at the level of individual phonetic elements, the design of our task and the nature of the coordination in this interactive context (realtime bidirection adaptation) led us to focus more broadly on the overall dynamics of speech synchronization at the syllabic level, rather than on specific linguistic units.

      We now state at the end of the Discussion section:

      “It is worth noting that the influence of specific speech units, such as consonants versus vowels, on speech coordination remains to be explored. In non-interactive contexts, participants show greater sensitivity during the production of stressed vowels, possibly reflecting heightened attentional or motor adjustments (Oschkinat & Hoole, 2022; Li & Lancia, 2024). In this study, the VP’s adaptation relies on sensitivity to spectral cues, particularly phonetic transitions, with some (e.g., formant transitions) being more salient than others. However, how these effects manifest in an interactive setting remains an open question, as both interlocutors continuously adjust their speech in real time. Future studies could investigate whether coordination signals, such as phase resets, preferentially align with specific parts of the syllable.” References cited:

      – Oschkinat, M., & Hoole, P. (2022). Reactive feedback control and adaptation to perturbed speech timing in stressed and unstressed syllables. Journal of Phonetics, 91, 101133.

      – Li, J., & Lancia, L. (2024). A multimodal approach to study the nature of coordinative patterns underlying speech rhythm. In Proc. Interspeech, 397-401.

      (4) In the discussion the results are related to a previously-described speech-induced suppression effect. However, it's not clear what the current results have to do with SIS, since the speaker's own voice is present and predictable from the forward model on every trial. Statements such as "Moreover, when the two speech signals come close enough in time, the patient possibly perceives them as its own voice" are highly speculative and apparently not supported by the data.

      We thank the reviewer for raising thoughtful concerns about our interpretation of the observed neural suppression as related to speaker-induced suppression (SIS). We agree that our study lacks a passive listening condition, which limits direct comparisons to the original SIS effect, traditionally defined as the suppression of neural responses to self-produced speech compared to externally-generated speech (Meekings & Scott, 2021).

      In response, we have reconsidered our terminology and interpretation. In the revised Discussion section, we refer to our findings as a "SIS-related phenomenon specific to the synchronous speech context". Unlike classic SIS paradigms, our interactive task involves simultaneous monitoring of self- and externally-generated speech, introducing additional attentional and coordinative demands.

      The revised Discussion also incorporates findings by Ozker et al. (2022, 2024), which link SIS and speech monitoring, suggesting that suppressing responses to self-generated speech facilitates error detection. We propose that the decrease in high-frequency activity (HFa) as verbal coordination increases reflects reduced error signals due to closer alignment between perceived and produced speech. Conversely, HFa increases with reduced coordination may signify greater prediction error.

      Additionally, we relate our findings to the "rubber voice" effect (Zheng et al., 2011; Lind et al., 2014; Franken et al., 2021), where temporally and phonetically congruent external speech can be perceived as self-generated. We speculate that this may occur in synchronous speech tasks when the participant's and VP's speech signals closely align. However, this interpretation remains speculative, as no subjective reports were collected to confirm this perception. Future studies could include participant questionnaires to validate this effect and relate subjective experience to neural measures of synchronization.

      Overall, our findings extend the study of SIS to dynamic, interactive contexts and contribute to understanding internal forward models of speech production in more naturalistic scenarios.

      We have now added these points to the discussion as follows:

      “The observed negative correlation between verbal coordination and high-frequency activity (HFa) in STG BA22 suggests a suppression of neural responses as the degree of behavioural synchrony increases. This result is reminiscent of findings on speaker-induced suppression (SIS), where neural activity in auditory cortex decreases during self-generated speech compared to externally-generated speech (Meekings & Scott, 2021; Niziolek et al., 2013). However, our paradigm differs from traditional SIS studies in two critical ways: (1) the speaker's own voice is always present and predictable from the forward model, and (2) no passive listening condition was included. Therefore, our findings cannot be directly equated with the original SIS effect.

      Instead, we propose that the suppression observed here reflects a SIS-related phenomenon specific to the synchronous speech context. Synchronous speech requires simultaneous monitoring of self- and externallygenerated speech, a task that is both attentionally demanding and coordinative. This aligns with evidence from Ozker et al. (2024, 2022), showing that the same neural populations in STG exhibit SIS and heightened responses to feedback perturbations. These findings suggest that SIS and speech monitoring are related processes, where suppressing responses to self-generated speech facilitates error detection. In our study, suppression of HFa as coordination increases may reflect reduced prediction errors due to closer alignment between perceived and produced speech signals. Conversely, increased HFa during poor coordination may signify greater mismatch, consistent with prediction error theories (Houde & Nagarajan, 2011; Friston et al., 2020). Furthermore, when self- and externally-generated speech signals are temporally and phonetically congruent, participants may perceive external speech as their own. This echoes the "rubber voice" effect, where external speech resembling self-produced feedback is perceived as self-generated (Zheng et al., 2011; Lind et al., 2014; Franken et al., 2021). While this interpretation remains speculative, future studies could incorporate subjective reports to investigate this phenomenon in more detail.” References cited:

      – Franken, M. K., Hartsuiker, R. J., Johansson, P., Hall, L., & Lind, A. (2021). Speaking With an Alien Voice: Flexible Sense of Agency During Vocal Production. Journal of Experimental Psychology-Human perception and performance, 47(4), 479-494. https://doi.org/10.1037/xhp0000799

      – Houde, J. F., & Nagarajan, S. S. (2011). Speech production as state feedback control. Frontiers in human neuroscience, 5, 82.

      – Lind, A., Hall, L., Breidegard, B., Balkenius, C., & Johansson, P. (2014). Speakers' acceptance of real-time speech exchange indicates that we use auditory feedback to specify the meaning of what we say. Psychological Science, 25(6), 1198-1205. https://doi.org/10.1177/0956797614529797

      – Meekings, S., & Scott, S. K. (2021). Error in the Superior Temporal Gyrus? A Systematic Review and Activation Likelihood Estimation Meta-Analysis of Speech Production Studies. Journal of Cognitive Neuroscience, 33(3), 422-444. https://doi.org/10.1162/jocn_a_01661

      – Niziolek C. A., Nagarajan S. S., Houde J. F (2013) What does motor efference copy represent? Evidence from speech production Journal of Neuroscience 33:16110–16116Ozker M., Doyle W., Devinsky O., Flinker A (2022) A cortical network processes auditory error signals during human speech production to maintain fluency PLoS Biology 20.

      – Ozker, M., Yu, L., Dugan, P., Doyle, W., Friedman, D., Devinsky, O., & Flinker, A. (2024). Speech-induced suppression and vocal feedback sensitivity in human cortex. eLife, 13, RP94198. https://doi.org/10.7554/eLife.94198

      – Zheng, Z. Z., MacDonald, E. N., Munhall, K. G., & Johnsrude, I. S. (2011). Perceiving a Stranger's Voice as Being One's Own: A 'Rubber Voice' Illusion? PLOS ONE, 6(4), e18655.

      (5) There are some seemingly arbitrary decisions made in the design and analysis that, while likely justified, need to be explained. For example, how were the cutoffs for moderate coupling vs phase-shifted coupling (k ~0.09) determined? This is noted as "rather weak" (line 212), but it's not clear where this comes from. Similarly, the ROI-based analyses are only done on regions "recorded in at least 7 patients" - how was this number chosen? How many electrodes total does this correspond to? Is there heterogeneity within each ROI?

      The reviewer is correct, we apologize for this missing information. We now specify that the coupling values were empirically determined on the basis of a pilot experiment in order to induce more or less synchronization, but keeping the phase-shifted coupling at a rather implicit level.  

      Concerning the definition of coupling as weak, one should consider that, in the Kuramoto model, the strength of coupling (k) is relative to the spread of the natural frequencies (Δω) in the system. In our study, the natural frequencies of syllables range approximately from 2 Hz to 10Hz, resulting in a frequency spread of Δω = 8 Hz. For coupling to strongly synchronize oscillators across such a wide range, k must be comparable to or exceed Δω. Thus, since k = 0.1 is far much smaller than Δω, it is therefore classified as weak coupling.

      We have now modified the Materials and methods section as follows:

      “More precisely, for a third of the trials the VP had a neutral behaviour (close to zero coupling: k = +/- 0.01). For a third it had a moderate coupling, meaning that the VP synchronised more to the participant speech (k = -0.09). And for the last third of the trials the VP had a moderate coupling but with a phase shift of pi/2, meaning that it moderately aimed to speak in between the participant syllables (k = + 0.09). The coupling values were empirically determined on the basis of a pilot experiment in order to induce more or less synchronization but keeping the phase-shifted coupling at a rather implicit level. In other terms, while participants knew that the VP would adapt, they did not necessarily know in which direction the coupling went.”

      Regarding the criterion of including regions recorded in at least 7 patients, our goal was to balance data completeness with statistical power. Given our total sample of 16 patients, this threshold ensures that each included region is represented in at least ~44% of the cohort, reducing the likelihood of spurious findings due to extremely small sample sizes. This choice also aligns with common neurophysiological analysis practices, where a minimum number of subjects (at least 2 in extreme cases) is required to achieve meaningful interindividual comparisons while avoiding excessive data exclusion. Additionally, this threshold maintains a reasonable tradeoff between maximizing patient inclusion and ensuring that statistical tests remain robust.

      We have now added more information in the Results section “Spectral profiles in the language network are nuanced by behaviour” on this point as follows:

      “To balance data completeness and statistical power, we included only brain regions recorded in at least 7 patients (~44% of the cohort) for the left hemisphere and at least 5 patients for the right hemisphere (~31% of the cohort), ensuring sufficient representation while minimizing biases due to sparse data.”

      Reviewer #2 (Public Review):

      Summary:

      This paper investigates the neural underpinnings of an interactive speech task requiring verbal coordination with another speaker. To achieve this, the authors recorded intracranial brain activity from the left hemisphere in a group of drug-resistant epilepsy patients while they synchronised their speech with a 'virtual partner'. Crucially, the authors were able to manipulate the degree of success of this synchronisation by programming the virtual partner to either actively synchronise or desynchronise their speech with the participant, or else to not vary its speech in response to the participant (making the synchronisation task purely one-way). Using such a paradigm, the authors identified different brain regions that were either more sensitive to the speech of the virtual partner (primary auditory cortex), or more sensitive to the degree of verbal coordination (i.e. synchronisation success) with the virtual partner (secondary auditory cortex and IFG). Such sensitivity was measured by (1) calculating the correlation between the index of verbal coordination and mean power within a range of frequency bands across trials, and (2) calculating the phase-amplitude coupling between the behavioural and brain signals within single trials (using the power of high-frequency neural activity only). Overall, the findings help to elucidate some of the left hemisphere brain areas involved in interactive speaking behaviours, particularly highlighting the highfrequency activity of the IFG as a potential candidate supporting verbal coordination.

      Strengths:

      This study provides the field with a convincing demonstration of how to investigate speaking behaviours in more complex situations that share many features with real-world speaking contexts e.g. simultaneous engagement of speech perception and production processes, the presence of an interlocutor, and the need for inter-speaker coordination. The findings thus go beyond previous work that has typically studied solo speech production in isolation, and represent a significant advance in our understanding of speech as a social and communicative behaviour. It is further an impressive feat to develop a paradigm in which the degree of cooperativity of the synchronisation partner can be so tightly controlled; in this way, this study combines the benefits of using prerecorded stimuli (namely, the high degree of experimental control) with the benefits of using a live synchronisation partner (allowing the task to be truly two-way interactive, an important criticism of other work using pre-recorded stimuli). A further key strength of the study lies in its employment of stereotactic EEG to measure brain responses with both high temporal and spatial resolution, an ideal method for studying the unfolding relationship between neural processing and this dynamic coordination behaviour.

      We sincerely appreciate the Reviewer's thoughtful and positive feedback on our manuscript.

      Weaknesses:

      One major limitation of the current study is the lack of coverage of the right hemisphere by the implanted electrodes. Of course, electrode location is solely clinically motivated, and so the authors did not have control over this. However, this means that the current study neglects the potentially important role of the right hemisphere in this task. The right hemisphere has previously been proposed to support feedback control for speech (likely a core process engaged by synchronous speech), as opposed to the left hemisphere which has been argued to underlie feedforward control (Tourville & Guenther, 2011). Indeed, a previous fMRI study of synchronous speech reported the engagement of a network of right hemisphere regions, including STG, IPL, IFG, and the temporal pole (Jasmin et al., 2016). Further, the release from speech-induced suppression during a synchronous speech reported by Jasmin et al. was found in the right temporal pole, which may explain the discrepancy with the current finding of reduced leftward high-frequency activity with increasing verbal coordination (suggesting instead increased speech-induced suppression for successful synchronisation). The findings should therefore be interpreted with the caveat that they are limited to the left hemisphere, and are thus likely missing an important aspect of the neural processing underpinning verbal coordination behaviour.

      We have now included, in the supplementary materials, data from the right hemisphere, although the coverage is a bit sparse (Figures S2, S4, S5, see our responses in the ‘Recommendation for the authors’ section, below). We have also revised the Discussion section to add the putative role of right temporal regions (see below as well).

      A further limitation of this study is that its findings are purely correlational in nature; that is, the results tell us how neural activity correlates with behaviour, but not whether it is instrumental in that behaviour. Elucidating the latter would require some form of intervention such as electrode stimulation, to disrupt activity in a brain area and measure the resulting effect on behaviour. Any claims therefore as to the specific role of brain areas in verbal coordination (e.g. the role of the IFG in supporting online coordinative adjustments to achieve synchronisation) are therefore speculative.

      We appreciate the reviewer’s observation regarding the correlational nature of our findings and agree that this is a common limitation of neuroimaging studies. While elucidating causal relationships would indeed require intervention techniques such as electrical stimulation, our study leverages the unique advantages of intracerebral recordings, offering the best available spatial and temporal resolution alongside a high signal-tonoise ratio. These attributes ensure that our data accurately reflect neural activity and its temporal dynamics, providing a robust foundation for understanding the relationship between neural processes and behaviour. Therefore, while causal claims are beyond the scope of this study, the precision of our methodology allows us to make well-supported observations about the neural correlates of synchronous speech tasks.

      Recommendations for the authors:

      Reviewing Editor Comment:

      After joint consultation, we are seeing the potential for the report to be strengthened and the evidence here to be deemed ultimately at least 'solid': to us (editors and reviewers) it seems that this would require both (1) clarifying/acknowledging the limitations of not having right hemisphere data, and (2) running some of the additional analyses the reviewers suggest, which should allow for richer examination of the data e.g. phase relationships in areas that correlate with synchronisation.

      We have now added data on the right hemisphere (RH) that we did not previously report due to a rather sparse sampling of the RH. These results are now reported in the Results section as well as in the Supplementary section, where we put all right hemisphere figures for all analyses (Figure S2, S4, S5). We have also run additional analyses digging into the phase relationship in areas that correlate with synchronisation (Figure S6). These additional analyses allowed us to improve the Discussion section as well.

      Reviewer #1 (Recommendations For The Authors):

      In some sections, the writing is a bit unclear, with both typos and vague statements that could be fixed with careful proofreading.

      We thank the reviewer for pointing out areas where the writing could be improved. We carefully proofread the manuscript to address typos and clarify any vague statements. Specific sections identified as unclear have been rephrased for better precision and readability.

      In Figure 1, the colors repeat, making it impossible to tell patients apart.

      We have now updated Figure 1 colormap to avoid redundancy and added the right hemisphere.

      Line 132: "16 unilateral implantations (9 left, 7 bilateral implantations)". Should this say 7 right hemisphere? If so, the following sentence stating that there was "insufficient cover [sic] of the right hemisphere" is unclear, since the number of patients between LH and RH is similar.

      The confusion was due to the fact that the lateralization refers to the presence/absence of electrodes in the Heschl’s gyrus (left : H’ ; right : H) exclusively.

      We have thus changed this section as follows:

      “16 patients (7 women, mean age 29.8 y, range 17 - 50 y) with pharmacoresistant epilepsy took part in the study. They were included if their implantation map covered at least partially the Heschl's gyrus and had sufficiently intact diction to support relatively sustained language production.” The relevant part (previously line 132) now states:

      “Sixteen patients with a total of 236 electrodes (145 in the left hemisphere) and 2395 contacts (1459 in the left hemisphere, see Figure 1). While this gives a rather sparse coverage of the right hemisphere, we decided, due to the rarity of this type of data, to report results for both hemispheres, with figures for the left hemisphere in the main text and figures for the right hemisphere in the supplementary section.”

      Reviewer #2 (Recommendations For The Authors):

      (1) To address the concern regarding the absence of data from the right hemisphere, I would advise the authors to directly acknowledge this limitation in their Discussion section, citing relevant work suggesting that the right hemisphere has an important role to play in this task (e.g. Jasmin et al., 2016). You should also make this clear in your abstract e.g. you could rewrite the sentence in line 40 to be: "Then, we recorded the intracranial brain activity of the left hemisphere in 16 patients with drug-resistant epilepsy...".

      We are grateful to the reviewer for this comment that incited us to look into the right hemisphere data. We have now included results in the right hemisphere, although the coverage is a bit sparse. We have also revised the Discussion section to add the putative role of right temporal regions. Interestingly, our results show, as suggested by the reviewer, a clear involvement of the RH in this task.

      First, the full brain analyses show a very similar implication of the RH as compared to the LH (see Figure below). We have now added in the Results section:

      “As expected, the whole language network is strongly involved, including both dorsal and ventral pathways (Fig 3A). More precisely, in the left temporal lobe the superior, middle and inferior temporal gyri, in the left parietal lobe the inferior parietal lobule (IPL) and in the left frontal lobe the inferior frontal gyrus (IFG) and the middle frontal gyrus (MFG). Similar results are observed in the right hemisphere, neural responses being present across all six frequency bands with medium to large modulation in activity compared to baseline (Figure S2A) in the same regions. Desynchronizations are present in the theta, alpha and beta bands while the low gamma and HFa bands show power increases.”

      As to compared to the left hemisphere, assessing brain-behaviour correlations in the right hemisphere does not provide the same statistical power, because some anatomical regions have very few electrodes. Nonetheless, we observe a strong correlation in the right IFG, similar to the one we previously reported in the left hemisphere, and we now report in the Results section:

      “The decrease in HFa along the dorsal pathway is replicated in the right hemisphere (Figure S4). However, while both the right STG BA41/42 and STG BA22 present a power increase (compared to baseline) — with a stronger increase for the STG BA41/42 — neither shows a significant correlation with verbal coordination (t(45)=-1.65, p=.1 ; t(8)=-0.67, p=.5 ; Student’s T test, FDR correction). By contrast, results in the right IFG BA44 are similar to the one observed in the left hemisphere with a significant power increase associated with a negative brainbehaviour correlation (t(17) = -3.11, p = .01 ; Student’s T test, FDR correction).”

      Interestingly, the phase-amplitude coupling analysis yields very similar results in both hemispheres (exception made for BA22). We have thus updated the Results section as follows:

      “Notably, when comparing – within the regions of interest previously described – the PAC with the virtual partner speech and the PAC with the phase difference, the coupling relationship changes when moving along the dorsal pathway: a stronger coupling in the auditory regions with the speech input, no difference between speech and coordination dynamics in the IPL and a stronger coupling for the coordinative dynamics compared to speech signal in the IFG (Figure 5B ). When looking at the right hemisphere, we observe the same changes in the coupling relationship when moving along the dorsal pathway, except that no difference between speech and coordination dynamics is present in the right secondary auditory regions (STG BA22; Figure S5).”

      We also included in the Discussion section the right hemisphere results also mentioning previous work of Guenther and the one of Jasmin. On the section “Left secondary auditory regions are more sensitive to coordinative behaviour” one can read:

      “Furthermore, the absence of correlation in the right STG BA22 (Figure S4) seems in first stance to challenge influential speech production models (e.g. Guenther & Hickok, 2016) that propose that the right hemisphere is involved in feedback control. However, one needs to consider the the task at stake heavily relied upon temporal mismatches and adjustments. In this context, the left-lateralized sensitivity to verbal coordination reminds of the works of Floegel and colleagues (2020, 2023) suggesting that both hemispheres are involved depending on the type of error: the right auditory association cortex monitoring preferentially spectral speech features and the left auditory association cortex monitoring preferentially temporal speech features. Nonetheless, the right temporal pole seems to be sensitive to speech coordinative behaviour, confirming previous findings using fMRI (Jasmin et al., 2016) and thus showing that the right hemisphere has an important role to play in this type of tasks (e.g. Jasmin et al., 2016).”

      References cited:

      – Floegel, M., Fuchs, S., & Kell, C. A. (2020). Differential contributions of the two cerebral hemispheres to temporal and spectral speech feedback control. Nature Communications, 11(1), 2839.

      – Floegel, M., Kasper, J., Perrier, P., & Kell, C. A. (2023). How the conception of control influences our understanding of actions. Nature Reviews Neuroscience, 24(5), 313-329.

      – Guenther, F. H., & Hickok, G. (2016). Neural models of motor speech control. In Neurobiology of language (pp. 725-740). Academic Press.

      (2) When discussing previous work on alignment during synchronous speech, you may wish to include a recently published paper by Bradshaw et al (2024); this manipulated the acoustics of the accompanist's voice during a synchronous speech task to show interactions between speech motor adaptation and phonetic convergence/alignment.

      We thank the reviewer for pointing to this recent and interesting paper. We added the article as reference as follows

      “Furthermore, synchronous speech favors the emergence of alignment phenomena, for instance of the fundamental frequency or the syllable onset (Assaneo et al., 2019 ; Bradshaw & McGettigan, 2021 ; Bradshaw et al., 2023; Bradshaw et al., 2024).”

      (3) Line 80: "Synchronous speech resembles to a certain extent to delayed auditory feedback tasks"- I think you mean "altered auditory feedback tasks" here.

      In the case of synchronous speech it is more about timing than altered speech signals, that is why the comparison is done with delayed and not altered auditory feedback. Nonetheless, we understand the Reviewer’s point and we have now changed the sentence as follows:

      “Synchronous speech resembles to a certain extent to delayed/altered auditory feedback tasks”

      (4) When discussing superior temporal responses during such altered feedback tasks, you may also want to cite a review paper by Meekings and Scott (2021).

      We thank the reviewer for this suggestion, indeed this was a big oversight!

      The paper is now quoted in the introduction as follows:

      “Previous studies have revealed increased responses in the superior temporal regions compared to normal feedback conditions (Hirano et al., 1997 ; Hashimoto & Sakai, 2003 ; Takaso et al., 2010 ; Ozerk et al., 2022 ; Floegel et al., 2020 ; see Meekings & Scott, 2021 for a review of error-monitoring and feedback control in the STG during speech production).”

      Furthermore, we updated the discussion part concerning the speaker-induced suppression phenomenon (see below our response to the point 10).

      (5) Line 125: "The parameters and sound adjustment were set using an external low-latency sound card (RME Babyface Pro Fs)". Can you please report the total feedback loop latency in your set-up? Or at the least cite the following paper which reports low latencies with this audio device.

      Kim, K. S., Wang, H., & Max, L. (2020). It's About Time: Minimizing Hardware and Software Latencies in Speech Research With Real-Time Auditory Feedback. Journal of Speech, Language, and Hearing Research, 63(8), 25222534. https://doi.org/10.1044/2020_JSLHR-19-00419

      We now report the total feedback loop latency (~5ms) and also cite the relevant paper (Kim et al., 2020).

      (6) Line 127 "A calibration was made to find a comfortable volume and an optimal balance for both the sound of the participant's own voice, which was fed back through the headphones, and the sound of the stimuli." What do you mean here by an 'optimal balance'? Was the participant's own voice always louder than the VP stimuli? Can you report roughly what you consider to be a comfortable volume in dB?

      This point was indeed unlcear. We have now changed as follows:

      “A calibration was made to find a comfortable volume and an optimal balance for both the sound of the participant's own voice, which was fed back through the headphones, and the sound of the stimuli. The aim of this procedure was that the patient would subjectively perceive their voice and the VP-voice in equal measure. VP voice was delivered at approximately 70dB.”

      (7) Relatedly, did you use any noise masking to mask the air-conducted feedback from their own voice (which would have been slightly out of phase with the feedback through the headphones, depending on your latency)?

      Considering the low-latency condition allowed with the sound card (RME Babyface Pro Fs), we did not use noise masking to mask the air-conducted feedback from the self-voice of the patients.

      (8) Line 141: "four short sentences were pre-recorded by a woman and a man." Did all participants synchronise with both the man and woman or was the VP gender matched to that of the participant/patient?

      We thank the reviewer for this important missing detail. We know changed the text as follows:

      “Four stimuli corresponding to four short sentences were pre-recorded by both a female and a male speaker. This allowed to adapt to the natural gender differences in fundamental frequency (i.e. so that the VP gender matched that of the patients). All stimuli were normalised in amplitude.”

      (9) Can you clarify what instructions participants were given regarding the VP? That is, were they told that this was a recording or a real live speaker? Were they naïve to the manipulation of the VP's coupling to the participant?

      We have now added this information to the task description as follows:

      “Participants, comfortably seated in a medical chair, were instructed that they would perform a real-time interactive synchronous speech task with an artificial agent (Virtual Partner, henceforth VP, see next section) that can modulate and adapt to the participant’s speech in real time.”

      “The third step was the actual experiment. This was identical to the training but consisted of 24 trials (14s long, speech rate ~3Hz, yielding ~1000 syllables). Importantly, the VP varied its coupling behaviour to the participant. More precisely, for a third of the sequences the VP had a neutral behaviour (close to zero coupling : k = +/- 0.01). For a third it had a moderate coupling, meaning that the VP synchronised more to the participant speech (k = - 0.09). And for the last third of the sequences the VP had a moderate coupling but with a phase shift of pi/2, meaning that it moderately aimed to speak in between the participant syllables (k = + 0.09). The coupling values were empirically determined on the basis of a pilot experiment in order to induce more or less synchronization, but keeping the phase-shifted coupling at a rather implicit level. In other terms, while participants knew that the VP would adapt, they did not necessarily know in which direction the coupling went.”  

      (10) The paragraph from line 438 entitled "Secondary auditory regions are more sensitive to coordinative behaviour" includes an interesting discussion of the relation of the current findings to the phenomenon of speech-induced suppression (SIS). However, the authors appear to equate the observed decrease in highfrequency activity as speech coordination increases with the phenomenon of SIS (in lines 456-457), which is quite a speculative leap. I would encourage the authors to temper this discussion by referring to SIS as a potentially related phenomenon, with a need for more experimental work to determine if this is indeed the same phenomenon as the decreases in high-frequency power observed here. I believe that the authors are arguing here for an interpretation of SIS as reflecting internal modelling of sensory input regardless of whether this is self-generated or other-generated; if this is indeed the case, I would ask the authors to be more explicit here that these ideas are not a standard part of the traditional account of SIS, which only includes internal modelling of self-produced sensory feedback.

      As stated in the public review, we thank both reviewers for raising thoughtful concerns about our interpretation of the observed neural suppression as related to speaker-induced suppression (SIS). We agree that our study lacks a passive listening condition, which limits direct comparisons to the original SIS effect, traditionally defined as the suppression of neural responses to self-produced speech compared to externally-generated speech (Meekings & Scott, 2021).

      In response, we have reconsidered our terminology and interpretation. In the revised discussion, we refer to our findings as a "SIS-related phenomenon specific to the synchronous speech context." Unlike classic SIS paradigms, our interactive task involves simultaneous monitoring of self- and externally-generated speech, introducing additional attentional and coordinative demands.

      The revised discussion also incorporates findings by Ozker et al. (2024, 2022), which link SIS and speech monitoring, suggesting that suppressing responses to self-generated speech facilitates error detection. We propose that the decrease in high-frequency activity (HFa) as verbal coordination increases reflects reduced error signals due to closer alignment between perceived and produced speech. Conversely, HFa increases with reduced coordination may signify greater prediction error.

      Additionally, we relate our findings to the "rubber voice" effect (Zheng et al., 2011; Lind et al., 2014; Franken et al., 2021), where temporally and phonetically congruent external speech can be perceived as self-generated. We speculate that this may occur in synchronous speech tasks when the participant's and VP's speech signals closely align. However, this interpretation remains speculative, as no subjective reports were collected to confirm this perception. Future studies could include participant questionnaires to validate this effect and relate subjective experience to neural measures of synchronization.

      Overall, our findings extend the study of SIS to dynamic, interactive contexts and contribute to understanding internal forward models of speech production in more naturalistic scenarios.

      We have now added these points to the discussion as follows:

      “The observed negative correlation between verbal coordination and high-frequency activity (HFa) in STG BA22 suggests a suppression of neural responses as the degree of synchrony increases. This result aligns with findings on speaker-induced suppression (SIS), where neural activity in auditory cortex decreases during self-generated speech compared to externally-generated speech (Meekings & Scott, 2021; Niziolek et al., 2013). However, our paradigm differs from traditional SIS studies in two critical ways: (1) the speaker's own voice is always present and predictable from the forward model, and (2) no passive listening condition was included. Therefore, our findings cannot be directly equated with the original SIS effect.

      Instead, we propose that the suppression observed here reflects a SIS-related phenomenon specific to the synchronous speech context. Synchronous speech requires simultaneous monitoring of self- and externally generated speech, a task that is both attentionally demanding and coordinative. This aligns with evidence from Ozker et al. (2024, 2022), showing that the same neural populations in STG exhibit SIS and heightened responses to feedback perturbations. These findings suggest that SIS and speech monitoring are related processes, where suppressing responses to self-generated speech facilitates error detection.

      In our study, suppression of HFa as coordination increases may reflect reduced prediction errors due to closer alignment between perceived and produced speech signals. Conversely, increased HFa during poor coordination may signify greater mismatch, consistent with prediction error theories (Houde & Nagarajan, 2011; Friston et al., 2020).”

      (11) Within this section, you also speculate in line 460 that "Moreover, when the two speech signals come close enough in time, the patient possibly perceives them as its own voice." I would recommend citing studies on the 'rubber voice' effect to back up this claim (e.g. Franken et al., 2021; Lind et al., 2014; Zheng et al., 2011).

      We are grateful to the Reviewer for this interesting suggestion. Directly following the previous comment, the section now states:

      “Furthermore, when self- and externally-generated speech signals are temporally and phonetically congruent, participants may perceive external speech as their own. This echoes the "rubber voice" effect, where external speech resembling self-produced feedback is perceived as self-generated (Zheng et al., 2011; Lind et al., 2014; Franken et al., 2021). While this interpretation remains speculative, future studies could incorporate subjective reports to investigate this phenomenon in more detail.”

      (12) As noted in my public review, since your methods are correlational, you need to be careful about inferring the causal role of any brain areas in supporting a specific aspect of functioning e.g. line 501-504: "By contrast, in the inferior frontal gyrus, the coupling in the high-frequency activity is strongest with the input-output phase difference (input of the VP - output of the speaker), a metric that reflects the amount of error in the internal computation to reach optimal coordination, which indicates that this region optimises the predictive and coordinative behaviour required by the task." I would argue that the latter part of this sentence is a conclusion that, although consistent with, goes beyond the current data in this study, and thus needs tempering.

      We agree with the Reviewer and changed the sentence as follows:

      “By contrast, in the inferior frontal gyrus, the coupling in the high-frequency activity is strongest with the inputoutput phase difference (input of the VP - output of the speaker), a metric that could possibly reflect the amount of error in the internal computation to reach optimal coordination. This indicates that this region could have an implication in the optimisation of the predictive and coordinative behaviour required by the task.”

    1. eLife Assessment

      This study reveals the important role of upstream open reading frames (uORFs) in limiting the translational variability of downstream coding sequences. Through a combination of computational simulations, comparative analyses of translation efficiency across different developmental stages in two closely related Drosophila species, and manipulative, experimental validation of translation buffering by an uORF for a gene, the authors provide convincing evidence supporting their conclusions. This work will be of broad interest to molecular biologists and geneticists.

    2. Reviewer #1 (Public review):

      Summary:

      The authors set out to explore the role of upstream open reading frames (uORFs) in stabilizing protein levels during Drosophila development and evolution. By utilizing a modified ICIER model for ribosome translation simulations and conducting experimental validations in Drosophila species, the study investigates how uORFs buffer translational variability of downstream coding sequences. The findings reveal that uORFs significantly reduce translational variability, which contributes to gene expression stability across different biological contexts and evolutionary timeframes.

      Strengths:

      (1) The study introduces a sophisticated adaptation of the ICIER model, enabling detailed simulation of ribosomal traffic and its implications for translation efficiency.<br /> (2) The integration of computational predictions with empirical data through knockout experiments and translatome analysis in Drosophila provides a compelling validation of the model's predictions.<br /> (3) By demonstrating the evolutionary conservation of uORFs' buffering effects, the study provides insights that are likely applicable to a wide range of eukaryotes.

      Weaknesses:

      (1) Although the study is technically sound, it does not clearly articulate the mechanisms through which uORFs buffer translational variability. A clearer hypothesis detailing the potential molecular interactions or regulatory pathways by which uORFs influence translational stability would enhance the comprehension and impact of the findings.<br /> (2) The study could be further improved by a discussion regarding the evolutionary selection of uORFs. Specifically, it would be beneficial to explore whether uORFs are favored evolutionarily primarily for their role in reducing translation efficiency or for their capability to stabilize translation variability. Such a discussion would provide deeper insights into the evolutionary dynamics and functional significance of uORFs in genetic regulation.

      Comments on revisions:

      The authors have adequately addressed my previous concerns.

    3. Reviewer #2 (Public review):

      uORFs, short open reading frames located in the 5' UTR, are pervasive in genomes. However, their roles in maintaining protein abundance are not clear. In this study, the authors propose that uORFs act as "molecular dam", limiting the fluctuation of the translation of downstream coding sequences. First, they performed in silico simulations using an improved ICIER model, and demonstrated that uORF translation reduces CDS translational variability, with buffering capacity increasing in proportion to uORF efficiency, length, and number. Next, they analysed the translatome between two related Drosophila species, revealing that genes with uORFs exhibit smaller fluctuations in translation between the two species and across different developmental stages within the same species. Moreover, they identified that bicoid, a critical gene for Drosophila development, contains a uORF with substantial changes in translation efficiency. Deleting this uORF in Drosophila melanogaster significantly affected its gene expression, hatching rates, and survival under stress conditions. Lastly, by leveraging public Ribo-seq data, the authors showed that the buffering effect of uORFs is also evident between primates and within human populations. Collectively, the study significantly advances our understanding of how uORFs regulate the translation of downstream coding sequences at the genome-wide scale, as well as during development and evolution. It would be particularly interesting to explore whether similar buffering functions are conserved in other organisms, and whether their regulatory effects could be harnessed for practical applications, such as improving crop traits or benefiting human health.

      Comments on revisions:

      The authors have fully addressed all of my concerns, and the revisions have substantially improved the manuscript. I have no further comments.

    4. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors set out to explore the role of upstream open reading frames (uORFs) in stabilizing protein levels during Drosophila development and evolution. By utilizing a modified ICIER model for ribosome translation simulations and conducting experimental validations in Drosophila species, the study investigates how uORFs buffer translational variability of downstream coding sequences. The findings reveal that uORFs significantly reduce translational variability, which contributes to gene expression stability across different biological contexts and evolutionary timeframes.

      We thank the reviewer for carefully reading our manuscript and providing thoughtful and constructive feedback. We believe the manuscript has been significantly improved by incorporating your suggestions. Please find our detailed responses and corresponding revisions below.

      Strengths:

      (1) The study introduces a sophisticated adaptation of the ICIER model, enabling detailed simulation of ribosomal traffic and its implications for translation efficiency.

      (2) The integration of computational predictions with empirical data through knockout experiments and translatome analysis in Drosophila provides a compelling validation of the model's predictions.

      (3) By demonstrating the evolutionary conservation of uORFs' buffering effects, the study provides insights that are likely applicable to a wide range of eukaryotes.

      We appreciate your positive feedback and thoughtful summary of the strengths of our study.

      Weaknesses:

      (1) Although the study is technically sound, it does not clearly articulate the mechanisms through which uORFs buffer translational variability. A clearer hypothesis detailing the potential molecular interactions or regulatory pathways by which uORFs influence translational stability would enhance the comprehension and impact of the findings.

      Thanks for your constructive comments. In the Discussion section of our previous submission (Original Lines 470-489), we proposed that uORFs function as “molecular dams” to smooth out fluctuations in ribosomal flow toward downstream CDS regions, primarily via mechanisms involving ribosome collision and dissociation. To further address your concern, we have expanded the Discussion and included a new model figure (Fig. 9) to more clearly articulate the potential biological and mechanistic basis by which translating 80S ribosomes may induce the dissociation of 40S ribosomes. The revised section (Lines 540–557) now reads:

      “Ribosome slowdown or stalling on mRNA due to rare codons [56,96-98] or nascent blocking peptides [99-102] frequently triggers ribosome collisions genome-wide [103-105]. Such collisions, especially among elongating 80S ribosomes, often activate ribosome quality control (RQC) pathways that recognize collision interfaces on the 40S subunit, leading to ribosomal subunit dissociation and degradation [106-108]. In mammals, ZNF598 specifically identifies collided ribosomes to initiate ubiquitin-dependent protein and mRNA quality control pathways [109-113]. Analogously, yeast employs Hel2-mediated ubiquitination of uS10, initiating dissociation via the RQC-trigger complex (RQT) [114]. Furthermore, the human RQT (hRQT) complex recognizes ubiquitinated ribosomes and induces subunit dissociation similarly to yeast RQT [115]. However, transient ribosome collisions can evade RQC by promoting resumed elongation through mechanical force provided by trailing ribosomes, thereby mitigating stalling [116]. Beyond 80S collisions, evidence increasingly highlights a distinct collision type involving scanning 40S subunits or pre-initiation (43S) complexes. Recently, an initiation RQC pathway (iRQC) targeting the small ribosomal subunit (40S) has been described, particularly involving collisions between scanning 43S complexes or between stalled 43S and elongating 80S ribosomes (Figure 9B) [117,118]. During iRQC, E3 ubiquitin ligase RNF10 ubiquitinates uS3 and uS5 proteins, resulting in 40S degradation [118]. This mechanism aligns closely with our ICIER model, proposing collision-driven 43S dissociation in the 5' UTRs. Future studies exploring these mechanisms in greater detail will clarify how uORFs modulate translational regulation through buffering effects.”

      (2) The study could be further improved by a discussion regarding the evolutionary selection of uORFs. Specifically, it would be beneficial to explore whether uORFs are favored evolutionarily primarily for their role in reducing translation efficiency or for their capability to stabilize translation variability. Such a discussion would provide deeper insights into the evolutionary dynamics and functional significance of uORFs in genetic regulation.

      Thank you for this insightful suggestion. We agree that understanding whether uORFs are evolutionarily favored for their role in translational repression or for their capacity to buffer translational variability is a compelling and unresolved question. Our study suggests that translational buffering, rather than translational repression alone, can also drive evolutionary selection favoring uORFs, although it remains challenging to empirically disentangle these functions due to their inherent linkage. We have expanded the discussion in the revised manuscript to address this point in more detail (Lines 494-513), which is reproduced as follows:

      “Previous studies have shown that a significant fraction of fixed uORFs in the populations of D. melanogaster and humans were driven by positive Darwinian selection 63,67, suggesting active maintenance through adaptive evolution rather than purely neutral or deleterious processes. While uORFs have traditionally been recognized for their capacity to attenuate translation of downstream CDSs, accumulating evidence now underscores their critical role in stabilizing gene expression under fluctuating cellular and environmental conditions [43,55,56]. Whether the favored evolutionary selection of uORFs acts primarily through their role in translational repression or translational buffering remains a compelling yet unresolved question, as these two functions are inherently linked. Indeed, highly conserved uORFs tend to be translated at higher levels, resulting not only in stronger inhibition of CDS translation [34,45,67] but also in a more pronounced buffering effect, as demonstrated in this study. This buffering capacity of uORFs potentially provides selective advantages by reducing fluctuations in protein synthesis, thus minimizing gene-expression noise and enhancing cellular homeostasis. This suggests that selection may favor uORFs that contribute to translational robustness, a hypothesis supported by findings in yeast and mammals showing that uORFs are significantly enriched in stressresponse genes and control the translation of certain master regulators of stress responses [41,42,94,95]. Our study suggests that translational buffering, rather than translational repression alone, can also drive evolutionary selection favoring uORFs, although it remains challenging to empirically disentangle these functions. Future comparative genomic analyses, coupled with experimental approaches such as ribosome profiling and functional mutagenesis, will be crucial in elucidating the precise evolutionary forces driving uORF conservation and adaptation.”

      Reviewer #2 (Public review):

      uORFs, short open reading frames located in the 5' UTR, are pervasive in genomes. However, their roles in maintaining protein abundance are not clear. In this study, the authors propose that uORFs act as "molecular dam", limiting the fluctuation of the translation of downstream coding sequences. First, they performed in silico simulations using an improved ICIER model, and demonstrated that uORF translation reduces CDS translational variability, with buffering capacity increasing in proportion to uORF efficiency, length, and number. Next, they analzed the translatome between two related Drosophila species, revealing that genes with uORFs exhibit smaller fluctuations in translation between the two species and across different developmental stages within the same specify. Moreover, they identified that bicoid, a critical gene for Drosophila development, contains a uORF with substantial changes in translation efficiency. Deleting this uORF in Drosophila melanogaster significantly affected its gene expression, hatching rates, and survival under stress condition. Lastly, by leveraging public Ribo-seq data, the authors showed that the buffering effect of uORFs is also evident between primates and within human populations. Collectively, the study advances our understanding of how uORFs regulate the translation of downstream coding sequences at the genome-wide scale, as well as during development and evolution.

      The conclusions of this paper are mostly well supported by data, but some definitions and data analysis need to be clarified and extended.

      We thank the reviewer for the thoughtful and constructive review. Your summary accurately captures the key findings of our study. We have carefully addressed all your concerns in the revised manuscript, and we believe it has been significantly improved based on your valuable input.

      (1) There are two definitions of translation efficiency (TE) in the manuscript: one refers to the number of 80S ribosomes that complete translation at the stop codon of a CDS within a given time interval, while the other is calculated based on Ribo-seq and mRNA-seq data (as described on Page 7, line 209). To avoid potential misunderstandings, please use distinct terms to differentiate these two definitions.

      Thank you for highlighting this important point, and we apologize for the confusion. The two definitions of translation efficiency (TE) in our manuscript arise from methodological differences between simulation and experimental analyses. To clarify, in the revised manuscript, we use “translation rate” in the context of simulations to describe the number of 80S ribosomes completing translation at the CDS stop codon per unit time. We retain the conventional “translation efficiency (TE)” for Ribo-seq–based measurements. 

      In this revised manuscript, we have added a more detailed explanation of TE in the revised manuscript (Lines 202–206), which now reads:

      “For each sample, we followed established procedures [62-66] to calculate the translational efficiency (TE) for each feature (CDS or uORF). TE serves as a proxy for the translation rate at which ribosomes translate mRNA into proteins, typically quantified by comparing the density of ribosome-protected mRNA fragment (RPF) to the mRNA abundance for that feature (see Materials and Methods).”

      (2) Page 7, line 209: "The translational efficiencies (TEs) of the conserved uORFs were highly correlated between the two species across all developmental stages and tissues examined, with Spearman correlation coefficients ranging from 0.478 to 0.573 (Fig. 2A)." However, the authors did not analyze the correlation of translation efficiency of conserved CDSs between the two species, and compare this correlation to the correlation between the TEs of CDSs. These analyzes will further support the authors conclusion regarding the role of conserved uORFs in translation regulation.

      In the revised manuscript, we have incorporated a comparison of translational efficiency (TE) correlations for conserved CDSs between the two species. We found that CDSs exhibit significantly higher interspecific TE correlations than uORFs, with Spearman’s rho ranging from 0.588 to 0.806. This suggests that uORFs tend to show greater variability in TE than CDSs, consistent with our model in which uORFs buffer fluctuations in downstream CDS translation. The updated results were included in the revised manuscript (Lines 223-227) as follows:

      “In contrast, TE of CDSs exhibited a significantly higher correlation between the two species in the corresponding samples compared to that of uORFs, with Spearman’s rho ranging from 0.588 to 0.806 (P = 0.002, Wilcoxon signed-rank test; Figure 2A). This observation is consistent with our simulation results, which indicate that uORFs experience greater translational fluctuations than their downstream CDSs.”

      (3) Page 8, line 217: "Among genes with multiple uORFs, one uORF generally emerged as dominant, displaying a higher TE than the others within the same gene (Fig. 2C)." The basis for determining dominance among uORFs is not explained and this lack of clarification undermines the interpretation of these findings.

      Thank you for pointing this out. We apologize for the confusion. In our study, a “dominant” uORF is defined as the one with the highest translation efficiency (TE) among all uORFs within the same gene. This designation is based solely on TE, which we consider a key metric for uORF activity, as it directly reflects translational output and potential regulatory impact. We have revised the manuscript to clarify this definition (Lines 232–244), now stating:

      “Among genes with multiple uORFs, we defined the uORF with the highest TE as the dominant uORF for that gene, as TE is one of the most relevant metrics for assessing uORF function 45,67…… These results suggest that genes with multiple uORFs tend to retain the same dominant uORF across developmental stages, indicating that the dominant uORFs may serve as the key translational regulator of the downstream CDS.

      (4) According to the simulation, the translation of uORFs should exhibit greater variability than that of CDSs. However, the authors observed significantly fewer uORFs with significant TE changes compared to CDSs. This discrepancy may be due to lower sequencing depth resulting in fewer reads mapped to uORFs. Therefore, the authors may compare this variability specifically among highly expressed genes.

      Thank you for this thoughtful observation. We agree that the lower proportion of uORFs showing significant TE changes compared to CDSs, as reported in Table 1, appears inconsistent with our conclusion that uORFs exhibit greater translational variability. However, this discrepancy is largely attributable to differences in sequencing depth and feature length—uORFs are generally much shorter and more weakly expressed than CDSs, resulting in fewer mapped reads and reduced statistical power (Figure S18A).

      To address this issue, we first followed your suggestion and restricted our analysis to genes with both mRNA and RPF RPKM values above the 50th percentile in D. melanogaster and D. simulans. While this filtering increased the total proportion of features with significant TE changes (due to improved read coverage), the proportion of significant uORFs still remained lower than that of CDSs (Table R1). This suggests that even among highly expressed genes, the disparity in read counts between uORFs and CDSs persists (Figure S18B), and thus the issue is not fully resolved.

      To better capture biological relevance, we compared the absolute values of log2(TE changes) between D. melanogaster and D. simulans for uORFs and their corresponding CDSs. Across all samples, uORFs consistently exhibit larger TE shifts than their downstream CDSs, supporting our model that uORFs act as translational buffers (Figure 3B).

      We have made relevant changes to report the new analysis in this revised manuscript. Specifically, in our original submission, we stated this observation with the sentence “The smaller number of uORFs showing significant TE changes compared to CDSs between D. melanogaster and D. simulans likely reflects their shorter length and reduced statistical power, rather than indicating that uORFs are less variable in translation than CDSs.” To make this point clearer, in the revised version (Lines 275-284), we rephrased this sentence which read as follows: 

      “Note that due to their shorter length and generally lower TE, uORFs had considerably lower read counts than CDSs, limiting the statistical power to detect significant interspecific TE differences for uORFs. This trend consistently holds whether analyzing all expressed uORFs (Figure S18A) or only highly expressed genes (Figure S18B). Thus, the fewer uORFs showing significant TE divergence likely reflects lower read counts and statistical sensitivity rather than reduced translational variability relative to CDSs. In fact, the absolute values of log2(fold change) of TE for uORFs between D. melanogaster and D. simulans were significantly greater than those observed for corresponding CDSs across all samples (P < 0.001, Wilcoxon signed-rank test; Figure 3B), suggesting that the magnitude of

      TE changes in CDSs is generally smaller than that in uORFs, due to the buffering effect of uORF.”

      Author response table 1.

      Proportion of uORFs and CDSs with significant TE changes before and after selecting HEGs

      (5) If possible, the author may need to use antibodies against bicoid to test the effect of ATG deletion on bicoid expression, particularly under different developmental stages or growth conditions.

      According to the authors' conclusions, the deletion mutant should exhibit greater variability in bicoid protein abundance. This experiment could provide strong support for the proposed mechanisms.

      Thank you for this excellent suggestion. We fully agree that testing Bcd protein levels across developmental stages or stress conditions using antibodies would be a strong validation of our model, which predicts greater variability in Bcd protein abundance upon uORF deletion.

      In fact, we attempted such experiments in both wild-type and mutant backgrounds. However, we encountered substantial difficulties in obtaining a reliable anti-Bcd antibody. Some Bcd antibodies referenced in the published literature were homemade and often shared among research groups as gifts [1-3] and some commercially available antibodies cited in previous studies are no longer supplied by vendors [4-6]. We managed to obtain a custom-made antibody from Professor Feng Liu, but unfortunately, it produced inconsistent and unsatisfactory results. Despite considerable effort—including during the COVID-19 pandemic—we were unable to identify a reagent suitable for robust and reproducible detection of Bcd protein.

      As an alternative, we used sucrose gradient fractionation followed by qPCR to directly measure the translation efficiency of bicoid in vivo. We believe this approach offers a clear and quantitative readout of translational activity, and it avoids potential confounding from protein degradation, which may vary across conditions and developmental stages. Nonetheless, we recognize the value of antibody-based validation and will pursue this direction in future work if reliable antibodies become available. We have added this limitation to the revised Discussion section (Lines 563–568) as follows:

      “We demonstrated that the bcd uORF represses CDS translation using sucrose gradient fractionation followed by qPCR—an approach that directly measures translation efficiency while minimizing confounding from RNA/protein degradation. However, detecting Bcd protein levels with antibodies across developmental stages or conditions in the mutants and wild-type controls would provide an even stronger validation of our model and should be explored in future studies.”

      Recommendations for the authors:  

      Reviewer #1 (Recommendations for the authors):

      (1) The authors should provide a more detailed explanation for the modifications made to the ICIER model. Specifically, an explanation of the biological or mechanistic rationale behind the ability of the 80S ribosome to cause upstream 40S ribosomes to dissociate from mRNA would help clarify this aspect of the model.

      Thank you for this suggestion. In the original submission, we described our modifications to the ICIER model in the section titled “An extended ICIER model for quantifying uORF buffering in CDS translation” (Lines 88-124 of the revised manuscript). 

      To further clarify the biological rationale behind this mechanism, we have now included a conceptual model figure (Figure 9) illustrating mechanistically how uORF translation can buffer downstream translation within a single mRNA molecule. Additionally, we expanded the Discussion to summarize the current understanding of how collisions between translating 80S ribosomes and scanning 40S subunits may lead to dissociation, referencing known initial ribosome quality control (iRQC) pathways. These revisions provide a clearer mechanistic framework for interpreting the buffering effects modeled in our simulations. The relevant part is reproduced from Discussion (Lines 540-557) which reads as follows:

      “Ribosome slowdown or stalling on mRNA due to rare codons [56,96-98] or nascent blocking peptides [99-102] frequently triggers ribosome collisions genome-wide [103-105]. Such collisions, especially among elongating 80S ribosomes, often activate ribosome quality control (RQC) pathways that recognize collision interfaces on the 40S subunit, leading to ribosomal subunit dissociation and degradation [106-108]. In mammals, ZNF598 specifically identifies collided ribosomes to initiate ubiquitin-dependent protein and mRNA quality control pathways [109-113]. Analogously, yeast employs Hel2-mediated ubiquitination of uS10, initiating dissociation via the RQC-trigger complex (RQT) [114]. Furthermore, the human RQT (hRQT) complex recognizes ubiquitinated ribosomes and induces subunit dissociation similarly to yeast RQT [115]. However, transient ribosome collisions can evade RQC by promoting resumed elongation through mechanical force provided by trailing ribosomes, thereby mitigating stalling [116]. Beyond 80S collisions, evidence increasingly highlights a distinct collision type involving scanning 40S subunits or pre-initiation (43S) complexes. Recently, an initiation RQC pathway (iRQC) targeting the small ribosomal subunit (40S) has been described, particularly involving collisions between scanning 43S complexes or between stalled 43S and elongating 80S ribosomes (Figure 9B) [117,118]. During iRQC, E3 ubiquitin ligase RNF10 ubiquitinates uS3 and uS5 proteins, resulting in 40S degradation [118]. This mechanism aligns closely with our ICIER model, proposing collision-driven 43S dissociation in the 5' UTRs. Future studies exploring these mechanisms in greater detail will clarify how uORFs modulate translational regulation through buffering effects.”

      (2) The figure legend references Figure 5C; however, this figure appears to be missing from the document.

      We apologize for the oversight. The missing panel previously referred to as Figure 5C has now been incorporated into the revised Figure 6A. The figure and its corresponding legend have been corrected accordingly in the updated manuscript.

      Reviewer #2 (Recommendations for the authors):

      This is an important study that enhances our understanding of the roles of uORFs in translational regulation. In addition to the suggestions provided in the public review, the following minor points should be addressed before publication in eLife:

      (1) Page 7, line 207: "We identified 18,412 canonical uORFs shared between the two species (referred to as conserved uORFs hereafter)." The term "canonical uORFs" requires clarification. Does this refer to uORFs with specific sequence features, conservation, or another defining characteristic?

      Thank you for pointing this out. We apologize for the lack of clarity. In our study, a canonical uORF is defined as an open reading frame (ORF) that initiates with a canonical AUG start codon located in the 5′ untranslated region (UTR) and terminates with a stop codon (UAA, UAG, or UGA) within the same mRNA. Conservation of uORFs is defined solely based on the presence of AUG start codons at orthologous positions in the 5′ UTR across species, regardless of differences in the stop codon.

      To clarify this definition, we have revised the sentence as follows (Lines 213-219): “We focused on canonical uORFs that initiate with an ATG start codon in the 5′ UTR and terminate with a stop codon (TAA, TAG, or TGA). Because the ATG start codon is the defining feature of a canonical uORF and tends to be more conserved than its downstream sequence [67], we defined uORF conservation based on the presence of the ATG start codon in the 5′ UTR of D. melanogaster and its orthologous positions in D. simulans, regardless of differences in the stop codon. Using this criterion, we identified 18,412 canonical uORFs with conserved start codons between the two species.”

      (2) Page 8, line 227: "Furthermore, the dominant uORFs showed a higher proportion of conserved uATGs than the other translated uORFs." There appears to be a typographical error. Should "other uATGs" instead read "other uORFs"?

      Thank you for pointing this out. As we addressed in response to your previous concern, in this study, we defined uORF conservation primarily based on the presence of their start codon (uATG) both in D. melanogaster and the orthologous sites of D. simulans, as the start codon is the defining feature of a uORF and tends to be more conserved than the remaining sequence, as demonstrated in our previous study [7]. We used the term “conserved uATGs” to reflect this definition and believe it accurately conveys the intended meaning in this context.

      (3) Page 8, line 240: "uORFs exhibited a significant positive correlation with the TE of their downstream CDSs in all samples analyzed (P < 0.001, Spearman's correlation)." A Spearman's rho of 0.11 or 0.21 may not practically represent a "significant" positive correlation. Consider rephrasing this as "a positive correlation."

      Thank you for the suggestion. We have revised the sentence in the manuscript to read (Lines 257-259): “uORFs exhibited a modest, yet statistically significant, positive correlation with the TE of their downstream CDSs across all samples analyzed (P < 0.001, Spearman’s correlation).”

      (4) Page 9, line 269: The analysis of interspecific TE changes between uORFs and their corresponding CDSs is a crucial piece of evidence supporting the authors' conclusions. Presenting this analysis as part of the figures, rather than in "Table 1," would improve clarity and accessibility.

      Thank you for this suggestion. In Table 1, we originally presented the number of uORFs and CDSs that showed significant differences in TE between D. melanogaster and D. simulans during various developmental stages. One key point we aimed to emphasize was that, although TE changes in uORFs and their downstream CDSs are positively correlated, there is a notable difference in the magnitude of these changes. To better convey this, we have summarized the core findings of Table 1 in graphical form.

      In Figure 3B of the revised version, we compared the absolute values of interspecific TE changes between CDS and uORF, showing that CDSs consistently exhibit smaller shifts than their upstream uORFs. This result further supports the translational buffering effect of uORFs on downstream CDS expression. We have included the updated results in the revised manuscript (Lines 281-284) as follows:

      “In fact, the absolute values of log2(fold change) of TE for uORFs between D. melanogaster and D. simulans was significantly greater than that observed for corresponding CDSs across all samples (P < 0.001, Wilcoxon signed-rank test; Figure 3B), suggesting that the magnitude of TE changes in CDSs is generally smaller than that in uORFs, due to the buffering effect of uORF.”

      (5) Page 9, line 279: The phrase "dominantly translated" needs clarification. Does it refer to Figure 2C, where one uORF is dominantly translated within a gene, or does it mean that the uORF's translation is higher than that of its corresponding CDS?

      We apologize for the obscurity. The phrase "dominantly translated" means one uORF with the highest TE compared to other uORFs within a gene. We have rephrased the relevant sentence in the revised version (Lines 299-304), which now reads:

      “To investigate how the conservation level and translation patterns of uORFs influence their buffering capacity on CDS translation, we categorized genes expressed in each pair of samples into three classes:

      Class I, genes with conserved uORFs that are dominantly translated (i.e., exhibiting the highest TE among all uORFs within the same gene) in both Drosophila species; Class II, genes with conserved uORFs that are translated in both species but not dominantly translated in at least one; and Class III, the remaining expressed genes.”

      (6) The sequencing data and analysis code should be made publicly available before publication to ensure transparency and reproducibility.

      Thank you for this suggestion. As described in the Data availability section, all deepsequencing data generated in this study, including single-ended mRNA-Seq and Ribo-Seq data of 10 developmental stages and tissues of Drosophila simulans and paired-end mRNA-Seq data of 0-2 h, 26 h, 6-12 h, and 12-24 h Drosophila melanogaster embryos, were deposited in the China National Genomics Data Center Genome Sequence Archive (GSA) under accession numbers CRA003198, CRA007425, and CRA007426. The mRNA-Seq and Ribo-Seq data for the different developmental stages and tissues of Drosophila melanogaster were published in our previous paper [8] and were deposited in the Sequence Read Archive (SRA) under accession number SRP067542.

      All original code has been deposited on GitHub: https://github.com/lujlab/uORF_buffer; https://github.com/lujlab/Buffer_eLife2025.

      Response reference

      (1) Li, X.Y., MacArthur, S., Bourgon, R., Nix, D., Pollard, D.A., Iyer, V.N., Hechmer, A., Simirenko, L., Stapleton, M., Luengo Hendriks, C.L., et al. (2008). Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6, e27. 10.1371/journal.pbio.0060027.

      (2) Horner, V.L., Czank, A., Jang, J.K., Singh, N., Williams, B.C., Puro, J., Kubli, E., Hanes, S.D., McKim, K.S., Wolfner, M.F., and Goldberg, M.L. (2006). The Drosophila calcipressin sarah is required for several aspects of egg activation. Curr Biol 16, 1441-1446. 10.1016/j.cub.2006.06.024.

      (3) Lee, K.M., Linskens, A.M., and Doe, C.Q. (2022). Hunchback activates Bicoid in Pair1 neurons to regulate synapse number and locomotor circuit function. Curr Biol 32, 2430-2441 e2433. 10.1016/j.cub.2022.04.025.

      (4) Wharton, T.H., Nomie, K.J., and Wharton, R.P. (2018). No significant regulation of bicoid mRNA by Pumilio or Nanos in the early Drosophila embryo. PLoS One 13, e0194865. 10.1371/journal.pone.0194865.

      (5) Wang, J., Zhang, S., Lu, H., and Xu, H. (2022). Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction. Nat Commun 13, 2714. 10.1038/s41467-022-30315-6.

      (6) Xu, H., Sepulveda, L.A., Figard, L., Sokac, A.M., and Golding, I. (2015). Combining protein and mRNA quantification to decipher transcriptional regulation. Nat Methods 12, 739-742. 10.1038/nmeth.3446.

      (7) Zhang, H., Wang, Y., Wu, X., Tang, X., Wu, C., and Lu, J. (2021). Determinants of genomewide distribution and evolution of uORFs in eukaryotes. Nat Commun 12, 1076. 10.1038/s41467-021-21394-y.

      (8) Zhang, H., Dou, S., He, F., Luo, J., Wei, L., and Lu, J. (2018). Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development. PLoS Biol 16, e2003903. 10.1371/journal.pbio.2003903.

    1. eLife Assessment

      These are valuable findings for those interested in how neural signals reflect auditory speech streams, and in understanding the roles of prediction, attention, and eye movements in this tracking. However, the evidence as it stands is incomplete. Further analyses are needed to clarify how the observed results relate to the relevant theoretical claims.

    2. Reviewer #1 (Public review):

      Summary:

      This study aimed at replicating two previous findings that showed (1) a link between prediction tendencies and neural speech tracking, and (2) that eye movements track speech. The main findings were replicated which supports the robustness of these results. The authors also investigated interactions between prediction tendencies and ocular speech tracking, but the data did not reveal clear relationships. The authors propose a framework that integrates the findings of the study and proposes how eye movements and prediction tendencies shape perception.

      Strengths:

      This is a well-written paper that addresses interesting research questions, bringing together two subfields that are usually studied in separation: auditory speech and eye movements. The authors aimed at replicating findings from two of their previous studies, which was overall successful and speaks for the robustness of the findings. The overall approach is convincing, methods and analyses appear to be thorough, and results are compelling.

      Weaknesses:

      Eye movement behavior could have presented in more detail and the authors could have attempted to understand whether there is a particular component in eye movement behavior (e.g., blinks, microsaccades) that drives the observed effects.

    3. Reviewer #2 (Public review):

      Summary

      Schubert et al. recorded MEG and eye tracking activity while participants were listening to stories in single-speaker or multi-speaker speech. In a separate task, MEG was recorded while the same participants were listening to four types of pure tones in either structured (75% predictable) or random (25%) sequences. The MEG data from this task was used to quantify individual 'prediction tendency': the amount by which the neural signal is modulated by whether or not a repeated tone was (un)predictable, given the context. In a replication of earlier work, this prediction tendency was found to correlate with 'neural speech tracking' during the main task. Neural speech tracking is quantified as the multivariate relationship between MEG activity and speech amplitude envelope. Prediction tendency did not correlate with 'ocular speech tracking' during the main task. Neural speech tracking was further modulated by local semantic violations in the speech material and by whether or not a distracting speaker was present. The authors suggest that part of the neural speech tracking is mediated by ocular speech tracking. Story comprehension was negatively related with ocular speech tracking.

      Strengths

      This is an ambitious study, and the authors' attempt to integrate the many reported findings related to prediction and attention in one framework is laudable. The data acquisition and analyses appear to be done with great attention to methodological detail. Furthermore, the experimental paradigm used is more naturalistic than was previously done in similar setups (i.e.: stories instead of sentences).

      Weaknesses

      While the analysis pipeline is outlined in much detail, some analysis choices appear ad-hoc and could have been more uniform and/or better motivated (other than: this is what was done before).

    4. Reviewer #3 (Public review):

      I thank the authors for their extensive revision of this paper, and I found some elements greatly improved.<br /> In particular, the authors do embrace a somewhat more speculative tone in the current version, which I think is fitting for this work, as the data seem (to me) to be not fully conclusive. The data set collected here is clearly valuable and unique (and I would encourage the authors to make it publicly available!), however, my overall impression is that the specific analyses reported here might not fully

      Despite the revised description of methods, results and figures, I still have trouble understanding many of the results and the authors conclusive interpretation of them. These are my main reservations:

      (1) Regarding "individual prediction tendency" - thank you for adding clarifying methodological details and showing the data in a new Figure (#2). Honestly, however, I still can't say that I fully understand the result. For example, why is there also a significant response in the random condition as well? And how do you interpret the interesting time-course (with a peak ~200ms prior to the stimulus, and a reduction overtime from there?<br /> Also (I may have missed this, but..) what neural data was used to train the classifier and derive the "prediction tendency" index? Was it just the broadband neural response? Is there a way to know which sensors contributed to this metric (e.g., are they predominantly auditory? Frontal?)? And is there a way to establish the statistical significance of this metric (e.g., how good the decoder actually was in predicting behavioral sensitivity?). I don't see any statistics in the results section describing the individual prediction tendency.

      (2) Regarding the TRF analysis - Thanks for clarifying the approach used to obtain 2-second long "segments" of speech tracking. This is an interesting approach, however I think quite new(?) , and for me it raises a whole new set of questions, as well as additional controls and data that I would have liked to see, to be convinced that results are significant. I will elaborate:

      - Do I understand correctly that you segment the real and predicted neural response into 2-second long segments and then calculate the Pearsons' correlation between them to assess the goodness of the model? This is very unclear, since in the methods section you state only that "the same" analysis was performed as for the full data - but what exactly? Clearly, values will be very different when using such short segments. I feel that additional details are still required (and perhaps data shown) to fully understand the "semantic violation" analysis of TRFs.

      - I would like to reiterate my previous comment regarding the use of permutation tests to verify the validity of TRF-based measures derived. This would be especially important when using new approaches (such as the segmentation used here). The authors argue that this is not needed since this was not done in their previously published study. However, this sounds a bit like "two wrongs make a right" argument... why not just do it, and let us know that this 2-second segmentation approach allows estimating reliable speech tracking?

      - Following up on my previous comment that defining "clusters" as at least two neighboring channels (Figure 3) - the fact that this is a default in Fieldtrip is by no means sufficient justification!. This seems quite liberal to me, especially given the many comparisons performed. Here too, permutations can help to determine the necessary data-driven threshold for corrections. This is of course critical for interpreting the result shown in Figures 3E&G that are critical "take home messages" of the paper - i.e., that the prediction-index from the first part of the experiment is related to speech tracking in the second part of the experiment. To my eyes, this does not look extremely convincing, but perhaps the authors can show more conclusive data to support this (e.g., scatter plots of the betas across participant?).<br /> - A similar point can be made for the effect of semantic violations (though here the scalp-level result is somewhat more clustered). The authors point out that the semantic effect is a "replication" of their result reported in Schubert et al. 2023, but if I am not mistaken the results there were somewhat different (as was the manipulation). It would be nice to explicitly discuss the similarity/difference between these effects.

      (3) Regarding the ocular-TRFs -

      - Maybe this is just me, but I believe that effects that are robust should be clearly visible in the data, without the need for fancy "black-box" statistical models. In the case of the ocular TRFs, it is hard for me to see how these time-courses are not just noise (and, again, a permutation test would have helped to convince me..). The inconsistent results for horizontal and vertical eye-movements vis a vis the experimental conditions (single vs. multi-speaker conditions) don't help either, despite the authors argument that these are "independent" - but why should this be the case, especially if there is nothing really to look at in this task?<br /> - I remain with this scepticism for the mediation-portion of the analysis as well... But perhaps replications from other groups or making the data public will help shed further light on this in the future.

      Minor<br /> - Thanks for adding information about the creation of semantic-violation stimuli. Since the violations and lexical-controls were taken from different audio recordings, it would have been nice to verify that differences between neural responses cannot be attributed to differences in articulations (e.g., by comparing their spectro-temporal properties).

    5. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      Summary:

      This study aimed at replicating two previous findings that showed (1) a link between prediction tendencies and neural speech tracking, and (2) that eye movements track speech. The main findings were replicated which supports the robustness of these results. The authors also investigated interactions between prediction tendencies and ocular speech tracking, but the data did not reveal clear relationships. The authors propose a framework that integrates the findings of the study and proposes how eye movements and prediction tendencies shape perception.

      Strengths:

      This is a well-written paper that addresses interesting research questions, bringing together two subfields that are usually studied in separation: auditory speech and eye movements. The authors aimed at replicating findings from two of their previous studies, which was overall successful and speaks for the robustness of the findings. The overall approach is convincing, methods and analyses appear to be thorough, and results are compelling.

      Weaknesses:

      Linking the new to the previous studies could have been done in more detail, and the extent to which results were replicated could have been discussed more thoroughly.

      Eye movement behavior could have been presented in more detail and the authors could have attempted to understand whether there is a particular component in eye movement behavior (e.g., microsaccades) that drives the observed effects.

      We would like to thank you for your time and effort in reviewing our work and we appreciate the positive comments!

      We extended our manuscript, now providing intermediate results on individual prediction tendency, which can be compared to our results from Schubert et al., (2023).

      Furthermore, we expanded our discussion now detailing the extent to which our results (do not) replicate the previous findings (e.g. differences in horizontal vs. vertical ocular speech tracking, lack of distractor tracking, link between ocular speech tracking and behavioral outcomes).

      While we agree with the reviewer that it is an important and most interesting question, to what extent individual features of gaze behavior (such as microsaccades, blinks etc.) contribute to the ocular speech tracking effect, it is beyond the scope of the current manuscript. It will be methodologically and conceptually challenging to distinguish these features from one another and to relate them to diverse cognitive processes. We believe that a separate manuscript is needed to give these difficult questions sufficient space for new methodological approaches and control analyses. The primary goal of this manuscript was to replicate the findings of Gehmacher et al. (2024) using similar methods and to relate them to prediction tendencies, attention, and neural speech tracking. 

      Reviewer #2 (Public review):

      Summary

      Schubert et al. recorded MEG and eye-tracking activity while participants were listening to stories in single-speaker or multi-speaker speech. In a separate task, MEG was recorded while the same participants were listening to four types of pure tones in either structured (75% predictable) or random (25%) sequences. The MEG data from this task was used to quantify individual 'prediction tendency': the amount by which the neural signal is modulated by whether or not a repeated tone was (un)predictable, given the context. In a replication of earlier work, this prediction tendency was found to correlate with 'neural speech tracking' during the main task. Neural speech tracking is quantified as the multivariate relationship between MEG activity and speech amplitude envelope. Prediction tendency did not correlate with 'ocular speech tracking' during the main task. Neural speech tracking was further modulated by local semantic violations in the speech material, and by whether or not a distracting speaker was present. The authors suggest that part of the neural speech tracking is mediated by ocular speech tracking. Story comprehension was negatively related to ocular speech tracking.

      Strengths

      This is an ambitious study, and the authors' attempt to integrate the many reported findings related to prediction and attention in one framework is laudable. The data acquisition and analyses appear to be done with great attention to methodological detail (perhaps even with too much focus on detail-see below). Furthermore, the experimental paradigm used is more naturalistic than was previously done in similar setups (i.e. stories instead of sentences).

      Weaknesses

      For many of the key variables and analysis choices (e.g. neural/ocular speech tracking, prediction tendency, mediation) it is not directly clear how these relate to the theoretical entities under study, and why they were quantified in this particular way. Relatedly, while the analysis pipeline is outlined in much detail, an overarching rationale and important intermediate results are often missing, which makes it difficult to judge the strength of the evidence presented. Furthermore, some analysis choices appear rather ad-hoc and should be made uniform and/or better motivated.

      We would like to thank you very much for supporting our paper and your thoughtful feedback!

      To address your concerns, that our theoretical entities as well as some of our analytical choices lack transparency, we expanded our manuscript in several ways:

      (1) We now provide the intermediate results of our prediction tendency analysis (see new Figure 2 of our manuscript). These results are comparable to our findings from Schubert et al. (2023), demonstrating that on a group level there is a tendency to pre-activate auditory stimuli of high probability and illustrating the distribution of this tendency value in our subject population.

      (2) We expanded our methods section in order to explain our analytical choices (e.g. why this particular entropy modulation paradigm was used to measure individual prediction tendency).

      (3) We now provide an operationalisation of the terms “neural speech tracking” and “ocular speech tracking” at their first mention, to make these metrics more transparent to the reader.

      (4) We are summarizing important methodological information ahead of each results section, in order to provide the reader with a comprehensible background, without the necessity to read through the detailed methods section. 

      (5) We expanded our discussion section, with a special emphasis on relating the key variables of the current investigation to theoretical entities.

      Reviewer #3 (Public review):

      Summary:

      In this paper, the authors measured neural activity (using MEG) and eye gaze while individuals listened to speech from either one or two speakers, which sometimes contained semantic incongruencies.

      The stated aim is to replicate two previous findings by this group: (1) that there is "ocular speech tracking" (that eye-movements track the audio of the speech), (2) that individual differences in neural response to tones that are predictable vs. not-predictable in their pitch is linked to neural response to speech. In addition, here they try to link the above two effects to each other, and to link "attention, prediction, and active sensing".

      Strengths:

      This is an ambitious project, that tackles an important issue and combines different sources of data (neural data, eye-movements, individual differences in another task) in order to obtain a comprehensive "model" of the involvement of eye-movements in sensory processing.

      The authors use many adequate methods and sophisticated data-analysis tools (including MEG source analysis and multivariate statistical models) in order to achieve this.

      Weaknesses:

      Although I sympathize with the goal of the paper and agree that this is an interesting and important theoretical avenue to pursue, I am unfortunately not convinced by the results and find that many of the claims are very weakly substantiated in the actual data.

      Since most of the analyses presented here are derivations of statistical models and very little actual data is presented, I found it very difficult to assess the reliability and validity of the results, as they currently stand. I would be happy to see a thoroughly revised version, where much more of the data is presented, as well as control analyses and rigorous and well-documented statistical testing (including addressing multiple comparisons).

      We thank you for your thoughtful feedback. We appreciate your concerns and will address them below in greater detail.

      These are the main points of concern that I have regarding the paper, in its current format.

      (1) Prediction tendencies - assessed by listening to sequences of rhythmic tones, where the pitch was either "predictable" (i.e., followed a fixed pattern, with 25% repetition) or "unpredictable" (no particular order to the sounds). This is a very specific type of prediction, which is a general term that can operate along many different dimensions. Why was this specific design selected? Is there theoretical reason to believe that this type of prediction is also relevant to "semantic" predictions or other predictive aspects of speech processing?

      Theoretical assumptions and limitations of our quantification of individual prediction tendency are now shortly summarized in the first paragraph of our discussion section. With this paradigm we focus on anticipatory “top-down” predictions, whilst controlling for possibly confounding “bottom-up” processes. Since this study aimed to replicated our previous work we chose the same entropy-modulation paradigm as in other studies from our group (e.g. Demarchi et al. 2019, Schubert et al. 2023;2024, Reisinger et al. 2024), which has proven to give reproducible findings of feature-specific preactivations of sounds in a context of low entropy. One advantage of this design is that it gives us the opportunity to directly compare the processing of “predictable” and “unpredictable” sounds of the same frequency in a time-resolved manner (this argument is now also included in the Methods section).

      Regarding the question to what extent this type of prediction might also be relevant to “semantic” predictions we would like to refer to our previous study (Schubert et al., 2023), where we explicitly looked at the interaction between individual prediction tendency and encoding of semantic violations in the cortex. (In short, there we found a spatially dissociable interaction effect, indicating an increased encoding of semantic violations that scales with prediction tendency in the left hemisphere, as well as a disrupted encoding of semantic violations for individuals with stronger prediction tendency in the right hemisphere.) We did not aim to replicate all our findings in the current study, but instead we focused on merging the most important results from two independent phenomena in the domain of speech processing and bringing them into a common framework. However, as now stated in our discussion, we believe that “predictions are directly linked to the interpretation of sensory information. This interpretation is likely to occur at different levels along the cognitive (and anatomical) hierarchy…” and that “this type of prediction is relevant for acoustic processing such as speech and music, whose predictability unfolds over time.”

      (2) On the same point - I was disappointed that the results of "prediction tendencies" were not reported in full, but only used later on to assess correlations with other metrics. Even though this is a "replication" of previous work, one would like to fully understand the results from this independent study. On that note, I would also appreciate a more detailed explanation of the method used to derive the "prediction tendency" metric (e.g, what portion of the MEG signal is used? Why use a pre-stimulus and not a post-stimulus time window? How is the response affected by the 3Hz steady-state response that it is riding on? How are signals integrated across channels? Can we get a sense of what this "tendency" looks like in the actual neural signal, rather than just a single number derived per participant (an illustration is provided in Figure 1, but it would be nice to see the actual data)? How is this measure verified statistically? What is its distribution across the sample? Ideally, we would want enough information for others to be able to replicate this finding).

      We now included a new figure (similar to Schubert et al. 2023) showing the interim results of the “prediction tendency” effect as well as individual prediction tendency values of all subjects.

      Furthermore we expanded the description of the “prediction tendency” metric in the Methods section, where we explain our analytical choices in more detail. In particular we used a pre-stimulus time window in order to capture “anticipatory predictions”. The temporally predictably design gives us the opportunity to capture this type of predictions. The integration across channels is handled by the multivariate pattern analysis (MVPA), which inherently integrates multidimensional data (as mentioned in the methods section we used data from 102 magnetometers) and links it to (in this case) categorical information.

      (3) Semantic violations - half the nouns ending sentences were replaced to create incongruent endings. Can you provide more detail about this - e.g., how were the words selected? How were the recordings matched (e.g., could they be detected due to audio editing?)? What are the "lexically identical controls that are mentioned"? Also, is there any behavioral data to know how this affected listeners? Having so many incongruent sentences might be annoying/change the nature of listening. Were they told in advance about these?

      We expanded the Methods section and included the missing information: 

      “We randomly selected half of the nouns that ended a sentence (N = 79) and replaced them with the other half to induce unexpected semantic violations. The swap of nouns happened in the written script before the audio material was recorded in order to avoid any effects of audio clipping. Narrators were aware of the semantic violations and had been instructed to read out the words as normal. Consequently all target words occurred twice in the text, once in a natural context (serving as lexical controls) and once in a mismatched context (serving as semantic violations) within each trial, resulting in two sets of lexically identical words that differed greatly in their contextual probabilities (see Figure 1F for an example). Participants were unaware of these semantic violations.” Since we only replaced 79 words with semantic violations in a total of ~ 24 minutes of audio material we believe that natural listening was not impaired. In fact none of the participants mentioned to have noticed the semantic violations during debriefing (even though they had an effect on speech tracking in the brain). 

      (4) TRF in multi-speaker condition: was a univariate or multivariate model used? Since the single-speaker condition only contains one speech stimulus - can we know if univariate and multivariate models are directly comparable (in terms of variance explained)? Was any comparison to permutations done for this analysis to assess noise/chance levels?

      For mTRF models it depends on the direction (“encoding” vs. “decoding”) whether or not the model is comparable to a univariate model. In our case of an encoding model the TRFs are fitted to each MEG channel independently. This gives us the possibility to explore the effect over different areas (whereas a multivariate “decoding” model would result in only one speech reconstruction value).

      In both conditions (single and multi speaker) a single input feature (the envelope of the attended speech stream) was used. Of course it would be possible to fit the model to use a multivariate encoding model, predicting the brain’s response to the total input of sounds. This would, however, target a slightly different question than ours as we aimed to investigate how much of the attended speech is tracked.

      Regarding your suggestion of a comparison to permutations to assess noise levels we would like to point out that we chose the same methodological approach as in our previous studies, that we aimed to replicate here. Indeed in these original studies no permuted versions (with exception of the mediation analysis where comparing a model with an additional input predictor to a single predictor model would not result in a fair comparison) have been used. We conducted the mTRF approach considering the guidelines of Crosse et al. (2016) to the best of our knowledge and in accordance with similar studies in this field.

      Crosse, M. J., Di Liberto, G. M., Bednar, A., & Lalor, E. C. (2016). The multivariate temporal response function (mTRF) toolbox: a MATLAB toolbox for relating neural signals to continuous stimuli. Frontiers in human neuroscience, 10, 604.

      (5) TRF analysis at the word level: from my experience, 2-second segments are insufficient for deriving meaningful TRFs (see for example the recent work by Mesik & Wojtczak). Can you please give further details about how the analysis of the response to semantic violations was conducted? What was the model trained on (the full speech or just the 2-second long segments?) Is there a particular advantage to TRFs here, relative - say - to ERPs (one would expect a relatively nice N400 response, not)? In general, it would be nice to see the TRF results on their own (and not just the modulation effects).

      We fully agree with the reviewers statement that 2-second segments would have been too short to derive meaningful TRFs. To investigate the effect of semantic violations, we used the same TRFs trained on the whole dataset (with 4-fold cross validation). The resulting true as well as the predicted data was segmented into single word epochs of 2 seconds. We selected semantic violations as well as their lexically identical controls and correlated true with predicted responses for every word. Thus, we conducted the same analysis as for the overall encoding effect, focusing on only part of the data. We have reformulated the Methods section accordingly to clear up this misunderstanding. Since the TRFs are identical to the standard TRFs from the overall neural speech tracking, they are not informative to the semantic violation effect. However, since the mTRF approach is the key method throughout the manuscript (and our main focus is not on the investigations of brain responses to semantic violations) we have favoured this approach over the classical ERF analysis. 

      (6) Another related point that I did not quite understand - is the dependent measure used for the regression model "neural speech envelope tracking" the r-value derived just from the 2sec-long epochs? Or from the entire speech stimulus? The text mentions the "effect of neural speech tracking" - but it's not clear if this refers to the single-speaker vs. twospeaker conditions or to the prediction manipulation. Or is it different in the different analyses? Please spell out exactly what metric was used in each analysis.

      As suggested we now provide a clear definition of each dependent metric for each analysis.

      “Neural speech tracking” refers to the correlation coefficients between predicted and true brain responses from the aforementioned encoding model, trained and tested on the whole audio material within condition (single vs. multi-speaker).

      Recommendations for the authors:

      Reviewing Editor Comments:

      The reviewers have provided a number of recommendations to improve the manuscript, particularly requesting that more data be reported, with an emphasis on the measurements themselves (eye movements and TRFs) rather than just the numerical outputs of mathematical models.

      We appreciate all the reviewers' and editor’s comments and effort to improve our manuscript. In the revised version we provide interim findings and missing data, updated figures that include an intuitive illustration of the metrics (such as TRFs), and a thoroughly revised discussion section where we focus on the relationship between our observed quantities and theoretical entities. We now offer operationalized definitions of the relevant concepts (“prediction tendency”, “active ocular sensing” and “selective attention”) and suggest how these entities might be related in the context of speech processing, based on the current findings. We are confident that this revision has improved the quality of our paper a lot and we are grateful for all the feedback and suggestions. 

      Reviewer #1 (Recommendations for the authors):

      (1) Participants had to fixate throughout the tasks. How did the authors deal with large eye movements that violated the instructed fixation?

      As described in the Methods section: “Participants were instructed to look at a black fixation cross at the center of a grey screen.” This instruction was not intended to enforce strict fixation but rather to provide a general reference point, encouraging participants to keep their gaze on the grey screen and avoid freely scanning the room or closing their eyes. Unlike trial-based designs, where strict fixation is feasible due to shorter trial durations, this approach did not impose rigid fixation requirements. Consequently, the threshold for "instruction violation" was inherently more flexible, and no additional preprocessing was applied to the gaze vectors.

      Fixating for such an extended period of time (1.5 hours?) is hard. Did fixation behavior change over time? Could (fixation) fatigue affect the correlations between eye movements and speech tracking? For example, fatigued participants had to correct their fixation more often and this drives, in part, the negative correlation with comprehension?

      Yes, participants spent approximately 2 hours in the MEG, including preparation time (~30 minutes). However, participants were given opportunities to rest their eyes between different parts and blocks of the experiment (e.g., resting state, passive listening, and audiobook blocks), which should help mitigate fatigue to some extent.

      That said, we agree that it is an intriguing idea that fatigue could drive the ocular speech tracking effect, with participants potentially needing to correct their gaze more as the experiment progresses. However, our analysis suggests this is unlikely for several reasons:

      (1) Cross-validation in encoding models: Ocular speech tracking effects were calculated using a 4-fold cross-validation approach (this detail has now been added to the Methods section; please see our response to public review #3). This approach reduces the influence of potential increases in gaze corrections over time, as the models are trained and validated on independent data splits.  Moreover, if there were substantial differences in underlying response magnitudes between folds - for instance, between the first and fourth fold - this would likely compromise the TRF's ability to produce valid response functions for predicting the left-out data. Such a scenario would not result in significant tracking, further supporting the robustness of the observed effects.

      (2) TRF time-course stability: If fatigue were driving increased gaze corrections, we would expect this to be reflected in a general offset (capturing the mean difference between folds) in the TRF time-courses shown in Figure 4 (right panel). However, no such trend / offset is evident.

      (3) Comparison of eye movement data: To directly investigate this possibility, we compared the amount of total eye movements between the first and last blocks for both the single and multi-speaker conditions. Total movement was calculated by first calculating the differences in pixel values between consecutive eye positions on both the x- and y-axes. The Euclidean distance was then computed for each difference, providing a measure of movement between successive time points. Summing these distances yielded the total movement for each block. Statistical analysis was performed separately for the single speaker (ASS) and multi-speaker (AMS) conditions. For each condition, paired comparisons were made between the first and last blocks (we resorted to non-parametric tests, if assumptions of normality were violated):

      For the single speaker condition (ASS), the normality assumption was not satisfied (p≤0.05p, Kolmogorov-Smirnov test). Consequently, a Wilcoxon signedrank test was conducted, which revealed no significant difference in total movements between the first and last blocks (z=−1.330, p=0.184). For the multi-speaker condition (AMS), the data met the normality assumption (p>0.05), allowing the use of a paired t-test. The results showed no significant difference in total movements between the first and last blocks (t=−0.184, p=0.855).

      The results are visualized in a bar plot (see below), where individual data points are displayed alongside the mean and standard error for each block. Statistical annotations indicate that neither condition demonstrated significant differences between the blocks. These findings suggest that total eye movements remained stable across the experimental conditions, regardless of whether participants were exposed to a single or multiple speakers.

      Author response image 1.

      (4) Behavioral responses: Participants’ behavioral responses did not indicate any decrease in comprehensibility for later blocks compared to earlier ones. Specifically, a comparison of comprehension scores between the first and last blocks revealed no significant difference in either the single-speaker condition (ASS; Wilcoxon signed-rank test Z=−0.5911, p=0.5545) or the multi-speaker condition (AMS; Wilcoxon signed-rank test: Z=0.5018, p=0.6158). These findings suggest that participants maintained consistent levels of comprehension throughout the experiment, regardless of the condition or block order. The results are visualized in a bar plot (see below), where individual data points are displayed alongside the mean and standard error for each block. Statistical annotations indicate that neither condition demonstrated significant differences between the blocks.

      Author response image 2.

      Together, these factors suggest that fatigue is unlikely to be a significant driver of the ocular speech tracking effects observed in this study.

      (2) The authors should provide descriptive statistics of fixation behavior /fixational eye movements. What was the frequency and mean direction of microsaccades, do they follow the main sequence, etc., quantify drift and tremor?

      Thank you for their suggestion regarding descriptive statistics. To address this, we computed the rates of microsaccades (which were extracted using the microsaccade detection algorithm as proposed in Liu, B., Nobre, A. C. & van Ede, F. Functional but not obligatory link between microsaccades and neural modulation by covert spatial attention. Nat. Commun. 13, 3503 (2022)) and fixations as these metrics are directly relevant to our study and the requests above.

      Microsaccade Rates:

      - Single speaker Condition: Mean = 2.306 Hz, SD = 0.363 Hz. ○ Multi speaker: Mean = 2.268 Hz, SD = 0.355 Hz.

      Fixation Rates:

      - Single speaker Condition: Mean = 2.858 Hz, SD = 1.617 Hz. ○ Multi speaker Condition: Mean = 2.897 Hz, SD = 1.542 Hz.

      These values fall within the expected ranges reported in the literature (fixation rates: 2– 4 Hz, microsaccade rates: ~0.5–2.5 Hz) and serve as a sanity check, confirming the plausibility of our eye-tracking data. Regarding the reviewer’s request for additional metrics (e.g., microsaccade direction, main sequence analysis, drift, and tremor), extracting these features would require advanced algorithms and analyses not supported by our current preprocessing pipeline or dataset. We hope that the provided metrics, which were the main focus of this study, serve as a sufficient sanity check and highlight the robustness of our data.

      Related to this, I am wondering whether microsaccades are the feature that drives speech tracking.

      This is an important and pressing question that we aim to address in future publications. Currently, our understanding - and the reason microsaccades and blinks are not analysed in this manuscript - is limited by methodological constraints. Specifically, microsaccades are binary response vectors, which are not compatible with TRF analyses. Addressing this would require adapting future models to handle timecontinuous binary response data or exploring alternative approaches, such as regression-based ERFs (for example as in Heilbron et al. 2022). As the primary goal of this manuscript was to replicate the findings of Gehmacher et al. (2024) using similar methods and to integrate these findings into an initial unified framework, we did not investigate additional eye movement features here. However, we agree that microsaccades (and also blinks, see below) likely contribute, at least in part, to the observed ocular speech tracking effects, and we now suggest this in the Discussion:  

      “Relatedly, it remains an open question whether microsaccades are a key feature driving ocular speech tracking. However, our current study does not analyze microsaccades due to methodological constraints: microsaccades are binary response vectors, which are incompatible with TRF analyses used here. Addressing this would require adapting models to handle time-continuous binary response data or potentially exploring alternative approaches, such as regression-based ERFs (e.g., as in Heilbron et al., 2022). While these limitations preclude microsaccade analysis in the current study, we hypothesize that they could enhance temporal precision and selectively amplify relevant sensory input, supporting auditory perception. Future studies should explore this possibility to uncover the specific contributions of microsaccades to speech tracking.”

      (3) Can the authors make sure that interpolated blinks did not drive any of the effects? Can interpolated blink trials be excluded?

      Using continuous audiobooks as stimuli meant that we could not exclude blink periods from the analysis without introducing substantial continuation artifacts in the TRF analysis. Importantly, the concept of covert motor routines and active sensing suggests that participants engage more strongly in motor routines - including ocular behaviors such as microsaccades and blinks - during tasks like speech tracking. These motor routines are inherently tied to individual gaze patterns, making microsaccades and blinks correlated with other ocular behaviors. This complicates efforts to disentangle their individual contributions to the observed ocular speech tracking effects.

      Engagement in these motor routines, as posited by active sensing, would naturally load onto various viewing behaviors, further intertwining their roles.

      Even if we were to examine correlations, such as the amount of blinks with the ocular speech tracking effect, it is unlikely to provide a clearer understanding due to these inherent overlaps. The methodological and conceptual challenge lies in distinguishing these features from one another and understanding their respective roles in driving the observed effects.

      However, the aim of this manuscript was not to dissect the ocular speech tracking effect in greater detail, but rather to relate it - based on similar analytical choices as in Gehmacher et al - to prediction tendencies, attention, and neural speech tracking. While it will be crucial in future work to differentiate these patterns and their connections to diverse cognitive processes, it is beyond the scope of this study to address all these questions comprehensively.

      We acknowledge that eye movements, including microsaccades and blinks (however, see challenges for this in response 2), remain underexplored in many experimental paradigms. Their interplay with cognitive processes - such as attention, prediction, and sensory integration - will undoubtedly be an important focus for future studies. 

      (4) Could the authors provide more details on how time shuffling was done for the eyemovement predictor, and include a circularly shifted version (or a version that does not destroy temporal contiguity) in their model comparisons? Some types of shuffling can result in unrealistic time series, which would end up in an unfair comparison with the model that has the real eye movement traces as predictors.

      We thank the reviewer for their insightful question regarding the time-shuffling procedure for the eye-movement predictor and for suggesting the inclusion of a circularly shifted version in our model comparisons. Below, we provide further details about our approach and the rationale behind it:

      (1) Random Shuffling: In our analysis, the eye-movement predictor was randomly shuffled over time, meaning that individual samples were randomly replaced. This method completely disrupts the temporal structure of the signal, providing a null model that directly tests whether the temporal mediation observed is due to the specific temporal relationship between ocular movements and envelope tracking.

      (2) Circular Shifting: While circular shifting maintains temporal contiguity, it introduces certain challenges in the context of TRF analysis. Specifically:

      - Adaptation to Shifts: The TRF model could adapt to the introduced shift, potentially reducing the validity of the null comparison.

      - Similarity due to Repetition: The broadband envelope exhibits strong repetitive patterns over time, such as rhythms inherent to speech. Circular shifting can therefore produce predictors that are very similar to the original signal. As a result, this similarity may lead to null distributions that do not adequately disrupt the temporal mediation we aim to test, making it less robust as a control.

      (3) Rationale for Random Shuffling: The primary goal of our mediation analysis is to determine whether there is a temporal mediation of envelope tracking by ocular movements. By deliberately destroying the temporal structure through random shuffling, we ensure that the null model tests for the specific temporal relationship that is central to our hypothesis. Circularly shifted predictors, on the other hand, may partially preserve temporal dependencies, making them less suitable for this purpose.

      In summary, while circular shifting is a valuable approach in other contexts, it is less appropriate for the specific goals of this study. We hope this explanation clarifies our methodological choices and demonstrates their alignment with the aims of our analysis.

      (5) Replication: I want to point out that it is great that the previous findings were in principle replicated. However, I would like to suggest a more nuanced evaluation of the replication:

      a) Instead of a (direct) replication, the present study should be called a 'conceptual replication', since modifications in design and procedure were made.

      Thank you very much for this suggestion! We now use the term ‘conceptual replication’ throughout the manuscript.

      b) Not all the findings from the Gehmacher et al., 2024 study were replicated to a full extent:

      Did the authors find indications of a vertical vs. horizontal tracking difference in the Gehmacher 2024 data? Could they check this in the Gehmacher 2024 data?

      The findings for horizontal and vertical gaze tracking in Gehmacher et al. (2024) are detailed in the supplementary material of that publication. Both single-speaker and multi-speaker target conditions showed significant speech tracking effects in both horizontal and vertical directions. However, there was a slightly stronger tracking effect for the single-speaker condition in the vertical direction. Due to the highly predictable structure of words in Gehmacher et al. effects here were probably overall boosted as compared to continuous audiobook listening, likely leading to the differentiation of horizontal and vertical gaze. See figures in Gehmacher et al. supplementary file for reference.

      c) Another difference between their previous and this study is the non-existent tracking of the multi-speaker distractor in this study. The authors should point this out clearly in the discussion and potentially provide an explanation.

      Thank you for highlighting this point! We now address this in the discussion:

      “Importantly, in contrast to Gehmacher et al. (2024), we did not observe ocular tracking of the multi-speaker distractor in this study. This difference is likely attributable to the simplistic single-trial, 5-word task structure in Gehmacher et al., which resulted in high temporal overlap between the target and distractor speech streams and likely drove the significant distractor-tracking effects observed in that study. The absence of such an effect during continuous listening in our study suggests that ocular tracking is indeed more specific to selective attention.”

      Minor:

      (1) I was a little surprised to not see an indication of eyes/eye movements in Figure 6. The intention of the authors might have been to create a general schematic illustration, but I find this a bit misleading. This paper provides nice evidence for a specific ocular effect in speech tracking. There is, to my knowledge, no indication that speech would be influenced by different kinds of active sensing (if there are, please include them in the discussion). Given that the visuomotor system is quite dominant in humans, it might actually be the case that the speech tracking the authors describe is specifically ocular.

      Taking into account all the reviewers' remarks on the findings and interpretations, we have updated this figure (now Fig. 7) in the manuscript to make it more specific and aligned with the revised discussion section. Throughout the manuscript, we now explicitly refer to active ocular sensing in relation to speech processing and have avoided the broader term 'active sensing' in this context. We hope these revisions address the concerns raised.

      (2) I find the part in the discussion (page 2, last paragraph) on cognitive processes hard to follow. I don't agree that 'cognitive processes' are easily separable from any of the measured responses (eye and brain). Referring to the example they provide, there is evidence that eye movements are correlated with brain activity that is correlated with memory performance. How, and more importantly, why would one separate those?

      Thank you for raising this important point. We have carefully considered your comments, particularly regarding the interplay between cognitive processes and measured responses (eye and brain), as well as the challenge of conceptually separating them. Additionally, we have incorporated Reviewer #2's query (13) into a unified and complementary reasoning. In response, we have rewritten the relevant paragraph in the discussion to provide a clearer and more detailed explanation of how ocular and neural responses contribute to speech processing in an interdependent manner. We hope this revision addresses your concerns and offers a more precise and coherent discussion on this topic:

      “Despite the finding that eye movements mediate neural speech tracking, the behavioural relevance for semantic comprehension appears to differ between ocular and neural speech tracking. Specifically, we found a negative association between ocular speech tracking and comprehension, indicating that participants with lower comprehension performance exhibited increased ocular speech tracking. Interestingly, no significant relationship was observed between neural tracking and comprehension.

      In this context, the negative association between ocular tracking and comprehension might reflect individual differences in how participants allocate cognitive resources. Participants with lower comprehension may rely more heavily on attentional mechanisms to process acoustic features, as evidenced by increased ocular tracking. This reliance could represent a compensatory strategy when higher-order processes, such as semantic integration or memory retrieval, are less effective. Importantly, our comprehension questions (see Experimental Procedure) targeted a broad range of processes, including intelligibility and memory, suggesting that this relationship reflects a trade-off in resource allocation between low-level acoustic focus and integrative cognitive tasks.

      Rather than separating eye and brain responses conceptually, our analysis highlights their complementary contributions. Eye movements may enhance neural processing by increasing sensitivity to acoustic properties of speech, while neural activity builds on this foundation to integrate information and support comprehension. Together, these systems form an interdependent mechanism, with eye and brain responses working in tandem to facilitate different aspects of speech processing.

      This interpretation is consistent with the absence of a difference in ocular tracking for semantic violations (e.g., words with high surprisal versus lexically matched controls), reinforcing the view that ocular tracking primarily reflects attentional engagement with acoustic features rather than direct involvement in semantic processing. This aligns with previous findings that attention modulates auditory responses to acoustic features (e.g., Forte et al., 2017), further supporting the idea that ocular tracking reflects mechanisms of selective attention rather than representations of linguistic content.

      Future research should investigate how these systems interact and explore how ocular tracking mediates neural responses to linguistic features, such as lexical or semantic processing, to better understand their joint contributions to comprehension.”.  

      (3) Attention vs. predictive coding. I think the authors end up with an elegant description of the observed effects, "as an "active sensing" mechanism that implements the attentional optimization of sensory precision." However, I feel the paragraph starts with the ill-posed question "whether ocular speech tracking is modulated not by predictive, but other (for example attentional) processes". If ocular tracking is the implementation of a process (optimization of sensory precision, aka attention), how could it be at the same time modulated by that process? In my opinion, adding the notion that there is a modulation by a vague cognitive concept like attention on top of what the paper shows does not improve our understanding of how speech tracking in humans works.

      Thank you for raising this point. We agree that it is critical to clarify the relationship between ocular speech tracking, attention, and predictive processes, and we appreciate the opportunity to refine this discussion.  

      To avoid the potential confusion that active ocular sensing represents on the one hand an implementation of selective attention on the other it seems to be modulated by it, we now use  the formulation “ocular speech tracking reflects attentional mechanisms rather than predictive processes.”

      To address your concern that the conceptualization of attention seems rather vague, we have revised the whole paragraph in order to redefine the theoretical entities in question (including selective attention) and to provide a clearer and more precise picture (see also our revised version of Fig. 6, now Fig. 7). We now focus on highlighting the distinct yet interdependent roles of selective attention and individual prediction tendencies for speech tracking.:

      “With this speculative framework we attempt to describe and relate three important phenomena with respect to their relevance for speech processing: 1) “Anticipatory predictions” that are created in absence of attentional demands and contain probabilistic information about stimulus features (here, inferred from frequency-specific pre-activations during passive listening to sound sequences). 2) “Selective attention” that allocates resources towards relevant (whilst suppressing distracting) information (which was manipulated by the presence or absence of a distractor speaker). And finally 3) “active ocular sensing”, which refers to gaze behavior that is temporally aligned to attended (but not unattended) acoustic speech input (inferred from the discovered phenomenon of ocular speech tracking). We propose that auditory inflow is, at a basic level, temporally modulated via active ocular sensing, which “opens the gates” in the sensory periphery at relevant timepoints. How exactly this mechanism is guided (for example where the information about crucial timepoints comes from, if not from prediction, and whether it requires habituation to a speechstream etc.) is yet unclear. Unlike predictive tendencies, active ocular sensing appears to reflect selective attention, manifesting as a mechanism that optimizes sensory precision. Individual differences with respect to anticipatory predictions on the other hand, seem to be independent from the other two entities, but nevertheless relevant for speech processing. We therefore support the notion that representational content is interpreted based on prior probabilistic assumptions. If we consider the idea that “a percept” of an (auditory) object is actually temporally and spatially distributed (across representational spacetime - see Fig. 7), the content of information depends on where and when it is probed (see for example Dennett, 1991 for similar ideas on consciousness). Having to select from multiple interpretations across space and time requires a careful balance between the weighting of internal models and the allocation of resources based on current goals. We suggest that in the case of speech processing, this challenge results in an independent adaptation of feature-based precision-weighting by predictions on the one hand and temporal precision-weighting by selective attention on the other.”

      Reviewer #2 (Recommendations for the authors):

      My main recommendation is outlined in the Weaknesses above: the overarching rationale for many analysis choices should be made explicit, and intermediate results should be shown where appropriate, so the reader can follow what is being quantified and what the results truly mean. Specifically, I recommend to pay attention to the following (in no particular order):

      (1) Define 'neural speech tracking' early on. (e.g.: 'The amount of information in the MEG signal that can multivariately be explained by the speech amplitude envelope.' (is that correct?))

      Thank you for pointing out that this important definition is missing. It is now defined at the first mention in the Introduction as follows: “Here (and in the following) “neural speech tracking” refers to a correlation coefficient between actual brain responses and responses predicted from an encoding model based solely on the speech envelope”.

      (2) Same for 'ocular speech tracking'. Here even reading the Methods does not make it unambiguous how this term is used.

      It is now defined at the first mention in the Introduction as follows: “Ocular speech tracking” (similarly to “neural speech tracking” refers to the correlation coefficient between actual eye movements and movements predicted from an encoding model based on the speech envelope”.

      In addition also define both (neural and ocular speech tracking) metrics in the Methods Section.

      (3) Related to this: for ocular speech tracking, are simply the horizontal and vertical eye traces compared to the speech envelope? If so, this appears somewhat strange: why should the eyes move more rightward/upward with a larger envelope? And the direction here depends on the (arbitrary) sign of right = positive, etc. (It would make more sense to quantify 'amount of movement' in some way, but if this is done, I missed it in Methods.)

      Thank you for your insightful comments. You are correct that the horizontal and vertical traces were used for ocular speech tracking, and no additional details were included in the Methods. While we agree that the observed rightward/upward movement may seem unusual, this pattern is consistent with previous findings, including those reported in Gehmacher et al. (2024). In that study, we discussed how ocular speech tracking could reflect a broader engagement of the motor system during speech perception. For example, we observed a general right-lateralized gaze bias when participants attended to auditory speech, which we hypothesized might resemble eye movements during text reading, with a similar temporal alignment (~200 ms). We also speculated that this pattern might differ in cultures that read text from right to left.

      We appreciate your suggestion to explore alternative methods for quantifying gaze patterns, such as the "amount of movement" or microsaccades. While these approaches hold promise for future studies, our primary aim here was to replicate previous findings using the same signal and analysis methods to establish a basis for further exploration.  

      (4) In the Introduction, specifically blink-related ocular activity is mentioned as being related to speech tracking (for which a reference is, incidentally, missing), while here, any blink-related activity is excluded from the analysis. This should be motivated, as it appears in direct contradiction.

      Thank you for pointing this out. The mention of blink-related ocular activity in the Introduction refers to findings by Jin et al. (2018), where such activity was shown to align with higher-order syntactic structures in artificial speech. We have now included the appropriate reference for clarity.

      While Jin et al. focused on blink-related activity, in the present study, we focused on gaze patterns to investigate ocular speech tracking, replicating findings from

      Gehmacher et al. (2024). This approach was motivated by our goal to validate previous results using the same methodology. Importantly to this point, the exclusion of blinks in our analysis was due to methodological constraints of TRF analysis, which requires a continuous response signal; blinks, being discrete and artifact-prone, are incompatible with this approach.

      To address your concern, we revised the Introduction to clarify this distinction and provide explicit motivation for focusing on gaze patterns. It now reads:

      “Along these lines, It has been shown that covert, mostly blink related eye activity aligns with higher-order syntactic structures of temporally predictable, artificial speech (i.e. monosyllabic words; Jin et al, 2018). In support of ideas that the motor system is actively engaged in speech perception (Galantucci et al., 2006; Liberman & Mattingly, 1985), the authors suggest a global entrainment across sensory and (oculo)motor areas which implements temporal attention. 

      In another recent study from our lab (Gehmacher et al., 2024), we showed that eye movements continuously track intensity fluctuations of attended natural speech, a phenomenon we termed ocular speech tracking. In the present study, we focused on gaze patterns rather than blink-related activity, both to replicate findings from

      Gehmacher et al. (2024) and because blink activity is unsuitable for TRF analysis due to its discrete and artifact-prone nature. Hence, “Ocular speech tracking” (similarly to “neural speech tracking” refers to the correlation coefficient between actual eye movements and movements predicted from an encoding model based on the speech envelope.”

      Jin, P., Zou, J., Zhou, T., & Ding, N. (2018). Eye activity tracks task-relevant structures during speech and auditory sequence perception. Nature communications, 9(1), 5374.

      (5) The rationale for the mediation analysis is questionable. Let speech envelope = A, brain activity = B, eye movements = C. The authors wish to claim that A -> C -> B. But it is equally possible that A -> B -> C. They reflect on this somewhat in Discussion, but throughout the rest of the paper, the mediation analysis is presented as specifically testing whether A -> B is mediated by C, which is potentially misleading.

      Indeed we share your concern regarding the directionality of the relationships in the mediation analysis. Our choice of ocular movements as a mediator was motivated by the fact that the relationship between acoustic speech and neural activity is well established, as well as previous results indicating that oculomotor activity contributes to cognitive effects in auditory attention (Popov et al., 2022). 

      Indeed, here we treat both interpretations (“ocular movements contribute to neural speech tracking” versus “neural activity contributes to ocular speech tracking”) as equal.  We now emphasise this point in our discussion quite thoroughly:

      “It is important to note that our current findings do not allow for inference on directionality. Our choice of ocular movements as a mediator was motivated by the fact that the relationship between acoustic speech and neural activity is well established, as well as previous results indicating that oculomotor activity contributes to cognitive effects in auditory attention (Popov et al., 2022). However, an alternative model may suggest that neural activity mediates the effect of ocular speech tracking. Hence, it is possible that ocular mediation of speech tracking may reflect a) active (ocular) sensing for information driven by (top-down) selective attention or b) improved neural representations as a consequence of temporally aligned increase of sensory gain or c) (not unlikely) both. In fact, when rejecting the notion of a single bottom-up flow of information and replacing it with a model of distributed parallel and dynamic processing, it seems only reasonable to assume that the direction of communication (between our eyes and our brain) will depend on where (within the brain) as well as when we look at the effect. Thus, the regions and time-windows reported here should be taken as an illustration of oculo-neural communication during speech processing rather than an attempt to "explain" neural speech processing by ocular movements.”

      (6) The mediation analysis can be improved by a proper quantification of the effect (sizes or variance explained). E.g. how much % of B is explained by A total, and how much of that can in turn be explained by C being involved? For drawing directional conclusions perhaps Granger causality could be used.

      In Figure 4 (now Figure 5) of our manuscript we use standardized betas (which correspond to effect sizes) to illustrate the mediation effect. With the current mTRF approach it is however not possible (or insightful) to compare the variance explained. It is reasonable to assume that variance in neural activity will be explained better when including oculomotor behavior as a second predictor along with acoustic simulation. However this increase gives no indication to what extent this oculomotor behavior was task relevant or irrelevant (since all kinds of “arbitrary” movements will be captured with brain activity and therefore lead to an increase in variance explained). For this reason we chose to pursue the widely accepted framework of mediation (Baron & Kenny, 1986). This (correlational) approach is indeed limited in its interpretations (see prev. response), however the goal of the current study was to replicate and illustrate the triad relationship of acoustic speech input, neural activity and ocular movements with no particular hypotheses on directionality.

      (7) Both prediction tendency and neural speech tracking depend on MEG data, and thus on MEG signal-to-noise ratio (SNR). It is possible some participants may have higher SNR recordings in both tasks, which may result in both higher (estimated) prediction tendency and higher (estimated) speech tracking. This would result in a positive correlation, as the authors observe. This trivial explanation should be ruled out, by quantifying the relative SNR and testing for the absence of a mediation here.

      We agree that for both approaches (MVPA and mTRF models) individual MEG SNR plays an important role. This concern has been raised previously and addressed in our previous manuscript (Schubert et al., 2023). First, it should be noted that our prediction tendency value is the result of a condition contrast (rather than simple decoding accuracy) which compensates for the influence of subject specific signal-to-noise ratio (as no vacuous difference in SNR is to be expected between conditions). Second, in our previous study we also used frequency decoding accuracy as a control variable to correlate with speech tracking variables of interest and found no significant effect.

      (8) Much of the analysis pipeline features temporal response functions (TRFs). These should be shown in a time-resolved manner as a key intermediate step.

      We now included the Neural Speech tracking TRFs into the Figure (now Figure 3).

      (9) Figure 2 shows much-condensed results from different steps in the pipeline. If I understand correctly, 2A shows raw TRF weights (averaged over some time window?), while 2B-F shows standardized mean posterior regressor weights after Bayesian stats? It would be very helpful to make much more explicit what is being shown here, in addition to showing the related TRFs.

      Thank you for pointing this out! The figure description so far has been indeed not very insightful on this issue. We now adapted the caption and hope this clarifies the confusion: “ Neural speech tracking is related to prediction tendency and word surprisal, independent of selective attention. A) Envelope (x) - response (y) relationships are estimated using deconvolution (Boosting). The TRF (filter kernel, h) models how the brain processes the envelope over time. This filter is used to predict neural responses via convolution. Predicted responses are correlated with  actual neural activity to evaluate model fit and the TRF's ability to capture response dynamics. Correlation coefficients from these models are then used as dependent variables in Bayesian regression models. (Panel adapted from Gehmacher et al., 2024b). B) Temporal response functions (TRFs) depict the time-resolved neural tracking of the speech envelope for the single speaker and multi speaker target condition, shown here as absolute values averaged across channels. Solid lines represent the group average. Shaded areas represent 95% Confidence Intervals. C–H) The beta weights shown in the sensor plots are derived from Bayesian regression models in A). For Panel C, this statistical model is based on correlation coefficients computed from the TRF models (further details can be found in the Methods Section). C) In a single speaker condition, neural tracking of the speech envelope was significant for widespread areas, most pronounced over auditory processing regions. D) The condition effect indicates a decrease in neural speech tracking with increasing noise (1 distractor). E) Stronger prediction tendency was associated with increased neural speech tracking over left frontal areas. F) However, there was no interaction between prediction tendency and conditions of selective attention. G) Increased neural tracking of semantic violations was observed over left temporal areas. H) There was no interaction between word surprisal and speaker condition, suggesting a representation of surprising words independent of background noise. Marked sensors indicate ‘significant’ clusters, defined as at least two neighboring channels showing a significant result. N = 29.”

      Gehmacher, Q., Schubert, J., Kaltenmaier, A., Weisz, N., & Press, C. (2024b). The "Ocular Response Function" for encoding and decoding oculomotor related neural activity. bioRxiv, 2024-11.

      (10) Bayesian hypothesis testing is not done consistently. Some parts test for inclusion of 0 in 94% HDI, while some parts adopt a ROPE approach. The same approach should be taken throughout. Additionally, Bayes factors would be very helpful (I appreciate these depend on the choice of priors, but the default Bambi priors should be fine).

      Our primary aim in this study was to replicate two recent findings: (1) the relationship between individual prediction tendencies and neural speech tracking, and (2) the tracking of the speech envelope by eye movements. To maintain methodological consistency with the original studies, we did not apply a ROPE approach when analyzing these replication effects. Instead, we followed the same procedures as the original work, focusing on the inclusion of 0 in the HDI for the neural effects and using the same methods for the ocular effects. Additionally, we were not specifically interested in potential null effects in these replication analyses, as our primary goal was to test whether we could reproduce the previously reported findings.

      For the mediation analysis, however, we chose to extend the original approach by not only performing the analysis in a time-resolved manner but also applying a ROPE approach. This decision was motivated by our interest in gaining more comprehensive insights — beyond the replication goals — by also testing for potential null effects, which can provide valuable information about the presence or absence of mediation effects.

      We appreciate your thoughtful feedback and hope this clarifies our rationale for the differing approaches in our Bayesian hypothesis testing. 

      Regarding Bayes Factors, 

      We understand that some researchers find Bayes Factors appealing, as they offer a seemingly simple and straightforward way to evaluate the evidence in favor of/ or against H0 in relation to H1 (e.g. BF10 > 102 =  Decisive; according to the Jeffreys Scale). However, in practice Bayes Factors are often misunderstood e.g. by interpreting Bayes Factor as posterior odds or not acknowledging the notion of relative evidence in the Bayes Factor (see Wong et al. 2022). Instead of using Bayes Factors, we prefer to rely on estimating and reporting the posterior distribution of parameters given the data, prior and model assumptions (in form of the 94% HDI). This allows for a continuous evaluation of evidence for a given hypothesis that is in our eyes easier to interpret as a Bayes Factor.

      Jeffreys, Harold (1998) [1961]. The Theory of Probability (3rd ed.). Oxford, England. p. 432. ISBN 9780191589676.

      Wong, T. K., Kiers, H., & Tendeiro, J. (2022). On the Potential Mismatch Between the Function of the Bayes Factor and Researchers’ Expectations. Collabra: Psychology, 8(1), 36357. https://doi.org/10.1525/collabra.36357

      (11) It would be helpful if Results could be appreciated without a detailed read of Methods. I would recommend a recap of each key methodological step before introducing the relevant Result. (This may also help in making the rationale explicit.)

      In addition to the short recaps of methods that were already present, and information on quantifications of neural and ocular tracking and bayes statistics (see responses 1, 2, 9), we now added the following parts below to the results sections. Please refer to them in the context of the manuscript where they should now complement a key recap of methodological steps necessary to readily understand each analysis and rational that led to the results:

      Individual prediction tendency is related to neural speech tracking:

      “Thus, this measure is a single value per subject, which comprises a) differences between two contextual probabilities (i.e. ordered vs. random) in b) feature-specific tone representations c) in advance of their observation (summed over a time-window of -0.3 - 0 s). Importantly, this prediction tendency was assessed in an independent entropy modulation paradigm (see Fig. 1). On a group level we found an increased tendency to pre-activate a stimulus of high probability (i.e. forward transition) in an ordered context compared to a random context (see Fig, 2A). This effect replicates results from our previous work (Schubert et al., 2023, 2024). Using the summed difference between entropy levels (ordered - random) across pre-stimulus time, one value was extracted per subject (Fig. 2B). This value was used as a proxy for “individual prediction tendency” and correlated with encoding of clear speech across different MEG sensors. [...]

      Neural speech tracking, quantified as the correlation coefficients between predicted and observed MEG responses to the speech envelope, was used as the dependent variable in Bayesian regression models. These models included condition (single vs. multi-speaker) as a fixed effect, with either prediction tendency or word surprisal as an additional predictor, and random effects for participants.”

      Eye movements track acoustic speech in selective attention:

      “For this, we separately predicted horizontal and vertical eye movements from the acoustic speech envelope using temporal response functions (TRFs). The resulting model fit (i.e. correlation between true and predicted eye movements) is commonly referred to as “speech tracking”. Bayesian regression models were applied to evaluate tracking effects under different conditions of selective attention (single speaker, attended multi-speaker, unattended multi-speaker). Furthermore, we assessed whether individual prediction tendency or semantic word surprisal influenced ocular speech tracking.”

      Neural speech tracking is mediated by eye movements:

      “This model evaluates to what extent gaze behaviour functions as a mediator between acoustic speech input and brain activity.”

      Neural and ocular speech tracking are differently related to comprehension: “Bayesian regression models were used to investigate relationships between neural/ocular speech tracking and comprehension or difficulty. Ocular speech tracking was analyzed separately for horizontal and vertical eye movements.”

      (12) The research questions in the Introduction should be sharpened up, to make explicit when a question concerns a theoretical entity, and when it concerns something concretely measured/measurable.

      We sharpened them up:

      “Taking into account the aforementioned study by Schubert and colleagues (2023), the two recently uncovered predictors of neural tracking (individual prediction tendency and ocular tracking) raise several empirical questions regarding the relationship between predictive processes, selective attention, and active ocular sensing in speech processing:

      (1) Are predictive processes related to active ocular sensing in the same way they are to neural speech tracking? Specifically, do individuals with a stronger tendency to anticipate predictable auditory features, as quantified through prestimulus neural representations in an independent tone paradigm, show increased or even decreased ocular speech tracking, measured as the correlation between predicted and actual eye movements? Or is there no relationship at all?

      (2) To what extent does selective attention influence the relationship between prediction tendency, neural speech tracking, and ocular speech tracking? For example, does the effect of prediction tendency or ocular speech tracking on neural tracking differ between a single-speaker and multi-speaker listening condition?

      (3) Are individual prediction tendency and ocular speech tracking related to behavioral outcomes, such as comprehension and perceived task difficulty? Speech comprehension is assessed through accuracy on comprehension questions, and task difficulty is measured through subjective ratings.

      Although predictive processes, selective attention, and active sensing have been shown to contribute to successful listening, their potential interactions and specific roles in naturalistic speech perception remain unclear. Addressing these questions will help disentangle their contributions and establish an integrated framework for understanding how neural and ocular speech tracking support speech processing.”

      (13) The negative relationship between story comprehension and ocular speech tracking appears to go against the authors' preferred interpretation, but the reflection on this in the Discussion is very brief and somewhat vague.

      Thank you for pointing this out. We have taken your comments into careful consideration and also incorporated Reviewer #1's query (Minor point 2) into a unified and complementary reasoning. We have rewritten the relevant paragraph in the discussion to provide a clearer and more detailed explanation. We hope this revision offers a more precise and less vague discussion on this important point.

      “Despite the finding that eye movements mediate neural speech tracking, the behavioural relevance for semantic comprehension appears to differ between ocular and neural speech tracking. Specifically, we found a negative association between ocular speech tracking and comprehension, indicating that participants with lower comprehension performance exhibited increased ocular speech tracking. Interestingly, no significant relationship was observed between neural tracking and comprehension.

      In this context, the negative association between ocular tracking and comprehension might reflect individual differences in how participants allocate cognitive resources. Participants with lower comprehension may rely more heavily on attentional mechanisms to process acoustic features, as evidenced by increased ocular tracking. This reliance could represent a compensatory strategy when higher-order processes, such as semantic integration or memory retrieval, are less effective. Importantly, our comprehension questions (see Experimental Procedure) targeted a broad range of processes, including intelligibility and memory, suggesting that this relationship reflects a trade-off in resource allocation between low-level acoustic focus and integrative cognitive tasks.

      Rather than separating eye and brain responses conceptually, our analysis highlights their complementary contributions. Eye movements may enhance neural processing by increasing sensitivity to acoustic properties of speech, while neural activity builds on this foundation to integrate information and support comprehension. Together, these systems form an interdependent mechanism, with eye and brain responses working in tandem to facilitate different aspects of speech processing.

      This interpretation is consistent with the absence of a difference in ocular tracking for semantic violations (e.g., words with high surprisal versus lexically matched controls), reinforcing the view that ocular tracking primarily reflects attentional engagement with acoustic features rather than direct involvement in semantic processing. This aligns with previous findings that attention modulates auditory responses to acoustic features (e.g., Forte et al., 2017), further supporting the idea that ocular tracking reflects mechanisms of selective attention rather than representations of linguistic content.

      Future research should investigate how these systems interact and explore how ocular tracking mediates neural responses to linguistic features, such as lexical or semantic processing, to better understand their joint contributions to comprehension.”.  

      (14) Page numbers would be helpful.

      We added the page numbers.

      Reviewer #3 (Recommendations for the authors):

      Results

      (1) Figure 2 - statistical results are reported in this figure, but they are not fully explained in the text, nor are statistical values provided for any of the analyses (as far as I can tell).

      Also, how were multiple comparisons dealt with (the choice of two neighboring channels seems quite arbitrary)? Perhaps for this reason, the main result - namely the effect of "prediction tendency" and "semantic violations" - is quite sparse and might not survive more a rigorous statistical criterion. I would feel more comfortable with these results if the reporting of the statistical analysis had been more thorough (ideally, including comparison to control models).

      We would like to thank you again for your detailed queries, comments, and questions on our work. We first of all adapted this figure (now Figure 3 in the manuscript, please see responses 8 and 9 to Reviewer #2) to help readers understand the metrics and values within each statistical analysis. In addition, we indeed did not include the detailed statistics in the text! We now added the missing statistic reports calculated as averages over ‘clusters’:

      “Replicating previous findings (Schubert et al., 2023), we found widespread encoding of clear speech (average over cluster: β = 0.035, 94%HDI = [0.024, 0.046]), predominantly over auditory processing regions (Fig. 3C), that was decreased (β = -0.018, 94%HDI = [0.029, -0.006]) in a multi-speaker condition (Fig. 3D). Furthermore, a stronger prediction tendency was associated with increased neural speech tracking (β = 0.014, 94%HDI = [0.004, 0.025]) over left frontal sensors (see Fig. 3E). We found no interaction between prediction tendency and condition (see Fig. 3F).” [...] “In a direct comparison with lexically identical controls, we found an increased neural tracking of semantic violations (β = 0.039, 94%HDI = [0.007, 0.071]) over left temporal areas (see Fig. 3G). Furthermore, we found no interaction between word surprisal and speaker condition (see Fig. 3H).”

      Regarding the "prediction tendency" effect, it is important to note that this finding replicates a result from Schubert et al. (2023). The left frontal location of this effect is also consistent over studies, which convinces us of the robustness of the finding. Furthermore, testing this relationship properly requires a mixed-effects model in order to account for the variability across subjects that is not explained by fixed effects and the repeated measures design. For this reason a random Intercept had to be fitted for each subject (1|subject in the respective model formula). This statistical requirement motivated our decision to use bayesian statistics as (at least to our knowledge) there is no implementation of a cluster-based permutation mixed effects model (yet). In order to provide a more conservative criterion (as bayesian statistics don’t require a multiple comparison correction) we chose to impose in addition the requirement of a “clustered” effect.

      The choice of using two neighboring channels is consistent with the default parameter settings in FieldTrip’s cluster-based permutation testing (cfg.minnbchan = 2). This parameter specifies the minimum number of neighboring channels required for a sample to be included in the clustering algorithm, ensuring spatial consistency in the identified clusters. This alignment ensures that our methodology is comparable to numerous prior studies in the field, where such thresholds are standard. While it is true that all statistical analyses involve some degree of arbitrariness in parameter selection (e.g., alpha levels or clustering thresholds), our approach reflects established conventions and ensures comparability with previous findings.

      While the original study utilized source space analyses, we replicated this effect using only 102 magnetometers. This choice was made for computational simplicity, demonstrating that the effect is robust even without source-level modeling. Similarly, the "semantic violation" effect, while perceived as sparse, is based solely on magnetometer data and - in our opinion - should not be viewed as overly sparse given the methods employed. This effect aligns with the two-neighbor clustering approach, ensuring spatial consistency across magnetometers. The results reflect the robustness of the effects within the constraints of magnetometer-level analyses.

      Overall, the methodological choices, including the choice of a bayesian linear mixed effects model, the use of two neighboring channels and the reliance on magnetometers, are grounded in established practices and methodological considerations. While stricter thresholds or alternative approaches might yield different results, our methods align with best practices in the field and ensure the robustness, comparability, and replicability of our findings.

      (2) Figure 3 - the difference between horizontal and vertical eye-movements. This result is quite confusing and although the authors do suggest a possible interpretation for this in the discussion, I do wonder how robust this difference is or whether the ocular signal (in either direction) is simply too noisy or the effect too small to be detected consistently across conditions. Also, the ocular-TRFs themselves are not entirely convincing in suggesting reliable response/tracking of the audio - despite the small-but-significant increase in prediction accuracy.

      The horizontal versus vertical comparison was conducted to explore potential differences in how these dimensions contribute to ocular tracking of auditory stimuli (please also see our response to Reviewer #1, Response 5b, that includes the vertical vs. horizontal effects of Gehmacher at al. 2024). It would indeed be interesting to develop a measure that combines the two directions into a more natural representation of 'viewing,' such as a combined vector. However, this approach would require the use of complex numbers to represent both magnitude and direction simultaneously, hence the development of novel TRF algorithms capable of modeling this multidimensional signal. While beyond the scope of the current study, this presents an exciting avenue for future research and would allow us to move closer to understanding ocular speech tracking and the robustness of these effects, above and beyond the already successful replication.

      It is also important to emphasize that ocular-TRFs are derived from (viewing) behavioral data rather than neural signals, and are thus inherently subject to greater variability across participants and time. This higher variability does not necessarily indicate a small or unreliable effect but reflects the dynamic and task-dependent nature of eye movement behavior. The TRFs with shaded error margins represent this variability, highlighting how eye movements are influenced by both individual differences and moment-to-moment changes in task engagement.

      Despite this inherent variability, the significant prediction accuracy improvements confirm that ocular-TRFs reliably capture meaningful relationships between eye movements and auditory stimuli. The observed differences between horizontal and vertical TRFs further support the hypothesis that these dimensions are differentially involved in the task, possibly driven by the specific roles they play in sensorimotor coupling.

      (3) Figure 4 - this figure shows source distribution of 3 PCA components, derived from the results of the mediation effect of eye movements on the speech-tracking. Here too I am having difficulty in interpreting what the results actually are. For one, all three components are quite widespread and somewhat overlapping, so although they are statistically "independent" it is hard to learn much from them about the brain regions involved and whether they truly represent separable contributions. Similarly difficult to interpret are the time courses, which share some similarities with the known TRFs to speech (especially PC3). I would have expected to find a cleaner "auditory" response, and clearer separation between sensory regions and regions involved in the control of eye movements. I also wonder why the authors chose not to show the sourcelocalization of the neural and ocular speech-tracking responses alone - this could have helped us between understand what "mediation" of the neural response might look like.

      We appreciate the reviewer’s interest in better understanding the source distribution and time courses of the PCA components. While we acknowledge that the widespread and overlapping nature of the components may make a more fine grained interpretation challenging, it is important to emphasize that our analysis simply reflects the data, hence we can only present and interpret what the analysis revealed.

      Regarding your suggestion to show the source localization of ocular speech tracking and neural speech tracking alone, we would like to point out that ocular tracking is represented by only one channel for vertical and one channel for horizontal eye movements. Thus, in this case the estimated source of the effect are the eyes themselves. We believe that the source localization of neural speech tracking has been a thoroughly studied topic in research so far (locating it to perisylvian, auditory areas with a stronger preference for the left hemisphere) and can also be seen in Schubert et al., (2023). Nevertheless, we believe the observed PCA components still provide valuable, and most importantly novel insights into the interplay between eye movements and neural responses in speech tracking.  

      Discussion/interpretation

      (1) Although I appreciate the authors' attempt to propose a "unified" theoretical model linking predictions about low-level features to higher features, and the potential involvement of eye movements in 'active sensing' I honestly think that this model is overambitious, given the data presented in the current study. Moreover, there is very little discussion of past literature and existing models of active sensing and hierarchical processing of speech, that could have helped ground the discussion in a broader theoretical context. The entire discussion contains fewer than 20 citations (some of which are by these authors) and needs to be substantially enriched in order to provide context for the authors' claims.

      Thank you very much for your thoughtful feedback and for appreciating our approach. We hope that the revised manuscript addresses your concerns. Specifically, we now emphasize that our proposal is a conceptual framework, with the main goal to operationale “prediction tendency”, “active ocular sensing”, and “selective attention” and to “organise these entities according to their assumed function for speech processing and to describe their relationship with each other.” We did this by thoroughly revising our discussion section with a clear emphasis on the definition of terms, for example: 

      “With this speculative framework we attempt to describe and relate three important phenomena with respect to their relevance for speech processing: 1) “Anticipatory predictions” that are created in absence of attentional demands and contain probabilistic information about stimulus features (here, inferred from frequency-specific pre-activations during passive listening to sound sequences). 2) “Selective attention” that allocates resources towards relevant (whilst suppressing distracting) information (which was manipulated by the presence or absence of a distractor speaker). And finally 3) “active ocular sensing”, which refers to gaze behavior that is temporally aligned to attended (but not unattended) acoustic speech input (inferred from the discovered phenomenon of ocular speech tracking).”

      Our theoretical proposals are now followed by a recap of our results that support the respective idea, for example: 

      “...these predictions are formed in parallel and carry high feature-specificity but low temporal precision (as they are anticipatory in nature). This idea is supported by our finding that pure-tone anticipation is visible over a widespread prestimulus interval, instead of being locked to sound onset”

      “....we suggest that active (ocular) sensing does not necessarily convey feature- or content-specific information, it is merely used to boost (and conversely filter) sensory input at specific timescales (similar to neural oscillations). This assumption is supported by our finding that semantic violations are not differentially encoded in gaze behaviour than lexical controls.”

      And we put a strong focus on highlighting the boundaries of these ideas, in order to avoid theoretical confusion, misunderstandings or implicit theoretical assumption that are not grounded in data, in particular: 

      “In fact, when rejecting the notion of a single bottom-up flow of information and replacing it with a model of distributed parallel and dynamic processing, it seems only reasonable to assume that the direction of communication (between our eyes and our brain) will depend on where (within the brain) as well as when we look at the effect. Thus, the regions and time-windows reported here should be taken as an illustration of oculo-neural communication during speech processing rather than an attempt to "explain" neural speech processing by ocular movements.”

      “Even though the terminology [“hierarchy”] is suggestive of a fixed sequence (similar to a multi storey building) with levels that must be traversed one after each other (and even the more spurious idea of a rooftop, where the final perceptual experience is formed and stored into memory), we distance ourselves from these (possibly unwarranted) ideas. Our usage of “higher” or “lower” simply refers to the observation that the probability of a feature at a higher (as in more associative) level affects the interpretation (and thus the representation and prediction) of a feature at lower (as in more segregated) levels (Caucheteux et al., 2023).”

      Additionally, we have made substantial efforts to present complementary results (see response to Reviewer #2, point 8) to further substantiate our interpretation. Importantly, we have updated the illustration of the model (see response to Reviewer #, minor point 1) and refined both our interpretations and the conceptual language in the Discussion. Furthermore, we have included additional citations where appropriate to strengthen our argument.

      We would also like to briefly note that this section of the Discussion aimed to highlight existing literature that bridges the gap our model seeks to address. However, as this is a relatively underexplored area, the references available are necessarily limited.

      (2) Given my many reservations about the data, as presented in the current version of the manuscript, I find much of the discussion to be an over-interpretation of the results. This might change if the authors are able to present more robust results, as per some of my earlier comments.

      We sincerely hope that our comprehensive revisions have addressed your concerns and improved the manuscript to your satisfaction.

    1. eLife Assessment

      The authors analyses describe a novel mechanism by which a retrotransposon-derived LTR may be involved in genomic imprinting and demonstrate imprinting of the ZDBF2 locus in rabbits and Rhesus macaques using allele-specific expression analysis. This imprinting of the ZDBF2 locus correlates with transcription of GPR1-AS orthologs. The accompanying genomic analysis is very well executed allowing for the conclusions reached in the manuscript. The revisions made at the request of the reviewers in this important manuscript strengthen the evidence from the genomic analyses, and as a result, the evidence is now convincing and will be informative to the genomics and developmental biology communities.

    2. Reviewer #1 (Public review):

      Summary:

      The study tests the conservation of imprinting of the ZBDF2 locus across mammals. ZDBF2 is known to be imprinted in mouse, human and rat. The locus has a unique mechanism of imprinting: although imprinting is conferred by a germline DMR methylated in oocytes, the DMR is upstream to ZDBF2 (at GPR1) and monoallelic methylation of the gDMR does not persist beyond early developmental stages. Instead, a lncRNA (GPR1-AS, also known as Liz in mouse) initiating at the gDMR is expressed transiently in embryos and sets up a secondary DMR (by mechanisms not fully elucidated) that then confers monoallelic expression of ZDBF2 in somatic tissues.

      In this study, the authors first interrogate existing placental RNA-seq datasets from multiple mammalian species, and detect GPR1-AS1 candidate transcripts in human, baboon, macaque and mouse, but not in about a dozen other mammals. Because of the varying depth, quality and nature of these RNA-seq libraries, the ability to definitely detect the GPR1-AS1 lncRNA is not guaranteed; therefore, they generate their own deep, directional RNA-seq data from tissues/embryos from five species, finding evidence of GPR1-AS in rabbit, chimpanzee, but not bovine, pig or opossum. From these surveys, the authors conclude that the lncRNA is present only in Euarchontoglires mammals. To test the association between GPR1-AS and ZDBF2 imprinting, they perform RT-PCR and sequencing in tissue from wallabies and cattle, finding biallelic expression of ZDBF2 in these species that also lack a detected GPR1-AS transcript. From inspection of the genomic location of the GPR1-AS first exon, the authors identify an overlap with a solo LTR of the MER21C retrotransposon family in those species in which the lncRNA is observed, except for some rodents, including mouse. However, they do detect a degree of homology (46%) to the MER21C consensus at the first exon on Liz in mouse. Finally, the authors explore public RNA-seq datasets to show that GPR1-AS is expression transiently during human preimplantation development, an expression dynamic that would be consistent with the induction of monoallelic methylation of a somatic DMR at ZDBF2 and consequent monoallelic expression.

      Strengths:

      The analysis uncovers a novel mechanism by which a retrotransposon-derived LTR may be involved in genomic imprinting.<br /> The genomic analysis is very well executed.<br /> New directional and deeply-sequenced RNA-seq datasets from placenta or trophectoderm of five mammalian species and marsupial embryos, which will be of value to the community.

      Weaknesses:

      Although the genomic analysis is very strong, the study remains entirely correlative. All of the data are descriptive, and much of the analysis is performed on RNA-seq and other datasets from the public domain; a small amount of primary data is generated by the authors.<br /> Evidence that the residual LTR in mouse is functionally relevant for Liz lncRNA expression is lacking.

      Comments on revision:

      The authors have responded very constructively to all points raised by me and the other reviewers. For example, the authors have gone to further, extensive efforts in seeking to identify an LTR at the mouse Liz locus - which is not found - but additional multiple genome alignments provide evidence for sequence conservation consistent with retention of a functional relic of the MER21C in rodent genomes. Moreover, they demonstrate the promoter activity of this mouse sequence region in transfections. They have also demonstrated imprinted expression of ZDBF2 in two additional species - rabbit and rhesus macaque - consistent with their model.

    3. Reviewer #2 (Public review):

      Summary:

      This work concerns the evolution of ZDBF2 imprinting in mammalian species via initiation of GPR1 antisense (AS) transcription from a lineage-specific long-terminal repeat (LTR) retrotransposon. It extends previous work describing the mechanism of ZDBF2 imprinting in mice and humans by demonstrating conservation of GPR1-AS transcripts in rabbits and non-human primates. By identifying the origin of GPR1-AS transcription as the LTR MER21C, the authors claim to account for how imprinting evolved in these species but not in those lacking the MER21C insertion. This illustrates the principle of LTR co-option as a means of evolving new gene regulatory mechanisms, specifically to achieve parent-of-origin allele specific expression (imprinting). Examples of this phenomenon have been described previously, but usually involve initiation of transcription during gametogenesis rather than post-fertilization, as in this work. The findings of this paper are therefore relevant to biologists studying imprinted genes or interested more generally in the evolution of gene regulatory mechanisms.

      Strengths:

      (1) The authors convincingly demonstrate the existence of GPR1-AS orthologs in specific mammalian lineages using high quality RNA-seq libraries collected from diverse mammalian species.

      (2) The authors demonstrate imprinting of the ZDBF2 locus in rabbits and Rhesus macaques using allele-specific expression analysis. The transcription of GPR1-AS orthologs therefore correlates with imprinting of the ZDBF2 locus.

      Weaknesses:

      (1) Experimental evidence directly linking GPR1-AS transcription to ZDBF2 imprinting in rabbits and non-human primates is lacking. Consideration should be given to the challenges associated with studying non-model species and manipulating repeat sequences. Further, this mechanism is established in humans and mice, so the authors' model is arguably sufficiently supported merely by the existence of GPR1-AS orthologs in other mammalian lineages.

    4. Reviewer #3 (Public review):

      Kobayashi et al identify MER21C as a common promoter of GPR1-AS/Liz in Euarchontoglires, which establishes a somatic DMR that controls ZFDB2 imprinting. In mice, MER21C appears to have diverged significantly from its primate counterparts and is no longer annotated as such.

      The authors used high-quality cross-species RNA-seq data to characterise GPR1-AS-like transcripts, which included generating new data in five different species. The association between MER21C/B elements and the promoter of GPR1-AS in most species is clear and convincing. The expression pattern of MER21C/B elements overall further supports their role in enabling correct temporal expression of GPR1-AS during embryonic development.

      In the revised version of the manuscript the authors provided additional support for the common evolutionary origin of the GPR1-AS/Liz promoter between primates and rodents. They also showed a more extensive concordance between the presence of GPR1-AS-like transcripts and ZDBF2 imprinting.

      Altogether, these findings robustly support the conclusions of the paper, shedding light into the events underlying the evolution of imprinting at the ZDBF2 locus.

    5. Author response:

      The following is the authors’ response to the original reviews

      Recommendations For The Authors:

      Reviewer #1 (Recommendations For The Authors): 

      Recommendations  Analysis: 

      (1) Given that a MER21B/C LTR was not immediately identified at the start site of the Liz lncRNA in the mouse, and its match is only 46%, this raises the question of whether an analogous LTR would be identified at the homologous location in other species on deeper analysis. The authors need to argue that what has been conserved in the LTR alone in mouse is the essential element conferring the ability to initiate transcription of Liz. A transient reporter assay might be sufficient to do this. 

      We believe that the 46% identity between the first exon of mouse Liz and the consensus sequence of MER21C is so weak that its traces as MER21C are too attenuated to be detected by standard in silico analyses, such as homology searches. For instance, when pairwise alignments are performed between the first exon of mouse Liz and the consensus sequences of solo-LTRs other than MER21C, MER21C does not emerge as the most similar sequence (Figure 5 – figure supplement 1). This is in stark contrast to similar analyses involving the first exon of human and rabbit GPR1AS (which overlaps with MER21C), where MER21C is identified as the most similar sequence. [pages: 26, 31-32]

      The positions of these LTRs were initially annotated using RepeatMasker. To ensure robust analysis, we performed additional searches with RepeatMasker under more sensitive conditions, adjusting search engines (e.g., RMblast to HMMER or Cross-match) and sensitivity settings. Nevertheless, MER21C or closely related LTRs were still undetectable in mouse, rat, and hamster (Figure 4 – figure supplement 1). However, a multiple genome alignment generated by Cactus/UCSC revealed a syntenic region corresponding to the first exon of human GPR1-AS, overlapping with LTR21C, in the genomes of mice, as well as rats and hamsters (Figure 4 – figure supplement 2). Although RepeatMasker did not annotate MER21C at the GPR1 locus in these species, homologous regions were observed across all selected Euarchontoglires. Due to the limitations of the Cactus alignment track in delineating precise homologous boundaries across species, extracting sequences for evolutionary tree construction was not feasible. Nevertheless, these findings support the hypothesis that the first exon of GPR1-AS (Liz in mice) originated from a MER21C insertion in the common ancestor of Euarchontoglires. [pages: 21, 24-25]

      A combination of traditional annotation of repetitive elements using RepeatMasker and the reconstruction of ancestral genomes through multiple genome alignment can reveal highly degenerated LTR relics. This approach is likely to point to significant future directions for research. This point is further elaborated in the discussion section. [page 42]

      Furthermore, in response to the reviewer's suggestion, we investigated the promoter activity of the GPR1-AS and Liz first exons, which are hypothesized to have originated from the same MER21C insertion. Using a dual reporter assay, we demonstrated that the first exon of mouse Liz exhibits promoter activity in a human cell line comparable to that of the human GPR1-AS promoter. Thus, despite the relatively low sequence similarity between the Liz first exon and the MER21C consensus sequence (46% as determined by pairwise alignment, Figure 5 – figure supplement 2), the promoter activity remains functionally conserved. We further discuss the potential functional motifs within the putative MER21C LTR-derived sequences in Figure 4B-D. Taken together, these findings suggest that despite a high level of degeneracy of the promoter region in rodents, including mice, the most parsimonious explanation for the origin of this regulatory element in rodents is the presence of the same LTR relic detectable in humans/primates, which is essential for robust transcription initiation of Liz and GPR1-AS, respectively. [pages: 27, 32]

      (2) Imprinting will depend on an initiating mechanism in the germline, in addition to events in the embryo that induce the secondary DMR at ZDBF2. The authors should therefore examine as far as possible the presence of a gDMR in the species with/without GPR1-AS1 and ZDBF2 imprinting. Whole-genome bisulphite sequencing data from oocytes and sperm should exist for some of the relevant species (e.g., pig, cow: Ivanova et al. 2020 PMID: 32393379; Lu et al. 2012 PMID: 34818044). 

      As the reviewer noted, the presence of a gDMR is essential for the establishment of imprinting. Following another reviewer's suggestion, we have now demonstrated that the ZDBF2 gene in rhesus monkeys is also subject to imprinting (see Figure 3C-D). We also acquired whole genome bisulfite sequencing data for rhesus monkey sperm and oocytes, identified DMRs between them, and discovered an oocyte-specifically methylated gDMR in the first exon of GPR1-AS (which overlaps with MER21C)(Figure 3 – figure supplement 1A). This finding is consistent with observations in humans and mice. Conversely, we obtained similar sequencing data for porcine and bovine sperm and oocytes and conducted the same analysis (Figure 3 – figure supplement 1A,B). However, we did not detect any oocyte-specific methylated gDMRs in the GPR1 intragenic region (where GPR1AS is transcribed from an intron of GPR1) in these species of the Laurasiatheria superorder. These results support the hypothesis that ZDBF2 is not imprinted in lineages outside the Euarchontoglires, the superorder which includes both rodents and primates. We have included these important DMR results as a supplement to Figure 3. [pages 16-21]

      Presentation: 

      (1) The first section of the Introduction would benefit from the inclusion of some additional general references on genomic imprinting. 

      We have added two review articles, Tucci et al. (2019) and Kobayashi (2021), as references in the first section of the Introduction. [page 5]

      (2) Introduction statement: "....nearly 200 imprinted genes have been identified in mice and humans. However, less than half of these genes overlapped in both species." This was the conclusion of one study (Tucci et al. 2016), so it would be better to provide a caveat to the statement "However, one comparative analysis suggested that fewer than half of these genes overlapped in both species". 

      The point being that the actual number of imprinted genes is still a matter of debate (see Edwards et al. 2023 PMID: 36916665), and the extent of overlap will depend on the strength of the evidence for each gene in the human and mouse imprinted gene lists. So, it is very difficult to put an accurate figure on the extent of overlap - but the authors' point is valid that there are species- or lineage-specific imprinted genes. 

      We have revised this sentence following reviewer #1's suggestion. [page 5]

      (3) Introduction statement: "The establishment of species-specific imprinting.....can be driven by various evolutionary events, including.....differences in the function of DNA methyltransferases". I am not aware that this has been described as an evolutionary event causing species-specific imprinting - without supporting evidence, I recommend to remove this suggestion. 

      We thank the reviewer for this comment and realize that we should have been more explicit here. We were referring to DNMT3C, a rodent-specific member of the DNMT3 family, which is responsible for the paternal methylation imprinting of Rasgrf1 in mice (Barau et al., Science, 2016), in association with the piRNA pathway and targeting of a specific retrotransposon within the DMR (Watanabe et al. Science, 2011). The Rasgrf1 gene is imprinted in mice but not considered imprinted in humans (though some conflicting data exist). While it is likely that the emergence of DNMT3C was a pre-requisite to the establishment of Rasgrf1 imprinting in evolutionary terms, clear evidence is lacking. Following the reviewer’s suggestion, we have removed the phrase "differences in the function of DNA methyltransferases" from the text. However, we have reintroduced this point in the Introduction section as a potential mechanism that may contribute to the establishment of species-specific imprinted genes, alongside the roles of ZNF445 and ZFP57, which regulate the maintenance of imprinting with partially divided roles between humans and mice. [page 6]

      (4) It would be very useful for readers to have a schema of the Gpr1/Zdbf2 locus that indicates the locations of the germline and somatic DMRs and their relationship to the Liz transcript. 

      (5) There is a summary figure amongst the Supplementary Figures (Suppl. Fig. 7) - it would be beneficial to readers to have this summary figure in the main text rather than the supplement. 

      Following reviewer #1’s suggestion, we have moved the regulatory system schema at the Gpr1/Zdbf2 locus, originally shown in Supplementary Figure 7, to the main text as Figure 7. In addition, in response to comment 4, we have revised the figure to explicitly depict the relationship between the Liz transcript and the establishment of the somatic DMR (sDMR), enhancing the clarity of the regulatory interactions at this locus. [page 38]

      (6) With a focus of the study on LTRs as cis-regulatory elements having been co-opted in genomic imprinting mechanisms - whether in the female germline (as in Bogutz et al. 2019) or in the current study as an activating element post-fertilisation - it is a real omission that the authors do not to refer to the role of tissue-specific LTRs as the candidate regulatory elements in non-canonical imprinting (see Hanna et al. 2019 PMID: 31665063). Please include in Introduction and/or Discussion. 

      We added a sentence explaining canonical and non-canonical imprinting and the cases where LTRs act as regulatory elements in non-canonical imprinting, with reference to the study of Hanna et al., as suggested. [page 6]

      (7) Discussion statement: "Two paternally expressed imprinted genes, PEG10/SIRH1 and PEG11/RTL1/SIRH2 have been identified in mammals. They encode GAG-POL proteins of sushi-ichi LTR retrotransposons and are essential for mammalian placenta formation and maintenance." 

      These sentences should be combined: "Two paternally expressed imprinted genes, PEG10/SIRH1, and PEG11/RTL1/SIRH2, that encode GAG-POL proteins of sushi-ichi LTR retrotransposons have been identified in mammals and are essential for mammalian placenta formation and maintenance." 

      We have revised this sentence according to reviewer #1's suggestion. [page 41]

      Reviewer #2 (Recommendations For The Authors): 

      When showing assembled GPR1-AS transcripts via genome browser tracks, it would be valuable to add normalized counts of reads mapping to each strand, in order to more convincingly demonstrate the existence of these transcripts. I ask for this because in my experience Stringtie will assemble transcripts that are only marginally supported by reads. 

      In response to Reviewer #2's suggestion, FPKM and TPM values for all StringTiepredicted GPR1-AS-like transcripts are now included in Figure 6. Each of these transcripts has a TPM value greater than 1, supporting their validity. [pages: 35]

      Reviewer #3 (Recommendations For The Authors): 

      (1) The tree in Figure 5A is one of the main arguments supporting the divergence of the mouse Liz promoter from a common MER21C element, but this contains only a handful of species, making it difficult to appreciate the full extent of its evolution. Presumably its faster mutation rate in mouse would also be supported by other closely related rodents, which would solidify the conclusion that the Liz promoter is derived from an ancient MER21C insertion. So my suggestion is to expand this tree substantially to other species, comparing sequences syntenic to the GPR1-AS/Liz promoter. 

      (2) It may also be worth trying different TE/LTR annotation tools and/or running Repeatmasker with different parameters, to see if an MER21C element is detected in mouse using a more sensitive approach. 

      In response to this suggestion, we performed computational analyses with RepeatMasker under various settings (e.g., switching search engines from RMblast to HMMER or Crossmatch, adjusting speed/sensitivity settings from default to slow). Despite these modifications, a MER21C element was not detected near the mouse Liz promoter. However, a multiple genome alignment track generated by Cactus/UCSC revealed a syntenic region, corresponding to the first exon of human GPR1-AS, which overlaps with LTR21C, also present in the genomes of mouse, rat, and hamster (Figure 4 – figure supplement 1). While RepeatMasker did not identify MER21C at the GPR1 locus in these species, homologous regions were observed across all selected Euarchontoglires. Although the Cactus alignment track does not delineate the exact boundaries of homologous regions across species (relative to humans) and thus precludes extracting each homologous sequence to construct an evolutionary tree, these findings support the hypothesis that the first exon of GPR1-AS (referred to as Liz in mice) originated from an ancient MER21C insertion in the common ancestor of Euarchontoglires. [pages: 21, 24-25]

      (3) According to Dfam, MER21C is not common to all eutherians, but specific to Boroeutheria, whilst MER21B is presumably specific to Euarchontoglires. To clarify MER21C/B evolution, it would be useful to show the number of elements present in select species from each group (including an outgroup). 

      (7) In Figure 4 it is hard to distinguish between red and purple. 

      Initially, we referenced Repbase (e.g., MER21C: Origin/Eutheria), but, as Reviewer #3 noted, Dfam should be the primary reference. We have now included the copy numbers of MER21C and MER21B for each genome in Figure 4, providing a clearer understanding of their evolutionary appearance (MER21C appears specific to Boroeutheria, while MER21B is specific to Euarchontoglires). Additionally, we adjusted the MER21B position color from purple to dark purple to improve visibility. Furthermore, we have also underlined the copy number of MER21C or MER21B located within the GPR1 region in each species. For example, in the Treeshrew genome, the LTR overlapping with GPR1-AS is annotated as MER21B, so we underlined the copy number of MER21B (2,305). These changes now clearly indicate whether homologous sequences to the first exon of GPR1-AS are annotated as MER21C or MER21B in each genome. [page 22]

      (4) Could the imprinting status of ZDBF2 not be determined in chimpanzees and rabbits? Or is it already known? Either way, a clarification would be useful to further support the concordance between GPR1-AS-like transcripts and ZDBF2 imprinting.

      The imprinting status of ZDBF2 had not previously been reported in chimpanzees, rhesus macaques, or rabbits, where GPR1-AS-like transcripts were identified. Therefore, we conducted allele-specific expression analysis of ZDBF2 using blood samples from rhesus macaques and rabbits. As expected, paternal-allele-specific expression of ZDBF2 was observed in both species, consistent with findings in humans and mice. These results have been added to Figure 3. Although we did not analyze the imprinting status in chimpanzees, we believe the existing data sufficiently support our hypothesis. [pages: 16, 19-20]

      (5) The authors briefly discuss the role of KRAB-ZFPs in controlling TE expression. An interesting addition would be to analyse the expression of the main KRAB-ZFP that binds to MER21C (ZFP789, according to data from PMID 28273063). This could be linked to the temporal control of MER21C expression. 

      In response to Reviewer #3's suggestion, we focused on the expression pattern of ZNF789 (noted by the reviewer as ZFP789), the primary KRAB-ZFP known to bind MER21C, as identified by Didier Trono’s group (PMID 28273063). Strikingly, our analysis reveals that ZNF789 is specifically downregulated at the 4-cell stage, which aligns with the timing of MER21C reactivation. While it remains to be determined whether this downregulation directly influences MER21C reactivation or the initiation of GPR1-AS expression, this finding is significant and consistent with our model. We have incorporated this information in Figure 5 – figure supplement 3. [pages: 33]

      (6) The sentence "Liz directs DNA methylation at the somatic DMR, which competes with ZDBF2 to repress the paternal allele" (introduction) was confusing to me. 

      This sentence has been revised to be more accurate as follows; Liz transcription counteracts the H3K27me3-mediated repression of Zdbf2 by promoting the deposition of antagonistic DNA methylation at the secondary DMR. [page 7]

      (8) In Figure 5 I take it that 'consensus motif' refers to ELF1/2? Maybe change the legend. 

      To clarify potential confusion around the term 'consensus motif,' which may have been mistaken for 'consensus MER21C' (the consensus sequence of MER21C-LTR from the Dfam database), we have revised the figure legend. We now refer to the motif as the "common motif," indicating the sequence common to all MER21C-derived sequences and overlapping with the first exon of GPR1-AS. [page 29]

    1. eLife Assessment

      The ExA-SPIM methodology developed here and characterized and supported by convincing evidence is an important development for the field of light sheet microscopy as the new technology provides an impressive field of view making it possible to image the entire expanded mouse brain at cellular and subcellular resolution.

    2. Reviewer #1 (Public Review):

      Summary:

      Glaser et al present ExA-SPIM, a light-sheet microscope platform with large volumetric coverage (Field of view 85mm^2, working distance 35mm ), designed to image expanded mouse brains in their entirety. The authors also present an expansion method optimized for whole mouse brains, and an acquisition software suite. The microscope is employed in imaging an expanded mouse brain, the macaque motor cortex and human brain slices of white matter.

      This is impressive work, and represents a leap over existing light-sheet microscopes. As an example, it offers a ~ fivefold higher resolution than mesoSPIM (https://mesospim.org/), a popular platform for imaging large cleared samples. Thus while this work is rooted in optical engineering, it manifests a huge step forward and has the potential to become an important tool in the neurosciences.

      Strengths:

      -ExA-SPIM features an exceptional combination of field of view, working distance, resolution and throughput.

      -An expanded mouse brain can be acquired with only 15 tiles, lowering the burden on computational stitching. That the brain does not need to be mechanically sectioned is also seen as an important capability.

      -The image data is compelling, and tracing of neurons has been performed. This demonstrates the potential of the microscope platform.

      Review of the revised manuscript:

      The authors have carefully addressed my previous concerns and suggestions.

    3. Reviewer #2 (Public Review):

      In this manuscript, Glaser et al. describe a new selective plane illumination microscope designed to image a large field of view that is optimized for expanded and cleared tissue samples. For the most part, the microscope design follows a standard formula that is common among many systems (e.g. Keller PJ et al Science 2008, Pitrone PG et al. Nature Methods 2013, Dean KM et al. Biophys J 2015, and Voigt FF et al. Nature Methods 2019). The primary conceptual and technical novelty is to use a detection objective from the metrology industry that has a large field of view and a large area camera. The authors characterize the system resolution, field curvature, and chromatic focal shift by measuring fluorescent beads in a hydrogel and then show example images of expanded samples from mouse, macaque, and human brain tissue.

      Glaser et al. have responded to the reviewer comments by removing some of the overstated claims from the prior manuscript and editing portions of the manuscript text to enhance the clarity. Although the manuscript would be stronger if the authors had been able to provide data that justified the original high-impact claims from the initial publication (e.g. that the images could be used for robust and automated neuronal tracing across large volumes), the amended manuscript text now more closely matches the supporting data. As with the initial submission, I believe that the microscope design and characterization is a useful contribution to the field and the data are quite stunning.

    4. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews: 

      Reviewer #1 (Public Review): 

      Summary: 

      Glaser et al present ExA-SPIM, a light-sheet microscope platform with large volumetric coverage (Field of view 85mm^2, working distance 35mm), designed to image expanded mouse brains in their entirety. The authors also present an expansion method optimized for whole mouse brains and an acquisition software suite. The microscope is employed in imaging an expanded mouse brain, the macaque motor cortex, and human brain slices of white matter. 

      This is impressive work and represents a leap over existing light-sheet microscopes. As an example, it offers a fivefold higher resolution than mesoSPIM (https://mesospim.org/), a popular platform for imaging large cleared samples. Thus while this work is rooted in optical engineering, it manifests a huge step forward and has the potential to become an important tool in the neurosciences. 

      Strengths: 

      - ExA-SPIM features an exceptional combination of field of view, working distance, resolution, and throughput. 

      - An expanded mouse brain can be acquired with only 15 tiles, lowering the burden on computational stitching. That the brain does not need to be mechanically sectioned is also seen as an important capability. 

      - The image data is compelling, and tracing of neurons has been performed. This demonstrates the potential of the microscope platform. 

      Weaknesses: 

      - There is a general question about the scaling laws of lenses, and expansion microscopy, which in my opinion remained unanswered: In the context of whole brain imaging, a larger expansion factor requires a microscope system with larger volumetric coverage, which in turn will have lower resolution (Figure 1B). So what is optimal? Could one alternatively image a cleared (non-expanded) brain with a high-resolution ASLM system (Chakraborty, Tonmoy, Nature Methods 2019, potentially upgraded with custom objectives) and get a similar effective resolution as the authors get with expansion? This is not meant to diminish the achievement, but it was unclear if the gains in resolution from the expansion factor are traded off by the scaling laws of current optical systems. 

      Paraphrasing the reviewer: Expanding the tissue requires imaging larger volumes and allows lower optical resolution. What has been gained?

      The answer to the reviewer’s question is nuanced and contains four parts. 

      First, optical engineering requirements are more forgiving for lenses with lower resolution. Lower resolution lenses can have much larger fields of view (in real terms: the number of resolvable elements, proportional to ‘etendue’) and much longer working distances. In other words, it is currently more feasible to engineer lower resolution lenses with larger volumetric coverage, even when accounting for the expansion factor. 

      Second, these lenses are also much better corrected compared to higher resolution (NA) lenses. They have a flat field of view, negligible pincushion distortions, and constant resolution across the field of view. We are not aware of comparable performance for high NA objectives, even when correcting for expansion.

      Third, although clearing and expansion render tissues ‘transparent’, there still exist refractive index inhomogeneities which deteriorate image quality, especially at larger imaging depths. These effects are more severe for higher optical resolutions (NA), because the rays entering the objective at higher angles have longer paths in the tissue and will see more aberrations. For lower NA systems, such as ExaSPIM, the differences in paths between the extreme and axial rays are relatively small and image formation is less sensitive to aberrations. 

      Fourth, aberrations are proportional to the index of refraction inhomogeneities (dn/dx). Since the index of refraction is roughly proportional to density, scattering and aberration of light decreases as M^3, where M is the expansion factor. In contrast, the imaging path length through the tissue only increases as M. This produces a huge win for imaging larger samples with lower resolutions. 

      To our knowledge there are no convincing demonstrations in the literature of diffraction-limited ASLM imaging at a depth of 1 cm in cleared mouse brain tissue, which would be equivalent to the ExA-SPIM imaging results presented in this manuscript.  

      In the discussion of the revised manuscript we discuss these factors in more depth. 

      - It was unclear if 300 nm lateral and 800 nm axial resolution is enough for many questions in neuroscience. Segmenting spines, distinguishing pre- and postsynaptic densities, or tracing densely labeled neurons might be challenging. A discussion about the necessary resolution levels in neuroscience would be appreciated. 

      We have previously shown good results in tracing the thinnest (100 nm thick) axons over cm scales with 1.5 um axial resolution. It is the contrast (SNR) that matters, and the ExaSPIM contrast exceeds the block-face 2-photon contrast, not to mention imaging speed (> 10x).  

      Indeed, for some questions, like distinguishing fluorescence in pre- and postsynaptic structures, higher resolutions will be required (0.2 um isotropic; Rah et al Frontiers Neurosci, 2013). This could be achieved with higher expansion factors.

      This is not within the intended scope of the current manuscript. As mentioned in the discussion section, we are working towards ExA-SPIM-based concepts to achieve better resolution through the design and fabrication of a customized imaging lens that maintains a high volumetric coverage with increased numerical aperture.  

      - Would it be possible to characterize the aberrations that might be still present after whole brain expansion? One approach could be to image small fluorescent nanospheres behind the expanded brain and recover the pupil function via phase retrieval. But even full width half maximum (FWHM) measurements of the nanospheres' images would give some idea of the magnitude of the aberrations. 

      We now included a supplementary figure highlighting images of small axon segments within distal regions of the brain.  

      Reviewer #2 (Public Review): 

      Summary: 

      In this manuscript, Glaser et al. describe a new selective plane illumination microscope designed to image a large field of view that is optimized for expanded and cleared tissue samples. For the most part, the microscope design follows a standard formula that is common among many systems (e.g. Keller PJ et al Science 2008, Pitrone PG et al. Nature Methods 2013, Dean KM et al. Biophys J 2015, and Voigt FF et al. Nature Methods 2019). The primary conceptual and technical novelty is to use a detection objective from the metrology industry that has a large field of view and a large area camera. The authors characterize the system resolution, field curvature, and chromatic focal shift by measuring fluorescent beads in a hydrogel and then show example images of expanded samples from mouse, macaque, and human brain tissue. 

      Strengths: 

      I commend the authors for making all of the documentation, models, and acquisition software openly accessible and believe that this will help assist others who would like to replicate the instrument. I anticipate that the protocols for imaging large expanded tissues (such as an entire mouse brain) will also be useful to the community. 

      Weaknesses: 

      The characterization of the instrument needs to be improved to validate the claims. If the manuscript claims that the instrument allows for robust automated neuronal tracing, then this should be included in the data. 

      The reviewer raises a valid concern. Our assertion that the resolution and contrast is sufficient for robust automated neuronal tracing is overstated based on the data in the paper. We are hard at work on automated tracing of datasets from the ExA-SPIM microscope. We have demonstrated full reconstruction of axonal arbors encompassing >20 cm of axonal length.  But including these methods and results is out of the scope of the current manuscript. 

      The claims of robust automated neuronal tracing have been appropriately modified.  

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors): 

      Smaller questions to the authors: 

      - Would a multi-directional illumination and detection architecture help? Was there a particular reason the authors did not go that route?

      Despite the clarity of the expanded tissue, and the lower numerical aperture of the ExA-SPIM microscope, image quality still degrades slightly towards the distal regions of the brain relative to both the excitation and detection objective. Therefore, multi-directional illumination and detection would be advantageous. Since the initial submission of the manuscript, we have undertaken re-designing the optics and mechanics of the system. This includes provisions for multi-directional illumination and detection. However, this new design is beyond the scope of this manuscript. We now mention this in L254-255 of the Discussion section.

      - Why did the authors not use the same objective for illumination and detection, which would allow isotropic resolution in ASLM? 

      The current implementation of ASLM requires an infinity corrected objective (i.e. conjugating the axial sweeping mechanism to the back focal plane). This is not possible due to the finite conjugate design of the ExA-SPIM detection lens.

      More fundamentally, pushing the excitation NA higher would result in a shorter light sheet Rayleigh length, which would require a smaller detection slit (shorter exposure time, lower signal to noise ratio). For our purposes an excitation NA of 0.1 is an excellent compromise between axial resolution, signal to noise ratio, and imaging speed. 

      For other potentially brighter biological structures, it may be possible to design a custom infinity corrected objective that enables ASLM with NA > 0.1.

      - Have the authors made any attempt to characterize distortions of the brain tissue that can occur due to expansion? 

      We have not systematically characterized the distortions of the brain tissue pre and post expansion. Imaged mouse brain volumes are registered to the Allen CCF regardless of whether or not the tissue was expanded. It is beyond the scope of this manuscript to include these results and processing methods, but we have confirmed that the ExA-SPIM mouse brain volumes contain only modest deformation that is easily accounted for during registration to the Allen CCF. 

      - The authors state that a custom lens with NA 0.5-0.6 lens can be designed, featuring similar specifications. Is there a practical design? Wouldn't such a lens be more prone to Field curvature? 

      This custom lens has already been designed and is currently being fabricated. The lens maintains a similar space bandwidth product as the current lens (increased numerical aperture but over a proportionally smaller field of view). Over the designed field of view, field curvature is <1 µm. However, including additional discussion or results of this customized lens is beyond the scope of this manuscript.

      Reviewer #2 (Recommendations For The Authors): 

      System characterization: 

      - Please state what wavelength was used for the resolution measurements in Figure 2.

      An excitation wavelength of 561 nm was used. This has been added to the manuscript text.

      - The manuscript highlights that a key advance for the microscope is the ability to image over a very large 13 mm diameter field of view. Can the authors clarify why they chose to characterize resolution over an 8diameter mm field rather than the full area? 

      The 13 mm diameter field of view refers to the diagonal of the 10.6 x 8.0 mm field of view. The results presented in Figure 1c are with respect to the horizontal x direction and vertical y direction. A note indicating that the 13 mm is with respect to the diagonal of the rectangular imaging field has been added to the manuscript text. The results were presented in this way to present the axial and lateral resolution as a function of y (the axial sweeping direction).

      - The resolution estimates seem lower than I would expect for a 0.30 NA lens (which should be closer to ~850 nm for 515 nm emission). Could the authors clarify the discrepancy? Is this predicted by the Zemax model and due to using the lens in immersion media, related to sampling size on the camera, or something else? It would be helpful if the authors could overlay the expected diffraction-limited performance together with the plots in Figure 2C. 

      As mentioned previously, the resolution measurements were performed with 561 nm excitation and an emission bandpass of ~573 – 616 nm (595 nm average). Based on this we would expect the full width half maximum resolution to be ~975 nm. The resolution is in fact limited by sampling on the camera. The 3.76 µm pixel size, combined with the 5.0X magnification results in a sampling of 752 nm. Based on the Nyquist the resolution is limited to ~1.5 µm. We have added clarifying statements to the text.

      - I'm confused about the characterization of light sheet thickness and how it relates to the measured detection field curvature. The authors state that they "deliver a light sheet with NA = 0.10 which has a width of 12.5 mm (FWHM)." If we estimate that light fills the 0.10 NA, it should have a beam waist (2wo) of ~3 microns (assuming Gaussian beam approximations). Although field curvature is described as "minimal" in the text, it is still ~10-15 microns at the edge of the field for the emission bands for GFP and RFP proteins. Given that this is 5X larger than the light sheet thickness, how do the authors deal with this? 

      The generated light sheet is flat, with a thickness of ~ 3 µm. This flat light sheet will be captured in focus over the depth of focus of the detection objective. The stated field curvature is within 2.5X the depth of focus of the detection lens, which is equivalent to the “Plan” specification of standard microscope objectives.

      - In Figure 2E, it would be helpful if the authors could list the exposure times as well as the total voxels/second for the two-camera comparison. It's also worth noting that the Sony chip used in the VP151MX camera was released last year whereas the Orca Flash V3 chosen for comparison is over a decade old now. I'm confused as to why the authors chose this camera for comparison when they appear to have a more recent Orca BT-Fusion that they show in a picture in the supplement (indicated as Figure S2 in the text, but I believe this is a typo and should be Figure S3). 

      This is a useful addition, and we have added exposure times to the plot. We have also added a note that the Orca Flash V3 is an older generation sCMOS camera and that newer variants exist. Including the Orca BT-Fusion. The BT-Fusion has a read noise of 1.0 e- rms versus 1.6 e- rms, and a peak quantum efficiency of ~95% vs. 85%. Based on the discussion in Supplementary Note S1, we do not expect that these differences in specifications would dramatically change the data presented in the plot. In addition, the typo in Figure S2 has been corrected to Figure S3.

      - In Table S1, the authors note that they only compare their work to prior modalities that are capable of providing <= 1 micron resolution. I'm a bit confused by this choice given that Figure 2 seems to show the resolution of ExA-SPIM as ~1.5 microns at 4 mm off center (1/2 their stated radial field of view). It also excludes a comparison with the mesoSPIM project which at least to me seems to be the most relevant prior to this manuscript. This system is designed for imaging large cleared tissues like the ones shown here. While the original publication in 2019 had a substantially lower lateral resolution, a newer variant, Nikita et al bioRxiv (which is cited in general terms in this manuscript, but not explicitly discussed) also provides 1.5-micron lateral resolution over a comparable field of view. 

      We have updated the table to include the benchtop mesoSPIM from Nikita et al., Nature Communications, 2024. Based on this published version of the manuscript, the lateral resolution is 1.5 µm and axial resolution is 3.3 µm. Assuming the Iris 15 camera sensor, with the stated 2.5 fps, the volumetric rate (megavoxels/sec) is 37.41.

      - The authors state that, "We systematically evaluated dehydration agents, including methanol, ethanol, and tetrahydrofuran (THF), followed by delipidation with commonly used protocols on 1 mm thick brain slices. Slices were expanded and examined for clarity under a macroscope." It would be useful to include some data from this evaluation in the manuscript to make it clear how the authors arrived at their final protocol. 

      Additional details on the expansion protocol may be included in another manuscript.

      General comments: 

      There is a tendency in the manuscript to use negative qualitative terms when describing prior work and positive qualitative terms when describing the work here. Examples include: 

      - "Throughput is limited in part by cumbersome and error-prone microscopy methods". While I agree that performing single neuron reconstructions at a large scale is a difficult challenge, the terms cumbersome and error-prone are qualitative and lacking objective metrics.

      We have revised this statement to be more precise, stating that throughput is limited in part by the speed and image quality of existing microscopy methods.

      - The resolution of the system is described in several places as "near-isotropic" whereas prior methods were described as "highly anisotropic". I agree that the ~1:3 lateral to axial ratio here is more isotropic than the 1:6 ratio of the other cited publications. However, I'm not sure I'd consider 3-fold worse axial resolution than lateral to be considered "near" isotropic.

      We agree that the term near-isotropic is ambiguous. We have modified the text accordingly, removing the term near-isotropic and where appropriate stating that the resolution is more isotropic than that of other cited publications.

      - In the manuscript, the authors describe the photobleaching in their imaging conditions as "negligible". Figure S5 seems to show a loss of 60% fluorescence after 2000 exposures (which in the caption is described as "modest"). I'd suggest removing these qualitative terms and just stating the values.

      We agree and have changed the text accordingly.

      - The results section for Figure 5 is titled "Tracing axons in human neocortex and white matter". Although this section states "larger axons (>1 um) are well separated... allowing for robust automated and manual tracing" there is no data for any tracing in the manuscript. Although I agree that the images are visually impressive, I'm not sure that this claim is backed by data.

      We have now removed the text in this section referring to automated and manual tracing.

    1. eLife Assessment

      This comprehensive study presents important findings that delineate how specific dopaminergic neurons (DANs) instruct aversive learning in Drosophila larvae exposed to high salt through an integration of behavioral experiments, imaging, and connectomic analysis. The work reveals how a numerically minimal circuit achieves remarkable functional complexity, with redundancies and synergies within the DL1 cluster that challenge our understanding of how few neurons generate learning behaviors. By establishing a framework for sensory-driven learning pathways, the study makes a compelling and substantial contribution to understanding associative conditioning while demonstrating conservation of learning mechanisms across Drosophila developmental stages.

    2. Reviewer #1 (Public review):

      In this paper Weber et al. investigate the role of 4 dopaminergic neurons of the Drosophila larva in mediating the association between an aversive high-salt stimulus and a neutral odor. The 4 DANs belong to the DL1 cluster and innervate non-overlapping compartments of the mushroom body, distinct from those involved in appetitive associative learning. Using specific driver lines for individual neurons, the authors show that activation of the DAN-g1 is sufficient to mimic an aversive memory and it is also necessary to form a high-salt memory of full strength, although optogenetic silencing of this neuron has only a partial phenotype. The authors use calcium imaging to show that the DAN-g1 is not the only DAN responding to salt. DAN-c1 and d1 also respond to salt, but they seem to play no role for the associative memory. DAN-f1, which does not respond to salt, is able to lead to the formation of a memory (if optogenetically activated), but it is not necessary for the salt-odor memory formation in normal conditions. However, when silenced together with DAN-g1, it enhances the memory deficit of DAN-g1. Overall, this work brings evidence of a complex interaction between DL1 DANs in both the encoding of salt signals and their teaching role in associative learning, with none of them being individually necessary and sufficient for both functions.

      Overall, the manuscript contributes interesting results that are useful to understand the organization and function of the dopaminergic system. The behavioral role of the specific DANs is accessed using specific driver lines which allow to test their function individually and in pairs. Moreover, the authors perform calcium imaging to test whether DANs are activated by salt, a prerequisite for inducing a negative association to it. Proper genetic controls are carried across the manuscript.

    3. Reviewer #2 (Public review):

      Summary:

      In this work the authors show that dopaminergic neurons (DANs) from the DL1 cluster in Drosophila larvae are required for the formation of aversive memories. DL1 DANs complement pPAM cluster neurons which are required for the formation of attractive memories. This shows the compartmentalized network organization of how an insect learning center (the mushroom body) encodes memory by integrating olfactory stimuli with aversive or attractive teaching signals. Interestingly, the authors found that the 4 main dopaminergic DL1 neurons act partially redundant, and that single cell ablation did not result in aversive memory defects. However, ablation or silencing of a specific DL1 subset (DAN-f1,g1) resulted in reduced salt aversion learning, which was specific to salt but no other aversive teaching stimuli tested. Importantly, activation of these DANs using an optogenetic approach was also sufficient to induce aversive learning in the presence of high salt. Together with the functional imaging of salt and fructose responses of the individual DANs and the implemented connectome analysis of sensory (and other) inputs to DL1/pPAM DANs this represents a very comprehensive study linking the structural, functional and behavioral role of DL1 DANs. This provides fundamental insight into the function of a simple yet efficiently organized learning center which displays highly conserved features of integrating teaching signals with other sensory cues via dopaminergic signaling.

      Strengths:

      This is a very careful, precise and meticulous study identifying the main larval DANs involved in aversive learning using high salt as a teaching signal. This is highly interesting because it allows to define the cellular substrates and pathways of aversive learning down to the single cell level in a system without much redundancy. It therefore sets the basis to conduct even more sophisticated experiments and together with the neat connectome analysis opens the possibility to unravel different sensory processing pathways within the DL1 cluster and integration with the higher order circuit elements (Kenyon cells and MBONs). The authors' claims are well substantiated by the data and balanced, putting their data in the appropriate context. The authors also implemented neat pathway analyses using the larval connectome data to its full advantage, thus providing network pathways that contribute towards explaining the obtained results.

      Weaknesses:

      Previous comments were fully addressed by the authors.

    4. Reviewer #3 (Public review):

      The study of Weber et al. provides a thorough investigation of the roles of four individual dopamine neurons for aversive associative learning in the Drosophila larva. They focus on the neurons of the DL-1 cluster which already have been shown to signal aversive teaching signals. But the authors go beyond the previous publications and test whether each of these dopamine neurons responds to salt or sugar, is necessary for learning about salt, bitter, or sugar, and is sufficient to induce a memory when optogenetically activated. In addition, previously published connectomic data is used to analyze the synaptic input to each of these dopamine neurons. The authors conclude that the aversive teaching signal induced by salt is distributed across the four DL-1 dopamine neurons, with two of them, DAN-f1 and DAN-g1, being particularly important. Overall, the experiments are well designed and performed, support the authors' conclusions, and deepen our understanding of the dopaminergic punishment system.

      Strengths:

      (1) This study provides, at least to my knowledge, the first in vivo imaging of larval dopamine neurons in response to tastants. Although the selection of tastants is limited, the results close an important gap in our understanding of the function of these neurons.

      (2) The authors performed a large number of experiments to probe for the necessity of each individual dopamine neuron, as well as combinations of neurons, for associative learning. This includes two different training regimen (1 or 3 trials), three different tastants (salt, quinine and fructose) and two different effectors, one ablating the neuron, the other one acutely silencing it. This thorough work is highly commendable, and the results prove that it was worth it. The authors find that only one neuron, DAN-g1, is partially necessary for salt learning when acutely silenced, whereas a combination of two neurons, DAN-f1 and DAN-g1, are necessary for salt learning when either being ablated or silenced.

      (3) In addition, the authors probe whether any of the DL-1 neurons is sufficient for inducing an aversive memory. They found this to be the case for two of the neurons, largely confirming previous results obtained by a different learning paradigm, parameters and effector.

      (4) This study also takes into account connectomic data to analyze the sensory input that each of the dopamine neurons receives. This analysis provides a welcome addition to previous studies and helps to gain a more complete understanding. The authors find large differences in inputs that each neuron receives, and little overlap in input that the dopamine neurons of the "aversive" DL-1 cluster and the "appetitive" pPAM cluster seem to receive.

      (5) Finally, the authors try to link all the gathered information in order to describe an updated working model of how aversive teaching signals are carried by dopamine neurons to the larva's memory center. This includes important comparisons both between two different aversive stimuli (salt and nociception) and between the larval and adult stages.

    5. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this paper Weber et al. investigate the role of 4 dopaminergic neurons of the Drosophila larva in mediating the association between an aversive high-salt stimulus and a neutral odor. The 4 DANs belong to the DL1 cluster and innervate non-overlapping compartments of the mushroom body, distinct from those involved in appetitive associative learning. Using specific driver lines for individual neurons, the authors show that activation of the DAN-g1 is sufficient to mimic an aversive memory and it is also necessary to form a high-salt memory of full strength, although optogenetic silencing of this neuron has only a partial phenotype. The authors use calcium imaging to show that the DAN-g1 is not the only DAN responding to salt. DAN-c1 and d1 also respond to salt, but they seem to play no role for the associative memory. DAN-f1, which does not respond to salt, is able to lead to the formation of a memory (if optogenetically activated), but it is not necessary for the salt-odor memory formation in normal conditions. However, when silenced together with DAN-g1, it enhances the memory deficit of DAN-g1. Overall, this work brings evidence of a complex interaction between DL1 DANs in both the encoding of salt signals and their teaching role in associative learning, with none of them being individually necessary and sufficient for both functions.

      Strengths:

      Overall, the manuscript contributes interesting results that are useful to understand the organization and function of the dopaminergic system. The behavioral role of the specific DANs is accessed using specific driver lines which allow to test their function individually and in pairs. Moreover, the authors perform calcium imaging to test whether DANs are activated by salt, a prerequisite for inducing a negative association to it. Proper genetic controls are carried across the manuscript.

      Weaknesses:

      The authors use two different approaches to silence dopaminergic neurons: optogenetics and induction of apoptosis. The results are not always consistent, but the authors discuss these differences appropriately. In general, the optogenetic approach is more appropriate as developmental compensations are not of major interest for the question investigated.

      The physiological data would suggest the role of a certain subset of DANs in salt-odor association, but a different partially overlapping set is necessary in behavioral assays (with a partial phenotype). No manipulation completely abolishes the salt-odor association, leaving important open questions on the identity of the neural circuits involved in this behavior.

      The EM data analysis reveals a non-trivial organization of sensory inputs into DANs, but it is difficult to extrapolate a link to the functional data presented in the paper.

      We would like to once again thank Reviewer 1 for the positive assessment of our work and for the valuable suggestions provided on the first revision of the manuscript. In this second revision, we have addressed the linguistic issues and most of the minor comments as recommended. We now hope that the current version of our manuscript meets the reviewer’s expectations both in terms of language and content.

      Reviewer #2 (Public review):

      Summary:

      In this work the authors show that dopaminergic neurons (DANs) from the DL1 cluster in Drosophila larvae are required for the formation of aversive memories. DL1 DANs complement pPAM cluster neurons which are required for the formation of attractive memories. This shows the compartmentalized network organization of how an insect learning center (the mushroom body) encodes memory by integrating olfactory stimuli with aversive or attractive teaching signals. Interestingly, the authors found that the 4 main dopaminergic DL1 neurons act partially redundant, and that single cell ablation did not result in aversive memory defects. However, ablation or silencing of a specific DL1 subset (DAN-f1,g1) resulted in reduced salt aversion learning, which was specific to salt but no other aversive teaching stimuli tested. Importantly, activation of these DANs using an optogenetic approach was also sufficient to induce aversive learning in the presence of high salt. Together with the functional imaging of salt and fructose responses of the individual DANs and the implemented connectome analysis of sensory (and other) inputs to DL1/pPAM DANs this represents a very comprehensive study linking the structural, functional and behavioral role of DL1 DANs. This provides fundamental insight into the function of a simple yet efficiently organized learning center which displays highly conserved features of integrating teaching signals with other sensory cues via dopaminergic signaling.

      Strengths:

      This is a very careful, precise and meticulous study identifying the main larval DANs involved in aversive learning using high salt as a teaching signal. This is highly interesting because it allows to define the cellular substrates and pathways of aversive learning down to the single cell level in a system without much redundancy. It therefore sets the basis to conduct even more sophisticated experiments and together with the neat connectome analysis opens the possibility to unravel different sensory processing pathways within the DL1 cluster and integration with the higher order circuit elements (Kenyon cells and MBONs). The authors' claims are well substantiated by the data and balanced, putting their data in the appropriate context. The authors also implemented neat pathway analyses using the larval connectome data to its full advantage, thus providing network pathways that contribute towards explaining the obtained results.

      Weaknesses:

      Previous comments were fully addressed by the authors.

      We sincerely thank Reviewer 2 for the positive evaluation of our work. We are glad that our responses in the first revision addressed the previous concerns and appreciate the reviewer’s constructive feedback once again.

      Reviewer #3 (Public review):

      Summary:

      The study of Weber et al. provides a thorough investigation of the roles of four individual dopamine neurons for aversive associative learning in the Drosophila larva. They focus on the neurons of the DL-1 cluster which already have been shown to signal aversive teaching signals. But the authors go beyond the previous publications and test whether each of these dopamine neurons responds to salt or sugar, is necessary for learning about salt, bitter, or sugar, and is sufficient to induce a memory when optogenetically activated. In addition, previously published connectomic data is used to analyze the synaptic input to each of these dopamine neurons. The authors conclude that the aversive teaching signal induced by salt is distributed across the four DL-1 dopamine neurons, with two of them, DAN-f1 and DAN-g1, being particularly important. Overall, the experiments are well designed and performed, support the authors' conclusions, and deepen our understanding of the dopaminergic punishment system.

      Strengths:

      (1) This study provides, at least to my knowledge, the first in vivo imaging of larval dopamine neurons in response to tastants. Although the selection of tastants is limited, the results close an important gap in our understanding of the function of these neurons.

      (2) The authors performed a large number of experiments to probe for the necessity of each individual dopamine neuron, as well as combinations of neurons, for associative learning. This includes two different training regimen (1 or 3 trials), three different tastants (salt, quinine and fructose) and two different effectors, one ablating the neuron, the other one acutely silencing it. This thorough work is highly commendable, and the results prove that it was worth it. The authors find that only one neuron, DAN-g1, is partially necessary for salt learning when acutely silenced, whereas a combination of two neurons, DAN-f1 and DAN-g1, are necessary for salt learning when either being ablated or silenced.

      (3) In addition, the authors probe whether any of the DL-1 neurons is sufficient for inducing an aversive memory. They found this to be the case for two of the neurons, largely confirming previous results obtained by a different learning paradigm, parameters and effector.

      (4) This study also takes into account connectomic data to analyze the sensory input that each of the dopamine neurons receives. This analysis provides a welcome addition to previous studies and helps to gain a more complete understanding. The authors find large differences in inputs that each neuron receives, and little overlap in input that the dopamine neurons of the "aversive" DL-1 cluster and the "appetitive" pPAM cluster seem to receive.

      (5) Finally, the authors try to link all the gathered information in order to describe an updated working model of how aversive teaching signals are carried by dopamine neurons to the larva's memory center. This includes important comparisons both between two different aversive stimuli (salt and nociception) and between the larval and adult stages.

      We would also like to thank Reviewer 3 for the positive assessment of our work. Many of the constructive comments provided were incorporated into the first revision, contributing significantly to the improved clarity and overall quality of the manuscript.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Here are some minor comments (and some semantics that could be addressed to improve the manuscript)

      Title: is the title correct given that c1 and d1 do not really signal punishment?

      We think the title is correct and would like to keep it as it is.

      L72 striatum misspelled

      We have corrected the error.

      L74 constitute instead of provide?

      We made the suggested modification in the text.

      L129: "But can these four individual DANs also process other sensory modalities?" other then what? What was used before?

      We have made the required change, which now allows us to contrast somatosensory and chemosensory information.

      L172: (Please refer to the discussion regarding the partial reduction of the memory); would be more natural to explain shortly here, or add a sentence before this parenthesis that point to the effect

      We made the requested change in the manuscript and added a short sentence before the parenthesis.

      L182: "DL1 neurons convey a dopaminergic aversive teaching signal" you cannot make this statement from just TH-GAL4!

      We agree - that's why we have completely revised the sentence and now further restricted it and also refer to further larval and adult published data

      L264: "possible redundancy among" I don't think you are testing a redundancy here, it is more likely a developmental compensation.

      We made the requested change in the sentence and added a potential developmental compensation as an interpretation of our results.

      L296: "to determine if the activation of individual DL1 DANs signals aspects of the natural high salt punishment," - how can the optogenetic activation tell something about aspects of the natural salt punishment? I understand the fact that salt is present, but still I find it inaccurate

      Our approach is based on the framework established by Bertram Gerber and colleagues over the past two decades in larval Drosophila research. According to this logic, memory recall is dependent on the specific properties of the test context, particularly the type and concentration of the stimulus presented on the test plate. Aversive memory retrieval occurs only when the test conditions closely match those of the training stimulus. Consequently, the larva's behavior on the test plate serves as an indicator of the memory content being recalled. We therefore adhere to this established methodology (Gerber & Hendel, 2006; Schleyer et al., 2011; Schleyer et al., 2015).

      L307 "DAN-f1 and DAN-g1 encode aspects of the natural aversive high salt teaching" you cannot conclude that given that f1 does not even respond to salt. I understand the logic of the salt during test, but I think it is still a stretched interpretation

      We agree and thus have deleted the sentence.

      L310 "Individual DL1 DANs are acutely necessary" this is too general, it seems that only one is

      We have changed the title and now clearly state that this is only one DAN of the DL1 cluster.

      Reviewer #2 (Recommendations for the authors):

      In Fig.6 the text flow could be optimized as the authors first mention Fig. 6E,F before they follow up with Fig. 6A-D.

      Thanks for bringing this up – we changed it in the revised version of the manuscript. Now 6A-D is mentioned first.

      In Fig.6 the finding that optogenetic inactivation but not ablation of DAN-g1 slightly but significantly reduces aversive salt learning suggests that there is an individual contribution of this DAN in this paradigm. The authors emphasize redundancy of DL1 DANs although the effect size seems comparable between DAN-g1 and DAN-f1,g1 silencing.

      In response to this concern and the one of reviewer 2, we have revised the section title and removed the final sentence of the section before to avoid placing emphasis on the potential redundancy of DL1 DANs within this results section.

      Reviewer #3 (Recommendations for the authors):

      The authors replied to each issue I raised, and revised their manuscript accordingly. In particular, regarding my major concern (the sufficiency of the neurons for salt-"specific" memories), I think the authors found a good solution.

      I have no further comments.

      We sincerely thank the reviewer for the positive feedback on our revision. We are pleased that the revised manuscript meets the expectations and appreciate the time and effort invested in the review process.

    1. eLife Assessment

      This study provides an important understanding of the contribution of different striatal subregions, the anterior Dorsal Lateral Striatum (aDLS) and the posterior Ventrolateral Striatum (pVLS), to auditory discrimination learning. The authors have included robust behavior combined with multiple observational and perturbation techniques. The data provided are convincing of the relevance of task-related activity in these two subregions during learning.

    2. Reviewer #1 (Public review):

      Summary:

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

      Comments on revisions:

      The authors have addressed some concerns raised in the initial review but some remain. In particular it is still unclear what conclusions can be drawn about task-related activity from scans that are performed 30 minutes after the behavioral task. I continue to think that a reorganization/analysis data according to event type would be useful and easier to interpret across the two brain areas, but the authors did not choose to do this. Finally, switching the cue-response association, I am convinced, would help to strengthen this study.

    3. Reviewer #2 (Public review):

      The study by Setogawa et al. aims to understand the role that different striatal subregions belonging to parallel brain circuits have in associative learning and discrimination learning (S-O-R and S-R tasks). Strengths of the study are the use of multiple methodologies to measure and manipulate brain activity in rats, from microPET imaging to excitotoxic lesions and multielectrode recordings across anterior dorsolateral (aDLS), posterior ventral lateral (pVLS)and dorsomedial (DMS) striatum.

      The main conclusions are that the aDLS promotes stimulus-response association and suppresses response-outcome associations. The pVLS is engaged in the formation and maintenance of the stimulus-response association. There is a lot of work done and some interesting findings however, the manuscript can be improved by clarifying the presentation and reasoning. The inclusion of important controls will enhance the rigor of the data interpretation and conclusions.

      Comments on revisions:

      The authors have made important revisions to the manuscript and it has improved in clarity. They also added several figures in the rebuttal letter to answer questions by the reviewers. I would ask that these figures are also made public as part of the authors' response or if not, included in the manuscript.

    1. eLife Assessment

      This study presents a valuable meta-analysis of two independent genome-wide association studies (GWASs) elucidating the role of plasma proteins as biomarkers for improving early detection of prostate cancer (PCa). The evidence supporting novel protein biomarkers of PCa risk is solid, although exploration of how these markers may also be shared with other prostate diseases would have strengthened the study. The work will be of interest to the field for elucidating novel variants of prostate cancer risk.

    2. Reviewer #1 (Public review):

      Summary:

      In Causal associations between plasma proteins and prostate cancer: a Proteome-Wide Mendelian Randomization, the authors present a manuscript which seeks to identify novel markers for prostate cancer through analysis of large biobank-based datasets and to extend this analysis to potential therapeutic targets for drugs. This is an area that is already extensively researched, but remains important, due to the high burden and mortality of prostate cancer globally.

      Strengths:

      The main strengths of the manuscript are the identification and use of large biobank data assets, which provide large numbers of cases and controls, essential for achieving statistical power. The databases used (deCODE, FinnGen, and the UK Biobank) allow for robust numbers of cases and controls. The analytical method chosen, Mendelian Randomization, is appropriate to the problem. Another strength is the integration of multi-omic datasets, here using protein data as well as GWAS sources to integrate genomic and proteomic data.

      Weaknesses:

      The main weaknesses of the manuscript relate to the following areas:

      (1) The failure of the study to analyse the data in the context of other closely related conditions such as benign prostatic hyperplasia (BPH) or lower urinary tract symptoms (LUTS), which have some pathways and biomarkers in common, such as inflammatory pathways (including complement) and specific markers such as KLK3. As a consequence, it is not possible for readers to know whether the findings are specific to prostate cancer or whether they are generic to prostate dysfunction. Given the prevalence of prostate dysfunction (half of men reaching their sixth decade), the potential for false positives and overtreatment from non-specific biomarkers is a major problem, resulting in the evidence presented in this manuscript being weak. Other researchers have addressed this issue using the same data sources as presented here, for example, in this paper, looking at BPH in the UK Biobank population.<br /> https://www.nature.com/articles/s41467-018-06920-9

      (2) There is no discussion of Gleason scores with regard to either biomarkers or therapies, and a general lack of discussion around indolent disease as compared with more aggressive variants. These are crucial issues with regard to the triage and identification of genomically aggressive localized prostate cancers. See, for example, the work set out in: https://doi.org/10.1038/nature20788 .

      (3) An additional issue is that the field of PCa research is fast-moving. The manuscript cites ~80 references, but too few of these are from recent studies, and many important and relevant papers are not included. The manuscript would be much stronger if it compared and contrasted its findings with more recent studies of PCa biomarkers and targets, especially those concerned with multi-omics and those including BPH.

      (4) The Methods section provides no information on how the Controls were selected. There is no Table providing cohort data to allow the reader to know whether there were differences in age, BMI, ethnic grouping, social status or deprivation, or smoking status, between the Cases and Controls. These types of data are generally recorded in Biobank data, so this sort of analysis should be possible, or if not, the authors' inability to construct an appropriately matched set of Controls should be discussed as a Limitation.

      Assessing impact:

      Because of the weaknesses of the approach identified above, without further additions to the manuscript, the likely impact of the work on the field is minimal. There is no significant utility of the methods and data to the community, because the data are pre-existing and are not newly introduced to the community in this work, and Mendelian randomization is a well-described approach in common use, and therefore, the assets and methods described in the manuscript are not novel. With regard to the authors achieving their aims, without assessing specificity and without setting their findings in the context of the latest literature, the authors (and readers) cannot know or assess whether the biomarkers identified or the druggable targets will be useful in the clinic.

      In conclusion, adding additional context and analysis to the manuscript would both help readers interpret and understand the work and would also greatly enhance its significance. For example, the UK Biobank includes data on men with BPH / LUTS, as analysed in this paper, for example, https://doi.org/10.1038/s41467-018-06920-9. By extending this analysis to identify which biomarkers and druggable targets are specific to PCa, and which are generic to prostate dysfunction, the authors would substantially reduce the risks of diagnostic false positives. This would help to manage the risks of inappropriate treatment or overtreatment.

    3. Reviewer #2 (Public review):

      This is potentially interesting work, but the analyses are attempted in a rather scattergun way, with little evident critical thought. The structure of the work (Results before Methods) can work in some manuscripts, but it is not ideal here. The authors discuss results before we know anything about the underlying data that the results come from. It gives the impression that the authors regard data as a resource to be exploited, without really caring where the data comes from. The methods can provide meaningful insights if correctly used, but while I don't have reasons to doubt that the analyses were conducted correctly, findings are presented with little discussion or interpretation. No follow-up analyses are performed.

      In summary, there are likely some gems here, but the whole manuscript is essentially the output from an analytic pipeline.

      Taking the researchers aims in turn:

      (1) Meta-GWAS - while combining two datasets together can provide additional insights, the contribution of this analysis above existing GWAS is not clear. The PRACTICAL consortium has already reported the GWAS of 70% of these data. What additional value does this analysis provide? (Likely some, but it's not clear from the text.) Also, the presentation of results is unclear - authors state that only 5 gene regions contained variants at p<5x10-8, but Figure 1 shows dozens of hits above 5x10-8. Also, the red line in Figure 1 (supposedly at 5x10-8) is misplaced.

      (2) Cross-phenotype analysis. It is not really clear what this analysis is, or why it is done. What is the iCPAGdb? A database? A statistical method? Why would we want to know cross-phenotype associations? What even are these? It seems that the authors have taken data from an online resource and have written a paragraph based on this existing data with little added value.

      (3) PW-MR. I can see the value of this work, but many details are unclear. Was this a two-sample MR using PRACTICAL + FinnGen data for the outcome? How many variants were used in key analyses? Again, the description of results is sparse and gives little added value.

      (4) Colocalization - seems clear to me.

      (5) Additional post-GWAS analyses (pathway + druggability) - again, the analyses seem to be performed appropriately, although little additional insight other than the reporting of output from the methods.

      Minor points:

      (6) The stated motivation for this work is "early detection". But causality isn't necessary for early detection. If the authors are interested in early detection, other analysis approaches are more appropriate.

      (7) The authors state "193 proteins were associated with PCa risk", but they are looking at MR results - these analyses test for disease associations of genetically-predicted levels of proteins, not proteins themselves.

      Strengths:

      The data and methods used are state-of-the-art.

      Weaknesses:

      The reader will have to provide their own translational insight.

    4. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In Causal associations between plasma proteins and prostate cancer: a Proteome-Wide Mendelian Randomization, the authors present a manuscript which seeks to identify novel markers for prostate cancer through analysis of large biobank-based datasets and to extend this analysis to potential therapeutic targets for drugs. This is an area that is already extensively researched, but remains important, due to the high burden and mortality of prostate cancer globally.

      Strengths:

      The main strengths of the manuscript are the identification and use of large biobank data assets, which provide large numbers of cases and controls, essential for achieving statistical power. The databases used (deCODE, FinnGen, and the UK Biobank) allow for robust numbers of cases and controls. The analytical method chosen, Mendelian Randomization, is appropriate to the problem. Another strength is the integration of multi-omic datasets, here using protein data as well as GWAS sources to integrate genomic and proteomic data.

      Thank you for your positive feedback regarding the overall quality of our work and we greatly appreciate you taking time and making effort in reviewing our manuscript.

      Weaknesses:

      The main weaknesses of the manuscript relate to the following areas:

      (1) The failure of the study to analyse the data in the context of other closely related conditions such as benign prostatic hyperplasia (BPH) or lower urinary tract symptoms (LUTS), which have some pathways and biomarkers in common, such as inflammatory pathways (including complement) and specific markers such as KLK3. As a consequence, it is not possible for readers to know whether the findings are specific to prostate cancer or whether they are generic to prostate dysfunction. Given the prevalence of prostate dysfunction (half of men reaching their sixth decade), the potential for false positives and overtreatment from non-specific biomarkers is a major problem, resulting in the evidence presented in this manuscript being weak. Other researchers have addressed this issue using the same data sources as presented here, for example, in this paper, looking at BPH in the UK Biobank population. https://www.nature.com/articles/s41467-018-06920-9

      Thank you for your valuable comment. We fully agree that biomarker development must prioritize specificity to avoid overtreatment. While our study is a foundational step toward identifying potential therapeutic targets or complementary biomarkers for prostate cancer (PCa)—not as a direct endorsement of these proteins for standalone clinical diagnosis. Mendelian randomization (MR) analysis strengthens causal inference by design, and we further ensured robustness through sensitivity analyses (e.g. MR-Egger regression for pleiotropy, Bonferroni correction for multiple testing). These methods distinguish true causal effects from nonspecific associations. Importantly, while PSA’s lack of specificity is widely recognized, its role in reducing PCa mortality underscores the value of biomarker-driven screening. Our findings align with the need to integrate multiple markers (e.g. combining a novel protein with PSA) to improve diagnostic precision. Translating these causal insights into clinical tools remains challenging but represents a necessary next step, and we emphasize that this work provides a rigorous starting point for future validation studies.

      (2) There is no discussion of Gleason scores with regard to either biomarkers or therapies, and a general lack of discussion around indolent disease as compared with more aggressive variants. These are crucial issues with regard to the triage and identification of genomically aggressive localized prostate cancers. See, for example, the work set out in: https://doi.org/10.1038/nature20788

      Thank you for pointing this out. We acknowledge that our original analysis did not directly address this critical issue due to a key data limitation: the publicly available GWAS summary statistics for PCa (from openGWAS and FinnGen) do not provide genetic associations stratified by phenotypic severity or molecular subtypes. This limitation precluded MR analysis of proteins specifically linked to aggressive disease. To partially bridge this gap, we integrate evidence from recent studies in the revised Discussion section to explore the relevance of potential biomarkers to aggressive PCa.

      (3) An additional issue is that the field of PCa research is fast-moving. The manuscript cites ~80 references, but too few of these are from recent studies, and many important and relevant papers are not included. The manuscript would be much stronger if it compared and contrasted its findings with more recent studies of PCa biomarkers and targets, especially those concerned with multi-omics and those including BPH.

      Thank you for your professional comments. We have rigorously updated the manuscript to include more recent publications and we systematically compare and contrast our findings with these recent studies in the revised Discussion section.

      (4) The Methods section provides no information on how the Controls were selected. There is no Table providing cohort data to allow the reader to know whether there were differences in age, BMI, ethnic grouping, social status or deprivation, or smoking status, between the Cases and Controls. These types of data are generally recorded in Biobank data, so this sort of analysis should be possible, or if not, the authors' inability to construct an appropriately matched set of Controls should be discussed as a Limitation.

      We thank the reviewer for raising this important methodological concern. We have expanded the Limitations section to state it.

      Reviewer #2 (Public review):

      This is potentially interesting work, but the analyses are attempted in a rather scattergun way, with little evident critical thought. The structure of the work (Results before Methods) can work in some manuscripts, but it is not ideal here. The authors discuss results before we know anything about the underlying data that the results come from. It gives the impression that the authors regard data as a resource to be exploited, without really caring where the data comes from. The methods can provide meaningful insights if correctly used, but while I don't have reasons to doubt that the analyses were conducted correctly, findings are presented with little discussion or interpretation. No follow-up analyses are performed.

      In summary, there are likely some gems here, but the whole manuscript is essentially the output from an analytic pipeline.

      We thank the reviewer for the thoughtful evaluation of our work.

      Taking the researchers aims in turn:

      (1) Meta-GWAS - while combining two datasets together can provide additional insights, the contribution of this analysis above existing GWAS is not clear. The PRACTICAL consortium has already reported the GWAS of 70% of these data. What additional value does this analysis provide? (Likely some, but it's not clear from the text.) Also, the presentation of results is unclear - authors state that only 5 gene regions contained variants at p<5x10-8, but Figure 1 shows dozens of hits above 5x10-8. Also, the red line in Figure 1 (supposedly at 5x10-8) is misplaced.

      Thank you very much for your feedback. Although the PRACTICAL consortium constituted the majority of PCa GWAS data, our meta-analysis integrating FinnGen data enhanced statistical power enabling robust detection of low-frequency variants with minor allele frequencies. Moreover, FinnGen's Finnish ancestry (genetic isolate) helps distinguish population-specific effects. The presentation of results showed the top 5 gene regions contained variants at p < 5×10<sup>-8</sup>. We apologize for not noticing that the red line was not displayed correctly in the original figures included in the manuscript. We have updated it in the revised manuscript.

      (2) Cross-phenotype analysis. It is not really clear what this analysis is, or why it is done. What is the iCPAGdb? A database? A statistical method? Why would we want to know cross-phenotype associations? What even are these? It seems that the authors have taken data from an online resource and have written a paragraph based on this existing data with little added value.

      We thank you for raising this issue. The iCPAGdb (interactive Cross-Phenotype Analysis of GWAS database) is an integrative platform that systematically identifies cross-phenotype associations and evaluates genetic pleiotropy by leveraging LD-proxy associations from the NHGRI-EBI GWAS Catalog. The pathogenesis and progression of prostate cancer constitute a complex pathophysiological continuum characterized by dynamic multisystem interactions, extending beyond singular molecular pathway dysregulation to encompass coordinated disruptions across endocrine regulation, immune microenvironment remodeling, and metabolic reprogramming. Therefore, it is indispensable for discriminating primary pathogenic drivers from secondary compensatory responses, ultimately informing the development of precision therapeutic strategies.

      (3) PW-MR. I can see the value of this work, but many details are unclear. Was this a two-sample MR using PRACTICAL + FinnGen data for the outcome? How many variants were used in key analyses? Again, the description of results is sparse and gives little added value.

      We thank you for raising this issue. Two-sample MR refers to an analytical design where genetic instruments for the exposure (plasma proteins) and genetic associations with the outcome (PCa) are derived from non-overlapping populations. This ensures complete sample independence between exposure and outcome datasets to avoid confounding biases, regardless of whether the outcome data originate from single or multiple cohorts. The meta-analysis of PRACTICAL and FinnGen GWAS generates 27,210 quality-controlled variants (p < 5×10<sup>-8</sup>, MAF ≥ 1%, LD-clumped r<sup>2</sup> < 0.1) used in key analyses.

      (4) Colocalization - seems clear to me.

      (5) Additional post-GWAS analyses (pathway + druggability) - again, the analyses seem to be performed appropriately, although little additional insight other than the reporting of output from the methods.

      The post-MR druggability and pathway analyses serve two primary scientific purposes: (1) therapeutic prioritization - systematically evaluating which MR-identified proteins represent tractable drug targets (either through existing FDA-approved agents or compounds in clinical development) with direct relevance to cancer or PCa management, and (2) mechanistic hypothesis generation - mapping these candidate proteins to coherent biological pathways to guide future functional validation studies investigating their causal roles in prostate carcinogenesis.

      Minor points:

      (6) The stated motivation for this work is "early detection". But causality isn't necessary for early detection. If the authors are interested in early detection, other analysis approaches are more appropriate.

      We appreciate your insightful feedback. While early detection is one motivation for this work, our primary goal extends to identifying causally implicated proteins that may serve as intervention targets for PCa prevention or therapy.  Establishing causality is critical for distinguishing biomarkers that drive disease pathogenesis from those that are secondary to disease progression, as the former holds greater specificity for early detection and prioritization of therapeutic targets. While we acknowledge that validation for early detection may require additional methodologies, MR analysis provides a foundational step by prioritizing candidate proteins with causal links to disease. This approach ensures that downstream efforts focus on biomarkers and targets with the greatest potential to alter disease trajectories, rather than merely correlative markers.

      (7) The authors state "193 proteins were associated with PCa risk", but they are looking at MR results - these analyses test for disease associations of genetically-predicted levels of proteins, not proteins themselves.

      In MR, the exposure of interest is the lifelong effect of genetically predicted protein levels. This approach is designed to infer causality while avoiding confounding and reverse causation, as genetic variants are fixed at conception and unaffected by disease processes. When we state “193 proteins were associated with PCa risk,” we specifically refer to proteins whose genetically predicted levels (based on instrument SNPs from protein QTLs) show causal links to PCa. Importantly, MR does not measure the direct association between observed protein concentrations and disease. Instead, it estimates the lifelong causal effect of protein levels predicted by genetics. This distinction is critical for disentangling cause from consequence. For example, a protein elevated due to tumor progression would not be identified as causal in MR if its genetic predictors are unrelated to PCa risk.

      We acknowledge that clinical translation requires further validation of these proteins in observational studies measuring actual protein levels. However, MR provides a robust first step by prioritizing candidates with causal roles, thereby reducing the risk of investing in biomarkers confounded by disease processes.

    1. eLife Assessment

      This study presents a valuable meta-analysis that highlights low and highly variable breast cancer survival rates across Africa, emphasizing the pressing need for public health in Africa. The evidence supporting the claims of the authors is solid, although a clarification of the crude 5-year survival rates would have strengthened the study. The work will be of interest to scientists working in the field of public health and breast cancer.

    2. Reviewer #1 (Public review):

      Summary:

      This meta-analysis synthesized data from 79 studies across 22 African countries, encompassing over 27,000 breast cancer patients, to estimate 5-year survival rates. The pooled survival rate was 48%, with substantial regional variation, ranging from 64% in Northern Africa to 32% in Western Africa. Survival outcomes were associated with socioeconomic indicators such as education level, Human Development Index (HDI), and Socio-demographic Index (SDI). Although no significant differences in survival were observed between sexes, non-Black Africans had better outcomes. Despite global advances in cancer care, breast cancer survival in Africa has largely stagnated since the early 2010s, underscoring the need for improved healthcare infrastructure, early detection, and equitable access to treatment.

      Strengths:

      The study has several strengths. It features a comprehensive literature search, adherence to the PRISMA reporting guideline, and prospective registration on PROSPERO, including documentation of protocol deviations. The authors employed rigorous meta-analytic techniques, including subgroup analyses and meta-regression, allowing for a nuanced investigation of potential effect modifiers.

      Weaknesses:

      Analyses of crude 5-year survival rates are inherently difficult to interpret, particularly in the absence of key clinical variables such as stage at diagnosis or whether cancers were detected through screening programs. This omission raises concerns about lead time bias, where earlier diagnosis (e.g., via screening) may falsely appear to improve survival without affecting actual mortality. The higher survival seen in North Africa, for example, may reflect earlier diagnosis rather than improved prognosis or care quality. In this context, the age of the study population is another important aspect.

      Relatedly, the representativeness of the included study populations is unclear. The data sources for individual studies - whether from national cancer registries or single tertiary hospitals -are not systematically reported. This distinction is crucial, as survival outcomes differ significantly between population-based and hospital-based cohorts. Without this contextual information, the generalizability of the findings is limited.

      The meta-regression analyses further raise concerns. The authors use study-level covariates (e.g., national HDI, average years of schooling) to explain variation in survival, yet they do not acknowledge the risk of ecological bias. Inferring individual-level effects from aggregated data is methodologically flawed, and the authors' causal interpretation of these associations is inappropriate, especially given the potential for confounding by unmeasured variables at both the individual and study levels.

      The assessment of publication bias is similarly problematic. While funnel plot asymmetry and a significant Egger's test are interpreted as evidence of bias, such methods are unreliable in meta-analyses of observational studies. Smaller studies may differ meaningfully from larger ones, not due to selective reporting, but because they may recruit patients from specialized tertiary centers where outcomes are poorer. The observed relationship between study size and survival may therefore reflect true differences in patient populations, not publication bias.

      Despite claiming to search for gray literature via Google Scholar, no such studies appear in the PRISMA flowchart. This is a missed opportunity. Gray literature - especially reports from cancer registries - could have enhanced the quality and completeness of the data. While cancer registration systems are not available in all African countries, several do exist, and the authors should have made greater efforts to incorporate routine surveillance data where available. Mortality data from vital statistics systems, available in some countries, could also have provided useful context or validation.

      The study's approach to quality assessment is limited. The scoring tool, adapted from Ssentongo et al., conflates completeness of reporting with risk of bias and fails to address key domains such as study population representativeness, selection bias, and lead time bias. Rather than calculating an overall quality score, the authors should have used a structured tool that evaluates risk of bias across defined domains-such as ROBINS-I, ROBINS-E, or tools developed for prevalence studies (e.g., Tonia et al., BMJ Mental Health, 2023). Cochrane guidance and the textbook by Egger, Higgins, and Davey Smith (DOI:10.1002/9781119099369) provide valuable resources for this purpose.

      The cumulative meta-analysis is not particularly informative, considering the massive heterogeneity in survival rates. It would be more meaningful to stratify the analysis by calendar period. In general, with such important heterogeneity, the calculation of an overall estimate does not add much.

      The authors spend quite some time discussing differences in survival between men and women and between the current and the 2018 estimates, despite the fact that the survival rates are similar, with widely overlapping confidence intervals. The use of a Z-test in this context is inappropriate as it ignores the heterogeneity between studies.

      Minor point:

      The terms retrospective and prospective are not particularly helpful - every longitudinal study of survival is retrospective. What the authors mean is whether or not the data were collected within a study designed to address this question, or whether existing data were used that were collected for another purpose. See also DOI: 10.1136/bmj.302.6771.249.

    3. Reviewer #2 (Public review):

      Summary:

      The study provides an updated literature review and meta-analysis for the 5-year survival estimates in breast cancer patients across continental Africa. The findings reveal substantial disparities between regions and other factors, highlighting the disadvantaged areas in Africa and the urgent need to address these inequities across the continent.

      Strengths:

      The main strengths of this study include:<br /> (1) the thorough literature search with an increasing number of included studies that enhances result reliability;<br /> (2) standard and appropriate statistical methods with clear reporting;<br /> (3) a comprehensive discussion.

      Overall, the paper is well-structured, clearly presented, and provides useful insights.

      Weaknesses:

      However, I have a few concerns that I would like the authors to address.

      (1) The conclusion "A country-wise comparison with 2018 estimates suggests a declining survival tendency, with WHO AFRO countries reporting the poorest estimates among other WHO regions." appears to have been drawn from the comparisons across both different regions and different time periods, which is incorrect! As shown in Figure 8, survival in Africa has increased from below 30% (WHO AFRO 2017) to around 50% (AFRICA 2024, presumably the current study). Section 3.5 is confusing and headed in the wrong direction. The key message in Figure 8 is that the current survival estimate in Africa is still lower than that of other WHO regions from a few years ago, highlighting the urgent need to improve survival in Africa.

      (2) The previous review by Ssentongo et al. classified countries into North Africa and sub-Saharan Africa (SSA), regions divided by the Sahara Desert. This classification is not only geographical-based, but also accounts for the significant differences in ethnicity, health system, and socioeconomic factors. North Africa (especially Egypt, Tunisia, Morocco) has better cancer registries, earlier detection, more treatment access, and therefore better survival outcomes (as shown in Figure 2). SSA tends to have worse outcomes, due to later-stage diagnosis, limited pathology, and access barriers. Given that the survival in women with breast cancer is among the lowest for several SSA countries, the study would benefit from an additional comparison between pooled estimates of North African and SSA, and comparisons with previous pooled estimates.

      (3) The authors classified studies under the female group. Females constituted at least 80% of the sample population, and subgroup analysis revealed only a marginal discrepancy in survival rates between the two sexes. However, most of the breast cancer patients and related studies consist predominantly of females. Given the non-negligible differences in various aspects between females and males, sensitivity analyses restricted to studies among females (as in Figure 2-3) would be informative for future research in breast cancer patients.

      (4) Stage at diagnosis and treatment are the strongest prognostic factors for breast cancer survival. Though data regarding these variables are not available for all studies, and it's complicated to compare or pool the results from different studies (as mentioned in the limitation), could the authors perform the regression analyses regarding early vs. late stages, and the percentage of treatment received? These two factors are too significant to overlook in studies on breast cancer survival.

      (5) The authors reported that studies published before 2019 had a higher survival than those conducted from 2019 onwards, which could be misleading and requires further explanation. As the authors noted ─"the year of publication may not be a reliable measure of the effect in question"─ a better approach would be to use the year of inclusion, i.e., the year the studies were conducted.

      (6) Northern and Western Africa both have the highest incidence of breast cancer in Africa, yet their 5-year survival estimates differ substantially. However, the authors have discussed the survival disparities without considering their similarly higher incidence rates. Could this disparity reflect different contributing factors, with the higher incidence rate in Northern Africa resulting from better screening programs (leading to more detections), while that in Western Africa stems from other epidemiological factors despite lower screening participation? Though the incidence rate is not the primary focus of this study, briefly exploring this dichotomy would enhance the discussion and provide valuable insights for readers.

    4. Author response:

      We thank the reviewing editors, senior editors, and reviewers for their time, efforts, and constructive feedback. We believe the points raised are addressable and we would like to proceed with a revised submission for further review. Specifically, we plan the following revisions:

      Editor’s Comments

      We will clarify study definitions to ensure the meaning of "5-year crude overall survival time" is explicit for readers.

      Reviewer 1 Comments

      - Clarify and supplement the work with detailed sources of study origin (cancer registries or single-center cohorts).

      - Conduct a multi-level hierarchical meta-analysis to address concerns of ecological fallacy in interpreting results.

      - Perform an ecological sensitivity analysis and clarify findings regarding small study effects.

      - Expand the search base significantly by including African local databases; preliminary searches have identified over 50 potentially eligible doctoral theses, dissertations, local journal articles, and gray literature, potentially adding data from five or more additional countries.

      Reviewer 2 Comments

      - Conduct subgroup analyses by sex and assess the influence of the percentage of males in mixed cohorts.

      - Enhance the limited meta-analysis and provide supplementary full forest plots for all analyses.

      - Clarify phrasing in sections identified by the reviewer.

      Additional Planned Clarifications and Analyses

      - Elucidate the role of cumulative meta-analysis in mitigating lead-time bias.

      - Include supplementary cumulative meta-analysis based on the year of investigation (instead of publication year).

      - Perform subgroup analyses by clinical staging, TNM grading, and treatment modalities where data from ≥10 studies is available.

      - Expand discussion on the merits of quality assessment versus risk of bias evaluation in large scale epidemiological and observational studies, in line with other studies of this scale.

      - Condense the comparison with 2018 estimates, as per reviewer suggestions.

      Clarification Regarding SSA vs. AU Classification

      We do not intend to compare survival between "Sub-Saharan Africa" (SSA) and North Africa, as this binary classification is historically rooted and does not reflect current African Union (AU) administrative or policy groupings. Our regional analyses will adhere to the AU’s contemporary regional framework to better reflect political, cultural, and healthcare system realities.

      On Registry Data

      We will clarify that we will not extract raw registry data, as such data is typically unprocessed and does not provide 5-year overall survival metrics. As such extracting raw, individual-level data from registries or vital statistics systems falls outside the methodological scope of a meta-analysis. Meta-analyses are designed to synthesize published survival estimates or those available from reports where survival analyses have already been conducted. Utilizing raw surveillance data would require primary data processing and survival analysis — effectively creating new data, not synthesizing existing results. This would represent a distinct study design, such as a pooled analysis or original cohort study, rather than a meta-analysis. Where registry reports present summary survival estimates (e.g., 5-year overall survival) in a format compatible with meta-analysis, we will certainly include them.

      All planned additional analyses will depend on data quality, consistency, and feasibility for pooling using state-of-the-art statistical techniques. Where pooling is not possible, we will transparently report limitations.

    1. eLife Assessment

      This valuable study provides a conceptual advance in our understanding of how membrane geometry modulates the balance between specific and non-specific molecular interactions, reversing multiphase morphologies in postsynaptic protein assemblies. Using a mesoscale simulation framework grounded in experimental binding affinities, the authors successfully recapitulate key experimental observations in both solution and membrane-associated systems, providing novel mechanistic insight into how spatial constraints regulate postsynaptic condensate organization. While the evidence supporting the conclusions is largely solid, a few aspects of the analysis and model proposed remain incomplete.

    2. Reviewer #1 (Public review):

      Summary:

      This study uses mesoscale simulations to investigate how membrane geometry regulates the multiphase organization of postsynaptic condensates. It reveals that dimensionality shifts the balance between specific and non-specific interactions, thereby reversing domain morphology observed in vitro versus in vivo.

      Strengths:

      The model is grounded in experimental binding affinities, reproduces key experimental observations in 3D and 2D contexts, and offers mechanistic insight into how geometry and molecular features drive phase behavior.

      Weaknesses:

      The model omits other synaptic components that may influence domain organization and does not extensively explore parameter sensitivity or broader physiological variability.

    3. Reviewer #2 (Public review):

      This is a timely and insightful study aiming to explore the general physical principles for the sub-compartmentalization--or lack thereof--in the phase separation processes underlying the assembly of postsynaptic densities (PSDs), especially the markedly different organizations in three-dimensional (3D) droplets on one hand and the two-dimensional (2D) condensates associated with a cellular membrane on the other. Simulation of a highly simplified model (one bead per protein domain) is carefully executed. Based on a thorough consideration of various control cases, the main conclusion regarding the trade-off between repulsive excluded volume interactions and attractive interactions among protein domains in determining the structures of 3D vs 2D model PSD condensates is quite convincing. The results in this manuscript are novel; however, as it stands, there is substantial room for improvement in the presentation of the background and the findings of this work. In particular, (i) conceptual connections with prior works should be better discussed, (ii) essential details of the model should be clarified, and (iii) the generality and limitations of the authors' approach should be better delineated. Specifically, the following items should be addressed (with the additional references mentioned below cited and discussed):

      (1) Excluded volume effects are referred to throughout the text by various terms and descriptions such as "repulsive force according to the volume" (e.g., in the Introduction), "nonspecific volume interaction", and "volume effects" in this manuscript. This is somewhat curious and not conducive to clarity, because these terms have alternate or connotations of alternate meanings (e.g., in biomolecular modeling, repulsive interactions usually refer to those with longer spatial ranges, such as that between like charges). It will be much clearer if the authors simply refer to excluded volume interactions as excluded volume interactions (or effects).

      (2) Inasmuch as the impact of excluded volume effects on subcompartmentalization of condensates ("multiple phases" in the authors' terminology), it has been demonstrated by both coarse-grained molecular dynamics and field-theoretic simulations that excluded volume is conducive to demixing of molecular species in condensates [Pal et al., Phys Rev E 103:042406 (2021); see especially Figures 4-5 of this reference]. This prior work bears directly on the authors' observation. Its relationship with the present work should be discussed.

      (3) In the present model setup, activation of the CaMKII kinase affects only its binding to GluN2Bc. This approach is reasonable and leads to model predictions that are essentially consistent with the experiment. More broadly, however, do the authors expect activation of the CaMKII kinase to lead to phosphorylation of some of the molecular species involved with PSDs? This may be of interest since biomolecular condensates are known to be modulated by phosphorylation [Kim et al., Science 365:825-829 (2019); Lin et al, eLife 13:RP100284 (2025)].

      (4) The forcefield for confinement of AMPAR/TARP and NMDAR/GluN2Bc to 2D should be specified in the main text. Have the authors explored the sensitivity of their 2D findings on the strength of this confinement?

      (5) Some of the labels in Figure 1 are confusing. In Figure 1A, the structure labeled as AMPAR has the same shape as the structure labeled as TARP in Figure 1B, but TARP is labeled as one of the smaller structures (like small legs) in the lower part of AMPAR in Figure 1A. Does the TARP in Figure 1B correspond to the small structures in the lower part of AMPAR? If so, this should be specified (and better indicated graphically), and in that case, it would be better not to use the same structural drawing for the overall structure and a substructure. The same issue is seen for NMDAR in Figure 1A and GluN2Bc in Figure 1B.

      (6) In addition to clarifying Figure 1, the authors should clarify the usage of AMPAR vs TARP and NMDAR vs GluN2Bc in other parts of the text as well.

      (7) The physics of the authors' model will be much clearer if they provide an easily accessible graphical description of the relative interaction strengths between different domain-representing spheres (beads) in their model. For this purpose, a representation similar to that given by Feric et al., Cell 165:1686-1697 (2016) (especially Figure 6B in this reference) of the pairwise interactions among the beads in the authors' model should be provided as an additional main-text figure. Different interaction schemes corresponding to inactive and activated CAMKII should be given. In this way, the general principles (beyond the PSD system) governing 3D vs 2D multiple-component condensate organization can be made much more apparent.

      (8) Can the authors' rationalization of the observed difference between 3D and 2D model PSD condensates be captured by an intuitive appreciation of the restriction on favorable interactions by steric hindrance and the reduction in interaction cooperativity in 2D vs 3D?

      (9) In the authors' model, the propensity to form 2D condensates is quite weak. Is this prediction consistent with the experiment? Real PSDs do form 2D condensates around synapses.

      (10) More theoretical context should be provided in the Introduction and/or Discussion by drawing connections to pertinent prior works on physical determinants of co-mixing and de-mixing in multiple-component condensates (e.g., amino acid sequence), such as Lin et al., New J Phys 19:115003 (2017) and Lin et al., Biochemistry 57:2499-2508 (2018).

      (11) In the discussion of the physiological/neurological significance of PSD in the Introduction and/or Discussion, for general interest it is useful to point to a recently studied possible connection between the hydrostatic pressure-induced dissolution of model PSD and high-pressure neurological syndrome [Lin et al., Chem Eur J 26:11024-11031 (2020)].

      (12) It is more accurate to use "perpendicular to the membrane" rather than "vertical" in the caption for Figure 3E and other such descriptions of the orientation of the CaMKII hexagonal plane in the text.

    4. Reviewer #3 (Public review):

      Summary:

      In this work, Yamada, Brandani, and Takada have developed a mesoscopic model of the interacting proteins in the postsynaptic density. They have performed simulations, based on this model and using the software ReaDDy, to study the phase separation in this system in 2D (on the membrane) and 3D (in the bulk). They have carefully investigated the reasons behind different morphologies observed in each case, and have looked at differences in valency, specific/non-specific interactions, and interfacial tension.

      Strengths:

      The simulation model is developed very carefully, with strong reliance on binding valency and geometry, experimentally measured affinities, and physical considerations like the hydrodynamic radii. The presented analyses are also thorough, and great effort has been put into investigating different scenarios that might explain the observed effects.

      Weaknesses:

      The biggest weakness of the study, in my opinion, has to do with a lack of more in-depth physical insight about phase separation. For example, the authors express surprise about similar interactions between components resulting in different phase separation in 2D and 3D. This is not surprising at all, as in 3D, higher coordination numbers and more available volume translate to lower free energy, which easily explains phase separation. The role of entropy is also significantly missing from the analyses. When interaction strengths are small, entropic effects play major roles.

      In the introduction, the authors present an oversimplified view of associative and segregative phase transitions based on the attractive and repulsive interactions, and I'm afraid that this view, in which all the observed morphologies should have clear pairwise enthalpic explanations, diffuses throughout the analysis. Meanwhile, I believe the authors correctly identify some relevant effects, where they consider specific/non-specific interactions, or when they investigate the reduced valency of CaMKII in the 2D system.

      Also, I sense some haste in comparing the findings with experimental observations. For example, the authors mention that "For the current four component PSD system, the product of concentrations of each molecule in the dilute phase is in good agreement with that of the experimental concentrations (Table S2)." But the data used here is the dilute phase, which is the remnant of a system prepared at very high concentrations and allowed to phase separate. The errors reported in Table S2 already cast doubt on this comparison. Or while the 2D system is prepared via confining the particles to the vicinity of the membrane, the different diffusive behavior in the membrane, in contrast to the bulk (i.e., the Saffman-Delbrück model), is not considered. This would thus make it difficult to interpret the results of a coupled 2D/3D system and compare them to the actual system.

    5. Author response:

      We thank all the reviewers for their thoughtful comments on our submitted manuscript.

      The main points made by all three reviewers were: to discuss the components of the omitted synapses and explore parameter sensitivity and broader physiological variability; to provide deeper physical insights into phase separation; to clarify terminology and provide better presentation and context in relation to previous studies.

      We fully agree with the first point, suggesting that parameter sensitivity and broader physiological variability should be explored. Our model omits scaffold proteins such as GKAP, Shank and Homer, which are present at the bottom of the PSD hierarchy. In addition, there are many other interactions in PSDs whose affinity is altered by phosphorylation, and the phase separation state of the condensate is likely to be affected by ionic concentration and other environmental factors. We will include a more detailed discussion of these environmental factors and a limitation of our study in the Discussion section. Furthermore, regarding to the sensitivity of the parameters, the reviewer's point that the membrane potential parameter is an important value is right since it directly regulates the difference between 3D and 2D systems. We plan to verify this by changing the strength of the membrane potential, and by running simulations again to see how much it affects the morphology of condensates.

      The second point is that we should provide deeper physical insight into phase separation in different dimensions. It would not be straightforward to directly estimate the entropy of the system due to the nature of the model. However, as pointed out, the difference of phase behavior can be elucidated through various simplified theories such as the lattice model. In this context, the reduced coordination number in 2D systems compared to 3D systems, and the decreased pseudo-attractive force due to the depletion effect, can offer rationalizations. We would like to add some theoretical discussion of these aspects with equations.

      Third, we will clarify terminology and provide better explanation in relation to previous studies. In some parts in manuscripts, such as complexes containing receptors, there were some disunity in terminology and lack of annotations in figures. We will improve the wording and visualization in the text for further clarity and add relevant references, as suggested by the reviewers.

      Also, as additionally suggested, scripts for the simulation and analysis together with the initial structure obtained will be deposited to Zenodo or GitHub.

    1. eLife Assessment

      This work presents an important technical advancement with the release of MorphoNet 2.0, a user-friendly, standalone platform for 3D+T segmentation and analysis in biological imaging. The authors provide convincing evidence of the tool's capabilities through illustrative use cases, though broader validation against current state-of-the-art tools would strengthen its position. The software's accessibility and versatility make it a resource that will be of value for the bioimaging community, particularly in specialized subfields.

    2. Reviewer #1 (Public review):

      The authors present a substantial improvement to their existing tool, MorphoNet, intended to facilitate assessment of 3D+t cell segmentation and tracking results, and curation of high-quality analysis for scientific discovery and data sharing. These tools are provided through a user-friendly GUI, making them accessible to biologists who are not experienced coders. Further, the authors have re-developed this tool to be a locally installed piece of software instead of a web interface, making the analysis and rendering of large 3D+t datasets more computationally efficient. The authors evidence the value of this tool with a series of use cases, in which they apply different features of the software to existing datasets and show the improvement to the segmentation and tracking achieved.

      While the computational tools packaged in this software are familiar to readers (e.g., cellpose), the novel contribution of this work is the focus on error correction. The MorphoNet 2.0 software helps users identify where their candidate segmentation and/or tracking may be incorrect. The authors then provide existing tools in a single user-friendly package, lowering the threshold of skill required for users to get maximal value from these existing tools. To help users apply these tools effectively, the authors introduce a number of unsupervised quality metrics that can be applied to a segmentation candidate to identify masks and regions where the segmentation results are noticeably different from the majority of the image.

      This work is valuable to researchers who are working with cell microscopy data that requires high-quality segmentation and tracking, particularly if their data are 3D time-lapse and thus challenging to segment and assess. The MorphoNet 2.0 tool that the authors present is intended to make the iterative process of segmentation, quality assessment, and re-processing easier and more streamlined, combining commonly used tools into a single user interface.

      One of the key contributions of the work is the unsupervised metrics that MorphoNet 2.0 offers for segmentation quality assessment. These metrics are used in the use cases to identify low-quality instances of segmentation in the provided datasets, so that they can be improved with plugins directly in MorphoNet 2.0. However, not enough consideration is given to demonstrating that optimizing these metrics leads to an improvement in segmentation quality. For example, in Use Case 1, the authors report their metrics of interest (Intensity offset, Intensity border variation, and Nuclei volume) for the uncurated silver truth, the partially curated and fully curated datasets, but this does not evidence an improvement in the results. Additional plotting of the distribution of these metrics on the Gold Truth data could help confirm that the distribution of these metrics now better matches the expected distribution.

      Similarly, in Use Case 2, visual inspection leads us to believe that the segmentation generated by the Cellpose + Deli pipeline (shown in Figure 4d) is an improvement, but a direct comparison of agreement between segmented masks and masks in the published data (where the segmentations overlap) would further evidence this.

      We would appreciate the authors addressing the risk of decreasing the quality of the segmentations by applying circular logic with their tool; MorphoNet 2.0 uses unsupervised metrics to identify masks that do not fit the typical distribution. A model such as StarDist can be trained on the "good" masks to generate more masks that match the most common type. This leads to a more homogeneous segmentation quality, without consideration for whether these metrics actually optimize the segmentation

      In Use case 5, the authors include details that the errors were corrected by "264 MorphoNet plugin actions ... in 8 hours actions [sic]". The work would benefit from explaining whether this is 8 hours of human work, trying plugins and iteratively improving, or 8 hours of compute time to apply the selected plugins.

    3. Reviewer #2 (Public review):

      Summary:

      This article presents Morphonet 2.0, a software designed to visualise and curate segmentations of 3D and 3D+t data. The authors demonstrate their capabilities on five published datasets, showcasing how even small segmentation errors can be automatically detected, easily assessed, and corrected by the user. This allows for more reliable ground truths, which will in turn be very much valuable for analysis and training deep learning models. Morphonet 2.0 offers intuitive 3D inspection and functionalities accessible to a non-coding audience, thereby broadening its impact.

      Strengths:

      The work proposed in this article is expected to be of great interest to the community by enabling easy visualisation and correction of complex 3D(+t) datasets. Moreover, the article is clear and well written, making MorphoNet more likely to be used. The goals are clearly defined, addressing an undeniable need in the bioimage analysis community. The authors use a diverse range of datasets, successfully demonstrating the versatility of the software.

      We would also like to highlight the great effort that was made to clearly explain which type of computer configurations are necessary to run the different datasets and how to find the appropriate documentation according to your needs. The authors clearly carefully thought about these two important problems and came up with very satisfactory solutions.

      Weaknesses:

      There is still one concern: the quantification of the improvement of the segmentations in the use cases and, therefore, the quantification of the potential impact of the software. While it appears hard to quantify the quality of the correction, the proposed work would be significantly improved if such metrics could be provided.

      The authors show some distributions of metrics before and after segmentations to highlight the changes. This is a great start, but there seem to be two shortcomings: first, the comparison and interpretation of the different distributions does not appear to be trivial. It is therefore difficult to judge the quality of the improvement from these. Maybe an explanation in the text of how to interpret the differences between the distributions could help. A second shortcoming is that the before/after metrics displayed are the metrics used to guide the correction, so, by design, the scores will improve, but does that accurately represent the improvement of the segmentation? It seems to be the case, but it would be nice to maybe have a better assessment of the improvement of the quality.

    4. Reviewer #3 (Public review):

      Summary:

      A very thorough technical report of a new standalone, open-source software for microscopy image processing and analysis (MorphoNet 2.0), with a particular emphasis on automated segmentation and its curation to obtain accurate results even with very complex 3D stacks, including timelapse experiments.

      Strengths:

      The authors did a good job of explaining the advantages of MorphoNet 2.0, as compared to its previous web-based version and to other software with similar capabilities. What I particularly found more useful to actually envisage these claimed advantages is the five examples used to illustrate the power of the software (based on a combination of Python scripting and the 3D game engine Unity). These examples, from published research, are very varied in both types of information and image quality, and all have their complexities, making them inherently difficult to segment. I strongly recommend the readers to carefully watch the accompanying videos, which show (although not thoroughly) how the software is actually used in these examples.

      Weaknesses:

      Being a technical article, the only possible comments are on how methods are presented, which is generally adequate, as mentioned above. In this regard, and in spite of the presented examples (chosen by the authors, who clearly gave them a deep thought before showing them), the only way in which the presented software will prove valuable is through its use by as many researchers as possible. This is not a weakness per se, of course, but just what is usual in this sort of report. Hence, I encourage readers to download the software and give it time to test it on their own data (which I will also do myself).

      In conclusion, I believe that this report is fundamental because it will be the major way of initially promoting the use of MorphoNet 2.0 by the objective public. The software itself holds the promise of being very impactful for the microscopists' community.

    5. Author response:

      eLife Assessment

      This work presents an important technical advancement with the release of MorphoNet 2.0, a user-friendly, standalone platform for 3D+T segmentation and analysis in biological imaging. The authors provide convincing evidence of the tool's capabilities through illustrative use cases, though broader validation against current state-of-the-art tools would strengthen its position. The software's accessibility and versatility make it a resource that will be of value for the bioimaging community, particularly in specialized subfields.

      We would like to thank the editors and reviewers for their careful and constructive evaluation of our manuscript “MorphoNet 2.0: An innovative approach for qualitative assessment and segmentation curation of large-scale 3D time-lapse imaging datasets”. We are grateful for the positive assessment of MorphoNet 2.0 as a valuable and accessible tool for the bioimaging community, and for the recognition of its technical advancements, particularly in the context of complex 3D+t segmentation tasks.

      The reviewers have highlighted several important points that we will address in the revised manuscript. These include:

      - The need for a clearer demonstration that improvements in unsupervised quality metrics correspond to actual improvements in segmentation quality. In response, we will provide comparisons with gold standard annotations where available and clarify how to interpret metric distributions.<br /> - The potential risk of circular logic when using unsupervised metrics to guide model training. We now explicitly discuss this limitation and emphasize the importance of external validation and expert input.<br /> - The value of comparing MorphoNet 2.0 to other tools such as FIJI and napari. We will include a comparative table to help readers understand MorphoNet’s positioning and complementarity.<br /> - The importance of clearer documentation and terminology. We will overhaul the help pages, standardize plugin naming, and add a glossary-style table to the manuscript.<br /> - Suggestions for future developments, such as mesh export and interoperability with napari, which we will explore for the revision.

      We appreciate the detailed feedback on both scientific and editorial aspects, including corrections to figures and text, and we will integrate all suggested revisions to improve the manuscript’s clarity and impact. We are confident that these changes will strengthen the manuscript and enhance the utility of MorphoNet 2.0 for the community.

      Public Reviews:

      Reviewer #1 (Public review):

      The authors present a substantial improvement to their existing tool, MorphoNet, intended to facilitate assessment of 3D+t cell segmentation and tracking results, and curation of high-quality analysis for scientific discovery and data sharing. These tools are provided through a user-friendly GUI, making them accessible to biologists who are not experienced coders. Further, the authors have re-developed this tool to be a locally installed piece of software instead of a web interface, making the analysis and rendering of large 3D+t datasets more computationally efficient. The authors evidence the value of this tool with a series of use cases, in which they apply different features of the software to existing datasets and show the improvement to the segmentation and tracking achieved.

      While the computational tools packaged in this software are familiar to readers (e.g., cellpose), the novel contribution of this work is the focus on error correction. The MorphoNet 2.0 software helps users identify where their candidate segmentation and/or tracking may be incorrect. The authors then provide existing tools in a single user-friendly package, lowering the threshold of skill required for users to get maximal value from these existing tools. To help users apply these tools effectively, the authors introduce a number of unsupervised quality metrics that can be applied to a segmentation candidate to identify masks and regions where the segmentation results are noticeably different from the majority of the image.

      This work is valuable to researchers who are working with cell microscopy data that requires high-quality segmentation and tracking, particularly if their data are 3D time-lapse and thus challenging to segment and assess. The MorphoNet 2.0 tool that the authors present is intended to make the iterative process of segmentation, quality assessment, and re-processing easier and more streamlined, combining commonly used tools into a single user interface.

      We sincerely thank the reviewer for their thorough and encouraging evaluation of our work. We are grateful that they highlighted both the technical improvements of MorphoNet 2.0 and its potential impact for the broader community working with complex 3D+t microscopy datasets. We particularly appreciate the recognition of our efforts to make advanced segmentation and tracking tools accessible to non-expert users through a user-friendly and locally installable interface, and for pointing out the importance of error detection and correction in the iterative analysis workflow. The reviewer’s appreciation of the value of integrating unsupervised quality metrics to support this process is especially meaningful to us, as this was a central motivation behind the development of MorphoNet 2.0. We hope the tool will indeed facilitate more rigorous and reproducible analyses, and we are encouraged by the reviewer’s positive assessment of its utility for the community.

      One of the key contributions of the work is the unsupervised metrics that MorphoNet 2.0 offers for segmentation quality assessment. These metrics are used in the use cases to identify low-quality instances of segmentation in the provided datasets, so that they can be improved with plugins directly in MorphoNet 2.0. However, not enough consideration is given to demonstrating that optimizing these metrics leads to an improvement in segmentation quality. For example, in Use Case 1, the authors report their metrics of interest (Intensity offset, Intensity border variation, and Nuclei volume) for the uncurated silver truth, the partially curated and fully curated datasets, but this does not evidence an improvement in the results. Additional plotting of the distribution of these metrics on the Gold Truth data could help confirm that the distribution of these metrics now better matches the expected distribution.

      Similarly, in Use Case 2, visual inspection leads us to believe that the segmentation generated by the Cellpose + Deli pipeline (shown in Figure 4d) is an improvement, but a direct comparison of agreement between segmented masks and masks in the published data (where the segmentations overlap) would further evidence this.

      We agree that demonstrating the correlation between metric optimization and real segmentation improvement is essential. We will add new analysis comparing the distributions of the unsupervised metrics with the gold truth data before and after curation. Additionally, we will provide overlap scores where ground truth annotations are available, confirming the improvement. We will also explicitly discuss the limitation of relying solely on unsupervised metrics without complementary validation.

      We would appreciate the authors addressing the risk of decreasing the quality of the segmentations by applying circular logic with their tool; MorphoNet 2.0 uses unsupervised metrics to identify masks that do not fit the typical distribution. A model such as StarDist can be trained on the "good" masks to generate more masks that match the most common type. This leads to a more homogeneous segmentation quality, without consideration for whether these metrics actually optimize the segmentation

      We thank the reviewer for this important and insightful comment. It raises a crucial point regarding the risk of circular logic in our segmentation pipeline. Indeed, relying on unsupervised metrics to select “good” masks and using them to train a model like StarDist could lead to reinforcing a particular distribution of shapes or sizes, potentially filtering out biologically relevant variability. This homogenization may improve consistency with the chosen metrics, but not necessarily with the true underlying structures.

      We fully agree that this is a key limitation to be aware of. We will revise the manuscript to explicitly discuss this risk, emphasizing that while our approach may help improve segmentation quality according to specific criteria, it should be complemented with biological validation and, when possible, expert input to ensure that important but rare phenotypes are not excluded.

      In Use case 5, the authors include details that the errors were corrected by "264 MorphoNet plugin actions ... in 8 hours actions [sic]". The work would benefit from explaining whether this is 8 hours of human work, trying plugins and iteratively improving, or 8 hours of compute time to apply the selected plugins.

      We will clarify that the “8 hours” refer to human interaction time, including exploration, testing, and iterative correction using plugins.

      Reviewer #2 (Public review):

      Summary:

      This article presents Morphonet 2.0, a software designed to visualise and curate segmentations of 3D and 3D+t data. The authors demonstrate their capabilities on five published datasets, showcasing how even small segmentation errors can be automatically detected, easily assessed, and corrected by the user. This allows for more reliable ground truths, which will in turn be very much valuable for analysis and training deep learning models. Morphonet 2.0 offers intuitive 3D inspection and functionalities accessible to a non-coding audience, thereby broadening its impact.

      Strengths:

      The work proposed in this article is expected to be of great interest to the community by enabling easy visualisation and correction of complex 3D(+t) datasets. Moreover, the article is clear and well written, making MorphoNet more likely to be used. The goals are clearly defined, addressing an undeniable need in the bioimage analysis community. The authors use a diverse range of datasets, successfully demonstrating the versatility of the software.

      We would also like to highlight the great effort that was made to clearly explain which type of computer configurations are necessary to run the different datasets and how to find the appropriate documentation according to your needs. The authors clearly carefully thought about these two important problems and came up with very satisfactory solutions.

      We would like to sincerely thank the reviewer for their positive and thoughtful feedback. We are especially grateful that they acknowledged the clarity of the manuscript and the potential value of MorphoNet 2.0 for the community, particularly in facilitating the visualization and correction of complex 3D(+t) datasets. We also appreciate the reviewer’s recognition of our efforts to provide detailed guidance on hardware requirements and access to documentation—two aspects we consider crucial to ensuring the tool is both usable and widely adopted. Their comments are very encouraging and reinforce our commitment to making MorphoNet 2.0 as accessible and practical as possible for a broad range of users in the bioimage analysis community.

      Weaknesses:

      There is still one concern: the quantification of the improvement of the segmentations in the use cases and, therefore, the quantification of the potential impact of the software. While it appears hard to quantify the quality of the correction, the proposed work would be significantly improved if such metrics could be provided.

      The authors show some distributions of metrics before and after segmentations to highlight the changes. This is a great start, but there seem to be two shortcomings: first, the comparison and interpretation of the different distributions does not appear to be trivial. It is therefore difficult to judge the quality of the improvement from these. Maybe an explanation in the text of how to interpret the differences between the distributions could help. A second shortcoming is that the before/after metrics displayed are the metrics used to guide the correction, so, by design, the scores will improve, but does that accurately represent the improvement of the segmentation? It seems to be the case, but it would be nice to maybe have a better assessment of the improvement of the quality.

      We thank the reviewer for this constructive and important comment. We fully agree that assessing the true quality improvement of segmentation after correction is a central and challenging issue. While we initially focused on changes in the unsupervised quality metrics to illustrate the effect of the correction, we acknowledge that interpreting these distributions may not be straightforward, and that relying solely on the metrics used to guide the correction introduces an inherent bias in the evaluation.

      To address the first point, we will revise the manuscript to provide clearer guidance on how to interpret the changes in metric distributions before and after correction, with additional examples to make this interpretation more intuitive.

      Regarding the second point, we agree that using independent, external validation is necessary to confirm that the segmentation has genuinely improved. To this end, we will include additional assessments using complementary evaluation strategies on selected datasets where ground truth is accessible, to compare pre- and post-correction segmentations with an independent reference. These results reinforce the idea that the corrections guided by unsupervised metrics generally lead to more accurate segmentations, but we also emphasize their limitations and the need for biological validation in real-world cases.

      Reviewer #3 (Public review):

      Summary:

      A very thorough technical report of a new standalone, open-source software for microscopy image processing and analysis (MorphoNet 2.0), with a particular emphasis on automated segmentation and its curation to obtain accurate results even with very complex 3D stacks, including timelapse experiments.

      Strengths:

      The authors did a good job of explaining the advantages of MorphoNet 2.0, as compared to its previous web-based version and to other software with similar capabilities. What I particularly found more useful to actually envisage these claimed advantages is the five examples used to illustrate the power of the software (based on a combination of Python scripting and the 3D game engine Unity). These examples, from published research, are very varied in both types of information and image quality, and all have their complexities, making them inherently difficult to segment. I strongly recommend the readers to carefully watch the accompanying videos, which show (although not thoroughly) how the software is actually used in these examples.

      We sincerely thank the reviewer for their thoughtful and encouraging feedback. We are particularly pleased that the reviewer appreciated the comparative analysis of MorphoNet 2.0 with both its earlier version and existing tools, as well as the relevance of the five diverse and complex use cases we selected. Demonstrating the software’s versatility and robustness across a variety of challenging datasets was a key goal of this work, and we are glad that this aspect came through clearly. We also appreciate the reviewer’s recommendation to watch the accompanying videos, which we designed to provide a practical sense of how the tool is used in real-world scenarios. Their positive assessment is highly motivating and reinforces the value of combining scripting flexibility with an interactive 3D interface.

      Weaknesses:

      Being a technical article, the only possible comments are on how methods are presented, which is generally adequate, as mentioned above. In this regard, and in spite of the presented examples (chosen by the authors, who clearly gave them a deep thought before showing them), the only way in which the presented software will prove valuable is through its use by as many researchers as possible. This is not a weakness per se, of course, but just what is usual in this sort of report. Hence, I encourage readers to download the software and give it time to test it on their own data (which I will also do myself).

      We fully agree that the true value of MorphoNet 2.0 will be demonstrated through its practical use by a wide range of researchers working with complex 3D and 3D+t datasets. In this regard, we will improve the user documentation and provide a set of example datasets to help new users quickly familiarize themselves with the platform. We are also committed to maintaining and updating MorphoNet 2.0 based on user feedback to further support its usability and impact.

      In conclusion, I believe that this report is fundamental because it will be the major way of initially promoting the use of MorphoNet 2.0 by the objective public. The software itself holds the promise of being very impactful for the microscopists' community.

    1. eLife Assessment

      Thick multicellular plant samples provide unique challenges when it comes to cryo-preservation, which has resulted in limited successful examples for structural studies using in situ cryo-electron tomography. To address this deficiency, this important study describes procedures for high-pressure-freezing, focused ion-beam milling, and cryo-electron tomography imaging of certain plant types. The results described in the paper provide solid evidence for the usefulness of the methods described, although some reservations remain about the applicability of the methods to a wider range of plant cell types.

    2. Reviewer #1 (Public review):

      Summary:

      This in situ cryo-ET workflow of selected plant structures provides several detailed strategies using plunge-freezing and the HPF waffle method and lift-out for notoriously difficult samples (compared to cell culture, yeast, and algae, which are far more prevalent in the literature).

      Strengths:

      A very difficult challenge whereby the authors demonstrate successful vitrification of selected plants/structures using waffle and lift-out approaches for cryoET. Because there are relatively few examples of multi-cellular plant cryo-ET in the literature, it is important for the scientific community to be motivated and have demonstrated strategies that it is achievable. This manuscript has a number of very helpful graphics and videos to help guide researchers who would be interested in undertaking that would help shorten the learning curve of admittedly tedious and complex workflows. This is a slow and tedious process, but you have to start somewhere, and I applaud the authors for sharing their experiences with others, and I expect will help other early adopters to come up to speed sooner.

      Weaknesses:

      While important, the specific specimen and cell-types selected that were successful (perhaps other plant specimen and tissues tried were unsuccessful and thus not reported) in this approach did not demonstrate success to broadly applicable to other much more prevalent and interesting and intensive areas plant biology and plant structures (some mentioned in more detail below).

      This manuscript is essentially a protocol paper and in its paragraph form, and even with great graphics, will definitely be difficult to follow and reproduce for a non-expert. Also considering the use of 3 different FIB-SEM platforms and 2 different cryo-FLM platforms, I wonder if a master graphic of the full workflow(s) could be prepared as a supplementary document that walks through the major steps and points to the individual figures at the critical steps to make it more accessible to the broader readership.

      Multiple times in the manuscript, important workflow details seemed to point to and be dependent on two "unpublished" manuscripts:

      (1) Line 583, 755, 790, 847-848, (Poge et al., will soon be published as a protocol).

      (2) Lines 140, 695, 716 (Capitanio et al., will soon be described in a manuscript).

      It is not clear if/when these would be publicly available. It may be important to wait until these papers can be included in published form.

    3. Reviewer #2 (Public review):

      Summary:

      Poge et al. present a workflow for studying plant tissue by combining high-pressure freezing, cryo-fluorescence microscopy, FIB milling, and cryo-electron tomography (cryo-ET). They tested various plant tissues, including Physcomitrium patens, Arabidopsis thaliana, and Limonium bicolor. The authors successfully produce thin lamellae suitable for cryo-ET studies. Using sub-tomogram averaging, they determined the Rubisco structure at subnanometer resolution, demonstrating the potential of this workflow for plant tissue studies.

      Strengths:

      This manuscript is likely the first to systematically apply FIB milling and cryo-ET to plant tissue samples. It provides a detailed methodological description, which is not only valuable for plant tissue studies but also adaptable to a broader range of biological tissue samples. The study compares the plunge freezing method with a high-pressure freezing method, demonstrating that high-pressure freezing can vitrify thick tissues while preserving their native state. Additionally, the authors explore two methods for plant tissue sample preparation, the "waffle" method and in-carrier high-pressure freezing combined with the "lift-out" approach. The "waffle" method is suitable for samples less than 25um, while the in-carrier high-pressure freezing method can process samples up to 100um.

      Weaknesses:

      The described workflow is very complicated and requires special expertise. The success rate of this workflow is not very high, particularly for high-pressure freezing and life-out technology. Further improvements are needed for automation and increasing throughput.

    4. Reviewer #3 (Public review):

      Summary:

      The authors aimed to improve cryo-TEM workflows for plant cells. The authors present details on high-pressure-freezing protocols to vitrify, ion-mill, and image certain plant cell types.

      Strengths:

      Clear step-by-step outline on how to preserve and image cryo samples derived from plants.

      Weaknesses:

      A general current weakness of cryo-TEM is the problem of vitrifying cells that are embedded in tissues. The vast majority of cells in the plant body are currently not accessible to this technology. This is not a weakness of this specific manuscript but a general problem.

      The manuscript is well organized and well written, and the discussion covers practically all questions I had while reading the results section. I only have a few comments, all of which I consider minor.

    1. eLife Assessment

      This study provides a valuable extension of credibility-based learning research by showing how feedback reliability can distort reward-learning biases in a disinformation-like bandit task. Although the paradigm is well controlled and the computational modelling rigorous, the evidential support is incomplete: key claims about learning from 50 %-credible feedback and heightened positivity bias at low credibility hinge on a single dataset, specific parameter definitions, and modelling assumptions not fully validated across studies. Clearer reporting of the discovery-study null result, behavioural tests of positivity bias, and standard information-criterion model comparisons are needed to solidify the conclusions and enhance generalizability.

    2. Reviewer #1 (Public review):

      This is a well-designed and very interesting study examining the impact of imprecise feedback on outcomes in decision-making. I think this is an important addition to the literature, and the results here, which provide a computational account of several decision-making biases, are insightful and interesting.

      I do not believe I have substantive concerns related to the actual results presented; my concerns are more related to the framing of some of the work. My main concern is regarding the assertion that the results prove that non-normative and non-Bayesian learning is taking place. I agree with the authors that their results demonstrate that people will make decisions in ways that demonstrate deviations from what would be optimal for maximizing reward in their task under a strict application of Bayes' rule. I also agree that they have built reinforcement learning models that do a good job of accounting for the observed behavior. However, the Bayesian models included are rather simple, per the author's descriptions, applications of Bayes' rule with either fixed or learned credibility for the feedback agents. In contrast, several versions of the RL models are used, each modified to account for different possible biases. However, more complex Bayes-based models exist, notably active inference, but even the hierarchical Gaussian filter. These formalisms are able to accommodate more complex behavior, such as affect and habits, which might make them more competitive with RL models. I think it is entirely fair to say that these results demonstrate deviations from an idealized and strict Bayesian context; however, the equivalence here of Bayesian and normative is, I think, misleading or at least requires better justification/explanation. This is because a great deal of work has been done to show that Bayes optimal models can generate behavior or other outcomes that are clearly not optimal to an observer within a given context (consider hallucinations for example) but which make sense in the context of how the model is constructed as well as the priors and desired states the model is given.

      As such, I would recommend that the language be adjusted to carefully define what is meant by normative and Bayesian and to recognize that work that is clearly Bayesian could potentially still be competitive with RL models if implemented to model this task. An even better approach would be to directly use one of these more complex modelling approaches, such as active inference, as the comparator to the RL models, though I would understand if the authors would want this to be a subject for future work.

      Abstract:

      The abstract is lacking in some detail about the experiments done, but this may be a limitation of the required word count. If word count is not an issue, I would recommend adding details of the experiments done and the results.<br /> One comment is that there is an appeal to normative learning patterns, but this suggests that learning patterns have a fixed optimal nature, which may not be true in cases where the purpose of the learning (e.g. to confirm the feeling of safety of being in an in-group) may not be about learning accurately to maximize reward. This can be accommodated in a Bayesian framework by modelling priors and desired outcomes. As such, the central premise that biased learning is inherently non-normative or non-Bayesian, I think, would require more justification. This is true in the introduction as well.

      Introduction:

      As noted above, the conceptualization of Bayesian learning being equivalent to normative learning, I think requires further justification. Bayesian belief updating can be biased and non-optimal from an observer perspective, while being optimal within the agent doing the updating if the priors/desired outcomes are set up to advantage these "non-optimal" modes of decision making.

      Results:

      I wonder why the agent was presented before the choice, since the agent is only relevant to the feedback after the choice is made. I wonder if that might have induced any false association between the agent identity and the choice itself. This is by no means a critical point, but it would be interesting to get the authors' thoughts.

      The finding that positive feedback increases learning is one that has been shown before and depends on valence, as the authors note. They expanded their reinforcement learning model to include valence, but they did not modify the Bayesian model in a similar manner. This lack of a valence or recency effect might also explain the failure of the Bayesian models in the preceding section, where the contrast effect is discussed. It is not unreasonable to imagine that if humans do employ Bayesian reasoning that this reasoning system has had parameters tuned based on the real world, where recency of information does matter; affect has also been shown to be incorporable into Bayesian information processing (see the work by Hesp on affective charge and the large body of work by Ryan Smith). It may be that the Bayesian models chosen here require further complexity to capture the situation, just like some of the biases required updates to the RL models. This complexity, rather than being arbitrary, may be well justified by decision-making in the real world.

      The methods mention several symptom scales- it would be interesting to have the results of these and any interesting correlations noted. It is possible that some of the individual variability here could be related to these symptoms, which could introduce precision parameter changes in a Bayesian context and things like reward sensitivity changes in an RL context.

      Discussion:

      (For discussion, not a specific comment on this paper): One wonders also about participants' beliefs about the experiment or the intent of the experimenters. I have often had participants tell me they were trying to "figure out" a task or find patterns even when this was not part of the experiment. This is not specific to this paper, but it may be relevant in the future to try and model participant beliefs about the experiment especially in the context of disinformation, when they might be primed to try and "figure things out".

      As a general comment, in the active inference literature, there has been discussion of state-dependent actions, or "habits", which are learned in order to help agents more rapidly make decisions, based on previous learning. It is also possible that what is being observed is that these habits are at play, and that they represent the cognitive biases. This is likely especially true given, as the authors note, the high cognitive load of the task. It is true that this would mean that full-force Bayesian inference is not being used in each trial, or in each experience an agent might have in the world, but this is likely adaptive on the longer timescale of things, considering resource requirements. I think in this case you could argue that we have a departure from "normative" learning, but that is not necessarily a departure from any possible Bayesian framework, since these biases could potentially be modified by the agent or eschewed in favor of more expensive full-on Bayesian learning when warranted.

      Indeed, in their discussion on the strategy of amplifying credible news sources to drown out low-credibility sources, the authors hint at the possibility of longer-term strategies that may produce optimal outcomes in some contexts, but which were not necessarily appropriate to this task. As such, the performance on this task- and the consideration of true departure from Bayesian processing- should be considered in this wider context.

      Another thing to consider is that Bayesian inference is occurring, but that priors present going in produce the biases, or these biases arise from another source, for example, factoring in epistemic value over rewards when the actual reward is not large. This again would be covered under an active inference approach, depending on how the priors are tuned. Indeed, given the benefit of social cohesion in an evolutionary perspective, some of these "biases" may be the result of adaptation. For example, it might be better to amplify people's good qualities and minimize their bad qualities in order to make it easier to interact with them; this entails a cost (in this case, not adequately learning from feedback and potentially losing out sometimes), but may fulfill a greater imperative (improved cooperation on things that matter). Given the right priors/desired states, this could still be a Bayes-optimal inference at a social level and, as such, may be ingrained as a habit that requires effort to break at the individual level during a task such as this.

      The authors note that this task does not relate to "emotional engagement" or "deep, identity-related issues". While I agree that this is likely mostly true, it is also possible that just being told one is being lied to might elicit an emotional response that could bias responses, even if this is a weak response.

    3. Reviewer #2 (Public review):

      This valuable paper studies the problem of learning from feedback given by sources of varying credibility. The solid combination of experiment and computational modeling helps to pin down properties of learning, although some ambiguity remains in the interpretation of results.

      Summary:

      This paper studies the problem of learning from feedback given by sources of varying credibility. Two bandit-style experiments are conducted in which feedback is provided with uncertainty, but from known sources. Bayesian benchmarks are provided to assess normative facets of learning, and alternative credit assignment models are fit for comparison. Some aspects of normativity appear, in addition to deviations such as asymmetric updating from positive and negative outcomes.

      Strengths:

      The paper tackles an important topic, with a relatively clean cognitive perspective. The construction of the experiment enables the use of computational modeling. This helps to pinpoint quantitatively the properties of learning and formally evaluate their impact and importance. The analyses are generally sensible, and parameter recovery analyses help to provide some confidence in the model estimation and comparison.

      Weaknesses:

      (1) The approach in the paper overlaps somewhat with various papers, such as Diaconescu et al. (2014) and Schulz et al. (forthcoming), which also consider the Bayesian problem of learning and applying source credibility, in terms of theory and experiment. The authors should discuss how these papers are complementary, to better provide an integrative picture for readers.

      Diaconescu, A. O., Mathys, C., Weber, L. A., Daunizeau, J., Kasper, L., Lomakina, E. I., ... & Stephan, K. E. (2014). Inferring the intentions of others by hierarchical Bayesian learning. PLoS computational biology, 10(9), e1003810.<br /> Schulz, L., Schulz, E., Bhui, R., & Dayan, P. Mechanisms of Mistrust: A Bayesian Account of Misinformation Learning. https://doi.org/10.31234/osf.io/8egxh

      (2) It isn't completely clear what the "cross-fitting" procedure accomplishes. Can this be discussed further?

      (3) The Credibility-CA model seems to fit the same as the free-credibility Bayesian model in the first experiment and barely better in the second experiment. Why not use a more standard model comparison metric like the Bayesian Information Criterion (BIC)? Even if there are advantages to the bootstrap method (which should be described if so), the BIC would help for comparability between papers.

      (4) As suggested in the discussion, the updating based on random feedback could be due to the interleaving of trials. If one is used to learning from the source on most trials, the occasional random trial may be hard to resist updating from. The exact interleaving structure should also be clarified (I assume different sources were shown for each bandit pair). This would also relate to work on RL and working memory: Collins, A. G., & Frank, M. J. (2012). How much of reinforcement learning is working memory, not reinforcement learning? A behavioral, computational, and neurogenetic analysis. European Journal of Neuroscience, 35(7), 1024-1035.

      (5) Why does the choice-repetition regression include "only trials for which the last same-pair trial featured the 3-star agent and in which the context trial featured a different bandit pair"? This could be stated more plainly.

      (6) Why apply the "Truth-CA" model and not the Bayesian variant that it was motivated by?

      (7) "Overall, the results from this study support the exact same conclusions (See SI section 1.2) but with one difference. In the discovery study, we found no evidence for learning based on 50%-credibility feedback when examining either the feedback effect on choice repetition or CA in the credibility-CA model (SI 1.2.3)" - this seems like a very salient difference, when the paper reports the feedback effect as a primary finding of interest, though I understand there remains a valence-based difference.

      (8) "Participants were instructed that this feedback would be "a lie 50% of the time but were not explicitly told that this meant it was random and should therefore be disregarded." - I agree that this is a possible explanation for updating from the random source. It is a meaningful caveat.

      (9) "Future studies should investigate conditions that enhance an ability to discard disinformation, such as providing explicit instructions to ignore misleading feedback, manipulations that increase the time available for evaluating information, or interventions that strengthen source memory." - there is work on some of this in the misinformation literature that should be cited, such as the "continued influence effect". For example: Johnson, H. M., & Seifert, C. M. (1994). Sources of the continued influence effect: When misinformation in memory affects later inferences. Journal of experimental psychology: Learning, memory, and cognition, 20(6), 1420.

      (10) Are the authors arguing that choice-confirmation bias may be at play? Work on choice-confirmation bias generally includes counterfactual feedback, which is not present here.

    4. Reviewer #3 (Public review):

      Summary

      This paper investigates how disinformation affects reward learning processes in the context of a two-armed bandit task, where feedback is provided by agents with varying reliability (with lying probability explicitly instructed). They find that people learn more from credible sources, but also deviate systematically from optimal Bayesian learning: They learned from uninformative random feedback, learned more from positive feedback, and updated too quickly from fully credible feedback (especially following low-credibility feedback). Overall, this study highlights how misinformation could distort basic reward learning processes, without appeal to higher-order social constructs like identity.

      Strengths

      (1) The experimental design is simple and well-controlled; in particular, it isolates basic learning processes by abstracting away from social context.

      (2) Modeling and statistics meet or exceed the standards of rigor.

      (3) Limitations are acknowledged where appropriate, especially those regarding external validity.

      (4) The comparison model, Bayes with biased credibility estimates, is strong; deviations are much more compelling than e.g., a purely optimal model.

      (5) The conclusions are interesting, in particular the finding that positivity bias is stronger when learning from less reliable feedback (although I am somewhat uncertain about the validity of this conclusion)

      Weaknesses

      (1) Absolute or relative positivity bias?

      In my view, the biggest weakness in the paper is that the conclusion of greater positivity bias for lower credible feedback (Figure 5) hinges on the specific way in which positivity bias is defined. Specifically, we only see the effect when normalizing the difference in sensitivity to positive vs. negative feedback by the sum. I appreciate that the authors present both and add the caveat whenever they mention the conclusion (with the crucial exception of the abstract). However, what we really need here is an argument that the relative definition is the *right* way to define asymmetry....

      Unfortunately, my intuition is that the absolute difference is a better measure. I understand that the relative version is common in the RL literature; however previous studies have used standard TD models, whereas the current model updates based on the raw reward. The role of the CA parameter is thus importantly different from a traditional learning rate - in particular, it's more like a logistic regression coefficient (as described below) because it scales the feedback but *not* the decay. Under this interpretation, a difference in positivity bias across credibility conditions corresponds to a three-way interaction between the exponentially weighted sum of previous feedback of a given type (e.g., positive from the 75% credible agent), feedback positivity, and condition (dummy coded). This interaction corresponds to the non-normalized, absolute difference.

      Importantly, I'm not terribly confident in this argument, but it does suggest that we need a compelling argument for the relative definition.

      (2) Positivity bias or perseveration?

      A key challenge in interpreting many of the results is dissociating perseveration from other learning biases. In particular, a positivity bias (Figure 5) and perseveration will both predict a stronger correlation between positive feedback and future choice. Crucially, the authors do include a perseveration term, so one would hope that perseveration effects have been controlled for and that the CA parameters reflect true positivity biases. However, with finite data, we cannot be sure that the variance will be correctly allocated to each parameter (c.f. collinearity in regressions). The fact that CA- is fit to be negative for many participants (a pattern shown more strongly in the discovery study) is suggestive that this might be happening. A priori, the idea that you would ever increase your value estimate after negative feedback is highly implausible, which suggests that the parameter might be capturing variance besides that it is intended to capture.

      The best way to resolve this uncertainty would involve running a new study in which feedback was sometimes provided in the absence of a choice - this would isolate positivity bias. Short of that, perhaps one could fit a version of the Bayesian model that also includes perseveration. If the authors can show that this model cannot capture the pattern in Figure 5, that would be fairly convincing.

      (3) Veracity detection or positivity bias?

      The "True feedback elicits greater learning" effect (Figure 6) may be simply a re-description of the positivity bias shown in Figure 5. This figure shows that people have higher CA for trials where the feedback was in fact accurate. But, assuming that people tend to choose more rewarding options, true-feedback cases will tend to also be positive-feedback cases. Accordingly, a positivity bias would yield this effect, even if people are not at all sensitive to trial-level feedback veracity. Of course, the reverse logic also applies, such that the "positivity bias" could actually reflect discounting of feedback that is less likely to be true. This idea has been proposed before as an explanation for confirmation bias (see Pilgrim et al, 2024 https://doi.org/10.1016/j.cognition.2023.105693 and much previous work cited therein). The authors should discuss the ambiguity between the "positivity bias" and "true feedback" effects within the context of this literature....

      The authors get close to this in the discussion, but they characterize their results as differing from the predictions of rational models, the opposite of my intuition. They write:

      Alternative "informational" (motivation-independent) accounts of positivity and confirmation bias predict a contrasting trend (i.e., reduced bias in low- and medium credibility conditions) because in these contexts it is more ambiguous whether feedback confirms one's choice or outcome expectations, as compared to a full-credibility condition.

      I don't follow the reasoning here at all. It seems to me that the possibility for bias will increase with ambiguity (or perhaps will be maximal at intermediate levels). In the extreme case, when feedback is fully reliable, it is impossible to rationally discount it (illustrated in Figure 6A). The authors should clarify their argument or revise their conclusion here.

      (4) Disinformation or less information?

      Zooming out, from a computational/functional perspective, the reliability of feedback is very similar to reward stochasticity (the difference is that reward stochasticity decreases the importance/value of learning in addition to its difficulty). I imagine that many of the effects reported here would be reproduced in that setting. To my surprise, I couldn't quickly find a study asking that precise question, but if the authors know of such work, it would be very useful to draw comparisons. To put a finer point on it, this study does not isolate which (if any) of these effects are specific to *disinformation*, rather than simply _less information._ I don't think the authors need to rigorously address this in the current study, but it would be a helpful discussion point.

      (5) Over-reliance on analyzing model parameters

      Most of the results rely on interpreting model parameters, specifically, the "credit assignment" (CA) parameter. Exacerbating this, many key conclusions rest on a comparison of the CA parameters fit to human data vs. those fit to simulations from a Bayesian model. I've never seen anything like this, and the authors don't justify or even motivate this analysis choice. As a general rule, analyses of model parameters are less convincing than behavioral results because they inevitably depend on arbitrary modeling assumptions that cannot be fully supported. I imagine that most or even all of the results presented here would have behavioral analogues. The paper would benefit greatly from the inclusion of such results. It would also be helpful to provide a description of the model in the main text that makes it very clear what exactly the CA parameter is capturing (see next point).

      (6) RL or regression?

      I was initially very confused by the "RL" model because it doesn't update based on the TD error. Consequently, the "Q values" can go beyond the range of possible reward (SI Figure 5). These values are therefore *not* Q values, which are defined as expectations of future reward ("action values"). Instead, they reflect choice propensities, which are sometimes notated $h$ in the RL literature. This misuse of notation is unfortunately quite common in psychology, so I won't ask the authors to change the variable. However, they should clarify when introducing the model that the Q values are not action values in the technical sense. If there is precedent for this update rule, it should be cited.

      Although the change is subtle, it suggests a very different interpretation of the model.

      Specifically, I think the "RL model" is better understood as a sophisticated logistic regression, rather than a model of value learning. Ignoring the decay term, the CA term is simply the change in log odds of repeating the just-taken action in future trials (the change is negated for negative feedback). The PERS term is the same, but ignoring feedback. The decay captures that the effect of each trial on future choices diminishes with time. Importantly, however, we can re-parameterize the model such that the choice at each trial is a logistic regression where the independent variables are an exponentially decaying sum of feedback of each type (e.g., positive-cred50, positive-cred75, ... negative-cred100). The CA parameters are simply coefficients in this logistic regression.

      Critically, this is not meant to "deflate" the model. Instead, it clarifies that the CA parameter is actually not such an assumption-laden model estimate. It is really quite similar to a regression coefficient, something that is usually considered "model agnostic". It also recasts the non-standard "cross-fitting" approach as a very standard comparison of regression coefficients for model simulations vs. human data. Finally, using different CA parameters for true vs false feedback is no longer a strange and implausible model assumption; it's just another (perfectly valid) regression. This may be a personal thing, but after adopting this view, I found all the results much easier to understand.

    1. eLife Assessment

      This important study of the inhibitory complex amacrines (CAM) in the vertical lobe of Octopus vulgaris delivers a solid standard for the structural characterization of an anatomical region likely to be key for memory processing in this unconventional but complex organism, as well as a helpful classification of CAM subtypes. This work will be of broad relevance to the fields of memory and evolutionary neuroscience.

    2. Reviewer #1 (Public review):

      The authors identified five complex amacrine cell (CAM) subtypes based on their morphology and synaptic connectivity. It's suggested that the differences in structure may be directly correlated with different functional roles. The authors also describe synaptic compartmentalization in the SFL tract relating to three types of CAM input regions, again implying a specialized role for these cells. The authors also identified neural progenitor cells, which suggests that the octopus's vertical lobe can undergo neurogenesis throughout its life.

      The work presented here is valuable and convincing. Below are some suggestions the authors may wish to incorporate:

      a) Quantitative measurements to define the CAM subtypes<br /> I think the categorization of the CAMs into five subtypes is convincing, however, I wonder how easily these categories could be identified by other researchers. Would it be possible for the authors to include additional quantitative measurements of these cell types to make their categorization less qualitative and more quantitative? For example, density, volume, and orientation of their dendritic fields?

      b) The definition of the neuritic backbone is included in the methods, but I found the term confusing when I first encountered it in the results, so I would suggest adding the definition to the results too.

      c) The authors wrote, 'Note that given the pronounced difference in diameters between the neuritic backbones (208.27 +/-87.95 nm) and axons (121.55 +/- 21.28 nm)'. What figure is this in?

      d) I am slightly confused about how the authors decided on the specific cubes to reflect the different synaptic compartments in the SFL tract. Is this organisation arranged/repeated vertically or horizontally throughout the SFL tract? The location of the cubes looks to me to be chosen at random, so more information here would be helpful.

      e) In Figure 2, could the authors plot the number of synapses per cube to make the result clearer, so that cube 1 has the lowest synaptic density and cube 2 has the highest?

      f) SAMs are ACh and excitatory<br /> The authors refer to SAMs as excitatory cholinergic. They should provide more detailed explanations/citations to back up this claim. Could SAMs be synthesizing any other neurotransmitters? Could there be a subpopulation of inhibitory SAMs?

      g) CAMs are GABA and inhibitory

      The 5 subtypes of CAMs described here have never been directly confirmed to be GABAergic. Could CAMs be synthesizing any other neurotransmitters? Could a subpopulation of CAMs be excitatory? I believe the authors should make this clearer to readers when referring to CAMs, perhaps by saying, 'hypothesized to be inhibitory neurons', or 'putative inhibitory neurons'.

      h) Fast neurotransmitters and neuromodulators<br /> The authors refer to neuromodulatory connections in their summary in Figure 4, however, cephalopod receptors have yet to be extensively functionally characterized, therefore, the role different molecules play as neurotransmitters or neuromodulators is not yet known. For example, many invertebrates are known to have functional diversity in their receptors: C. elegans has both excitatory and inhibitory receptors for a range of neurotransmitters, anionic ACh- and glutamate-gated channels, and cationic peptide-gated channels have also been identified in some molluscs. So, probably the authors should be cautious in speculating about how a particular transmitter/modulator acts in the octopus brain.

      i) In the methods, the authors refer to "an adult Octopus", what age and size was it? I also know this is Octopus vulgaris, but it would be good to specify it here.

      j) A general comment about all figures. All panels should have a letter associated with them to make it easier to refer to them in the text. For example, in Figure 4, please also add letters to the main schematic, the CAM subtypes, and the VL wiring diagram. In addition, D and E are missing boxes on the main schematic. It's also not immediately obvious that A-E are zooms of the larger schematic; perhaps this could be made clearer with colours or arrows. Please also add names to the CAM subtypes.

      a) Typo: 'Additionally, the unique characteristics of LTP in the octopus VL, such as its reliance on a NO-dependent mechanism, independent of de novo protein synthesis, persistent activation of (Turchetti-Maia et al., 2018).'

    3. Reviewer #2 (Public review):

      Summary:

      The paper examines the diversity of complex amacrine neurons in the ventral lobe of the adult octopus brain, a structure involved in learning and memory. The work builds on a recent paper by the authors that described the connectivity of the much larger population of simple amacrine (SAM) interneurons from the same pioneering EM volume.

      Strengths:

      While the EM volume only provides a snapshot of a tiny fraction of an adult octopus' brain, the authors can make specific conclusions and formulate precise hypotheses about neuron function, synaptic pathways, and developmental trajectories. One example is the reconstruction of a putative maturation sequence for the SAM neuronal lineage, based on the correlation of soma position and the number of synapses, uncovering a plausible developmental sequence of cell morphologies, with interesting parallels to vertebrate neurogenesis.

      Weaknesses:

      The weakness of the study is that it is examining a relatively small volume (260 × 390 × 27 µm), and several neurons are only incompletely reconstructed. It also remains unclear approximately how many neurons remain to be reconstructed from this volume.

      To improve the presentation, the authors should consider showing videos with the volumetric reconstructions of the different types with their partners/synapses and their relation to the SFL track and SAMs. Such videos would help the reader to appreciate the morphological differences between the cell types. The authors could also consider carrying out further morphological analyses to strengthen their cell-type classification, including Sholl value, radial density of input and output synapses, the number of branch nodes, and similar measures.

    4. Reviewer #3 (Public review):

      (1) The authors described "the excitatory glutamatergic SFL axons and cholinergic SAM inputs". However, the evidence of their transmitter specificity has not been provided. Compelling evidence was neither provided nor discussed in the context of the study.

      (2) Specific interference for inhibitory or excitatory synapses based on EM or other studies must be detailed and elaborated

      (3) Different local microcircuits (submodules) referred to in the text should be better described and more specifically defined.

      (4) I would recommend incorporating a more detailed description of synapses and, especially, synaptic vesicles, clarifying their diversity and similarity across cell subtypes. Are there any differences between cholinergic and glutamatergic synaptic vesicles, postsynaptic densities, or other features...? It would be good, if possible, to explicitly clarify: how many vesicles per different types of synapses? How many synapses per neuron of different types? How many inputs and outputs per a given neuron?

      (5) Authors discuss retrograde messengers like NO? Is there any identifiable morphological type of neuron(s) or synapses that might be nitrergic?

      (6) It would be good to provide separate illustrations showing the detailed organization of any glial cell or different types of glial cells they identified in this study. Authors mainly discuss glial processes but refer to "recognized glial types, such as radial glia and astrocyte-like glia" without specific illustrations, which can be deciphered from their EM data. What are vesicular organizations within different types of glial cells?

      (7) The authors also discuss "supervising inputs of inhibitory (pain) and neuromodulatory (supervising) signals", without any details. It would be important to provide these details in the discussion. Specifically, I suggest incorporating comments about differences/similarities of transmitters and morphology between pain and modulatory pathways/signaling/circuits.

    5. Reviewer #4 (Public review):

      Summary:

      The authors present a follow-up to their initial publication of a volume EM reconstruction of a part of the Octopus vulgaris vertical lobe (VL) (Bidel, Meirovitch et al., eLife 2023). In their previous study, they presented a swath of novel observations pertaining to the neuron types making up the VL and their synaptic connectivity. Here, the authors present an extension of those findings in which they (1) demonstrate that the Complex Amacrine cells (CAMs), which they identified previously, can be grouped into at least 5 distinct subclasses; (2) show that there appears to be distinct compartments in the SFL tract that contain specific synapse types; and (3) present morphological evidence that there may be a neurogenic niche in the VL. The findings are intriguing, advance our understanding of memory circuitry in octopus and across the phylogenetic tree, and open new avenues for deeper investigation.

      Strengths:

      A deeper dissection of the morphologies of CAMs and their distinct complements of synapse types is valuable. The identification of multiple categories of CAMs makes it clearer how the very simple SFL-to-SAM connectivity is likely enriched by a population of diverse interneurons.

      The observation that synapse types may be compartmentalized in the superior frontal lobe tract is an intriguing one, and invites more extensive segmentation and future anatomical studies to further characterize the precise architecture of these compartments.

      Finally, the evidence of the possibility of a neurogenic niche in the VL is exciting as it suggests that ongoing neurogenesis may be a common feature of memory circuitry, perhaps contributing to keeping the representation space of the circuit flexible and adequately sparse.

      Weaknesses:

      A key weakness is the reconstruction and grouping of the CAMs:

      (1) CAMs are relatively few in number compared to SAMs, and as such, only 53 are reconstructed in this study. Of those 53 cells, 18 were not classified into one of the 5 categories the authors designate, begging the question of how robust those categories are.

      (2) Related to (1), in Figure 1B, the proportions given in the bar graph are given cumulatively across the entire population of each category. The proportions should be presented as means within each category to adequately capture the variability of the small sample sizes.

      (3) While the xy dimensions of the serial section EM volume are adequate to capture relatively whole cells and neuronal arbors, the volume is only 27µm thick. Thus, many neurite branches are likely truncated in the z-dimension. This may have contributed to ~1/3 of CAMs eluding categorization. However, it is hard to estimate the effect this may have had without knowing the extent of the truncation. It may be worth the authors' time to count the proportion of CAM neurites that are cut off at the edges of the volume.

      (4) The authors state that CAMs appear to have axons and dendrites based on neurite widths. This is an interesting finding, given that amacrine cells are generally thought to possess only one type of neurite, which both send and receive synaptic potentials, and therefore deserves more attention. Is the distribution of neurite widths indeed bimodally distributed? Can the axons and dendrites be differentiated by examining the presence and absence of synaptic vesicle pools, respectively?

      In Figure 2, the compartmentalization of synapse types is intriguing; however, due to the 3D nature of the data, it is difficult to appreciate clearly from the panels presented. This is particularly true for the suggestion that glia may be forming a barrier around these compartments. This could be rectified by providing Neuroglancer links for these specific reconstructions (neurites, synapses, and glia).

      Lastly, although the identification of a putative neurogenic niche is tantalizing, morphological data alone is only an initial hint. Although the chances are slim, it would be more convincing if the authors could identify any actively dividing cells in the proposed niche. More likely, further work, for instance, immunofluorescence, which the lab has previously shown to be viable in octopus, will be needed to add weight to the claim.

    1. eLife Assessment

      This is an important study introducing a stimulus-computable model of multisensory perception that extends an existing framework to accept raw, stimulus-level inputs (i.e., image- and soundscape-computable). The author demonstrates how low-level correlation detection can drive both illusions and cue integration, and the model bridges diverse stimuli, behaviors, and species. The model and evidence provided are deemed generally convincing and of broad applicability, potentially impacting areas across neuroscience, psychology, and computational cognitive science. There are, however, certain aspects of the work considered incomplete, particularly as they relate to explaining details pertinent to model fitting.

    2. Reviewer #1 (Public review):

      Summary:

      Parise presents another instantiation of the Multisensory Correlation Detector model that can now accept stimulus-level inputs. This is a valuable development as it removes researcher involvement in the characterization/labeling of features and allows analysis of complex stimuli with a high degree of nuance that was previously unconsidered (i.e., spatial/spectral distributions across time). The author demonstrates the power of the model by fitting data from dozens of previous experiments, including multiple species, tasks, behavioral modalities, and pharmacological interventions.

      Strengths:

      One of the model's biggest strengths, in my opinion, is its ability to extract complex spatiotemporal co-relationships from multisensory stimuli. These relationships have typically been manually computed or assigned based on stimulus condition and often distilled to a single dimension or even a single number (e.g., "-50 ms asynchrony"). Thus, many models of multisensory integration depend heavily on human preprocessing of stimuli, and these models miss out on complex dynamics of stimuli; the lead modality distribution apparent in Figures 3b and c is provocative. I can imagine the model revealing interesting characteristics of the facial distribution of correlation during continuous audiovisual speech that have up to this point been largely described as "present" and almost solely focused on the lip area.

      Another aspect that makes the MCD stand out among other models is the biological inspiration and generalizability across domains. The model was developed to describe a separate process - motion perception - and in a much simpler organism - Drosophila. It could then describe a very basic neural computation that has been conserved across phylogeny (which is further demonstrated in the ability to predict rat, primate, and human data) and brain area. This aspect makes the model likely able to account for much more than what has already been demonstrated with only a few tweaks akin to the modifications described in this and previous articles from Parise.

      What allows this potential is that, as Parise and colleagues have demonstrated in those papers since our (re)introduction of the model in 2016, the MCD model is modular - both in its ability to interface with different inputs/outputs and its ability to chain MCD units in a way that can analyze spatial, spectral, or any other arbitrary dimension of a stimulus. This fact leaves wide open the possibilities for types of data, stimuli, and tasks a simplistic, neutrally inspired model can account for.

      And so it's unsurprising (but impressive!) that Parise has demonstrated the model's ability here to account for such a wide range of empirical data from numerous tasks (synchrony/temporal order judgement, localization, detection, etc.) and behavior types (manual/saccade responses, gaze, etc.) using only the stimulus and a few free parameters. This ability is another of the model's main strengths that I think deserves some emphasis: it represents a kind of validation of those experiments, especially in the context of cross-experiment predictions (but see some criticism of that below).

      Finally, what is perhaps most impressive to me is that the MCD (and the accompanying decision model) does all this with very few (sometimes zero) free parameters. This highlights the utility of the model and the plausibility of its underlying architecture, but also helps to prevent extreme overfitting if fit correctly (but see a related concern below).

      Weaknesses:

      There is an insufficient level of detail in the methods about model fitting. As a result, it's unclear what data the models were fitted and validated on. Were models fit individually or on average group data? Each condition separately? Is the model predictive of unseen data? Was the model cross-validated? Relatedly, the manuscript mentions a randomization test, but the shuffled data produces model responses that are still highly correlated to behavior despite shuffling. Could it be that any stimulus that varies in AV onset asynchrony can produce a psychometric curve that matches any other task with asynchrony judgements baked into the task? Does this mean all SJ or TOJ tasks produce correlated psychometric curves? Or more generally, is Pearson's correlation insensitive to subtle changes here, considering psychometric curves are typically sigmoidal? Curves can be non-overlapping and still highly correlated if one is, for example, scaled differently. Would an error term such as mean-squared or root mean-squared error be more sensitive to subtle changes in psychometric curves? Alternatively, perhaps if the models aren't cross-validated, the high correlation values are due to overfitting?

      While the model boasts incredible versatility across tasks and stimulus configurations, fitting behavioral data well doesn't mean we've captured the underlying neural processes, and thus, we need to be careful when interpreting results. For example, the model produces temporal parameters fitting rat behavior that are 4x faster than when fitting human data. This difference in slope and a difference at the tails were interpreted as differences in perceptual sensitivity related to general processing speeds of the rat, presumably related to brain/body size differences. While rats no doubt have these differences in neural processing speed/integration windows, it seems reasonable that a lot of the differences in human and rat psychometric functions could be explained by the (over)training and motivation of rats to perform on every trial for a reward - increasing attention/sensitivity (slope) - and a tendency to make mistakes (compression evident at the tails). Was there an attempt to fit these data with a lapse parameter built into the decisional model as was done in Equation 21? Likewise, the fitted parameters for the pharmacological manipulations during the SJ task indicated differences in the decisional (but not the perceptual) process and the article makes the claim that "all pharmacologically-induced changes in audiovisual time perception" can be attributed to decisional processes "with no need to postulate changes in low-level temporal processing." However, those papers discuss actual sensory effects of pharmacological manipulation, with one specifically reporting changes to response timing. Moreover, and again contrary to the conclusions drawn from model fits to those data, both papers also report a change in psychometric slope/JND in the TOJ task after pharmacological manipulation, which would presumably be reflected in changes to the perceptual (but not the decisional) parameters.

      The case for the utility of a stimulus-computable model is convincing (as I mentioned above), but its framing as mission-critical for understanding multisensory perception is overstated, I think. The line for what is "stimulus computable" is arbitrary and doesn't seem to be followed in the paper. A strict definition might realistically require inputs to be, e.g., the patterns of light and sound waves available to our eyes and ears, while an even more strict definition might (unrealistically) require those stimuli to be physically present and transduced by the model. A reasonable looser definition might allow an "abstract and low-dimensional representation of the stimulus, such as the stimulus envelope (which was used in the paper), to be an input. Ultimately, some preprocessing of a stimulus does not necessarily confound interpretations about (multi)sensory perception. And on the flip side, the stimulus-computable aspect doesn't necessarily give the model supreme insight into perception. For example, the MCD model was "confused" by the stimuli used in our 2018 paper (Nidiffer et al., 2018; Parise & Ernst, 2025). In each of our stimuli (including catch trials), the onset and offset drove strong AV temporal correlations across all stimulus conditions (including catch trials), but were irrelevant to participants performing an amplitude modulation detection task. The to-be-detected amplitude modulations, set at individual thresholds, were not a salient aspect of the physical stimulus, and thus only marginally affected stimulus correlations. The model was of course, able to fit our data by "ignoring" the on/offsets (i.e., requiring human intervention), again highlighting that the model is tapping into a very basic and ubiquitous computational principle of (multi)sensory perception. But it does reveal a limitation of such a stimulus-computable model: that it is (so far) strictly bottom-up.

      The manuscript rightly chooses to focus a lot of the work on speech, fitting the MCD model to predict behavioral responses to speech. The range of findings from AV speech experiments that the MCD can account for is very convincing. Given the provided context that speech is "often claimed to be processed via dedicated mechanisms in the brain," a statement claiming a "first end-to-end account of multisensory perception," and findings that the MCD model can account for speech behaviors, it seems the reader is meant to infer that energetic correlation detection is a complete account of speech perception. I think this conclusion misses some facets of AV speech perception, such as integration of higher-order, non-redundant/correlated speech features (Campbell, 2008) and also the existence of top-down and predictive processing that aren't (yet!) explained by MCD. For example, one important benefit of AV speech is interactions on linguistic processes - how complementary sensitivity to articulatory features in the auditory and visual systems (Summerfield, 1987) allow constraint of linguistic processes (Peelle & Sommers, 2015; Tye-Murray et al., 2007).

      References

      Campbell, R. (2008). The processing of audio-visual speech: empirical and neural bases. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1493), 1001-1010. https://doi.org/10.1098/rstb.2007.2155<br /> Nidiffer, A. R., Diederich, A., Ramachandran, R., & Wallace, M. T. (2018). Multisensory perception reflects individual differences in processing temporal correlations. Scientific Reports 2018 8:1, 8(1), 1-15. https://doi.org/10.1038/s41598-018-32673-y<br /> Parise, C. V, & Ernst, M. O. (2025). Multisensory integration operates on correlated input from unimodal transient channels. ELife, 12. https://doi.org/10.7554/ELIFE.90841<br /> Peelle, J. E., & Sommers, M. S. (2015). Prediction and constraint in audiovisual speech perception. Cortex, 68, 169-181. https://doi.org/10.1016/j.cortex.2015.03.006<br /> Summerfield, Q. (1987). Some preliminaries to a comprehensive account of audio-visual speech perception. In B. Dodd & R. Campbell (Eds.), Hearing by Eye: The Psychology of Lip-Reading (pp. 3-51). Lawrence Erlbaum Associates.<br /> Tye-Murray, N., Sommers, M., & Spehar, B. (2007). Auditory and Visual Lexical Neighborhoods in Audiovisual Speech Perception: Trends in Amplification, 11(4), 233-241. https://doi.org/10.1177/1084713807307409

    3. Reviewer #2 (Public review):

      Summary:

      Building on previous models of multisensory integration (including their earlier correlation-detection framework used for non-spatial signals), the author introduces a population-level Multisensory Correlation Detector (MCD) that processes raw auditory and visual data. Crucially, it does not rely on abstracted parameters, as is common in normative Bayesian models," but rather works directly on the stimulus itself (i.e., individual pixels and audio samples). By systematically testing the model against a range of experiments spanning human, monkey, and rat data, the authors show that their MCD population approach robustly predicts perception and behavior across species with a relatively small (0-4) number of free parameters.

      Strengths:

      (1) Unlike prior Bayesian models that used simplified or parameterized inputs, the model here is explicitly computable from full natural stimuli. This resolves a key gap in understanding how the brain might extract "time offsets" or "disparities" from continuously changing audio-visual streams.

      (2) The same population MCD architecture captures a remarkable range of multisensory phenomena, from classical illusions (McGurk, ventriloquism) and synchrony judgments, to attentional/gaze behavior driven by audio-visual salience. This generality strongly supports the idea that a single low-level computation (correlation detection) can underlie many distinct multisensory effects.

      (3) By tuning model parameters to different temporal rhythms (e.g., faster in rodents, slower in humans), the MCD explains cross-species perceptual data without reconfiguring the underlying architecture.

      Weaknesses:

      (1) The authors show how a correlation-based model can account for the various multisensory integration effects observed in previous studies. However, a comparison of how the two accounts differ would shed light on the correlation model being an implementation of the Bayesian computations (different levels in Marr's hierarchy) or making testable predictions that can distinguish between the two frameworks. For example, how uncertainty in the cue combined estimate is also the harmonic mean of the unimodal uncertainties is a prediction from the Bayesian model. So, how the MCD framework predicts this reduced uncertainty could be one potential difference (or similarity) to the Bayesian model.

      2) The authors show a good match for cue combination involving 2 cues. While Bayesian accounts provide a direction extension to more cues (also seen empirically, for eg, in Hecht et al. 2008), discussion on how the MCD model extends to more cues would benefit the readers.

      Likely Impact and Usefulness:

      The work offers a compelling unification of multiple multisensory tasks- temporal order judgments, illusions, Bayesian causal inference, and overt visual attention - under a single, fully stimulus-driven framework. Its success with natural stimuli should interest computational neuroscientists, systems neuroscientists, and machine learning scientists. This paper thus makes an important contribution to the field by moving beyond minimalistic lab stimuli, illustrating how raw audio and video can be integrated using elementary correlation analyses.

    1. eLife Assessment

      The study conducted by Hurtado et al. offers important insights and solid evidence regarding the prediction of drug combinations for cancer treatment. By leveraging disease-specific drug response profiles and single-cell transcriptional signatures, this research not only demonstrates a novel and effective approach to identifying potential drug synergies but it also enhances our understanding of the underlying mechanisms of drug response prediction.

    2. Reviewer #1 (Public review):

      Summary:

      Identifying drugs that target specific disease phenotypes remains a persistent challenge. Many current methods are only applicable to well-characterized small molecules, such as those with known structures. In contrast, methods based on transcriptional responses offer broader applicability because they do not require prior information about small molecules. Additionally, they can be rapidly applied to new small molecules. One of the most promising strategies involves the use of "drug response signatures"-specific sets of genes whose differential expression can serve as markers for the response to a small molecule. By comparing drug response signatures with expression profiles characteristic of a disease, it is possible to identify drugs that modulate the disease profile, indicating a potential therapeutic connection.

      This study aims to prioritize potential drug candidates and to forecast novel drug combinations that may be effective in treating triple-negative breast cancer (TNBC). Large consortia, such as the LINCS-L1000 project, offer transcriptional signatures across various time points after exposing numerous cell lines to hundreds of compounds at different concentrations. While this data is highly valuable, its direct applicability to pathophysiological contexts is constrained by the challenges in extracting consistent drug response profiles from these extensive datasets. The authors use their method to create drug response profiles for three different TNBC cell lines from LINCS.<br /> To create a more precise, cancer-specific disease profile, the authors highlight the use of single-cell RNA sequencing (scRNA-seq) data. They focus on TNBC epithelial cells collected from 26 diseased individuals compared to epithelial cells collected from 10 healthy volunteers. The authors are further leveraging drug response data to develop inhibitor combinations.

      Strengths:

      The authors of this study contribute to an ongoing effort to develop automated, robust approaches that leverage gene expression similarities across various cell lines and different treatment regimen, aiming to predict drug response signatures more accurately. There remains a gap in computational methods for inferring drug responses at the cell subpopulation level, which the authors are trying to address.

      Weaknesses:

      The major deficiencies in this revised manuscript are a lack of benchmarking against established methods, clarification of method limitations, and experimental validation.

      (1) The manuscript still lacks a direct comparison between the retriever tool and well-established methods. How does it perform compared to metaLINCS? Evaluating its performance relative to existing approaches is essential to demonstrate its added value and robustness.<br /> (2) The study remains limited by the absence of experimental validation. Are there supporting data from biological models or clinical trials? Figure 5F is important as this is the validation of the identified compounds in three cell lines. In the previous review, it was noted that the identified drugs had only a modest effect on cell viability. Furthermore, the efficacy of QL-XII-47 and GSK-690693 was found to be cell-line specific-showing activity against BT20 (the cell line used for LINCS transcriptional signature generation) but not against CAL120 and DU4475, which were not included in the signature derivation process. This raises concerns about the tool's ability to predict effective drugs. Additionally, the combination may have an effect because the drugs were tested at high concentrations. How does this effect compare in non-TNBC or normal immortalized breast cell lines? Finally, the DU4475 data were not reproducible, and the experiment must be repeated to ensure reliable comparisons.<br /> (3) A previous review requested a discussion on the limitations of the retriever tool, but the authors instead focused on the well-documented constraints of the LINCS dataset. Clearly defining limitations of the retriever will be critical for evaluating its potential applications and reliability.<br /> (4) Description of the database that the authors used should be corrected. Two examples are below:<br /> "The LINCS-L1000 project published transcriptional profiles of several cell lines." Exploring LINCS metadata will help to introduce the reader to this impressive catalog.<br /> "The portal then returns a ranked list of compounds that are likely to have an inverse effect on disease-associated gene expression levels". When selecting small molecules for use in LINCS-L1000 platform, no link was established between the compounds and disease-associated gene expression levels.<br /> (5) Fig. 3 presents data on differentially expressed genes. However, without indicating whether these genes are up- or downregulated, it is difficult to assess their relevance to TNBC phenotypes and cancer burden.<br /> Additionally, presenting the new Biological Process Gene Ontology analysis in a format similar to Fig. 3C would be beneficial. The statement that these processes are closely related to cancer deregulation is somewhat vague. Instead, the findings may be discussed in relation to each enriched pathway, specifically in the context of TNBC biology and available treatments.

    3. Reviewer #2 (Public review):

      Summary:

      In their study, Osorio and colleagues present 'retriever,' an innovative computational tool designed to extract disease-specific transcriptional drug response profiles from the LINCS-L1000 project. This tool has been effectively applied to TNBC, leveraging single-cell RNA sequencing data to predict drug combinations that may effectively target the disease. The public review highlights the significant integration of extensive pharmacological data with high-resolution transcriptomic information, which enhances the potential for personalized therapeutic applications.

      Strengths:

      A key finding of the study is the prediction and validation of the drug combination QL-XII-47 and GSK-690693 for the treatment of TNBC. The methodology employed is robust, with a clear pathway from data analysis to experimental confirmation.

      Comments on revisions:

      I commend the authors for their thorough and thoughtful revisions, which have significantly strengthened the manuscript. The expanded discussion on the limitations of the LINCS-L1000 dataset and the inherent challenges of imputation techniques provides critical context for interpreting the tool's predictive accuracy. The addition of clinical implications, including strategies for integrating retriever into clinical trial design and its broader applicability to other diseases, enhances the translational relevance of the work. Addressing drug resistance mechanisms in the context of combination therapy further underscores the biological rationale for the approach.

      The transparency regarding computational requirements and ethical considerations-particularly data privacy, bias mitigation, and model validation-demonstrates a responsible and forward-thinking approach to computational biology. These additions not only improve the manuscript's rigor but also set a precedent for ethical practices in personalized medicine research.

      With these revisions, the authors have effectively addressed prior concerns and elevated the impact of their work. The manuscript now presents a compelling case for the retriever as a valuable tool in precision oncology.

    4. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer 1:

      Summary:

      Identifying drugs that target specific disease phenotypes remains a persistent challenge. Many current methods are only applicable to well-characterized small molecules, such as those with known structures. In contrast, methods based on transcriptional responses offer broader applicability because they do not require prior information about small molecules. Additionally, they can be rapidly applied to new small molecules. One of the most promising strategies involves the use of “drug response signatures”-specific sets of genes whose differential expression can serve as markers for the response to a small molecule. By comparing drug response signatures with expression profiles characteristic of a disease, it is possible to identify drugs that modulate the disease profile, indicating a potential therapeutic connection.

      This study aims to prioritize potential drug candidates and to forecast novel drug combinations that may be effective in treating triple-negative breast cancer (TNBC). Large consortia, such as the LINCS-L1000 project, offer transcriptional signatures across various time points after exposing numerous cell lines to hundreds of compounds at different concentrations. While this data is highly valuable, its direct applicability to pathophysiological contexts is constrained by the challenges in extracting consistent drug response profiles from these extensive datasets. The authors use their method to create drug response profiles for three different TNBC cell lines from LINCS.

      To create a more precise, cancer-specific disease profile, the authors highlight the use of single-cell RNA sequencing (scRNA-seq) data. They focus on TNBC epithelial cells collected from 26 diseased individuals compared to epithelial cells collected from 10 healthy volunteers. The authors are further leveraging drug response data to develop inhibitor combinations.

      Strengths:

      The authors of this study contribute to an ongoing effort to develop automated, robust approaches that leverage gene expression similarities across various cell lines and different treatment regimens, aiming to predict drug response signatures more accurately. The authors are trying to address the gap that remains in computational methods for inferring drug responses at the cell subpopulation level.

      Weaknesses:

      One weakness is that the authors do not compare their method to previous studies. The authors develop a drug response profile by summarizing the time points, concentrations, and cell lines. The computational challenge of creating a single gene list that represents the transcriptional response to a drug across different cell lines and treatment protocols has been previously addressed. The Prototype Ranked List (PRL) procedure, developed by Iorio and co-authors (PNAS, 2010, doi:10.1073/pnas.1000138107), uses a hierarchical majority-voting scheme to rank genes. This method generates a list of genes that are consistently overexpressed or downregulated across individual conditions, which then hold top positions in the PRL. The PRL methodology was used by Aissa and co-authors (Nature Comm 2021, doi:10.1038/s41467-021-21884-z) to analyze drug effects on selective cell populations using scRNA-seq datasets. They combined PRL with Gene Set Enrichment Analysis (GSEA), a method that compares a ranked list of genes like PRL against a specific set of genes of interest. GSEA calculates a Normalized Enrichment Score (NES), which indicates how well the genes of interest are represented among the top genes in the PRL. Compared to the method described in the current manuscript, the PRL method allows for the identification of both upregulated and downregulated transcriptional signatures relevant to the drug’s effects. It also gives equal weight to each cell line’s contribution to the drug’s overall response signature.

      The authors performed experimental validation of the top two identified drugs; however, the effect was modest. In addition, the effect on TNBC cell lines was cell-line specific as the identified drugs were effective against BT20, whose transcriptional signatures from LINCS were used for drug identification, but not against the other two cell lines analyzed. An incorrect choice of genes for the signature may result in capturing similarities tied to experimental conditions (e.g., the same cell line) rather than the drug’s actual effects. This reflects the challenges faced by drug response signature methods in both selecting the appropriate subset of genes that make up the signature and managing the multiple expression profiles generated by treating different cell lines with the same drug.

      We appreciate the reviewer’s thoughtful feedback and their suggestion to refer to the Prototype Ranked List (PRL) manuscript. Unfortunately, since this methodology for the PRL isn’t implemented in an open-source package, direct comparison with our approach is challenging. Nonetheless, we investigated whether using ranks would yield similar results for the most likely active drug pairs identified by retriever. To do this, we calculated and compared the rankings of the average effect sizes provided by retriever. Although the Spearman (ρ \= 0.98) correlation coefficient was high, we observed that key genes are disadvantaged when using ranks compared to effect sizes. This difference is particularly evident in the gene set enrichment analysis, where using average ranks identified only one pathway as statistically significantly enriched. The code to replicate these analyses is available at https://github.com/dosorio/L1000-TNBC/blob/main/Code/.

      Author response image 1.

      Given the similarity in purpose between retriever and the PRL approach, we have added the following statement to the introduction: “Previously, this goal was approached using a majority-voting scheme to rank genes across various cell types, concentrations, and time points. This approach generates a prototype ranked list (PRL) that represents the consistent ranks of genes across several cell lines in response to a specific drug.”

      Regarding the experimental validation, we believe there is a misunderstanding about the evidence we provided. We would like to claridy that we used three different TNBC cell lines: CAL120, BT20, and DU4475. It’s important to note that CAL120 and DU4475 were not included in the signature generation process. Despite this, we observed effects that exceeded the additive effects expectations, particularly in the CAL120 cell line (Figure 5, Panel F).

      Reviewer 2:

      Summary:

      In their study, Osorio and colleagues present ‘retriever,’ an innovative computational tool designed to extract disease-specific transcriptional drug response profiles from the LINCS-L1000 project. This tool has been effectively applied to TNBC, leveraging single-cell RNA sequencing data to predict drug combinations that may effectively target the disease. The public review highlights the significant integration of extensive pharmacological data with high-resolution transcriptomic information, which enhances the potential for personalized therapeutic applications.

      Strengths:

      A key finding of the study is the prediction and validation of the drug combination QL-XII-47 and GSK-690693 for the treatment of TNBC. The methodology employed is robust, with a clear pathway from data analysis to experimental confirmation.

      Weaknesses:

      However, several issues need to be addressed. The predictive accuracy of ’retriever’ is contingent upon the quality and comprehensiveness of the LINCS-L1000 and single-cell datasets utilized, which is an important caveat as these datasets may not fully capture the heterogeneity of patient responses to treatment. While the in vitro validation of the drug combinations is promising, further in vivo studies and clinical trials are necessary to establish their efficacy and safety. The applicability of these findings to other cancer types also warrants additional investigation. Expanding the application of ’retriever’ to a broader range of cancer types and integrating it with clinical data will be crucial for realizing its potential in personalized medicine. Furthermore, as the study primarily focuses on kinase inhibitors, it remains to be seen how well these findings translate to other drug classes.

      We thank the reviewer for their thoughtful and constructive feedback. We appreciate your insights and agree that several important considerations need to be addressed.

      We recognize that the predictive accuracy of retriever depends on the LINCS-L1000 and single-cell datasets. These resources may not fully represent the complete range of transcriptional responses to disease and treatment across different patients. As you mentioned, this is an important limitation. However, we believe that by extrapolating the evaluation of the most likely active compound to each individual patient, we can help address this issue. This approach will provide valuable insights into which patients in the study are most likely to respond positively to treatment.

      On the in-vitro validation of drug combinations, we agree that while promising, these results are not sufficient on their own to establish clinical efficacy. Additional in-vivo studies will be essential in assessing the therapeutic potential and safety of these combinations, and clinical trials will be an important next step to validate the translational impact of our findings.

      Lastly, we appreciate the reviewer’s comment about the focus of our study on kinase inhibitors. This result was unexpected, as we tested the full set of compounds from the LINCS-L1000 project. We agree that exploring other top candidates, including different drug classes, will be important for assessing how broadly retriever approach can be applied.

      Reviewing Editor:

      I appreciate the interesting and potentially impactful nature of your research; the reviewers have some concerns that I believe need to be addressed. While your research addresses an important and timely topic in cancer treatment, the current manuscript does not provide a substantial advance in its present form.

      The significance of your findings is substantial, as you present a novel computational tool, ’retriever,’ which has the potential to revolutionize personalized cancer treatment strategies by predicting effective drug combinations for triple-negative breast cancer (TNBC). The integration of single-cell RNA-seq data with the LINCS-L1000 project’s transcriptional profiles is a powerful approach that could lead to more targeted and effective therapies. However, the manuscript would benefit from a more explicit discussion of how your work advances the field beyond current methodologies, particularly in the context of drug repurposing and combinatorial therapy.

      The strength of the evidence presented is robust, as evidenced by the systematic testing of 152 drug response profiles and 11,476 drug combinations. The identification of QL-XII-47 and GSK-690693 as promising treatment candidates for TNBC is a significant outcome that warrants further exploration. To enhance the manuscript, it would be beneficial to include a more detailed analysis of the biological pathways and mechanisms of action associated with these drugs, as well as a broader experimental validation beyond the cell lines tested.

      Taken together, I encourage you to address the issues raised and consider resubmitting a revised version of your work.

      Following the suggestions of the reviewing editor, we have included a more detailed discussion on how retriever advances the field, especially in the context of drug repurposing and combinatorial therapy in precision medicine, going beyond current methodologies.

      We agree with the suggestion of the editor to offer a more detailed analysis of the biological pathways and mechanisms of action related to these drugs. Consequently, we have expanded our evaluation of these mechanisms. We utilized the Biological Process Gene Ontology to identify changes associated with the mechanisms of each compound individually, as well as the proposed drug combination. Our findings reveal that the statistically significant processes are closely related to cancer deregulation, cross-validating our previous report using the Cancer Hallmarks.

      Author response image 2.

      Recommendations for the authors:

      Reviewer 1:

      (1) The LINCS-L1000 project is introduced in the manuscript as a resource for published transcriptional profiles of several cell lines. Since the original citation, it has been expanded into a vast resource, and the description probably needs to reflect the recent version of LINCS.

      We agree with the reviewer that the LINCS-L1000 project is introduced in the manuscript as a resource for transcriptional profiles of several cell lines. Since the original citation, the project has grown into a much larger resource.

      To reflect this, we have added a 2022 citation that summarizes efforts to link omics signatures with biological mechanisms using iLINCS: Pilarczyk, Marcin, et al. ”Connecting omics signatures and revealing biological mechanisms with iLINCS.” Nature communications 13.1 (2022): 4678.

      Reviewer 2:

      (1) It would be beneficial for the manuscript if the authors could expand on the potential limitations inherentto the ’retriever’ tool. This discussion could insightfully address how the foundational assumptions of the analysis may influence the predictive accuracy and the extent to which dataset quality could affect the reliability of the outcomes.

      We agree with the reviewer that expanding on the limitations of retriever would help raise awareness of the underlying assumptions in the analysis and how they affect the predictive accuracy and reliability of the results.

      The following paragraph was added to the Discussion section: “Although retriever represents a significant advancement in extracting disease-specific drug response profiles from the LINCS-L1000 dataset. Several limitations must be considered when interpreting its results. One key limitation is the restricted scope of gene expression data in the LINCS-L1000 project, which includes expression profiles for only 1,000 genes. While this gene set provides valuable insights into broad transcriptional changes, it may not fully capture the complexity of cellular responses to drug treatments. A possible solution to this limitation relies on imputation techniques to address the missing quantification in the gene expression matrix. The accuracy of the imputed values is dependent on the quality of the imputation model and the completeness of the available data. Consequently, there is an inherent risk that the imputed values may not accurately represent the true and complete underlying biological response.”

      (2) Enhancing the manuscript with a more detailed exploration of the clinical ramifications of the study’s findings would be valuable. The authors might consider including how these predictions could be strategically incorporated into the design of clinical trials, thereby bridging the gap between computational predictions and clinical application.

      We appreciate the opportunity provided by the reviewer to expand on the potential of retriever for the design of clinical trials and clinical application.

      The following paragraph was added to the discussion section: “Finally, we have shown that the approach implemented in retriever method can predict effective drug combinations for patients with triplenegative breast cancer (TNBC), but its potential goes beyond that. It can also be applied to single-cell RNA sequencing data from individual tumors and other diseases for which a the single-cell transcriptomic profile of a normal control population is available. In line with this, the LINCS project has released datasets for iPSC-derived cardiomyocytes and motor neurons, opening up new possibilities for precision medicine not only in cancer but also in a variety of other diseases. By predicting the most effective drug and combination treatments for each patient, clinical trials can be designed to target the right populations with the responsive transcriptional phenotype, leading to more successful outcomes.”

      (3) It would be insightful if the authors could discuss the potential for drug resistance in the context of thedrug combinations identified by ’retriever’. An analysis of this phenomenon could provide critical insights into the longevity and effectiveness of the proposed treatment strategies.

      We agree with the reviewer that the potential for drug resistance is a critical consideration when evaluating any therapeutic strategy in cancer, especially when using drug combinations. While the current study focuses on identifying effective drug pairings using ‘retriever’, we recognize that the emergence of resistance could limit their long-term utility. We have addressed the topic within the introduction: “Nonetheless, monotherapy in cancer is highly susceptible to the development of resistance following an initial response to treatment. Combination therapy, or the simultaneous administration of multiple drugs to treat a disease, has evolved into the standard pharmacological regimen for treating complex diseases such as cancer. Combination therapy prevent tumor evolution and help inhibit the development of drug resistance in cancer, thereby improving patient survival.”

      (4) Providing details regarding the computational resources necessary for the implementation of ’retriever’,along with any limitations associated with these requirements, could greatly enhance the transparency and reproducibility of the methodology. Such information would be instrumental for other researchers seeking to apply this tool in their own work.

      The following paragraph was added to the data availability section of the manuscript: “The retriever package is available from the Kuijjer Lab repository https://github.com/kuijjerlab/retriever or from the CRAN repositories at https://cran.r-project.org/package=retriever, and it is implemented as an R multiplatform package that can run on standard laptops or desktops with around 16 GB of RAM, making it accessible for most users. It is designed to work on Windows, macOS, and Linux. While the package can function with modest hardware, performance may vary based on dataset size and complexity. For larger datasets, systems with more RAM or cloud-based resources may improve efficiency.”

      (5) A thoughtful discussion on the ethical considerations surrounding the use of patient-derived data in thedevelopment and validation of ’retriever’ would round out the manuscript. Addressing issues of data privacy and the ethical use of such data could set a precedent for responsible research practices in the field of computational biology and personalized medicine.

      We agree with the reviewer on the need of discussing the ethical considerations surrounding the use of patient-derived data in the validation, development and re-purposing of drugs for disease treatment.

      The following paragraph was added to the discussion section: “We want to highlight the important ethical considerations involved in using patient-derived data for drug development and repurposing, particularly around data privacy, informed consent, and the reliability of predictive models. To protect patient privacy, it is crucial to adhere to data protection laws, such as HIPAA and GDPR, and to rigorously de-identify data to minimize the risk of re-identification. Additionally, datasets must be diverse and representative to prevent bias, ensuring that predictive models are applicable to a broad population. Computational models should undergo extensive validation before being used in clinical settings to ensure their accuracy and transparency. Ethical protocols for data sharing must also be established to respect patient autonomy and control over their data. Furthermore, continuous monitoring and validation of drug predictions are necessary to ensure treatment safety, effectiveness, and fairness.”

    1. eLife Assessment

      This manuscript presents a valuable minimal model of habituation which is quantified by information theoretic measures. The results here could be of use in interpreting habituation behavior in a range of biological systems. The evidence presented is solid, and uses simulations of the minimal model to recapitulate several hallmarks of habituation from a simple model.

    2. Reviewer #2 (Public review):

      In this study, the authors aim to investigate habituation, the phenomenon of increasing reduction in activity following repeated stimuli, in the context of its information theoretic advantage. To this end, they consider a highly simplified three-species reaction network where habituation is encoded by a slow memory variable that suppresses the receptor and therefore the readout activity. Using analytical and numerical methods, they show that in their model the information gain, the difference between the mutual information between the signal and readout after and before habituation, is maximal for intermediate habituation strength. Furthermore, they demonstrate that the Pareto front corresponding to an optimization strategy that maximizes the mutual information between signal and readout in the steady-state and minimizes dissipation in the system also exhibits similar intermediate habituation strength. Finally, they briefly compare predictions of their model to whole-brain recordings of zebrafish larvae under visual stimulation.

      The author's simplified model serves as a good starting point for understanding habituation in different biological contexts as the model is simple enough to allow for some analytic understanding but at the same time exhibits most basic properties of habituation in sensory systems. Furthermore, the author's finding of maximal information gain for intermediate habituation strength via an optimization principle is, in general, interesting. However, the following points remain unclear:

      (1) How general is their finding that the optimal Pareto front coincides with the region of maximal information gain? For instance, what happens if the signal H_st (H_max) isn't very strong? Does it matter that in this case, H_st only has a minor influence on delta Q_R? In the binary switching case, what happens if H_max is rather different from H_st (and not just 20% off)? Or in a case where the adapted value corresponds to the average of H_max and H_min?

      (2) The comparison to experimental data isn't very convincing. For instance, is PCA performed simultaneously on both the experimental data set and on the model or separately? What are the units of the PCs in Fig. 6(b,c)? Given that the model parameters are chosen so that the activity decrease in the model is similar to the one in the data (i.e., that they show similar habituation in terms of the readout), isn't it expected that the dynamics in the PC1/2 space look very similar?

    3. Reviewer #3 (Public review):

      The authors use a generic model framework to study the emergence of habituation and its functional role from information-theoretic and energetic perspectives. Their model features a receptor, readout molecules, and a storage unit, and as such, can be applied to a wide range of biological systems. Through theoretical studies, the authors find that habituation (reduction in average activity) upon exposure to repeated stimuli should occur at intermediate degrees to achieve maximal information gain. Parameter regimes that enable these properties also result in low dissipation, suggesting that intermediate habituation is advantageous both energetically and for the purpose of retaining information about the environment.

      A major strength of the work is the generality of the studied model. The presence of three units (receptor, readout, storage) operating at different time scales and executing negative feedback can be found in many domains of biology, with representative examples well discussed by the authors (e.g. Figure 1b). A key takeaway demonstrated by the authors that has wide relevance is that large information gain and large habituation cannot be attained simultaneously. When energetic considerations are accounted for, large information gain and intermediate habituation appear to be the favorable combination.

      Comments on the revision:

      The authors have adequately addressed the points I raised during the initial review. The text has been clarified at multiple instances, and the treatment of energy expenditure is now more rigorous. The manuscript is much improved both in terms of readability and scientific content.

    4. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public Review):

      Summary: 

      The manuscript by Nicoletti et al. presents a minimal model of habituation, a basic form of non-associative learning, addressing both from dynamical and information theory aspects of how habituation can be realized. The authors identify that negative feedback provided with a slow storage mechanism is sufficient to explain habituation.

      Strengths: 

      The authors combine the identification of the dynamical mechanism with information-theoretic measures to determine the onset of habituation and provide a description of how the system can gain maximum information about the environment.

      We thank the reviewer for highlighting the strength of our work and for their comments, which we believe have been instrumental in significantly improving our work and its scope. Below, we address all their concerns.

      Weaknesses: 

      I have several main concerns/questions about the proposed model for habituation and its plausibility. In general, habituation does not only refer to a decrease in the responsiveness upon repeated stimulation but as Thompson and Spencer discussed in Psych. Rev. 73, 16-43 (1966), there are 10 main characteristics of habituation, including (i) spontaneous recovery when the stimulus is withheld after response decrement; dependence on the frequency of stimulation such that (ii) more frequent stimulation results in more rapid and/or more pronounced response decrement and more rapid spontaneous recovery; (iii) within a stimulus modality, the less intense the stimulus, the more rapid and/or more pronounced the behavioral response decrement; (iv) the effects of repeated stimulation may continue to accumulate even after the response has reached an asymptotic level (which may or may not be zero, or no response). This effect of stimulation beyond asymptotic levels can alter subsequent behavior, for example, by delaying the onset of spontaneous recovery. 

      These are only a subset of the conditions that have been experimentally observed and therefore a mechanistic model of habituation, in my understanding, should capture the majority of these features and/or discuss the absence of such features from the proposed model. 

      We are really grateful to the reviewer for pointing out these aspects of habituation that we overlooked in the previous version of our manuscript. Indeed, our model is able to capture most of these 10 observed behaviors, specifically: 1) habituation; 2) spontaneous recovery; 3) potentiation of habituation; 4) frequency sensitivity; 5) intensity sensitivity; 6) subliminal accumulation. Here, we are following the same terminology employed in Eckert et al., Current Biology 34, 5646–5658 (2024), the paper highlighted by the reviewer. We have dedicated a section of the revised version of the manuscript to these hallmarks, substantiating the validity of our framework as a minimal model to have habituation. We remark that these are the sole hallmarks that can be discussed by considering one single external stimulus and that can be identified without ambiguity in a biochemical context. This observation is again in line with Eckert et al., Current Biology 34, 5646–5658 (2024).

      In the revised version, we employ the same strategy of the aforementioned work to determine when the system can be considered “habituated”. Indeed, we introduce a response threshold that is now discussed in the manuscript. We also included a note in the discussions stating that, since any biochemical model will eventually reach a steady state, subliminal accumulation, for example, can only be seen with the use of a threshold. The introduction of different storage mechanisms, ideally more detailed at a molecular level, can shed light on this conceptual gap. This is an interesting direction of research.

      Furthermore, the habituated response in steady-state is approximately 20% less than the initial response, which seems to be achieved already after 3-4 pulses, the subsequent change in response amplitude seems to be negligible, although the authors however state "after a large number of inputs, the system reaches a time-periodic steady-state". How do the authors justify these minimal decreases in the response amplitude? Does this come from the model parametrization and is there a parameter range where more pronounced habituation responses can be observed? 

      The reviewer is correct, but this is solely a consequence of the specific set of parameters we selected. We made this choice solely for visualization purposes in the previous version. In the revised version, in the section discussing the hallmarks of habituation, we also show other parameter choices when the response decrement is more pronounced. Moreover, we remark that the contour plot of \Delta⟨U> clearly shows that the decrement can largely exceed the 20% threshold presented in the previous version.

      In the revised version, also in light of the works highlighted by the reviewer, we decided to move the focus of the manuscript to the information-theoretic advantage of habituation. As such, we modified several parts of the main text. Also, in the region of optimal information gain, habituation is at an intermediate level. For this reason, we decided to keep the same parameter choice as the previous version in Figure 2.

      We stated that the time-periodic steady-state is reached “after a large number of stimuli” from a mathematical perspective. However, by using a habituation threshold, as done in Eckert et al., Current Biology 34, 5646–5658 (2024), we can state that the system is habituated after a few stimuli for each set of parameters. This aspect is highlighted in the revised version of the manuscript (see also the point above).

      The same is true for the information content (Figure 2f) - already at the first pulse, IU, H ~ 0.7 and only negligibly increases afterwards. In my understanding, during learning, the mutual information between the input and the internal state increases over time and the system extracts from these predictions about its responses. In the model presented by the authors, it seems the system already carries information about the environment which hardly changes with repeated stimulus presentation. The complexity of the signal is also limited, and it is very hard to clarify from the presented results, whether the proposed model can actually explain basic features of habituation, as mentioned above. 

      As for the response decrement of the readout, we can certainly choose a set of parameters for which the information gain is higher. In the revised version, we also report the information at the first stimulation and when the system is habituated to give a better idea of the range of these quantities. At any rate, as the referee correctly points out, it is difficult to give an intuitive interpretation of the information in our minimal model.

      It is also important to remark that, since the readout population and the receptor both undergo fast dynamics (with appropriate timescales as discussed in the text), we are not observing the transient gain of information associated with the first stimulus. As such, the mutual information presents a discontinuous behavior that resembles the dynamics of the readout, thereby starting at a non-zero value already at the first stimulus.

      Additionally, there have been two recent models on habituation and I strongly suggest that the authors discuss their work in relation to recent works (bioRxiv 2024.08.04.606534; arXiv:2407.18204).

      We thank the reviewer for pointing out these relevant references. In the revised version, we highlighted that we discuss the information-theoretic aspects of habituation, while the aforementioned references focus on the dynamics of this phenomenon.

      Reviewer #1 (Recommendations for the authors):

      I would also like to note here the simplification of the proposed biological model - in particular, that the receptor can be in an active/passive state, as well as proposing the Nf-kB signaling module as a possible molecular realization. Generally, a large number of cell surface receptors including RTKs of GPCRs have much more complex dynamics including autocatalytic activation that generally leads to bistability, and the Nf-kB has been demonstrated to have oscillatory even chaotic dynamics (works of Savas Tsay, Mogens Jensen and others). Considering this, the authors should at least discuss under which conditions these TNF-Alpha signaling could potentially serve as a molecular realisation for habituation. 

      We thank the reviewer for bringing this to our attention. In the previous version, we reported the TNF signaling network only to show a similar coarse-grained modular structure. However, following a suggestion of reviewer #2, we decided to change Figure 1 to include a simplified molecular scheme of chemotaxis rather than TNF signaling, to avoid any source of confusion about this issue.

      Also, a minor point: Figures 2d-e are cited before 2a-c. 

      We apologize for the oversight. The structure of the Figures and their order is now significantly different, and they are now cited in the correct order. 

      Reviewer #2 (Public review):

      In this study, the authors aim to investigate habituation, the phenomenon of increasing reduction in activity following repeated stimuli, in the context of its information-theoretic advantage. To this end, they consider a highly simplified three-species reaction network where habituation is encoded by a slow memory variable that suppresses the receptor and therefore the readout activity. Using analytical and numerical methods, they show that in their model the information gain, the difference between the mutual information between the signal and readout after and before habituation, is maximal for intermediate habituation strength. Furthermore, they demonstrate that the Pareto front corresponds to an optimization strategy that maximizes the mutual information between signal and readout in the steady state, minimizes some form of dissipation, and also exhibits similar intermediate habituation strength. Finally, they briefly compare predictions of their model to whole-brain recordings of zebrafish larvae under visual stimulation. 

      The author's simplified model might serve as a solid starting point for understanding habituation in different biological contexts as the model is simple enough to allow for some analytic understanding but at the same time exhibits all basic properties of habituation in sensory systems. Furthermore, the author's finding of maximal information gain for intermediate habituation strength via an optimization principle is, in general, interesting. However, the following points remain unclear or are weakly explained: 

      We thank the reviewer for deeming our work interesting and for considering it a solid starting point for understanding habituation in biological systems.

      (1) Is it unclear what the meaning of the finding of maximal information gain for intermediate habituation strength is for biological systems? Why is information gain as defined in the paper a relevant quantity for an organism/cell? For instance, why is a system with low mutual information after the first stimulus and intermediate mutual information after habituation better than one with consistently intermediate mutual information? Or, in other words, couldn't the system try to maximize the mutual information acquired over the whole time series, e.g., the time series mutual information between the stimulus and readout?

      This is a delicate aspect to discuss and we thank the referee for the comment. In the revised version, we report information gain, initial and final information, highlighting that both gain and final information are higher in regions where habituation is present. They have qualitatively similar behavior and highlight a clear information-theoretic advantage of this dynamical phenomenon. An important point is that, to determine the optimal Pareto front, we consider a prolonged stimulus and its associated steady-state information. Therefore, from the optimization point of view, there is no notion of “information gain” or “final information”, which are intrinsically dynamical quantities. As a result, the fact that optimal curve lies in the region of optimal information gain is a-priori not expected and hints at the potential crucial role of this feature. In the revised version, we elucidate this aspect with several additional analyses.

      We would like to add that, from a naive perspective, while the first stimulation will necessarily trigger a certain (non-zero) mutual information, multiple observations of the same stimulus have to reflect into accumulated information that consequently drives the onset of observed dynamical behaviors, such as habituation.

      (2) The model is very similar to (or a simplification of previous models) for adaptation in living systems, e.g., for adaptation in chemotaxis via activity-dependent methylation and demethylation. This should be made clearer.

      We apologize for having missed this point. Our choice has been motivated by the fact that we wanted to avoid confusion between the usual definition of (perfect) adaptation and habituation. However, we now believe that this is not the case for the revised manuscript, and we now include chemotaxis as an example in Figure 1.

      (3) It remains unclear why this optimization principle is the most relevant one. While it makes sense to maximize the mutual information between stimulus and readout, there are various choices for what kind of dissipation is minimized. Why was \delta Q_R chosen and not, for instance, \dot{\Sigma}_int or the sum of both? How would the results change in that case? And how different are the results if the mutual information is not calculated for the strong stimulation input statistics but for the background one?

      We thank the reviewer for the suggestion. We agree that a priori, there is no reason to choose \delta Q_R or a function of the internal energy flux J_int (that, in the revised version, we are using in place of \dot\Sigma_int following the suggestion of reviewer #3). The rationale was to minimize \delta Q_R since this dissipation is unavoidable and stems from the presence of the storage inhibiting the receptor through the internal pathway. Indeed, considering the existence of two different pathways implementing sensing and feedback, the presence of any input will result in a dissipation produced by the receptor. This energy consumption is reflected in \delta Q_R.

      In the revised version, we now include in the optimization principle two energy contributions (see Eq. (14) of the revised manuscript): \delta Q_R and E_int, which is the energy consumption associated with the driven storage production per unit energy. All Figures have been updated accordingly. The results remain similar, as \delta Q_R still represents the main contribution, especially at high \beta.

      Furthermore, in the revised version, we include examples of the Pareto optimization for different values of input strength. As detailed both in the main text and the Supplementary Information, changing the value of ⟨H⟩ moves the Pareto frontier in the (\beta, \sigma) space, since the signal needs to be strong enough for the system to distinguish it from the intrinsic thermal noise (controlled by beta). We also show that if the system is able to tune the inhibition strength \kappa, the Pareto frontiers at different ⟨H⟩ collapse into a single curve. This shows that, although the values of, e.g., the mutual information, depend on ⟨H⟩, the qualitative behavior of the system in this regime is effectively independent of it. We also added more details about this in the Supplementary Information.

      (4) The comparison to the experimental data is not too strong of an argument in favor of the model. Is the agreement between the model and the experimental data surprising? What other behavior in the PCA space could one have expected in the data? Shouldn't the 1st PC mostly reflect the "features", by construction, and other variability should be due to progressively reduced activity levels? 

      The agreement between data and model is not surprising - we agree on this - since the data exhibit habituation. However, we believe that the fact that our minimal model is able to capture the features of a complex neural system just by looking at the PCs, without any explicit biological details, is non-trivial. We also stress that the 1st PC only reflects the feature that captures most of the variance of the data and, as such, it is difficult to have a-priori expectations on what it should represent. In the case of the data generated from the model, most of the variance of the activity comes from the switching signal, and similar considerations can be made for the looming stimulations in the data. We updated the manuscript to clarify this point.

      Reviewer #2 (Recommendations for the authors):

      (1) The abstract makes it sound like a new finding is that habituation is due to a slow, negative feedback mechanism. But, as mentioned in the introduction, this is a well-known fact. 

      We agree with the reviewer. We have revised the abstract.

      (2) Figure 2c Why does the range of Delta Delta I_f include negative values if the corresponding region is shaded (right-tilted stripes)? 

      The negative values in the range are those attained in the shaded region with right-tilted stripes. We decided to include them in the colorbar for clarity, since Delta Delta I_f is also plotted in the region where it attains negative values.

      (3) What does the Pareto front look like if the optimization is done for input statistics given by ⟨H⟩_min? 

      In the revised version, we include examples of the Pareto optimization for different values of input strength. As detailed both in the main text and the Supplementary Information, changing the value of ⟨H⟩ moves the Pareto frontier in the (\beta, \sigma) space, since the strength of the signal is crucial for the system to discriminate input and thermal noise (see also the answers above).

      In particular, in Figure 4 we explicitly compare the results of the Pareto optimization (which is done with a static input of a given statistics) with the dynamics of the model for different values of ⟨H⟩ in two scenarios, i.e., adaptive and non-adaptive inhibition strength (see answers above for details).

      We also remark that ⟨H⟩_min represents the background signal that the system is not trying to capture, which is why we never used it for optimization.

      (4) From the main text, it is rather difficult to understand how the comparison to the experimental data was performed. How was the PCA done exactly? What are the "features" of the evoked neural response? 

      The PCA on data is performed starting from the single-neuron calcium dynamics. To perform a far comparison, we reconstruct a similar but extremely simplified dynamics using our model as explained in Methods to perform the PCA on analogous simulated data. We added a comment on this in the revised version. While these components capture most of the variance in the data, their specific interpretation is usually out of reach and we believe that it lies beyond the scope of this theoretical work. We also remark that the model does not contain all these biological details - a strong aspect in our opinion - and, as such, it cannot capture specific biological features.

      Reviewer #3 (Public review):

      The authors use a generic model framework to study the emergence of habituation and its functional role from information-theoretic and energetic perspectives. Their model features a receptor, readout molecules, and a storage unit, and as such, can be applied to a wide range of biological systems. Through theoretical studies, the authors find that habituation (reduction in average activity) upon exposure to repeated stimuli should occur at intermediate degrees to achieve maximal information gain. Parameter regimes that enable these properties also result in low dissipation, suggesting that intermediate habituation is advantageous both energetically and for the purpose of retaining information about the environment. 

      A major strength of the work is the generality of the studied model. The presence of three units (receptor, readout, storage) operating at different time scales and executing negative feedback can be found in many domains of biology, with representative examples well discussed by the authors (e.g. Figure 1b). A key takeaway demonstrated by the authors that has wide relevance is that large information gain and large habituation cannot be attained simultaneously. When energetic considerations are accounted for, large information gain and intermediate habituation appear to be a favorable combination. 

      We thank the reviewer for this positive assessment of our work and its generality.

      While the generic approach of coarse-graining most biological detail is appealing and the results are of broad relevance, some aspects of the conducted studies, the problem setup, and the writing lack clarity and should be addressed: 

      (1) The abstract can be further sharpened. Specifically, the "functional role" mentioned at the end can be made more explicit, as it was done in the second-to-last paragraph of the Introduction section ("its functional advantages in terms of information gain and energy dissipation"). In addition, the abstract mentions the testing against experimental measurements of neural responses but does not specify the main takeaways. I suggest the authors briefly describe the main conclusions of their experimental study in the abstract.

      We thank the reviewer for raising this point. In the revised version, we have changed the abstract to reflect the reviewer’s points and the new structure and results of the manuscript.

      (2) Several clarifications are needed on the treatment of energy dissipation. 

      -   When substituting the rates in Eq. (1) into the definition of δQ_R above Eq. (10), "σ" does not appear on the right-hand side. Does this mean that one of the rates in the lower pathway must include σ in its definition? Please clarify.

      We apologize to the reviewer for this typo. Indeed, \sigma sets the energy scale of feedback and, as such, it appears in the energetic driving given by the feedback on the receptor, i.e., in Eq. (1) together with \kappa. This typo has been corrected in the revised manuscript, and all subsequent equations are consistent.

      -   I understand that the production of storage molecules has an associated cost σ and hence contributes to dissipation. The dependence of receptor dissipation on ⟨H⟩, however, is not fully clear. If the environment were static and the memory block was absent, the term with ⟨H⟩ would still contribute to dissipation. What would be the nature of this dissipation?

      In the spirit of building a paradigmatic minimal model with a thermodynamic meaning, we considered H to act as an external thermodynamic driving. Since this driving acts on a different pathway with respect to the one affected by the storage, the receptor is driven out of equilibrium by its presence.

      By eliminating the memory block, we would also be necessarily eliminating the presence of the pathway associated with the storage effect (“internal pathway” in the manuscript), since its presence is solely due to the existence of a storage population. Therefore, in this case, the receptor would be a 2-state, 1-pathway system and, as such, it would always satisfy an effective detailed balance. As a consequence, the definition of \delta Q_R reported in the manuscript would not hold anymore and the receptor would not exhibit any dissipation. Thus, in a static environment and without a memory block, no receptor dissipation would be present. We would also like to stress that our choice to model two different pathways has been motivated by the observation that the negative feedback acts along a different pathway in several biochemical and biological examples. We made some changes to the model description in the revised version and we hope that this aspect has been clarified.

      -   Similarly, in Eq. (9) the authors use the ratio of the rates Γ_{s → s+1} and Γ_{s+1 → s} in their expression for internal dissipation. The first-rate corresponds to the synthesis reaction of memory molecules, while the second corresponds to a degradation reaction. Since the second reaction is not the microscopic reverse of the first, what would be the physical interpretation of the log of their ratio? Since the authors already use σ as the energy cost per storage unit, why not use σ times the rate of producing S as a metric for the dissipation rate? 

      We agree with the referee that the reverse reaction we considered is not the microscopic reverse of the storage production. In the case of a fast readout population, we employed a coarse-grained view to compute this entropy production. To be more precise, we gladly welcomed the referee’s suggestion in the revised version and modified the manuscript accordingly. As suggested, we now employ the energy flux associated with the storage production to estimate the internal dissipation (see new Fig. 3). 

      In the revised version, we also use this quantity in the optimization procedure in combination with \deltaQ_R (see new Fig. 4) to have a complete characterization of the system’s energy consumption. The conclusions are qualitatively identical to before, but we believe that now they are more solid from a theoretical perspective. For this important advance in the robustness and quality of our work, we are profoundly grateful to the referee.

      (3) Impact of the pre-stimulus state. The plots in Figure 2 suggest that the environment was static before the application of repeated stimuli. Can the authors comment on the impact of the pre-stimulus state on the degree of habituation and its optimality properties? Specifically, would the conclusions stay the same if the prior environment had stochastic but aperiodic dynamics? 

      The initial stimulus is indeed stochastic with an average constant in time and mimics the background (small) signal. We apply the (strong) stimulation when the system already reached a stationary state with respect to the background. As it can be appreciated in Fig. 2 of the revised version, the model response depends on the pre-stimulus level, since it sets the storage concentration before the stimulation arrives and, as such, the subsequent habituation dynamics. This dependence is important from a dynamical perspective. The information-theoretic picture has been developed, as said above, by letting the system relax before the first stimulus. This eliminates this arbitrary dependence and provides a clearer idea of the functional advantages of habituation. Moreover, the optimization procedure is performed in a completely different setting, with no pre-stimulus at all, since we only have one prolonged stimulation. We hope that the revised version is clearer on all these points.

      (4) Clarification about the memory requirement for habituation. Figure 4 and the associated section argue for the essential role that the storage mechanism plays in habituation. Indeed, Figure 4a shows that the degree of habituation decreases with decreasing memory. The graph also shows that in the limit of vanishingly small Δ⟨S⟩, the system can still exhibit a finite degree of habituation. Can the authors explain this limiting behavior; specifically, why does habituation not vanish in the limit Δ⟨S⟩ -> 0?

      We apologize for the lack of clarity and we thank the reviewer for spotting this issue. In Figure 4 (now Figure 5 in the revised manuscript) Δ⟨S⟩ is not exactly zero, but equal to 0.15% at the final point. It appeared as 0% in the plot due to an unwanted rounding in the plotting function that we missed. This has been fixed in the revised version, thank you.

      Reviewer #3 (Recommendations for the authors):

      (1) Page 2 | "Figure 1b-e" should be "Figure 1b-d" since there is no panel (e) in Figure 1. 

      (2) Figure 1a | In the top schematic, the symbol "k" is used, while in the rest of the text, the proportionality constant is denoted by κ. 

      We thank the reviewer for pointing this out. Figure 1 has been revised and the panels are now consistent. The proportionality constant (the inhibition strength) has also been fixed.

      (3) Figure 1a | I find the upper part of the schematic for Storage hard to perceive. I understand the lower part stands for the degradation reaction for storage molecules. The upper part stands for the synthesis reaction catalyzed by the readout population. I think the bolded upper arrow would explain it sufficiently well; the left/right arrows, together with the crossed green circle make that part of the figure confusing. Consider simplifying. 

      We decided to remove the left/right arrows, as suggested by the reviewer, as we agree that they were unnecessarily complicating the schematic. We hope that the revised version will be easier to understand.

      (4)Page 3 | It would be helpful to tell what the temporal statistics of the input signal $p_H(h,t)$ is, i.e. <h(t) h(t')>. Looking at the example trajectory in Figure 1a, consecutive signal values do not seem correlated. 

      We agree with the reviewer that this is an important detail and worth mentioning. We now explicitly state that consecutive values are not correlated, for simplicity. 

      (5)Figure 2 | I believe the label "EXTERNAL INPUT" refers to the *average* external input, not one specific realization (similar to panels (d) and (e) that report on average metrics). I suggest you indicate this in the label, or, what may be even better, add one particular realization of the stochastic input to the same graph.

      We thank the reviewer for spotting this. We now write that what we show is the average external signal. We prefer this solution rather than showing a realization of the stochastic input, since it is more consistent with the rest of the plots, where we always show average quantities. We also note that Figure 2 is now Figure 3 in the revised manuscript.

      (6)Figure 2d | The expression of Δ⟨U⟩ is the negative of the definition in Eq. (5). It should be corrected. 

      In the revised version, both the definitions in Figure 2 (now Figure 3) and in the text (now Eq. (11)) are consistent.

      (7) Figure 3(d-e) caption | "where ⟨U⟩ starts to be significantly smaller than zero." There, it should be Δ⟨U⟩ instead of ⟨U⟩. 

      Thanks again, we corrected this typo.

    1. eLife Assessment

      This study presents an important set of new tools to facilitate Cre or Dre-mediated recombination in mice. The characterization of these new tools was done using solid and validated methodology. The work convincingly demonstrates the efficient gene knockout capability of these models and will progress the field.

    2. Reviewer #1 (Public review):

      This is a simple and potentially valuable approach to reduce Cre leak in amplified systems designed to improve CreER use across alleles. The revised work is improved with a direct comparison to the Benedito iSure-Cre line, providing some practical guidance for investigators. The authors do not address the issue of Cre toxicity or mosaic efficiency with low Tamoxifen use.

      The major improvement in my mind is the inclusion of Supp Fig 7 where the authors compare their loxCre to iSureCre. The discussion is somewhat improved, but still fails to discuss significant issues such as Cre toxicity in detail. As noted by most reviewers, without a biological question, the paper is entirely a technical description of a couple of new tools. Whether and to what extent journals such as eLife should publish every new technical innovation without rigorous functional comparison to prior tools is an important question raised by this study. There is already a plethora of available techniques, most of which look better on paper than they function in mice.

      However, I do feel that these tools will be of potential use to the field.

    3. Reviewer #2 (Public review):

      This work presents new genetic tools for enhanced Cre-mediated gene deletion and genetic lineage tracing. The authors optimise and generate mouse models that convert temporally controlled CreER or DreER activity to constitutive Cre expression, coupled with the expression of tdT reporter for the visualizing and tracing of gene-deleted cells. This was achieved by inserting a stop cassette into the coding region of Cre, splitting it into N- and C-terminal segments. Removal of the stop cassette by Cre-lox or Dre-rox recombination results in the generation of modified Cre that is shown to exhibit similar activity to native Cre. The authors further demonstrate efficient gene knockout in cells marked by the reporter using these tools, including intersectional genetic targeting of pericentral hepatocytes.

      The new models offer several important advantages. They enable tightly controlled and highly effective genetic deletion of even alleles that are difficult to recombine. By coupling Cre expression to reporter expression, these models reliably report Cre-expressing i.e. gene-targeted cells and circumvent false positives that can complicate analyses in genetic mutants relying on separate reporter alleles. Moreover, the combinatorial use of Dre/Cre permits intersectional genetic targeting, allowing for more precise fate mapping.

      The study and the new models have also limitations. The demonstration of efficient deletion of multiple floxed alleles in a mosaic fashion, a scenario where the lines would demonstrate their full potential compared to already existing models, has not been tested in the current study. Mosaic genetics is increasingly recognized as a key methodology for assessing cell-autonomous gene functions. The challenge lies in performing such experiments, as low doses of tamoxifen needed for inducing mosaic gene deletion may not be sufficient to efficiently recombine multiple alleles in individual cells while at the same time accurately reporting gene deletion. In addition, as discussed by the authors, a limitation of this line is the constitutive expression of Cre, which is associated with toxicity in some cases.

      Comments on revisions: I have no further comments.

    4. Reviewer #3 (Public review):

      Shi et al describe a new set of tools to facilitate Cre or Dre-recombinase-mediated recombination in mice. The strategies are not completely novel but have been pursued previously by the lab, which is world-leading in this field, and by others. The authors report a new version of the iSuRe-Cre approach, which was originally developed by Rui Benedito's group in Spain. Shi et al describe that their approach shows reduced leakiness compared to the iSuRe-Cre line. Furthermore, a new R26-roxCre-tdT mouse line was established after extensive testing, which enables efficient expression of the Cre recombinase after activation of the Dre recombinase. The authors carefully evaluated efficiency and leakiness of the new line and demonstrated the applicability by marking peri-central hepatocytes in an intersectional genetics approach. The paper represents the result of enormous, carefully executed efforts. Although I would have preferred to see a study which uses the wonderful new tools to address a major biological question, carefully conducted technical studies have an enormous value for the scientific community, clearly justifying publication.

      The new mouse lines generated in this study will enhance the precision of genetic manipulation in distinct cell types and greatly facilitate future work in numerous laboratories. The authors expertly eradicated weaknesses from initial submissions. Remaining open questions regarding potential toxicity of expressing multiple recombinases and fluorescence reports were convincingly answered.

    5. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      (1) It is a nice study but lacks some functional data required to determine how useful these alleles will be in practice, especially in comparison with the figure line that stimulated their creation.

      We are grateful for this comment. For the usefulness of these alleles, Figure 3 shows that specific and efficient genetic manipulation of one cell subpopulation can be achieved by mating across the DreER mouse strain to the rox-Cre mouse strain. In addition, Figure 7 shows that R26-loxCre-tdT can effectively ensure Cre-loxP recombination on some gene alleles and for genetic manipulation. The expression of the tdT protein is aligned with the expression of the Cre protein (Alb roxCre-tdT and R26-loxCre-tdT, Figure 2 and Figure 5), which ensures the accuracy of the tracing experiments. We believe more functional data can be shown in future articles that use mice lines mentioned in this manuscript.

      (2) The data in Figure 5 show strong activity at the Confetti locus, but the design of the newly reported R26-loxCre line lacks a WPRE sequence that was included in the iSure-Cre line to drive very robust protein expression.

      Thank you for bringing up this point in the manuscript. In the R26-loxCre-tdT mice knock-in strategy, the WPRE sequence is added behind the loxCre-P2A-tdT sequence, as shown in Supplementary Figure 9.

      (3) The most valuable experiment for such a new tool would be a head-to-head comparison with iSure (or the latest iSure version from the Benedito lab) using the same CreER and target foxed allele. At the very least a comparison of Cre protein expression between the two lines using identical CreER activators is needed.

      Thank you for your valuable and insightful comment. The comparison results of R26-loxCre-tdT with iSuRe-Cre using Alb-CreER and targeting R26-Confetti can be found in Figure 6, according to the reviewer’s suggestion.

      (4) Why did the authors not use the same driver to compare mCre 1, 4, 7, and 10? The study in Figure 2 uses Alb-roxCre for 1 and 7 and Cdh5-roxCre for 4 and 10, with clearly different levels of activity driven by the two alleles in vivo. Thus whether mCre1 is really better than mCre4 or 10 is not clear.

      Response: or two mCre versions that work efficiently. For example, if Alb-mCre1 was competitive with Cdh5-mCre10, we can use them for targeting genes in different cell types, broadening the potential utility of these mice.

      (5) Technical details are lacking. The authors provide little specific information regarding the precise way that the new alleles were generated, i.e. exactly what nucleotide sites were used and what the sequence of the introduced transgenes is. Such valuable information must be gleaned from schematic diagrams that are insufficient to fully explain the approach.

      Response: We appreciate your thoughtful suggestions. The schematic figures, along with the nucleotide sequences for the generation of mice, can be found in the revised Supplementary Figure 9.

      Reviewer #2 (Public Review):

      (1) The scenario where the lines would demonstrate their full potential compared to existing models has not been tested.

      Thank you for your thoughtful and constructive comment. The comparative analysis of R26-loxCre-tdT with iSuRe-Cre, employing Alb-CreER to target R26-Confetti, is provided in Figure 6.

      (2) The challenge lies in performing such experiments, as low doses of tamoxifen needed for inducing mosaic gene deletion may not be sufficient to efficiently recombine multiple alleles in individual cells while at the same time accurately reporting gene deletion. Therefore, a demonstration of the efficient deletion of multiple floxed alleles in a mosaic fashion would be a valuable addition.

      Thank you for your constructive comments. Mosaic analysis using sparse labeling and efficient gene deletion would be our future direction using roxCre and loxCre strategies.

      3) When combined with the confetti line, the reporter cassette will continue flipping, potentially leading to misleading lineage tracing results.

      Thank you for your professional comments. Indeed, the confetti used in this study can continue flipping, which would lead to potentially misleading lineage tracing results. Our use of R26-Confetti is to demonstrate the robustness of mCre for recombination. Some multiple-color mice lines that don’t flip have been published, for example, R26-Confetti2(PMID: 30778223) and Rainbow (PMID: 32794408). These reporters could be used for tracing Cre-expressing cells, without concerns of flipping of reporter cassettes.

      (4) Constitutive expression of Cre is also associated with toxicity, as discussed by the authors in the introduction.

      Thank you for your professional comments. The toxicity of constitutive expression of Cre and the toxicity associated with tamoxifen treatment in CreER mice line (PMID: 37692772) are known to the field. This study can’t solve the toxicity of the constitutive expression of Cre in this work. Many mouse lines with constitutive Cre driven by different promoters are present across various fields, representing similar toxicity. To solve this issue, it would be possible to construct a new strategy that enables the removal of Cre after its expression.

      Reviewer #3 (Public Review):

      (1) Although leakiness is rather minor according to the original publication and the senior author of the study wrote in a review a few years ago that there is no leakiness(https://doi.org/10.1016/j.jbc.2021.100509).

      Thank you so much for your careful check. In this review (PMID: 33676891), the writer’s comments on iSuRe-Cre are on the reader's side, and all summary words are based on the original published paper (PMID: 31118412). Currently, we have tested iSuRe-Cre in our hands. We did detect some leakiness in the heart and muscle, but hardly in other tissues as shown in Author response image 1.

      Author response image 1.

      Leakiness in Alb CreER;iSuRe-Cre mouse line. Pictures are representative results for 5 mice. Scale bars, white 100 µm.

      (2) I would have preferred to see a study, which uses the wonderful new tools to address a major biological question, rather than a primarily technical report, which describes the ongoing efforts to further improve Cre and Dre recombinase-mediated recombination.

      Response: We gratefully appreciate your valuable comment. The roxCre and loxCre mice mentioned in this study provide more effective methods for inducible genetic manipulation in studying gene function. We hope that the application of our new genetic tools could help address some major biological questions in different biomedical fields in the future.

      (3) Very high levels of Cre expression may cause toxic effects as previously reported for the hearts of Myh6-Cre mice. Thus, it seems sensible to test for unspecific toxic effects, which may be done by bulk RNA-seq analysis, cell viability, and cell proliferation assays. It should also be analyzed whether the combination of R26-roxCre-tdT with the Tnni3-Dre allele causes cardiac dysfunction, although such dysfunctions should be apparent from potential changes in gene expression.

      We are sorry that we mistakenly spelled R26-loxCre-tdT into R26-roxCre-tdT in our manuscript. We have not generated the R26-roxCre-tdT mouse line. We also thank the reviewer for concerns about the toxicity of high Cre expression. The toxicity of constitutive expression of Cre and the toxicity of tamoxifen treatment of CreER mice line (PMID: 37692772) are known to the field. This study can’t solve the toxicity of the constitutive expression of Cre in this work. Many mouse lines with constitutive Cre driven by different promoters are present across various fields, representing similar toxicity. To solve this issue, it would be possible to construct a new strategy that enables the removal of Cre after its expression.

      (4) Is there any leakiness when the inducible DreER allele is introduced but no tamoxifen treatment is applied? This should be documented. The same also applies to loxCre mice.

      In this study, we come up with new mice tool lines, including Alb roxCre1-tdT, Cdh5 roxCre4-tdT, Alb roxCre7-GFP, Cdh5 roxCre10-GFP and R26-loxCre-tdT. As the data shown in Supplementary Figure 1, Supplementary Figure 2, and Figure 4D, Alb roxCre1-tdT, Cdh5 roxCre4-tdT, Alb roxCre7-GFP, Cdh5 roxCre10-GFP and R26-loxCre-tdT are not leaky. Therefore, if there is any leakiness driven by the inducible DreER or CreER allele, the leakiness is derived from the DreER or CreER. Additional pertinent experimental data can be referenced in Figure S4C, Figure S7A-B, and Figure S8A.

      (5) It would be very helpful to include a dose-response curve for determining the minimum dosage required in Alb-CreER; R26-loxCre-tdT; Ctnnb1flox/flox mice for efficient recombination.

      Thank you for your suggestion. We value your feedback and have incorporated your suggestion to strengthen our study. Relevant experimental data can be referenced in Figure S8E-G.

      (6) In the liver panel of Figure 4F, tdT signals do not seem to colocalize with the VE-cad signals, which is odd. Is there any compelling explanation?

      The staining in Figure 4F in the revision is intended to deliver optimized and high-resolution images.

      (7) The authors claim that "virtually all tdT+ endothelial cells simultaneously expressed YFP/mCFP" (right panel of Figure 5D). Well, it seems that the abundance of tdT is much lower compared to YFP/mCFP. If the recombination of R26-Confetti was mainly triggered by R26-loxCre-tdT, the expression of tdT and YFP/mCFP should be comparable. This should be clarified.

      Thank you so much for your careful check. We checked these signals carefully and didn't find the “much lower” tdT signal. As the file-loading website has a file size limitation, the compressed image results in some signal unclear. We attached clear high-resolution images here. Author response image 2 shows how we split the tdT signal and compared it with YFP/mCFP.

      Author response image 2.

      (8) In several cases, the authors seem to have mixed up "R26-roxCre-tdT" with "R26-loxCre-tdT". There are errors in #251 and #256.Furthermore, in the passage from line #278 to #301. In the lines #297 and #300 it should probably read "Alb-CreER; R26-loxCretdT; Ctnnb1flox/flox" rather than "Alb-CreER;R26-tdT2;Ctnnb1flox/flox".

      We are grateful for these careful observations. We have corrected these typos accordingly.

      Recommendations for the authors:

      Reviewer #1:

      (1) However, for it to be useful to investigators a more direct comparison with the Benedito iSure line (or the latest version) is required as that is the crux of the study.

      Thank you for emphasizing this point, which we have now addressed in the revised manuscript and Figure 6.

      (2) I would like to know how the authors will make these new lines available to outside investigators.

      Please contact the lead author by email to consult about the availability of new mouse lines developed in this study.

      (3) The discussion is overly long and fails to address potential weaknesses. Much of it reiterates what was already said in the results section.

      We are thankful for your critical evaluation, which has helped us improve our discussion.

      Reviewer #2:

      (1) Assessing the efficiency and accuracy of the lines in mosaic deletions of multiple alleles and reporting them in single cells after low-dose tamoxifen exposure would be highly beneficial to demonstrate the full potential of the models.

      We appreciate your careful consideration of this issue. Our future endeavors will focus on mosaic analysis utilizing sparse labeling and efficient gene deletion, employing both roxCre and loxCre strategies.

      (2) Performing FACS analysis to confirm that all targeted (Cre reporter-positive) cells are also tdT-positive would provide more precise data and avoid vague statements like 'virtually all' or 'almost complete' in the results section:

      Line 166: Although mCre efficiently labeled virtually all targeted cells (Figure S3A-E)...

      Line 293: ... and not a single tdT+ hepatocyte 293 expressed Cyp2e1 (Figure 6D)... However, the authors do not provide any quantification. FACS would be ideal here.

      Line 244: ...expression of beta-catenin and GS almost disappeared in the 4W mutant sample... The resolution in the provided PDF is not adequate for assessment.

      Line 296: ... revealed almost complete deletion of Ctnnb1 in the Alb-CreER;R26-tdT2;Ctnnb1flox/flox mice...

      Thank you for suggesting these improvements, which have strengthened the robustness of our conclusions. In the revised version, we have incorporated FACS results that correspond to related sections. Additionally, a quantification statement has been included in the statistical analysis section. We appreciate your meticulous review and comments, which have significantly improved the clarity of our manuscript.

      (3) In the beginning of the results section, it is not clear which results are from this study and which are known background information (like Figure 1A). For example, it is not clear if Figure 1C presents data from R26-iSuRe-Cre. Please revise the text to more clearly present the experimental details and new findings.

      Thank you for this observation. Figure 1C belongs to this study, and the revised version has been modified to the related statement for improved clarity.

      (4) Experimental details regarding the genetic constructs and genotyping of the new knock-in lines are missing. Are R26 constructs driven by the endogenous R26 promoter or were additional enhancers used?

      Thank you for emphasizing this point. The schematic figures and nucleotide sequences for the generation of mice can be found in the revised Supplementary Figure 9, which can help to address this issue.

      (5) The method used to quantify mCre activity in terms of reporter+ target cells is not specified. From images or by FACS?

      Additionally, if images were used for quantification, it would be important to provide details on the number of images analyzed, the number of cells counted per image, and how individual cells were identified.

      Thank you for your comment. We have included the quantification statement in the statistical analysis section. Analyzing R26-Confetti+ target cells using FACS is challenging due to the limitations of the sorting instrument. Consequently, we quantified the related data by images. Each dot on the chart represents one sample, and the quantification for each mouse was conducted by averaging the data from five 10x fields taken from different sections.

      (6) Line 160: These data demonstrate that roxCre was functionally efficient yet non-leaky. Functional efficiency in vivo was not shown in the preceding experiments.

      Functional efficiency in vivo can be referred to in Figures S1-S2 and S4C.

      (7) It would be useful to provide a reference for easy vs low-efficiency recombination of different reporter alleles (lines 56-58).

      We are grateful for this comment, as it has allowed us to improve the clarity of our explanation. Consequently, we have made the necessary modifications.

      (8) Discussion on the potential drawbacks and limitations of the lines would be useful.

      We are thankful for your evaluation, which has significantly contributed to the enhancement of our discourse.

    1. eLife Assessment

      This analysis of the formation of the oral-aboral body axis in cnidarians, the sister group of bilaterians, is a significant and fundamental contribution to the field of Wnt signalling and planar cell polarity, particularly in or understanding in gradient formation, non-canonical Wnt signalling and Wnt-Frizzled interactions in cnidarians. The evidence supporting the conclusions is compelling and has the potential to contribute to a deeper understanding of the origin and evolution of Wnt signalling in cnidarians and metazoans in general. These findings, which are presented in a thoughtful and scholarly manner, will be of broad interest to developmental and evolutionary biologists.

    2. Reviewer #1 (Public review):

      Summary:

      This noteworthy paper examines the role of planar cell polarity and Wnt signalling in body axis formation of the hydrozoan Clytia. In contrast to the freshwater polyp Hydra or the sea anemone Nematostella, Clytia represents a cnidarian model system with a complete life cycle (planula larva-polyp-medusa). In this species, classical experiments have demonstrated that a global polarity is established from the oral end of the embryos (Freeman, 1981). Prior research has demonstrated that Wnt3 plays a role in the formation of the oral organiser in Clytia and other cnidarians, acting in an autocatalytic feedback-loop with β-catenin. However, the question of whether and to what extent an oral-aboral gradient of Wnt activity is established remained unanswered. This gradient is thought to control both tissue differentiation and tissue polarity. The planar cell polarity (PCP) pathway has been linked to this polarity, although it is generally considered to be β-catenin independent.

      Comments on major strengths and weaknesses:

      Beautiful and solid experiments to clarify the role of canonical Wnt signalling and PCP core factors in coordinating planar cell polarity of Clytia. The authors have conducted a series of sophisticated experiments utilising morpholinos, mRNA microinjections and immunofluorescent visualisation of PCP. The objective of these experiments was to address the function of Wnt3, β-catenin and PCP core proteins in the coordination of the global polarity of Clytia embryos. The authors conclude that PCP plays a role in regulating polarity along the oral-aboral axis of embryos and larvae. This offers a conceivable explanation for how polarity information is established and distributed globally during Clytia embryogenesis, with implications for our understanding of axis formation in cnidarians and the evolution of Wnt signalling in general. - While the experiments are well-designed and executed, there are some criticisms, questions or suggestions that should be addressed.

      (i) Wnt3 cue and global PCP. PCP has been described in detail in a previous paper on Clytia (Momose et al, 2012): its orientation along the oral-aboral body axis (ciliary basal body positioning studies), and its function in directional polarity during gastrulation (Stbm-, Fz1-, and Dsh-MO experiments). I wonder if this part could be shortened. What is new, however, are the knockdown and Wnt3-mRNA rescue experiments, which provide a deeper insight into the link between Wnt3 function in the blastopore organiser as a source or cue for axis formation. These experiments demonstrate that the Wnt3 knockdown induces defects equivalent to PCP factor knockdown, but can be rescued by Wnt3-mRNA injection, even at a distance of 200 µm away from the Wnt-positive area. The experimental set-up of these new molecular experiments follows in important aspects those of Freeman's experiments of 1981 (who in turn was motivated to re-examine Teissier's work of 1931/1933 ...). Freeman did not use the term "global polarity" but the concept of an axis-inducing source and a long-range tissue polarity can be traced back to both researchers.

      (ii) PCP propagation and β-catenin. The central but unanswered question in this study focuses on the interaction between Wnt3 and PCP and the propagation of PCP. Wnt3 has been described in cnidarians but also in vertebrates and insects as a canonical Wnt interacting with β-catenin in an autocatalytic loop. The surprising result of this study is that the action of Wnt3 on PCP orientation is not inhibited in the presence of a dominant-negative form of CheTCF (dnTCF) ruling out a potential function of β-catenin in PCP. This was supported by studies with constitutively active β-catenin (CA-β-cat) mRNA which was unable to restore PCP coordination nor elongation of Wnt3-depleted embryos but did restore β-catenin-dependent gastrulation. Based on these data, the authors conclude that Wnt3 has two independent roles: Wnt/β-catenin activation and initial PCP orientation (two step model for PCP formation). However, the molecular basis for the interaction of Wnt3 with the PCP machinery and how the specificity of Wnt3 for both pathways is regulated at the level of Wnt-receiving cells (Fz-Dsh) remains unresolved. - Also, with respect to PCP propagation, there is no answer with respect to the underlying mechanisms. The authors found that PCP components are expressed in the mid-blastula stage, but without any further indication of how the signal might be propagated, e.g., by a wavefront of local cell alignment. Here, it is necessary to address the underlying possible cellular interactions more explicitly.

      (iii) The proposed two step model for PCP formation has important evolutionary implications in that it excludes the current alternate model according to which a long-range Wnt3-gradient orients PCP ("Wnt/β-catenin-first"). Nevertheless, the initial PCP orientation by Wnt3 - as proposed in the two-step-model - is not explained at all on the molecular level. Another possible, but less well discussed and studied option for linking Wnt3 with PCP action could be a role of other Wnt pathways. The authors present compelling evidence that Wnt3 is the most highly expressed Wnt in Clytia at all stages of development. The authors convincingly show that Wnt3 is the most highly expressed Wnt in Clytia at all stages of development (Fig. S1). However, Wnt7 is also more highly expressed, which makes it a candidate for signal transduction from canonical Wnts to PCP Wnts. An involvement of Wnt7 in PCP regulation has been described in vertebrates (http://dx.doi.org/10.1016/j.celrep.2013.12.026). This would challenge the entire discussion and speculation on the evolutionary implications according to which PCP Wnt signaling comes first (PCP-first scenario") and canonical Wnt signaling later in metazoan evolution.

      (iv) The discussion, including Figure 6, is strongly biased towards the traditional evolutionary scenario postulating a choanzoan-sponge ancestry of metazoans. Chromosome-linkage data of pre-metazoans and metazoans (Schulz et al., 2023; https://doi.org/10 (1038/s41586-023-05936-6) now indicate a radically different scenario according to which ctenophores represent the ancestral form and are sister to sponges, cnidarians and bilaterians (the Ctenophora-sister hypothesis). This also has implications for the evolution of Wnt signalling, as discussed in the recent Nature Genetics Review by Holzem et al. (2024) (https://doi.org/10.1038/s41576-024-00699-w). Furthermore, it calls into question the hypothesis of a filter-feeding multicellular gastrula-like ancestor as proposed by Haeckel (Maegele et al., 2023). These papers have not yet been referenced, but they would provide a more robust discussion.

      General appraisal:

      The authors have carefully addressed all important points raised in this review. Aims and results support their conclusions.

      Impact of the work, utility of methods and data:

      As stated above, there will be a major impact on our understanding of the role of Wnt signaling in gradient formation and particularly the role of non canonical wnt signaling. As mentioned above, this will have a major impact on our understanding of the role of Wnt signalling in gradient formation, particularly the role of non-canonical Wnt signalling. - It will also be important to better understand the role of Wnt-Frizzled interactions in these basal organisms, as cnidarians have a smaller repertoire of Frizzled receptors compared to the relatively complete repertoire of Wnt subfamilies. This may imply that Wnt 3 is active in both canonical and PCP.

      Additional context:

      With regard to the question of the evolution of the body plan and Wnt signalling, it would be helpful and important for readers unfamiliar with cnidarians to know that the Hydrozoa/Medusozoa, to which Clytia belongs, are an "evolutionary derived group" within the Cnidaria, as opposed to the Anthozoa (e.g. sea anemone Nematostella). Hydrozoans possess planula larvae that are devoid of a mouth and any form of feeding mechanism, relying instead on the yolk of a fertilised egg for sustenance. The substantial divergence between the Anthozoa and Medusozoa was accompanied by significant gene reductions within the Medusozoa, which likely exerts an influence on the evolution of Wnt signalling in this group as well. This should not detract from the value of the work, but may help to put it in perspective.

    3. Reviewer #2 (Public review):

      Summary:

      Canonical Wnt signaling has previously been shown to be responsible for correct patterning of the oral-aboral axis as well as germ layer formation in several cnidarians. The post-gastrula stage, the planula larvae is not only elongated, it has a specific swimming direction due to the decentralized cellular positioning and slanted anchoring of the cilia. This, in turn, is in most other animals the result of a Wnt-Planar-cell polarity pathway. This paper by Uveira et al investigates the role of Wnt3 signaling in serving as a local cue for the PCP pathway which then is responsible for the orientation of the cilia and elongation of the planula larva of the hydrozoan Clytia hemisphaerica. Wnt3 was shown before to activate the canonical pathway via ß-catenin and to act as an axial organizer. The authors provide compelling evidence for this somewhat unusual direct link between the pathways through the same signaling molecule, Wnt3. In conclusion, they propose a two-step model: 1) local orientation by Wnt3 secretion 2) global propagation by the PCP pathway over the whole embryo.

      Strengths:

      In a series of elegant and also seemingly sophisticated experiments, they show that Wnt3 activates the PCP pathway directly, as it happens in the absence of canonical Wnt signaling (e.g. through co-expression of dnTCF). Conversely, constitutive active ß-catenin was not able to rescue PCP coordination upon Wnt3 depletion, yet restored gastrulation. This uncouples the effect of Wnt3 on axis specification and morphogenetic movements from the elongation via PCP. Through transplantation of single blastomeres providing a local source of Wnt3, they also demonstrate the reorganization of cellular polarity immediately adjacent to the Wnt3 expressing cell patch. These transplantation experiments also uncover that mechanical cues can also trigger the polarization, suggesting a mechanotransduction or direct influence on subcellular structures, e.g. actin fiber orientation.

      This is a beautiful and elegant study addressing an important question. The results have significant implications also for our understanding of the evolutionary origin of axis formation and the link of these two ancient pathways, which in most animals are controlled by distinct Wnt ligands and Frizzled receptors. The quality of the data is stunning and the paper is written in a clear and succinct manner. This paper has the potential to become a widely cited milestone paper.

      Weaknesses:

      I can not detect any major weaknesses. The work only raises a few more follow-up questions, which the authors are invited to comment on.

      I acknowledge the revisions made by the authors. Some open questions remain that need to be addressed in future work, and I accept the limitations of this study, as argued by the authors. Besides the elegant and high-quality experiments, I also appreciate the thoughtful and inspiring discussion.

    4. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      (1) Wnt3 cue and global PCP. PCP has been described in detail in a previous paper on Clytia (Momose et al, 2012): its orientation along the oral-aboral body axis (ciliary basal body positioning studies), and its function in directional polarity during gastrulation (Stbm-, Fz1-, and Dsh-MO experiments). I wonder if this part could be shortened. What is new, however, are the knockdown and Wnt3-mRNA rescue experiments, which provide a deeper insight into the link between Wnt3 function in the blastopore organiser as a source or cue for axis formation. These experiments demonstrate that the Wnt3 knockdown induces defects equivalent to PCP factor knockdown, but can be rescued by Wnt3-mRNA injection, even at a distance of 200 µm away from the Wnt-positive area. The experimental set-up of these new molecular experiments follows in important aspects those of Freeman's experiments of 1981 (who in turn was motivated to re-examine Teissier's work of 1931/1933 ...). Freeman did not use the term "global polarity" but the concept of an axis-inducing source and a long-range tissue polarity can be traced back to both researchers.

      We appreciate the reviewer’s insightful comments for evolutionary biology and cnidarian developmental biology.

      Concerning the presentation of the basic PCP structure of Clytia embryo epidermal cells, we prefer to retain this section unless there is a strict limit on manuscript length. These experiments provide background information necessary to establish the biological system for the readers. The structures of cells, notably cell adhesion, cilia, and the cytoskeleton, are essential components of this system.

      We have restored sentences concerning the historical contributions of Freeman and Teissier from a previous version of the manuscript.

      Freeman’s work offered two key insights. The first is the concept that cell polarity spreads and self-organizes over the distances revealed by the tissue orientation of aggregate embryonic cells (Freeman, 1981 https://doi.org/10.1007/BF00867804), which was termed “global polarity” in a review by Primus and Freeman (2004 https://doi.org/10.1002/bies.20031). This concept closely resembles the modern understanding of PCP coordination mechanisms mediated by core PCP interactions. Remarkably, Freeman proposed this idea in the early 1980s, at the same time of the first characterization of PCP mutants in Drosophila (Gubb and Garcia-Bellido 1982). The second is the role of egg polarity in defining the axis. Freeman demonstrated that the position of the first cleavage furrow predicts the oral-aboral axis by a series of sophisticated experiments. This was a milestone for the studies of cnidarian body axis development.

      However, some of Freeman’s interpretations were misleading. In the 1981 paper, he stated:

      "Polarity

      Other work that I have done has established that the anterior-posterior axis of the planula is set up at the time of the first cleavage; the site where cleavage is initiated specifies the posterior pole of this axis (Freeman 1980). The experiment reported here in which embryos were cut into halves and each half regulated to form a normal planula with the same polarity properties as the embryo it is from provides evidence that these polarity properties are remarkably stable at all developmental stages tested ranging from 4 cell to postgastrula embryos. "

      Freeman hypothesised that cell polarity at the 2- or 4-cell stage, referred to as the “polarity of first cell cleavage,” is directly inherited as the global polarity observed in later developmental stages.

      In the review by Primus and Freeman (2004), two hypotheses were introduced: (1) maternally localised factors, such as mRNA, determine the axis, and (2) cell polarity of cleavage furrow formation, is inherited to later stages and determines the axis. Freeman described these two hypotheses as mutually exclusive. However, we now know that cell polarity at early cleavage stages does not directly contribute to global polarity/PCP. Instead, Wnt/β-catenin signaling is regionally activated by maternally localised mRNAs distributed along the egg polarity (Momose, 2007; Momose, 2008), which maintain Wnt3 localisation and direct morphological axis patterning. Our study shown in this article unified these hypotheses.

      On the second point, as the reviewer noted, Freeman indeed revisited the work of Georges Teissier (Teissier, 1931), who conducted similar experiments on Amphisbetia embryos. It was Teissier who first described how the egg polarity is preserved in later stages and defines the axis. Teissier, however, carefully avoided asserting continuity between egg and blastula polarities, allowing for the possibility of “rétablissement” (re-establishment). As Teissier stated:

      "…On constate, en second lieu, que la polarité de l’œuf se conserve dans chacun de se fragment et que le maintien ou le rétablissement de cette polarité sont indispensables à un développement normal. Un fragment d’œuf ou de morula n’a aucune partie ni aucun blastomère qui soit rigoureusement déterminé comme endoderme, mais possède, par contre, un pôle antérieur et un pôle postérieur bien définis.…

      Mais cette proposition, qui ne semble pourtant guère dépasser la simple constatation des faits, soulève de grave difficulté. Elle donne en effet à la polarité, propriété encore bien mystérieuse, un rôle morphogénétique de premier ordre et implique des conséquences trop importantes pour qu’on puisse l’accepter sans un très sérieux examen.

      Comme je ne pense pas que les questions relatives à la nature des localisation germinales, à l’existence et au fonctionnement des organisateurs de l’œuf des Cœlentérés, puissant, dans l’état actuel de nos connaissances, être discutées utilement, je ne veux voir dans la proposition précédente qu’une façons commode et tout provisoire de systématiser les faits."

      English translation:

      “We note also that the polarity of the egg is preserved in each fragment and that the maintenance or re-establishment of this polarity is essential for normal development. A fragment of egg or morula has no part or blastomere that is rigorously determined as endoderm, but has, on the other hand, a well-defined anterior and posterior pole....

      But this proposition, which hardly seems to go beyond the simple observation of facts, raises serious difficulties. It gives polarity, still a mysterious property, a morphogenetic role of the first order, and implies consequences too important to be accepted without very serious examination.

      As I do not believe that questions concerning the nature of germinal localisation, or the existence and functioning of the egg organisers in Coelenterates, can, in the present state of our knowledge, be usefully discussed, I prefer only to see in the foregoing proposition a convenient and very provisional way of systematising the facts.”

      Teissier, G. (1931). Étude Expérimentale du Développement de Quelques Hydraires. Ann. Sc. Nat. Zool 14, 5–59.

      Teissier's interpretation and caution were reasonable.

      Our work connects recent molecular research on axis specification mechanisms in cnidarians with the classic experimental studies of Freeman and Teissier. We believe it is essential to present and acknowledge their conceptual contributions.  We have updated the Discussion to include these points.

      (2) PCP propagation and β-catenin. The central but unanswered question in this study focuses on the interaction between Wnt3 and PCP and the propagation of PCP. Wnt3 has been described in cnidarians but also in vertebrates and insects as a canonical Wnt interacting with β-catenin in an autocatalytic loop. The surprising result of this study is that the action of Wnt3 on PCP orientation is not inhibited in the presence of a dominant-negative form of CheTCF (dnTCF) ruling out a potential function of β-catenin in PCP. This was supported by studies with constitutively active β-catenin (CA-β-cat) mRNA which was unable to restore PCP coordination nor elongation of Wnt3-depleted embryos but did restore β-catenin-dependent gastrulation. Based on these data, the authors conclude that Wnt3 has two independent roles: Wnt/β-catenin activation and initial PCP orientation (two-step model for PCP formation). However, the molecular basis for the interaction of Wnt3 with the PCP machinery and how the specificity of Wnt3 for both pathways is regulated at the level of Wnt-receiving cells (Fz-Dsh) remain unresolved. Also, with respect to PCP propagation, there is no answer with respect to the underlying mechanisms. The authors found that PCP components are expressed in the mid-blastula stage, but without any further indication of how the signal might be propagated, e.g., by a wavefront of local cell alignment. Here, it is necessary to address the underlying possible cellular interactions more explicitly.

      The question of how Wnt3 interacts with the core PCP complex remains open for future investigation. An obvious hypothesis is that one of the Frizzled receptors binds Wnt3 ligands. For additional details, please refer to the response to Reviewer 2’s comment. Regarding other non-classic Wnt receptors, studies in the developing mouse limb have demonstrated that a Wnt5a gradient controls PCP polarisation via ROR receptors and graded Strabismus phosphorylation (Gao et al., 2011, https://doi.org/10.1016/j.devcel.2011.01.001). However, in this context, the Wnt5a gradient influences the frequency of polarised cells rather than PCP orientation. In Clytia, we performed gene knockdown experiments targeting ROR and RYK receptors using Morpholinos but did not observe any effect on axial patterning, suggesting that these receptors are unlikely to be involved in Wnt3 interaction.

      Concerning PCP propagation mechanisms, these are well-characterized in both Drosophila and vertebrates and conserved across taxa. The localised Fz-Fmi complex at the apical cortex of a cell interacts with the oppositely localised Stbm-Fmi complex in neighbouring cells, enabling coordination of PCP between directly adjacent cells. This interaction provides a comprehensive explanation for PCP propagation mechanisms. In Drosophila, the “domineering non-autonomy” effect is a well-documented phenomenon where PCP orientation autonomously propagates from core PCP mutant mosaic patches. Overall, PCP propagation is a conserved and robust mechanism across metazoans.

      (3) The proposed two-step model for PCP formation has important evolutionary implications in that it excludes the current alternate model according to which a long-range Wnt3-gradient orients PCP ("Wnt/β-catenin-first"). Nevertheless, the initial PCP orientation by Wnt3 - as proposed in the two-step model - is not explained at all on the molecular level. Another possible, but less well-discussed and studied option for linking Wnt3 with PCP action could be the role of other Wnt pathways. The authors present compelling evidence that Wnt3 is the most highly expressed Wnt in Clytia at all stages of development. The authors convincingly show that Wnt3 is the most highly expressed Wnt in Clytia at all stages of development (Figure S1). However, Wnt7 is also more highly expressed, which makes it a candidate for signal transduction from canonical Wnts to PCP Wnts. An involvement of Wnt7 in PCP regulation has been described in vertebrates (http://dx.doi.org/10.1016/j.celrep.2013.12.026). This would challenge the entire discussion and speculation on the evolutionary implications according to which PCP Wnt signaling comes first (PCP-first scenario") and canonical Wnt signaling later in metazoan evolution.

      First of all, we apologise that the expression profile of Wnt7originally provided in Figure S1 was incorrect; Wnt7 is not expressed in the embryonic stage. The error came from the accession number XLOC_034538 assigned to two transcripts, Wnt7 and Ataxin10, in the published genome assembly. Once the expression profile is revised in this light, the data are consistent with the in situ hybridisation data published in Momose et al. (2012, https://doi.org/10.1242/dev.084251). Wnt3 is the only Wnt ligand detectable between egg and gastrula stages. We appreciate the reviewer highlighting this issue and have corrected Figure S1

      If we understand correctly, the reviewer raises the possibility that Wnt3's downstream canonical Wnt/β-catenin pathway activates the expression of other Wnt genes, which in turn orient the PCP. Indeed, we showed that the expression of Wnt1 (previously called WntX2), Wnt2 (WntX1A), Wnt5 and Wnt6 (Wnt9) all becomes undetectable at the planula stage following Wnt3-MO injection (Momose et al., 2012). So, it is a reasonable concern.

      This possibility can be excluded because the canonical pathway activation by CA-β-cat does not restore PCP in Wnt3-MO-injected embryos and Wnt3 can orient PCP without Wnt/β-catenin pathway activity in the presence of dominant negative TCF (dnTCF). Concerning Wnt1b and Wnt11b, these transcripts are maternally stored and even more abundant than Wnt3. However, we can conclude that these do not have any role in axis patterning based on the complete axis loss in Wnt3-MO morphants.

      Lastly, it should of course be remembered that the chronological order of characters appearing in a developmental process does not necessarily reflect their appearance in evolution from ancestral to modern.

      (4) The discussion, including Figure 6, is strongly biased towards the traditional evolutionary scenario postulating a choanzoan-sponge ancestry of metazoans. Chromosome-linkage data of pre-metazoans and metazoans (Schulz et al., 2023; https://doi.org/10(1038/s41586-023-05936-6) now indicate a radically different scenario according to which ctenophores represent the ancestral form and are sister to sponges, cnidarians and bilaterians (the Ctenophora-sister hypothesis). This has also implications for the evolution of Wnt signalling, as discussed in the recent Nature Genetics Review by Holzem et al. (2024) (https://doi.org/10.1038/s41576-024-00699-w). Furthermore, it calls into question the hypothesis of a filter-feeding multicellular gastrula-like ancestor as proposed by Haeckel (Maegele et al., 2023). These papers have not yet been referenced, but they would provide a more robust discussion.

      I overlooked the excellent work of Holzem and colleagues. I appreciate this suggestion. The work, unfortunately, focusses mainly on the Wnt/β-catenin pathway. The PCP pathway consists of not only core PCP (Fmi Stbm, Pk, Dgo, Fz and Dsh) but many other components, such as Rho GTPase, which are all dealt with as "PCP” in this review. While the full set of core PCP is present only in the phylum Cnidaria and bilaterians, Pk and Dgo are present in choanoflagellate and Rho GTPase or ROCK are present even in Fungi (Lapébie et al,  2011 DOI 10.1002/bies.201100023). Holzem et al., described PCP as absent in ctenophores, likely based on the lack of Fmi/Stbm, while claiming its presence in fungi based on Rho GTPase and ROCK. This led to their argument that the Wnt/β-catenin pathway is more ancestral, supported by the absence of PCP components in ctenophores alongside the ctenophore-sister hypothesis.

      This likely reflects the limited attention given to PCP in the metazoan evolutionary biology community. Our work sheds light on the importance of PCP regulation in metazoan evolution. In the revised Discussion, we emphasise this point together with the importance of cell biology studies in basal metazoans and compare them based on functional studies.

      The observation of Aiptasia’s predatory “gastrula-like” larvae is indeed fascinating. Understanding how early metazoan ancestors obtained nutrients is a key to uncovering the origins of metazoans. However, the relevance of this work to metazoan evolution remains unclear. Predatory nutrient uptake is common among cnidarians, and the findings of Maegele et al. could suggest that the predatory gastrula-like state is ancestral, with the symbiotic state being derived, within Cnidaria, but does not notably support it in metazoa. Also, it has to be clarified how predation is defined. Fundamentally, there is little distinction between filter-feeding and predatory feeding regarding heterotrophy; both feeding types require digestive machinery. If active feeding behaviour is the essence of predation, this would be better addressed as an evolutionary neurobiology or neuroscience question. Another mystery is what the metazoan ancestors took as food if they were predatory; there has to be a non-predatorial metazoan, as a food, already present before them.<br /> Overall, Maegele’s work seems premature to be incorporated into the metazoan evo-devo discussion. In either case, the standard approach would involve comparative studies across taxa. It will be interesting to see follow-up works on comparative and functional genomics of predatory/digestive machinery within phylum cnidaria and across metazoan, including sponge and ctenophores.

      Reviewer #2 (Recommendations for the authors):

      We appreciate the reviewer’s expertise and recommendations regarding Wnt and PCP signalling. It would be our great pleasure if our work is seen and referenced by the cell biology community using model animals.

      (1) According to the 2-step model, one would expect that there is a temporal gradient in the spreading of the PCP from oral to aboral. Is there any indication for this?

      The best indication of a spatial and temporal gradient of PCP establishment observed so far is at the blastula stage (Fig.2B). PCP gradually becomes coordinated starting at 9 hpf, when PCP is slightly better organised close to the Wnt3-positive area (oral) compared to distal (aboral) areas. We did live imaging with tagged Poc1 to track the positions of centrioles in each cell (Fig. 2E), but this did not provide any further information about the spreading of the PCP. We hypothesise that there is a delay between PCP polarisation—established through the subcellular localisation of core PCP components—and its structural manifestation as ciliary positioning and orientation. This delay likely varies between cells, preventing the formation of a precise spatial PCP wave. We hope in the future to address this temporal aspect by live-imaging of core PCP proteins labelled with fluorescent proteins.

      (2) PCP is likely to be an all-or-nothing effect, while axial patterning is dose-dependent. is there a critical dose of Wnt3 level required to kick off the PCP pathway?

      We agree that the PCP phenotype is all-or-nothing.  Although we did not perform a quantitative test, we have not seen any intermediate phenotypes in Wnt3-rescue experiments. In our experimental condition (100 ng/µl mRNA), the Wnt3 mRNA injection into a blastomere consistently restores the body axis (via PCP) of Wnt3-MO injected embryos. No axis restoration was observed at 1 ng/µl. At 10 ng/µl, some embryos showed a restored elongated axis, while others showed no axis. The volume of injection is not precisely controllable and can easily vary two-fold, so we assume the limit is somewhere around 10 ng/µl. This contrasts with endoderm rescue via Wnt/β-catenin activation by GSK-β-inhibitors (alsterpaullone) or the constitutively active β-catenin (CA-β-cat), which occurs in a dose-dependent manner (ex. Supplementary Figure S2).

      (3) The key question left unaddressed is whether Wnt3 signals through one or two different Frizzled receptors? Which Frizzled receptors are candidates for this? Could they be knocked down to see which pathway (or both) is affected?

      How Wnt3 orientates the PCP system is an extremely interesting question that needs to be answered, and we plan to address this in the future. In Clytia, four Frizzled genes have been identified in the genome: CheFz1 (vertebrate counterpart of Fz1, 2, 3, 6 and 7), CheFz2 (Fz5 and 8), CheFz3 (Fz9/10) and CheFz4 (Fz4). Knockdown of CheFz1, hereby called Fz1, by Morpholino showed a PCP phenotype (Momose 2012, supplementary data). For a long time, we have suspected that the most likely candidate for PCP mediation is CheFz1. The Wnt3-rescue experiment in CheFz1-blocked background (similar experiment to Figure 3E, F) could potentially have answered this question. No PCP orientation would be expected even near the Wnt3-mRNA injected area if CheFz1 was the Wnt3 receptor for PCP orientation. Unfortunately, no reliable PCP phenotype was observed in this experiment, so this experiment was not included in the manuscript. We initially thought this was due to incomplete suppression of CheFz1 mRNA translation by the Morpholino when used at sub-toxic doses. But we now favour the alternative explanation that Fz1 does not mediate the Wnt3 signal responsible for initiating PCP orientation. We have previously shown that Fz1 is required for the Wnt/ β-catenin pathway (indicated by nuclear β-catenin localisation Momose 2007), which is then required to maintain Wnt3 expression. We cannot rule out that the PCP phenotype obtained previously following Fz1 knockdown (supplementary data in Momose 2012) is an indirect effect of Wnt3 downregulation.

      In future work, we plan to test the PCP involvement of the other Clytia Frizzleds, notably CheFz2 and CheFz4, which are not present as maternal mRNAs but are zygotically expressed in the early gastrula stage. CheFz3 is unlikely to be a candidate because it is aborally localised and acts as a negative receptor for the Wnt/β-catenin pathway (Momose 2007). Lastly, in unpublished experiments, no axial phenotype was obtained with ROR and RYK knockdown by Morpholino (T. Momose unpublished). 

      Based on these considerations, our current working hypothesis is that Wnt3 somehow stabilises or activates one of the Frizzled receptors acting as a core PCP protein in a polarised manner, likely at the oral side of each cell (Stbm is localised at the aboral side), which breaks the PCP symmetry and is propagated across the body axis.

      A few lines have been added to the discussion regarding this point.

      (4) Is there also PCP within the Wnt3 expressing domain? In other words, (and linked to question 2), does PCP require a certain concentration of Wnt3 or a gradient of Wnt3 in order to provide an orientation?

      In the context of a simple Wn3-MO rescue experiment, PCP is coordinated within the Wnt3-positive area. But this could be because PCP can propagate in both orientations, so it does not answer the question. In the Wnt3-rescue experiments in Fmi-MO and Stbm-MO embryos, PCP seemed better oriented close to the boundary between Wnt3-positive and -negative areas, in particular outside the Wnt3-positive area and rather uncoordinated deep in the middle of Wnt3-RNA positive area. 

      If Wnt3 expression is uniform across an embryo, as achieved by Wnt3-mRNA injection into the egg, the axis will be lost entirely (Momose 2008). We interpret these observations as indicating that Wnt3 expression "contrasts" (or steep gradients) act as the PCP orientation cue rather than a permissive manner.

      In normal development, mRNA expression detected by in situ hybridisation has a slight gradient, but we do not have any information about the endogenous protein distribution.

      We greatly appreciate the reviewer’s insightful comments. A few sentences addressing points (2) and (4) have been added. The graphical models in Figures 4 and 6A have been updated. While these are relatively minor changes to the manuscript, they significantly impact future perspectives.

      Minor comments:

      (1) Labeling in some of the figures is too small and not legible, e.g. Figures 4E-H. Please check and improve.

      Agreed. Some labelling was way too small (2.5 points). This has been corrected. The minimum font size is now 6-point for most labelling in the revised Figures. 

      (2) Page 13: ...and allow us to novel scenarios for PCP-driven axis symmetry breaking... seems to lack the verb "propose"

      Corrected.

    1. eLife Assessment

      This paper provides a compelling and rigorous quantitative analysis of the turnover and maintenance of CD4+ tissue-resident memory T cell clones, in the skin and the lamina propria. It provides a fundamental advance in our understanding of CD4 T cell regulation. Interestingly, in both tissues, maintenance involves an influx from progenitors on the time scale of months. The evidence that is based on fate mapping and mathematical inference is strong, although open questions on the interpretation of the Ki67-based fate mapping remain.

    2. Reviewer #1 (Public review):

      Summary:

      Compelling and clearly described work that combines two elegant cell fate reporter strains with mathematical modelling to describe the kinetics of CD4+ TRM in mice. The aim is to investigate the cell dynamics underlying maintenance of CD4+TRM.

      The main conclusions are that 1) CD4+ TRM are not intrinsically long-lived 2) even clonal half lives are short: 1 month for TRM in skin, even shorter (12 days) for TRM in lamina propria 3) TRM are maintained by self-renewal and circulating precursors.

      Strengths:

      (1) Very clearly and succinctly written. Though in some places too succinctly! See suggestions below for areas I think could benefit from more detail.

      (2) Powerful combination of mouse strains and modelling to address questions that are hard to answer with other approaches.

      (3) The modelling of different modes of recruitment (quiescent, neutral, division linked) is extremely interesting and often neglected (for simpler neutral recruitment).

      Comments on revised version: This reviewer is satisfied with the author responses and the changes made in the manuscript.

    3. Reviewer #2 (Public review):

      This manuscript addresses a fundamental problem of immunology - the persistence mechanisms of tissue-resident memory T cells (TRMs). It introduces a novel quantitative methodology, combining the in vivo tracing of T cell cohorts with rigorous mathematical modeling and inference. Interestingly, the authors show that immigration plays a key role for maintaining CD4+ TRM populations in both skin and lamina propria (LP), with LP TRMs being more dependent on immigration than skin TRMs. This is an original and potentially impactful manuscript.

      Comments on revised version: This reviewer is satisfied with the author responses and the changes made in the manuscript.

    4. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review):

      Summary:

      Compelling and clearly described work that combines two elegant cell fate reporter strains with mathematical modelling to describe the kinetics of CD4+ TRM in mice. The aim is to investigate the cell dynamics underlying the maintenance of CD4+TRM.

      The main conclusions are that:

      (1) CD4+ TRM are not intrinsically long-lived.

      (2) Even clonal half-lives are short: 1 month for TRM in skin, and even shorter (12 days) for TRM in lamina propria.

      (3) TRM are maintained by self-renewal and circulating precursors.

      Strengths:

      (1) Very clearly and succinctly written. Though in some places too succinctly! See suggestions below for areas I think could benefit from more detail.

      (2) Powerful combination of mouse strains and modelling to address questions that are hard to answer with other approaches.

      (3) The modelling of different modes of recruitment (quiescent, neutral, division linked) is extremely interesting and often neglected (for simpler neutral recruitment).

      Weaknesses/scope for improvement:

      (1) The authors use the same data set that they later fit for generating their priors. This double use of the same dataset always makes me a bit squeamish as I worry it could lead to an underestimate of errors on the parameters. Could the authors show plots of their priors and posteriors to check that the priors are not overly-influential? Also, how do differences in priors ultimately influence the degree of support a model gets (if at all)? Could differences in priors lead to one model gaining more support than another?

      We now show the priors and posteriors overlaid in Figure S2. The posteriors lie well within the priors, giving us confidence that the priors are not overly influential.

      (2) The authors state (line 81) that cells were "identified as tissue-localised by virtue of their protection from short-term in vivo labelling (Methods; Fig. S1B)". I would like to see more information on this. How short is short term? How long after labelling do cells need to remain unlabelled in order to be designated tissue-localised (presumably label will get to tissue pretty quickly -within hours?). Can the authors provide citations to defend the assumption that all label-negative cells are tissue-localised (no false negatives)?

      And conversely that no label-positive cells can be found in the tissue (no false positives)? I couldn't actually find the relevant section in the methods and Figure S1B didn't contain this information.

      We did describe the in vivo labeling in the first section of Methods (it was for 3 mins before sacrifice). The two aims of Fig S1B were to show the gating strategy (label-positive and negatives from tissue samples were clearly separated) and to address the false-positive issue. Less than 3% of cells in our tissue samples were positive; therefore, at most 3% of truly tissue-resident cells acquired the i.v. label, and likely less. Excluding those (as we did) therefore makes little difference to our analyses in terms of cell numbers. False negative rates are expected to be extremely low; labeling within circulating cells is typically >99% (see refs in Methods).

      (3) Are the target and precursor populations from the same mice? If so is there any way to reflect the between-individual variation in the precursor population (not captured by the simple empirical fit)? I am thinking particularly of the skin and LP CD4+CD69- populations where the fraction of cells that are mTOM+ (and to a lesser extent YFP+) spans virtually the whole range. Would it be nice to capture this information in downstream predictions if possible?

      This is a great point. We do indeed isolate all populations from each mouse. We are very aware of the advantages of using this grouping of information to reduce within-mouse uncertainty – we employ this as often as we can. The issue here was that the label content within the tissue (target) at any time depends on the entire trajectory of the label frequency in the precursor, in that mouse, up to that point. We can’t identify this curve for each animal individually – so we are obliged to use a population average.

      To mitigate this lack of pairing we do take a very conservative approach and fit this empirical function describing the trajectories of YFP and mTom in precursors at the same time as the label kinetics in the target; that is, we account for uncertainty in label influx in our fits and parameter estimates.

      Another issue is that to be sure that we are performing model selection appropriately, we only use the distribution of the likelihood on the target observations when comparing support for different precursors with LOO-IC. If we had been able to pair the precursor and target data in some way, the two would then be entangled and model comparison across precursors would not be possible.

      We’ve added some of this to the discussion.

      (4) In Figure 3, estimates of kinetics for cells in LP appear to be more dependent on the input model (quiescent/neutral/division-linked) than the same parameters in the skin. Can the authors explain intuitively why this is the case?

      This is a nice observation and it has a fairly straightforward explanation. As we pointed out in the paper, estimated rates of self renewal become more sensitive to the mode of recruitment the greater the rate of influx. If immigrants are quiescent, all Ki67 in the tissue has to be explained by self renewal. If all new immigrants are Ki67 high, the estimate of the rate of self renewal within the tissue will be lower. Across the board, the estimated rates of influx into gut were consistently higher than those in skin, and so the sensitivity of parameters to the mode of recruitment was much more obvious at that site.

      The importance of this trade-off for the division linked model can also be seen when you look at the neutral and quiescent models; they give similar parameter estimates because the Ki67 levels within all precursor populations were all less than 25% and so those two modes of recruitment are difficult to distinguish.

      (5) Can the authors include plots of the model fits to data associated with the different strengths of support shown in Figure 4? That is, I would like to know what a difference in the strength of say 0.43 compared with 0.3 looks like in "real terms". I feel strongly that this is important. Are all the fits fantastic, and some marginally better than others? Are they all dreadful and some are just less dreadful? Or are there meaningful differences?

      This is another good point (and from the author recommendations list, is your most important concern).

      We find that a fairly common issue is that models that are clearly distinguished by information criteria or LRTs can often give visually quite similar fits. Our experience is that this is partly due to the fact that models are usually fit on transformed scales (e.g. log for cell counts, logit for fractions) to normalise residuals, and this uncertainty is compressed when one looks at fits on the observed scale (e.g. linear). Another issue in our case is that for each model (precursor, target, and mode of recruitment) we fit 6 time courses simultaneously. Visual comparisons of fits of different models can then be a little difficult or misleading; apparently small differences in each fitted timecourse can add up to quite significant changes in the combined likelihood. We added this to the Discussion.

      The number of models is combinatorial (Fig. 4) so showing them all seems a bit cumbersome. But now in the supporting information (Fig. S3), for each target we show the best, second best, and the worst model fits overlaid, to give a sense of the dynamic range of the models we considered. As you will now see, visual differences among the most strongly supported models were not huge (but refer to our point just above). Measures of out-of-sample prediction error (LOO-IC) discriminated between these models reasonably well, though (weights shown in Fig. 4).

      It’s also worth mentioning here that we have substantially greater confidence in the identity of the precursors than in the precise modes of recruitment - you can see this clearly in the groupings of weights in Figure 4A. We did comment on this in the text but now emphasise it more.

      (6) Figure 4 left me unclear about exactly which combinations of precursors and targets were considered. Figure 3 implies there are 5 precursors but in Figure 4A at most 4 are considered. Also, Figure 4B suggests skin CD69- were considered a target. This doesn't seem to be specified anywhere.

      Thanks for pointing this out. When we were considering CD4+ EM in bulk as target, this population includes CD69- cells; in those fits, therefore, we couldn't use CD69- as a precursor. We now clarify this in the caption. Thanks also for the observation about Figure 4B; we didn’t consider CD69- cells as a target, so we’ve also made that clearer.

      Reviewer #2 (Public review):

      This manuscript addresses a fundamental problem of immunology - the persistence mechanisms of tissue-resident memory T cells (TRMs). It introduces a novel quantitative methodology, combining the in vivo tracing of T-cell cohorts with rigorous mathematical modeling and inference. Interestingly, the authors show that immigration plays a key role in maintaining CD4+ TRM populations in both skin and lamina propria (LP), with LP TRMs being more dependent on immigration than skin TRMs. This is an original and potentially impactful manuscript. However, several aspects were not clear and would benefit from being explained better or worked out in more detail.

      (1) The key observations are as follows:

      a) When heritably labeling cells due to CD4 expression, CD4+ TRM labeling frequency declines with time. This implies that CD4+ TRMs are ultimately replenished from a source not labeled, hence not expressing CD4. Most likely, this would be DN thymocytes.

      That’s correct.

      b) After labeling by Ki67 expression, labeled CD4+ TRMs also decline - This is what Figure 1B suggests. Hence they would be replaced by a source that was not in the cell cycle at the time of labeling. However, is this really borne out by the experimental data (Figure 2C, middle row)? Please clarify.

      (2) For potential source populations (Figure 2D): Please discuss these data critically. For example, CD4+ CD69- cells in skin and LP start with a much lower initial labeling frequency than the respective TRM populations. Could the former then be precursors of the latter?

      A similar question applies to LN YFP+ cells. Moreover, is the increase in YFP labeling in naïve T cells a result of their production from proliferative thymocytes? How well does the quantitative interpretation of YFP labeling kinetics in a target population work when populations upstream show opposite trends (e.g., naïve T cells increasing in YFP+ frequency but memory cells in effect decreasing, as, at the time of labeling, non-activated = non-proliferative T cells (and hence YFP-) might later become activated and contribute to memory)?

      These are good (and related) points. We've added some text to the discussion, paragraphs 2 and 3; we reproduce it here, slightly expanded.

      Fig 1B was a schematic but did faithfully reflect the impact of any waning of YFP in precursor on its kinetic in the targets. However, in our experiments, as you noted, the kinetics of YFP in most of the precursor populations were quite flat. This was due in part to memory subsets being sustained by the increasing levels of YFP within naïve cells from the cohort of thymocytes labeled during treatment. There is also likely some residual permanent labeling of lymphocyte progenitor populations. We discussed this in Lukas Front Imm 2023. (The latter is not a problem; all that matters for our analysis is that we generate a reasonable empirical description of the label kinetics in naive cells, however it arises). YFP is therefore not cleanly washed out in the periphery; and so for models with circulating memory as the tissue precursor, the flatness of their YFP curves leads to rather flat curves in the tissues.

      The mTom labelling was more informative as it was clearly diluted out of all peripheral populations by mTom-negative descendants of thymically-derived cells, as you point out in (a).

      Regarding (2), re: interpreting the initial levels of labels in precursors and targets. The important point here is that YFP and mTom were induced quickly in all populations we studied; therefore our inferences regarding precursors and targets aren’t informed by the initial levels of levels in each. (Imagine a slow precursor feeding a rapidly dividing target; YFP levels in the former would start lower than those in the latter). The causal issue that we think you’re referring to would matter if one expects the targets to begin with no label at all; for instance, in our busulfan chimeric mouse model (e.g. Hogan PNAS 2015) new, thymically derived ‘labelled’ (donor) cells progressively infiltrate replete ‘unlabelled’ (host) populations. In that case, one can immediately reject certain differentiation pathways by looking the sequence of accrual of donor cells in different subsets.

      The trends in YFP and mTom frequencies after treatment do matter for pathway inference, though, because precursor kinetics must leave an imprint on the target. For the case you mentioned, with opposite trends in label kinetics, such models would unlikely to be supported strongly; indeed, we never saw strong support for naïve cells (strongly increasing YFP) as a direct precursor of TRM (fairly flat).

      We’ve added a condensed version of this to the Discussion.

      (3) Please add a measure of variation (e.g., suitable credible intervals) to the "best fits" (solid lines in Figure 2).

      Added.

      (4) Could the authors better explain the motivation for basing their model comparisons on the Leave-OneOut (LOO) cross-validation method? Why not use Bayesian evidence instead?

      Bayes factors are very sensitive to priors and are either computationally unstable if calculated with importance sampling methods, or very expensive to calculate, if ones uses the more stable bridge sampling method. (We also note that fitting just a single model here takes a substantial amount of time). Further, using BF can be unreliable unless one of the models is close to the 'true' data generating model; though they seem to work well, we can be sure that none of our models are! For us, a more tractable and real-world selection criterion is based on the usefulness of a model, for which predictive performance is a reasonable proxy. In this case the mean out-of-sample prediction error (which LOO-IC reflects) is a wellestablished and valid means of ascribing support to different models.

    1. eLife Assessment

      This important study addresses an essential morphogenetic process-epithelial fusion-by identifying the transcription factor Hamlet as a potential master regulator. Using a combination of genetic, cell biological, and omics approaches, including a comprehensive RNAi screen and high-quality imaging, the authors provide compelling evidence for Hamlet's role in coordinating cell fate and differentiation. The findings are robust and of broad interest to developmental biologists and geneticists.

    2. Reviewer #1 (Public review):

      Summary:

      Wang et al. identify Hamlet, a PR-containing transcription factor, as a master regulator of reproductive development in Drosophila. Specifically, the fusion between the gonad and genital disc that is necessary for development of a continuous testes and seminal vesicle tissue essential for fertility. To do so, the authors generate novel Hamlet null mutants by CRISPR/Cas9 gene editing and characterize the morphological, physiological, and gene expression changes of the mutants using immunofluorescence, RNA-seq, cut-tag, and in-situ analysis. Thus, Hamlet is discovered to regulate a unique expression program, which includes Wnt2 and Tl, that is necessary for testis development and fertility.

      Strengths:

      This is a rigorous and comprehensive study that identifies the Hamlet dependent gene expression program mediating reproductive development in Drosophila. The Hamlet transcription targets are further characterized by Gal4/UAS-RNAi confirming their role in reproductive development. Finally, the study points to a role for Wnt2 and Tl as well as other Hamlet transcriptionally regulated genes in epithelial tissue fusion.

      Weaknesses:

      None noted.

    3. Reviewer #2 (Public review):

      Strengths:

      Wang and colleagues successfully uncovered an important function of the Drosophila PRDM16/PRDM3 homolog Hamlet (Ham) - a PR domain containing transcription factor with known roles in the nervous system in Drosophila. To do so, they generated and analyzed new mutants lacking the PR domain, and also employed diverse preexisting tools. In doing so, they made a fascinating discovery: They found that PR-domain containing isoforms of ham are crucial in the intriguing development of the fly genital tract. Wang and colleagues found three distinct roles of Ham: (1) Specifying the position of the testis terminal epithelium within the testis, (2) allowing normal shaping and growth of the anlagen of the seminal vesicles and paragonia and (3) enabling the crucial epithelial fusion between the seminal vesicle and the testis terminal epithelium. The mutant blocks fusion even if the parts are positioned correctly. The last finding is especially important, as there are few models allowing one to dissect the molecular underpinnings of heterotypic epithelial fusion in development. Their data suggest that they found a master regulator of this collective cell behavior. Further, they identified some of the cell biological players downstream of Ham, like for example E-Cadherin and Crumbs. In a holistic approach, they performed RNAseq and intersected them with the CUT&TAG-method, to find a comprehensive list of downstream factors directly regulated by Ham. Their function in the fusion process was validated by a tissue-specific RNAi screen. Meticulously, Wang and colleagues performed multiplexed in situ hybridization and analyzed different mutants, to gain a first understanding of the most important downstream-pathways they characterized - which are Wnt2 and Toll.

      This study pioneers a completely new system. It is a model for exploring a process crucial in morphogenesis across animal species, yet not well-understood. Wang and colleagues not only identified a crucial regulator of heterotypic epithelial fusion but took on the considerable effort of meticulously pinning down functionally important downstream effectors by using many state-of-the-art methods. This is especially impressive, as dissection of pupal genital discs before epithelial fusion is a time-consuming and difficult task. This promising work will be the foundation future studies build on, to further elucidate how this epithelial fusion works, for example on a cell biological and biomechanical level.

      Weaknesses:

      The developing testis-genital disc system has many moving parts. Myotube migration was previously shown to be crucial for testis shape. This means, that there is the potential of non-tissue autonomous defects upon knockdown of genes in the genital disc or the terminal epithelium, affecting myotube behavior which in turn affects epithelial fusion, as myotubes might create the first "bridge" bringing the two epithelia together. Nevertheless, this is outside the scope of this work and could be addressed in the future.

    4. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1 (Public review): 

      Summary: 

      Wang et al. identify Hamlet, a PR-containing transcription factor, as a master regulator of reproductive development in Drosophila. Specifically, the fusion between the gonad and genital disc is necessary for the development of continuous testes and seminal vesicle tissue essential for fertility. To do this, the authors generate novel Hamlet null mutants by CRISPR/Cas9 gene editing and characterize the morphological, physiological, and gene expression changes of the mutants using immunofluorescence, RNA-seq, cut-tag, and in-situ analysis. Thus, Hamlet is discovered to regulate a unique expression program, which includes Wnt2 and Tl, that is necessary for testis development and fertility. 

      Strengths: 

      This is a rigorous and comprehensive study that identifies the Hamlet-dependent gene expression program mediating reproductive development in Drosophila. The Hamlet transcription targets are further characterized by Gal4/UAS-RNAi confirming their role in reproductive development. Finally, the study points to a role for Wnt2 and Tl as well as other Hamlet transcriptionally regulated genes in epithelial tissue fusion. 

      We appreciate that the reviewer thinks our study is rigorous.

      Weaknesses: 

      The image resolution and presentation of figures is a major issue in this study. As a nonexpert, it is nearly impossible to see the morphological changes as described in the results. Quantification of all cell biological phenotypes is also lacking therefore reducing the impact of this study to those familiar with tissue fusion events in Drosophila development. 

      In the revised version, we have improved the image presentation and resolution. For all the images with more than two channels, we included single-channel images, changed the green color to lime and the red to magenta, highlighted the testis (TE) and seminal vescicles to make morphological changes more visible.  

      We had quantification for marker gene expression in the original version, and now also included quantification for cell biological phenotypes which are generally with 100% penetrance.  

      Reviewer #2 (Public review): 

      Strengths: 

      Wang and colleagues successfully uncovered an important function of the Drosophila PRDM16/PRDM3 homolog Hamlet (Ham) - a PR domain-containing transcription factor with known roles in the nervous system in Drosophila. To do so, they generated and analyzed new mutants lacking the PR domain, and also employed diverse preexisting tools. In doing so, they made a fascinating discovery: They found that PR-domain containing isoforms of ham are crucial in the intriguing development of the fly genital tract. Wang and colleagues found three distinct roles of Ham: (1) specifying the position of the testis terminal epithelium within the testis, (2) allowing normal shaping and growth of the anlagen of the seminal vesicles and paragonia and (3) enabling the crucial epithelial fusion between the seminal vesicle and the testis terminal epithelium. The mutant blocks fusion even if the parts are positioned correctly. The last finding is especially important, as there are few models allowing one to dissect the molecular underpinnings of heterotypic epithelial fusion in development. Their data suggest that they found a master regulator of this collective cell behavior. Further, they identified some of the cell biological players downstream of Ham, like for example E-Cadherin and Crumbs. In a holistic approach, they performed RNAseq and intersected them with the CUT&TAG-method, to find a comprehensive list of downstream factors directly regulated by Ham. Their function in the fusion process was validated by a tissue-specific RNAi screen. Meticulously, Wang and colleagues performed multiplexed in situ hybridization and analyzed different mutants, to gain a first understanding of the most important downstream pathways they characterized, which are Wnt2 and Toll. 

      This study pioneers a completely new system. It is a model for exploring a process crucial in morphogenesis across animal species, yet not well understood. Wang and colleagues not only identified a crucial regulator of heterotypic epithelial fusion but took on the considerable effort of meticulously pinning down functionally important downstream effectors by using many state-of-the-art methods. This is especially impressive, as the dissection of pupal genital discs before epithelial fusion is a time-consuming and difficult task. This promising work will be the foundation future studies build on, to further elucidate how this epithelial fusion works, for example on a cell biological and biomechanical level. 

      We appreciate that the reviewer thinks our study is orginal and important.

      Weaknesses: 

      The developing testis-genital disc system has many moving parts. Myotube migration was previously shown to be crucial for testis shape. This means, that there is the potential of non-tissue autonomous defects upon knockdown of genes in the genital disc or the terminal epithelium, affecting myotube behavior which in turn affects fusion, as myotubes might create the first "bridge" bringing the epithelia together. The authors clearly showed that their driver tools do not cause expression in myoblasts/myotubes, but this does not exclude non-tissue autonomous defects in their RNAi screen. Nevertheless, this is outside the scope of this work. 

      We thank the reviewer’s consideration of non-tissue autonomous defects upon gene knockdown. The driver, hamRSGal4, drives reporter gene expression mainly in the RS epithelia, but we did observe weak expression of the reporter in the myoblasts before they differentiate into myotubes. Thus, we could not rule out a non-tissue autonomou effect in the RNAi screen. So we now included a statement in the result, “Given that the hamRSGal4 driver is highly expressed in the TE and SV epithelia, we expect highly effective knockdown occurs only in these epithelial cells. However, hamRSGal4 also drives weak expression in the myoblasts before they differentiated into myotubes (Supplementary Fig. 5B), which may result in a non-tissue autonomous effect when knocking down the candidate genes expressed in myoblasts.”

      However, one point that could be addressed in this study: the RNAseq and CUT&TAG experiments would profit from adding principal component analyses, elucidating similarities and differences of the diverse biological and technical replicates. 

      Thanks for the suggestion. We now have included the PCA analyses in supplementary figure 6A-B and the corresponding description in the text. The PCA graphs validated the consistency between biological replicates of the RNA-seq samples. The Cut&Tag graphs confirm the consistency between the two biological replicates from the GFP samples, but show a higher variability between the w1118 replicates. Importantly, we only considered the overlapped peaks pulled by the GFP antibody from the ham_GFP genotype and the Ham antibody from the wildtype (w1118) sample as true Ham binding sites. 

      Recommendations for the authors:  

      Reviewer #1 (Recommendations for the authors): 

      Major Concern: 

      (1) The image resolution and presentation of figures (Figures 2, 5, 6, and 7) is a major issue in this study. As a non-expert, it is nearly impossible to see the morphological changes as described in the results. Images need to be captured at higher resolution and zoomed in with arrows denoting changes as described. Individual channels, particularly for intensity measurement need to be shown in black and white in addition to merged images. Images also need pseudo-colored for color-blind individuals (i.e. no red-green staining). 

      The images were captured at a high resolution, but somehow the resolution was drammaticlly reduced in the BioRxiv PDF. We try to overcome this by directly submitting the PDF in the Elife submission system. In the revised version, we have included single-channel images, changed the green and red colors to lime and magenta for color blindness. We also highlighted the testis (TE) and seminal vescicle structures in the images to make morphological changes more visible.  

      (2) The penetrance of morphological changes observed in RT development is also unclear and needs to be rigorously quantified for data in Figures 2, 5, and 7. 

      We now included quantification for cell biological phenotypes which are generally with 100% penetrance. The percentage of the penetrance and the number of animals used are indicated in each corresponding image.  

      Reviewer #2 (Recommendations for the authors): 

      Major Points 

      (1) Lines 193- 220 I would strongly suggest pointing out the obvious shape defects of the testes visible in Figure 2A ("Spheres" instead of "Spirals"). These are probably a direct consequence of a lack in the epithelial connection that myotubes require to migrate onto the testis (in a normal way) as depicted in the cartoons, allowing the testis to adopt a spiral shape through myotube-sculpting (Bischoff et al., 2021), further confirming the authors' findings! 

      Good point. In the revised text, we have added more description of the testis shape defects and pointed out a potential contribution from compromised myotube migration.   

      (2) Line 216: "Often separated from each other". Here it would be important to mention how often. If the authors cannot quantify that from existing data, I suggest carrying it out in adult/pharate adult genital tracts (if there is no strong survivor bias due to the lethality of stronger affected animals), as this is much easier than timing prepupae. This should be a quick and easy experiment. 

      Because it is hard to tell whether the separation of the SV and TE was caused by developmental defects or sometimes could be due to technical issues (bad dissection), we now change the description to, “control animals always showed connected TE and SV, whereas ham mutant TE and SV tissues were either separated from each other, or appeared contacted but with the epithelial tubes being discontinuous (Fig. 2B).” Additionally, we quantified the disconnection phenotype, which is 100% penetrance in 18 mutant animals. This quantification is now included in the figure. 

      (3) Lines 289-305, Figure 3. I could only find how many replicates were analyzed in the RNAseq/CUT&Tag experiments in the Material & Methods section. I would add that at least in the figure legends, and perhaps even in the main text. Most importantly, I would add a Principal Component Analysis (one for RNAseq and one for the CUT&TAG experiment), to demonstrate the similarity of biological replicates (3x RNaseq, 4x Cut&Tag) but also of the technical replicates (RNAseq: wt & wt/dg, ham/ham & ham/df, GD & TE; CUT&TAG: Antibody & GFP-Antibody, TG&TE...). This should be very easy with the existing data, and clearly demonstrate similarities & differences in the different types of replicates and conditions. 

      Principle component analysis and its description are now added to Supplementary Fig 6 and the main text respectively. 

      (4) Line 321; Supplementary Table 1: In the table, I cannot find which genes are down- or upregulated - something that I think is very important. I would add that, and remove the "color" column, which does not add any useful information. 

      In Supplementary table 1, the first sheet includes upregulated genes while the second sheet includes downregulated genes. We removed the column “color” as suggested.  

      (5) Line 409: SCRINSHOT was carried out with candidate genes from the screen. One gene I could not find in that list was the potential microtubule-actin crosslinker shot. If shot knockdown caused a phenotype, then I would clearly mention and show it. If not, I would mention why a shot is important, nonetheless. 

      shot is one of the candidate target genes selected from our RNA-seq and Cut&Tag data. However, in the RNAi screen, knocking down shot with the available RNAi lines did not cause any obvious phenotype. These could be due to inefficient RNAi knockdown or redundancy with other factors. We anyway wanted to examine shot expression pattern in the developing RS, give the important role of shot in epithelial fusion (Lee S., 2002). Using SCRINSHOT, we could detect epithelial-specific expression of shot, implying its potential function in this context. We now revised the text to clarify this point. 

      Minor points 

      (1) Cartoons in Figure 1: The cartoons look like they were inspired by the cartoon from Kozopas et al., 1998 Fig. 10 or Rothenbusch-Fender et al., 2016 Fig 1. I think the manuscript would greatly profit from better cartoons, that are closer to what the tissue really looks like (see Figure 1H, 2G), to allow people to understand the somewhat complicated architecture. The anlagen of the seminal vesicles/paragonia looks like a butterfly with a high columnar epithelium with a visible separation between paragonia/seminal vesicles (upper/lower "wing" of the "butterfly"). Descriptions like "unseparated" paragonia/seminal vesicle anlagen, would be much easier to understand if the cartoons would for example reflect this separation. It would even be better to add cartoons of the phenotypic classes too, and to put them right next to the micrographs. (Another nitpick with the cartoons: pigment cells are drastically larger and fewer in number (See: Bischoff et al., 2021 Figure 1E & MovieM1).) 

      Thanks for the suggestion. We have updated Figure 1 by adding additional illustrations showing the accessory gland and seminal vesicle structures in the pupal stage and changing the size of pigment cells.

      (2) Line 95-121 I would also briefly introduce PR domains, here. 

      We have added a brief descripition of the PR domains.

      (3) Line 152, 158, 160, 162. When first reading it, I was a bit confused by the usage of the word sensory organ. I would at least introduce that bristles are also known as external mechanosensory organs. 

      We have now revised the description to “mechano-sensory organ”.

      eg. Line 184, 194, and many more. Most times, the authors call testis muscle precursors "myoblasts". This is correct sometimes, but only when referring to the stage before myoblast-fusion, which takes place directly before epithelial fusion (28 h APF). Postmyoblast-fusion (eg. during migration onto the testis), these cells should be called myotubes or nascent myotubes, as the fly muscle community defined the term myoblast as the singlenuclei precursors to myotubes. 

      We have now revised the description accordingly.  

      (4) Line 217/Figure 2B. It looks like there is a myotube bridge between the testis and the genital disc. I would point that out if it's true. If the authors have a larger z-stack of this connection, I suggest creating an MIP, and checking if there are little clusters of two/three/four nuclei packed together. This would clearly show that the cells in between are indeed myotubes (granted that loss of ham does not introduce myoblast-fusion-defects). 

      We do not have a Z-stack of this connection, and thus can not confirm whether the cells in this image are myotubes. However, we found that mytubes can migrate onto the testis and form the muscular sheet in the ham mutant despite reduced myotube density. At the junction there are myotubes, suggesting that loss of ham does not introduce myoblast-fusion defects. These results are now included in the revised manuscript, supplementary Fig. 5 C-D.

      (5) Line 231/Supplementary Fig. 3C-G: I would add to the cartoons, where the different markers are expressed. 

      We have added marker gene expression in the cartoons.

      (6) Line 239. I don't see what Figure 1A/1H refers to, here. I would perhaps just remove it. 

      Yes, we have removed it.

      (7) Line 232. I would rephrase the beginning of the sentence to: Our data suggest Ham to be... 

      Yes, we have revised it.

      (8) Line 248-250/Figure 2F. Clonal analyses are great, but I think single channels should be shown in black and white. Also, a version without the white dashed line should be shown, to clearly see the differences between wt and ham-mutant cells. 

      Now single channel images from the green and red images are presented in Supplementary Figures. This particular one is in Supplementary Figure 3B. 

      (9) Line 490. The Toll-9 phenotype was identified on the sterility effect/lack-of-spermphenotype alone, and it was deduced, that this suggests connection defects. By showing the right focus plane in Fig S8B (lower right), it should be easy to directly show whether there is a connection defect or not. Also, one would expect clearer testis-shaping defects, like in ham-mutants, as a loss of connection should also affect myotube migration to shape the testis. This is just a minor point, as it only affects supplementary data with no larger impact on the overall findings, even if Toll-9 is shown not to have a defect, after all. 

      We find that scoring defects at the junction site at the adult stage is difficult and may not be always accurate. Instead, we score the presence of sperms in the SV, which indirectly but firmly suggests successful connection between the TE and SV. We have now included a quantification graph, showing the penetrance of the phentoype in the new Supplementary Fig.14C. There were indeed morphological defects of TE in Toll-9 RNAi animals. We now included the image and quantification in the new Supplementary Fig.14B.

    1. eLife Assessment

      This important study reports on a basis for neurabin-mediated specification of substrate choice by protein phosphatase-1. The data from the comprehensive approach using structural, biochemical, and computational methods are compelling. This paper is broadly relevant to those investigating various cellular signaling cascades that entail phosphorylation as the main mechanism.

    2. Reviewer #1 (Public review):

      Summary:

      In this manuscript the Treisman and colleagues address the question of how protein phosphatase 1 (PP1) regulatory subunits (or PP1-interacting protein (PIPs)) confer specificity on the PP1 catalytic subunit which by itself possesses little substrate specificity. In prior work the authors showed that the PIP Phactrs confers specificity by remodelling a hydrophobic groove immediately adjacent to the PP1 catalytic site through residues within the RVxF- ø ø -R-W string of Phactrs. Specifically, the residues proximal and including the 'W' of the RVxF- ø ø -R-W string remodel the hydrophobic groove. Other residues the of the RVxF- ø ø -R-W string (i.e. the RVxF- ø ø -R) are not involved in this remodelling.

      The authors suggest that the RVxF- ø ø -R-W string is a conserved feature of many PIPs including PNUTS, Neurabin/spinophilin and R15A. However from a sequence and structural perspective only the RVxF- ø ø -R- is conserved. The W is not conserved in most and in the R15A structure (PDB:7NZM) the Trp side chain points away from the hydrophobic channel - this could be a questionable interpretation due to model building into the low resolution cryo-EM map (4 A).

      In this paper the authors convincingly show that Neurabin confers substrate specificity through interactions of its PDZ domain with the PDZ domain-binding motif (PBM) of 4E-BP. They show the PBM motif is required for Neurabin to increase PP1 activity towards 4E-BP and a synthetic peptide modelled on 4E-BP and also a synthetic peptide based on IRSp53 with a PBM added. The PBM of 4E-BP1 confers high affinity binding to the Neurabin PDZ domain. A crystal structure of a PP1-4E-BP1 fusion with Neurabin shows that the PBM of 4E-BP interacts with the PDZ domain of Neurabin. No interactions of 4E-BP and the catalytic site of PP1 are observed. Cell biology work showed that Neurabin-PP1 regulates the TOR signalling pathway by dephosphorylating 4E-BPs.

      Strengths:

      This work demonstrates convincingly using a variety of cell biology, proteomics, biophysics and structural biology that the PP1 interacting protein Neurabin confers specificity on PP1 through an interaction of its PDZ domain with a PDZ-binding motif of 4E-BP1 proteins. Remodelling of the hydrophobic groove of the PP1 catalytic subunit is not involved in Neurabin-dependent substrate specificity, in contrast to how Phactrs confers specificity on PP1. The active site of the Neurabin/PP1 complex does not recognise residues in the vicinity of the phospho-residue, thus allowing for multiple phospho-sites on 4E-BP to be dephosphorylated by Neurabin/PP1. This contrasts with substrate specificity conferred by the Phactrs PIP that confers specificity of Phactrs/PP1 towards its substrates in a sequence-specific context by remodelling the hydrophobic groove immediately adjacent to the catalytic. The structural and biochemical insights are used to explore the role of Neurabin/PP1 in dephosphorylation 4E-BPs in vivo, showing that Neurabin/PP1 regulates the TOR signalling pathway, specifically mTORC1-dependent translational control.

      Weaknesses:

      The only weakness is the suggestion that a conserved RVxF- ø ø -R-W string exists in PIPs. The 'W' is not conserved in sequence and 3-dimensions in most of the PIPs discussed in this manuscript. The lack of conservation of the W would be consistent with the finding based on multiple PP1-PIP structures that apart from Phactrs, no other PIP appears to remodel the PP1 hydrophobic channel.

      Comments on revisions:

      The authors have addressed my comments.

      One aspect of the manuscript and response to reviewers is misleading regarding the statement: 'Like many PIPs, they interact with PP1 using the previously defined "RVxF", "ΦΦ", and "R" motifs (Choy et al, 2014).' This statement, and similar in the authors' response, implies that Choy et al discovered the "RVxF" and "ΦΦ" motifs. The Choy et al, 2014 paper reports the discovery of the "R" motif. The "RVxF" and "ΦΦ" motifs were discovered and reported in earlier papers not cited in the authors' manuscript. Perhaps the authors can correct this.

    3. Reviewer #2 (Public review):

      This manuscript explores the molecular mechanisms that are involved in substrate recognition by the PP1 phosphatase. The authors previously showed that the PP1 interacting protein (PPI), PhactrI, conferred substrate specificity by remodelling the PP1 hydrophobic substrate groove. In this work, the authors aimed to understand the key determinant of how other PIPs, Neurabin and Spinophilin, mediate substrate recognition.

      The authors generated a few PP1-PIP fusion constructs, undertook TMT phosphoproteomics and validated their method using PP1-Phactr1/2/3/4 fusion constructs. Using this method, the authors identified phsophorylation sites controlled by PP1-Neurabin and focussed their work on 4E-BP1, thereby linking PP1-Neurabin to mTORC1 signalling. Upon validating that PP1-Neurabin dephosphorylates 4E-BP1, they determined that 4E-BP1 PBM binds to the PDZ domain of Neurabin with an affinity that was greater than 30 fold as compared to other substrates. PP1-Neurabin dephosphorylated 4E-BP1WT and IRSp53WT with a catalytic efficiency much greater than PP1 alone. However, PP1-Neurabin bound to 4E-BP1 and IRSp53 mutants lacking the Neurabin PDZ domain with a catalytic efficiency lesser than that observed with 4E-BP1WT. These results indicate the involvement of the PDZ domain in facilitating substrate recruitment by PP1-Neurabin. Interestingly, PP1-Phactr1 dephosphorylation of 4E-BP1 phenocopies PP1 alone, while PP1-Phactr1 dephosphorylates IRSp53 to a much higher extent than PP1 alone. These results highlights the importance of the PDZ domain and also shed light on how different PP1-PIP holoenzymes mediate substrate recognition using distinct mechanisms. The authors also show that the remodelling of the hydrophobic PP1 substrate groove which is essential for substrate recognition by PP1-Phactr1, was not required by PP1-Neurabin. Additionally, the authors also resolved the structure of a PP1-4E-BP1 fusion with the PDZ-containing C-terminal of Neurabin and observed that the Neurabin/PP1-4E-BP1 complex structure was oriented at 21{degree sign} to that in the unliganded Spinophilin/PP1 complex (resolved by Ragusa et al., 2010) owing to a slight bend in the C-terminal section that connects it to the RVxF-ΦΦ-R-W string. Since, no interaction was observed with the remodelled PP1-Neurabin hydrophobic groove, the authors utilised AlphaFold3 to further answer this. They observed a high confidence of interaction between the groove and phosphorylated substrate and a low confidence of interaction between the groove and unphosphorylated substrate, thereby suggesting that the hydrophobic groove remodelling is not involved in PP1-Neurabin recognition and dephosphorylation of 4E-BP1.

      In this work, the authors provide novel insights into how Neurabin depends on the interaction between its PDZ domain and PBM domains of potential substrates to mediate its recruitment by PP1. Additionally, they uncover a novel PP1-Neurabin substrate, 4E-BP1. They systematically employ phosphoproteomics, biochemical and structural methods to investigate substrate specifity in a robust fashion. Furthermore, the authors also compares the interactions between PP1-Neurabin to 4E-BP1 and IRSp53 (PP1-Phactr1 substrate) with PP1-Phactr1, to showcase the specificity of the mode of action employed by these complexes in mediating substrate specificity. The authors do employ an innovative PP1-PIP fusion strategy previously explored by Oberoi et al., 2016 and the authors themselves in Fedoryshchak et al., 2020. This method, allows for a more controlled investigation of the interactions between PP1-PIPs and its substrates. Furthermore, the authors have substantially characterised the importance of the PDZ domain using their fusion constructs, however, I believe that a further exploration into either structural or AlphaFold3 modelling of PBM domain substrate mutants, or a Neurabin PDZ-domain mutant might further strengthen this claim. Overall, the paper makes a substantial contribution to understanding substrate recognition and specificity in PP1-PIP complexes. The study's innovative methods, biological relevance, and mechanistic insights are strengths, but whether this mechanism occurs in a physiological context is unclear.

    4. Reviewer #3 (Public review):

      Protein Phosphatase 1 (PP1), a vital member of the PPP superfamily, drives most cellular serine/threonine dephosphorylation. Despite PP1's low intrinsic sequence preference, its substrate specificity is finely tuned by over 200 PP1-interacting proteins (PIPs), which employ short linear motifs (SLIMs) to bind specific PP1 surface regions. By targeting PP1 to cellular sites, modifying substrate grooves, or altering surface electrostatics, PIPs influence substrate specificity. Although many PIP-PP1-substrate interactions remain uncharacterized, the Phactr family of PIPs uniquely imposes sequence specificity at dephosphorylation sites through a conserved "RVxF-ΦΦ-R-W" motif. In Phactr1-PP1, this motif forms a hydrophobic pocket that favors substrates with hydrophobic residues at +4/+5 in acidic contexts (the "LLD motif"), a specificity that endures even in PP1-Phactr1 fusions. Neurabin/Spinophilin remodel PP1's hydrophobic groove in distinct ways, creating unique holoenzyme surfaces, though the impact on substrate specificity remains underexplored. This study investigates Neurabin/Spinophilin specificity via PDZ domain-driven interactions, showing that Neurabin/PP1 specificity is governed more by PDZ domain interactions than by substrate sequence, unlike Phactr1/PP1.

      A significant strength of this work is the use of PP1-PIP fusion proteins to effectively model intact PP1•PIP holoenzymes by replicating the interactions that remodel the PP1 interface and confer site-specific substrate specificity. When combined with proteomic analyses to assess phospho-site depletion in mammalian cells, these fusions offer critical insights into holoenzyme specificity, revealing new candidate substrates for Neurabin and Spinophilin. The studies present compelling evidence that the PDZ domain of PP1-Neurabin directs its specificity, with the remodeled PP1 hydrophobic groove interactions having minimal impact. This mechanism is supported by structural analysis of the PP1-4E-BP1 substrate fusion bound to a Neurabin construct, highlighting the 4E-BP1/PDZ interaction. This work delivers crucial insights into PP1-PIP holoenzyme function, combining biochemical, proteomic, and structural approaches. It validates the PP1-PIP fusion protein model as a powerful tool, suggesting it may extend to studying additional holoenzymes. While an extremely useful model, it must be considered unlikely the PP1-PIP fusions fully recapitulate the specificity and regulation of the holoenzyme.

    5. Author response:

      The following is the authors’ response to the original reviews

      Response to the public reviews:

      We are very pleased to see these positive reviews of our preprint.

      Reviewers 1 and 3 raise issues around PIP-PP1 interactions.

      (1) Role of the “RVxF-ΦΦ-R-W string”

      Most PIPs interact with the globular PP1 catalytic core through short linear interaction motifs (SLiMs) and Choy et al (PNAS 2014) previously showed that many PIPs interact with PP1 through conserved trio of SLiMs, RVxF-ΦΦ-R, which is also present in the Phactrs.

      Previous structural analysis showed the trajectory of the PPP1R15A/B, Neurabin/Spinphilin (PPP1R9A/B), and PNUTS (PPP1R10) PIPs across the PP1 surface encompasses not only the RVxF-ΦΦ-R trio, but also additional sequences C-terminal to it (Chen et al, eLife, 2015). This extended trajectory is maintained in the Phactr1-PP1 complex (Fedoryshchak et al, eLife (2020). Based on structural alignment we proposed the existence of an additional hydrophobic “W” SLiM that interacts with the PP1 residues I133 and Y134.

      The extended “RVxF-ΦΦ-R-W” interaction brings sequences C-terminal to the “W” SLiM into the vicinity of the hydrophobic groove that adjoins the PP1 catalytic centre. In the Phactr1/PP1 complex, these sequences remodel the groove, generating a novel pocket that facilitates sequence-specific substrate recognition.

      This raises the possibility that sequences C-terminal to the extended “RVxF-ΦΦ-R-W string” in the other complexes also confer sequence-specific substrate recognition, and our study aims to test this hypothesis. Indeed, the hydrophobic groove structures of the Neurabin/Spinophilin/PP1 and Phactr1/PP1 complexes differ significantly (Ragusa et al, 2010; see Fedoryshchak et al 2020, Fig2 FigSupp1).

      (2) Orientation of the W side chain

      Reviewer 1 points out that in the substrate-bound PP1/PPP1R15A/Actin/eIF2 pre-dephosphorylation complex the W sidechain is inverted with respect to its orientation in  PP1-PPP1R15B complex (Yan et al, NSMB 2021). The authors proposed that this may reflect the role of actin in assembly of the quaternary complex. This does not necessarily invalidate the notion that sequences C-terminal to the “W” motif might play a role in actin-independent substrate recognition, and we therefore consider our inclusion of the R15A/B fusions in our analysis to be reasonable.

      (3) Conservation of W

      The motif ‘W’ does not mandate tryptophan - Phactrs and PPP1R15A/B indeed have W at this position but Neurabin/spinophilin contain VDP, which makes similar interactions. Similarly the “RVxF” motifs in Phactr1, Neurabin/Spinophilin, PPP1R15A/B and PNUTS are LIRF, KIKF, KV(R/T)F and TVTW respectively.

      In our revision, we will present comparisons of the differentially remodelled/modified PP1 hydrophobic groove in the various complexes, discuss the different orientations of the tryptophan in the previously published PPP1R15A/PP1 and PPP1R15B/PP1 structures. We will also address the other issues raised by the referees.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Comments and suggestions for revisions

      (1) The authors do not provide strong evidence that the interactions of the 'W' of the RVxF- øø -R-W string with the hydrophobic groove of PP1 is conserved in PIPs. Whereas the RVxF motif is well conserved and validated since its discovery in 1997, as are the øø - (an extension of the RVxF motif), and the 'R', the conservation of the Trp residue in the RVxF-øø-R-W string is not conserved.

      We did not mean to imply that the W motif is conserved amongst all PIPs.

      Most PIPs interact with the globular PP1 catalytic core through short linear interaction motifs (SLiMs). Choy et al (PNAS 2014) previously showed that many PIPs interact with PP1 through a conserved trio of SLiMs, RVxF-ΦΦ-R, which is also present in the Phactrs.

      Previous structural analysis showed that the PPP1R15A/B, Neurabin/Spinophilin (PPP1R9A/B), and PNUTS (PPP1R10) PIPs share a trajectory across the PP1 surface that encompasses not only the RVxF-ΦΦ-R SLIMs, but also additional sequences C-terminal to the R SLIM (Chen et al, eLife, 2015). This trajectory is also shared by the Phactr1-PP1 complex (Fedoryshchak et al, eLife, 2020). Based on this structural alignment we proposed the existence of an additional hydrophobic “W” SLiM that interacts with the PP1 residues I133 and Y134 (See Fedoryshchak et al, 2020, Figure 1 figure supplement 2).

      Introduction, paragraph 2 is rewritten to make this clearer.

      The sequence and positions of W differ in amino acid type and position relative to the RVxF-øø-R string.

      The motif ‘W’ does not mandate tryptophan, it is our name for a common structurally aligned motif: although the Phactrs and PPP1R15A/B indeed have W at this position, Neurabin and spinophilin contain VDP, which nevertheless makes similar interactions. Similarly the _“_RVxF” motifs in Phactr1, Neurabin/Spinophilin, PPP1R15A/B and PNUTS are LIRF, KIKF, KV(R/T)F and TVTW respectively.

      In the Discussion the authors state that the hydrophobic groove of PP1 is remodelled by Neurabin. However, details of this are not described or shown in the manuscript.

      The shared trajectory determined by the RVxF-øø-R-W string brings the sequences C-terminal to the W SLIM into the vicinity of the PP1 hydrophobic groove. In the Phactr1/PP1 holoenzyme this generates a novel pocket required for substrate recognition (Fedoryshchak et al, 2020). These observations raised the possibility that sequences C-terminal to the “W” motif in the other RVxF-øø-R-W PIPs also play a role in substrate recognition.

      Introduction paragraph 3 now cites a new Figure 1-S2, which shows how the hydrophobic groove is remodelled in the various different PIP/PP1 complexes. A revised Figure 1A now indicates the hydrophobic residues defining the hydrophobic groove by grey shading.

      (2) To add to the confidence of the structure, the authors should include a 2Fo-Fc simulated annealing omit map, perhaps showing the R and W interactions of the RVxF-øø-R-W string.

      This is now included as new Figure 6 Figure supplement 1. Note that in Neurabin, the W motif is VDP, where the valine and proline sidechains interact similarly to the tryptophan (see also new Figure 1-S2G,H).

      We also add a new supplementary Figure 6-S1 comparing our PBM-liganded Neurabin PDZ domain with the previously published unliganded structure (Ragusa et al 2010).

      (3) Page 16. The authors state that spinophilin remodels the PP1 hydrophobic groove differently from Phactrs. Arguably spinophilin does not remodel the PP1 hydrophobic groove at all. There are no contacts between spinophilin and the PP1 hydrophobic groove in the spinophilin-PP1 structure, correlating with the absence of 'W" in the RVxF-øø-R-W string in spinophilin.

      The VDP sequence corresponding to the W motif in spinophilin and neurabin makes analogous contacts to those made by the W in Phactr1 (see Fedoryshchak et al 2020).

      Remodelling is meant in the sense of altering the structure of the major groove by bringing new sequences into its vicinity rather than necessarily directly interacting with it. The spinophilin/PP1 and Phactr/PP1 hydrophobic grooves are compared in new Figure 1-S2 (see also Fedoryshchak et al 2020, Figure 2 figure supplement 1)

      (4) Page 8. For the cell-based/proteomics-dephosphorylation assay in Figure 2, it isn't clear why there were no dephosphorylation sites detected for the PPP1R15A/B-PP1 fusion (except PPP6R1 S531 for PPP1R15B). One might have expected a correlation with PP1 alone. Does this imply that PPP1R15A/B are inhibiting PP1 catalytic activity? Was the activity tested in vitro?

      The R15A/B data are compared to average abundance of all the phosphosites in the dataset, including those of PP1.

      We have not tested for a general inhibitory effect of R15A/B on PP1 activity. Many PIPs including R15A/B do occlude one or more of the PP1 substrate groove and therefore generally act as inhibitors of PP1 activity against some potential substrates, while enhancing activities against others.

      Other points 

      (4) Figure S1: Colour sequence similarities/identities.

      Done

      (6) Figures: Structure figures lacked labels:

      Figure 1A, label PP1, Phactrs etc.

      Done

      Figure 6, label PP1, Neurabin, previous Neurabin structure (Fig. 6C), hydrophobic groove, PDZ domain, etc.

      Done

      (7) Statistical analysis. p values should be shown for data in:

      Figure 5.

      To avoid cluttering the Figure, a new sheet, “statistical significance” has been added to Supplementary Table 3, summarizing the analysis.

      Figure 1.

      Figure amended (now figure 1-S1).

      (8) Some inconsistency with labels, eg '34-WT' used in Fig. 5C, whereas '34A-WT' (better) in Methods.

      Now changed to 34A etc where used.

      (9) Page 6. PPP1R9A/B is not shown in Figure 1A and Figure S1A.

      PPP1R9A/B are Neurabin and spinophilin - now clarified in Introduction paragraph 2, Results paragraph 1, Discussion paragraph 1.

      (10) Page 7: lines 4, 'site' not 'side'.

      Done

      (11) Page 9: DTL and CAMSAP3 were found to be dephosphorylated in the PP1-Neurabin/spinophilin screen. Are these PDZ-binding proteins?

      Neither DTL nor CAMSAP3 contain C-terminal hydrophobic residues characteristic of classical PBMs. Sentence added in Discussion, paragraph 5

      (12) Page 12 and Figure 5 and S5: The synthetic p4E-BP1 and IRSp53WT peptides with PBM should be given more specific names to indicate the presence of the PBM.

      We have renamed 4E-BP1<sup>WT</sup> and IRSp53<sup>WT</sup> to 4E-BP1<sup>PBM</sup> and  IRSp53<sup>PBM</sup> respectively, emphasising the inclusion of the wildtype or mutated PBM from 4E-BP1 on these peptides.

      Text, Figure 5, and Figure S5 all revised accordingly.

      (13) Give PDB code for spinophilin-PP1 complex coordinates shown in Figure 6C.

      PDB codes for the various PIP/PP1 complexes now given in new Figure 1-S2 and revised Figure 6C.

      Reviewer #2 (Recommendations for the authors):

      The work undertaken by the authors is extensive and robust, however, I believe that some improvement in the writing and some detailed explanation of certain results sections would help with the presentation of the work and clarity for the readers.

      (1) The introduction should contain more information about the interaction between PP1 and Neurabin, given that this is the focus of the paper. This would give the reader the necessary background required to follow the paper.

      Introduction paragraph 2 revised to describe the different SLIMs in more detail. New Figure 1-S2 shows detail of the different remodelled hydrophobic grooves in the various PIP/PP1 complexes.

      (2) More information on PP1-IRSp53L460A has to be added before discussing results in S1B.

      Sentence explaining that IRSp53 L460 docks with the remodelled PP1 hydrophobic groove in the Phactr1/PP1 holoenzyme added in Results paragraph 2.

      (3) Page 6: "as expected, the +5 residue L460A mutation, which impairs dephosphorylation by the intact Phactr1/PP1 holoenzyme, impaired sensitivity to all the fusions, indicating that they recognise phosphorylated IRSp53 in a similar way (Figure S1B)". Statistics between IRSp53 and IRSp53L460A across PP1-PIPs need to be conducted before concluding the above. From the graph and the images, the impairment to dephosphorylation is not convincing.

      For each of the four PP1-Phactr fusions, the IRSp53 L460A peptide shows significantly less reactivity than the IRSp53WT peptide (p<0.05 for each fusion).

      Since the proteomics studes in Figure 2 show that the substrate specificity of the four PP1-Phactr1 fusions is virtually identical, we combined the data for the four different fusions. The IRSp53 L460A peptide shows significantly less reactivity than the IRSp53WT peptide in this analysis (p< 0.0001). This result shown in revised Figure S1B and legend.

      (4) mCherry-4E-BP1(118+A), in which an additional C-terminal alanine should still allow TOSmediated phosphorylation, but prevent PDZ interaction. Does 4EBP1 (118+A) actually prevent interaction between PP1-Neurabin? This interaction needs to be validated, especially since spinophilin was shown to bind to multiple regions of PP1.

      It is not clear what the referee is asking for here. The biochemical analysis in Figure 4C shows that the C-terminus of 4E-BP1 constitutes a classical PBM. The X-ray crystallography in Figure 6 confirms this, demonstrating H-bond interactions between the 4E-BP1 C-terminal carboxylate and main chain amides of L514, G515 and I516.

      We consider the possibility that the 4E-BP1(118+A) mutant inhibits the activity of PP1-neurabin via a mechanism other than direct blocking 4E-BP1 / PDZ interaction to be unlikely for the following reasons:

      (1) Addition of a C-terminal alanine will disrupt the PBM interaction because the extra residue sterically blocks access to the PBM-binding groove. This is the most parsimonious explanation, and is based on our solid structural and biochemical evidence that the 4E-BP1 C-terminus is a classical PBM.

      (2) Alphafold3 modelling predicts Neurabin PDZ / 4E-BP1 PBM interaction with high confidence (shown in Figure 6-S2E), but it does not predict any PDZ interaction with 4E-BP1(118+A). Note added in Figure 6-S2 legend.

      (3) Recognition of the 4E-BP1(118+A) mutation without loss of binding affinity would require that the mutant becapable of binding formally equivalent to recognition of an “internal” PDZ-binding peptide. Recognition of such “internal peptides” is dependent on their adopting a specifically constrained conformation, which typically requires reorganisation of the PDZ carboxylate-binding GLGF loop. Such “internal site” recognition typically involves more than one residue C-terminal to the conventional PDZ “0” position (see Penkert et al NSMB 2004, doi:10.1038/nsmb839; Gee et al JBC 1998, DOI: 10.1074/jbc.273.34.21980; Hillier et al 1999, Science PMID: 10221915).

      (5) It is nice to see that the various PP1-Phactr fusions have around 60% substrate overlap between them. Would it be possible to compare these results with previously published mass spec data of Phactr1XXX from the group? There is mention of some substrates being picked up, but a comparison much like in Figure 2E would be more informative about the extent to which the described method captures relevant information.

      This is difficult to do directly as the PP1-Phactr fusion data are from human cells while that in Fedoryshchak et al 2020 is from mouse.

      However, manual curation shows that of the 28 top hits seen in our previous analysis of Phactr1XXX in NIH3T3 cells, 18 were also detectable in the HEK293 system; of these, 13 were also detected as as PP1-Phactr fusion hits. Data summarised in new Figure 2-S1C. Text amended in Results, “Proteomic analysis...”, paragraph 2.

      (6) Figure 3D Why are the levels of pT70, pT37/46 and total protein in vector controls much lower as compared to 0nM Tet in PP1-Neurabin conditions? It is also weird that given total protein is so low, why are the pS65/101 levels high compared to the rest?

      We think it likely these phenomena reflect a low level expression of PP1-Neurabin expression in uninduced cells. Now noted in Figure 3D legend, basal PP1-Neurabin expression shown in new Figure 3-S1C. This alters the relative levels of the different species detected by the total 4E-BP1 antibody in favour of the faster migrating forms, which are less phosphorylated than the slower ones, and the total amount increases about 2-fold (Figure 3D, compare 0nM Tet lanes).

      The altered p65/101-pT70 ratio is also likely to reflect the leaky PP1-Neurabin expression, since the relative intensities of the various phosphorylated species are dependent on both the relative rates of phosphorylation and dephosphorylation. Expression of a phosphatase would therefore be expected to differentially affect the phosphorlyation levels of different sites according to their reactivity.

      (7) Figure 3E: Does inhibiting mTORC further reduce translation when PP1-Neurabin is expressed? If this is the case, this might suggest that they might not necessarily be mTORC inhibitors?

      We have not done this experiment. Since Rapamycin cannot be guaranteed to completely block 4E-BP1 phosphorylation, and PP1-Neurabin cannot be guaranteed to completely dephosphorylate 4E-BP1, any further reduction upon their combination would be hard to interpret.

      (8) Substrate interactions with the remodelled PP1 hydrophobic groove do not affect PP1-Neurabin specificity. Is there evidence that PP1-Neurabin remodels the hydrophobic groove? Is it not possible that Neurabin does not remodel the PP1 groove to begin with and hence there is no effect observed with the various mutants? If this is not the case, it should be explained in a bit more detail.

      Comparison of the Neurabin/PP1 and Phactr1/PP1 structures shows that the hydrophobic groove is remodelled differently in the two complexes. Now shown in new Figure 1-S2B,C,G.

      (9) Figure 5B has a lot of interesting information, which I believe has not been discussed at all in the results section.

      To help interpretation of the enzymology in Figure 5 we have renamed 4E-BP1WT and IRSp53WT to 4E-BP1PBM and IRSp53PBM respectively, emphasising the inclusion of the wildtype or mutated PBM from 4E-BP1 on these peptides. Text in Results, “PDZ domain interaction…”, paragraph 1, and Figures 5 and S5 revised accordingly.

      Why does the 4E-BP1Mut affect catalytic efficiency of PP1 alone when compared with WT, while no difference is observed with IRSp53WT and mutant?

      We do not understand the basis for the differential reactivity of 4E-BP1PBM and 4E-BP1MUT with PP1 alone; we suspect that it reflects the hydrophobicity change resulting from the MDI -> SGS substitution. However this is unlikely to be biologically significant as PP1 is sequestered in PIP-PP1 complexes.

      Importantly, the two PP1 fusion proteins behave consistently in this assay – the presence of the intact PBM increases reactivity with PP1-Neurabin, but has no effect on dephosphorylation by PP1-Phactr1.

      Why does PP1 alone not have a difference between IRSp53WT and mutant, while PP1-Neurabin does have a difference?

      This is due to the presence of the PBM in IRSp53WT (now renamed IRSp53PBM), which affects increases affinity for PP1 Neurabin, but not PP1 alone. Likewise, PP1-Phactr1, which does not possess a PDZ domain, is also unaffected by the integrity of the PBM.

      (7) “Strikingly, alanine substitutions at +1 and +2 in 4E-BP1WT increased catalytic efficiency by both fusions, perhaps reflecting changes at the catalytic site itself (Figure 5E, Figure S5E)”. This could be expanded upon, because this suggests a mechanism that makes the substrate refractory to PDZ/hydrophobic groove remodelling?

      We favour the idea that this reflects a requirement to balance dephosphorylation rates between the multiple 4E-BP1 phosphorylation sites, especially if multiple rounds of dephosphorylation occur for each PBM—PDZ interaction. Additional sentences added in Discussion paragraph 7.

      (8) Typographical errors and minor comments:

      a) PIPs can target PP1 to specific subcellular locations, and control substrate specificity through autonomous substrate-binding domains, occupation or extension of the substrate grooves, or modification of PP1 surface electrostatics.

      b) Phosphophorylation side site abundances within triplicate samples from the same cell line were comparable between replicates (Figure 2B).

      c) While the alanine substitutions had little effect, conversion of +4 to +6 to the IRSp534E-BP1 sequence LLD increased catalytic efficiency some 20-fold (Figure 5C, Figure S5C). 

      d) Figure 3E labels are not clear. The graph can be widened to make the labels of the conditions clearer.

      All corrected

      Reviewer #3 (Recommendations for the authors):

      This was a very well-written manuscript.

      However, I was looking for a summary mechanistic figure or cartoon to help me navigate the results.

      I noted a few typos in the text.

      New summary Figure 5-S2 added, cited in results, and discussed in Discussion paragraph 6,7.

    1. eLife assessment

      This study offers a useful discussion of the well-accepted abundance-occupancy relationship in macroecology. While using the ebird large dataset to revisit the theme is interesting, multiple unresolved confounding factors exist, leaving the results inadequate to overturn the repeatedly confirmed abundancy-occupancy relationship.

    2. Reviewer #1 (Public review):

      Summary:

      This article presents an analysis that challenges established abundance-occupancy relationships (AORs) by utilizing the largest known bird observation database. The analysis yields contentious outcomes, raising the question of whether these findings could potentially refute AORs.

      Strengths:

      The study employed an extensive aggregation of datasets to date to scrutinize the abundance-occupancy relationships (AORs).

      Weaknesses:

      The authors should thoroughly address the correlation between checklist data and global range data, ensuring that the foundational assumptions and potential confounding factors are explicitly examined and articulated within the study's context.

      In the revision, the authors have refined their findings to birds and provided additional clarifications and discussion. However, the primary concerns raised by reviewers remain inadequately addressed. My main concern continues to be whether testing AOR at a global scale is meaningful given the numerous confounding factors involved. With the current data and analytical approach, these confounders appear inseparable. The study would be significantly strengthened if the authors identified specific conditions under which AORs are valid.

    3. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      This article presents a meta-analysis that challenges established abundance-occupancy relationships (AORs) by utilizing the largest known bird observation database. The analysis yields contentious outcomes, raising the question of whether these findings could potentially refute AORs.

      We thank the Reviewer for their positive comments.

      Strengths:

      The study employed an extensive aggregation of datasets to date to scrutinize the abundance-occupancy relationships (AORs).

      We thank the Reviewer for their positive comments.

      Weaknesses:

      While the dataset employed in this research holds promise, a rigorous justification of the core assumptions underpinning the analytical framework is inadequate. The authors should thoroughly address the correlation between checklist data and global range data, ensuring that the foundational assumptions and potential confounding factors are explicitly examined and articulated within the study's context.

      We thank the Reviewer for these comments. We agree that more justification and transparency is needed of the core assumptions that form the foundation of our methods. In our revised version, we have taken the following steps to achieve this:

      - Altered the title to be more explicit about the core assumptions, which now reads: “Local-scale relative abundance is decoupled from global range size”

      - We have added more details on why and how we treat global range size as a measure of ‘occupancy.’

      - We have added a section that discusses the limitations of using eBird relative abundance

      Reviewer #2 (Public Review):

      Summary:

      The goal is to ask if common species when studied across their range tend to have larger ranges in total. To do this the authors examined a very large citizen science database which gives estimates of numbers, and correlated that with the total range size, available from Birdlife. The average correlation is positive but close to zero, and the distribution around zero is also narrow, leading to the conclusion that, even if applicable in some cases, there is no evidence for consistent trends in one or other direction.

      We thank the Reviewer for these comments.

      Strengths:

      The study raises a dormant question, with a large dataset.

      We thank the Reviewer for these comments. We intended to take a longstanding question and attempt to apply novel datasets that were not available mere decades ago. While we do not imply that we have ‘solved’ the question, we hope this work highlights the potential for further interrogation using these large datasets.

      Weaknesses:

      This study combines information from across the whole world, with many different habitats, taxa, and observations, which surely leads to a quite heterogeneous collection.

      We agree that there is a heterogeneous collection of data across many habitats, taxa, and observations. However, rather than as a weakness, we see this as a significant strength. Our work assumes we are averaging over this variability to assess for a large-scale pattern in the relationship - something that was potentially a limitation of previous work, as these large datasets were often focused on particular contexts (e.g., much work focused solely on the UK), which we believe could limit some of the generalizability of the previous work. However, the reviewer makes a fair point in regard to the heterogeneity of data collection. We have now added some text in the discussion which is explicit about this - see the new section named “Potential limitations of current work and future work –-although our findings challenge some long-held assumptions about the consistency of the abundance-occupancy relationship, our work only deals with interspecific AORs among birds, synthesizing observations of potentially heterogeneous locations, context and quality”.

      First, scale. Many of the earlier analyses were within smaller areas, and for example, ranges are not obviously bounded by a physical barrier. I assume this study is only looking at breeding ranges; that should be stated, as 40% of all bird species migrate, and winter limitation of populations is important. Also are abundances only breeding abundances or are they measured through the year? Are alien distributions removed?

      Second, consider various reasons why abundance and range size may be correlated (sometimes positively and sometimes negatively) at large scales. Combining studies across such a large diversity of ecological situations seems to create many possibilities to miss interesting patterns. For example:

      (1) Islands are small and often show density release.

      See comment below.

      (2) North temperate regions have large ranges (Rapoport's rule) and higher population sizes than the tropics.

      See comment below.

      (3) Body size correlates with global range size (I am unsure if this has recently been tested but is present in older papers) and with density. For example, cosmopolitan species (barn owl, osprey, peregrine) are relatively large and relatively rare.

      See comment below.

      (4) In the consideration of alien species, it certainly looks to me as if the law is followed, with pigeon, starling, and sparrow both common and widely distributed. I guess one needs to make some sort of statement about anthropogenic influences, given the dramatic changes in both populations and environments over the past 50 years.

      See comment below. We also added a sentence in the methods that highlighted we did not remove alien ranges and provided reasons why. Still, we do acknowledge the dramatic changes in populations and environments over the past 50 years (see the new section  “Potential limitations of current work and futur work”)

      (5) Wing shape correlates with ecological niche and range size (e.g. White, American Naturalist). Aerial foraging species with pointed wings are likely to be easily detected, and several have large ranges reflecting dispersal (e.g. barn swallow).

      We agree that all of the points above are interesting data explorations. As said above, our main purpose was to highlight the potential for further interrogation using these large datasets. However, we have added some additional text in the discussion that explicitly mentions/encourages these additional data explorations. We hope people will pick up on the potential for these data and explore them further.

      Third, biases. I am not conversant with ebird methodology, but the number appearing on checklists seems a very poor estimate of local abundance. As noted in the paper, common species may be underestimated in their abundance. Flocking species must generate large numbers, skulking species few. The survey is often likely to be in areas favorable to some species and not others. The alternative approach in the paper comes from an earlier study, based on ebird but then creating densities within grids and surely comes with similar issues.

      We agree that if we were interested in the absolute abundance of a given species, the local number on an eBird checklist would be a poor representation. However, our study aims not to estimate absolute abundance but to examine relative abundance among species on each checklist. By focusing on relative abundance, we leverage eBird data's strengths in detecting the presence and frequency of species across diverse locations and times, thereby capturing community composition trends that can provide meaningful insights despite individual checklist biases. This approach allows us to assess the comparative prominence of species in the community as reported by the observer, providing a consistent metric of relative abundance. Despite detectability biases, the structure of eBird checklists reflects the observer’s encounter rates with each species under similar conditions, offering a valuable snapshot of relative species composition across sites and times. The key to our assumption is that these biases discussed are not directional and, therefore, random throughout the sampling process, which would translate to no ‘real’ bias in our effect size of interest.

      Range biases are also present. Notably, tropical mountain-occupying species have range sizes overestimated because holes in the range are not generally accounted for (Ocampo-Peñuela et al., Nature Communications). These species are often quite rare, too.

      We thanks the reviewer for pointing to this issue and reference. We included a discussion on these biases in our limitations section and reference Ocampo-Peñuela et al. to emphasize the need for improved spatial resolution in range data for more accurate AOR assessments.”More precise range-size estimates would also improve the accuracy of AOR assessments, since species range data are often overestimated due to the failure to capture gaps in actual distributions ”

      Fourth, random error. Random error in ebird assessments is likely to be large, with differences among observers, seasons, days, and weather (e.g. Callaghan et al. 2021, PNAS). Range sizes also come with many errors, which is why occupancy is usually seen as the more appropriate measure.

      If we consider both range and abundance measurements to be subject to random error in any one species list, then the removal of all these errors will surely increase the correlation for that list (the covariance shouldn't change but the variances will decrease). I think (but am not sure) that this will affect the mean correlation because more of the positive correlations appear 'real' given the overall mean is positive. It will definitely affect the variance of the correlations; the low variance is one of the main points in the paper. A high variance would point to the operation of multiple mechanisms, some perhaps producing negative correlations (Blackburn et al. 2006).

      We agree random errors can affect estimates, but as we wrote above, random errors, regardless of magnitudes, would not bias estimates. After accounting for sampling error (a part of random errors), little variance is left to be explained as we have shown in the MS. This suggests that many of the random errors were part of the sampling errors. And this is where meta-analysis really shines.

      On P.80 it is stated: "Specifically, we can quantify how AOR will change in relation to increases in species richness and sampling duration, both of which are predicted to reduce the magnitude of AORs" I haven't checked the references that make this statement, but intuitively the opposite is expected? More species and longer durations should both increase the accuracy of the estimate, so removing them introduces more error? Perhaps dividing by an uncertain estimate introduces more error anyway. At any rate, the authors should explain the quoted statement in this paper.

      It would be of considerable interest to look at the extreme negative and extreme positive correlations: do they make any biological sense?

      Extremely high correlations would not make any biological sense if these observations were based on large sample sizes. However, as shown in Figure 2, all extreme correlations come from small sample sizes (i.e., low precision), as sampling theory expects (actually our Fig 2 a text-book example of the funnel shape). Therefore, we do not need to invoke any biological explanations here.

      Discussion:

      I can see how publication bias can affect meta-analyses (addressed in the Gaston et al. 2006 paper) but less easily see how confirmation bias can. It seems to me that some of the points made above must explain the difference between this study and Blackburn et al. 2006's strong result.

      We agree. Now, we extended an explanation of why confirmation bias could result in positive AOR. Yet, we point out confirmation bias is a very common phenomena which we cite relevant citations in the original MS. The only way to avoid confirmation bias is to conduct a study blind but this is not often possible in ecological work.

      “Meta-research on behavioural ecology identified 79 studies on nestmate recognition, 23 of which were conducted blind. Non-blind studies confirmed a hypothesis of no aggression towards nestmates nearly three times more often. It is possible that confirmation bias was at play in earlier AOR studies.”

      Certainly, AOR really does seem to be present in at least some cases (e.g. British breeding birds) and a discussion of individual cases would be valuable. Previous studies have also noted that there are at least some negative and some non-significant associations, and understanding the underlying causes is of great interest (e.g. Kotiaho et al. Biology Letters).

      We agree. And yes, we pointed out these in our introduction.

      Reviewer #3 (Public Review):

      Summary:

      This paper claims to overturn the longstanding abundance occupancy relationship.

      Strengths:

      (1) The above would be important if true.

      (2) The dataset is large.

      We have clarified this point by changing the title to emphasize that we do not suggest overturning AORs entirely but instead provide a refined view of the relationship at a global scale. Our results suggest a weaker and more context-dependent AOR than previously documented. We hope our revised title and additional clarifications in the text convey our intent to contribute to a more nuanced understanding rather than a whole overturning of the AOR framework.

      Weaknesses:

      (1) The authors are not really measuring the abundance-occupancy relationship (AOR). They are measuring abundance-range size. The AOR typically measures patches in a metapopulation, i.e. at a local scale. Range size is not an interchangeable notion with local occupancy.

      We have refined this in our revision to be more explicitly focused on global range size. However, we note that the classic paper by Bock and Richlefs (1983, Am Nat) also refers to global (species entire) range size in the context of the AOR. Importantly, Bock and Richlefs pointed out the importance of using species’ entire ranges; without such uses, there will be sampling artifacts creating positive AORs when using arbitrary geographical ranges, which were used in some studies of AORs. So we highlight that our work is well in line with the previous work, allowing us to question the longstanding macroecological work. One of the issues of AOR has been how to define occupancy and global range size, which provides a relatively ambiguous measure, which is why we used this measure.

      (2) Ebird is a poor dataset for this. The sampling unit is non-standard. So abundance can at best be estimated by controlling for sampling effort. Comparisons across space are also likely to be highly heterogenous. They also threw out checklists in which abundances were too high to be estimated (reported as "X"). As evidence of the biases in using eBird for this pattern, the North American Breeding Bird Survey, a very similar taxonomic and geographic scope but with a consistent sampling protocol across space does show clear support for the AOR.

      Yes, we agree the sampling unit is non-standard. However, this is a significant strength in that it samples across much heterogeneity (as discussed in response to Reviewer 2, above). We were interested in relative abundance and not direct absolute abundance per se, which is accurate, especially since we did control for sampling effort.

      We appreciate the reviewer’s attention to our data selection criteria. We excluded checklists containing ‘X’ entries to minimize biases in our abundance estimates. The 'X' notation is often used for the most common species, reflecting the observer's identification of presence without specifying a count. This approach was chosen to avoid disproportionately inflating presence data for these abundant species, which could distort the relative abundance calculations in our analysis. By excluding such checklists, we aimed to retain consistency and ensure that local abundance estimates were representative across all species on each checklist. We have revised our manuscript to clarify this methodological choice and hope this explanation addresses the reviewer’s concern. We modified our text in the methods to make the entries ‘X’ clearer (see the Method section).

      (3) In general, I wonder if a pattern demonstrated in thousands of data sets can be overturned by findings in one data set. It may be a big dataset but any biases in the dataset are repeated across all of those observations.

      Overturning a major conclusion requires careful work. This paper did not rise to this level.

      We appreciate the reviewer’s caution regarding broad conclusions based on a single dataset, even one as large as eBird. Our intention was not to definitively overturn the abundance-occupancy relationship (AOR) but to re-evaluate it with the most extensive and globally representative dataset currently available. We recognise that potential biases in citizen science data, such as observer variation, may influence our findings, and we have taken steps to address these in our methodology and limitations sections. We see this work as a contribution to an ongoing discourse, suggesting that AOR may be less universally consistent than previously believed, mainly when tested with large-scale citizen science data. We hope this study will encourage additional research that tests AORs using other expansive datasets and approaches, further refining our understanding of this classic macroecological relationship. However, we have left our broad message about instigating credible revolution and also re-examining ecological laws.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) The investigation focuses solely on interspecific relationships among birds; thus, the extrapolation of these conclusions to broader ecological contexts requires further validation.

      We have now added this point to our new section: “Although our findings challenge some long-held assumptions about the consistency of the abundance-occupancy relationship, our work only deals with interspecific AORs among birds, so we hope this work serves as a foundation for further investigations that utilize such comprehensive datasets.”

      (2) The rationale for combining data from eBird - a platform predominantly representing individual observations from urban North America - with the more globally comprehensive BirdLife International database needs to be substantiated. The potential underrepresentation of global abundance in the eBird checklist data could introduce a sampling bias, undermining the foundational premises of AORs.

      We agree with the limitation of ebird sampling coverage, but it should not bias our results. In statistical definitions, bias is directional, and if not directional, it will become statistical noise, making it difficult to detect the signal. In fact, our meta-analyses adjust what statisticians call sampling bias and it is the strength of meta-analysis.

      (3) In the full mixed-effect model, checklist duration and sampling variance (inversely proportional to sample size N) are treated as fixed effects. However, these variables are likely to be negatively correlated, which could introduce multicollinearity, inflating standard errors and diminishing the statistical significance of other factors, such as the intercept. This calls into question the interpretation of insignificance in the results.

      Multicollinearity is an issue with sample sizes. For example, with small datasets, correlations of 0.5 could be an issue, and such an issue would usually show up as a large SE. We do not have such an issue with ~ 17 million data points. Please refer to this paper.

      Freckleton, Robert P. "Dealing with collinearity in behavioural and ecological data: model averaging and the problems of measurement error." Behavioral Ecology and Sociobiology 65 (2011): 91-101.

      (4) The observed low heterogeneity may stem from discrepancies in sampling for abundance versus occupancy, compounded by uncertainties in reporting behavior.

      If we assume everybody underreports common species or overreports rare species, this could happen. However, such an assumption is unlikely. If some people report accurately (but not others), we should see high heterogeneity, which we do not observe).  We have touched upon this point in our original MS.

      (5) The contribution and implementation of phylogenetic comparative analysis remain ambiguous and were not sufficiently clarified within the study.

      We need to add more explanation for the global abundance analysis

      “To statistically test whether there was an effect of abundance and occupancy at the macro-scale, we used phylogenetic comparative analysis.  This analysis also addresses the issue of positive interspecific AORs potentially arising from not accounting for phylogenetic relatedness among species examined ”

      (6) The use of large N checklists could skew the perceived rarity or commonality of species, potentially diminishing the positive correlation observed in AORs. A consistent observer effect could lead to a near-zero effect with high precision.

      Regardless of the number of N species in checklists (seen in Fig 2), correlations are distributed around zero. This means there is nothing special about large N checklists. 

      (7) The study should acknowledge and discuss any discrepancies or deviations from previous literature or expected outcomes.

      We felt we had already done this as we discussed the previous meta-analysis and what we expected from this meta-analysis.  Nevertheless, we have added some relevant sentences in the new version of MS.

      In addition to these major points, there are several minor concerns:

      (1) Figure 2B lacks discussion, and the metric for the number of observations is not clarified. Furthermore, the labeling of the y-axis appears to be incorrect.

      Thank you very much for pointing out this shortcoming. Now, the y-axis label has been fixed and we mention 2B in the main text.

      (2) The study should provide a clear, mathematical expression of the multilevel random effect models for greater transparency.

      Many thanks for this point, and now we have added relevant mathematical expressions in Table S6.

      (3) On Line 260, the term "number of species" should be refined to "number of species in a checklist," ideally represented by a formula for precision.

      This ambiguity has been mended as suggested.

      Please provide the data and R code linked to the outputs.

      The referee must have missed the link (https://github.com/itchyshin/AORs) in our original MS. In addition to our GitHub repository link, we now have added a link to our Zenodo repository (https://doi.org/10.5281/zenodo.14019900).

      Reviewer #3 (Recommendations For The Authors):

      The authors cite Rabinowitz's 7 forms of rarity paper as a suggestion that previous findings also break the AOR. In fact empirical studies of the 7 forms of rarity typically find that all three forms of rareness vs commonness are heavily correlated (e.g. Yu & Dobson 2000).

      We thank the reviewer for drawing attention to Yu & Dobson (2000) and similar studies that find positive correlations among the axes of rarity. Ref 3 is correct in that Rabinowitz’s (1981) framework does not require that local abundance and geographic range size be uncorrelated for every species; instead, it highlights conceptual scenarios where a species may be common locally yet have a restricted distribution (or vice versa).

      Empirical analyses such as Yu & Dobson (2000) show that, on average, these axes can be correlated, which may align with conventional AOR findings in some taxonomic groups. However, Rabinowitz’s key insight was that exceptions do occur, so these exceptions demonstrate that strong positive AORs may not be universally applicable. Our results do not claim that Rabinowitz’s framework “breaks” the AOR outright; instead, we use it to underscore that local abundance can, in principle, be “decoupled” from global occupancy.  Whether the correlation found by Yu & Dobson (2000) implies a positive AOR, requires a detailed simulation study, which is an interesting avenue for future research. 

      Thus, citing Rabinowitz serves to highlight the potential heterogeneity and complexity of abundance–occupancy relationships rather than to refute every positive correlation reported in the literature. Our findings suggest that when examined at large spatiotemporal scales (with unbiased sampling), the overall AOR signal may be less robust than traditionally believed. This is consistent with Rabinowitz’s view that local abundance and global range can vary along independent axes. Now we added

      “Although studies using her framework found positive correlations between species range and local abundance.”

    1. eLife Assessment

      This important theoretical study shows that active hexatic topological defects in epithelia play a crucial role in enabling collective cell flows. While the use of coarse-grained hydrodynamic models to describe cell-scale behavior has limitations, the study provides solid evidence supporting its claims. These findings will interest both biophysicists studying collective cell behaviors and biologists investigating epithelial flows during development.

    2. Reviewer #1 (Public review):

      Summary:

      This paper investigates the physical mechanisms underlying cell intercalation, which then enables collective cell flows in confluent epithelia. The authors show that T1 transitions (the topological transitions responsible for cell intercalation) correspond to the unbinding of groups of hexatic topological defects. Defect unbinding, and hence cell intercalation and collective cell flows, are possible when active stresses in the tissue are extensile. This result helps to rationalize the observation that many epithelial cell layers have been found to exhibit extensile active nematic behavior.

      Strengths:

      The authors obtain their results based on a combination of active hexanematic hydrodynamics and a multiphase field (MPF) model for epithelial layers, whose connection is a strength of the paper. With the hydrodynamic approach, the authors find the active flow fields produced around hexatic topological defects, which can drive defect unbinding. Using the MPF simulations, the authors show that T1 transitions tend to localize close to hexatic topological defects.

      Weaknesses:

      Citations are sometimes not comprehensive. Cases of contractile behavior found in collective cell flows, which would seemingly contradict some of the authors' conclusions, are not discussed.

      I encourage the authors to address the comments and questions below.

      (1) In Equation 1, what do the authors mean by the cluster's size \ell? How is this quantity defined? The calculations in the Methods suggest that \ell indicates the distance between the p-atic defects and the center of the T1 cell cluster, but this is not clearly defined.

      (2) The multiphase field model was developed and reviewed already, before the Loewe et al. 2020 paper that the authors cite. Earlier papers include Camley et al. PNAS 2014, Palmieri et al. Sci. Rep. 2015, Mueller et al. PRL 2019, and Peyret et al. Biophys. J. 2019, as reviewed in Alert and Trepat. Annu. Rev. Condens. Matter Phys. 2020.

      (3) At what time lag is the mean-squared displacement in Figure 3f calculated? How does the choice of a lag time affect these data and the resulting conclusions?

      (4) The authors argue that their results provide an explanation for the extensile behavior of cell layers. However, there are also examples of contractile behavior, such as in Duclos et al., Nat. Phys., 2017 and in Pérez-González et al., Nat. Phys., 2019. In both cases, collective cell flows were observed, which in principle require cell intercalations. How would these observations be rationalized with the theory proposed in this paper? Can these experiments and the theory be reconciled?

    3. Reviewer #2 (Public review):

      Summary:

      This paper studies the role of hexatic defects in the collective migration of epithelia. The authors emphasize that epithelial migration is driven by cell intercalation events and not just isolated T1 events, and analyze this through the lens of hexatic topological defects. Finally, the authors study the effect of active and passive forces on the dynamics of hexatic defects using analytical results, and numerical results in both continuum and phase-field models.

      The results are very interesting and highlight new ways of studying epithelial cell migration through the analysis of the binding and unbinding of hexatic defects.

      Strengths:

      (1) The authors convincingly argue that intercalation events are responsible for collective cell migration, and that these events are accompanied by the formation and unbinding of hexatic topological defects.

      (2) The authors clearly explain the dynamics of hexatic defects during T1 transitions, and demonstrate the importance of active and passive forces during cell migration.

      (3) The paper thoroughly studies the T1 transition through the viewpoint of hexatic defects. A continuum model approach to study T1 transitions in cell layers is novel and can lead to valuable new insights.

      Weaknesses:

      (1) The authors could expand on the dynamics of existing hexatic defects during epithelial cell migration, in addition to how they are created during T1 transitions.

      (2) The different terms in the MPF model used to study cell layer dynamics are not fully justified. In particular, it is not clear why the model includes self-propulsion and rotational diffusion in addition to nematic and hexatic stresses, and how these quantities are related to each other.

      (3) The authors could provide some physical intuition on what an active extensile or contractile term in the hexatic order parameter means, and how this is related to extensility and contractility in active nematics and/or for cell layers.

    4. Reviewer #3 (Public review):

      Summary:

      In this manuscript, the authors discuss epithelial tissue fluidity from a theoretical perspective. They focus on the description of topological transitions whereby cells change neighbors (T1 transitions). They explain how such transitions can be described by following the fate of hexatic defects. They first focus on a single T1 transition and the surrounding cells using a hydrodynamic model of active hexatics. They show that successful T1 intercalations, which promote tissue fluidity, require a sufficiently large extensile hexatic activity in the neighborhood of the cells attempting a T1 transition. If such activity is contractile or not sufficiently extensile, the T1 is reversed, hexatic defects annihilate, and the epithelial network configuration is unchanged. They then describe a large epithelium, using a phase field model to describe cells. They show a correlation between T1 events and hexatic defects unbinding, and identify two populations of T1 cells: one performing T1 cycles (failed T1), and not contributing to tissue migration, and one performing T1 intercalation (successful T1) and leading to the collective cell migration.

      Strengths:

      The manuscript is scientifically sound, and the variety of numerical and analytical tools they use is impressive. The approach and results are very interesting and highlight the relevance of hexatic order parameters and their defects in describing tissue dynamics.

      Weaknesses:

      (1) Goal and message of the paper.

      a) In my opinion, the article is mainly theoretical and should be presented as such. For instance, their conclusions and the consequences of their analysis in terms of biology are not extremely convincing, although they would be sufficient for a theory paper oriented to physicists or biophysicists. The choice of journal and potential readership should be considered, and I am wondering whether the paper structure should be re-organized, in order to have side-by-side the methods and the results, for instance (see also below).

      b) Currently, the two main results sections are somewhat disconnected, because they use different numerical models, and because the second section only marginally uses the results from the first section to identify/distinguish T1 (see also below).

      (2) Quite surprisingly, the authors use a cell-based model to describe the macroscopic tissue-scale behavior, and a hydrodynamic model to describe the cell-based events. In particular, their hydrodynamic description (the active hexatic model) is supposed to be a coarse-grained description, valid to capture the mesoscopic physics, and yet, they use it to describe cell-scale events (T1 transitions). For instance, what is the meaning of the velocity field they are discussing in Figure 2? This makes me question the validity of the results of their first part.

      (3) The quality of the numerical results presented in the second part (phase field model) could be improved.

      a) In terms of analysis of the defects. It seems that they have all the tools to compare their cell-resolved simulations and their predictions about how a T1 event translates into defects unbinding. However, their analysis in Figure 3e is relatively minimal: it shows a correlation between T1 cells and defects. But it says nothing about the structure and evolution of the defects, which, according to their first section, should be quite precise. I believe it should be possible to identify and quantify more precisely the unbinding or annihilation of the defects and hence to characterize more precisely the T1 events.

      b) In terms of clarity of the presentation. For instance, in Figure 3f, they plot the mean-square displacement as a function of a defect density. I thought that MSD was a time-dependent quantity: they must therefore consider MSD at a given time, or averaged over time (in that case, what they are showing is rather an effective diffusivity). They should, in any case, be explicit about what their definition of this quantity is.

      c) In terms of statistics. For instance, Figure 3g is used to study the role of rotational diffusion on the average time between T1s. The error bars in this figure are huge and make their claims hardly supported. It is, for instance, hard to believe that the dynamics of T1 cycles are unaffected by D_r. In the limit where D_r vanishes, for instance, there should be no T1 and the period of a T1 cycle should diverge, which is not observed. Their claim of a "monotonic decay" of the average time between intercalations is also not fully supported given their statistics.

    1. eLife Assessment

      This important study addresses the question of how large-scale events such as the COVID-19 pandemic can change people's beliefs and their updates. Using a well-validated task, the authors find that belief updating becomes less optimistically biased during COVID-19 compared to before it. In this revision, due to the addition of more model-based analyses and power calculations, they have generated convincing evidence for their primary claim that the pandemic significantly impacted people's belief updating away from optimistic belief updating. As with many manipulations outside the experimenters' control, it remains unclear which psychological factor impacted by the pandemic drives the group differences, and sample sizes are, by necessity, on the smaller side as data cannot readily be acquired. However, the authors are commended for doing power analyses, showing their sensitivity, and recognizing the limitations of their study.

    2. Reviewer #1 (Public review):

      This manuscript uses a well-validated behavioural estimation task to investigate the degree to which optimistic belief updating was attenuated during the 2020 global pandemic. Online participants estimated how likely different negative life events were to happen to them in the future and were given statistics about these events. Belief updating (measured as the degree to which estimations changed after viewing the statistics) was less optimistically biased during the pandemic (compared to outside of it). This resulted from reduced updating from "good news" (better than expected information). Computational models were used to try to unpack how statistics were integrated and used to revise beliefs. Two families of models were compared - an RL set of models where "estimation errors" (analogous to prediction errors in classic RL models) predict belief change and a Bayesian set of models where an implied likelihood ratio was calculated (derived from participants estimations of their own risk and estimation of the base rate risk) and used to predict belief change. The authors found evidence that the former set of models accounted for updating better outside of the pandemic, but the latter accounted for updating during the pandemic. In addition, the RL model provides evidence that learning was asymmetrically positively biased outside of the pandemic but symmetric during it (as a result of reduced learning rates from good news estimation errors).

      Strengths

      Understanding whether biases in learning are fixed modes of information processing or flexible and adapt in response to environmental shocks (like a global pandemic or economic recession) is an important area of research relevant to a wide range of fields, including cognitive psychology, behavioural economics, and computational psychiatry. The study uses a well-validated task, and the authors conduct a power analysis to show that the sample sizes are appropriate. Furthermore, the authors test that their results hold in both a between-group analysis (the focus of the main paper) and a within-group analysis (mainly in the supplemental).

      The finding that optimistic biases are reduced in response to acute stress, perceived threat, and depression has been shown before using this task both in the lab (social stress manipulation), in the real world (firefighters on duty), and clinical groups (patients with depression). However, the work does extend these findings here in important ways:

      (1) Examining the effect of a new real-world adverse event (the pandemic).<br /> (2) The reduction in optimistic updating here arises due to reduced updating from positive information (previously, in the case of environmental threat, this reduction mainly arose from increased sensitivity to negative information).<br /> (3) Leveraging new RL-inspired computational approaches, demonstrating that the bias - and its attenuation - can be captured using trial-by-trial computational modelling with separate learning rates for positive and negative estimation errors.

      The authors now take great care to caveat that the findings cannot directly attribute the observed lack of optimistically biased belief updating during lockdown to psychological causes such as heightened anxiety and stress.

      The authors have added model recovery results. Whilst there are some cases within a family (RL or Bayesian) of models where they can be confused (e.g., Bayesian model 10-the winning model during the pandemic-sometimes gets confused with Bayesian model 9), there is no confusion between families of models (RL models don't get confused with Bayesian models and vice versa), which is reassuring.

      Weaknesses

      The authors now conduct model recovery (SI Figure 5) and show how the behaviour of the two best-fitting models (Rational Bayesian model and optimistically biased RL-like model) approximates the actual data observed by showing them alongside each other (Figure 1b). It seems from Figure 1b that the 2 models predict similar behaviour for bad news but diverge for good news, with the optimistically biased RL-like model predicting greater updates than the rational Bayesian model. However, it is difficult to tell from the figure (partly because of the y-axis scale) how much of a divergence this is and how distinctive a pattern relative to the other models. I think the interpretation could be improved further by a clearer sense of the behavioural signatures of each model, enabling them to be reliably teased apart from one another in the model recovery.

    3. Reviewer #2 (Public review):

      The authors investigated how experiencing the COVID-19 pandemic affected optimism bias in updating beliefs about the future. They ran a between-subjects design testing participants on cognitive tasks before, during and after the lift of the sanitary state of emergency during the pandemic. The authors show that optimism bias varied depending on the context in which it was tested. Namely, it disappeared during COVID-19 and it re-emerged at the time of lift of sanitary emergency measures. Via advanced computational modelling they are able to thoroughly characterise the nature of such alterations, pinpointing specific mechanisms underlying the lack of optimistic bias during the pandemic.

      Strengths pertain to the comprehensive assessment of the results via computational modelling, and from a theoretical point of view, the notion that environmental factors can affect cognition. Power analysis was conducted to ensure that the study was powered to observe the effect of interest despite the relatively small sample size.

      As the authors also noted, a major impediment to the interpreting the findings pertains to the lack of additional measures. While information on, for example, risk perception or need for social interaction were collected from participants during the pandemic, the fact that these could not be included in the analysis hindered the interpretation of findings. While the interpretation of the findings remains challenging, this work offers an example of the influence of real-life conditions on the belief-updating process.

    4. Author response:

      The following is the authors’ response to the original reviews

      Reviewer #1:

      Summary:

      This manuscript uses a well-validated behavioral estimation task to investigate how optimistic belief updating was attenuated during the 2020 global pandemic. Online participants recruited during and outside of the pandemic estimated how likely different negative life events were to happen to them in the future and were given statistics about these events happening. Belief updating (measured as the degree to which estimations changed after viewing the statistics) was less optimistically biased during the pandemic (compared to outside of it). This resulted from reduced updating from "good news" (better than expected information). Computational models were used to try to unpack how statistics were integrated and used to revise beliefs. Two families of models were compared - an RL set of models where "estimation errors" (analogous to prediction errors in classic RL models) predict belief change and a Bayesian set of models where an implied likelihood ratio was calculated (derived from participants estimations of their own risk and estimation of the base rate risk) and used to predict belief change. The authors found evidence that the former set of models accounted for updating better outside of the pandemic, but the latter accounted for updating during the pandemic. In addition, the RL model provides evidence that learning was asymmetrically positively biased outside of the pandemic but symmetric during it (as a result of reduced learning rates from good news estimation errors).

      Strengths:

      Understanding whether biases in learning are fixed modes of information processing or flexible and adapt in response to environmental shocks (like a global pandemic or economic recession) is an important area of research relevant to a wide range of fields, including cognitive psychology, behavioral economics, and computational psychiatry. The study uses a well-validated task, and the authors conduct a power analysis to show that the sample sizes are appropriate. Furthermore, the authors test that their results hold in both a between-group analysis (the focus of the main paper) and a within-group analysis (mainly in the supplemental).

      The finding that optimistic biases are reduced in response to acute stress, perceived threat, and depression has been shown before using this task both in the lab (social stress manipulation), in the real world (firefighters on duty), and clinical groups (patients with depression). However, the work does extend these findings here in important ways:

      (1) Examining the effect of a new real-world adverse event (the pandemic).<br /> (2) The reduction in optimistic updating here arises due to reduced updating from positive information (previously, in the case of environmental threat, this reduction mainly arose from increased sensitivity to negative information).<br /> (3) Leveraging new RL-inspired computational approaches, demonstrating that the bias - and its attenuation - can be captured using trial-by-trial computational modeling with separate learning rates for positive and negative estimation errors.

      Weaknesses:

      Some interpretation and analysis (the computational modeling in particular) could be improved.

      On the interpretation side, while the pandemic was an adverse experience and stressful for many people (including myself), the absence of any measures of stress/threat levels limits the conclusions one can draw. Past work that has used this task to examine belief updating in response to adverse environmental events took physiological (e.g., SCR, cortisol) and/or self-report (questionnaires) measures of mood. In SI Table 1, the authors possibly had some questionnaire measures along these lines, but this might be for the participants tested during the pandemic.

      Thank you for this review.

      We agree that the lack of physiological and self-report measures of stress, threat, and perceived uncertainty limits the interpretation of findings regarding potential psychological factors. Some self-reported anxiety and perceived risk measures experienced during the lockdowns were collected in a subset of participants (n=40, counting n=21 tested before and during the 1st strict lockdown, and n=19 tested solely during the 1st lockdown). These reports were given retrospectively at the time of release of the 1st lockdown in summer 2020 when the pandemic was still unfolding (SI Table 1).

      Exploratory correlations revealed some noteworthy trends. We found that participants who reported to have perceived a bigger risk of death due to contagion were also those who were less optimistically biased when updating their beliefs about adverse future life risks during the first strict COVID-19-related lockdown (Pearson’s r = -0.36, p = 0.02).

      Moreover, parameter estimates from the computational models of belief updating showed associations with specific survey responses: The rational Bayesian model’s scaling parameter correlated positively with adherence to distancing measures (r = 0.41, p = 0.01) and negatively with the need for social contact (r = -0.37, p = 0.02). This result indicated that participants who were updating their beliefs faster were more likely to follow preventive guidelines and felt less social craving. Meanwhile, the asymmetry parameter correlated negatively with mask wearing (r = -0.41, p = 0.01), positively with physical contact with close others (r = 0.32, p = 0.04) and satisfaction with social interactions (r = 0.33, p = 0.04). This suggests that participants who displayed some asymmetry in belief updating during the COVID-19 pandemic were less likely to comply with mask-wearing rules and more likely to engage in social interactions.

      However, these results did not survive correction for multiple comparisons and the sample size for correlational analyses is in the lower range. The subjective measures of anxiety and fear of contagion did not significantly correlate to the updating bias, or any other variable measured by the belief updating task (e.g. estimation error, updating magnitude).

      We now further discuss on page 12 the limitation, which reads:

      “We did not collect physiological measures of stress or information about the COVID-19 infection status of participants, which precludes a direct exploration of the immediate effects of experiencing the infection on belief-updating behavior and the potential interaction with anxiety and stress levels. Although subjective ratings of the perceived risk of death from COVID-19 correlated negatively to the beliefs updating bias measured during the pandemic, this result was obtained retrospectively in a subset of participants (SI section 4). We thus cannot directly attribute the observed lack of optimistically biased belief updating during the lockdown to psychological causes such as heightened anxiety and stress. This limitation is noteworthy, as the impact of experiencing the pandemic on belief updating about the future could differ between those who directly experienced infection and those who remained uninfected. It is also important to acknowledge that our study was timely and geographically limited to the context of the COVID-19 outbreak in France. Cultural variations and differences in governmental responses to contain the spread of SARS-CoV-2 may have impacted the optimism biases in belief updating differently.”

      On the analysis side, it was unclear what the motivation was for the different sets of models tested. Both families of models test asymmetric vs symmetric learning (which is the main question here) and have similar parameters (scaling and asymmetry parameters) to quantify these different aspects of the learning process. Conceptually, the different behavioral patterns one could expect from the two families of models needed to be clarified.

      Thank you for raising this point. We agree that a clearer conceptual distinction between the two model families can help strengthen the interpretation of our findings. We have added the following considerations to the introduction on pages 2–3, which now reads:

      “The underlying mechanism of optimistically biased belief updating involves an asymmetry in learning from positive and negative belief-disconfirming information[2,3,4], which can unfold in two ways following Reinforcement learning (RL) or Bayes rule[5].

      Conceptually, Reinforcement learning (RL) and Bayesian models of belief updating are complementary but make different assumptions about the hidden process humans may use to adjust their beliefs when faced with information that contradicts them. The RL models assume belief updating is proportional to the estimation error. The key idea of the estimation error expresses the difference between how much someone believes they will experience a future life event and the actual prevalence of the event in the general population. This difference can be positive or negative. A scaling and an asymmetry parameter quantify the propensity to consider the estimation error magnitude and its valence, respectively. These two free parameters form the learning rate, which indicates how fast and biased participants update their beliefs.

      In contrast, Bayesian models assume that following Bayes’ rule the posterior, updated belief is a new hypothesis, formed by pondering prior knowledge with new evidence. The prior knowledge consists in information about the prevalence of life events in the general population. The new evidence comprises various alternative hypotheses. It examines how likely a specific event is to occur or not occur for oneself, compared to the likelihood that it will happen or not happen to others. This probabilistic adjustment of beliefs about future life events can be considered as an approximation of a participant’s confidence in the future. The two free parameters of the Bayesian belief updating model scale how much the initial belief deviates from the updated, posterior belief (i.e., scaling parameter) and the propensity to consider the valence of this deviance (i.e., asymmetry parameter).

      Although RL-like and Bayesian updating models make different assumptions about the updating strategy, they are complementary and powerful formalizations of human reasoning. Both models provide insight into hidden, latent variables of the updating process. Most notably, the learning rate and its components, the scaling and asymmetry parameters, which can vary between individuals and contexts and, through this variance, offer possible explanations for the idiosyncrasy in belief-updating behavior and its cognitive biases. “

      Do the "winning" models produce the main behavioral patterns in Figure 1, and are they in some way uniquely able to do so, for instance? How would updating look different for an optimistic RL learner versus an optimistic Bayesian RL learner?

      We now show that the winning models can reproduce the main behavioral patterns (revised Figure 1b).

      Moreover, we plotted estimated and observed average belief updating for each participant (n=123) using the overall best-fitting asymmetrical RL-like updating model shown in SI Figure 6.

      Would the asymmetry parameter in the former be correlated with the asymmetry parameter in the latter? Moreover, crucially, would one be able to reliably distinguish the models from one another under the model estimation and selection criteria that the authors have used here (presenting robust model recovery could help to show this)?

      The asymmetry parameter estimated with the optimistically biased RL- and Bayesian models did correlate (r = 0.735; p < 0.001).

      However, we argue that while the observed updating behavior and estimated free parameters are similar for RL-like and Bayesian learners, the underlying assumed cognitive processes differed and are identifiable. To test this assumption, we have added a model recovery analysis now reported in the supplement section 2c and main manuscript’s methods section pages 24–25.

      As shown in SI Figure 5 confusion matrix, there is evidence for strong recovery of nearly all models, and importantly for the two winning models: the optimistically biased RL-like model and the rational Bayesian model of belief updating. This analysis thus rules out that the two model families were confused and mitigate concerns about the validity of the model selection.

      Note, one exception was observed. The RL-like and Bayesian updating models that assumed no scaling and asymmetry were best recovered by their respective models that estimated the asymmetry parameter. Many factors could explain this. For example, it could be that the models, which assumed asymmetry, but no scaling, may have captured some bias in updating due to noise generated by the zero parameter models.

      A justification is also needed to focus on the "RL-like updating model with an asymmetry and scaling learning rate component" in Figure 3. As I understand it, this model fits best outside of the pandemic, but another model - the Rational Bayesian Model - does worse (and does the best during the pandemic). What model best combines the groups (outside and inside the pandemic)?

      We thank the reviewer for highlighting the need to justify our focus on the biased RL-like updating model in Figure 3. The model chosen for parameter comparison was selected based on a model comparison procedure conducted across all 12 models, including data from all participants (both those tested outside and during the pandemic, n=123). This model comparison revealed that Model 1 — the RL model with both asymmetry and scaling learning rate parameters estimated — provided the best fit across the entire dataset (Ef = 0.40, pxp = 0.99). As such, we focused on this model for parameter comparisons in Figure 3 to ensure consistency with the model comparison results and to interpret the parameters in the context of the overall best-fitting model. We added this information on top of the model parameter comparison results on page 8. Moreover, SI Figure 6 in the supplements shows how this model reproduces the observed belief updating in each of the 123 participants.

      Why do the authors use absolute belief updating (|UPD|) in the first linear mixed effects model (equation iv)? Since an update is calculated differently depending on whether information calls for an update in an upward or downward direction, I do not understand the need to do this (and it means that updates that go in the wrong direction - away from the information - are counted as positive)

      Thank you for driving our attention to this point. The ‘absolute belief updating’ note was incorrect, and we apologize for the confusion. To be precise, we did not use absolute updating values in our analyses. Belief updating was assumed on each trial to go either toward the base rate (e.g., Update = E2 – E1) for negative estimation errors or away from it for positive estimation errors (e.g., Update = E1 – E2). Updates that went in the wrong direction, further away from the base rate, were thus counted and included in the analysis with their negative sign. We have corrected this important point in equation iv of the methods section on page 19.

      Figure 4: The task schema does not show a confidence rating for base rates.

      Thank you for catching this. We have now added the confidence ratings for base rates to the task in Figure 4b in the revised version of the manuscript. We have furthermore corrected a typo in Figure 4a: The sample size for the group 3 tested in Mai 2021 now indicates 31.

      The authors report that base rates are uniformly distributed - this is quite different to other instances of the task where base rates are normally distributed (ideally around the midpoint of the scale). Why this deviation in the design?

      We used life events and base rates like those used in past studies of belief updating (Garrett and Sharot 2017, Sharot et al. 2011, Garrett et al. 2017, Korn et al. 2017), which were normal to uniformly distributed (W = 0.952, p = 0.088, Shapiro-Wilk test). The base rates ranged between 10% and 70%, with a mean of 40%. Participants rated their estimates between 3% and 77%, which ensured that for most likely (base rate = 70%) and most unlikely events (base rate = 10%) there was the same space (7%) to update beliefs toward the base rates. Moreover, all statistical models included the absolute estimation errors as a control for variance potentially explained by different estimation error magnitude[42,43]. We added this extra base rate information to the methods section’s task description on page 16.

      The task is comprised of only negative life events, which arguably this hinders the generalizability of the results. The authors could mention this as a limitation (there has been a significant quantity of debate about this point in relation to this task: see the work from Ulrike Hahn's lab).

      We have added a paragraph to the discussion page 13 to provide a rationale for using only adverse events. This paragraph now reads:

      “In this study we tested how actual adverse experiences affect the updating of negative future outlooks in healthy participants and in analogy to studies conducted in depressed patients[19,20,24] following the cognitive model of depression[37]. One open question is whether findings were specific to the adverse event framing[38,39,40]. We argue that under normal, non-adverse contexts belief updating should also be optimistically biased for positive life events, as shown by previous research[41,42]. However, how context such as experiencing a challenging or favorable situation influence the updating of beliefs about positive and negative outlooks remains an open question.”

      It would be useful to show the parameter recovery for all parameters (not just the learning rates) and the correlation between parameters (both in simulations and in the fitted parameters).

      We apologize for being unclear on this part. The models included two free parameters that were the components of the learning rates: The scaling and the asymmetry parameter. We now have added parameter recovery analyses for the scaling and asymmetry components of the learning rates for (1) the Bayesian model of belief updating during the pandemic, and (2) the RL-like model of belief updating outside the pandemic to the supplement (SI section 2b, SI Figure 4).

      Reviewer #2:

      The authors investigated how experiencing the COVID-19 pandemic affected optimism bias in updating beliefs about the future. They ran a between-subjects design testing for participants on cognitive tasks before, during, and after lifting the sanitary state of emergence during the pandemic. The authors show that optimism bias varied depending on the context in which it was tested. Namely, it disappeared during COVID-19 and re-emerged at the time of lift of sanitary emergency measures. Through advanced computational modeling, they are able to thoroughly characterize the nature of such alternations, pinpointing specific mechanisms underlying the lack of optimistic bias during the pandemic.

      Strengths pertain to the comprehensive assessment of the results via computational modeling and from a theoretical point of view to the notion that environmental factors can affect cognition. However, the relatively small sample size for each group is a limitation.

      Thank you for this review.

      We acknowledge that sample sizes in each group are lower, especially when breaking down the participant sample into four sub-samples tested in the different contexts. To mitigate concerns we checked the power of the observed context by valence interaction on belief updating. To this aim we simulated new belief updates using the parameters from the best fitting optimistic RL-like model of observed belief updating outside the pandemic, and the rational Bayesian model of observed belief updating during the pandemic. At each iteration we performed a linear mixed effects model analysis of the simulated belief updates[44] analogous to equation iv in the main text. The frequency across 1000 iterations with which the LMEs detected a significant interaction of valence by context on simulated belief updating was 75 %. This frequency indicates the power of the valence by context interaction on observed belief updating. In other words, false negatives were 25% likely, which meant type II errors of failing to reject the null hypothesis when the effect was there. We have added these extra analyses to the main manuscript’s results section page 4 and method’s section page 20.

      A major impediment interpreting of the findings is the need for additional measures. While the information on for example, risk perception or the need for social interaction was collected from participants during the pandemic, the fact that these could not be included in the analysis hinders the interpretation of findings, which is now generally based on data collected during the pandemic, for example, reporting increased stress. While authors suggest an interpretation in terms of uncertainty of real-life conditions it is currently difficult to know if that factor drove the effect. Many concurrent elements might have accounted for the findings. This limits understanding of the underlying mechanisms related to changes in optimism bias.

      We agree with the reviewer on the limitation arising from the lack of physiological and self-report measures of stress, threat, and perceived uncertainty. To address this point and a similar point raised by reviewer 1 we have added a section to the supplement (SI section 4) that now reports explorative correlations between questionnaire responses of subjective perceptions of risk and anxiety, behavior (e.g. mask wearing, social distancing) and belief updating measured during the 1st strict lockdown.

      We now also further discuss this limitation on page 12 of the main text’s discussion.

      I recommend that the authors spend more time on explaining the belief-updating task in the presentation of the experiment.

      Thank you for this advice. We now provide a clearer and more detailed description of the belief-updating task in the main manuscript’s methods section and have updated Figure 4b to display the confidence rating event in the task schema.

      The task description now reads:

      “As illustrated in Figure 4b, each of the 40 trials began with presenting an adverse life event. Participants estimated their own risk and the risk of someone else their age and gender. Then the base rate of the event occurring in the general population was displayed on the computer screen. Participants rated their confidence in the accuracy of the presented base rate. Finally, they re-estimated their risk for experiencing the event now informed by the base rate.”

      The experimental task seems to include a self-other dimension, which is completely disregarded in the analysis. It would be interesting to explore whether the effect of diluted optimism bias during the pandemic is specific to information about self vs. Other.

      We appreciate the reviewer's observation regarding the self-versus-other dimension in the belief updating task design. As now shown in SI Figure 2 the participants indeed displayed an optimism bias: They estimated that adverse events are more likely to happen to others than to themselves (ß = 3.02, SE = 0.86, t (232) = 3.53, p = 5.09e-04, 95% CI [1.33 – 4.71]; SI Figure 2; SI Table 18). This effect was observed overall participants. The pandemic context had no significant effect (ß = -1.91, SE = 3.00, t (232) = -0.64, p = 0.52, 95% CI [-7.82 – 4.00]; SI Table 18). Moreover, following previous studies of optimistically biased belief updating we tested the effect of estimation errors (EE) calculated on the difference between the estimate for someone else (eBR) and the base rate (BR), following: EE = eBR – BR[4,5,25,26]. When categorizing trials as good news or bad news based on this alternative EE calculation the context-by-EE valence interaction remained significant (SI Table 6).

      We conclude from these additional analyses that experiencing the pandemic specifically influenced belief updating but did not affect optimism biases in initial beliefs about the future.

      Please provide an English translation of the instructions for the task.

      We now provide an English translation of the task instructions in the Supplement section 5.

    1. eLife Assessment

      Jung et al. present valuable work on the relationship between gamma-aminobutyric acid (GABA) levels within the anterior temporal lobes (ATL) to semantic memory while accounting for inter-individual differences. They provide solid evidence suggesting that inhibitory continuous theta burst transcranial magnetic stimulation (cTBS TMS) increased GABA concentration and decreased the blood-oxygen dependent signal (BOLD) during a semantic task. The results will be of interest to researchers studying the neurobiology of semantic cognition.

    2. Reviewer #1 (Public review):

      This study presents valuable findings on the GABA and BOLD changes induced by continuous theta burst stimulation (cTBS) and on the relationships between ATL GABA level and performance in a semantic task. However, I'm afraid that the current results are incomplete to support some primary claims of the paper, for example, the purported inverted-U-shaped relationship between GABA levels in the ATL and semantic task performance. The influence of practice effects also complicates the interpretation of the results. Additional concerns include potential double dipping in the analysis depicted in Figure 3A and the use of inconsistent behavioral measures (IE and accuracy) across various analyses.

      The authors have made two beneficial revisions in this round: (1) acknowledging the insufficient data points supporting the inverted U-shaped curve; (2) attempting to control for practice effects. However, I believe unresolved issues remain:

      (1) The authors have not addressed my specific concern about Figure 4D - the analysis attempts to fit an inverted U-shaped curve to the data without distinguishing between data points influenced by practice effects and those unaffected, rendering its reliability questionable.

      (2) The authors appear to have misunderstood my question regarding Figure 3A. This issue is unrelated to practice effects. My point was that even if we randomly generated pre- and post-test data points and grouped/analyzed them according to the authors' methodology, we would still likely reproduce the pattern in Figure 3A due to the double dipping problem. Thus, this statistical analysis and its conclusions currently lack methodological validity.

      (3) Regarding the inconsistency in behavioral measures, the authors' explanation fails to remove my concerns. If the authors argue that accuracy is the most appropriate behavioral dependent variable for this study, why did they employ inverse efficiency in some of their analyses? My understanding is that a study should either consistently use the single most suitable measure or report multiple measures while providing adequate discussion of inconsistent results.

    3. Reviewer #3 (Public review):

      As a result of a number of rounds of reviews and consultations between reviewers, Jung et al. present important work on the relationship between gamma-aminobutyric acid (GABA) levels within the anterior temporal lobes (ATL) to semantic memory while accounting for inter-individual differences. They provide solid evidence suggesting that inhibitory continuous theta burst transcranial magnetic stimulation (cTBS TMS) increased GABA concentration and decreased the blood-oxygen dependent signal (BOLD) during a semantic task.

      The authors fully addressed my comments from the first and second rounds of reviews, and I do not have additional concerns. I have, however, scaled down my short assessment, given the concerns of reviewers 1 and 2.

    4. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study examined the changes in ATL GABA levels induced by cTBS and its relationship with BOLD signal changes and performance in a semantic task. The findings suggest that the increase in ATL GABA levels induced by cTBS is associated with a decrease in BOLD signal. The relationship between ATL GABA levels and semantic task performance is nonlinear, and more specifically, the authors propose that the relationship is an inverted U-shaped relationship.

      Strengths:

      The findings of the research regarding the increase of GABA and decrease of BOLD caused by cTBS, as well as the correlation between the two, appear to be reliable. This should be valuable for understanding the biological effects of cTBS.

      Weakness:

      I am pleased to see the authors' feedback on my previous questions and suggestions, and I believe the additional data analysis they have added is helpful. Here are my reserved concerns and newly discovered issues.

      (1) Regarding the Inverted U-Shaped Curve In the revised manuscript, the authors have accepted some of my suggestions and conducted further analysis, which is now presented in Figure 3B. These results provide partial support for the authors' hypothesis. However, I still believe that the data from this study hardly convincingly support an inverted U-shaped distribution relationship.

      The authors stated in their response, "it is challenging to determine the optimal level of ATL GABA," but I think this is achievable. From Figures 4C and 4D, the ATL GABA levels corresponding to the peak of the inverted U-shaped curve fall between 85 and 90. In my understanding, this can be considered as the optimal level of ATL GABA estimated based on the existing data and the inverted U-shaped curve relationship. However, in the latter half of the inverted U-shaped curve, there are quite few data points, and such a small number of data points hardly provides reliable support for the quantitative relationship in the latter half of the curve. I suggest that the authors should at least explicitly acknowledge this and be cautious in drawing conclusions. I also suggest that the authors consider fitting the data with more types of non-linear relationships, such as a ceiling effect (a combination of a slope and a horizontal line), or a logarithmic curve.

      We appreciate R1’s comments. Inverted U-shaped relationships are well-established in neuroscience, particularly in the context of neurotransmitter concentrations (e.g., dopamine, acetylcholine, noradrenaline) and their influence on cognitive functions such as working memory and cognitive control (Aston-Jones & Cohen., 2005; Cools & D'Esposito., 2011; Vijayraghavan et al., 2007; He & Zempel., 2013). Recently, Ferri et al. (2017) demonstrated an inverted U-shaped relationship between excitation-inhibition balance (EIB: the ratio of Glx and GABA) and multisensory integration, showing that both excessive and insufficient inhibition negatively impact functionality. Given that GABA is the brain’s primary inhibitory neurotransmitter, our findings suggest that ATL GABA may play a similar regulatory role in semantic memory function.

      While our statistical modelling approach demonstrated that the inverted U-shaped function was the best-fitting model for our current data in explaining the relationship between ATL GABA and semantic memory, we acknowledge the limitation of having fewer data points in the latter half (right side) of the curve, where excessive ATL GABA levels are associated with poorer semantic performance. Following R1’s suggestion, we have explicitly acknowledged this limitation in the revised manuscript and exercised caution in our discussion.

      Discussion, p.17, line 408

      "However, our findings should be interpreted with caution due to the limitation of having fewer data points in the latter half (right side) of the inverted U-shaped curve. Future studies incorporating GABA agonists could help further validate and refine these findings."

      Following R1’s latter suggestion, we tested a logarithmic curve model. The results showed significant relationships between ATL GABA and semantic performance (R<sup>2</sup> = 0.544, p < 0.001) and between cTBS-induced changes in ATL GABA and semantic performance (R<sup>2</sup> = 0.202, p < 0.001). However, the quadratic (inverted U-shaped) model explained more variance than the logarithmic model, as indicated by a higher R<sup>2</sup> and lower BIC. Model comparisons further confirmed that the inverted U-shaped model provided the best fit for both ATL GABA in relation to semantic performance (Fig. 4C) and cTBS-induced ATL GABA changes in relation to semantic function (Fig. 4D).

      Author response table 1.

      (2) In Figure 2F, the authors demonstrated a strong practice effect in this study, which to some extent offsets the decrease in behavioral performance caused by cTBS. Therefore, I recommend that the authors give sufficient consideration to the practice effect in the data analysis.

      One issue is the impact of the practice effect on the classification of responders and non-responders. Currently, most participants are classified as non-responders, suggesting that the majority of the population may not respond to the cTBS used in this study. This greatly challenges the generalizability of the experimental conclusions. However, the emergence of so many non-responders is likely due to the prominent practice effect, which offsets part of the experimental effect. If the practice effect is excluded, the number of responders may increase. The authors might estimate the practice effect based on the vertex simulation condition and reclassify participants after excluding the influence of the practice effect.

      Another issue is that considering the significant practice effect, the analysis in Figure 4D, which mixes pre- and post-test data, may not be reliable.

      We appreciate Reviewer 1’s thoughtful comments regarding the practice effect and its potential impact on our findings. Our previous analysis revealed a strong practice effect on reaction time (RT), with participants performing tasks faster in the POST session, regardless of task condition (Fig. S3). Given our hypothesis that inhibitory ATL cTBS would disrupt semantic task performance, we accounted for this by using inverse efficiency (IE), which combines accuracy and RT. This analysis demonstrated that ATL cTBS disrupted semantic task performance compared to both control stimulation (vertex) and control tasks, despite the practice effect (i.e., faster RT in the POST session), thereby supporting our hypothesis. These findings may suggest that the effects of ATL cTBS were more subtly reflected in semantic task accuracy rather than RT.

      Regarding inter-individual variability in response to rTMS/TBS, prior studies have shown that 50–70% of participants are non-responders, either do not respond or respond in an unexpected manner (Goldsworthy et al., 2014; Hamada et al., 2013; Hinder et al., 2014; Lopez-Alonso et al., 2014; Maeda et al., 2000a; Müller-Dahlhaus et al., 2008). Our previous study (Jung et al., 2022) using the same semantic task and cTBS protocol was the first to explore TBS-responsiveness variability in semantic memory, where 12 out of 20 participants (60%) were classified as responders. The proportion of responders and non-responders in the current study aligns with previous findings, suggesting that this variability is expected in TBS research.

      However, we acknowledge R1’s concern that the strong practice effect may have influenced responder classification. To address this, we estimated the practice effect using the vertex stimulation condition and reclassified participants accordingly by adjusting ATL stimulation performance (IE) relative to vertex stimulation performance (IE). This reclassification identified nine responders (an increase of two), aligning with the typical responder proportion (52%) reported in the TBS literature. Overall, we replicated the previous findings with improved statistical robustness.

      A 2×2×2 ANOVA was conducted with task (semantic vs. control) and session (PRE vs. POST) as within-subject factors, and group (responders vs. non-responders) as a between-subject factor. The analysis revealed a significant interaction between the session and group (F<sub>1, 15</sub> = 10.367, p = 0.006), a marginally significant interaction between the session and task (F<sub>1, 15</sub> = 4.370, p = 0.054), and a significant 3-way interaction between the session, task, and group (F<sub>1, 15</sub> = 7.580, p = 0.015). Post hoc t-tests showed a significant group difference in semantic task performance following ATL stimulation (t = 2.349, p = 0.033). Post hoc paired t-test demonstrated that responders exhibited poorer semantic task performance following the ATL cTBS (t = -5.281, p < 0.001), whereas non-responders showed a significant improvement (t = 3.206, p = 0.007) (see Figure. 3A).

      Notably, no differences were observed between responders and non-responders in the control task performance across pre- and post-stimulation sessions, confirming that the practice effect was successfully controlled (Figure. 3B).

      We performed a 2 x 2 ANOVA with session (pre vs. post) as a within subject factor and with group (responders vs. non-responders) as a between subject factor to examine the effects of group in ATL GABA levels. The results revealed a significant main effect of session (F<sub>1, 14</sub> = 39.906, p < 0.001) and group (F<sub>1, 14</sub> = 9.677, p = 0.008). Post hoc paired t-tests on ATL GABA levels showed a significant increase in regional ATL GABA levels following ATL stimulation for both responders (t = -3.885, p = 0.002) and non-responders (t = -4.831, p = 0.001). Furthermore, we replicated our previous finding that baseline GABA levels were significantly higher in responders compared to non-responders (t = 2.816, p = 0.007) (Figure. 3C). This pattern persisted in the post-stimulation session (t = 2.555, p = 0.011) (Figure. 3C).

      Accordingly, we have revised the Methods and Materials (p 26, line 619), Results (p11, line 233-261), and Figure 3.

      (3) The analysis in Figure 3A has a double dipping issue. Suppose we generate 100 pairs of random numbers as pre- and post-test scores, and then group the data based on whether the scores decrease or increase; the pre-test scores of the group with decreased scores will have a very high probability of being higher than those of the group with increased scores. Therefore, the findings in Figure 3A seem to be meaningless.

      Yes, we agreed with R1’s comments. However, Figure 3A illustrates interindividual responsiveness patterns, while Figure 3B demonstrates that these results account for practice effects, incorporating new analyses.

      (4) The authors use IE as a behavioral measure in some analyses and use accuracy in others. I recommend that the authors adopt a consistent behavioral measure.

      We appreciate Reviewer 1’s suggestion. In examining the relationship between ATL GABA and semantic task performance, we have found that only semantic accuracy—not reaction time (RT) or inverse efficiency (IE)—shows a significant positive correlation and regression with ATL GABA levels and semantic task-induced ATL activation, both in our previous study (Jung et al., 2017) and in the current study. ATL GABA levels were not correlated with semantic RT (Jung et al., 2017: r = 0.34, p = 0.14, current study: r = 0.26, p = 0.14). It should be noted that there were no significant correlations between ATL GABA levels and semantic inverse efficiency (IE) in both studies (Jung et al., 2017: r = 0.13, p = 0.62, current study: r = 0.22, p = 0.44). As a result, we found no significant linear and non-linear relationship between ATL GABA levels and RT (linear function R<sup>2</sup> = 0.21, p =0.45, quadratic function: R<sup>2</sup> = 0.17, p = 0.21) and between ATL GABA levels and IE (linear function R<sup>2</sup> = 0.24, p =0.07, quadratic function: R<sup>2</sup> = 2.24, p = 0.12).

      The absence of a meaningful relationship between ATL GABA and semantic RT or IE may be due to the following reasons: 1) RT is primarily associated with premotor and motor activation during semantic processing rather than ATL activation; 2) ATL GABA is likely to play a key role in refining distributed semantic representations through lateral inhibition, which sharpens the activated representation (Jung et al., 2017; Liu et al. 2011; Isaacson & Scanziani., 2011). This sharpening process may contribute to more accurate semantic performance (Jung et al., 2017). In our semantic task, for example, when encountering a camel (Fig. 1B), multiple semantic features (e.g., animal, brown, desert, sand, etc.) are activated. To correctly identify the most relevant concept (cactus), irrelevant associations (tree) must be suppressed—a process that likely relies on inhibitory mechanisms. Given this theoretical framework, we have used accuracy as the primary measure of semantic performance to elucidate the ATL GABA function.

      Reviewer #2 (Public review):

      Summary:

      The authors combined inhibitory neurostimulation (continuous theta-burst stimulation, cTBS) with subsequent MRI measurements to investigate the impact of inhibition of the left anterior temporal lobe (ATL) on task-related activity and performance during a semantic task and link stimulation-induced changes to the neurochemical level by including MR spectroscopy (MRS). cTBS effects in the ATL were compared with a control site in the vertex. The authors found that relative to stimulation of the vertex, cTBS significantly increased the local GABA concentration in the ATL. cTBS also decreased task-related semantic activity in the ATL and potentially delayed semantic task performance by hindering a practice effect from pre to post. Finally, pooled data with their previous MRS study suggest an inverted u-shape between GABA concentration and behavioral performance. These results help to better understand the neuromodulatory effects of non-invasive brain stimulation on task performance.

      Strengths:

      Multimodal assessment of neurostimulation effects on the behavioral, neurochemical, and neural levels. In particular, the link between GABA modulation and behavior is timely and potentially interesting.

      Weaknesses:

      The analyses are not sound. Some of the effects are very weak and not all conclusions are supported by the data since some of the comparisons are not justified. There is some redundancy with a previous paper by the same authors, so the novelty and contribution to the field are overall limited. A network approach might help here.

      Reviewer #3 (Public review):

      Summary:

      The authors used cTBS TMS, magnetic resonance spectroscopy (MRS), and functional magnetic resonance imaging (fMRI) as the main methods of investigation. Their data show that cTBS modulates GABA concentration and task-dependent BOLD in the ATL, whereby greater GABA increase following ATL cTBS showed greater reductions in BOLD changes in ATL. This effect was also reflected in the performance of the behavioural task response times, which did not subsume to practice effects after AL cTBS as opposed to the associated control site and control task. This is in line with their first hypothesis. The data further indicates that regional GABA concentrations in the ATL play a crucial role in semantic memory because individuals with higher (but not excessive) GABA concentrations in the ATLs performed better on the semantic task. This is in line with their second prediction. Finally, the authors conducted additional analyses to explore the mechanistic link between ATL inhibitory GABAergic action and semantic task performance. They show that this link is best captured by an inverted U-shaped function as a result of a quadratic linear regression model. Fitting this model to their data indicates that increasing GABA levels led to better task performance as long as they were not excessively low or excessively high. This was first tested as a relationship between GABA levels in the ATL and semantic task performance; then the same analyses were performed on the pre and post-cTBS TMS stimulation data, showing the same pattern. These results are in line with the conclusions of the authors.

      Comments on revisions:

      The authors have comprehensively addressed my comments from the first round of review, and I consider most of their answers and the steps they have taken satisfactorily. Their insights prompted me to reflect further on my own knowledge and thinking regarding the ATL function.

      I do, however, have an additional and hopefully constructive comment regarding the point made about the study focusing on the left instead of bilateral ATL. I appreciate the methodological complexities and the pragmatic reasons underlying this decision. Nevertheless, briefly incorporating the justification for this decision into the manuscript would have been beneficial for clarity and completeness. The presented argument follows an interesting logic; however, despite strong previous evidence supporting it, the approach remains based on an assumption. Given that the authors now provide the group-level fMRI results captured more comprehensively in Supplementary Figure 2, where the bilateral pattern of fMRI activation can be observed in the current data, the authors could have strengthened their argument by asserting that the activation related to the given semantic association task in this data was bilateral. This would imply that the TMS effects and associated changes in GABA should be similar for both sites. Furthermore, it is worth noting the approach taken by Pobric et al. (2007, PNAS), who stimulated a site located 10 mm posterior to the tip of the left temporal pole along the middle temporal gyrus (MTG) and not the bilateral ATL.

      We appreciate the reviewer’s constructive comment regarding the focus on the left ATL rather than bilateral ATL in our study. Accordingly, we have added the following paragraph in the Supplementary Information.

      “Justification of target site selection and cTBS effects

      Evidence suggests that bilateral ATL systems contribute to semantic representation (for a review, see Lambon Ralph., 2017). Consistent with this, our semantic task induced bilateral ATL activation (Fig. S2). Thus, stimulating both left and right ATL could provide a more comprehensive understanding of cTBS effects and its GABAergic function.

      Previous rTMS studies have applied inhibitory stimulation to the left vs. right ATL, demonstrating that stimulation at either site significantly disrupted semantic task performance (Pobric et al., 2007, PNAS; Pobric et al., 2010, Neuropsychologia; Lambon Ralph et al., 2009, Cerebral Cortex). Importantly, these studies reported no significant difference in rTMS effects between left and right ATL stimulation, suggesting that stimulating either hemisphere produces comparable effects on semantic processing. In the current study, we combined cTBS with multimodal imaging to investigate its effects on the ATL. Given our study design constraints (including the need for a control site, control task, and control stimulation) and limitations in scanning time, we selected the left ATL as the target region. This choice also aligned with the MRS voxel placement used in our previous study (Jung et al., 2017), allowing us to combine datasets and further investigate GABAergic function in the ATL. Accordingly, cTBS was applied to the peak coordinate of the left ventromedial ATL (MNI -36, -15, -30) as identified by previous fMRI studies (Binney et al., 2010; Visser et al., 2012).

      Given that TMS pulses typically penetrate 2–4 cm, we acknowledge the challenge of reaching deeper ventromedial ATL regions. However, our findings indicate that cTBS effectively modulated ATL function, as evidenced by reduced task-induced regional activity, increased ATL GABA concentrations, and poorer semantic performance, confirming that TMS pulses successfully influenced the target region. To further validate these effects, we conducted an ROI analysis centred on the ventromedial ATL (MNI -36, -15, -30), which revealed a significant reduction in ATL activity during semantic processing following ATL stimulation (t = -2.43, p = 0.014) (Fig. S7). This confirms that cTBS successfully modulated ATL activity at the intended target coordinate.”

      We appreciate R3's comment regarding the approach taken by Pobric et al. (2007, PNAS), who stimulated a site 10 mm posterior to the tip of the left temporal pole along the middle temporal gyrus (MTG). This approach has been explicitly discussed in our previous papers and reviews (e.g., Lambon Ralph, 2014, Proc. Royal Society B). Our earlier use of lateral ATL stimulation at this location (Pobric et al. 2007; Lambon Ralph et al. 2009; Pobric et al. 2010) was based on its alignment with the broader ATL region commonly atrophied in semantic dementia (cf. Binney et al., 2010 for a direct comparison of SD atrophy, fMRI data and the TMS region). Since these original ATL TMS investigations, a series of distortion-corrected or distortion-avoiding fMRI studies (e.g., Binney et al 2010; Visser et al, various, Hoffman et al., various; Jackson et al., 2015) have demonstrated graded activation differences across the ATL. While weaker activation is present at the original lateral ATL (MTG) stimulation site, the peak activation is maximal in the ventromedial ATL—a finding that was also observed in the current study. Accordingly, we selected the ventromedial ATL as our target site for stimulation.

      Following these points, we have revised the manuscript in the Methods and Materials.

      Transcranial magnetic stimulation p23, line 525-532,

      “Previous rTMS studies targeted a lateral ATL site 10 mm posterior to the temporal pole on the middle temporal gyrus (MTG) (Pobric et al. 2007; Lambon Ralph et al. 2009; Pobric et al. 2010), aligning with the broader ATL region typically atrophied in semantic dementia  (Binney et al. 2010). However, distortion-corrected fMRI studies (Binney et al. 2010; Visser et al. 2012) have revealed graded activation differences across the ATL, with peak activation in the ventromedial ATL. Based on these findings, we selected the target site in the left ATL (MNI -36, -15, -30) from a prior distortion-corrected fMRI study (Binney et al. 2010; Visser et al. 2012 that employed the same tasks as our study (for further details, see the Supplementary Information).”

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      The authors have responded to all my comments and I found most of the responses reasonable and sufficient. However, I have one remaining point: I pointed out before that the scope of this paper is somehow narrow and asked for a network analysis. I found the response to my question somehow puzzling since the authors write:

      "However, it is important to note that we did not find any significant correlations between ATL GABA changes and cTBS-induced changes in the functional connectivity. Consequently, we are currently preparing another paper that specifically addresses the network-level changes induced by ATL cTBS."

      I don't understand the logic here. Even in the absence of significant correlations between ATL GABA changes and cTBS-induced changes in connectivity, it would be interesting to know how baseline connectivity is correlated with the induced changes. I am not sure if it is adequate to squeeze another paper out of the dataset instead of reporting it here as suggested.

      We apologise that our previous response was not clear. To examine cTBS-induced network-level changes, we conducted ROI analyses targeting key semantic regions, including the bilateral ATL, inferior frontal gyrus (IFG), and posterior middle temporal gyrus (pMTG), as well as Psychophysiological Interactions (PPI) using the left ATL as a seed region. The ROI analysis revealed that ATL stimulation significantly decreased task-induced activity in the left ATL (target region) while increasing activity in the right ATL and left IFG. PPI analyses showed that ATL stimulation enhanced connectivity between the left ATL and the right ATL (both ventromedial and lateral ATL), bilateral IFG, and bilateral pMTG, suggesting that ATL stimulation modulates a bilateral semantic network.

      Building on these findings, we conducted Dynamic Causal Modeling (DCM) to estimate and infer interactions among predefined brain regions across different experimental conditions (Friston et al., 2003). The bilateral ventromedial ATL, lateral ATL, IFG, and pMTG were defined as network nodes with mutual connections. Our model examined cTBS effects at the left ATL under both baseline (intrinsic) and semantic task (modulatory) conditions, estimating 56 intrinsic parameters for baseline connectivity and testing 16 different modulatory models to assess cTBS-induced connectivity changes during semantic processing. Here, we briefly summarize the key DCM analysis results: 1) ATL cTBS significantly altered effective connectivity between the left and right lateral and ventromedial ATL in both intrinsic and modulatory conditions; 2) cTBS increased modulatory connectivity from the right to the left ATL compared to vertex stimulation.

      Given the complexity and depth of these findings, we believe that a dedicated paper focusing on the network-level effects of ATL cTBS is necessary to provide a more comprehensive and detailed analysis, which extends beyond the scope of the current study. It should be noted that no significant relationship was found between ATL GABA levels and ATL connectivity in both PPI and DCM analyses.

      Reviewer #3 (Recommendations for the authors):

      In response to my comment about the ATL activation being rather medial in the fMRI data and my concern about the TMS pulse perhaps not reaching this site, the authors offer an excellent solution to demonstrate TMS effects to such a medial ATL coordinate. I think that the analyses and figures they provide as a response to this comment and a brief explanation of this result should be incorporated into supplementary materials for methodologically oriented readers. Also, perhaps it would be beneficial to discuss that the effect of TMS on vATL remains a matter of further research to see not just if but also how TMS pulse reaches target coordinates, given the problematic anatomical location of the region.

      We appreciate R3’s suggestion. Please, see our reply above.

    1. eLife assessment

      Using an elegant and thorough experimental design, Thomazeau et al show that, in the developing mouse visual cortex, presynaptic NMDA receptors at layer 5 neocortical synapses mediate spike-timing dependent LTD via JNK2, non-ionotropic signaling. These fundamental findings shed light on how NMDA receptors can tune synaptic function without acting as coincidence detectors. The experiments are supported by compelling evidence, gathered through mouse transgenics and quadruple patch clamp recordings from cortical slices.

    2. Reviewer #1 (Public review):

      Summary:

      The results offer compelling evidence that L5-L5 tLTD depends on presynaptic NMDARs, a concept that has previously been somewhat controversial.

      It documents the novel finding that presynaptic NMDARs facilitate tLTD through their metabotropic signaling mechanism.

      Strengths:

      The experimental design is clever and clean.

      The approach of comparing the results in cell pairs where NMDA is deleted either presynaptically or postsynaptically is technically insightful and yields decisive data.

      The MK801 experiments are also compelling.

      Weaknesses:

      No major weaknesses were noted by this reviewer.

    3. Reviewer #2 (Public review):

      Summary:

      The study characterized the dependence of spike-timing-dependent long-term depression (tLTD) on presynaptic NMDA receptors and the intracellular cascade after NMDAR activation possibly involved in the observed decrease in glutamate probability release at L5-L5 synapses of the visual cortex in mouse brain slices.

      Strengths:

      The genetic and electrophysiological experiments are thorough. The experiments are well-reported and mainly support the conclusions. This study confirms and extends current knowledge by elucidating additional plasticity mechanisms at cortical synapses, complementing existing literature.

      Weaknesses:

      While one of the main conclusions (preNMDARs mediating presynaptic LTD) is resolved in a very convincing genetic approach, the second main conclusion of the manuscript (non-ionotropic preNMDARs) relies on the use of a high concentration of extracellular blockers (MK801, 2 mM; 7-clorokinurenic acid: 100 microM), but no controls for the specific actions of these compounds are shown. In addition, no direct testing for ions passing through preNMDAR has been performed.

      It is not known if the results can be extrapolated to adult brain as the data were obtained from 11-18 days-old mice slices, a period during which synapses are still maturing and the cortex is highly plastic.

    4. Reviewer #3 (Public review):

      Summary:

      In this manuscript, "Neocortical Layer-5 tLTD Relies on Non-Ionotropic Presynaptic NMDA Receptor Signaling", Thomazeau et al. seek to determine the role of presynaptic NMDA receptors and the mechanism by which they mediate expression of frequency-independent timing-dependent long-term depression (tLTD) between layer-5 (L5) pyramidal cells (PCs) in the developing mouse visual cortex. By utilizing sophisticated methods, including sparse Cre-dependent deletion of GluN1 subunit via neonatal iCre-encoding viral injection, in vitro quadruple patch clamp recordings, and pharmacological interventions, the authors elegantly show that L5 PC->PC tLTD is (1) dependent on presynaptic NMDA receptors, (2) mediated by non-ionotropic NMDA receptor signaling, and (3) is reliant on JNK2/Syntaxin-1a (STX1a) interaction (but not RIM1αβ) in the presynaptic neuron. The study elegantly and pointedly addresses a long-standing conundrum regarding the lack of frequency dependence of tLTD.

      Strengths:

      The authors did a commendable job presenting a very polished piece of work with high-quality data that this Reviewer feels enthusiastic about. The manuscript has several notable strengths. Firstly, the methodological approach used in the study is highly sophisticated and technically challenging and successfully produced high-quality data that were easily accessible to a broader audience. Secondly, the pharmacological interventions used in the study targeted specific players and their mechanistic roles, unveiling the mechanism in question step-by-step. Lastly, the manuscript is written in a well-organized manner that is easy to follow. Overall, the study provides a series of compelling evidence that leads to a clear illustration of mechanistic understanding.

      I have a couple of small items below, which the authors can address in a minor revision if they so wish.

      Minor comments:

      (1) For the broad readership, a brief description of JNK2-mediated signaling cascade underlying tLTD, including its intersection with CB1 receptor signaling may be desired.

      (2) The authors used juvenile mice, P11 to P18 of age. It is a typical age range used for plasticity experiments, but it is also true that this age range spans before and after eye-opening in mice (~P13) and is a few days before the onset of the classical critical period for ocular dominance plasticity in the visual cortex. Given the mechanistic novelty reported in the study, can authors comment on whether this signaling pathway may be age-dependent?

    1. eLife Assessment

      This study offers valuable insights into the role of post-translational modifiers, specifically SUMO2ylation at K81 in p66Shc, and its impact on endothelial function through reactive oxygen species. A series of compelling experiments demonstrated that lysine 81 of p66Shc is the site of SUMO2 conjugation, which is crucial for mitochondrial localization and essential for S36 phosphorylation, leading to specific pathological effects. The combination of cell overexpression and animal studies provides solid data supporting this mechanistic link.

    2. Reviewer #1 (Public review):

      Summary:

      The authors describe a role of sumoylation at K81 in p66Shc which affects endothelial dysfunction. This explores a new mechanism for understanding the role of PTMs in cellular processes.

      Strengths:

      The experiments are well planned and the results are well represented.<br /> Vascular tonality experiments were carried out nicely, given the amount of time and effort one needs to put in to get clean results from these experiments.

      Weaknesses:

      (1) The production of ROS has been measured in a very superficial way.<br /> The term "ROS" confers a plethora of chemical species which exerts different physiological effects on different cells and situations.<br /> Mitochondria through one of the source , but not the only source of ROS production. Only measuring ROS with mitosox do not reflect the cellular condition of ROS in a specific condition. I would suggest authors consider doing IF of oxidative stress specific markers , carbonyl group and also, maybe, Amplex red for determining average oxidative stress and ros production in the cells.<br /> (2) 8-OHG signal seems very confusing in Figure 7E. 8-ohg is supposed to be mainly in the nucleus and to some extent in mitochondria. The signal is very diffused in the images. I would suggest a higher magnification and better resolution images for 8-ohg. Also, the VWF signal is pretty weak whereas it should be strong given the staining is in aorta. Authors should redo the experiments.<br /> (3) PCA analysis is quite not clear. Why is there a convergence among the plots? Authors should explain. Also, I would suggest that the authors do the analysis done in Figure 8B again with R based packages. IPA, though being user-friendly, mostly does not yield meaningful results and the statistics carried out is not accurate. Authors should redo the analysis in R or Python whichever is suitable for them.<br /> (4) The MS analysis part seems pretty vague in methods. Please rewrite.

    3. Reviewer #2 (Public review):

      Summary:

      The article builds on the earlier work that both p66Shc and SUMOylation are essential nitric oxide (NO) based development of endothelial vasculature (PMID: 10580504; 28760777 and 35187108). The current manuscript brings forward a finding of how SUMO2ylation of p66Shc mediated ROS production which is essential for endothelial cells. They further identify that lysine 81 of p66Shc is the residue which is conjugated to SUMO2 and is crucial for mitochondrial localization. They further show that K81 SUMO2ylation is essential for S36 phosphorylation.

      Strengths:

      Convincingly shows that p66Shc is SUMO2ylated on lysine 81 in cells and also shows that the phosphorylation (serine 36) reduces upon loss of this critical SUMOylation site.

      Weaknesses:

      All the experiments performed here are in overexpression background therefore, it would be crucial to show that p66Shc is SUMO2ylated at physiological levels.

    4. Reviewer #3 (Public review):

      Summary:

      The authors set out to determine how SUMO2 impairs endothelial function through direct modification of the protein p66Shc. p66Shc is known to promote reactive oxygen species production, and here the authors demonstrate that SUMO2 modifies p66Shc at lysine-81, resulting in increased phosphorylation, mitochondrial translocation. These are prosed to mediate the detrimental effects of SUMO2 in a mouse model of hyperlipidemia.

      Strengths:

      A major strength of this work is the multi-pronged approach combining biochemical assays, proteomic analyses, and a genetically modified mouse model expressing a SUMOylation resistant mutant of p66Shc. These experiments comprehensively illustrate that lysine-81 SUMOylation of p66Shc is necessary for the observed endothelial dysfunction in hyperlipidemic conditions.

      Weaknesses:

      One notable weakness is that the link between the observed cellular changes and the ultimate in vivo phenotype remains only partially explored. While the authors successfully show that p66ShcK81R knockin mice are protected from endothelial dysfunction in a hyperlipidemic context, additional experiments characterizing the broader tissue-specific roles, or examining further endothelial assays in vivo, would strengthen the mechanistic conclusions. It would also be beneficial to see more direct evaluations of p66Shc subcellular localization in the protective knockin mice to complement the proteomic findings.

      Despite these gaps, the data broadly support the authors' main conclusions. The authors lay out a plausible mechanistic pathway for how hyperlipidemia and increased global SUMOylation can converge on the oxidative stress pathway to provoke vascular dysfunction.

      The likely impact of this work on the field is noteworthy. Beyond clarifying how a single post-translational modification event can influence the pathophysiology of endothelial cells, the study provides a model for investigating broader roles of SUMO2 in other cardiovascular conditions and highlights the importance of identifying additional SUMOylation sites and their downstream impact.

      In conclusion, by demonstrating the direct SUMOylation of p66Shc at lysine-81 and linking that modification to endothelial dysfunction in a hyperlipidemic mouse model, this paper offers valuable insights into how broadly acting post-translational modifiers can evoke specific pathological effects.

    5. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      (1) The production of ROS has been measured in a very superficial way.

      The term "ROS" confers a plethora of chemical species which exerts different physiological effects on different cells and situations.

      Mitochondria through one of the source, but not the only source of ROS production. Only measuring ROS with mitosox do not reflect the cellular condition of ROS in a specific condition. I would suggest authors consider doing IF of oxidative stress specific markers , carbonyl group and also, maybe, Amplex red for determining average oxidative stress and ros production in the cells.

      We agree with the reviewer that a detailed analysis of ROS production and its markers would strengthen the manuscript. Accordingly, we will perform the Amplex Red assay for Figure 1.

      (2) 8-OHG signal seems very confusing in Figure 7E. 8-ohg is supposed to be mainly in the nucleus and to some extent in mitochondria. The signal is very diffused in the images. I would suggest a higher magnification and better resolution images for 8-ohg. Also, the VWF signal is pretty weak whereas it should be strong given the staining is in aorta. Authors should redo the experiments.

      The reviewer’s comment is correct regarding the expected signal. We will repeat the assays. However, we would like to note that the flat morphology of the endothelial cell monolayer on the aortic surface may limit the visualization of subcellular signal differentiation when transversely sectioned.

      (3) PCA analysis is quite not clear. Why is there a convergence among the plots? Authors should explain. Also, I would suggest that the authors do the analysis done in Figure 8B again with R based packages. IPA, though being user-friendly, mostly does not yield meaningful results and the statistics carried out is not accurate. Authors should redo the analysis in R or Python whichever is suitable for them.

      Thank you for your valuable feedback. We acknowledge the concern regarding the PCA analysis and the convergence observed in the plots. In the revised manuscript, we will revise our interpretation to clarify this observation.

      Additionally, we appreciate your suggestion to use R-based packages for pathway analysis. We will make efforts to regenerate the analysis presented in Figure 8B using R to enhance the statistical robustness and reproducibility of our results.

      (4) The MS analysis part seems pretty vague in methods. Please rewrite.

      We will revise the methods section to improve the legibility.

      Reviewer #2 (Public review):

      All the experiments performed here are in overexpression background therefore, it would be crucial to show that p66Shc is SUMO2ylated at physiological levels.

      To address this concern, we will attempt to assess p66Shc-SUMO2 levels under physiological conditions. However, we would like to highlight a technical limitation: the currently available antibodies do not distinguish p66Shc from other isoforms, nor SUMO2 from SUMO3. Therefore, enriching for the endogenous p66Shc-SUMO2 adduct will require novel tools and techniques, which we are actively exploring.

      Reviewer #3 (Public review):

      One notable weakness is that the link between the observed cellular changes and the ultimate in vivo phenotype remains only partially explored. While the authors successfully show that p66ShcK81R knockin mice are protected from endothelial dysfunction in a hyperlipidemic context, additional experiments characterizing the broader tissue-specific roles, or examining further endothelial assays in vivo, would strengthen the mechanistic conclusions. It would also be beneficial to see more direct evaluations of p66Shc subcellular localization in the protective knockin mice to complement the proteomic findings.

      That is an excellent suggestion. We will determine the tissue specific distribution of endogenous p66ShcK81R.

      Despite these gaps, the data broadly support the authors' main conclusions. The authors lay out a plausible mechanistic pathway for how hyperlipidemia and increased global SUMOylation can converge on the oxidative stress pathway to provoke vascular dysfunction.

      The likely impact of this work on the field is noteworthy. Beyond clarifying how a single post-translational modification event can influence the pathophysiology of endothelial cells, the study provides a model for investigating broader roles of SUMO2 in other cardiovascular conditions and highlights the importance of identifying additional SUMOylation sites and their downstream impact.

      In conclusion, by demonstrating the direct SUMOylation of p66Shc at lysine-81 and linking that modification to endothelial dysfunction in a hyperlipidemic mouse model, this paper offers valuable insights into how broadly acting post-translational modifiers can evoke specific pathological effects.

    1. eLife Assessment

      This valuable paper shows image correlation spectroscopy (ICS) as a new tool to analyze the clustering of proteins involved in DNA damage response (DDR). The convincing evidence presented demonstrates that ICS is more sensitive than traditional foci counting. This new method provides an alternative tool to quantify immunostained foci for researchers in the fields of DDR and cell biology.

    2. Reviewer #1 (Public review):

      Summary:

      This manuscript assesses the utility of spatial image correlation spectroscopy (ICS) for measuring physiological responses to DNA damage. ICS is a long-established (~1993) method, similar to fluorescence correlation spectroscopy, for deriving information about the fluorophore density that underlies the intensity distributions of images.

      The revisions to the current manuscript have improved the understanding of the strengths and limitations of the spatial ICS method. In particular, since the measurements are obtaining complementary information to traditional focus counting, one does not expect a simple linear relationship between the quantities obtained by ICS and by immunostaining. The explanations are satisfactory to me and, I expect, to the interested reader.

      Additionally, I am satisfied with the code availability now that it is placed on Github.

    3. Reviewer #2 (Public review):

      This valuable study presents image correlation spectroscopy (ICS) an alternative method to foci counting as a quantitative measurement of recruitment of DNA damage response associated proteins to chromatin following exposure of cells to various genotoxic agents. The evidence presented to demonstrate that this method is more sensitive than traditional foci counting is convincing, although the two methods provide similar results for many of the comparisons. This work will be of interest to scientists using immunostaining to study DNA repair.

      Comments on revisions:

      The authors adequately addressed the comments raised and improved the manuscript. The authors accurately state that there is subjectivity in foci counting, e.g., different thresholds and/or algorithms produce different absolute counts. In addition, the conditions for pre-extraction also introduce variability, and any pre-extraction may inadvertently remove meaningful signal. Yet it is unclear whether these differences in absolute counts impact the conclusions that can be drawn from these experiments, which do not usually make a claim about the absolute number of foci, but rather a comparison between two different conditions with the same pre-extraction conditions and the same threshold/counting algorithm applied, with appropriate controls. Moreover, when the authors compared ICS to foci counting, the results were largely similar, although ICS was superior in a few instances. Overall, how transitioning from the widely-used foci counting method to ICS will offer a major advantage is unclear.

    4. Reviewer #3 (Public review):

      Summary:

      This paper described a new tool called "Image Correlation Spectroscopy; ICS) to detect clustering fluorescence signals such as foci in the nucleus (or any other cellular structures). The authors compared ICS DA (degree of aggregation) data with Imaris Spots data (and ImageJ Find Maxima data) and found a comparable result between the two analyses and that the ICS sometimes produced a better quantification than the Imaris software. Moreover, the authors extended the application of ICS to detect cell-cycle stages by analyzing the DAPI image of cells. This is a useful tool without the subjective bias of researchers and provides novel quantitative values in cell biology.

      Strengths:

      The authors developed a new tool to detect and quantify the aggregates of immuno-fluorescent signals, which is a center of modern cell biology, such as the fields of DNA damage responses (DDR), including DNA repair. This new method could detect the "invisible" signal in cells without pre-extraction, which could prevent the effect of extracted materials on the pre-assembled ensembles, a target for the detection. This would be an alternative method for the quantification of fluorescent signals relative to conventional methods.

      Comments on revisions:

      The authors addressed previous comments properly.

    5. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This manuscript assesses the utility of spatial image correlation spectroscopy (ICS) for measuring physiological responses to DNA damage. ICS is a long-established (~1993) method similar to fluorescence correlation spectroscopy, for deriving information about the fluorophore density that underlies the intensity distributions of images. The authors first provide a technical but fairly accessible background to the theory of ICS, then compare it with traditional spot-counting methods for its ability to analyze the characteristics of γH2AX staining. Based on the degree of aggregation (DA) value, the authors then survey other markers of DNA damage and uncover some novel findings, such as that RPA aggregation inversely tracks the sensitivity to PARP inhibitors of different cell lines.

      The need for a more objective and standardized tool for analyzing DNA damage has long been felt in the field and the authors argue convincingly for this. The data in the manuscript are in general well-supported and of high quality, and show promise of being a robust alternative to traditional focus counting. However, there are a number of areas where I would suggest further controls and explanations to strengthen the authors' case for the robustness of their ICS method.

      Strengths:

      The spatial ICS method the authors describe and demonstrate is easy to perform and applicable to a wide variety of images. The DDR was well-chosen as an arena to showcase its utility due to its well-characterized dose-responsiveness and known variability between cell types. Their method should be readily useable by any cell biologist wanting to assess the degree of aggregation of fluorescent tags of interest.

      Weaknesses:

      The spatial ICS method, though of longstanding history, is not as intuitive or well-known as spot-based quantitation. While the Theory section gives a standard mathematical introduction, it is not as accessible as it could be. Additionally, the values of TNoP and DA shown in the Results are not discussed sufficiently with regard to their physical and physiological interpretation.

      We agree that a major limitation in adaption of this approach is a deeper understanding of the theory and results. We have updated the theory section to include further discussion (Page 4 line 132)

      The correlation of TNoP with γH2AX foci is high (Figure 2) and suggestive that the ICS method is suitable for measuring the strength of the DDR. The authors correctly mention that the number of spots found using traditional means can vary based on the parameters used for spot detection. They contrast this with their ICS detection method; however, the actual robustness of spatial ICS is not given equal consideration.

      We found it difficult to give equal consideration of robustness to ICS. The major limitation of traditional approaches is proper selection of an intensity threshold that is necessary to define and separate foci from background intensity. However, ICS does not employ a threshold, therefore we could not test different thresholding applications in ICS as we did with traditional methods. In our view the absence of the need for a threshold is profoundly advantageous. The only inputs we employ in the ICS analysis are used to segment cell nuclei, yet these have no impact on the ICS calculation and are necessary for any analysis of the DDR.

      Reviewer #2 (Public review):

      Summary:

      Immunostaining of chromatin-associated proteins and visualization of these factors through fluorescence microscopy is a powerful technique to study molecular processes such as DNA damage and repair, their timing, and their genetic dependencies. Nonetheless, it is well-established that this methodology (sometimes called "foci-ology") is subject to biases introduced during sample preparation, immunostaining, foci visualization, and scoring. This manuscript addresses several of the shortcomings associated with immunostaining by using image correlation spectroscopy (ICS) to quantify the recruitment of several DNA damage response-associated proteins following various types of DNA damage.

      The study compares automated foci counting and fluorescence intensity to image correlation spectroscopy degree of aggregation study the recruitment of DNA repair proteins to chromatin following DNA damage. After validating image correlation spectroscopy as a reliable method to visualize the recruitment of γH2AX to chromatin following DNA damage in two separate cell lines, the study demonstrates that this new method can also be used to quantify RPA1 and Rad51 recruitment to chromatin following DNA damage. The study further shows that RPA1 signal as measured by this method correlates with cell sensitivity to Olaparib, a widely-used PARP inhibitor.

      Strengths:

      Multiple proof-of-concept experiments demonstrate that using image correlation spectroscopy degree of aggregation is typically more sensitive than foci counting or foci intensity as a measure of recruitment of a protein of interest to a site of DNA damage. The sensitivity of the SKOV3 and OVCA429 cell lines to MMS and the PARP inhibitors Olaparib and Veliparib as measured by cell viability in response to increasing amounts of each compound is a valuable correlate to the image correlation spectroscopy degree of aggregation measurements.

      Weaknesses:

      The subjectivity of foci counting has been well-recognized in the DNA repair field, and thus foci counts are usually interpreted relative to a set of technical and biological controls and across a meaningful time period. As such:

      (1) A more detailed description of the numerous prior studies examining the immunostaining of proteins such as γH2AX, RAD51, and RPA is needed to give context to the findings presented herein.

      We apologize for not providing enough detail. We have added further references and discussion. γH2AX foci counting, in particular, has been used in thousands of previous studies. (Pages 18 line 513 and 517)

      (2) The benefits of adopting image correlation spectroscopy should be discussed in comparison to other methods, such as super-resolution microscopy, which may also offer enhanced sensitivity over traditional microscopy.

      Thank you for raising this point. We have added this discussion (page 19 line 553). The limiting factor that ICS addresses is the partition coefficient of signal in a foci or cluster versus outside the cluster. Super-resolution will not necessarily improve this unless it is resolved down to single molecule counting. However, one would still need to evaluate how to define a cluster or foci in the background of non-cluster distribution.

      (3) Additional controls demonstrating the specificity of their antibodies to detection of the proteins of interest should be added, or the appropriate citations validating these antibodies included.

      We have added text stating that we only use validated antibodies (page 6 line 193). One thing to note is that we are measuring differences between treatment conditions, thus, if an antibody has non-specific labeling of proteins of cellular structures that do not change upon treatment, our approach would overcome this limitation.

      Reviewer #3 (Public review):

      Summary:

      This paper described a new tool called "Image Correlation Spectroscopy; ICS) to detect clustering fluorescence signals such as foci in the nucleus (or any other cellular structures). The authors compared ICS DA (degree of aggregation) data with Imaris Spots data (and ImageJ Find Maxima data) and found a comparable result between the two analyses and that the ICS sometimes produced a better quantification than the Imaris. Moreover, the authors extended the application of ICS to detect cell-cycle stages by analyzing the DAPI image of cells. This is a useful tool without the subjective bias of researchers and provides novel quantitative values in cell biology.

      Strengths:

      The authors developed a new tool to detect and quantify the aggregates of immunofluorescent signals, which is a center of modern cell biology, such as the fields of DNA damage responses (DDR), including DNA repair. This new method could detect the "invisible" signal in cells without pre-extraction, which could prevent the effect of extracted materials on the pre-assembled ensembles, a target for the detection. This would be an alternative method for the quantification of fluorescent signals relative to conventional methods.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Major comments:

      (1) The ICS theory section is essential and based on an excellent review from one of the authors. It would benefit greatly from a diagram showing where the quantities 𝒈(𝟎, 𝟎), 𝝎𝟎, and 𝒈inf come from in the 2D Gaussian fit, ideally for two cases where these quantities differ (i.e., how they correspond to different DA or TNoP values). In my opinion, this addition would greatly increase the manuscript's accessibility for DDR researchers. The citation of the review at the beginning would also be a plus.

      We have added the review citation at the front of the theory section (page 3 line 87).We have highlighted where g(0,0), the most critical measurement for determination of TNoP and DA, derives from in Figure 2D. However, it is difficult to describe all the curve fit parameters in an image as they have some interdependency on each other and thus labeling one in a single image would not independently capture how they might be observed in a different curve fit.

      (2) The TNoP measured in Figure 2 is a quantity about 2000-3000 times greater than the number of "traditionally detected" foci by both methods and the linear relations have very low Y intercepts. Can the authors comment explicitly on the physical interpretation of this number - are 2 to 3 thousand independent particles present within each "focus" detected by traditional means? If so, then what might one "particle" correspond to? (a single secondary antibody or fluorophore? a nucleosome?). In a similar vein, the X intercepts lie at around 25 foci, meaning that in images with fewer than that number of foci detected by ImageJ or Imaris, the ICS method should detect zero TNoP - is this in line with the authors' predictions? Is it possible that a first-order line fit is not the most appropriate relation between the two methods?

      We apologize for our brevity here. Since DA proved to be a more useful metric we did not spend much effort discussing TNoP. TNoP correlates to the number of clustered particles, or non-diffuse fluorophores. TNoP is the inverse of the number of individual particles per nucleus, but the value is not a direct measure of foci. If a sample had no clustering at all, the number of individual particles would be at a maximum and the TNoP would be at a minimum. However, as fluorophores cluster, the number of individual particles (i.e. non-clustered fluorophores) decreases, which increases the TNoP value. Therefore, TNoP has a correlation to the number of foci detected through traditional measurements, as we found here. Yet, TNoP is a relative measurement and cannot be compared across different conditions. Similar to foci counting, TNoP is unable to factor the size or intensity of each cluster, thus DA is a more appropriate quantification of the DNA damage response.

      The value of TNoP is dependent on the fitted point spread function and the area of the nucleus. The y=0 intercept of TNoP is defined by the optical setup and is not expected to necessarily go through x=0. Intriguingly, other groups have found that some foci identified through traditional measurements are actually clusters of multiple smaller foci, thus the concept of what a foci represents is difficult to interpret. Thus, here we aimed to show a general correlation of TNoP with foci count through traditional methods to reflect how ICS is similar to foci counting, then employed DA to overcome the limitations of defining a foci.

      We have tried to clarify this in the text (page 8, line 266)

      (3) Some suggestions to address the robustness of ICS:

      For a given sample (i.e. one segmented nucleus), the calculation of DA and TNoP should be similar between different images of that same nucleus taken at different times, similar to how the number of traditionally detected foci would be fairly invariant. In particular, it should be shown that these values are not just scaling with the higher normalized intensity seen in stronger DDR responses. In the same vein, the linear relationship between TNoP and "foci" should not change even if the confocal settings are slightly different (i.e., higher/lower illumination intensity) as long as the condition stipulated by the authors in the Discussion holds ("ICS can be implemented on any fluorescence image as long as the square relative fluorescence intensity fluctuations are detectable above noise fluctuations."). To show, as the title states, that spatial ICS is a robust tool, it would be desirable to demonstrate this with a series of images of the same cell at the same or varying excitation intensities.

      Thank you for your suggestions. Indeed, the calculation will be the same over sequential images of the same cell. Observations of dose dependent DA that does not correlate with intensity for RPA1 and RAD51 results (Fig. S5) directly demonstrates that DA does not just scale with intensity.

      We would not expect the TNoP to change with confocal setting, however we show in Figure 1 that the number of foci does indeed change with intensity settings as captured by thresholds. Therefore, any interpretation of TNoP vs. foci count would be very difficult to make at different microscope settings. To ensure we are fairly comparing ICS to existing analysis we keep the settings the same and measure changes between conditions.

      (4) More information is needed on how intensity normalization was performed. The Methods states "Measurements across experiments were normalized by the control in each dataset." The DMSO (0mM drug) plots all appear to have a mean of 1.0, so it appears the values for each set of control nuclei were divided by their own mean, and then the values for each set of experimental nuclei were divided by the mean value of all 3 controls as an aggregate; is this correct?

      We apologize for not being more clear. Thank you for raising this point. We normalized data to a control from each experimental group. Thus, in figures 3,4 and 5 data were collected over multiple experiments with one control per experiment and each treatment condition included in each experiment. Therefore, we normalized each result to the corresponding control from that imaging session. However, in Figure 8 we ran experiments at much higher throughput with multiple controls per experiment, thus the data were normalized to the overall average of the controls, which is why the control averages are not all at a value of 1. We have clarified this in the text. (Page 7 line 218).

      (5) Some more information about the ICS analysis should be given if the full code is not provided - in particular, how the nucleus mask was implemented on the "signal" channel (were the edges abruptly set to zero or was a window function introduced to avoid edge effects in the discrete FFT?

      Thank you for raising this point. We have added the code to GitHub - github.com/ dubachLab/ics. The signal region was established by simply applying the nuclear mask from the DAPI channel to the IF channel. Each region is padded with average intensity value at the edges for 2x the dimensions of the ROI to remove edge effects in the FFT.

      Minor comments:

      (1) Figure 3, 4, 5: I think it would aid figure readability if channels were labeled in the images themselves, not just in the legend.

      Thank you for the suggestion, we tried doing this and struggle to fit a label with the layout of the images. We were also concerned about interpretation of data in each column and the potential to assign data to each figure if they were so prominently labeled.

      (2) Supplemental Figures are mislabeled; the order given in the legends is S1, S2, S3, S2, S3. S4 is called out in the main text where it should be S5.

      Thank you for catching this error. We have made the necessary corrections. S4 contains data on cellular response to the drugs, while S5 contains intensity data in response to MMS.

      (3) It should be stated for each Figure what kind of microscopy was performed - I assume that it is confocal for everything except when widefield is explicitly stated, but for clarity please add this information.

      Indeed, this is correct, we have indicated which microscopy was used for each figure.

      (4) The MATLAB code and full (uncropped) Western blots should be provided as supplemental data if possible.

      We have included a GitHub link for the code and un-cropped western blots.

      (5) The p values from significance tests should indicate whether multiple comparisons correction was necessary (if suggested by Prism) and performed.

      Apologies for a lack of clarity but this was not necessary, significance was calculated vs. the next lower dose (e.g. 10 micromolar vs. 1 micromolar). We have clarified this in the methods (page 7 line 221).

      Reviewer #2 (Recommendations for the authors):

      Major points:

      In addition to the weaknesses noted above, to encourage widespread adoption of this method, the authors should make the tools that they used for their analysis publicly available. In a few instances (e.g., compare Figures 3J and 3L), other methods outperform DA. It would be meaningful to discuss when especially DA may be a better measure than others (such as intensity or number of foci).

      We have made code available on Github. We expect results, such as those in Figures 3J and 3L where intensity is significantly higher at the highest concentration but DA is not are reflective of the underlying biology and this may be interpreted differently under different experimental conditions. Imaris spots (Fig. 3K) also does not capture a significant increase at the highest dose of olaparib, suggesting that intensity may raise but it doesn’t not generate more foci. These results are likely highly dependent on the mechanism of olaparib at such a high concentration and the DDR response. We are hesitant to draw biological conclusions from these results and instead would like to highlight the capacity of ICS to evaluate the DDR, therefore we don’t want to make any broad comments about different applications.

      Minor points:

      (1) Pg. 12: "We used MMS to induce DNA damage in SKOV3 and OVCA429 cells. As expected, normalized intensity for RPA1 and RAD51 values (Figure S5) did not display a dose dependence on MMS concentration."

      Please provide a citation for the claim that RPA1 and RAD51 normalized intensities do not display a dose dependence on MMS concentration.

      These were data that we generated. We were not expecting an intensity change as that would presumably require increased protein generation in response to MMS, compared to gH2AX where the phospho-specific H2AX is generated in the DDR.

      (2) Pg. 12: "Similar to RPA1, RAD51 does not form distinguishable foci in the nuclei in cells without preextraction (Fig. 5)." Please provide a citation for this claim.

      We did not do pre-extraction and our results don’t produce changes in distinguishable foci. We provided citations discussing how, without pre extraction, foci formation for these proteins is not obvious (REF 38 and 39).

      (3) I noted that the authors cite one paper [38] apparently showing that RPA and Rad51 do not always form foci, however, this is in the C. elegans germline in response to micro irradiation, therefore I am not sure that it is applicable to human cells.

      We apologize for referencing a paper on C elegans. Most papers looking at RPA and RAD51 in the DDR use pre-extraction as it seems necessary to observe foci. Therefore, there are not as many papers, that we could find, that do not use pre-extraction. Reference 39 is in Hela cells.

      Reviewer #3 (Recommendations for the authors):

      Major points:

      (1) Page 8, the second paragraph: In the Result section, it is better to describe how the authors carried out immuno-staining (without pre-extract subtraction) and ICS briefly, although the method is described in detail in the Method section.

      Thank you for the suggestion, we have added this description (page 8, line 259)

      (2) In Figure 5K-P: The authors analyzed "invisible" RAD51 foci on the image (Fig. 5L, M, O, and P) without pre-extraction. As a control experiment, it is useful to check whether pre-extraction would provide "visible" RAD51 foci and to examine the similar MMS concentration dependency shown in Figure 5R (or 5T). This would strengthen the power of the ICS analysis.

      Thank you for the suggestion. In our hands, pre-extraction is extremely subjective. We have tried performing pre-extraction but find highly variable results depending on conditions. Therefore, we did not include any pre-extraction here. We expect that performing these experiments may or may not agree with results in Figure 5 largely because we are unable to achieve repeatable pre-extraction foci counting.

      (3) Figure 6D (and 6C) looks very interesting. It would be important to show the interpretation of this correlation shown in the graph. Although the authors argued that ICS analysis results shown in the graph could provide new insight into the DDR (page 14, last line 5), as shown in another part, it is important to carry out the same analysis by using Imaris Spots. Moreover, it is interesting to apply the analysis to RAD51 foci (shown in Figure 5), given that the PARPi effect is enhanced in the absence of RAD51mediated recombination.

      We completely agree that this analysis may generate interesting results to help interpret the DDR response to PARP inhibition. These experiments are part of an ongoing follow up study where we extend the use of ICS to other parts of the DDR and investigate protein clustering across several proteins with impact on PARPi response. Therefore, since the focus of this manuscript is introducing ICS as a tool to study the DDR, we believe that omitting those data here does not deter from the central points of the manuscript. We including results in Figure 6 because we wanted to show how ICS could impact DDR research. Furthermore, combined with our advances shown in Figures 7 and 8, we are currently working on adapting ICS to be high-throughput and much simpler than Imaris spots for handling large datasets needed to generate results like those in Figure 6.

      Minor points:

      (1) Figure 1I, blue arrows: These showed an area with a higher background. Because of a low magnification, it is very hard to see the difference from the other areas of the background. It is better to show a magnified image of the representative region with a higher background.

      We hope that readers can see the higher intensity in the diffuse area. We attempted to construct a zoomed in area, but that either blocked a significant portion of the nonzoomed image or added complexity to the figure. We have noted that images in Figure S1 are larger and more obviously capture an increase in background intensity.

      (2) Figure 2 legend, line 5, the same as "A)": This should be "B".

      Here, the number of independent particle clusters is intended to be the same as A, the difference is that the independent particles are clusters in C and individual fluorophores in A.

      (3) Page 9, the first paragraph, last line, foci formation, and foci composition: These should be "focus formation and focus composition".

      We have changed this.

      (4) Page 15, the first paragraph, line 5, palbociclib, camptothecin, or etoposide: please explain what kinds of the drugs are.

      We have added that these drugs cause cells to stall at different cell cycle stages. Explaining the drugs would take considerable room in the text.

      (5) Page 16, the first paragraph, line 1, bleomycin: Please explain what this drug is.

      Similar to above, we have stated that this drug causes DNA damage, going into detail would take several sentences.

    1. eLife Assessment

      This study presents a useful finding for the ferroptosis-mediated tumor microenvironment (TME) in triple-negative breast cancer (TNBC) using public single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing data. The data were collected and analyzed using solid and validated methodology and can be used as a starting point for functional studies of TME in TNBC. The work will be of interest to medical biologists working in the field of TNBC.

    2. Reviewer #2 (Public review):

      Summary:

      This study aims to explore the ferroptosis-related immune landscape of TNBC through the integration of single-cell and bulk RNA sequencing data, followed by the development of a risk prediction model for prognosis and drug response. The authors identified key subpopulations of immune cells within the TME, particularly focusing on T cells and macrophages. Using machine learning algorithms, the authors constructed a ferroptosis-related gene risk score that accurately predicts survival and the potential response to specific drugs in TNBC patients.

      Strengths:

      The study identifies distinct subpopulations of T cells and macrophages with differential expression of ferroptosis-related genes. The clustering of these subpopulations and their correlation with patient prognosis is highly insightful, especially the identification of the TREM2+ and FOLR2+ macrophage subtypes, which are linked to either favorable or poor prognoses. The risk model thus holds potential not only for prognosis but also for guiding treatment selection in personalized oncology.

    3. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Triple-negative breast cancer (TNBC) accounts for approximately 15-20% of all breast cancers. Compared to other types of breast cancer, TNBC exhibits highly aggressive clinical characteristics, a greater likelihood of metastasis, poorer clinical outcomes, and lower survival rates. Immunotherapy is an important treatment option for TNBC, but there is significant heterogeneity in treatment response. Therefore, it is crucial to accurately identify immunosuppressive patients before treatment and actively seek more effective therapeutic approaches for TNBC patients.

      Strengths:

      In this work, the authors collected and integrated data from single cells and large volumes of RNA sequencing and RNA-SEQ to analyze the TME landscape mediated by genes associated with iron death. On this basis, the prediction model of prognosis and treatment response of 131 patients was constructed using a machine learning algorithm, which is beneficial to provide individualized and precise treatment guidance for breast cancer patients.

      Thank you for your appreciation of our work. We are encouraged by your positive feedback and will continue to explore new avenues in personalized medicine for breast cancer.

      Weaknesses:

      However, there are still some issues that need to be clarified:

      (1) The description of the research background is too brief and concise, and it is necessary to add some information about the limitations of existing methods and the differences and advantages of this study compared with other published relevant studies, so as to better highlight the necessity and research value of this study.

      Thank you for your suggestions. We have supplemented the research background and compared the differences between this study and other studies, further highlighting the research value of our study.

      (2) This study is a retrospective analysis of a public data set and lacks experimental validation and prospective experiments to support the results of bioinformatics analysis. This should be added to the acknowledgment of limitations in the study.

      Thank you for the constructive feedback. We also acknowledge that the lack of experimental evidence is one of the limitations of this study. Therefore, we plan to conduct in vivo and in vitro experiments in our future research to support the findings of our bioinformatics analysis, and have already supplemented the relevant content in the limitations of Discussion.

      Reviewer #2 (Public review):

      Summary:

      This study aims to explore the ferroptosis-related immune landscape of TNBC through the integration of single-cell and bulk RNA sequencing data, followed by the development of a risk prediction model for prognosis and drug response. The authors identified key subpopulations of immune cells within the TME, particularly focusing on T cells and macrophages. Using machine learning algorithms, the authors constructed a ferroptosis-related gene risk score that accurately predicts survival and the potential response to specific drugs in TNBC patients.

      Strengths:

      The study identifies distinct subpopulations of T cells and macrophages with differential expression of ferroptosis-related genes. The clustering of these subpopulations and their correlation with patient prognosis is highly insightful, especially the identification of the TREM2+ and FOLR2+ macrophage subtypes, which are linked to either favorable or poor prognoses. The risk model thus holds potential not only for prognosis but also for guiding treatment selection in personalized oncology.

      Thank you for your thorough review and insightful comments.

      Weaknesses:

      The study has a relatively small sample size, with only 9 samples analyzed by scRNA-seq. Given the typically high heterogeneity of the tumor microenvironment (TME) in cancer patients, this may affect the accuracy of the conclusions. The scRNA-seq analysis focuses on the expression of ferroptosis-related genes in various cells within the TME. In contrast, bulk RNA sequencing uses data from tumor samples, and the results between the two analyses are not consistent. The bulk RNA sequencing results may not accurately capture the changes happening in the microenvironment.

      Thank you for your constructive feedback. Although this study only included 9 samples, given the limited availability of scRNA-seq datasets for untreated TNBC in public databases, we chose to utilize a dataset that contains a relatively larger number of untreated TNBC samples. We are fully aware of the complexity and high heterogeneity of the TME. Despite the limited sample size, we first conducted rigorous quality control on the data and, based on this, preliminarily revealed the landscape of the TME mediated by ferroptosis-related genes. These findings provide a new perspective for understanding the biological mechanisms underlying the onset and progression of breast cancer. To enhance the reliability and generalizability of our research results, we plan to strive to expand the sample size in future work and consider integrating other omics technologies, such as proteomics and metabolomics, with scRNA-seq data for a more in-depth exploration of the complex interactions within the TME.

      We also agree with your viewpoint that scRNA-seq data reveals gene expression within individual cells, while bulk RNA-seq data reveals the average gene expression in tumor tissues, and there are differences in data acquisition and processing methods between the two. However, we believe that there are also some close connections between them in terms of gene expression levels. By comparing the expression specificity of marker genes for specific cell types in breast cancer tissues, we found that they are correlated with patient prognosis, and the results have been validated in both internal and external validation sets. Thank you once again for your valuable suggestions, which will play an important guiding role in our subsequent research.

      Reviewer #1 (Recommendations for the authors):

      (1) The breast cancer scRNA-seq dataset files of GSE176078 include 10 TNBC primary tumors (DOI:10.1016/j.compbiomed.2023.107066). However, in this study, only 9 cases were listed, please explain the reason for the data exclusion.

      Thank you for your questions. Although it was clearly stated in the original paper that "To elucidate the cellular architecture of breast cancers, we analyzed 26 primary pre-treatment tumors, including 11 ER+, 5 HER2+ and 10 TNBCs, by scRNA-Seq (Supplementary Table 1)," upon downloading and carefully examining the patient information in Supplementary Table 1, we only included 9 patients explicitly labeled as TNBC in our study (https://pmc.ncbi.nlm.nih.gov/articles/PMC9044823/#SD1).

      (2) The description of the technique in the methods section should be more detailed, such as parameter settings, quality control standards, etc.

      Thank you for your valuable suggestions. We have already supplemented the relevant content in the methods section.

      (3) Please check and correct formatting errors to improve readability, such as lines 176 and 177.

      We were really sorry for our careless mistakes. Thank you for your reminder. We have corrected the “Pseudotime analysis with scRNA-seq data helps to obtain an approximate landscape of gene expression dynamics” into “Pseudotime analysis of scRNA-seq snapshot data helps to provide an approximate landscape of gene expression dynamics”. And we have further checked and revised the formatting errors of the manuscript.

      Reviewer #2 (Recommendations for the authors):

      (1) In multiple sections of the paper, abbreviations are used without being defined when first mentioned.

      We were really sorry for our careless mistakes. Thank you for your reminder. We have already added definitions for the abbreviations in both the abstract and the main text.

      (2) The authors should analyze whether the transcription factors in Figure 2 are correlated with the expression of ferroptosis-related genes.

      Thank you for your valuable feedback. Some transcription factors in Figure 2 correlate with the expression of ferroptosis-related genes, which we have supplemented in the Discussion.

      (3) Figures 3d and 4e lack explanations for the axis values, and for Figure 4e, is the unit of the y-axis labeled "survival" in days?

      Thank you for your valuable feedback. We apologize for the lack of explanations for the axis values in Figures 3d and 4e and we have made revisions to both figures accordingly. We have noted that the unit "survival" on the y-axis of Figure 4e is in years, and we have already made the necessary supplement to clarify this. Thank you very much for your reminder.

      (4) The authors conducted their analysis using public databases but did not cite the original literature, nor did they discuss the similarities and differences between their findings and those in the original studies.

      Thank you for your valuable suggestions, and we deeply apologize for our carelessness. We have supplemented the original literature in the references and discussed the differences between this study and the original literature in the Discussion.

      (5) Some figures, particularly those involving heatmaps and t-SNE plots (e.g., Figures 1 and 3), present dense and complex data that may be challenging for readers to interpret. The heatmaps (Figure 1e-f and 3d) include many genes, but it is unclear how these genes were selected, and the scale of gene expression differences is difficult to interpret. Simplifying these figures by focusing on the most differentially expressed and clinically relevant genes (e.g., those with prognostic value) would improve readability.

      Thank you for your valuable suggestions. The t-SNE plots in Figures 1 and 3 primarily serve as a dimensionality reduction technique to visually present the clustering of multiple cells or samples based on gene expression, aiding readers in quickly identifying cell subpopulations. The heatmaps, on the other hand, are mainly used to showcase the differential expression of ferroptosis-related genes across different clinicopathological classifications and cell subpopulations, with varying shades of color helping readers quickly recognize gene expression differences among different cell subpopulations. The genes included in the heatmaps (Figures 1e-f and 3d) are sourced from the FerrDb website. We have uploaded the list of ferroptosis-related genes used in this study as Supplementary Table 1 and added the relevant steps in Method 2.3.

      (6) The study analyzes the expression of ferroptosis-related genes in different immune cells within the TME. The authors should discuss how these changes in gene expression may impact the function and behavior of immune cells.

      Thank you for your valuable feedback. We have supplemented the discussion with detailed effects of the main differential genes (FOLR2 and TREM2) on the tumor immune response.

      (7) The authors analyzed the expression of ferroptosis-related genes in immune cells using single-cell sequencing data. However, they subsequently applied the selected genes to perform a risk factor analysis in tumor cells. Is the expression and function of these genes the same in immune cells and tumor cells? This seems questionable.

      Thank you very much for your suggestion. We also believe that there may be differences in the expression and function of genes between immune cells and tumor cells. However, some genes may exhibit similarities in their expression and function in immune cells and tumor cells, especially within the tumor immune microenvironment, due to the complex and tight interactions between immune cells and tumor cells (as shown in Figures 1d and 2h), and their expression levels can be related to the onset, progression, and prognosis of tumors.

      (8) While the risk score model based on ferroptosis-related genes is promising, it lacks experimental validation, which weakens the strength of the conclusions. The authors should consider conducting in vitro or in vivo experiments. These functional studies would provide essential evidence to support the model's predictive capability.

      Thank you for the constructive feedback. We fully recognize the importance of conducting functional studies to substantiate the predictive capability of the model. Therefore, we plan to conduct in vitro and in vivo experiments in our future research to provide the necessary evidence and further validate the model's effectiveness.

      (9) The manuscript predicts sensitivity to 27 drugs based on the risk score, but it lacks mechanistic insight into why patients in the high-risk group might be more responsive to certain drugs. Including a more detailed discussion of the molecular mechanisms underlying this drug sensitivity, particularly linking ferroptosis-related genes to drug metabolism or efficacy, would provide a stronger rationale for the clinical application of these findings.

      Thank you very much for your valuable suggestions. In the discussion, we thoroughly analyzed the mechanism of action of the drugs (ABT-263 and erlotinib) with the greatest difference in sensitivity between high-risk and low-risk groups, as well as their correlation with ferroptosis.

    1. eLife Assessment

      This important work shows the biological processes and detailed mechanisms involving testosterone's influence on seminal plasma metabolites in mice. Evidence supporting the up regulation of metabolic enzymes and the role of ACLY is solid, though the precise contributions of fatty acids to sperm motility requires further elucidation.

    2. Reviewer #1 (Public review):

      Summary:

      In this revised report, Yamanaka and colleagues investigate a proposed mechanism by which testosterone modulates seminal plasma metabolites in mice. Based on limited evidence in previous versions of the report, the authors softened the claim that oleic acid derived from seminal vesicle epithelium strongly affects linear progressive motility in isolated cauda epididymal sperm in vitro. Though the report still contains somewhat ambiguous references to the strength of the relationship between fatty acids and sperm motility.

      Strengths:

      Often, reported epidydimal sperm from mice have lower percent progressive motility compared with sperm retrieved from the uterus or by comparison with human ejaculated sperm. The findings in this report may improve in vitro conditions to overcome this problem, as well as add important physiological context to the role of reproductive tract glandular secretions in modulating sperm behaviors. The strongest observations are related to the sensitivity of seminal vesicle epithelial cells to testosterone. The revisions include the addition of methodological detail, modified language to reflect the nuance of some of the measurements, as well as re-performed experiments with more appropriate control groups. The findings are likely to be of general interest to the field by providing context for follow-on studies regarding the relationship between fatty acid beta oxidation and sperm motility pattern.

      Weaknesses:

      The connection between media fatty acids and sperm motility pattern remains inconclusive.

    3. Reviewer #2 (Public review):

      Using a combination of in vivo studies with testosterone-inhibited and aged mice with lower testosterone levels as well as isolated mouse and human seminal vesicle epithelial cells the authors show that testosterone induces an increase in glucose uptake. They find that testosterone induces a difference in gene expression with a focus on metabolic enzymes. Specifically, they identify increased expression of enzymes regulating cholesterol and fatty acid synthesis, leading to increased production of 18:1 oleic acid. The revised version strengthens the role of ACLY as the main regulator of seminal vesicle epithelial cell metabolic programming. The authors propose that fatty acids are secreted by seminal vesicle epithelial cells and are taken up by sperm, positively affecting sperm function. A lipid mixture mimicking the lipids secreted by seminal vesicle epithelial cells, however, only has a small and mostly non-significant effect on sperm motility, suggesting the authors were not apply to pinpoint the seminal vesicle fluid component that positively affects sperm function.

    4. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this revised report, Yamanaka and colleagues investigate a proposed mechanism by which testosterone modulates seminal plasma metabolites in mice. The authors identify oleic acid as a particularly important metabolite, derived from seminal vesicle epithelium, that stimulates linear progressive motility in isolated cauda epidydimal sperm in vitro. The authors provide additional experimental evidence of a testosterone dependent mechanism of oleic acid production by the seminal vesicle epithelium.

      Strengths:

      Often, reported epidydimal sperm from mice have lower percent progressive motility compared with sperm retrieved from the uterus or by comparison with human ejaculated sperm. The findings in this report may improve in vitro conditions to overcome this problem, as well as add important physiological context to the role of reproductive tract glandular secretions in modulating sperm behaviors. The strongest observations are related to the sensitivity of seminal vesicle epithelial cells to testosterone. The revisions include addition of methodological detail, modified language to reflect the nuance of some of the measurements, as well as re-performed experiments with more appropriate control groups. The findings are likely to be of general interest to the field by providing context for follow-on studies regarding the relationship between fatty acid beta oxidation and sperm motility pattern.

      Thank you for summarizing and your positive evaluation of our study.

      Weaknesses:

      Support for the proposed mechanism is stronger in this revised report than in the previous report, but there are many challenges in measuring sperm metabolism and its direct relationship with motility patterns. This study is no exception and largely relies on correlations between various experiments in lieu of direct testing. Additionally, the discussion is framed from a human pre-clinical perspective, and it should be noted that the reproductive physiology between mice and humans is very different.

      Thank you for pointing out the challenges in our paper. We appreciate your comment on the limited evidence supporting the direct relationship between sperm metabolism and motility patterns under current experimental conditions. Based on your and reviewer2’s suggestions, we have decided to remove the experiments and discussion on the “effects of OA on sperm metabolism, motility and fertility (Fig. 7, Supplemental Figure 5A and C-F.)” and the corresponding parts in the Discussion section from the paper. (See also Reviewer 2's main comment) These data mainly show correlations, and did not show direct evidence of causality. Instead, we added a new experiment to the manuscript, in which a lipid mixture that mimics the fatty acid profile secreted testosterone-dependently from seminal vesicle epithelial cells was added to the sperm culture medium (New Supplemental Figure 5, Lines 259-268). In this experiment, motility parameters were measured using CASA. This experiment evaluates the direct effects of lipid exposure on sperm motility. With these revisions, we are able to focus on the metabolic changes caused by testosterone in seminal vesicle epithelial cells, which are the central focus of our research. We have added a short statement agreeing the potential importance of OA and our intention to more rigorously investigate the role of OA in sperm function in subsequent studies (Lines 402-407).

      Furthermore, we have revised text, clearly state the limitations of the species difference and clarify that the translational aspects to humans are speculative (Lines 383-384, 395-397, 408-410).

      We appreciate your guidance. We believe that these changes will strengthen our research.

      Reviewer #2 (Public review):

      Using a combination of in vivo studies with testosterone-inhibited and aged mice with lower testosterone levels as well as isolated mouse and human seminal vesicle epithelial cells the authors show that testosterone induces an increase in glucose uptake. They find that testosterone induces a difference in gene expression with a focus on metabolic enzymes. Specifically, they identify increased expression of enzymes regulating cholesterol and fatty acid synthesis, leading to increased production of 18:1 oleic acid. The revised version strengthens the role of ACLY as the main regulator of seminal vesicle epithelial cell metabolic programming. 18:1 oleic acid is secreted by seminal vesicle epithelial cells and taken up by sperm, inducing an increase in mitochondrial respiration. The difference in sperm motility and in vivo fertilization in the presence of 18:1 oleic acid and the absence of testosterone, however, is small. Additional experiments should be included to further support that oleic acid positively affects sperm function.

      Thank you very much for carefully reading the manuscript and for your comments. We appreciate your understanding that the role of ACLY in metabolic programming of seminal vesicle epithelial cells has been strengthened in the revised version. On the other hand, we agree with your view that the increase in sperm motility and fertilization rate by oleic acid is minimal under the current experimental conditions. We agree that further evidence is needed to support our conclusion regarding the positive effects of oleic acid on sperm function. Based on your comments and our re-evaluation of the data, we have decided to remove the experiments and discussion on “OA and sperm motility” from the current paper (Fig. 7, Supplemental Figure 5A and C-F). In the revised paper, we have significantly toned down the claims on the previous role of oleic acid and instead focused on the metabolic regulatory mechanisms of seminal vesicle epithelial cells.

      We hope that these revisions address your concerns and improve the overall clarity of the manuscript.

      Recommendations for the authors:

      Note from the reviewing editor: The reviewers agree that the revised manuscript is significantly improved and view the work as important. Both reviewers agree that the evidence for testosterone effects on seminal vesicle epithelial cells to support fatty acid synthesis is strong and suggest that the authors tone down their conclusion of oleic acid effect on sperm motility as the effect is very small. With this minor changes, the evidence to support the conclusion of the study is viewed as solid.

      Thank you for recognizing the improvements that we have made to our manuscript and for appreciating the importance of our research. We also appreciate your assessment that the evidence for the effect of testosterone on seminal vesicle epithelial cells that support fatty acid synthesis is solid.

      On the other hand, we agree with the two reviewers that the effect of oleic acid on sperm motility is limited and that the relevant data do not measure a direct relationship. Therefore, we have decided to withdraw the data set on the effect of oleic acid on sperm (Fig. 7, Supplemental Figure 5A and C-F) and focus this paper on seminal vesicle epithelial cells (in response to reviewer 2's suggestion). Given that testosterone-induced lipid (Fatty acid) synthesis in seminal vesicle epithelial cells is a key aspect of our study, we have included additional experiments in the revised manuscript to show how lipids affect sperm (New Supplemental Figure5, Lines 259-263).

      With these revisions, the manuscript emphasizes the importance of testosterone-dependent fatty acid synthesis in seminal vesicle epithelial cells and the fact that this includes oleic acid. The title has also been partially revised in line with these revisions.

      Reviewer #1 (Recommendations for the authors):

      Minor Comments:

      (1) The authors indicate in the methods that extracellular flux analysis was normalized to cell count. However, the y-axis units in Figs 4, 8, 9 and SFig 9 are not normalized.

      (2) The OA label appears to be missing from Fig 7A. Additionally, the scale bar is offset in one of the images and the length of the scale bar does not appear to be mentioned in the figure legend.

      Thank you for raising these points. We have corrected.

      Fig. 7 has been withdrawn in response to Reviewer 2's suggestion.

      Reviewer #2 (Recommendations for the authors):

      With the experiments included in their revised version the authors strengthen their conclusions about testosterone-induced metabolic reprogramming in seminal vesicle cells resulting in reduced proliferation. The experiments surrounding ACLY are well-designed and give insights into the underlying molecular mechanisms. For other parts, the manuscript became less clear and it is often hard to follow the author's line of thoughts for their conclusions.

      Based on the experiments shown in the manuscript this reviewer is still not convinced that OA positively affects sperm function. The changes in linear motility are minor, blastocyst levels are lower and the authors do not show that OA alone positively affects cleavage rate during AI. Without additional experiments that show a stronger effect on sperm function, the authors should consider focusing the manuscript exclusively on seminal vesicle epithelial cells.

      Thank you for your constructive comments on our paper. We thank the reviewer for pointing out that the effect of oleic acid (OA) on sperm function is limited in our current experiments. As reviewer 1 also pointed out, we agree that further experiments and improved methodology are needed to reliably demonstrate the functional effects of OA on sperm. Because the strength of the data on the direct relationship between fatty acids in seminal fluid and improved sperm function is currently insufficient, we have removed the data set for oleic acid and sperm motility (Fig. 7, Supplemental Figure 5A and C-F) and focused on the “the mechanism of metabolic regulation of testosterone in seminal vesicle epithelial cells”. We have consistently narrowed the focus of the paper to the theme of “how testosterone changes energy metabolism in seminal vesicle epithelial cells”. In accordance with this change, the structure of the paper has also been partially revised (red text in the manuscript). With these revisions, the main point of the paper focuses on the mechanism by which testosterone regulates metabolic pathways in the seminal vesicle epithelial cells.

      For more detailed revisions, please see the responses to your comments below.

      (1) 45-55 still need major revision. It will not become clear to the reader what the authors mean by epididymal maturation. 'Ability to fertilize in in vitro?' Epididymal sperm are moving linearly in the absence of seminal vesicle fluid. Increased progressive motility, hyperactivation, and the ability to undergo the acrosome reaction are induced upon exposure to seminal vesicle fluid. The authors should introduce the concept of capacitation and that capacitation can be induced in vitro by exposure to bicarbonate and a cholesterol acceptor.

      Thank you for pointing out the ambiguity of epididymal maturation, the need to clarify the concept of capacitation, and the role of seminal plasma in this context. The revised text explains that epididymal maturation only gives sperm their potential ability to fertilize. It also explains that it is the subsequent capacitation process—inducible in vitro by incubation with bicarbonate and cholesterol acceptors—that gives full fertilization potential. On the other hands, we emphasize that in vivo, seminal plasma, which contains both capacitation-promoting and decapacitation factors, plays a key role in fine-tuning the timing of capacitation, ensuring that sperm acquire fertilization competence at the appropriate moment. We hope that these revisions clarify our intended meaning and strengthen the overall message of the paragraph. (lines 42-54)

      “Sperm that have completed spermatogenesis in the testis acquire their potential to fertilize while maturing in the epididymis (5–7). The physiological change of sperm during fertilization process are collectively referred to as “capacitation”. This change includes a large amplitude of flagella (called hyperactivation) and developing the capacity to undergo the acrosome reaction, and can be induced by culturing sperm collected from the epididymis in a medium containing bicarbonate and cholesterol acceptors (8, 9). However, once capacitation is complete, sperm cannot maintain that state for a long time. Therefore, even if epididymal sperm that have not been exposed to seminal plasma are artificially inseminated into the cervix or uterus, the fertilization rate remains low (10–12). That is because, in vivo, during ejaculation, exposure of epididymal sperm to seminal plasma masks the unintended capacitation as they pass through the female reproductive tract and ensures fertilization of sperm that reach the oviduct (13). In other words, seminal plasma plays an important role in fine-tuning the timing of sperm capacitation and in maintaining the sustained sperm motility needed to reach the oviduct.”

      (2) 81: Similar as in their rebuttal the authors should further elute on the connection between fructose, citrate, and testosterone. That still does not become clear. Based on the author's explanation in the rebuttal, why are citrate and fructose levels higher when the animals are castrated?

      We thank you for the opportunity to clarify our statement regarding the relationship between fructose, citrate, and testosterone. Our original explanation was intended to reflect the fact that testosterone from the testes has a stimulating effect on the accessory reproductive glands, and to report that the concentrations of fructose and citric acid were higher in the non-castrated (control) animals than in the castrated animals. In castrated animals, the absence of testosterone leads to decreased activity of these glands and, consequently, lower levels of these metabolites. To make this clear, we have revised the manuscript as follows. (lines 76-82)

      “Several specific factors produced by the male accessory glands that contribute to seminal plasma and impact male fertility have been elucidated. For example, surgical removal of seminal vesicles in male mice and rats was associated with infertility (17, 22, 23). The observations that fructose (24) and citric acid (25) concentrations in seminal plasma of control mice and rats are higher than in castrated animals suggest that the specific metabolism of the accessory glands might be affected by testosterone derived from the testes, which activate intracellular androgen receptors (AR; NR3C4) required for gene regulation of transcription.”

      (3) 111: This reviewer does not understand the author's obsession with reporting linear motility. Sperm are moving linearly when isolated from the epididymis. Again, increase of progressive motility is a well-defined hallmark of capacitation and primarily used in the field when discussing changes in sperm motility during capacitation. This reviewer is assuming that the changes in progressive vs linear motility in Fig. 7 are not significant because the data is more scattered. The % increase seems to be approximately the same. The same is true for Fig. 8. The increase in LIN is so small and not dose-dependent that this reviewer is not comfortable making that one of the main conclusions of the manuscript.

      Our claim is based on the observation that seminal vesicle secretions significantly improve the linear motility (VSL and LIN) of sperm even in an environment that does not contain capacitation-inducing factors such as BSA. We interpret this as a survival strategy for sperm to pass through the female reproductive tract efficiently. Therefore, we believe that this does not mean that the meaning of “progressive motility” in the context of conventional capacitation is the same as that of progressive motility observed in seminal plasma.

      However, the reviewer's point that the current data set does not sufficiently support what the minor increase in linear motility caused by oleic acid means is agreed with. Therefore, we have decided to withdraw the dataset on the effect of oleic acid on sperm motility (Fig. 7, Supplemental Figure 5A and C-F) and have revised the conclusion. (Lines 406-410)

      (4) 128: For the mitochondrial membrane potential measurements the authors should mention that they included antimycin as a control. The manuscript would benefit from including scatter plots with unloaded controls to support their gating strategy. In its current stage, the gating between low and high membrane potential seems arbitrary.

      Thank you for pointing this out. We have included an explanation of antimycin as a control in the main text (Lines 920-921). In addition, we have added some reference scatter plots and also added an explanation of the gating strategy between low and high membrane potentials (Supplemental Figure 1C and D, Lines 1101-1104). We hope this change will make the manuscript clearer.

      (5) 190: What do the authors mean by: 'However, there was no difference in the Oligomycin-sensitive ECAR, indicating that testosterone may increase glucose metabolism but does not enhance the expression of a group of enzymes involved in the glycolytic pathway.'

      Our original intention was to state that testosterone probably increases basal glycolytic flux via increased glucose uptake (as supported by the GLUT4 translocation data), but does not increase maximal glycolytic capacity, as indicated by the lack of difference in oligomycin-sensitive ECAR.

      However, as Reviewer 1 previously pointed out, we agree that the assay conditions themselves, such as the use of oligomycin to inhibit oxidative mitochondria, may create non-physiological conditions and not fully reflect the energy distribution in vivo. Under these conditions, there is a possibility that the flow of glycolysis will increase artificially as a compensatory reaction, and parameters such as “maximum glycolytic capacity” should have been interpreted with caution.

      Therefore, we have revised the manuscript to clarify that our data are a single-time point under defined experimental conditions and do not necessarily provide direct insight into changes in expression or activity of individual glycolytic enzymes.

      “These data indicate that testosterone enhances glucose utilization. This leads to the interpretation that testosterone increases the flow of glycolysis by increasing glucose uptake and alters metabolic flux distribution.” (Lines 186-188)

      (6) 205: Could the authors elaborate further on how they came to this conclusion: 'These results suggest that testosterone does not reduce transient enzyme activity in mitochondria but rather weakens the metabolic pathway of the mitochondrial TCA cycle and/or the electron transport chain due to the changes in gene expression patterns in seminal vesicle epithelial cells.' Based on their results at this point the authors have no insights about changes in enzyme activity or gene expression that might explain the phenotype.

      Our statement is based on the following observations. In testosterone-treated cells, the addition of glucose increased ECAR, suggesting an increase in glycolytic flux due to an increase in glucose uptake. On the other hand, mitochondrial respiratory parameters (basal respiration, oligomycin-sensitive respiration, FCCP-uncoupled respiration, and reserve respiratory capacity) were significantly decreased under testosterone treatment.

      From these results, it was speculated that testosterone promotes the redistribution of metabolic flux, directing it away from mitochondrial oxidative phosphorylation and towards the glycolytic pathway and, possibly, lipid synthesis. However, as the reviewers correctly point out, at this point, we have not directly measured changes in the activity or expression of individual enzymes in the TCA cycle or ETC. Therefore, in the next experiment, we extracted mRNA from the cells and performed gene expression analysis using real-time PCR. To make this clear, we have revised the manuscript as follows.

      “Overall, these data indicate that testosterone promotes the redistribution of metabolic flux. In other words, testosterone increased glycolysis in seminal vesicle epithelial cells while decreasing mitochondrial respiration. To determine whether these changes were accompanied by changes in gene expression of specific metabolic-related enzymes, we analyzed gene expression levels.” (Lines 201-205)

      (7) 219: Characterizing ACLY as an enzyme of the ETC is misleading. ACLY is a cytosolic enzyme that connects the TCA cycle with fatty acid synthesis.

      We would like to thank you for pointing out that the description of the function of ACLY could be misunderstood. We agree that characterizing ACLY as an enzyme of the ETC could be misleading. Therefore, we have revised the sentence to clearly indicate that ACLY is a cytosolic enzyme that links the TCA cycle with fatty acid synthesis. The revised text is as follows:

      "Interestingly, testosterone significantly increased the expression of Acly, which encodes a cytoplasmic enzyme that converts citrate transported from the TCA cycle into acetyl-CoA, a substrate that is essential for fatty acid synthesis." (lines216-218)

      (8) 228: Which results support that ETC proteins were upregulated by flutamide?

      We appreciate the reviewer for this point. In preliminary experiments, we analyzed ETC protein expression using real-time qPCR. Our data show that treatment with flutamide significantly upregulates the expression of genes involved in mitochondrial ETC, such as mtND6, while decreasing the expression of the lipogenic genes Acly and Acc. These additional data are now presented in Supplementary Figure S3B. (lines 223-226)

      (9) 245: Aren't the authors showing in Fig. 5 that glut4 expression is reduced in seminal vesicle epithelial cells upon testosterone treatment? How does that fit into the author's hypothesis?

      Thank you for pointing this out. We have already responded to a similar comment from Reviewer 3 in a previous revision. Please refer to our response to Reviewer 3 in a previous version.

      (10) 285: Based on the author's results OA increases the oocyte cleavage rate but then reduces the rate of blastocyst to cleaved oocyte. Doesn't that mean OA affects negatively early development?

      We thank the reviewer for the insightful comment. The one-hour pre-treatment is designed to reflect the transient exposure of sperm to the seminal plasma during ejaculation. In this context, it is unlikely that such a short exposure would impair the overall developmental potential of the embryo. However, although pre-conditioning with oleic acid does not ultimately affect the development of the offspring, it may lead to a decrease in the blastocyst rate at a certain point (approximately 96-120 hours after fertilization). We agree that additional research is needed to demonstrate this.

      Therefore, because the experiments related to the effects of oleic acid on sperm and fertilization are currently incomplete, we have decided to withdraw them for future research.

      (11) 305: What happens to pyruvate and lactate levels when ACLY expression is reduced?

      We appreciate the reviewer’s question regarding the fate of pyruvate and lactate when ACLY expression is reduced. In the absence of testosterone (Ctrl), the expression level of ACLY decreases. At this time, the concentration of pyruvate in the culture medium increased compared to that of testosterone (Testo; Fig. 4D,E). This is probably a reflection of the fact that when the expression of ACLY is suppressed, the rate at which the products of the glycolytic pathway are converted to the fat-producing pathway (i.e., the conversion of citrate to acetyl-CoA) decreases.

      On the other hand, lactate levels did not change significantly. This suggests that the flow of lactate production via lactate dehydrogenase is relatively constant, independent of metabolic reprogramming by ACLY.

      Therefore, our data suggest that a decrease in ACLY expression leads to a decrease in pyruvate demand, while lactate production is maintained. We interpret these findings as supporting the idea that ACLY is important for directing the carbon produced by the glycolytic pathway to lipid synthesis (by transporting citrate from the mitochondria).

      We hope that this explanation clarifies the interpretation of the data.

      Minor revision:

      189: ECAR: extracellular acidification rate. Please correct.

      We have corrected this. (Lines 184-185)

      199: Pyruvate is not synthesized, it is metabolized from PEP. Please correct.

      The following corrections have been made. “pyruvate is metabolized from phosphoenolpyruvic acid through glycolysis”. (Lines 194-195)

      In addition, minor revisions were made to improve the clarity of the overall text.

    1. eLife Assessment

      This useful manuscript provides a newly curated database (termed AACDB) of antibody-antigens structural information, alongside annotations that are either taken and from the PDB, or added de-novo. Sequences, structures, and annotations can be easily downloaded from the AACDB website, speeding up the development of structure-based algorithms and analysis pipelines to characterize antibody-antigen interactions. The methodology presented for this data curation is solid. The curated dataset will be of broad interest and value to researchers interested in antibody-antigen interactions.

    2. Reviewer #1 (Public review):

      This work introduces and describes a useful curation pipeline of antibody-antigen structures downloaded from the PDB database. The antibody-antigen structures are presented in a new database called AACDB - with associated website - alongside annotations that were either corrected from those present in the PDB database, or added de-novo with solid methodology. Sequences, structures and annotations can be very easily downloaded from the AACDB website, speeding up the development of structure-based algorithms and analysis pipelines to characterize antibody-antigen interactions. However, AACDB is missing some important annotations that I believe would greatly enhance its usefulness, such as binding affinity annotations.

      I think the potentially most significant contribution of this database is the manual data curation to fix errors present in the PDB entries, by cross-referencing with the literature. The authors also seem to describe, whenever possible, the procedures they took to correct the annotations.

      I have personally verified some of the examples presented by the authors, and found that SAbDab appears to fix the mistakes related to mis-identification of antibody chains, but not other annotations.

      "(1) the species of the antibody in 7WRL was incorrectly labeled as "SARS coronavirus B012" in both PDB and SabDab" → I have verified the mistake and fix, and that SAbDab does not fix is, just uses the pdb annotation.<br /> "(2) 1NSN, the resolution should be 2.9 , but it was incorrectly labeled as 2.8" → I have verified the mistake and fix, and that saabdab does not fix it, just uses the PDB annotation.<br /> "(3) mislabeling of antibody chains as other proteins (e.g. in 3KS0, the light chain of B2B4 antibody was misnamed as heme domain of flavocytochrome b2)" → SAbDab fixes this as well in this case.<br /> "(4) misidentification of heavy chains as light chains (e.g. both two chains of antibody were labeled as light chain in 5EBW)" → SAbDab fixes this as well in this case.

      I believe the splitting of the pdb files is a valuable contribution as it standardizes the distribution of antibody-antigen complexes. Indeed, there is great heterogeneity in how many copies of the same structure are present in the structure uploaded to the PDB, generating potential artifacts for machine learning applications to pick up on. That being said, I have two thoughts both for the authors and the broader community. First, in the case of multiple antibodies binding to different epitopes on the same antigen, one should not ignore the potentially stabilizing effect that the binding of one antibody has on the complex, thereby enabling the binding of the second antibody. In general, I urge the community to think about what is the most appropriate spatial context to consider when modeling the stability of interactions from crystal structure data. Second, and in a similar vein, some antigens occur naturally as homomultimers - e.g. influenza hemagglutinin is a homotrimer. Therefore, to analyze the stability of a full-antigen-antibody structure, I believe it would be necessary to consider the full homo-trimer, whereas in the current curation of AACDB with the proposed data splitting, only the monomers are present.

      I think the annotation of interface residues is a very useful addition to structural datasets.

      I am, however, not convinced of the utility of *change* in SASA as a useful metric for identifying interacting residues, beyond what is already identified via pairwise distances between the antibody and antigen residues. If we had access to the unbound conformation of most antibodies and antigens, then we could analyze the differences in structural conformations upon binding, which can be in part quantified by change in SASA. However, as only bound structures are usually available, one is usually force to approximate a protein's unbound structure by computationally removing its binding partner - as it seems to me the authors of this work are doing.

      Some obvious limitations of AACDB in its current form include:

      AACDB only contains entries with protein-based antigens of at most 50 amino-acids in length. This excludes non-protein-based antigens, such as carbohydrate- and nucleotide-based, as well as short peptide antigens.<br /> AACDB does not include annotations of binding affinity, which are present in SAbDab and have been proven useful both for characterizing drivers of antibody-antigen interactions (cite https://www.sciencedirect.com/science/article/pii/S0969212624004362?via%3Dihub) and for benchmarking antigen-specific antibody-design algorithms (cite https://www.biorxiv.org/content/10.1101/2023.12.10.570461v1))

    3. Reviewer #2 (Public review):

      Summary:

      Antibodies, thanks to their high binding affinity and specificity to cognate protein targets, are increasingly used as research and therapeutic tools. In this work, Zhou et al. have created, curated and made publicly available a new database of antibody-antigen complexes to support research in the field of antibody modelling, development and engineering.

      Strengths:

      The authors have performed a manual curation of antibody-antigen complexes from the Protein Data Bank, rectifying annotation errors; they have added two methods to estimate paratope-epitope interfaces; they have produced a web interface capable of effective visualisation and of summarising the key useful information in one page. The database is also cross-linked to other databases that contain information relevant to antibody developability and therapeutic applications.

      Weaknesses:

      The database does not import all the experimental information from PDB and contains only complexes with large protein targets.

      Comments on revisions: I thank the authors for having incorporated my feedback and I look forward to the next releases of this database.

    4. Author response:

      The following is the authors’ response to the original reviews

      Public reviews:

      Reviewer #1:

      (1) This manuscript introduces a useful curation pipeline of antibody-antigen structures downloaded from the PDB database. The antibody-antigen structures are presented in a new database called AACDB, alongside annotations that were either corrected from those present in the PDB database or added de-novo with a solid methodology. Sequences, structures, and annotations can be very easily downloaded from the AACDB website, speeding up the development of structure-based algorithms and analysis pipelines to characterize antibody-antigen interactions. However, AACDB is missing some key annotations that would greatly enhance its usefulness.

      Here are detailed comments regarding the three strengths above:

      I think potentially the most significant contribution of this database is the manual data curation to fix errors present in the PDB entries, by cross-referencing with the literature. However, as a reviewer, validating the extent and the impact of these corrections is hard, since the authors only provided a few anecdotal examples in their manuscript.

      I have personally verified some of the examples presented by the authors and found that SAbDab appears to fix the mistakes related to the misidentification of antibody chains, but not other annotations.

      (a) "the species of the antibody in 7WRL was incorrectly labeled as "SARS coronavirus B012" in both PDB and SabDab" → I have verified the mistake and fix, and that SAbDab does not fix is, just uses the pdb annotation.

      (b) "1NSN, the resolution should be 2.9 , but it was incorrectly labeled as 2.8" → I have verified the mistake and fix, and that sabdab does not fix it, just uses the PDB annotation.

      (c) "mislabeling of antibody chains as other proteins (e.g. in 3KS0, the light chain of B2B4 antibody was misnamed as heme domain of flavocytochrome b2)" → SAbDab fixes this as well in this case.

      (d) "misidentification of heavy chains as light chains (e.g. both two chains of antibody were labeled as light chain in 5EBW)" → SAbDab fixes this as well in this case.

      I personally believe the authors should make public the corrections made, and describe the procedures - if systematic - to identify and correct the mistakes. For example, what was the exact procedure (e.g. where were sequences found, how were the sequences aligned, etc.) to find mutations? Was the procedure run on every entry?

      We appreciate the reviewer’s valuable feedback. Our correction procedures combined manual curation with systematic sequence analysis. While most metadata discrepancies were resolved through cross-referencing original literature, we implemented a structured approach for identifying mutations in specific cases. For PDB entries labeled as variants (e.g., "Bevacizumab mutant" or "Ipilimumab variant Ipi.106") where the "Mutation(s)" field was annotated as "NO," we retrieved the canonical therapeutic antibody sequence from Thera-SAbDab, then performed pairwise sequence alignment against the PDB entry using BLAST program to identified mutated residues.

      This procedure was not applied to all entries, as mutations are context-dependent. Therapeutic antibodies have well-defined reference sequences, enabling systematic alignment. For antibodies lacking unambiguous wild-type references (e.g., research-grade or non-therapeutic antibodies), mutation annotations were directly inherited from the PDB or literature.

      All corrections have been publicly archived in AACDB. We have added a detailed discussion of this issue in the section “2.3 Metadata” of revised manuscript.

      (2) I believe the splitting of the pdb files is a valuable contribution as it standardizes the distribution of antibody-antigen complexes. Indeed, there is great heterogeneity in how many copies of the same structure are present in the structure uploaded to the PDB, generating potential artifacts for machine learning applications to pick up on. That being said, I have two thoughts both for the authors and the broader community. First, in the case of multiple antibodies binding to different epitopes on the same antigen, one should not ignore the potentially stabilizing effect that the binding of one antibody has on the complex, thereby enabling the binding of the second antibody. In general, I urge the community to think about what is the most appropriate spatial context to consider when modeling the stability of interactions from crystal structure data. Second, and in a similar vein, some antigens occur naturally as homomultimers - e.g. influenza hemagglutinin is a homotrimer. Therefore, to analyze the stability of a full-antigen-antibody structure, I believe it would be necessary to consider the full homo-trimer, whereas, in the current curation of AACDB with the proposed data splitting, only the monomers are present.

      We sincerely appreciate the reviewer’s insightful comments regarding the splitting of PDB files and we appreciate the opportunity to address the reviewer’s thoughtful concerns.

      Firstly, when two antibodies bind to distinct epitopes on the same antigen, we would like to clarify that this scenario can be divided into two cases based on the experimental context: Case1: When two antibodies bind to distinct epitopes on the same antigen, and their complexes are determined in separate structures. For example, SAR650984 (PDB: 4CMH) and daratumumab (PDB: 7DHA) target CD38 at non-overlapping epitopes. These two antibody-antigen complexes were determined independently, and their structures do not influence each other. Case 2 : When the crystal structure contains a ternary complex with two antibodies and an antigen, as in the example of 6OGE discussed in Section 2.2 of our manuscript. After reviewing the original literature, the experiment confirmed that the order of Fab binding does not affect the formation of the ternary complex, and the binding of one antibody does not enhance the binding of the other. This supports the rationale for splitting 6OGE into two separate structures. However, we acknowledge that not all ternary complexes in the PDB provide such detailed experimental descriptions in their original literature. We agree with the reviewer that in some cases, one antibody may stabilize the structure to facilitate the binding of a second antibody. For instance, in 3QUM, the 5D5A5 antibody stabilizes the structure, enabling the binding of the 5D3D11 antibody to human prostate-specific antigen. Such sandwich complexes are indeed valuable for identifying true epitopes and paratopes. Importantly, splitting the structure does not alter the interaction sites.

      Secondly, we fully agree with the reviewer that for antigens that naturally exist as homomultimers (e.g., influenza hemagglutinin as a homotrimer), the full multimeric structure should be considered when analyzing stability. In such cases, users can directly utilize the original PDB structures provided in their multimeric form. Our splitting approach is intended to provide an additional option for cases where monomeric analysis is sufficient or preferred, but it does not preclude the use of the original multimeric structures when necessary.

      (3) I think the manuscript is lacking in justification about the numbers used as cutoffs (1A^2 for change in SASA and 5A for maximum distance for contact) The authors just cite other papers applying these two types of cutoffs, but the underlying physico-chemical reasons are not explicit even in these papers. I think that, if the authors want AACDB to be used globally for benchmarks, they should provide direct sources of explanations of the cutoffs used, or provide multiple cutoffs. Indeed, different cutoffs are often used (e.g. ATOM3D uses 6A instead of 5A to determine contact between a protein and a small molecule https://datasets-benchmarks-proceedings.neurips.cc/paper/2021/hash/c45147dee729311ef5b5c3003946c48f-Abstract-round1.html). I think the authors should provide a figure with statistics pertaining to the interface atoms. I think showing any distribution differences between interface atoms determined according to either strategy (number of atoms, correlation between change in SASA and distance...) would be fundamental to understanding the two strategies. I think other statistics would constitute an enhancement as well (e.g. proportion of heavy vs. light chain residues).

      Some obvious limitations of AACDB in its current form include:

      AACDB only contains entries with protein-based antigens of at most 50 amino acids in length. This excludes non-protein-based antigens, such as carbohydrate- and nucleotide-based, as well as short peptide antigens.

      AACDB does not include annotations of binding affinity, which are present in SAbDab and have been proven useful both for characterizing drivers of antibody-antigen interactions (cite https://www.sciencedirect.com/science/article/pii/S0969212624004362?via%3Dihub) and for benchmarking antigen-specific antibody-design algorithms (cite https://www.biorxiv.org/content/10.1101/2023.12.10.570461v1)).

      We thank the reviewer for raising this critical point about the cutoff values used in AACDB. In the current study, the selection of the threshold value is very objective; the threshold chosen in the manuscript is summarized based on existing literature, and we have provided more literature support in the manuscript. The criteria for defining interacting amino acids in established tools, typically do not set the ΔSASA exceed 1 Å2 and the distance exceed 6 Å. While our manuscript emphasizes widely accepted thresholds for consistency with prior benchmarks, AACDB explicitly provides raw ΔSASA and distance values for all annotated residues. Users can dynamically filter the data from downloaded files by excluding entries exceeding their preferred thresholds (e.g., selecting 5Å instead of 6Å). This ensures adaptability to diverse research needs. In the revised version, we reset the distance threshold to 6 Å and calculated the interacting amino acids in order to give the user a wider range of choices. In the section “3.2 Database browse and search” of revised manuscript, we provide a description of the flexible choice of thresholds for practical use.

      Furthermore, distance and ΔSASA are two distinct metrics for evaluating interactions. Distance directly quantifies spatial proximity between atoms, reflecting physical contacts such as van der Waals interactions or hydrogen bonds, and is ideal for identifying direct spatial adjacency. ΔSASA, on the other hand, measures changes in solvent accessibility of residues during binding, capturing the contribution of buried surfaces to binding free energy. Even for residues not in direct contact, reduced SASA due to conformational changes may indicate indirect functional roles.

      As demonstrated through comparisons on the detailed information pages, the sets of interacting amino acids defined by these two methods differ by only a few residues, with no significant variation in their overall distributions. However, since interaction patterns vary significantly across different complexes, analyzing residue distributions across all structures using both criteria is not feasible.

      We thank the reviewer for highlighting these limitations. AACDB currently focuses on protein-based antigens ≤50 amino acids to prioritize structural consistency, which excludes non-protein antigens and shorter peptides. While affinity annotations are critical for benchmarking antibody design tools, these data were not integrated in this release due to insufficient data verification caused by internal team constraints. We acknowledge these gaps and plan to expand antigen diversity and incorporate affinity metrics in future updates.

      Reviewer #2:

      Summary:

      Antibodies, thanks to their high binding affinity and specificity to cognate protein targets, are increasingly used as research and therapeutic tools. In this work, Zhou et al. have created, curated, and made publicly available a new database of antibody-antigen complexes to support research in the field of antibody modelling, development, and engineering.

      Strengths:

      The authors have performed a manual curation of antibody-antigen complexes from the Protein Data Bank, rectifying annotation errors; they have added two methods to estimate paratope-epitope interfaces; they have produced a web interface that is capable of both effective visualisation and of summarising the key useful information in one page. The database is also cross-linked to other databases that contain information relevant to antibody developability and therapeutic applications.

      Weaknesses:

      The database does not import all the experimental information from PDB and contains only complexes with large protein targets.

      Thank you for the valuable feedback. As previously responded to Reviewer 1, due to limitations within our team, comprehensive data integration from PDB has not been achieved in the current version. We acknowledge the significance of expanding the database to encompass a broader range of experimental information and complexes with diverse target sizes. Regrettably, immediate updates to address these limitations are not feasible at this time. Nevertheless, we are committed to enhancing the database in upcoming upgrades to provide users with a more comprehensive and inclusive resource

      Recommendations for the authors:

      Reviewer #1:

      (1) Line 194: "produce" → "produced"

      We thank the reviewer for the feedback. We have checked the grammar and spelling carefully in the revised manuscript.

      (2) As mentioned in the public review, I think adding binding affinity annotations would greatly enhance the use cases for the database.

      We thank the reviewer for the suggestion. As the response in “Public review”. Due to team constraints, these data are not integrated into this release but are being collated. We recognize these gaps and plan to expand antigenic diversity and incorporate affinity metrics in future updates.

      (3) I think adding a visualization of interface atoms and contacts on an entry's webpage would be useful for someone exploring specific entries. It also would be useful if the authors provided a pymol command to select interface residues since that's a procedure any structural biologist is likely to do.

      We sincerely appreciate the reviewer’s constructive suggestions. In response to the request for enhanced visualization and accessibility of interface residue information, we have implemented the following improvements: (1) Web Interface Visualization. On the entry-specific webpage, we have added an interactive visualization window that highlights the antigen-antibody interaction interface using distinct colors. The interaction interface visualization has been incorporated into Figure 5 of the revised manuscript, with a detailed description. (2) PyMOL Command Accessibility. The “Help” page now provides step-by-step PyMOL commands to select and visualize interface residues.

      (4) I think the authors should provide headers to the files containing interface residues according to the change-in-SASA criterion, as they do for those computed according to contact. This would avoid unnecessary confusion - however slight - and make parsing easier. I was initially confused by the meaning of the last column, though after a minute I understood it to be the change in SASA.

      We thank the reviewer for providing such detailed feedback. We thank the reviewer for the comment and the suggestion. We have provided headers for the files of the interacting residues defined by ΔSASA.

      (5) Line 233: "AACDB's data processing pipeline supports mmCIF files" → The meaning and implications of this statement are not obvious to me, and are mentioned nowhere else in the paper. Do you mean that in AACDB there are structure entries that the RCSB PDB database only has in mmCIF file format, and not .pdb format? So, effectively, there are some entries in AACDB that are not in any other antibody-specific database?I checked and, as of Dec 3rd, 2024, there are 41 structures in AACDB that are NOT in SAbDab. Manually checking 5 of those 41 structures, none are mmCIF-only structures.

      We thank the reviewer for the valuable comment. Because of the size of the structures within certain entries, representing them in a single PDB format data file is not feasible due to the excessive number of atoms and polymer chains they contain. As a result, PDB stores these structures in “mmcif” format files. In AACDB, 47 entries, such as 7SOF, 7NKT, 7B27, and 6T9D, are only available in the “mmCIF” format from the PDB. The “.pdb” and “.cif” files contain atomic coordinates in distinct text formats, and the segmentation of these structure files is automatically conducted based on manually annotated antibody-antigen chains. To accommodate this, we have incorporated these considerations into our file processing pipeline, thereby enabling a fully automated file segmentation process. Additionally, we employed Naccess to calculate interatomic distances. However, since this software only accepts .pdb format files as input, we also converted all split .cif files into .pdb format within our fully automated pipeline. We apologize for the lack of clarity in the original manuscript and have included a more detailed explanation in the "2.2 PDB Splitting" section of the revised manuscript.

      Reviewer #2:

      (1) In SabDab and PDB, experimental binding affinities are also reported: could the authors comment on whether they also imported this information and double-checked it against the original paper? If it wasn't imported, that might discourage some users and should be considered as an extension for the future.

      We thank the reviewer for the comment and the suggestion. As the response in “Public review”. Due to current resource constraints, quantitative affinity data has not been incorporated into this release but is undergoing systematic curation. We explicitly recognize these limitations and propose a two-pronged strategy for future iterations: (1) broadening antigen diversity coverage through expanded structural sampling, and (2) integrating quantitative binding affinity measurements. In the Discussion section, we have included description outlining the planned enhancements.

      (2) Line 49-50: the references mentioned in connection to deep learning methods for antibody-antigen predictions seem a bit limited given the amount of articles in this field, with 3 of 4 references on one method only (SEPPA), could the authors expand this list to reflect a bit more the state of the art?

      We thank the reviewer for the suggestion. We agree that more relevant studies should be listed and therefore more references are provided in the revised manuscript.

      When mentioning the limitations of the existing databases, it feels a bit that the criticism is not fully justified. For instance:

      Line 52-53: could the authors elaborate on the reasons why such an identification is challenging? (Isn't it possible to make an efficient database-filtered search? Or rather, should one highlight that a more focussed resource is convenient and why?)

      Thank you for feedback. In this study, the keywords "antibody complex," "antigen complex," and "immunoglobulin complex," were employed during data collection. PDB returned over 30,000 results, of which only one-tenth met our criteria after rigorous filtering. This demonstrates that keyword searches, while useful, inherently limit result precision and introduce substantial redundancy, likely due to the PDB's search mechanism. That’s why we illustrated the significant challenges in identifying antibody-antigen complexes from general protein structures in the PDB.

      Line 55: reading the website http://www.abybank.org/abdb/, it would be fairer to say that the web interface lacks updates, as the database and the code have gone through some updates. Could the authors provide a concrete example of the reason why: 'The AbDb database currently lacks proper organization and management of this valuable data.'?

      We thank the reviewer for highlighting this issue. In our original manuscript, the statement that the AbDb database "lacks proper organization and management" was based on the absence of explicit statement regarding data updates on its official website at the time of submission, even though internal updates to its content may have occurred. We fully respect the long-standing contributions of AbDb to antibody structural research, and our comments were solely directed at the specific state of the database at that time. As the reviewer noted, following the release of our preprint, we have also taken note of AbDb's recent updates. To reflect the latest developments and avoid potential misinterpretation, we have revised the original statement in revised manuscript.

      Also 'this rapid updating process may inadvertently overlook a significant amount of information that requires thorough verification,': it's difficult for me to understand what this means in practice. Could the authors clarify if they simply mean that SabDab collects information from PDB and therefore tends to propagate annotation errors from there? If yes, I think it's enough to state it in these terms, and for sure I agree that the reason is that correcting these annotation errors requires a substantial amount of work.

      We thank the reviewer for providing such detailed feedback on the manuscript. We acknowledge that SabDab represents a highly valuable contribution to the field, and its rapid update mechanism has significantly advanced related research areas. However, as stated by the reviewer, we aim to clarify that SabDab primarily relies on automated metadata extraction from the PDB for annotation, and its rapid update process inherently inherits raw data from upstream sources. According to their paper, manual curation is only applied when the automated pipeline fails to resolve structural ambiguities. This workflow—dependent on PDB annotations with limited manual verification—may propagate errors provided by PDB. Examples include species misannotation and mutation status misinterpretation. We fully agree with the reviewer's observation that correcting errors in such cases necessitates labor-intensive manual curation, which is a core motivation for our study.

      Line 86: why 'Structures that consisted solely of one type of antibody were excluded'? Why exclude complexes with antigens shorter than 50 amino acids? These complexes are genuine antibody-antigen complexes.

      We thank the reviewer for the valuable question. The AACBD database is dedicated to curating structural data of antigen-antibody complexes. Structures featuring only a single antibody type are classified as free antibodies and systematically excluded from the database due to the absence of protein-bound partners. During data screening , we retained sequences shorter than 50 amino acids by categorizing them as peptides rather than eliminating them outright. The current release exclusively encompasses complexes with protein-based antigens. Meanwhile, complexes involving peptide, haptens, and nucleic acid antigens are undergoing systematic curation, with planned inclusion in future updates to broaden antigen category representation.

      Line 96 needs a capital letter at the beginning.

      Line 107: 'this would generate' → 'this generates' (given it is something that has been implemented, correct?).

      Line 124: missing an 'of'.

      Line 163: inspiring by -> inspired by.

      Thank you for feedback. All of the above grammatical or spelling errors have been revised in the manuscript.

      Line 109-111: apart from the example, it would be good to spell out the general rule applied to anti-idiotypic antibodies.

      We thank the reviewer for the valuable feedback. For anti-idiotypic antibodies complex. the partner antibody is treated as a dual-chain antigen, , necessitating individual evaluation of heavy chain and light chain interactions with the anti-idiotypic component. We have given a general rule for anti-idiotypic antibodies in section “2.2 PDB splitting” of revised manuscript.

      Line 155-159: could the authors provide references for the two choices (based on sasa and any-atom distance) that they adopted to define interacting residues?

      We thank the reviewer for the comment and the suggestion. As the same as the response to reviewer #1 in Public review. The interacting residues definition and the threshold chosen in the manuscript is summarized based on existing literature. We have added additional references for support in section “1.Introduction”. Our resource does not provide a fixed amino acid list. Instead, all interacting residues are explicitly documented alongside their corresponding ΔSASA (solvent-accessible surface area changes) and intermolecular distances, allowing researchers to flexibly select residue pairs based on customized thresholds from downloadable datasets. Furthermore, aligning with widely adopted criteria in current literature—where interactions are defined by ΔSASA >1 Ų and atomic distances <6 Å, we have recalibrated our analysis in the revised version. Specifically, we replaced the previous 5 Å distance threshold with a 6 Å cutoff to recalculate interacting residues.

      Line 176-178: could the authors re-phrase this sentence to clarify what they mean by 'change in the distribution'?

      We thank the reviewer for the suggestion. Our search was conducted with an end date of November 2023. However, Figure 3B includes an entry dated 2024. Upon reviewing this record, we identified that the discrepancy arises from the supersession of the 7SIX database entry (originally released in December 2022) by the 8TM1 version in January 2024. This version update explains the apparent chronological inconsistency. We regret any lack of clarity in our original description and have revised the corresponding section in the manuscript to explicitly clarify this change of database.

      Caption Figure 3: please spell out all the acronyms in the figure. Provide the date when the last search was performed (i.e., the date of the last update of these statistics).

      We thank the reviewer for the comment. We have systematically expanded all acronyms and included update dates for statistics in the legend of Figure 3. Corresponding changes have also been made to the statistical pages on the website.

      Finally, it would be advisable to do a general check on the use of the English language (e.g. I noted a few missing articles). In Figure 5 DrugBank contains typos.

      We sincerely appreciate the reviewer's meticulous attention to linguistic precision. We have corrected the typographical error in Figure 5 and conducted a comprehensive review of the entire manuscript to ensure accuracy and clarity.

    1. eLife Assessment

      The authors present an important set of data implicating ETFDH as an epigenetically suppressed gene in cancer with tumor suppressive functions. The evidence is solid, with the authors demonstrating that ETFDH suppression results in accumulation of amino acids that impact metabolism via hyperactive mTORC1.

    2. Reviewer #1 (Public review):

      In their manuscript, Papadopoli et al explore the role of ETFDH in transformation. They note that ETFDH protein levels are decreased in cancer, and that deletion of ETFDH in cancer cell lines results in increased tumorigenesis, elevated OXPHOS and glycolysis, and a reduction in lipid and amino acid oxidation. The authors attribute these effects to increased amino acid levels stimulating mTORC1 signaling and driving alterations in BCL6 and EIF4EBP1. They conclude that ETFDH1 is epigenetically silenced in a proportion of neoplasms, suggesting a tumor-suppressive function. Overall, the authors logically present clear data and perform appropriate experiments to support their hypotheses. I only have a few minor points related to the semantics of a few of the author's statements.

      Minor Points

      Authors state, "we identified ETF dehydrogenase (ETFDH) as one of the most dispensable metabolic genes in neoplasia." Surely there are thousands of genes that are dispensable for neoplasia. Perhaps the authors can revise this sentence and similar sentiments in the text.

      Authors state, " These findings show that ETFDH loss elevates glutamine utilization in the CAC to support mitochondrial metabolism." While elevated glutamine to CAC flux is consistent with the statement that increased glutamine, the authors have not measured the effect of restoring glutamine utilization to baseline on mitochondrial metabolism. Thus, the causality implied by the authors can only be inferred based on the data presented. Indeed, the increased glutamine consumption may be linked to the increase in ROS, as glutamate efflux via system xCT is a major determinant of glutamine catabolism in vitro.

      Authors state that the mechanism described is an example of "retrograde signaling". However, the mechanism seems to be related to a reduction in BCAA catabolism, suggesting that the observed effects may be a consequence of altered metabolic flux rather than a direct signaling pathway. The data presented do not delineate whether the observed effects stem from disrupted mitochondrial communication or from shifts in nutrient availability and metabolic regulation.

      The authors should discuss which amino acids that are ETFDH substrates might affect mTORC1 activity, or consider whether other ETFDH substrates might also affect mTORC1 in their discussion. Along these lines, the authors might consider discussing why amino acids that are not ETFDH substrates are increased upon ETFDH loss.

    3. Reviewer #2 (Public review):

      Summary:

      The altered metabolism of tumors enables their growth and survival. Classically, tumor metabolism often involves increased activity of a given pathway in intermediary metabolism to provide energy or substrates needed for growth. Papadopoli et al. investigate the converse - the role of mitochondrial electron transfer flavoprotein dehydrogenase (ETFDH) in cancer metabolism and growth. The authors present compelling evidence that ETFDH insufficiency, which is detrimental in non-malignant tissues, paradoxically enhances bioenergetic capacity and accelerates neoplastic growth in cancer cells in spite of the decreased metabolic fuel flexibility that this affords tumor cells. This is achieved through the retrograde activation of the mTORC1/BCL-6/4E-BP1 axis, leading to metabolic and signaling reprogramming that favors tumor progression.

      Strengths:

      This review focuses primarily on the cancer metabolism aspects of the manuscript.

      The study provides robust evidence linking ETFDH insufficiency to enhanced cancer cell bioenergetics and tumor growth.

      The use of multiple cancer cell lines and in vivo models strengthens the generalizability of the findings.

      The mechanistic insights into the mTORC1/BCL-6/4E-BP1 axis and its role in metabolic reprogramming are of general interest within and outside the immediate field of tumor metabolism.

      Weaknesses:

      The ETFDH knockout experiments are well-controlled by the addback of sgRNA-resistant ETFDH, but do not determine if the catalytic activity of this enzyme is required for the phenotypes induced by ETFDH loss.

      Although this is not critical, it would be nice to see if the increased labeled aspartate pools result in higher nucleotide pools to support tumor growth.

      Conclusion:

      This manuscript provides significant insights into the role of ETFDH insufficiency in cancer metabolism and growth. The findings highlight the potential of targeting the mTORC1/BCL-6/4E-BP1 axis in ETFDH-deficient cancers. The compelling data support the conclusions presented in the manuscript, which will be valuable to the cancer metabolism community.

    4. Author response:

      We are highly appreciative of your constructive criticism and that you found that our findings of interest and significance. Based on your helpful suggestions, we plan to revise the paper as following:

      (1) Although ETFDH is reduced, but not mutated across neoplasia, we appreciate your point pertinent to catalytically activity of ETFDH. To this end, in the revision we are planning to compare the effects of rescues using wild type ETFDH or one of the MADD-associated mutants with compromised catalytic activity.

      (2) We intend to measure steady-state nucleotide levels as a function of ETFDH status in the cell. If time and/or funding allow, we will also perform appropriate labelling experiments.

      (3) We will revise the text of the manuscript to address the minor points raised by the reviewers.

      Again, we would like to thank you for helpful comments, which we aim to address as outlined above and hopefully further improve our report.

    1. eLife Assessment

      This important paper reports the discovery of calcarins, a protein family that seems to be involved in calcification in the calcareous sponge Sycon ciliatum, significantly enhancing our understanding of the molecular and cellular mechanisms underlying spicule formation in sponges and the evolution of carbonate biomineralization. The conclusions are supported by compelling evidence based on an integrated analysis that combines transcriptomics, genomics, proteomics, and precise in situ hybridization. These findings will be of broad interest to cell biologists, biochemists, and evolutionary biologists.

    2. Reviewer #1 (Public review):

      To elucidate the mechanisms and evolution of animal biomineralization, Voigt et al. focused on the sponge phylum - the earliest branching extant metazoan lineages exhibiting biomineralized structures - with a particular emphasis on deciphering the molecular underpinnings of spicule formation. This study centered on calcareous sponges, specifically Sycon ciliatum, as characterized in previous work by Voigt et al. In S. ciliatum, two morphologically distinct spicule types are produced by a set of two different types of cells that secrete extracellular matrix proteins, onto which calcium carbonate is subsequently deposited. Comparative transcriptomic analysis between a region with active spicule formation and other body regions identified 829 candidate genes involved in this process. Among these, the authors focused on the calcarine gene family, which is analogous to the Galaxins, the matrix proteins known to participate in coral calcification. The authors performed three-dimensional structure prediction using AlphaFold, examined mRNA expression of Calcarin genes in spicule-forming cell types via in situ hybridization, conducted proteomic analysis of matrix proteins isolated from purified spicules, and carried out chromosome arrangement analysis of the Calcarin genes.

      Based on these analyses, it was revealed that the combination of Calcarin genes expressed during spicule formation differs between the founder cells-responsible for producing diactines and triactines-and the thickener cells that differentiate from them, underscoring the necessity for precise regulation of Calcarin gene expression in proper biomineralization. Furthermore, the observation that 4 Calcarin genes are arranged in tandem arrays on the chromosome suggests that two rounds of gene duplication followed by neofunctionalization have contributed to the intricate formation of S. ciliatum spicules. Additionally, similar subtle spatiotemporal expression patterns and tandem chromosomal arrangements of Galaxins during coral calcification indicate parallel evolution of biomineralization genes between S. ciliatum and aragonitic corals.

      Strengths:

      (1) An integrative research approach, encompassing transcriptomic, genomic, and proteomic analyses as well as detailed FISH.

      (2) High-quality FISH images of Calcarin genes, along with a concise summary clearly illustrating their expression patterns, is appreciated.

      (3) It was suggested that thickener cells originate from founder cells. To the best of my knowledge, this is the first study to demonstrate trans-differentiation of sponge cells based on the cell-type-specific gene expression, as determined by in situ hybridization.

      (4) The comparison between Calcarins of Calcite sponge and Galaxins of aragonitic corals from various perspective-including protein tertiary structure predictions, gene expression profiling during calcification, and chromosomal sequence analysis to reveal significant similarities between them.

      (5) The conclusions of this paper are generally well supported by the data; however, some FISH images require clearer indication or explanation.

      (6) Figure S2 (B, C, D): The fluorescent signals in these images are difficult to discern. If the authors choose to present signals at such low magnification, enhancing the fluorescence signals would improve clarity. Additionally, incorporating Figure S2A as an inset within Figure S2E may be sufficient to convey the necessary information about signal localization.

      (7) Figure S3A: The claim that Cal2-expressing spherical cells are closely associated with the choanoderm at the distal end of the radial tube is difficult to follow. Are these Cal2-expressing spherical cells interspersed among choanoderm cells, or are they positioned along the basal surface of the choanoderm? Clarifying their precise localization and indicating it in the image would strengthen the interpretation.

      (8) To further highlight the similarities between S.ciliatum and aragonitic corals in the molecular mechanisms of calcification, consider including a supplementary figure providing a concise depiction of the coral calcification process. This would offer valuable context for readers.

    3. Reviewer #2 (Public review):

      Summary:

      This paper reports on the discovery of calcarins, a protein family that seems involved in calcification in the sponge Sycon ciliatum, based on specific expression in sclerocytes and detection by mass spectrometry within spicules. Two aspects stand out: (1) the unexpected similarity between Sycon calcarins and the galaxins of stony corals, which are also involved in mineralization, suggesting a surprising, parallel co-option of similar genes for mineralization in these two groups; (2) the impressively cell-type-specific expression of specific calcarins, many of which are restricted to either founder or thickener cells, and to either diactines, triactines, or tetractines. The finding that calcarins likely diversified at least partly by tandem duplications (giving rise to gene clusters) is a nice bonus.

      Strengths:

      I enjoyed the thoroughness of the paper, with multiple lines of evidence supporting the hypothesized role of calcarins: spatially and temporally resolved RNAseq, mass spectrometry, and whole-mount in situ hybridization using CISH and HCR-FISH (the images are really beautiful and very convincing). The structural predictions and the similarity to galaxins are very surprising and extremely interesting, as they suggest parallel evolution of biomineralization in sponges and cnidarians during the Cambrian explosion by co-option of the same "molecular bricks".

      Weaknesses:

      I did not detect any major weakness, beyond those inherent to working with sponges (lack of direct functional inhibition of these genes) or with fast-evolving gene families with complex evolutionary histories (lack of a phylogenetic tree that would clarify the history of galaxins/calcarins and related proteins).

    4. Reviewer #3 (Public review):

      Summary:

      The study explores the extent to which the biomineralization process in the calcitic sponge Sycon ciliatum resembles aragonitic skeleton formation in stony corals. To investigate this, the authors performed transcriptomic, genomic, and proteomic analyses on S. ciliatum and examined the expression patterns of biomineralization-related genes using in situ hybridization. Among the 829 differentially expressed genes identified in sponge regions associated with spicule formation, the authors focused on calcarin genes, which encode matrix proteins analogous to coral galaxins. The expression patterns of calcarins were found to be diverse but specific to particular spicule types. Notably, these patterns resemble those of galaxins in stony corals. Moreover, the genomic organization of calcarine genes in S. ciliatum closely mirrors that of galaxin genes in corals, suggesting a case of parallel evolution in carbonate biomineralization between calcitic sponges and aragonitic corals.

      Strengths:

      The manuscript is well written, and the figures are of high quality. The study design and methodologies are clearly described and well-suited to addressing the central research question. Particularly noteworthy is the authors´ integration of various omics approaches with molecular and cell biology techniques. Their results support the intriguing conclusion that there is a case of parallel evolution in skeleton-building gene sets between calcitic sponges and aragonitic corals. The conclusions are well supported by the data and analyses presented.

      Weaknesses:

      The manuscript is strong, and I have not identified any significant weaknesses in its current form.

    5. Author response:

      We sincerely thank all reviewers for their thoughtful, detailed, and supportive evaluations of our manuscript. We are very pleased that the reviewers appreciated the integrative approach of our study, the quality of the imaging and analyses, and the insights provided into the parallel evolution of biomineralization mechanisms in sponges and corals.

      We are carefully considering all the suggestions made, including those regarding the improvement of figure clarity and the clarification of certain image interpretations. These comments are extremely valuable, and we are preparing a detailed point-by-point reply to accompany our revised manuscript.

      It was also brought to our attention that the links to the Zenodo repository were incorrect. We apologize for this oversight and any inconvenience it may have caused and will updae the links in our revised manuscript. In the meantime, the correct Zenodo repositories can be accessed using the following links:

      https://zenodo.org/records/14755899

      https://zenodo.org/records/13847772

      We again thank the reviewers for their constructive feedback, which will help us to further strengthen the manuscript.

    1. eLife Assessment

      This study provides important insights into the regulation of neuroblast lifespan and proliferation in the Drosophila mushroom body, identifying Krüppel (Kr) as a key transcription factor promoting timely termination of these neuroblasts by repressing Imp expression, and proposes an antagonistic role of Krüppel homolog 1 (Kr-h1), whose overexpression leads to prolonged mushroom body neuroblast proliferation and tumor-like expansion. The findings are impactful for researchers interested in temporal patterning and neural development, and the methods and data analysis are solid, however, the precise regulatory interactions between Kr and Kr-h1 and their modes of action remain incompletely tested. Further experiments would be required to fully elucidate the mechanistic interplay between the factors involved.

    2. Reviewer #1 (Public review):

      Summary:

      In this manuscript, the authors investigated factors required for neural progenitors to exit the cell cycle before the adult stage. They first show that Kr is turned on in pupal stage MBNBs, and depletion of Kr from pupal stage NBs leads to retention of MBNBs into the adult stage. Then they demonstrate that these retained NBs maintain the expression of Imp, and co-depletion of Imp abolishes the extended neurogenesis. Further, they show that co-depletion of kr-h1 significantly reduces the retained MBNBs caused by loss of kr, suggesting antagonistic genetic interactions between these two. In addition, they demonstrate that over-expressing Kr-h1 leads to the striking phenotype of tumor-like neuroblast overgrowth in adult brains.

      Strengths:

      (1) The authors leveraged well-controlled, powerful genetic tools (including temporal control of RNAi knockdown using the Gal80ts system), and provided strong evidence that Kr expression in pupal stage MBNBs is required to repress Imp and promote the end of neurogenesis. Similarly, the experimental result of co-depleting Kr-h1 and Kr, and the striking phenotype upon Kr-h1 mis-expression, support the antagonistic roles played by Kr-h1 and Kr in this process.

      (2) The sample sizes, quantification methods, and p-values are well documented for all experiments. In most parts, the data presented strongly support their conclusions.

      (3) Identification of two transcription factors with opposite roles in controlling cell cycle exit, and their possible interactions with the Imp/Syp axis, is highly significant for the study on how the proliferation of neural progenitors is regulated and limited before the adult stage.

      Weaknesses:

      (1) The nature of the KrIf-1 allele is not clear. It is mentioned that this allele leads to misexpression of Kr in various tissues. However, it is not clear if Kr is mis-expressed or lost in MBNBs in the KrIf-1 mutant. If Kr is mis-expressed in MBNBs in the KrIf-1 mutant, then it would be difficult to explain why both loss of Kr and mis-expression of Kr in MBNBs lead to the same NB retention phenotype. The authors should examine Kr expression in MBNBs in the KrIf-1 mutant.

      (2) Some parts of the regulations and interactions between Kr, Kr-h1, Imp, Syp, and E93 are not well-defined. For example, the data suggest that Kr is turned on in the pupal stage MBNBs, and is required to end neurogenesis through repressing Imp and Kr-h1. To further support this conclusion, the authors can examine if Kr-h1 expression is up-regulated in kr-RNAi. The authors suggested that Kr-h1 may act upstream or in parallel to Imp/Syp, but also suggested that Kr-h1 may repress E93. The expression of Imp, Syp, and E93 can be examined in brains with Kr-h1 mis-expression to determine where Kr-h1 acts. If Imp expression is elevated when Kr-h1 is mis-expressed, then Kr-h1 may act upstream of Imp. If Imp/Syp expression does not change, then Kr-h1 may act on the E93 level.

    3. Reviewer #2 (Public review):

      Summary:

      In this paper, the authors study the role of Kruppel in regulating the survival of mushroom body neuroblasts. They first confirm that adult wild-type brains have no proliferation and report that Kruppel mutants and Kruppel RNAi in neuroblasts show a few proliferative clones; they show that these proliferative clones are localized in the mushroom body. They then show that Kruppel is expressed mostly during pupal stages and acts by downregulating the expression of Imp, which has been shown to positively regulate neuroblast proliferation and survival. Expectedly, this also affects neuronal diversity in the mushroom body, which is enriched in gamma neurons that are born during the Imp-expression window. Finally, they show that Kr acts antagonistically to Kr-h1, which is expressed predominantly in larval stages.

      Strengths:

      The main strength of this paper is that it identified a novel regulator of Imp expression in the mushroom body neuroblasts. Imp is a conserved RNA-binding protein that has been shown to regulate neural stem cell proliferation and survival in different animals.

      Weaknesses:

      (1) The main weakness of the paper is that the authors want to test adult neurogenesis in a system where no adult neurogenesis exists. To achieve this, they force neuroblasts to survive in adulthood by altering the genetic program that prevents them from terminating their proliferation. If this was reminiscing about "adult neurogenesis", the authors should at least show how adult neurons incorporate into the mushroom body even if they are born much later. On the contrary, this more likely resembles a tumorigenic phenotype, when stem cells divide way past their appropriate timing.

      (2) Moreover, the figures are, in many cases, hard to understand, and the interpretation of the figures doesn't always match what one sees. The manuscript would benefit from better figures; for example, in Figure 2C, Miranda expression in insc>GFP in Kr-IF-1 is not visible.

      (3) The authors describe a targeted genetic screen, but they don't describe which genes were tested, how they were chosen, and why Kruppel was finally selected.

      (4) The authors argue that Kr does not behave as a typical tTF in MBNBs. However, they show no expression in the embryo, limited expression in the larva and early pupa, and a peak around P24-P48. This sounds like a temporally regulated expression of a transcription factor. Importantly, they mentioned that they tested their observations against different datasets (FlyAtlas2, modENCODE, and MBNB-lineage-specific RNA-seq data), but they don't provide the data.

      (5) Finally, the contribution of Kr to the neuronal composition of the mushroom body is expected (since Imp is known to regulate neuronal diversity in the MB), but the presentation in the paper is very incomplete.

      Unfortunately, based on the above, I am not convinced that the authors can use this framework to infer anything about adult neurogenesis. Therefore, the impact of this work is limited to the role of Kruppel in regulating Imp, which has already been shown to regulate the extent of neuroblast division, as well as the neuronal types that are born at different temporal windows.

    4. Reviewer #3 (Public review):

      Summary:

      Drosophila neuroblasts (NBs) serve as a well-established model for studying neural stem cell biology. The intrinsic genetic programs that control their mitotic potential throughout development have been described in remarkable detail, highlighting a series of sequentially expressed transcription factors and RNA-binding proteins that together constitute the temporal patterning system.

      However, the mechanisms that limit the number of NB divisions remain largely unknown in a specific subset of NBs known as mushroom body neuroblasts (MB NBs). Unlike other NBs, which terminate proliferation before or shortly after the onset of metamorphosis, MB NBs continue dividing until the end of metamorphosis, ceasing only just before adulthood.<br /> In this study, the authors identify the transcription factor Krüppel (Kr), a member of the conserved Krüppel-like family, as temporally regulated in MB NBs. They demonstrate that Kr knockdown during pupal stages maintains expression of the RNA-binding protein Imp and results in prolonged MB NB proliferation into adulthood. Their data suggest that Kr contributes to the timely silencing of Imp during metamorphosis. The authors further identify Kr-h1, a related transcription factor, as a potential antagonist. While Kr-h1 appears dispensable for the timely termination of MB NBs under normal conditions, its overexpression leads to their continued proliferation and tumor-like expansion in adults.

      This work provides the first evidence for a transcription factor-driven temporal regulation mechanism in MB NBs, offering new insight into the control of neural stem cell self-renewal. Given the evolutionary conservation of Krüppel-like factors, this study may have broader implications for the neural stem cell field.

      Strengths:

      (1) The study possibly identifies a new series of temporal transcription factors that are specific for mushroom body neuroblasts.

      (2) The mechanism could be conserved in vertebrates.

      Weaknesses:

      Some proposed regulatory interactions, particularly between Kr, Kr-h1, and other temporal factors like Imp, Chinmo, and E93, have not been thoroughly investigated, which weakens the support for the proposed model. Additional experimental validation is needed to confirm these relationships and strengthen the mechanistic framework.

    5. Author response:

      We thank the editors and reviewers for their thoughtful and constructive evaluation of our manuscript, “Krüppel Regulates Cell Cycle Exit and Limits Adult Neurogenesis of Mushroom Body Neural Progenitors in Drosophila.” We are pleased that all reviewers recognised the novelty and significance of identifying Krüppel (Kr) as a key transcription factor promoting timely termination of mushroom body neuroblast (MBNB) proliferation, and the potential antagonistic function of Kr-h1.

      We appreciate the helpful suggestions aimed at improving the mechanistic clarity and presentation of our findings. Below, we outline how we plan to address the major points raised in the full revision.

      (1) Characterisation of the KrIf-1 allele and Kr expression

      We agree that clarifying the nature of the KrIf-1 allele is important. In response to this concern, we will examine Kr expression in KrIf-1 mutant larval, pupal, and adult brains using immunostaining and available reporter lines. These experiments will help determine whether the observed neuroblast retention phenotype correlates with altered Kr expression in MBNBs.

      (2) Regulatory relationships between Kr, Kr-h1, Imp, Syp, Chinmo, and E93

      We are currently performing additional experiments to clarify the interactions among these temporal factors. For instance, we are testing whether Kr-h1 overexpression alters the expression of Imp, Syp, and E93. We have obtained a published E93 antibody from Dr Chris Doe (Syed et al., 2017) and will include E93 expression analysis in our revised manuscript.

      While Chinmo is of interest, its expression is well established to be regulated downstream of Imp/Syp via mRNA stability (Liu et al., 2015; Ren et al., 2017). Given that we currently lack reliable tools to assess Chinmo levels, we will focus primarily on Imp, Syp, and E93 as readouts for Kr/Kr-h1 function. If we succeed in obtaining Chinmo antibodies or reporter lines in time, we will include corresponding data.

      (3) Expression of Kr-h1 in MBNBs

      We fully agree that direct evidence for Kr-h1 expression in MBNBs is important. To address this, we have obtained the Kr-h1::GFP BAC transgenic line (BDSC #96786) and are currently using it to assess Kr-h1 expression in MBNBs. We also tested an anti–Kr-h1 antibody previously reported by Kang et al. (2017), developed in the context of fat body studies, but it did not yield clear signals in larval MBNBs. However, previous work by Shi et al. (2007) clearly demonstrated Kr-h1 expression in the developing MB, including MBNBs, using a custom antibody developed by their lab. We also contacted the Lee lab to request this antibody, but unfortunately, it is no longer available. We will include the results obtained using the GFP BAC line in the revised manuscript and, if needed, pursue RNA in situ hybridisation to further validate Kr-h1 expression in MBNBs.

      (4) Temporal Kr knockdown and MARCM analysis

      We appreciate the suggestion to validate our RNAi-based temporal knockdown results using MARCM. We plan to perform MBNB-specific MARCM analysis following the strategy described by Rossi et al. (2020). However, this approach requires additional time due to the logistics of acquiring the necessary fly stocks, generating appropriate genetic combinations, and conducting clonal analyses. While we will make every effort to include these data, we note that RNAi-based knockdown offers the advantage of temporal reversibility and has been essential for assessing stage-specific requirements in our current study.

      (5) Details of the targeted genetic screen

      Kr was initially identified as part of a broader, ongoing effort to screen for candidate transcription factors and cell cycle regulators involved in neuroblast cell cycle exit and/or quiescence. As this screen is still preliminary and incomplete, we prefer not to include the full dataset at this stage. Instead, we will revise the manuscript to clarify that Kr was prioritised for further investigation based on the striking MBNB-specific phenotype observed upon RNAi-mediated knockdown and in the KrIf-1 mutant, rather than through a completed screening process.

      (6) Clarifying the model (Figure 6D) and interactions

      We will revise the proposed model to distinguish between experimentally supported interactions and speculative ones. As noted above, we will primarily focus on the Imp/Syp and E93 axis in relation to Kr and Kr-h1 activity. Chinmo will be omitted from the model unless further data become available to support its inclusion.

      (7) Clarifications on figures and data presentation

      We appreciate the feedback on figure clarity. We will revise figures such as 1B, 2C, and 3A to improve legibility and presentation. We will also correct typographical errors and figure references, and clarify the activity patterns of the GAL4 drivers. Specifically, while UASmCD8::GFP expression driven by OK107-GAL4 is markedly weaker in MBNBs than in their neuronal progeny (as seen, for example, in Figure S3C), the driver remains active and functionally relevant in MBNBs. We believe the weak expression in MBNBs likely explains the absence of a NB retention phenotype in OK107>KrIR adult brains (see main text, Lines 374–376). As suggested by the reviewer, we will clarify this point earlier in the manuscript and can include additional data showing OK107>GFP expression patterns in pupal MB lineages as supplementary material.

      (8) Analysis of public datasets

      We will include results from our analysis of publicly available datasets such as FlyAtlas2, modENCODE, and a time-course RNA-seq dataset specific to MBNBs (Liu et al., 2015). While the spatial resolution of FlyAtlas2 and modENCODE is limited, the MBNB dataset provides valuable temporal information up to 36 h after puparium formation (APF). From this dataset, we observe that Kr expression remains consistently low throughout development, with only a modest increase at 84 h ALH (mean TPM ~11) and 36 h APF (~7), suggesting it does not undergo strong transcriptional regulation in MBNBs. In contrast, Kr-h1 is highly expressed during early larval stages (24–84 h ALH; mean TPM ~55–60) and shows a marked suppression by 36 h APF (mean TPM ~2), consistent with its proposed role in promoting MBNB proliferation. Importantly, Eip93F (E93) exhibits a reciprocal pattern to Kr-h1—with minimal expression until 84 h ALH (mean TPM ~24), followed by a substantial induction at 36 h APF (mean TPM ~104), aligning with its known role in triggering neuroblast termination. These temporal expression dynamics support our model that Kr-h1 and E93 function in opposition during the transition from proliferative to terminating neuroblast states. We will summarise these findings in the revised manuscript, along with appropriate discussion of dataset limitations.

      We hope this provisional response conveys our strong commitment to thoroughly addressing the reviewers’ concerns and improving the manuscript. We are currently carrying out additional experiments and will submit a revised version with new data and enhanced clarity in due course.

      References:

      Kang et al., 2017. Sci Rep. 7(1):16369. doi: 10.1038/s41598-017-16638-1.

      Shi et al., 2007. Dev Neurobiol. 67(11):1614–1626. doi: 10.1002/dneu.20537.

      Rossi et al., 2020. eLife. 9:e58880. doi: 10.7554/eLife.58880.

      Liu et al., 2015. Science. 350(6258):317–320. doi: 10.1126/science.aad1886.

      Ren et al., 2017. Curr Biol. 27(9):1303–1313. doi: 10.1016/j.cub.2017.03.018. Syed et al., 2017. eLife. 6:e26287. doi: 10.7554/eLife.26287.

    1. eLife Assessment

      The findings in this manuscript are important because they demonstrate the key role of metabolism in insect development. The data were collected and analyzed using solid and validated methodologies, but the evidence is incomplete, as the extent of the involvement of AOX activity in vivo and in physiological conditions is not addressed. This manuscript will be of interest for the fields of mitochondrial bioenergetics, metabolism and development.

    2. Reviewer #1 (Public review):

      Summary:

      The manuscript by Garcia et al. describes how the expression of a respiratory chain alternative oxidase (AOX) from the tunicate Ciona intestinalis, capable of transferring electrons directly from reduced coenzyme Q (CoQ) to oxygen, is able to induce an increase in the mass of Drosophila melanogaster larvae and an accelerated development, especially when the larvae are kept at low temperatures. In order to explain this phenomenon, the paper addresses the modifications in the activity and levels of the 'canonical' electron transfer system (ETS), i.e., complexes I-IV and of the ATP synthase. In addition, the abundance of different metabolites as well as the NAD+/NADH ratios are measured, finding significant differences between the larvae.

      Strengths:

      The observations of differences in growth, body mass and food intake in the wt D. melanogaster larvae vs. those expressing the AOX transgene are solid. The evidence that mild uncoupling of the ETS might accelerate development of the fly larvae is convincing.

      Weaknesses:

      Some of the observations, especially those concerning the origin of the metabolic remodelling in AOX-expressing larvae, are left unexplained, and the argumentation is somewhat speculative. What the authors mean by "reconfiguration" of the mitochondrial electron transfer system is not clear. If this implies that there is an actual change in ETS function and/or structural organisation in the presence of AOX, this conclusion is not supported by the experimental data. In addition, the influence of AOX activity in the mitochondrial ETS system is tested in vitro in the presence of saturating concentrations of substrates. The real degree to which AOX activity is actually influencing ETS activity in vivo remains unknown.

    3. Reviewer #2 (Public review):

      Summary:

      This manuscript presents intriguing findings about the role of alternative oxidase (AOX) from the tunicate Ciona intestinalis in accelerating growth and development when expressed in Drosophila melanogaster.

      Strengths:

      The study is overall well-constructed, including appropriate analysis. Likewise, the manuscript is written clearly and supported by high-quality figures. The present study provides valuable insights into AOX's role in Drosophila development. The paper attempts to explore a unique mechanism by which AOX influences Drosophila development, providing insights into mitochondrial respiration and its physiological effects. This is relevant for understanding mitochondrial dysfunction and potential therapeutic applications. The study employs a variety of approaches, including calorimetry, infrared thermography, and genetic analyses, to investigate AOX's impact on metabolism and development.

      Weaknesses:

      There are a number of methodological limitations and substantial gaps in the interpretation of the data presented, which reduces the strength of its conclusions. For instance, there is a misunderstanding of the non-proton motive nature of the AOX - it does not uncouple respiration, merely decouple it as it neither contributes to nor dissipates the proton motive force, in contrast to chemical uncouplers or proton uncouplers such as UCPs. The authors need to reassess their data in light of the above.

    4. Author response:

      Reviewer #1 (Public review):

      Summary:

      The manuscript by Garcia et al. describes how the expression of a respiratory chain alternative oxidase (AOX) from the tunicate Ciona intestinalis, capable of transferring electrons directly from reduced coenzyme Q (CoQ) to oxygen, is able to induce an increase in the mass of Drosophila melanogaster larvae and an accelerated development, especially when the larvae are kept at low temperatures. In order to explain this phenomenon, the paper addresses the modifications in the activity and levels of the 'canonical' electron transfer system (ETS), i.e., complexes I-IV and of the ATP synthase. In addition, the abundance of different metabolites as well as the NAD+/NADH ratios are measured, finding significant differences between the larvae.

      Strengths:

      The observations of differences in growth, body mass and food intake in the wt D. melanogaster larvae vs. those expressing the AOX transgene are solid. The evidence that mild uncoupling of the ETS might accelerate development of the fly larvae is convincing."

      We appreciate the reviewer’s attention to our results and hope we can improve the manuscript to address all criticism appropriately.

      Weaknesses:

      Some of the observations, especially those concerning the origin of the metabolic remodelling in AOX-expressing larvae, are left unexplained, and the argumentation is somewhat speculative. What the authors mean by "reconfiguration" of the mitochondrial electron transfer system is not clear. If this implies that there is an actual change in ETS function and/or structural organisation in the presence of AOX, this conclusion is not supported by the experimental data. In addition, the influence of AOX activity in the mitochondrial ETS system is tested in vitro in the presence of saturating concentrations of substrates. The real degree to which AOX activity is actually influencing ETS activity in vivo remains unknown.

      Indeed, the term “reconfiguration” may seem a little too strong. However, we do have preliminary structural data on larval mitochondria indicating that the term is adequate in this context. We plan to work on obtaining concrete data to sustain our claims that AOX imparts significant functional and structural remodeling of the organelle, which would be consistent with our respirometry and BN-PAGE data. If the data turns out not to be robust enough, we will consider replacing the term with one that better reflects our findings.

      We also realize that the in vivo data we are presenting (body mass, mobility, food intake) are indirect measurements of metabolism and that a more direct approach is necessary to assess the real degree to which AOX influences ETS activity in vivo. To address this issue, we plan to expand our pharmacological treatments of the larval development and to measure whole larval oxygen consumption.

      Reviewer #2 (Public review):

      Summary:

      This manuscript presents intriguing findings about the role of alternative oxidase (AOX) from the tunicate Ciona intestinalis in accelerating growth and development when expressed in Drosophila melanogaster.

      Strengths:

      The study is overall well-constructed, including appropriate analysis. Likewise, the manuscript is written clearly and supported by high-quality figures. The present study provides valuable insights into AOX's role in Drosophila development. The paper attempts to explore a unique mechanism by which AOX influences Drosophila development, providing insights into mitochondrial respiration and its physiological effects. This is relevant for understanding mitochondrial dysfunction and potential therapeutic applications. The study employs a variety of approaches, including calorimetry, infrared thermography, and genetic analyses, to investigate AOX's impact on metabolism and development.

      We sincerely thank the reviewer for recognizing the strengths and acknowledging the novelty of our study.

      Weaknesses:

      There are a number of methodological limitations and substantial gaps in the interpretation of the data presented, which reduces the strength of its conclusions. For instance, there is a misunderstanding of the non-proton motive nature of the AOX - it does not uncouple respiration, merely decouple it as it neither contributes to nor dissipates the proton motive force, in contrast to chemical uncouplers or proton uncouplers such as UCPs. The authors need to reassess their data in light of the above.

      The reviewer is absolutely right about the non-proton motive nature of AOX. We will reassess our data considering that AOX decouples respiration and, if necessary and possible, we will add new experiments to address the methodological limitations raised by the reviewer.

    1. eLife Assessment

      This important study advances our understanding of vertebrate forelimb development, specifically the contribution of Hox genes to zebrafish pectoral fin formation. While there are reservations about some of the descriptions and interpretations of the data, the results are mostly convincing. The authors have employed a robust and extensive genetic approach to tackle a key and unresolved question. The findings will be of broad interest to developmental and evolutionary biologists.

    2. Reviewer #1 (Public review):

      Summary:

      The authors have used gene deletion approaches in zebrafish to investigate the function of genes of the hox clusters in pectoral fin "positioning" (but perhaps more accurately pectoral fin "formation").

      Strengths:

      The authors have employed a robust and extensive genetic approach to tackle an important and unresolved question.

      The results are largely presented in a very clear way.

      Weaknesses:

      The Abstract suggests that no genetic evidence exists in model organisms for a role of Hox genes in limb positioning. There are, however, several examples in mouse and other models (both classical genetic and other) providing evidence for a role of Hox genes in limb position, which is elaborated on in the Introduction.

      It would perhaps be more accurate to state that several lines of evidence in a range of model organisms (including the mouse) support a role for Hox genes in limb positioning. The author's work is not weakened by a more inclusive introduction that cites the current literature more comprehensively.

      It would be helpful for the authors to make a clear distinction between "positioning" of the limb/fin and whether a limb/fin "forms" at all, independent of the relative position of this event along the body axis.

      Discussion of why the zebrafish is sensitive to Hoxb loss with reference to the fin, but mouse Hoxb mutants do make a limb?

      Is this down to exclusive expression of Hoxbs in the zebrafish pectoral fin forming region rather than a specific functional role of the protein? This is important as it has implications for the interpretation of results throughout the paper and could explain some apparently conflicting results.

      Why is Hoxba more potent than Hoxbb? Is this because Hoxba has Hox4/5 present, while Hoxbb has only Hoxb5? Hoxba locus has retained many more Hox genes in cluster than hoxbb; therefore, one might expect to see greater redundancy in this locus).

      Deletion of either Hoxa or Hoxd in the background of the Hoxba mutant does have some effect. Is this a reflection of protein function or expression dynamics of Hoxa/Hoxd genes?

      Can we really be confident that there is a "transformation of pectoral fin progenitor cells into cardiac cells"?

      The failure to repress Nkx2.5 in the posterior (pelvic fin) domain is clear, but have these cells actually acquired cardiac identity? They would be expected to express Tbx5a (or b) as cardiac precursors, but this domain does not broaden. There is no apparent expansion of the heart (field)/domain or progenitors beyond the 16 somite stage. The claimed "migration" of heart precursors in the mutant is not clear. The heart/cardiac domain that does form in the mutant is not clearly expanded in the mutant. The domain of cmlc2 looks abnormal in the mutant, but I am not convinced it is "enlarged" as claimed by the authors. The authors have not convincingly shown that "the cells that should form the pectoral fin instead differentiate into cardiac cells."

      The only clear conclusion is the loss of pectoral fin-forming cells rather than these fin-forming cells being "transformed" into a new identity. It would be interesting to know what has happened to the cells of the pectoral fin-forming region in these double mutants.

      It is not clear what the authors mean by a "converse" relationship between forelimb/pectoral fin and heart formation. The embryological relationship between these two populations is distinct in amniotes.

      The authors show convincing data that RA cannot induce Tbx5a in the absence of Hob clusters, but I am not convinced by the interpretation of this result. The results shown would still be consistent with RA acting directly upstream of tbx5a, but merely that RA acts in concert with hox genes to activate tbx5a. In the absence of one or the other, Tbx5a would not be expressed. It is not necessary that RA and hoxbs act exclusively in a linear manner (i.e., RA regulates hoxb that in turn regulates tbx5a).

      The authors have carried out a functional test for the function of hoxb6 and hoxb8 in the hemizygous hoxb mutant background. What is lacking is any expression analysis to demonstrate whether Hoxb6b or Hoxb8b are even expressed in the appropriate pectoral fin territory to be able to contribute to pectoral fin development, either in this assay or in normal pectoral fin development.

      (The term "compensate" used in this section is confusing/misleading.)

      The authors' confounding results described in Figures 6-7 are consistent with the challenges faced in other model organisms in trying to explore the function of genes in the hox cluster and the known redundancy that exists across paralogous groups and across individual clusters.

      Given the experimental challenges in deciphering the actual functions of individual or groups of hox genes, a discussion of the normal expression pattern of individual and groups of hox genes (and how this may change in different mutant backgrounds) could be helpful to make conclusions about likely normal function of these genes and compensation/redundancy in different mutant scenarios.

    3. Reviewer #2 (Public review):

      Summary:

      The authors of this manuscript performed a fascinating set of zebrafish mutant analyses on hox cluster deletion and pinpointed the cause of the pectoral fin loss in one combinatorial hox cluster mutant of Hoxba and Hoxbb.

      Strengths:

      The study is based on a variety of existing experimental tools that enabled the authors' past construction of hox cluster mutants, and is well-designed. The manuscript is well written to report the authors' findings on the mechanism that positions the pectoral fin.

      Weaknesses:

      The study does not focus on the other hox clusters other than ba and bb, and is confined to the use of zebrafish, as well as the comparison with existing reports from mouse experiments.

    4. Author response:

      We appreciate the reviewers' positive feedback on our paper. We especially thank them for their evaluation of the genetic analysis, which required a significant amount of timef time. We acknowledge that several aspects of our interpretation and description of the results need correction, as noted by both reviewers. Additionally, we recognize the importance of providing a more comprehensive overview of previous findings, including those conducted in mice, in the manuscript. In the revised version, we will thoroughly address the reviewers' concerns.

      Both reviewers emphasized the need for further validation to ascertain whether the specific requirement of Hox genes in the Hoxba and Hoxbb clusters for pectoral fin bud formation is due to their expression patterns or the functional roles of Hox proteins. This consideration has been on our agenda for some time; however, our submitted paper does not sufficiently address this aspect. In the revised manuscript, we will conduct a comprehensive analysis of the expression patterns of Hox genes in zebrafish to draw informed conclusions on this matter.