10,000 Matching Annotations
  1. Dec 2024
    1. Reviewer #1 (Public review):

      The origin recognition complex (ORC) is an essential loading factor for the replicative Mcm2-7 helicase complex. Despite ORC's critical role in DNA replication, there have been instances where the loss of specific ORC subunits has still seemingly supported DNA replication in cancer cells, endocycling hepatocytes, and Drosophila polyploid cells. Critically, all tested ORC subunits are essential for development and proliferation in normal cells. This presents a challenge, as conditional knockouts need to be generated, and a skeptic can always claim that there were limiting but sufficient ORC levels for helicase loading and replication in polyploid or transformed cells. That being said, the authors have consistently pushed the system to demonstrate replication in the absence or extreme depletion of ORC subunits.

      Here, the authors generate conditional ORC2 mutants to counter a potential argument with prior conditional ORC1 mutants that Cdc6 may substitute for ORC1 function based on homology. They also generate a double ORC1 and ORC2 mutant, which is still capable of DNA replication in polyploid hepatocytes. While this manuscript provides significantly more support for the ability of select cells to replicate in the absence or near absence of select ORC subunits, it does not shed light on a potential mechanism.

      The strengths of this manuscript are the mouse genetics and the generation of conditional alleles of ORC2 and the rigorous assessment of phenotypes resulting from limiting amounts of specific ORC subunits. It also builds on prior work with ORC1 to rule out Cdc6 complementing the loss of ORC1.

      The weakness is that it is a very hard task to resolve the fundamental question of how much ORC is enough for replication in cancer cells or hepatocytes. Clearly, there is a marked reduction in specific ORC subunits that is sufficient to impact replication during development and in fibroblasts, but the devil's advocate can always claim minimal levels of ORC remaining in these specialized cells.

      The significance of the work is that the authors keep improving their conditional alleles (and combining them), thus making it harder and harder (but not impossible) to invoke limiting but sufficient levels of ORC. This work lays the foundation for future functional screens to identify other factors that may modulate the response to the loss of ORC subunits.

      This work will be of interest to the DNA replication, polyploidy, and genome stability communities.

    2. Reviewer #2 (Public review):

      This manuscript proposes that primary hepatocytes can replicate their DNA without the six-subunit ORC. This follows previous studies that examined mice that did not express ORC1 in the liver. In this study, the authors suppressed expression of ORC2 or ORC1 plus ORC2 in the liver.

      Comments:

      (1) I find the conclusion of the authors somewhat hard to accept. Biochemically, ORC without the ORC1 or ORC2 subunits cannot load the MCM helicase on DNA. The question arises whether the deletion in the ORC1 and ORC2 genes by Cre is not very tight, allowing some cells to replicate their DNA and allow the liver to develop, or whether the replication of DNA proceeds via non-canonical mechanisms, such as break-induced replication. The increase in the number of polyploid cells in the mice expressing Cre supports the first mechanism, because it is consistent with few cells retaining the capacity to replicate their DNA, at least for some time during development.

      (2) Fig 1H shows that 5 days post infection, there is no visible expression of ORC2 in MEFs with the ORC2 flox allele. However, at 15 days post infection, some ORC2 is visible. The authors suggest that a small number of cells that retained expression of ORC2 were selected over the cells not expressing ORC2. Could a similar scenario also happen in vivo?

      (3) Figs 2E-G shows decreased body weight, decreased liver weight and decreased liver to body weight in mice with recombination of the ORC2 flox allele. This means that DNA replication is compromised in the ALB-ORC2f/f mice.

      (4) Figs 2I-K do not report the number of hepatocytes, but the percent of hepatocytes with different nuclear sizes. I suspect that the number of hepatocytes is lower in the ALB-ORC2f/f mice than in the ORC2f/f mice. Can the authors report the actual numbers?

      (5) Figs 3B-G do not report the number of nuclei, but percentages, which are plotted separately for the ORC2-f/f and ALB-ORC2-f/f mice. Can the authors report the actual numbers?

      (6) Fig 5 shows the response of ORC2f/f and ALB-ORC2f/f mice after partial hepatectomy. The percent of EdU+ nuclei in the ORC2-f/f (aka ALB-CRE-/-) mice in Fig 5H seems low. Based on other publications in the field it should be about 20-30%. Why is it so low here? The very low nuclear density in the ALB-ORC2-f/f mice (Fig 5F) and the large nuclei (Fig 5I) could indicate that cells fire too few origins, proceed through S phase very slowly and fail to divide.

      (7) Fig 6F shows that ALB-ORC1f/f-ORC2f/f mice have very severe phenotypes in terms of body weight and liver weight (about on third of wild-type!!). Fig 6H and 6I, the actual numbers should be presented, not percentages. The fact that there are EYFP negative cells, implies that CRE was not expressed in all hepatocytes.

      (8) Comparing the EdU+ cells in Fig 7G versus 5G shows very different number of EdU+ cells in the control animals. This means that one of these images is not representative. The higher fraction of EdU+ cells in the double-knockout could mean that the hepatocytes in the double-knockout take longer to complete DNA replication than the control hepatocytes. The control hepatocytes may have already completed DNA replication, which can explain why the fraction of EdU+ cells is so low in the controls. The authors may need to study mice at earlier time points after partial hepatectomy, i.e. sacrifice the mice at 30-32 hours, instead of 40-52 hours.

      (9) Regarding the calculation of the number of cell divisions during development: the authors assume that all the hepatocytes in the adult liver are derived from hepatoblasts that express Alb. Is it possible to exclude the possibility that pre-hepatoblast cells that do not express Alb give rise to hepatocytes? For example the cells that give rise to hepatoblasts may proliferate more times than normal giving rise to a higher number of hepatoblasts than in wild-type mice.

      (10) My interpretation of the data is that not all hepatocytes have the ORC1 and ORC2 genes deleted (eg EYFP-negative cells) and that these cells allow some proliferation in the livers of these mice.

    3. Reviewer #3 (Public review):

      Summary:

      The authors address the role of ORC in DNA replication and that this protein complex is not essential for DNA replication in hepatocytes. They provide evidence that ORC subunit levels are substantially reduced in cells that have been induced to delete multiple exons of the corresponding ORC gene(s) in hepatocytes. They evaluate replication both in purified isolated hepatocytes and in mice after hepatectomy. In both cases, there is clear evidence that DNA replication does not decrease at a level that corresponds with the decrease in detectable ORC subunit and that endoreduplication is the primary type of replication observed. It remains possible that small amounts of residual ORC are responsible for the replication observed, although the authors provide arguments against this possibility. The mechanisms responsible for DNA replication in the absence of ORC are not examined.

      Strengths:

      The authors clearly show that there are dramatic reductions in the amount of the targeted ORC subunits in the cells that have been targeted for deletion. They also provide clear evidence that there is replication in a subset of these cells and that it is likely due to endoreduplication. Although there is no replication in MEFs derived from cells with the deletion, there is clearly DNA replication occurring in hepatocytes (both isolated in culture and in the context of the liver). Interestingly, the cells undergoing replication exhibit enlarged cell sizes and elevated ploidy indicating endoreduplication of the genome. These findings raise the interesting possibility that endoreduplication does not require ORC while normal replication does.

      Weaknesses:

      There are two significant weaknesses in this manuscript. The first is that although there is clearly robust reduction of the targeted ORC subunit, the authors cannot confirm that it is deleted in all cells. For example, the analysis in Fig. 4B would suggest that a substantial number of cells have not lost the targeted region of ORC2. Although the western blots show stronger effects, this type of analysis is notorious for non-linear response curves and no standards are provided. The second weakness is that there is no evaluation of the molecular nature of the replication observed. Are there changes in the amount of location of Mcm2-7 loading that is usually mediated by ORC? Does an associated change in Mcm2-7 loading lead to the endoreduplication observed? After numerous papers from this lab and others claiming that ORC is not required for eukaryotic DNA replication in a subset of cells, we still have no information about an alternative pathway that could explain this observation.

      The authors frequently use the presence of a Cre-dependent eYFP expression as evidence that the ORC1 or ORC2 genes have been deleted. Although likely the best visual marker for this, it is not demonstrated that the presence of eYFP ensures that ORC2 has been targeted by Cre. For example, based on the data in Fig. 4B, there seems to be a substantial percentage of ORC2 genes that have not been targeted while the authors report that 100% of the cells express eYFP.

    4. Author response:

      eLife Assessment

      This descriptive manuscript builds on prior research showing that the elimination of Origin Recognition Complex (ORC) subunits does not halt DNA replication. The authors use various methods to genetically remove one or two ORC subunits from specific tissues and observe continued replication, though it may be incomplete. The replication appears to be primarily endoreduplication, indicating that ORC-independent replication may promote genome reduplication without mitosis. Despite similar findings in previous studies, the paper provides convincing genetic evidence in mice that liver cells can replicate and undergo endoreduplication even with severely depleted ORC levels. While the mechanism behind this ORC-independent replication remains unclear, the study lays the groundwork for future research to explore how cells compensate for the absence of ORC and to develop functional approaches to investigate this process. The reviewers agree that this valuable paper would be strengthened significantly if the authors could delve a bit deeper into the nature of replication initiation, potentially using an origin mapping experiment. Such an exciting contribution would help explain the nature of the proposed new type of Mcm loading, thereby increasing the impact of this study for the field at large.<br />

      We appreciate the reviewers’ suggestion. Till now we know of only one paper that mapped origins of replication in regenerating mouse liver, and that was published two months back in Cell (PMID: 39293447).  We want to adopt this method, but we do not need it to answer the question asked.  We have mapped origins of replication in ORC-deleted cancer cell lines and compared to wild-type cells in Shibata et al., BioRXiv (PMID: 39554186) (it is under review).  We report the following:  Mapping of origins in cancer cell lines that are wild type or engineered to delete three of the subunits, ORC1, ORC2 or ORC5 shows that specific origins are still used and are mostly at the same sites in the genome as in wild type cells. Of the 30,197 origins in wild type cells (with ORC), only 2,466 (8%) are not used in any of the three ORC deleted cells and 18,319 (60%) are common between the four cell types. Despite the lack of ORC, excess MCM2-7 is still loaded at comparable rates in G1 phase to license reserve origins and is also repeatedly loaded in the same S phase to permit re-replication. 

      Citation: Specific origin selection and excess functional MCM2-7 loading in ORC-deficient cells. Yoshiyuki Shibata, Mihaela Peycheva, Etsuko Shibata, Daniel Malzl, Rushad Pavri, Anindya Dutta. bioRxiv 2024.10.30.621095; doi: https://doi.org/10.1101/2024.10.30.621095 (PMID: 39554186)

      Public Reviews:

      Reviewer #1 (Public review):

      The origin recognition complex (ORC) is an essential loading factor for the replicative Mcm2-7 helicase complex. Despite ORC's critical role in DNA replication, there have been instances where the loss of specific ORC subunits has still seemingly supported DNA replication in cancer cells, endocycling hepatocytes, and Drosophila polyploid cells. Critically, all tested ORC subunits are essential for development and proliferation in normal cells. This presents a challenge, as conditional knockouts need to be generated, and a skeptic can always claim that there were limiting but sufficient ORC levels for helicase loading and replication in polyploid or transformed cells. That being said, the authors have consistently pushed the system to demonstrate replication in the absence or extreme depletion of ORC subunits.

      Here, the authors generate conditional ORC2 mutants to counter a potential argument with prior conditional ORC1 mutants that Cdc6 may substitute for ORC1 function based on homology. They also generate a double ORC1 and ORC2 mutant, which is still capable of DNA replication in polyploid hepatocytes. While this manuscript provides significantly more support for the ability of select cells to replicate in the absence or near absence of select ORC subunits, it does not shed light on a potential mechanism.

      The strengths of this manuscript are the mouse genetics and the generation of conditional alleles of ORC2 and the rigorous assessment of phenotypes resulting from limiting amounts of specific ORC subunits. It also builds on prior work with ORC1 to rule out Cdc6 complementing the loss of ORC1.

      The weakness is that it is a very hard task to resolve the fundamental question of how much ORC is enough for replication in cancer cells or hepatocytes. Clearly, there is a marked reduction in specific ORC subunits that is sufficient to impact replication during development and in fibroblasts, but the devil's advocate can always claim minimal levels of ORC remaining in these specialized cells.

      The significance of the work is that the authors keep improving their conditional alleles (and combining them), thus making it harder and harder (but not impossible) to invoke limiting but sufficient levels of ORC. This work lays the foundation for future functional screens to identify other factors that may modulate the response to the loss of ORC subunits.

      This work will be of interest to the DNA replication, polyploidy, and genome stability communities.

      Thank you.

      Reviewer #2 (Public review):

      This manuscript proposes that primary hepatocytes can replicate their DNA without the six-subunit ORC. This follows previous studies that examined mice that did not express ORC1 in the liver. In this study, the authors suppressed expression of ORC2 or ORC1 plus ORC2 in the liver.

      Comments:

      (1) I find the conclusion of the authors somewhat hard to accept. Biochemically, ORC without the ORC1 or ORC2 subunits cannot load the MCM helicase on DNA. The question arises whether the deletion in the ORC1 and ORC2 genes by Cre is not very tight, allowing some cells to replicate their DNA and allow the liver to develop, or whether the replication of DNA proceeds via non-canonical mechanisms, such as break-induced replication. The increase in the number of polyploid cells in the mice expressing Cre supports the first mechanism, because it is consistent with few cells retaining the capacity to replicate their DNA, at least for some time during development.

      In our study, we used EYFP as a marker for Cre recombinase activity. ~98% of the hepatocytes in tissue sections and cells in culture express EYFP, suggesting that the majority of hepatocytes successfully expressed the Cre protein to delete the ORC1 or ORC2 genes. To assess deletion efficiency, we employed sensitive genotyping and Western blotting techniques to confirm the deletion of ORC1 and ORC2 in hepatocytes isolated from Alb-Cre mice. Results in Fig. 2C and Fig. 6D demonstrate the near-complete absence of ORC2 and ORC1 proteins, respectively, in these hepatocytes.

      The mutant hepatocytes underwent at least 15–18 divisions during development. The inherited ORC1 or ORC2 protein present during the initial cell divisions, would be diluted to less than 1.5% of wild-type levels within six divisions, making it highly unlikely to support DNA replication, and yet we observe hepatocyte numbers that suggest there was robust cell division even after that point.

      Furthermore, the EdU incorporation data confirm DNA synthesis in the absence of ORC1 and ORC2. Specifically, immunofluorescence showed that both in vitro and in vivo, EYFP-positive hepatocytes (indicating successful ORC1 and ORC2 deletion) incorporated EdU, demonstrating that DNA synthesis can occur without ORC1 and ORC2.

      Finally, the Alb-ORC2f/f mice have 25-37.5% of the number of hepatocyte nuclei compared to WT mice (Table 2).  If that many cells had an undeleted ORC2 gene, that would have shown up in the genotyping PCR and in the Western blots.

      (2) Fig 1H shows that 5 days post infection, there is no visible expression of ORC2 in MEFs with the ORC2 flox allele. However, at 15 days post infection, some ORC2 is visible. The authors suggest that a small number of cells that retained expression of ORC2 were selected over the cells not expressing ORC2. Could a similar scenario also happen in vivo?

      This would not explain the significant incorporation of EdU in hepatocytes that do not have detectable ORC by Western blots and that are EYFP positive.  Also note that for MEFs we are delivering the Cre by AAV infection in vitro, so there is a finite probability that a cell will not receive Cre and will not delete ORC2.  However, in vivo, the Alb-Cre will be expressed in every cell that turns on albumin.  There is no escaping the expression of Cre.

      (3) Figs 2E-G shows decreased body weight, decreased liver weight and decreased liver to body weight in mice with recombination of the ORC2 flox allele. This means that DNA replication is compromised in the ALB-ORC2f/f mice.

      It is possible that DNA replication is partially compromised or may slow down in the absence of ORC2. However, it is important to emphasize that livers with ORC2 deletion remain capable of DNA replication, so much so that liver function and life span are near normal. Therefore, some kind of DNA replication has to serve as a compensatory mechanism in the absence of ORC2 to maintain liver function and support regeneration.

      (4) Figs 2I-K do not report the number of hepatocytes, but the percent of hepatocytes with different nuclear sizes. I suspect that the number of hepatocytes is lower in the ALB-ORC2f/f mice than in the ORC2f/f mice. Can the authors report the actual numbers?

      We show in Table 2 that the Alb-Orc2f/f mice have about 25-37.5% of the hepatocytes compared to the WT mice.

      (5) Figs 3B-G do not report the number of nuclei, but percentages, which are plotted separately for the ORC2-f/f and ALB-ORC2-f/f mice. Can the authors report the actual numbers?

      In all the FACS experiments in Fig. 3B-G we collect data for a total of 10,000 nuclei (or cells).  For Fig. 3E-G we divide the 10,000 nuclei into the bottom 40% on the EYFP axis (EYFP low, which is mostly EYFP negative) as the control group, and EYFP high (top 20% on the EYFP axis) test group.  We will mention this in the revision and label EYFP negative and positive as EYFP low and high.

      (6) Fig 5 shows the response of ORC2f/f and ALB-ORC2f/f mice after partial hepatectomy. The percent of EdU+ nuclei in the ORC2-f/f (aka ALB-CRE-/-) mice in Fig 5H seems low. Based on other publications in the field it should be about 20-30%. Why is it so low here? The very low nuclear density in the ALB-ORC2-f/f mice (Fig 5F) and the large nuclei (Fig 5I) could indicate that cells fire too few origins, proceed through S phase very slowly and fail to divide.

      The percentage of EdU+ nuclei in the ORC2f/f without Alb-Cre mice is 8%, while in PMID 10623657, the 10% of wild type nuclei incorporate  EdU at 42 hr post partial hepatectomy (mid-point between the 36-48 hr post hepatectomy that was used in our study).  The important result here is that in the ORC2f/f mice with Alb-Cre (+/-) we are seeing significant EdU incorporation. We will also correct the X-axis labels in 5F, 5I, 7E and 7F to reflect that those measurements were not made at 36 hr post-resection but later (as was indicated in the schematic in Fig. 5A).

      (7) Fig 6F shows that ALB-ORC1f/f-ORC2f/f mice have very severe phenotypes in terms of body weight and liver weight (about on third of wild-type!!). Fig 6H and 6I, the actual numbers should be presented, not percentages. The fact that there are EYFP negative cells, implies that CRE was not expressed in all hepatocytes.

      The liver to body weight ratio is what one has to look at, and it is 70% of the WT.  In females the liver and body weight are low (although in proportion to each other), which maybe is what the reviewer is talking about.  However, the fact that liver weight and body weight are not as low in males, suggest that this is a gender (hormone?) specific effect and not a DNA replication defect.  We have another paper also in BioRXiv (Su et al.) that suggests that ORC subunits have significant effect on gene expression, so it is possible that that is what leads to this sexual dimorphism in phenotype.

      The bottom 40% of nuclei on the EYFP axis in the FACS profiles (what was labeled EYFP negative but will now be called EYFP low) contains mostly non-hepatocytes that are genuinely EYFP negative.   Non-hepatocytes (bile duct cells, endothelial cells, Kupffer cells, blood cells) are a significant part of cells in the dissociated liver (as can be seen in the single cell sequencing results in PMID: 32690901).  Their presence does not mean that hepatocytes are not expressing Cre.  Hepatocytes mostly are EYFP positive, as can be seen in the tissue sections (where the hepatocytes take up most of visual field) and in cells in culture.  Also if there are EYFP negative hepatocyte nuclei in the FACS, that still does not rule out EYFP presence in the cytoplasm.  The important point from the FACS is that the EYFP high nuclei (which have expressed Cre for the longest period) are polyploid relative to the EYFP low nuclei.

      (8) Comparing the EdU+ cells in Fig 7G versus 5G shows very different number of EdU+ cells in the control animals. This means that one of these images is not representative. The higher fraction of EdU+ cells in the double-knockout could mean that the hepatocytes in the double-knockout take longer to complete DNA replication than the control hepatocytes. The control hepatocytes may have already completed DNA replication, which can explain why the fraction of EdU+ cells is so low in the controls. The authors may need to study mice at earlier time points after partial hepatectomy, i.e. sacrifice the mice at 30-32 hours, instead of 40-52 hours.

      The apparent difference that the reviewer comments on stems from differences in nuclear density in the images in Fig. 7G and 5G (also quantitated in Fig. 7F and 5F).  The quantitation in Fig. 7H and 5H show that the % of EdU plus cells are comparable (5-8%). 

      (9) Regarding the calculation of the number of cell divisions during development: the authors assume that all the hepatocytes in the adult liver are derived from hepatoblasts that express Alb. Is it possible to exclude the possibility that pre-hepatoblast cells that do not express Alb give rise to hepatocytes? For example the cells that give rise to hepatoblasts may proliferate more times than normal giving rise to a higher number of hepatoblasts than in wild-type mice.

      Single cell sequencing of mouse liver at e11 shows hepatoblasts expressing hepatocyte specific markers (PMID: 32690901).  All the cells annotated from the single-cell seq analysis are differentiated cells arguing against the possibility that undifferentiated endodermal cells (what the reviewer probably means by pre-hepatoblasts) exist at e11.  The following review (https://www.ncbi.nlm.nih.gov/books/NBK27068/) says: “The differentiation of bi-potential hepatoblasts into hepatocytes or BECs begins around e13 of mouse development. Initially hepatoblasts express genes associated with both adult hepatocytes (Hnf4α, Albumin) ...”  Thus, we can be certain that undifferentiated endodermal cells are unlikely to persist on e11 and that hepatoblasts at e11 express albumin.  Our calculation of number of cell divisions in Table 2 begins from e12.

      The reviewer maybe suggesting that ORC deletion leads to the immediate demise of hepatoblasts (despite having inherited ORC protein from the endodermal cells) causing undifferentiated endodermal cells to persist and proliferate much longer than in normal development.  We consider it unlikely, but if true it will be amazing new biology, both by suggesting that deletion of ORC immediately leads to the death of the hepatoblasts (despite a healthy reserve of inherited ORC protein) and by suggesting that there is a novel feedback mechanism from the death/depletion of hepatoblasts leading to the persistence and proliferation of undifferentiated endodermal cells.

      (10) My interpretation of the data is that not all hepatocytes have the ORC1 and ORC2 genes deleted (eg EYFP-negative cells) and that these cells allow some proliferation in the livers of these mice.

      Please see the reply in question #1.  Particularly relevant: “Finally, the Alb-ORC2f/f mice have 25-37.5% of the number of hepatocyte nuclei compared to WT mice (Table 2).  If that many cells had an undeleted ORC2 gene, that would have shown up in the genotyping PCR and in the Western blots.

      Reviewer #3 (Public review):

      Summary:

      The authors address the role of ORC in DNA replication and that this protein complex is not essential for DNA replication in hepatocytes. They provide evidence that ORC subunit levels are substantially reduced in cells that have been induced to delete multiple exons of the corresponding ORC gene(s) in hepatocytes. They evaluate replication both in purified isolated hepatocytes and in mice after hepatectomy. In both cases, there is clear evidence that DNA replication does not decrease at a level that corresponds with the decrease in detectable ORC subunit and that endoreduplication is the primary type of replication observed. It remains possible that small amounts of residual ORC are responsible for the replication observed, although the authors provide arguments against this possibility. The mechanisms responsible for DNA replication in the absence of ORC are not examined.

      Strengths:

      The authors clearly show that there are dramatic reductions in the amount of the targeted ORC subunits in the cells that have been targeted for deletion. They also provide clear evidence that there is replication in a subset of these cells and that it is likely due to endoreduplication. Although there is no replication in MEFs derived from cells with the deletion, there is clearly DNA replication occurring in hepatocytes (both isolated in culture and in the context of the liver). Interestingly, the cells undergoing replication exhibit enlarged cell sizes and elevated ploidy indicating endoreduplication of the genome. These findings raise the interesting possibility that endoreduplication does not require ORC while normal replication does.

      Weaknesses:

      There are two significant weaknesses in this manuscript. The first is that although there is clearly robust reduction of the targeted ORC subunit, the authors cannot confirm that it is deleted in all cells. For example, the analysis in Fig. 4B would suggest that a substantial number of cells have not lost the targeted region of ORC2. Although the western blots show stronger effects, this type of analysis is notorious for non-linear response curves and no standards are provided. The second weakness is that there is no evaluation of the molecular nature of the replication observed. Are there changes in the amount of location of Mcm2-7 loading that is usually mediated by ORC? Does an associated change in Mcm2-7 loading lead to the endoreduplication observed? After numerous papers from this lab and others claiming that ORC is not required for eukaryotic DNA replication in a subset of cells, we still have no information about an alternative pathway that could explain this observation.

      We do not see a significant deficit in MCM2-7 loading (amount and rate) in cancer cell lines where we have deleted ORC1, ORC2 or ORC5 genes separately in Shibata et al. bioRxiv 2024.10.30.621095; doi: https://doi.org/10.1101/2024.10.30.621095 (PMID: 39554186)

      The authors frequently use the presence of a Cre-dependent eYFP expression as evidence that the ORC1 or ORC2 genes have been deleted. Although likely the best visual marker for this, it is not demonstrated that the presence of eYFP ensures that ORC2 has been targeted by Cre. For example, based on the data in Fig. 4B, there seems to be a substantial percentage of ORC2 genes that have not been targeted while the authors report that 100% of the cells express eYFP.

      The PCR reactions in Fig. 4B are still contaminated by DNA from non-hepatocyte cells:  bile duct cells, endothelial, Kupfer cells and blood cells.  Under the microscope  culture we can recognize the hepatocytes unequivocally from their morphology. <2% of the hepatocyte cells in culture in Fig. 4C are EYFP-.

    1. eLife Assessment

      In this useful manuscript, the authors performed scRNA-seq on a diverse cohort of 15 early-stage cervical cancer patients. Correlative data is provided to support the possible establishment of an immunosuppressive microenvironment near SCL26A3+ cells, and an association of these cells with upstaging at time of surgery. However without more extensive validation, the evidence supporting the conclusions remains incomplete. Overall, this paper will provide a potentially helpful dataset for researchers studying cervical cancer.

    2. Reviewer #1 (Public review):

      Summary:

      The authors in this manuscript performed scRNA-seq on a cohort of 15 early-stage cervical cancer patients with a mixture of adeno- and squamous cell carcinoma, HPV status, and several samples that were upstaged at the time of surgery. From their analyses they identified differential cell populations in both immune and tumour subsets related to stage, HPV status, and whether a sample was adenocarcinoma or squamous cell. Putative microenvironmental signaling was explored as a potential explanation for their differential cell populations. Through these analyses the authors also identified SLC26A3 as a potential biomarker for later stage/lymph node metastasis which was verified by IHC and IF. The dataset is likely useful for the community. The accuracy and clarity have been improved from the previous version, and additional immunofluorescence supporting the existence of their proposed cluster is now present. That said, there remain some issues with the strength of some claims (particularly in the abstract and results sections) and some of the cell type definitions.

      Strengths

      The dataset could be useful for the community<br /> SLC26A3 could potentially be a useful marker to predict lymph node metastasis with further study

      Weaknesses

      Casual language is used in the abstract around immunosuppressive microenvironment and signal cross-talk between Epi_10_CYSTM1 cluster and Tregs. The data show localization that supports a possible interaction and probable cytokines, but functional experiments would be needed to establish causality.

      In the description of the single cell data processing there is no mention of batch effect correction. Given that many patients were analyzed, and no mention was made of pooling or deconvolution, it must be assumed these were run separately which invariably leads to batch effects. Given the good overlays across patients some batch correction must have been performed. How was batch effect correction performed?

      While statistics were added to the clinical correlates, it would appear that single variables are being assessed one at a time by chi-squared analysis. This ignores the higher order structure of the data and the correlations between some variables resulting in potentially spurious findings. This is compounded as some categories had below 5 observations violating the assumptions of a chi-squared test.

      The description of all analytical steps remains quite truncated. While the inclusion of annotated code is useful, a full description of which tools were used, with which settings, and why each were chosen, is a minimum needed to properly interpret the results. This is as important in a mainly analytical paper as the experimental parameters.

      Validation of the clustering results remains a problem. The only details provided are that FindClusters was used. This depends on a manual choice of multiple parameters including the k-nearest neighbours included, whether Louvain or Leiden clustering is used, the resolution parameter, and others (how many variable genes/PCs etc...). Why were these parameters selected, how do you know that you're not over or under-clustering.

      The cluster Epi_10_CYSTM1 remains somewhat problematic. None of the additional data supports its existence outside of the single patient who has cells from that population. Additionally, it falls well outside of any of the other Epithelial cells to the point that drawing it as part of a differentiation order doesn't even make sense. Indeed, most of the upregulated pathways in this cluster appear to be related to class II antigen presentation which would fit better with a dendritic cell/macrophage than an epithelial cell. While the IF at the end does support the existence of the cluster, numbers are still very limited, and this doesn't have data on the antigen presenting function. At the least a strong disclaimer should be included in the text that this population is essentially exclusive to one sample in the scRNA data.

      The linkage between the cluster types and IHC for prediction of lymph node metastasis is tenuous. Most of the strongly cluster associated markers were not predictive despite their clusters being theoretically enriched. This inability to recognize the clusters in additional samples using alternative methods does not give confidence that these clusters are robust. SLC26A3 being associated with upstaging may very well be a useful marker, however, given the lack of association of the other markers, it may be premature to say this is due to the same Epi_10_CYSTM1 cluster.

      There are multiple issues in the classification of T cells and neutrophils. In the analysis of T cell subset, all CD4+ T cells are currently scored as Tregs, what happened to the T-helper cells? Additionally, Activated T and Cytotoxic T both seem to contain CD8+ cells, but all their populations have equivalent expression of the activation marker CD69. Moreover, the "Cytotoxic" ones also express TIGIT, HAVCR2 and LAG3 which are generally exhaustion markers. For neutrophils, several obviously different clusters have been grouped together (Neu_1 containing two diametrically opposite cell clouds being an obvious example).

      Again in the CellChat section of the results causal language is being repeatedly used. These are just possible interactions, not validated ones. While the co-localization in the provided IF images certainly supports the co-localization, this still is only correlative and doesn't prove causality.

      Minor Issues<br /> The sentence "However, due to the low morbidity of ADC, in-depth investigations are insufficient" could be misinterpreted. Morbidity generally refers to the severity or health burden rather than the frequency of cases, though it's true in some studies prevalence is used for the overall impact of the disease on a population and referred to as morbidity. In this instance though, "incidence" or "prevalence" would be clearer word choices.

      The previous rebuttal states that clusters/cell type calls were refined to eliminate issues such as epithelial cells creeping into the T cell cluster, however, the cell %s have not been altered according to the change tracking. Shouldn't all the %s have been altered even if only slightly?

    3. Reviewer #2 (Public review):

      Summary:

      Peng et al. present a study using scRNA-seq to examine phenotypic properties of cervical cancer, contrasting features of both adenocarcinomas (ADC) and squamous cell carcinoma (SCC), and HPV-positive and negative tumours. They propose several key findings: unique malignant phenotypes in ADC with elevated stemness and aggressive features, interactions of these populations with immune cells to promote an immunosuppressive TME, and SLC26A3 as a biomarker for metastatic (>=Stage III ) tumours.

      Strengths:

      This study provides a valuable resource of scRNA-seq data from a well-curated collection of patient samples. The analysis provides a high-level view of the cellular composition of cervical cancers. The authors introduce some mechanistic explanations of immunosuppression and the involvement of regulatory T cells that is intriguing.

      Weaknesses:

      I believe many of the proposed conclusions are over-interpretations or unwarranted generalizations of the single-cell analysis. I believe there may also be some artifacts in the data that may not reflect true biology--eg. The presentation of KRT+ neutrophils, which may reflect doublets with cancer cells. In some cases there is mention of quality control steps to remove contaminant cell clusters, but there is no method or supplemental figure to describe and/or justify these steps.

      The key limitation is related to the "ADC-specific" Epi_10_CYSTM1 cluster, which is a central focus of the paper. This population only contains cells from one of the 11 ADC samples and represents only a small fraction of the malignant cells from that sample. Yet, this population is used to derive SLC26A3 as a potential biomarker. SLC26A3 transcripts are only detected in this small population of cells (none of the other ADC samples), which makes me question the specificity of the IHC staining on the validation cohort. The manuscript does not address why this marker is so rare in the scRNA-seq data, but abundant in the IHC.

      While I understand it may be out of the scope of this individual study, many of the conclusions are inferred from the data analysis with little follow-up in experimental models or orthogonal assays.

    4. Author response:

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

      Public reviews:

      Reviewer #1 (public review):

      (1) The link between the background in the introduction and the actual study and findings is often tenuous or not clearly explained. A re-working of the intro to better set up and link to the study questions would be beneficial.

      We have rewritten the introduction of the manuscript and clearly stated the study questions we were aiming for:

      In paragraph 1-we have stated clearly that we need to study why ADC type of cervical cancer is more aggressive. (Line 58 - 77)

      In paragraph 2- we have stated clearly that we need to find valuable biomarkers to help diagnose lymph node metastasis, which may compensate the shortage of radiological imaging tools and reduce the rate of misdiagnosis. (Line 78 - 100)

      In paragraph 3- we have stated clearly that HPV negative cases is a special group of cervical cancer and we aim to study its cellular features. (Line 101 - 108)

      In paragraph 4- we have stated clearly that we need to decode cell-to-cell interaction mode in the tumor immune microenvironment of ADC using scRNA-seq. (Line 109 - 123)

      (2) For the sequencing, which kit was used on the Novaseq6000?

      For sequencing, we used the Chromium Controller and Chromium Single Cell 3’Reagent Kits (v3 chemistry CG000183) on the Novaseq6000. We feel sorry for lacking this quite important part and have already add the information in Methods section. (Line 196- 197)

      (3) Additional details are needed for the analysis pipeline. How were batch effects identified/dealt with, what were the precise functions and settings for each step of the analysis, how was clustering performed and how were clusters validated etc. Currently, all that is given is software and sometimes function names which are entirely inadequate to be able to assess the validity of the analysis pipeline. This could alternatively be answered by providing annotated copies of the scripts used for analysis as a supplement.

      We apologize for the inadequacy of descriptions of data analysis process. We have already provided a new part of “data processing” with more details in the Methods section (Line 202 - 221). In addition, we have also provided annotated copies of scripts in the supplementary data as Supplementary Data 1.

      (4) For Cell type annotation, please provide the complete list of "selected gene markers" that were used for annotation.

      We have already added the list of marker genes for cell type annotation in the revised manuscript as Supplementary Table 3.

      (5) No statistics are given for the claims on cell proportion differences throughout the paper (for cell types early, epithelial sub-clusters later, and immune cell subsets further on). This should be a multivariate analysis to account for ADC/SCC, HPV+/- and Early/Late stage.

      We feel sorry for lacking statistics when performing analyses of comparisons. In the revision, we have already used statistic approaches to analyze the differences between each set of group comparison. As a result, the corresponding figures have been revised, accordingly.

      For examle, Fig. 1F, Fig. 2D, Fig. 4E, Fig. 5D, Fig. 6D had been re-analyzed to compare ADC/SCC;Supplementary Fig. 1A, Supplementary Fig. 2A, Supplementary Fig. 4A, Supplementary Fig. 5A, Supplementary Fig. 6A had been re-analyzed to compare HPV+/HPV-; Supplementary Fig. 1B, Supplementary Fig. 2B, Supplementary Fig. 4B, Supplementary Fig. 5B, Supplementary Fig. 6B had been re-analyzed to compare Early/Late stage. All P values have been listed in the figure legends.

      (6) The Y-axis label is missing from the proportion histograms in Figure 2D. In these same panels, the bars change widths on the right side. If these are exclusively in ADC, show it with a 0 bar for SCC, not doubling the width which visually makes them appear more important by taking up more area on the plot.

      We feel sorry for impreciseness when presenting histograms of Fig. 2D and we have also revised other figures with similar mistakes, such as Fig. 1F,  Fig. 5D. As for the width of bars, which is due to output style of data processing, we have already corrected all similar mistakes alongside the whole manuscript, for example, Fig. 2D and Supplementary Fig. 2A-B.

      (7) Throughout the manuscript, informatic predictions (differentiation potential, malignancy score, stemness, and trajectory) are presented as though they're concrete facts rather than the predictions they are. Strong conclusions are drawn on the basis of these predictions which do not have adequate data to support. These conclusions which touch on essentially all of the major claims made in the manuscript would need functional data to validate, or the claims need to be very substantially softened as they lack concrete support. Indeed, the fact that most of the genes examined that were characteristic of a given cluster did not show the expected expression patterns in IHC highlights the fact that such predictions require validation to be able to draw proper inferences.

      Thank you for your insightful comments. As you noted, several conclusions were initially based on bioinformatics predictions. Thus in the revised manuscript, we have rewritten all relevant descriptions in a more softened way, particularly in the paragraph of “epithelial cells” in Results section, as well as the conclusions derived from bioinformatics predictions in other paragraphs throughout the manuscript. We hope our revised descriptions will enhance the precision of our work.

      For example, in paragraph “The sub-clusters of epithelial cells in ADC exhibit elevated stem-like features (from Line 353)”, many over-affirmative disriptions had been re-written in Line 353, 362, 371, 375, 379, 383, 390, 392. From Line 395 to 399, the conclusion had been revised as “The observation of cluster Epi_10_CYSTM1 and its possible specificity to ADC makes us question whether or not it may be related to the aggressiveness of ADC” compared to the previous “This observation may partially indicate that high stemness cluster Epi_10_CYSTM1 is essential for ADC to present more aggressive features”. From Line 400 to 408, conclusions from GO analyses had also been rewritten.

      In paragraph “ADC-specific epithelial cluster-derived gene SLC26A3 is a potential prognostic marker for lymph node metastasis (from Line 422)”, many conclusions based on predictions had been revises, such as Line 424 - 428, Line 439 - 441, Line 451 - 453, Line 455 - 457, Line 458 - 459, Line 471 - 473, Line 478 - 481, Line 484 - 486, Line 489, etc.

      In paragraph “Tumor associated neutrophils (TANs) surrounding ADC tumor area may contribute to the formation of a malignant microenvironment (from Line 536)”, we have changed the descriptions based on bio-infomative predictions, such as Line 560, Line 561, Line 565, Line 566, Line 572, Line 576 - 577, etc.

      In paragraph “Crosstalk among tumor cells, Tregs and neutrophils establishes the immunosuppressive TIME in ADC (from Line 601)”, we have already corrected the all the affirmative descriptions, such as Line 604, Line 612, Line 614, Line 626, Line 628 - 629, Line 641, Line 654 – 655, etc.

      All the changes have also been listed in Revision Notes in detail.

      (8) The cluster Epi_10_CYSTM1 which is the basis for much of the paper is present in a single individual (with a single cell coming from another person), and heavily unconnected from the rest of the epithelial populations. If so much emphasis is placed on it, the existence of this cluster as a true subset of cells requires validation.

      We appreciate this suggestion. We agree that the majority of Epi_10_CYSTM1 cells are derived from sample S7. The fact that we have detected this cluster in only one patient may be due to sampling differences and the inherent heterogeneity of tumor specimens. However, the relatively high number of cells in this cluster from one stage III patient suggests its presence in ADC patients and highlights its potential as a diagnostic marker for clinical staging. To further investigate whether this cluster is generally existing in ADC patients, we have identified and selected candidate genes, such as SLC26A3, ORM1, and ORM2, as representative markers of this cluster, which demonstrated high specificity (as shown in Fig. 3B). We then performed IHC staining on a total of 56 tissue samples, and the results showed positive expressions of these markers in the majority of stage IIIC tumor tissues, confirming the existence of this cell cluster (as shown in Supplementary Fig. 3E). In our revised manuscript, we have included an in-depth discussion of this issue in the seventh paragraph of the Discussion section (From Line 801).

      (9) Claims based on survival analysis of TCGA for Epi_10_CYSTM1 are based on a non-significant p-value, though there is a slight trend in that direction.

      Thank you for your insightful comment. From the data of TCGA survival analysis for Epi_10, we found a not-so-slight trend of difference between groups (with a small P value). As a result, we presented this data and hoped to add more strength to the clinical significance of this cluster. However, this indeed caused controversy because the P value is non-significant. As a result, we have already deleted this data in the revised manuscript.

      (10) The claim "The identification of Epi_10_CYSTM1 as the only cell cluster found in patients with stage IIICp raises the possibility that this cluster may be a potential marker to diagnose patients with lymph node metastasis." This is incorrect according to the sample distributions which clearly show cells from the patient who has EPI_10_CYSTM1 in multiple other clusters. This is then used as justification for SLC26A3 which appears to be associated with associated with late stage, however, in the images SLC26A3 appears to be broadly expressed in later tumours rather than restricted to a minor subset as it should be if it were actually related to the EPI_10_CYSTM1 cluster.

      We feel thankful for this question. The conclusion that “The identification of Epi_10_CYSTM1 as the only cell cluster found in patients with stage IIICp raises the possibility that this cluster may be a potential marker to diagnose patients with lymph node metastasis” has indeed been written too concrete according to the sample distribution. We feel sorry for this and have already corrected the description into “As one of stage IIIC-specific cell clusters, the cluster of Epi_10_CYSTM1, with its representative marker gene SLC26A3, presents potential diagnostic value to predict lymph node metastasis” from Line 478-481.

      However, based on our results, we do think this cluster is a potential diagnostic marker and the hypothesis is right. As for SLC26A3, we have specifically added a new paragraph (from Line 801 - 822) in Discussion section to discuss the rationality and necessity of selecting this gene as our central focus, and the reasons why SLC26A3 should be the representative of cluster Epi_10_CYSTM1. As you noted, SLC26A3 appears to be broadly expressed in later tumors rather than restricted to a minor subset in the images. We apologize for any misunderstanding caused. When presenting the IHC data, we only showed the strongly positive areas of each slide to emphasize the differences. In our revision, we have included whole slide scanning images of the IHC samples, clearly showing that SLC26A3 is restricted to a part of the tumors (Supplementary Fig.9).

      (11) The authors claim that cytotoxic T cells express KRT17, and KRT19. This likely represents a mis-clustering of epithelial cells.

      We apologize for using data without noticing the contamination of T cells with few epithelial cells. We have re-performed quality control to exclude contamination and re-analyzed all data of T cells. In the reviesed manuscript, we have therefore updated completely new data for T cells in both Fig. 4 and Supplementary Fig. 4.

      (12) Multiple claims are made for specific activities based on GO term biological process analysis which while not contradictory to the data, certainly are by no means the only explanation for it, nor directly supported.

      Our initial purpose was to use GO analysis as supports for our conclusions. However, we know these are only claims but not evidence, which is also the problem of our writing techniques as in question (7). Therefore, in our revised manuscript, we have already deleted GO data and descriptions in the paragraphs of “T cell (Fig.4)”(from Line 495) and “B/plasma cell (Fig.6)” (from Line 579), because the predictions are quite irrelevant to our conclusions.

      However, in the sections of “epithelial cell (Fig.2)” (from Line 352) and “neutrophils (Fig.5)” (from Line 536), we retained the GO data and rewrote the conclusions, because these analyses have provided us with valuable information regarding the role of specific cell clusters in ADC progression. Furthermore, our subsequent analyses, such as CellChat, have further validated the accuracy of the findings from the GO analysis. We do think this logically supports the whole storyline of the study.

      Reviewer #2 (public review):

      (1) I believe that many of the proposed conclusions are over-interpretations or unwarranted generalizations of the single-cell analysis. These conclusions are often based on populations in the scRNA-seq data that are described as enriched or specific to a given group of samples (eg. ADC). This conclusion is based on the percentage of cells in that population belonging to the given group; for example, a cluster of cells that dominantly come from ADC. The data includes multiple samples for each group, but statistical approaches are never used to demonstrate the reproducibility of these claims.

      We feel sorry that many of the conclusions have been written in an over-affirmative way but lack profound supporting evidences. In our revision, we have already optimized the writing techniques and re-written all conclusions or descriptions related to only bio-informatic predictions. Moreover, we have performed statistical re-analyses on all data and rearranged the related figures.

      For example, in Line 352, we have changed the sub-title “The sub-clusters of epithelial cells exhibit elevated stem-like features to promote the aggressiveness of ADC” into “The sub-clusters of epithelial cells in ADC exhibit elevated stem-like features”. In this paragraph, many over-affirmative discriptions such as “exclusively”, “significant”, “overwhelmingly”, “remarkably” have been deleted. From Line 486-493, the conclusion of “Moreover, SLC26A3 could be employed as a marker for the Epi_10_CYSTM1 cluster, aiding in the diagnosis of lymph node metastasis to prevent post-surgical upstaging in ADC patients in the future” have been changed into “our results propose that SLC26A3 might be considered as a diagnostic marker to predict lymph node metastasis in ADC patients”. Similar over-affirmative descriptions and conclusions had also been re-written in the other paragraphs, which has been refered to question (7) above.

      (2) This leads to problematic conclusions. For example, the "ADC-specific" Epi_10_CYSTM1 cluster, which is a central focus of the paper, only contains cells from one of the 11 ADC samples and represents only a small fraction of the malignant cells from that sample (Sample 7, Figure 2A). Yet, this population is used to derive SLC26A3 as a potential biomarker. SLC26A3 transcripts were only detected in this small population of cells (none of the other ADC samples), which makes me question the specificity of the IHC staining on the validation cohort.

      We sincerely feel grateful for this question. This is a quite important question as it is also pointed out by reviewer#1 in question (8) above. In the revised manuscript, we have already optimized our descriptions and have added detailed explanation for the importance of SLC26A3 in the Discussion section  (from Line 802 - 823). We agree that the majority of Epi_10_CYSTM1 cells are derived from sample S7. The fact that we detected this cluster in only one patient may be due to sampling differences and the inherent heterogeneity of tumor specimens. However, the relatively high number of cells in this cluster from one stage III patient suggests its presence in ADC and highlights its potential as a diagnostic marker for staging ADC. To further investigate whether this cluster is generally present in ADC patients, we identified and selected candidate genes, such as SLC26A3, ORM1, and ORM2, as representative markers of this cluster, which demonstrated high specificity (as shown in Fig. 3B). We then performed IHC staining on 56 cases of tissue samples, and the results showed positive expression of these markers in the majority of stage III tumor tissues, confirming the existence of this cell cluster (as shown in Supplementary Fig. 3E). In our revised manuscript, we have included an in-depth discussion of this issue in the seventh paragraph of the Discussion section.

      (3) This is compounded by technical aspects of the analysis that hinder interpretation. For example, it is clear that the clustering does not perfectly segregate cell types. In Figures 2B and D, it is evident that C4 and C5 contain mixtures of cell type (eg. half of C4 is EPCAM+/CD3-, the other half EPCAM-/CD3+). These contaminations are carried forward into subclustering and are not addressed. Rather, it is claimed that there is a T cell population that is CD3- and EPCAM+, which does not seem likely.

      Thank you for your insightful comment. This important point is also raised by reviewer#1 above. In the revised manuscript, we have reanalyzed our scRNA-seq data and listed the canonical marker genes for cell type annotation. Most importantly, as for T cells and its sub-clustering, we have performed quality control and re-analyzed all data for T cells, with contamination excluded. In the reviesed manuscript, we have added the re-analyzed data for T cells in both Fig. 4 and Supplementary Fig. 4.

      Recommendations for the authors:

      Reviewer #1 (recommendations for the authors):

      The text would substantially benefit from an editorial revision of language usage.

      We sincerely feel grateful for this suggestion. In our revision, we have conducted language editing and carefully rewritten our manuscript. The changes have been clearly marked in the tracked version of the revised manuscript.

      Reviewer #2 (recommendations for the authors):

      (1) Use statistical approaches to claim enrichment/specificity of populations to given groups (ADC, HPV, etc). Analysis packages like Milo for differential abundance testing would be very helpful.

      We feel grateful for this suggestion. In our revision, we have performed statistical analyses for all groups of comparison data. Meanwhile, we have rearranged the figures based on these statistical results, for example, Fig. 1F, Fig. 2D, Fig. 4E, Fig. 5D, Fig. 6D, Supplementary Fig. 1A-B, Supplementary Fig. 2A-B, Supplementary Fig. 4A-B, Supplementary Fig. 5A-B, Supplementary Fig. 6A-B.

      (2) In the subclustering, consider a round of quality control to ensure that all cells are of the cell type they are claimed to be. Contaminant clusters/cells could be filtered out or reassigned. This could be supplemented with an automated annotation approach using cell-type references.

      We feel thankful for this suggestion. As a result, we have provided copies of scripts in the supplementary data to ensure the quality control of cell type annotation.

      (3) An explanation for why SLC26A3 is so rare in the scRNA-seq data, but seemingly common in the IHC staining would be helpful. I am concerned about the specificity of the stain.

      We apologize for lacking adequate explanation of SLC26A3 and cluster Epi_10_CYSTM1. This is a quite crucial question as it has been listed above in question (8) of reviewer #1 and question (2) of reviewer #2 (public review section). In the revised manuscript, we have added intenstive discussion about this question in the seventh paragraph of Disccusion section (from Line 801 - 822). In fact, because of the heterogeneity among different individuals and different tumor regions even within one sample, Epi_10_CYSTM1 seemed to be derived from only one sample. However, the relatively high number of cells in this cluster from one late-stage (stage IIIC) patient suggests its presence in ADC and highlights its potential as a diagnostic marker for staging ADC. Furthermore, we have identified SLC26A3, ORM1 and ORM2 as specific markers of this cluser and performed IHC staining. With a positive expression of these markers, the existence of this cluster has been indirectly proved (as shown in Fig. 3B).

    1. Author response:

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

      The authors agree with the reviewers that future studies are needed to dissect the mechanisms of eIF3 binding to 3'UTRs and their impact on translation, and the impact of this binding on cellular fate.


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

      eLife Assessment

      This valuable study reveals extensive binding of eukaryotic translation initiation factor 3 (eIF3) to the 3' untranslated regions (UTRs) of efficiently translated mRNAs in human pluripotent stem cell-derived neuronal progenitor cells. The authors provide solid evidence to support their conclusions, although this study may be enhanced by addressing potential biases of techniques employed to study eIF3:mRNA binding and providing additional mechanistic detail. This work will be of significant interest to researchers exploring post-transcriptional regulation of gene expression, including cellular, molecular, and developmental biologists, as well as biochemists.

      We thank the reviewers for their positive views of the results we present, along with the constructive feedback regarding the strengths and weaknesses of our manuscript, with which we generally agree. We acknowledge our results will require a deeper exploration of the molecular mechanisms behind eIF3 interactions with 3'-UTR termini and experiments to identify the molecular partners involved. Additionally, given that NPC differentiation toward mature neurons is a process that takes around 3 weeks, we recognize the importance of examining eIF3-mRNA interactions in NPCs that have undergone differentiation over longer periods than the 2-hr time point selected in this study. Finally, considering the molecular complexity of the 13subunit human eIF3, we agree that a direct comparison between Quick-irCLIP and PAR-CLIP will be highly beneficial and will determine whether different UV crosslinking wavelengths report on different eIF3 molecular interactions. Additional comments are given below to the identified weaknesses.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The authors perform irCLIP of neuronal progenitor cells to profile eIF3-RNA interactions upon short-term neuronal differentiation. The data shows that eIF3 mostly interacts with 3'-UTRs - specifically, the poly-A signal. There appears to be a general correlation between eIF3 binding to 3'-UTRs and ribosome occupancy, which might suggest that eIF3 binding promotes protein

      Strengths:

      The study provides a wealth of new data on eIF3-mRNA interactions and points to the potential new concept that eIF3-mRNA interactions are polyadenylation-dependent and correlate with ribosome occupancy.

      Weaknesses:

      (1) A main limitation is the correlative nature of the study. Whereas the evidence that eIF3 interacts with 3-UTRs is solid, the biological role of the interactions remains entirely unknown. Similarly, the claim that eIF3 interactions with 3'-UTR termini require polyadenylation but are independent of poly(A) binding proteins lacks support as it solely relies on the absence of observable eIF3 binding to poly-A (-) histone mRNAs and a seeming failure to detect PABP binding to eIF3 by co-immunoprecipitation and Western blotting. In contrast, LC-MS data in Supplementary File 1 show ready co-purification of eIF3 with PABP.

      We agree the molecular mechanisms underlying the crosslinking between eIF3 and the end of mRNA 3’-UTRs remains to be determined. We also agree that the lack of interaction seen between eIF3 and PABP in Westerns, even from HEK293T cells, is a puzzle. The low sequence coverage in the LC-MS data gave us pause about making a strong statement that these represent direct eIF3 interactions, given the similar background levels of some ribosomal proteins.

      (2) Another question concerns the relevance of the cellular model studied. irCLIP is performed on neuronal progenitor cells subjected to neuronal induction for 2 hours. This short-term induction leads to a very modest - perhaps 10% - and very transient 1-hour-long increase in translation, although this is not carefully quantified. The cellular phenotype also does not appear to change and calling the cells treated with differentiation media for 2 hours "differentiated NPCs" seems a bit misleading. Perhaps unsurprisingly, the minor "burst" of translation coincides with minor effects on eIF3-mRNA interactions most of which seem to be driven by mRNA levels. Based on the ~15-fold increase in ID2 mRNA coinciding with a ~5-fold increase in ribosome occupancy (RPF), ID2 TE actually goes down upon neuronal induction.

      We agree that it will be interesting to look at eIF3-mRNA interactions at longer time points after induction of NPC differentiation. However, the pattern of eIF3 crosslinking to the end of 3’-UTRs occurs in both time points reported here, which is likely to be the more general finding in what we present.

      (3) The overlap in eIF3-mRNA interactions identified here and in the authors' previous reports is minimal. Some of the discrepancies may be related to the not well-justified approach for filtering data prior to assessing overlap. Still, the fundamentally different binding patterns - eIF3 mostly interacting with 5'-UTRs in the authors' previous report and other studies versus the strong preference for 3'-UTRs shown here - are striking. In the Discussion, it is speculated that the different methods used - PAR-CLIP versus irCLIP - lead to these fundamental differences. Unfortunately, this is not supported by any data, even though it would be very important for the translation field to learn whether different CLIP methodologies assess very different aspects of eIF3-mRNA interactions.

      We agree the more interesting aspect of what we observe is the difference in location of eIF3 crosslinking, i.e. the end of 3’-UTRs rather than 5’-UTRs or the pan-mRNA pattern we observed in T cells. The reviewer is right that it will be important in the future to compare PAR-CLIP and Quick-irCLIP side-by-side to begin to unravel the differences we observe with the two approaches.

      Reviewer #2 (Public review):

      Summary:

      The paper documents the role of eIF3 in translational control during neural progenitor cell (NPC) differentiation. eIF3 predominantly binds to the 3' UTR termini of mRNAs during NPC differentiation, adjacent to the poly(A) tails, and is associated with efficiently translated mRNAs, indicating a role for eIF3 in promoting translation.

      Strengths:

      The manuscript is strong in addressing molecular mechanisms by using a combination of nextgeneration sequencing and crosslinking techniques, thus providing a comprehensive dataset that supports the authors' claims. The manuscript is methodologically sound, with clear experimental designs.

      Weaknesses:

      (1) The study could benefit from further exploration into the molecular mechanisms by which eIF3 interacts with 3' UTR termini. While the correlation between eIF3 binding and high translation levels is established, the functionality of these interactions needs validation. The authors should consider including experiments that test whether eIF3 binding sites are necessary for increased translation efficiency using reporter constructs.

      We agree with the reviewer that the molecular mechanism by which eIF3 interacts with the 3’UTR termini remains unclear, along with its biological significance, i.e. how it contributes to translation levels. We think it could be useful to try reporters in, perhaps, HEK293T cells in the future to probe the mechanism in more detail.

      (2) The authors mention that the eIF3 3' UTR termini crosslinking pattern observed in their study was not reported in previous PAR-CLIP studies performed in HEK293T cells (Lee et al., 2015) and Jurkat cells (De Silva et al., 2021). They attribute this difference to the different UV wavelengths used in Quick-irCLIP (254 nm) and PAR-CLIP (365 nm with 4-thiouridine). While the explanation is plausible, it remains a caveat that different UV crosslinking methods may capture different eIF3 modules or binding sites, depending on the chemical propensities of the amino acid-nucleotide crosslinks at each wavelength. Without addressing this caveat in more detail, the authors cannot generalize their findings, and thus, the title of the paper, which suggests a broad role for eIF3, may be misleading. Previous studies have pointed to an enrichment of eIF3 binding at the 5' UTRs, and the divergence in results between studies needs to be more explicitly acknowledged.

      We agree with the reviewer that the two methods of crosslinking will require a more detailed head-to-head comparison in the future. However, we do think the title is justified by the fact that we see crosslinking to the termini of 3’-UTRs across thousands of transcripts in each condition. Furthermore, the 3’-UTR crosslinking is enriched on mRNAs with higher ribosome protected fragment counts (RPF) in differentiated cells, Figure 3F.

      (3) While the manuscript concludes that eIF3's interaction with 3' UTR termini is independent of poly(A)-binding proteins, transient or indirect interactions should be tested using assays such as PLA (Proximity Ligation Assay), which could provide more insights.

      This is a good idea, but would require a substantial effort better suited to a future publication. We think our observations are interesting enough to the field to stimulate future experimentation that we may or may not be most capable of doing in our lab.

      Reviewer #3 (Public review):

      Summary:

      In this manuscript by Mestre-Fos and colleagues, authors have analyzed the involvement of eIF3 binding to mRNA during differentiation of neural progenitor cells (NPC). The authors bring a lot of interesting observations leading to a novel function for eIF3 at the 3'UTR.

      During the translational burst that occurs during NPC differentiation, analysis of eIF3-associated mRNA by Quick-irCLIP reveals the unexpected binding of this initiation factor at the 3'UTR of most mRNA. Further analysis of alternative polyadenylation by APAseq highlights the close proximity of the eIF3-crosslinking position and the poly(A) tail. Furthermore, this interaction is not detected in Poly(A)-less transcripts. Using Riboseq, the authors then attempted to correlate eIF3 binding with the translation efficacy of mRNA, which would suggest a common mechanism of translational control in these cells. These observations indicate that eIF3-binding at the 3'UTR of mRNA, near the poly(A) tail, may participate to the closed-loop model of mRNA translation, bridging 5' and 3', and allowing ribosomes recycling. However, authors failed to detect interactions of eIF3, with either PABP or Paip1 or 40S subunit proteins, which is quite unexpected.

      Strength:

      The well-written manuscript presents an attractive concept regarding the mechanism of eIF3 function at the 3'UTR. Most mRNA in NPC seems to have eIF3 binding at the 3'UTR and only a few at the 5'end where it's commonly thought to bind. In a previous study from the Cate lab, eIF3 was reported to bind to a small region of the 3'UTR of the TCRA and TCRB mRNA, which was responsible for their specific translational stimulation, during T cell activation. Surprisingly in this study, the eIF3 association with mRNA occurs near polyadenylation signals in NPC, independently of cell differentiation status. This compelling evidence suggests a general mechanism of translation control by eIF3 in NPC. This observation brings back the old concept of mRNA circularization with new arguments, independent of PABP and eIF4G interaction. Finally, the discussion adequately describes the potential technical limitations of the present study compared to previous ones by the same group, due to the use of Quick-irCLIP as opposed to the PAR-CLIP/thiouridine.  

      Weaknesses:

      (1) These data were obtained from an unusual cell type, limiting the generalizability of the model.

      We agree that unraveling the mechanism employed by eIF3 at the mRNA 3’-UTR termini might be better studied in a stable cell line rather than in primary cells.

      (2) This study lacks a clear explanation for the increased translation associated with NPC differentiation, as eIF3 binding is observed in both differentiated and undifferentiated NPC. For example, I find a kind of inconsistency between changes in Riboseq density (Figure 3B) and changes in protein synthesis (Figure 1D). Thus, the title overstates a modest correlation between eIF3 binding and important changes in protein synthesis.

      We thank the reviewer for this question. Riboseq data and RNASeq data are not on absolute scales when comparing across cell conditions. They are normalized internally, so increases in for example RPF in Figure 3B are relative to the bulk RPF in a given condition. By contrast, the changes in protein synthesis measured in Figure 1D is closer to an absolute measure of protein synthesis. 

      (3) This is illustrated by the candidate selection that supports this demonstration. Looking at Figure 3B, ID2, and SNAT2 mRNA are not part of the High TE transcripts (in red). In contrast, the increase in mRNA abundance could explain a proportionally increased association with eIF3 as well as with ribosomes. The example of increased protein abundance of these best candidates is overall weak and uncertain.

      We agree that using TE as the criterion for defining increased eIF3 association would not be correct. By “highly translated” we only mean to convey the extent of protein synthesis, i.e. increases in ribosome protected fragments (RPF), rather than the translational efficiency.

      (4) Despite several attempts (chemical and UV cross-linking) to identify eIF3 partners in NPC such as PABP, PAIP1, or proteins from the 40S, the authors could not provide any evidence for such a mechanism consistent with the closed-loop model. Overall, this rather descriptive study lacks mechanistic insight (eIF3 binding partners).

      We agree that it will be important to identify the molecular mechanism used by eIF3 to engage the termini of mRNA 3’-UTRs. Nevertheless, the identification of eIF3 crosslinking to that location in mRNAs is new, and we think will stimulate new experiments in the field.

      (5) Finally, the authors suspect a potential impact of technical improvement provided by QuickirCLIP, that could have been addressed rather than discussed.

      We agree a side-by-side comparison of eIF3 crosslinks captured by PAR-CLIP versus QuickirCLIP will be an important experiment to do. However, NPCs or other primary cells may not be the best system for the comparison. We think using an established cell line might be more informative, to control for effects such as 4-thiouridine toxicity.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) The Western blot signals for SLC38A2 and ID2 are close to the membrane background and little convincing. Size markers are missing.

      We agree these antibodies are not great. They are the best we could find, unfortunately. We have included originals of all western blots and gels as supplementary information. It’s important to note that the Riboseq data for ID2 and SLC38A2 are consistent with the western blots. See Figure 3C and Figure 3–figure supplement 3B.

      (2) Figure 1 - Figure Supplement 1 appears to present data from a single experiment. This is far less than ideal considering the minor differences measured.

      Thanks for the comment. This is a representative experiment showing the early time course. We have added a second experiment with two different treatments that show the same pattern in the puromycin assay, in Figure 1–figure supplement 1.

      (3) Figure 3F: One wonders what this would look like if TE was plotted instead of RPF. Figure 3 - Figure Supplement 4 seems to show something along those lines. However, the data are not mentioned in the main results section are quite unclear. Why are data separated into TE high and low? Doesn't TE high in differentiated cells equal TE low in undifferentiated cells?

      This is an interesting question. Note that in Figure 3B, n=6300 genes show no change in TE upon differentiation, compared to a total of n=2127 that show a change in TE, with most of those changes not very large. We have now replotted Figure 3F comparing irCLIP read counts in 3’-UTRs to RPF read counts, which shows a significant positive correlation, regardless of whether we look at undifferentiated or differentiated NPCs (See Figure 3F and a new Figure 3– figure supplement 4A). We also compare irCLIP reads in 3’-UTRs to TE values, which show no correlation (See Figure 3G and Figure 3–figure supplement 4B).

      Figure 3-figure supplement 4 was actually a response to a previous round of review (at PLOS Biology) to a rather technical question from a reviewer. We think this figure and associated text should be removed. Instead, we now include supplementary tables with the processed RPF and TE values, for reference (Supplemental files 4-6). We omitted these in the original submission when they should have been included. We also abandoned comparing undifferentiated and differentiated NPCs, and instead look directly at irCLIP reads vs. RPFs or TE, regardless of NPC state, as noted above (Figure 3F, G, and Figure 3–figure supplement 4).

      (4) Figure 3C: The data should be plotted on the same y-axis scale. This would make a visual assessment of the differences in mRNA and RFP levels more intuitive.

      Thanks for this suggestion. We have rescaled the plots as requested.

      Reviewer #2 (Recommendations for the authors):

      (1) The quality of the Western blots in several figures is quite poor. Notably, Figure 1C seems to be a composite gel, as each blot appears to come from a different gel. Additionally, in Supplementary Figure 1A, there is only a single data point, yet the authors indicate that this image is representative of multiple assays. The lack of error bars in this figure raises a question vis-a-vis the reproducibility of the experiments.

      Thanks for the comments. We now include all the original gels as supplementary information. As noted above, the antibodies for ID2 and SLC38A2 are not great, we agree. And as we noted above, the Riboseq data for ID2 and SLC38A2 are consistent with the western blots.

      (2) For the top 500 targets of undifferentiated and differentiated NPCs in the Quick-irCLIP assay, the manuscript does not clarify how many targets are common and how many are unique to each condition. This information is important for understanding the extent of overlap and differentiation-specific interactions of eIF3 with mRNAs. Providing this data would strengthen the interpretation of the results.

      There are 449 of the top 500 hits in common between undifferentiated and differentiated NPCs. We have now added this information to the text, to add clarity. 

      (3) The manuscript does not provide detailed percentages or numbers regarding the overlap between iCLIP and APA-Seq peaks. Clarifying this overlap, particularly in terms of how many of the APA sites are also targets of eIF3, would bolster the understanding of how these two datasets converge to support the authors' conclusions.

      This is a difficult calculation to make, due to the fact that APA-Seq reads are generally much longer than the Quick-irCLIP reads. This is why we focused instead on quantifying the percent of Quick-irCLIP peaks (which are more narrow) overlap with predicted polyadenylation sequences, in Figure 2-figure supplement 1.

      Reviewer #3 (Recommendations for the authors):

      (1) Perform Quick-irCLIP in HEK293 cells to infer technical limitations and/or to generalize the model. The authors will then compare again eIF3 binding site in Jurkat, HEK293, and NPC.

      This is an experiment we plan to do for a future publication, given that we would want to repeat both Quick-irCLIP and PAR-CLIP at the same time.

      (2) Select mRNA candidates with high or low TE changes and analyze eIF3 binding and RPF density and protein abundance along NPC differentiation to support the role of eIF3 binding in stimulating translation.

      We agree looking at time courses in more depth would be interesting. However, this would require substantial experimentation, which is better suited to a future study. Furthermore, now that we have moved away from comparing undifferentiated NPCs and differentiated NPCs when examining TE and RPF values (Figure 3 and Figure 3–figure supplement 4), we think the results now support a more general mechanism of translation reflected in the irCLIP 3’-UTR vs. RPF correlation, independent of NPC state.

      (3) Analyze the interaction of eIF3 with eIF4G and other known partners. This will really provide an improvement to the manuscript. The lack of interaction between eIF3 and the 40S is quite surprising.

      We agree more work needs to be done on the mechanistic side. These are experiments we think would be best to carry out in a stable cell line in the future, rather than primary cells.

      (4) Perform Oligo-dT pulldown (or cap column if possible) and analyze the relative association of PABP, eIF3, and eIF4F on mRNA in NPC versus HEK293. This will clarify whether this mechanism of mRNA translation is specific to NPC or not.

      Thanks for this suggestion. We are uncertain how it would be possible to deconvolute all the possible ways to interpret results from such an experiment. We agree thinking about ways to study the mechanism will keep us occupied for a while.

      (5) Citations in the text indicate the first author, whereas the references are numbered! 

      Our apologies for this oversight. This was a carryover from previous formatting, and has been fixed.

    2. eLife Assessment

      This valuable study shows previously unappreciated binding of the eukaryotic translation initiation factor 3 (eIF3) to the poly(A) tail proximal portion of 3' untranslated regions (UTRs) of mRNAs that are efficiently translated in neuronal progenitors. The authors' conclusions are supported by solid experimental evidence which is based on several orthogonal systems biology approaches. This article is of considerable interest to the broad spectrum of biomedical researchers interested in studying post-transcriptional regulation of gene expression.

    3. Joint Public Review:

      Reviewers thought that the authors addressed some, but not all the concerns raised in the previous round of a review.

      Strengths: The authors employed a battery of next-generation sequencing and crosslinking techniques (e.g., Quick-irCLIP, APA-Seq, and Ribo-Seq) to describe a previously unappreciated binding of eIF3 to the 3'UTRs of the mRNAs. It is also shown that eIF3:3'UTR binding occurs in the vicinity of poly(A) tail of mRNAs that are actively translated in neuronal progenitor cells derived from human pluripotent stem cells. Collectively, these findings provide evidence for the role of eIF3 in regulating translation from the 3'UTR end of the mRNA.

      Weaknesses: In addition to these clear strengths of the article, some weaknesses were observed pertinent to the lack of mechanistic data. It was therefore thought that the experiments aiming to dissect the mechanisms of eIF3 binding to 3'UTRs and their impact on translation warrant future studies. Finally, establishing the impact of the proposed eIF3:3'UTR binding mechanism of translational regulation on cellular fate is required to further support the biological importance of the observed phenomena. It was found that this should also be addressed in the follow up studies.

    1. eLife Assessment

      Yu and colleagues used two-sample MR to test the effect of PUFA on cerebral aneurysms. They found that genetically predicted omega-3 and DHA decreased the risk for Intracranial Aneurysm and Subarachnoid Haemorrhage. This work is useful and the revised version provides solid evidence to support the claims.

    2. Reviewer #1 (Public Review):

      Summary:

      The authors performed two-sample MR combined with sensitivity analyses and colocalization to test the effect of PUFA on cerebral aneurysms. They found that genetically predicted omega-3 and DHA decreased the risk for intracranial aneurysm (IA) and subarachnoid haemorrhage (SAH) but not for unruptured IA (uIA).

      Strengths:

      PUFA on the risk of cerebral aneurysms is of clinical importance; the authors performed multiple sensitivity analyses to ensure MR fulfils its assumptions.

    3. Reviewer #2 (Public Review):

      Summary:

      In the manuscript, Yu et al reported a two-sample Mendelian randomization study to evaluate the causation between polyunsaturated fatty acids (PUFA) and cerebral aneurysm, based on summary statistics from published genome-wide association studies. The authors identified that omega-3 fatty acids and Docosahexaenoic acid decreased the risk for intracranial aneurysm (IA) and aneurysmal subarachnoid haemorrhage (aSAH). COLOC analysis suggested that the acids and IA, aSAH likely share causal variants in gene fatty acid desaturase 2.

      Strengths:

      The methodology is sound, with appropriate sensitivity analysis.

      Weaknesses:

      The results did not provide significant novel findings.

    4. Author response:

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

      Public Reviews:

      Reviewer #1 (Public Review):

      (1) In my opinion, the major weakness is the selection of IVs, the same IVs should be used for each exposure, especially when the outcomes (IA, SAH, and uIA) are closely related. The removal of IVs was inconsistent, for example, why was LPA rs10455872 removed for SAH but not for uIA? (significantly more IVs were used for uIA). The authors should provide more details for the justification of the removal of IVs other than only indicating "confounder" in supplementary tables. The authors should also perform additional analyses including all IVs and IVs from other PUFA GWAS.

      We apologized for our negligence. We reconducted a two-sample MR analysis following the removal of rs10455872 from the uIA, which yielded unaltered ORs and 95% confidence intervals. The P-value was once again found to be statistically insignificant. These results demonstrate the robustness of our MR analyses and indicate that this SNP does not exert an influence on the overall results. (see Figure 4)

      For SNP selection, we adhered rigorously to the established Mendelian randomization analysis process for the screening of instrumental variables. "Confounder" is mean that a current explicit influencer that is explicitly associated with the outcome variable. Following the removal of such confounding SNPs, the analysis of heterogeneity and pleiotropy is repeated on several occasions in MR analysis using radical MR, MRPRESSO, IVW-radical and Egger-radical, with each iteration involving the removal of the corresponding anomalous SNPs until all instances of pleiotropy and heterogeneity have been eliminated, it can be observed that the final single-nucleotide polymorphism (SNP) for each group is not identical. Therefore, It can be observed that the final SNPs for each group is not identical.

      (2) In addition, it seems that the SNPs in the FADS locus were driving the MR association, while FADS is a very pleiotropic locus associated with many lipid traits, removing FADS could attenuate the MR effect. The authors should perform a sensitivity analysis to remove this locus.

      Thanks for the reviewer’s suggestion. In our revised manuscript, We reconducted MR analysis of the positive results after the removal of the FADS2 and its SNPs within 500 kb of the FADS2 locus. This analysis demonstrated that there was no significant causal pathogenic association between PUFA and IA, aSAH. This result validated that SNP: rs174564 was a significant factor driving the causal association between PUFAs and CA. (See page 6, line155-157 and Figure 8)

      (3) Instead of removing multiple "confounder" IVs which I think may bias the MR results due to very closely related lipid traits, the authors should perform multivariable MR to identify independent effects of PUFAs to IA, conditioning on other PUFAs and/or other lipids.

      Thanks for the reviewer’s suggestion. In our revised manuscript, we employed MVMR through adjust for HDL cholesterol, LDL cholesterol, total cholesterol and triglycerides, to remove bias from closely related lipid traits. The application of MVMR analysis serves to reinforce the robustness of our conclusions. (See page 6, line151-153 and Figure5-7)

      (4) Colocalization was not well described, the authors should include the colocalization results for each locus in a supplementary table. They also mentioned "a large PP for H4 (PP.H4 above 0.75) strongly supports shared causal variants affecting both gene expression and phenotype". The authors should make sure that the colocalization was performed using the expression data of each gene or using the GWAS summary of each PUFA locus.

      I apologize for our negligence. We have added the detailed results of the COLOC for each locus in the supplementary table. (See supplementary table 6)

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) I suggest the authors consult Borges et al., 2022 (doi: 10.1186/s12916-022-02399-w) for PUFA IV selection, and perform sensitivity analysis based on Borges et al., 2022 IVs and another PUFA GWAS (such as J Kettunen et al., 2016, doi: 10.1038/ncomms11122).

      Thanks for the reviewer’s suggestion. In order to provide further evidence of the robustness of the results of our analyses, we conducted MVMR and a sensitivity analysis after excluding SNPs within 500 kb of the FADS2 locus, as recommended by Borges et al. (2022). (See page 6, line151-157 and Figure 5-8)

      In regard to the article by J. Kettunen et al. (2016), we found that the validation dataset from which the article was sourced was insufficient in terms of sample size and lacked the requisite statistical efficacy to be used for validation purposes.

      (2) The authors justified that colocalization is to determine if "PUFAs are mediators in the hereditary causative route of cerebral aneurysm", which I don't think is the case.

      Colocalization is to determine whether an MR estimate is not confounded by LD.

      I apologize for our incorrect description. We have made careful modification in our revised manuscript, as follows: “There is consistent evidence that PUFAs have a beneficial causal effect on cerebral aneurysm. In order to determine an MR estimate is not confounded by LD, we used COLOC to identify shared causal SNP between PUFAs and cerebral aneurysms”. (See page 7-8, line 215-217)

      (3) Supplementary tables 2-4 were a bit confusing to me, I suggest the authors provide one supplementary table for each exposure.

      Thanks for the reviewer’s suggestion. Supplementary tables 2_1-2_5 shows the exposure data for the five PUFAs associated with IA, supplementary tables 3_1-3_5 shows the exposure data for the five PUFAs associated with aSAH and supplementary tables 4_1-4_5 shows the exposure data for the five PUFAs associated with UIA. Each exposure is represented by a distinct table.

      (4) Figure 1 legend: I can't find multivariable MR in the figure/method.

      I apologize for our negligence. In our revised manuscript, we have added the MVMR methodology. We also have modified Figure 1 and Figure 1 legend. (See Figure 1, Figure 1 legend and page 6, line 151-153)

      (5) LOO analysis was mentioned in methods and results but I could not find the results for LOO.

      I apologize for our negligence. In our revised manuscript, we have described the results of the LOO, as follows: “The leave-one-out plot demonstrates that there is a potentially influential SNP (rs174564) driving the causal link between PUFA and cerebral aneurysm.” (See page 7, line 209-210)

      (6) Finally, the authors should proofread their manuscript as many sentences are difficult to read, such as:

      Line 183: "...MR methods revealed consistency", "However, there was no any causal relationship..."

      Line 200: "For achieve that..."

      I apologize for our incorrect description. We have modified these descriptions in our revised manuscript, as follows: “The results demonstrated consistency in the outcomes and directionality of the various MR methods employed” and “In order to determine an MR estimate is not confounded by LD, we used COLOC to identify shared causal SNP between PUFAs and cerebral aneurysms”. (See page 7, line 187-188 and line 215-217).

      Reviewer #2 (Recommendations For The Authors):

      (1) Are there any previous epidemiological studies on the association between PUFA and cerebral aneurysm? It will be helpful to introduce this background.

      Thanks for the reviewer’s suggestion. The epidemiology of PUFA with aneurysm in other sites, such as the abdominal aorta, are described in the Introduction section. Although there is a paucity of large-scale multicenter clinical epidemiological studies examining the relationship between PUFAs and cerebral aneurysms, we are endeavoring to infer a prior association between PUFAs and cerebral aneurysms with the aid of Mendelian randomization analysis.

      (2) The authors performed a leave-one-out analysis but did not explain much about the results. The leave-one-out analysis seems to provide some evidence that some SNP is driving the results, like rs174564 in Supplementary Figure 5-1.

      I apologize for our negligence. In our revised manuscript, we have described the results of the leave-one-out analysis, as follows: “The leave-one-out plot demonstrates that there is a potentially influential SNP (rs174564) driving the causal link between PUFA and cerebral aneurysm”. (See page 7, line209-214)”.

      (3) In the discussion (line 211), the authors mentioned omega-6 fatty acids increased the risk of IA and aSAH, omega-3 fatty acids decreased the risk for IA and aSAH, but omega-6 by omega-3 decreased the risk of IA and aSAH. This seems to be different from the figures.

      I apologize for our incorrect description. We have modified this description in our revised manuscript, as follows: “We demonstrated that the omega-3 fatty acids, DHA and, omega-3-pct causally decreased the risk for IA and aSAH. And omega-6 by omega-3 causally increased the risk of IA and aSAH”. (See page 8, line228-230)

      Minor:

      (4) Some grammar errors need to be checked, such as:

      In line 200, "For achieve that, we tested for shared causative SNPs between PUFAs and cerebral aneurysm using COLOC".

      In line 123, "Fourth, to eliminate unclear, palindromic and associated with known confounding factors (body mass index (McDowell et 125 al., 2018), blood pressure (Sun et al., 2022), type 2 diabetes (Tian et al., 2022), high-density lipoprotein (Huang et al., 2018)) SNPs."

      I apologize for our incorrect description. We have modified these descriptions in our revised manuscript, as follows: “Fourth, remove SNPs that are obscure, palindromic, and linked to recognized confounding variables (body mass index (McDowell et al., 2018), blood pressure (Sun et al., 2022), type 2 diabetes (Tian et al., 2022), high-density lipoprotein (Huang et al., 2018))” and “In order to determine an MR estimate is not confounded by LD, we used COLOC to identify shared causal SNP between PUFAs and cerebral aneurysms”. (See page 5, line 124-127 and page 7 line215-217)

    1. eLife Assessment

      This work provides important findings characterizing potential synaptic mechanisms supporting the role of midline thalamus-hippocampal projections in fear memory extinction in mice. The methods and approaches were considered solid, though some evidence is incomplete as there are some concerns with the analytical approaches used for some aspects of the study. This work will be of interest to those in the field of thalamic regulation and fear memory.

    2. Reviewer #1 (Public review):

      The findings of Ziolkowska and colleagues show that a specific projection from the nucleus reuniens of the thalamus (RE) to dorsal CA1 of the hippocampus plays an important role in fear extinction learning in male and female mice. In and of itself, this is not a new finding. Yet, the potential novelty and excitement comes from the authors' identification of structural alterations from RE projecting neurons to the specific stratum lacunosum moleculare subregion of CA1 after learning. The authors use a range of anatomical and functional approaches to demonstrate structural synaptic changes in dorsal CA1 that parallel the necessary role of RE inputs in modulating extinction learning. The significance of these findings was previously hampered by several technical shortcomings in the experimental design and interpretation. The authors adequately addressed some of the design concerns raised in the previous round, along with the interpretive critique that they couldn't localize the timing of effects to consolidation as originally claimed. Nevertheless, the authors provided an inadequate response to the concern regarding their misapplication of Ns and missing controls in one experiment.

      In the previous review, a major methodological weakness in the experimental design involved the widespread misapplication of Ns used for the statistical analyses. Much of the anatomical analyses of structural synaptic changes in the RE-CA1 pathway used N = number of axons (Figs. 1, 2), N = number of dendrites (Figs. 3, 4), and N = number of sections (Fig. 7). In each instance it was recommended that N = animal number should be used. Reasons for this are as follows: this is standard practice in neuroanatomical research; using N = branch/ dendrite/ bouton/ spine number artificially inflates the statistical power and this incorrectly assumes independence of observations; using N = number of sections, etc., doesn't account for imbalances in the number of observations that vary from animal to animal that may skew group results.

      In the authors' response, they generally concurred, but then they followed up with the defense that the number of items was too few in some cases, or absent in others, to permit using N = animal number. While they changed some of their data to N = animal numbers, other aspects of their data remained as-is. The description of the statistics in the figure legend is also dense and difficult to follow in places. Ns should be checked in the legend and figure to make sure they're correct, as at least one error was noted (e.g., see Fig. 2C). Overall, the authors' response falls short of the standard of rigor that helps to reinforce scientific findings from reliability and reproducibility concerns when generating more data to increase Ns (i.e., the number of animals) would have been the better choice.

      Another persistent concern from the previous review is that, in the electron microscopic analyses of dendritic spines (Fig. 5), the authors only compared fear acquisition versus extinction training. One critique was that the lack of inclusion of a naïve control group made it difficult to understand how these structural synaptic changes are occurring relative to baseline. It was also noted that the authors appropriately included naïve controls in other experiments in the paper. In the revised submission the authors simply added in naïve control data to their previous histogram. It is not considered good practice to collect, process, or analyze data one group at a time, as this would be prone to cohort effects or experimental bias. These data should be discarded and the experiment should be run correctly with randomized cases in each group, or instead these data should be eliminated from the report since there is a key control group missing. Again, the nature of the authors' response perpetuates the aforementioned concern that data collection and analysis in this report may fall short of an acceptable standard of rigor.

    3. Reviewer #2 (Public review):

      Summary:

      Ziółkowska et al. characterize the synaptic mechanisms at the basis of the RE-dCA1 contribution to the consolidation of fear memory extinction. In particular, they describe a layer specific modulation of RE-dCA1 excitatory synapses modulation associated to contextual fear extinction which is impaired by transient chemogenetic inhibition of this pathway. These results indicate that RE activity-mediated modulation of synaptic morphology contributes to contextual fear extinction

      Strengths:

      The manuscript is well conceived, the statistical analysis is solid and methodology appropriate. The strength of this work is that it nicely builds up on existing literature and provides new molecular insight on a thalamo-hippocampal circuit previously known for its role in fear extinction. In addition, the quantification of pre- and post-synapses is particularly thorough.

      Weaknesses:

      The results illustrated in this manuscript show nice incremental evidence about the neural mechanisms contributing to the RE-CA1 modulation of fear extinction. The novelty of this manuscript is therefore not exceptional, but still highly relevant for the field.

    4. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      The findings of Ziolkowska and colleagues show that a specific projection from the nucleus reuniens of the thalamus (RE) to dorsal hippocampal CA1 neurons plays an important role in fear extinction learning in male and female mice. In and of itself, this is not a particularly new finding, although the authors' identification of structural alterations from within dorsal CA1 stratum lacunosum moleculare (SLM) as a candidate mechanism for the learning-related plasticity is potentially novel and exciting. The authors use a range of anatomical and functional approaches to demonstrate structural synaptic changes in dorsal CA1 that parallel the necessary role of RE inputs in modulating extinction learning. Yet, the significance of these findings is substantially limited by several technical shortcomings in the experimental design, and the authors' central interpretation. Otherwise, there remain several strengths in the design and interpretation that offset some of these concerns.

      Given that much is already known about the role of RE and hippocampus in modulating fear learning and extinction, it remains unclear whether addressing these concerns would substantially increase the impact of this study beyond the specific area of speciality. Below, several major weaknesses will be highlighted, followed by several miscellaneous comments.

      Methodological:

      (1) One major methodological weakness in the experimental design involves the widespread misapplication of Ns used for the statistical analyses. Much of the anatomical analyses of structural synaptic changes in the RE-CA1 pathway use N = number of axons (Figs. 1, 2), N = number of dendrites (Figs. 3, 4), and N = number of sections (Fig. 7; note that there are 7 figures in total). In every instance, N = animal number should be used. It is unclear which of these results would remain significant if N = animal number were used in each or how many more animals would be required. This is problematic since these data comprise the main evidence for the authors' central conclusion that specific structural synaptic changes are associated with fear extinction learning.

      We do agree with the reviewer that N = animal number is the preferred way to present data in most of our experiments. However, in some experimental groups we observed a very low number of entries. For example, in the 5US group we found RE+/+ spines only in 3 out of 6 analyzed animals. We believe that this observation is not due to technical problems as mCherry virus transduction required to find RE+/+ spines is similar in all experimental groups and we analyzed similar volumes of tissue. While this result still allows the calculation of density of RE+/+ spines per animal it generates no entries for spine area and PSD95 mean gray value if N = animal number. Hence, we decided to use N=animals to calculate spines and boutons densities, and N=dendritic spines/boutons to calculate other spine/bouton parameters. 

      (2) There is a lack of specific information regarding what constitutes learning with respect to behavioral freezing. It is never clearly stated what specific intervals are used over which freezing is measured during acquisition, extinction, and in extinction retrieval tests. Additionally, assessment of freezing during retrieval at 5- and 30-min time points doesn't lay to rest the possibility that there were differences in the decay rate over the 30-min period (also see below).

      We added a detailed description of how learning was assessed.

      ln 125-134: “For assessment of learning we used percent of time spent by animals freezing (% freezing). Freezing behavior was defined as complete lack of movement, except respiration. To assess within-session learning (working memory) we compared pre- and post-US freezing frequency (the first 148 sec vs last 30 sec) during the CFC session (day 1). To assess formation of long-term contextual fear memory, we compared pre-US freezing (day 1) and the first 5 minutes of the Extinction session (day 2). To assess within session contextual fear extinction we ran 2-way ANOVA to assess the effect of time and manipulation on freezing frequency. Freezing data were analyzed in 5-minute bins. To assess formation of long-term contextual fear extinction memory we compared the first 5 minutes of the Extinction session (day 2) and Test session (day 3).”

      As suggested by the reviewer, we also added data for all six 5-minut bins of Extinction sessions.

      (3) A minor-to-moderate methodological weakness concerns the authors' decision to utilize saline injected groups as controls for the chemogenetics experiments (Figs. 5, 6). The correct design is to have a CNO-only group with the same viral procedure sans hM4Di. This concern is partly mitigated by the inclusion of a CNO vs. saline injection control experiment (Fig. 6).

      Figure 5 does not describe a chemogenetic experiment.

      We added new groups with control virus (CNO vs saline) to Figure 6 (now Fig. 6D and H).

      The chemogenetic experiment shown on Figure 7 has all 4 experimental groups (Control vs hM4Di and saline vs CNO).

      (4) In the electron microscopic analyses of dendritic spines (Fig. 5), comparison of only the fear acquisition versus extinction training, and the lack of inclusion of a naïve control group, makes it difficult to understand how these structural synaptic changes are occurring relative to baseline. It is noteworthy that the authors utilize the tripartite design in other anatomical analyses (Fig. 2-4).

      We added data for the Naive mice to Figure 5.

      (5) Interpretation:

      The main interpretive weakness in the study is the authors' claim that their data shows a role for the RE-CA1 pathway in memory consolidation (i.e., see Abstract). This claim is based on the premise that, although RE-CA1 pathway inactivation with CNO treatment 30 min prior to contextual fear extinction did not affect freezing at 5- and 30-min time points relative to saline controls, these rats showed greater freezing when tested on extinction retrieval 24 h thereafter. First, the data do not rule out possible differences in the decay rate of freezing during extinction training due to CNO administration. Next, the fact that CNO is given prior to training still leaves open the possibility that acquisition was affected, even if there were not any frank differences in freezing. Support for this latter possibility derives from the fact that mice tested for extinction retrieval as early as 5 min after extinction training (Fig. 6C) showed the same impairments as mice tested 24 h later (Figs. 6A). Further, all the structural synaptic changes argued to underlie consolidation were based on analysis at a time point immediately following extinction training, which is too early to allow for any long-term changes that would underlie memory consolidation, but instead would confer changes associated with the extinction training event.

      We do agree with the reviewer that our data do not allow us to conclude whether RE-CA1 pathway is involved in acquisition or consolidation of CFE memory. Therefore, we avoid those terms in the manuscript. We just conclude that RE→CA1 participates in the CFE.

      Reviewer #2 (Public review):

      Summary:

      Ziółkowska et al. characterize the synaptic mechanisms at the basis of the REdCA1 contribution to the consolidation of fear memory extinction. In particular, they describe a layer specific modulation of RE-dCA1 excitatory synapses modulation associated to contextual fear extinction which is impaired by transient chemogenetic inhibition of this pathway. These results indicate that RE activity-mediated modulation of synaptic morphology contributes to the consolidation of contextual fear extinction

      Strengths:

      The manuscript is well conceived, the statistical analysis is solid and methodology appropriate. The strength of this work is that it nicely builds up on existing literature and provides new molecular insight on a thalamo-hippocampal circuit previously known for its role in fear extinction. In addition, the quantification of pre- and post-synapses is particularly thorough.

      Weaknesses:

      The findings in this paper are well supported by the data more detailed description of the methods is needed.

      (1) In the paragraph Analysis of dCA1 synapses after contextual fear extinction (CFE), more experimental and methodological data should be given in the text:

      - how was PSD95 used for the analysis, what was the difference between RE. Even if Thy1-GFP mice were used in Fig.2, it appears they were not used for bouton size analysis. To improve clarity, I suggest moving panel 2C to Figure 3. It is not clear whether all RE axons were indiscriminately analysed in Fig. 2 or if only the ones displaying colocalization with both PSD95 and GFP were analysed. If GFP was not taken into account here, analysed boutons could reflect synapses onto inhibitory neurons and this potential scenario should be discussed.

      PSD-95 immunostaining in close apposition to boutons was used to identify RE buttons innervating CA1 (Fig 1 and 2). In these cases PSD-95 signal was not quantified. PSD-95 in close apposition to dendritic spines was used as a proxy of PSDs in CA1 (Figure 3, 4 and 7). In these cases we assessed the integrated mean gray value of PSD-95 signal per dendritic spine (Figure 3, 4) or per ROI (Figure 7). This is explained in detail in the section Confocal microscopy and image quantification (ln 149-172).

      GFP signal was not taken into account during boutons analysis. This is explained in the materials and methods section Confocal microscopy and image quantification (ln 149-172).

      We indicate that PSD-95 is a marker of excitatory synapses located both on excitatory and inhibitory neurons.

      Ln 258: RE boutons were identified in SO and SLM as axonal thickenings in close apposition to PSD-95-positive puncta (a synaptic scaffold used as a marker of excitatory synapses located both on excitatory and inhibitory neurons (Kornau et al., 1995; El-Husseini et al., 2000; Chen et al., 2011; Dharmasri et al., 2024).

      We also cite literature demonstrating that RE projects to the hippocampal formation and forms asymmetric synapses with dendritic spines and dendrites, suggesting innervation of excitatory synapses on both excitatory and aspiny inhibitory neurons (ln 673).

      As advised by the reviewer the Figure 2C panel was moved to Figure 3 (now it is Fig 3A).

      (2) in the methods: The volume of intra-hippocampal CNO injections should be indicated. The concentration of 3 uM seems pretty low in comparison with previous studies. CNO source is missing.

      This section has been rewritten to be more clear. The concentration of CNO was chosen based on the previous studies (Stachniak et al., 2014).

      ln 103: “Cannula placement. Mice were anesthetized by inhalation of 3–5% isoflurane (IsoFlo; Abbott Animal Health) in oxygen and positioned in a stereotaxic frame (51503, Stoelting, Wood Dale, IL, USA). Two holes were drilled in the skull, and a double guide cannulae (2 mm apart and 2 mm long; 26GA, Plastics One) was lowered into the holes such that the cannula tip was located over dorsal CA1 area (2 mm posterior to bregma, ±1 mm lateral, and −1.3 mm vertical). Cannulae were kept patent by using 33-gauge internal dummy cannulae (Plastics One). The animals were used in contextual fear conditioning 21 days after the cannulation. Animals received bilateral CNO (3 μM, 0.2 μl per side for 1 min; Tocris Bioscience, Cat. No. 4936) (Stachniak et al., 2014) or saline injections (0.2 μl per side) 30 minutes before Extinction session via intrahippocampal injection cannulae (33-gauge). After the infusion, the cannula was left in place for 30 seconds. The cannula placement was verified by histology, and only data from animals with correct cannula implants were included in statistical analyses.”

      (3) More details of what software/algorithm was used to score freezing should be included.

      Freezing was automatically scored with VideoFreeze™ Software (Med Associates Inc.).

      (4) Antibody dilutions for IHC should be indicated. Secondary antibody incubation time should be indicated.

      The missing information is added.

      ln 144: “Next, sections were incubated in 4°C overnight with primary antibodies directed against PSD-95 (1:500, Millipore, MAB 1598), washed three times in 0.3% Triton X-100 in PBS and incubated in room temperature for 90 minutes with a secondary antibody bound with Alexa Fluor 647 (1:500, Invitrogen, A31571).”

      (5) No statement about code and data availability is present.

      The statements are added.

      ln 785: Row data and the code used for analysis of confocal data is available at OSF (https://osf.io/bnkpx/).

      Reviewer #3 (Public review):

      Summary:

      This paper examined the role of nucleus reuniens (RE) projections to dorsal CA1 neurons in context fear extinction learning. First, they show that RE neurons send excitatory projections to the stratum oriens (SO) and the stratum lacunosum moleculare (SLM), but not the stratum radiatum (SR). After context fear conditioning, the synaptic connections between RE and dCA1 neurons in the SLM (but not the SO) are weakened (reduced bouton and spine density) after mice undergo context fear conditioning. This weakening is reversed by extinction learning, which leads to enhanced synaptic connectivity between RE inputs and dendrites in the SLM. Control experiments demonstrate that the observed changes are due to extinction and not caused by simple exposure to the context. Extinction learning also induced increases in the size (volume and surface area) of the post-synaptic density (PSD) in SLM. To establish the functional role of RE inputs to dCA1, the researchers used an inhibitory DREADD to silence this pathway during extinction learning. They observe that extinction memory (measured 2-hours or 24-hours later) is impaired by this inhibition. Control experiments show that the extinction memory deficit is not simply due to increased freezing caused by inactivation of the pathway or injections of CNO. Inhibiting the RO projection during extinction learning also reduced the levels of PSD-95 protein levels in the spines of dCA1 neurons.

      Strengths:

      Based on their results, the authors conclude that, "the RE→SLM pathway participates in the updating of fearful context value by actively regulating CFE-induced molecular and structural synaptic plasticity in the SLM.". I believe the data are generally consistent with this hypothesis, although there is an important control condition missing from the behavioral experiments.

      Weaknesses:

      (1) A defining feature of extinction learning is that it is context specific (Bouton, 2004). It is expressed where it was learned, but not in other environments. Similarly, it has been shown that internal contexts (or states) also modulate the expression of extinction (Bouton, 1990). For example, if a drug is administered during extinction learning, it can induce a specific internal state. If this state is not present during subsequent testing, the expression of extinction is impaired just as it is when the physical context is altered (Bouton, 2004). It is possible that something similar is happening in Figure 6. In these experiments, CNO is administered to inactivate the RE-dCA1 projection during extinction learning. The authors observe that this manipulation impairs the expression of extinction the next day (or 2-hours later). However, the drug is not given again during the test. Therefore, it is possible that CNO (and/or inactivation of the RE-dCA1 pathway) induces a state change during extinction that is not present during subsequent testing. Based on the literature cited above, this would be expected to disrupt fear extinction as the authors observed. To determine if this alternative explanation is correct, the researchers need to add groups that receive CNO during extinction training and subsequent extinction testing. If the deficits in extinction expression reported in Figure 6 result from a state change, then these groups should not exhibit an impairment. In contrast, if the authors' account is correct, then the expression of extinction should still be disrupted in mice that receive CNO during training and testing.

      We do agree with the reviewer that such an experiment would be interesting. However, it could be also confusing as we could not distinguish whether the possible behavioral effects are related to the state-dependent aspects of CFE or impaired recall of CFE. Importantly, previous studies showed that RE is crucial for extinction recall (Totty et al., 2023). We also show that CFE memory is impaired not only when the animals recall CFE without CNO (day 3) but also with CNO (day 4) (Figure 6C). Moreover, we do not see the effects of CNO on CFE in the control groups (Figure 6D and H). So we believe that it is unlikely that CNO results in state-dependent CFE.

      (2) In their analysis of dCA1 synapses after contextual fear extinction (CFE) (Figure 4), the authors should have compared Ctx and Ctx-Ctx animals against naïve animals (as they did in Figure 3) when comparing 5US and Ext with naïve animals. Otherwise, the authors cannot make the following conclusion; "since changes of SLM synapses were not observed in the animals exposed to the familiar context that was not associated with the USs, our data support the role of the described structural plasticity at the RE→SLM synapses in CFE, rather than in processing contextual information in general.".

      We assume that the key experimental groups to conclude about synaptic plasticity related to particular behavior are the groups that differ just by one factor/experience. For CFE that would be mice sacrificed immediately before and after CFE session (Figure 2 & 3); on the other hand to conclude about the effects of the re-exposure to the neutral context mice sacrificed before and after second exposure to the neutral context are needed (Figure 4). The naive group, as it differs by at least two manipulations from the Ext and Ctx-Ctx groups, is interesting but not crucial in both cases. This group would be necessary if we focused on the memories of FC or novel context. However, these topics are not the main focus of the current manuscript. Still, the naive group is shown on Figures 2 & 3 to check if CFE brings spine parameters to the levels observed in mice with low freezing.

      We have re-written the cited paragraph to be more precise in our conclusions.

      "Overall, our data demonstrate that synapses in all dCA1 strata undergo structural or molecular changes relevant to CFC and/or CFE. However, only in SLM CFE-induced synaptic changes are likely to be directly regulated by RE inputs as they appear on RE+ dendrites and spines. Since such changes of SLM synapses were not observed in the animals re-exposed to the neutral context, our data support the role of the described structural plasticity at the RE→SLM synapses in CFE, rather than in processing contextual information in general."

      (3) In the materials and methods section, the description of cannula placements is confusing and needs to be rewritten.

      This section has been rewritten.

      ln 103: “Cannula placement. Mice were anesthetized by inhalation of 3–5% isoflurane (IsoFlo; Abbott Animal Health) in oxygen and positioned in a stereotaxic frame (51503, Stoelting, Wood Dale, IL, USA). Two holes were drilled in the skull, and a double guide cannulae (2 mm apart and 2 mm long; 26GA, Plastics One) was lowered into the holes such that the cannula tip was located over dorsal CA1 area (2 mm posterior to bregma, ±1 mm lateral, and −1.3 mm vertical). Cannulae were kept patent by using 33-gauge internal dummy cannulae (Plastics One). The animals were used in contextual fear conditioning 21 days after the cannulation. Animals received bilateral CNO (3 μM, 0.2 μl per side for 1 min; Tocris Bioscience, Cat. No. 4936) (Stachniak et al., 2014) or saline injections (0.2 μl per side) 30 minutes before Extinction session via intrahippocampal injection cannulae (33-gauge). After the infusion, the cannula was left in place for 30 seconds. The cannula placement was verified by histology, and only data from animals with correct cannula implants were included in statistical analyses.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Other/ Minor:

      In the beginning of the second paragraph on p. 21 of the Results section, it states that "RE-dCA1 has no effect on working memory," although it was not clear what data the authors were referring to support this conclusion.

      We refer there to the changes of freezing behavior within the CFE session. This is explained now.

      Reviewer #2 (Recommendations for the authors):

      No statement about code and data availability is present.

      The statements are added.

      ln 785: “Row data and the code used for analysis of confocal data is available at OSF (https://osf.io/bnkpx/).”

    1. eLife Assessment

      The important study established a large-scale objective and integrated multiple optical microscopy systems to demonstrate their potential for long-term imaging of the developmental process. The convincing imaging data cover a wide range of biological applications, such as organoids, mouse brains, and quail embryos, but enhancing image quality can further enhance the method's effectiveness. This work will appeal to biologists and imaging technologists focused on long-term imaging of large fields.

    2. Reviewer #1 (Public review):

      Summary:

      The authors are trying to develop a microscopy system that generates data output exceeding the previous systems based on huge objectives.

      Strengths:

      They have accomplished building such a system, with a field of view of 1.5x1.0 cm2 and a resolution of up to 1.2 um. They have also demonstrated their system performance on samples such as organoids, brain sections, and embryos.

      Weaknesses:

      To be used as a volumetric imaging technique, the authors only showcase the implementation of multi-focal confocal sectioning. On the other hand, most of the real biological samples were acquired under the wide-field illumination, and processed with so-called computational sectioning. Despite the claim that it improves the contrast, sometimes I felt that the images were oversharpened and the quantitative nature of these fluorescence images may be perturbed.

    3. Reviewer #2 (Public review):

      Summary:

      This manuscript introduced a volumetric trans-scale imaging system with an ultra-large field-of-view (FOV) that enables simultaneous observation of millions of cellular dynamics in centimeter-wide 3D tissues and embryos. In term of technique, this paper is just a minor improvement of the authors' previous work, which is a fluorescence imaging system working at visible wavelength region (https://www.nature.com/articles/s41598-021-95930-7).

      Strengths:

      In this study, the authors enhanced the system's resolution and sensitivity by increasing the numerical aperture (NA) of the lens. Furthermore, they achieved volumetric imaging by integrating optical sectioning and computational sectioning. This study encompasses a broad range of biological applications, including imaging and analysis on organoids, mouse brains, and quail embryos, respectively. Overall, this method is useful and versatile.

      Weaknesses:

      What is the unique application that only can be done by this high-throughput system remains vague. Meanwhile, there are also several outstanding issues in this paper, such as the lack of technical advances, unclear method details and non-standardized figures.

      Comments on revisions:

      The revised manuscript has significantly improved in response to the initial review comments, particularly with the detailed additions regarding the objective lens and confocal imaging modes, which enhance the clarity and comprehensibility of the paper. While the structure and arguments are much clearer overall, there are still key issues that need to be addressed, specifically regarding algorithm validation, computational sectioning presentation, and volume imaging rate.

      Algorithm Validation:<br /> The validation of the algorithm's accuracy is not sufficiently robust. Reviewer 1's comment is entirely reasonable, and the authors should validate the algorithm's accuracy using well-established methods as ground truth. In the revised version, the authors attempt to demonstrate the fidelity of the algorithm by employing deep learning methods for high-accuracy cell recognition. However, this validation relies solely on comparisons between deep learning results and manual annotation results. The problem lies in the fact that both manual annotations and deep learning outcomes are derived from algorithm-processed data, which fails to prove the authenticity or validity of the data itself. To strengthen the validation, the authors should incorporate independent, gold-standard methods for comparison.

      Computational Sectioning:<br /> In the revised manuscript, the authors effectively demonstrate the ability of optical sectioning to improve axial resolution using fluorescent beads, as shown in Fig. S3, which is a strong point. However, the manuscript lacks a direct comparison for computational sectioning and does not provide a clear evaluation of axial resolution before and after applying computational sectioning. While some related information is included in Figs. 5.C and D, the details are insufficient, and intensity profiles are absent. I recommend that the authors include more direct visual demonstrations of computational sectioning, along with comparisons of axial resolution before and after applying computational sectioning. This would better showcase the method's effectiveness.

      Volume Imaging Rate:<br /> The manuscript currently omits critical details about the method's volume imaging rate. In the description of the quail embryo imaging experiment, key parameters such as exposure time and imaging speed are missing. Additionally, the manuscript does not discuss the maximum imaging rate supported by the system in confocal mode. The volume imaging rate is an essential factor for biological researchers to evaluate the applicability of the technique. Therefore, this information should be included, ideally in the abstract and introduction. Furthermore, the authors could describe how the volume imaging rate performs under different conditions and discuss its potential applications across various biological research contexts. Including such details would significantly enhance the paper's utility and appeal to the broader research community.

      These adjustments will further strengthen the manuscript and address the reviewers' concerns effectively.

    4. Author response:

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

      Reviewer #1 (Public Review): 

      Summary: 

      The authors are trying to develop a microscopy system that generates data output exceeding the previous systems based on huge objectives. 

      Strengths: 

      They have accomplished building such a system, with a field of view of 1.5x1.0 cm2 and a resolution of up to 1.2 um. They have also demonstrated their system performance on samples such as organoids, brain sections, and embryos. 

      Weaknesses: 

      To be used as a volumetric imaging technique, the authors only showcase the implementation of multi-focal confocal sectioning. On the other hand, most of the real biological samples were acquired under wide-field illumination, and processed with so-called computational sectioning. Despite the claim that it improves the contrast, sometimes I felt that the images were oversharpened and the quantitative nature of these fluorescence images may be perturbed. 

      Reviewer #2 (Public Review): 

      Summary: 

      This manuscript introduced a volumetric trans-scale imaging system with an ultra-large field-of-view (FOV) that enables simultaneous observation of millions of cellular dynamics in centimeter-wide 3D tissues and embryos. In terms of technique, this paper is just a minor improvement of the authors' previous work, which is a fluorescence imaging system working at visible wavelength region (https://www.nature.com/articles/s41598-021-95930-7). 

      Strengths: 

      In this study, the authors enhanced the system's resolution and sensitivity by increasing the numerical aperture (NA) of the lens. Furthermore, they achieved volumetric imaging by integrating optical sectioning and computational sectioning. This study encompasses a broad range of biological applications, including imaging and analysis of organoids, mouse brains, and quail embryos, respectively. Overall, this method is useful and versatile. 

      Weaknesses: 

      The unique application that only can be done by this high-throughput system remains vague. Meanwhile, there are also several outstanding issues in this paper, such as the lack of technical advances, unclear method details, and nonstandardized figures. 

      Here, we address the first part of the Weaknesses concerning the unique application, and will respond to the latter part in the Reply to the Recommendations.

      We are developing 'large field of view with cellular resolution' imaging technique, aiming to apply it to the observation of multicellular systems consisting of a large number of cells. Our proposed optical system has achieved optical performance that enables simultaneous observation of more than one million cells in a single field of view. In this paper, we have succeeded in adding three-dimensional imaging capability while maintaining the size of this two-dimensional field of view. By simultaneously observing the dynamics of a large number of cells, we can reveal spatio-temporal sequences in state transitions (pattern formation, pathogenesis, embryogenesis, etc.) in multicellular systems and discover cells that serve as a starting point. These were mentioned in the 1st and 2nd paragraphs of the Introduction section (Line 48-, 58-) and discussed in the 4th paragraph of Discussion section (Line 398-) of the main text. While our previous work on two-dimensional specimens has shown its validity, the present work demonstrated that temporal changes of multicellular systems in three-dimensional specimens can be observed at the single-cell level.

      Ideally, we aim to achieve the same level of depth observation capability as the FOV size in the lateral direction. However, at present, the penetration depth for living specimens is limited to a few hundred micrometers due to non-transparency, while the lateral FOV size exceeds 1 cm. The current optical performance is well-suited for systems where development occurs within a thin volume but a large area, such as the quail embryo presented in this paper (Fig. 6 in the revised manuscript). In addition to quail embryos, this technique can also be applied to the developmental systems of highly transparent model organisms, such as zebrafish. Furthermore, for chemically cleared specimens, even those thicker than 1.5 mm, as shown in this paper (Fig. 5 in the revised manuscript), can be observed. Besides organs other than the brain, it could also be applied to imaging entire living organisms. However, for observation depths up to 10 mm, such as in the whole mouse brain, a mechanism to compensate for spherical aberration is required, which we consider the next step in our technological development.

      Recommendations for the authors: 

      Reviewer #1 (Recommendations For The Authors): 

      (1) I suggest that authors shall re-examine the quantitative nature of their image processing algorithm. Also, I wonder whether there are parameters that could be adjusted, as images in Figure 3D and 4E seem to be oversharpened with potential loss of information. 

      As the reviewer pointed out, we recognized that there was an insufficient explanation of the image processing.

      Therefore, descriptions on the quantitative nature and parameter adjustments have been added to the text (Materials and Methods, Line 552) and the Supplementary File (Fig. S4-5, Note 2), and these have been referenced in the main text. A summary is given below.

      The adjustable parameters in our method include the cutoff frequency of the smoothing filter used in the background light estimation. If the cutoff frequency is too high, the focal plane component will be included in the “background”; if it is too low, background light will remain in the focal plane. The cutoff frequency needs to be optimized within this range. In this optimization, neither the size of the cell itself nor the performance of the optical system was considered; instead, we utilized the concept of independent component analysis (ICA). This approach is taken because the size and structure of cells vary from sample to sample, and the optical properties also vary with wavelength and location, making it impractical to consider each factor for every case. ICA employs a blind separation method, which is based on the principle that individual signals deviate from the normal (Gaussian) distribution, while the superimposition of signals tends to bring the distribution closer to the Gaussian distribution. Several indices have been proposed to quantify the non-Gaussian nature of the distribution, including kurtosis, skewness, negentropy, and mutual information. Among these measures, we empirically found skewness to be the most suitable and robust, and therefore adopted it for our algorithm. The optimal parameters were selected using a subset of the data before applying the calculations of the entire dataset. The determined values were then applied to the entire dataset.

      Regarding the oversharpening, we believe that it rarely occurs in the image data shown in the manuscript. In a case where low-frequency structures and high-frequency structures are mixed in the focal plane, oversharpeninglike effect can occur because of the disappearance of low-frequency structures, which is discussed in Supplementary File (Note 2, Figs. S5D). However, in the case of a sample with nearly uniform spatial frequency, such as the nucleus observed in this study, oversharpening is unlikely to occur by setting appropriate parameters as described above. If it appears that some images are oversharpened in the figures, it is due to the contrast of the image.

      (2) On the other hand, I am curious how a wide-field fluorescence system may reliably extract information from a denselylabeled sample within axial volume of 200 um, as they showed in the mouse brain in Figure 4. Thus I am skeptical regarding the fidelity and completeness of the signals and cells recorded there. It would be ideal if the authors could benchmark their system performance with a two-photon microscope system, which serves as the ground truth. 

      The reviewer's suggestion is reasonable; however, we are unfortunately unable to observe the same sample using a two-photon microscope. Instead, we will explain these differences from a theoretical perspective. Two-photon microscopes used for brain imaging typically employ objective lenses with a numerical aperture (NA) of at least 0.5, allowing for 3D imaging with depth resolution ranging from several micrometers down to sub-micrometer levels. In contrast, our method uses a lens system with NA of 0.25, and the optical configuration (focusing NA, pinhole size) are not optimized for resolution (Note 2 in Supplementary File), thus the longitudinal resolution (FWHM) is about 14 microns (Fig. 3E in the revised manuscript). This difference is significant in the brain imaging, where our method may not fully separate all cells in close proximity along the depth axis, as shown in the bottom panels (xz-plane) of Fig. 5F of the revised manuscript. Nevertheless, we believe that cell nuclei can be accurately detected in this 3D image using appropriate cell detection methods based on deep learning. To support this claim, we conducted cell detection using the state-of-the-art cell detection platform ELEPHANT and incorporated the results into Fig. 5 (Fig. 5G-I). This figure demonstrates that even with the current spatial resolution, accurate detection of cell nuclei is achievable.

      We accordingly added one paragraph (Line 285) in the main text to explain the cell detection method and discuss the results. We also added one section into Materials and Methods for more detail of the cell detection (Line 650).

      In conjunction with the revision, the developer of ELEPHANT (K. Sugawara) has been included as a co-author.

      Reviewer #2 (Recommendations For The Authors): 

      In my opinion, the following concerns need to be addressed. 

      Major comments: 

      (1) The proposed system's crucial element involves the development of a giant lens system with a numerical aperture (NA) of 0.25. However, a comprehensive introduction and explanation of this significant giant lens system are missing from the manuscript. I strongly suggest that the authors supplement the relevant content to provide a clearer understanding of this integral component. 

      A detailed description of the giant lens system has been added to the main text (Optical Configuration and Performance, Line 83) and the Materials and Methods section (Wide -field imaging system (AMATERAS-2w) configuration, Line 446). A diagram of the lens configuration has also been included in Fig. 1A. In conjunction with these additions, two engineers from SIGMAKOKI CO. LTD., who made significant contributions to the design and manufacturing of the lens system, have been included as co-authors.

      (2) The manuscript introduces a computational sectioning technique, based on iteratively filtering technology. However, the accuracy of this algorithm is not sufficiently validated. 

      It is challenging to discuss accuracy of the processing results compared to the ground truth, because the ground truth is unknown for any of the experiments. Instead, in the Supplementary File (Notes 2, Figures S4-5), we show how the processing results for the measured and simulated data vary with the parameter (cutoff frequency), illustrating the characteristics of our method. The results suggest that by optimally pre-selecting the parameter, it is possible to successfully separate the in-focus and out-of-focus components. This discussion is related to our response to the first recommendation made by the reviewer #1. Please review our response to Reviewer #1 regarding parameter optimization and oversharpening. Here, as an addition, we describe a discussion of the conditions that must be met in order to perform the calculation correctly, as described below (also included in Note 2, Limitation of the computational sectioning).

      To apply this method, certain requirements must be met regarding cutoff spatial frequency and intensity. Regarding cutoff spatial frequency, the algorithm utilizes a low-pass filter with a single cutoff frequency, which can make it challenging to accurately extract structures in the focal plane when structures of varying sizes and shapes are mixed within the sample. This is illustrated by the simulation shown in Fig. S5 and described in Note 2. Conversely, regarding intensity, if the structure’s intensity in the focal plane is weak compared to the Gaussian fluctuations in the background intensity, it becomes difficult to extract the structure. However, intensity fluctuations can be reduced by applying a 3x3 moving average filter to the entire image as a pre-processing step before applying the baseline estimation algorithm. 

      In the experimental data presented in this paper (Figs. 4-6 in the revised manuscript), the spatial frequency issue was not significant because the target structures, which are stained nuclei, appear to be of nearly uniform size in the focal plane. The second issue, related to intensity, is also addressed in Fig. 4, as the signal intensity from the focal plane is sufficient to overcome background light in almost all regions. In the mouse brain example, the use of confocal imaging suppresses background light, allowing the structures in the focal plane to be accurately extracted.

      (3) I didn't see a detailed description of the confocal imaging in the manuscript. If it adheres to conventional confocal technology, then the question arises: what truly constitutes the novel aspect of this technique? 

      The principle of confocal imaging and optics is based on the use of a pinhole array, a system also employed commercially by CrestOptics (X-Light, Italy). Prior to the 1990s, when the configuration utilizing Yokogawa Electric's pinhole array and microlens array pairs became popular, pinhole array-only setups were the norm, and are now considered somewhat traditional. We do not claim novelty in the optical configuration itself, but rather in the design of a confocal optical system tailored for our original large-field (low-magnification) imaging system with a relatively high NA. The pinhole array disk we designed features significantly smaller pinholes and correspondingly tighter pinhole spacing than those used for high-magnification observation purposes. We believe that this unique size and arrangement provides sufficient novelty.

      We have revised the manuscript to clearly emphasize what we believe constitutes the novelty of this technique (paragraphs starting from Line 166 and Line 183). We have also added a discussion on our confocal optical configuration and its spatial resolution in the Supplementary File (Note 1, Fig. S2-3).

      (4) Light-sheet and light-field microscopy, as two emerging 3D microscopy techniques which has theoretically higher throughput than confocal, are not sufficiently introduced in this manuscript. 

      In the previous version, we briefly mentioned light-sheet and light-field microscopy, but we recognized that more detailed explanations were necessary and should be included in the manuscript. We have added several sentences to the main text (Line 159-165). A summary is provided below. 

      Light-sheet microscopy requires the illumination light to propagate over long distances within the specimen, and many applications necessitate the use of transparency-enhanced tissue. Even when the sample is highly transparent, no existing technique can form thin optical sections as long as 1 cm. Therefore, light-sheet microscopy is not an effective method for the thin, wide, three-dimensional objects that are the focus of this project. Regarding light-field microscopy, it features a trade-off where the number of pixels in the two-dimensional plane is reduced in exchange for the ability to record three-dimensional fluorescence distribution information in a single shot. In our imaging system, the pixel spacing is set to be comparable to the Nyquist Frequency to observe as many cells as possible, meaning that no more additional pixels can be sacrificed. Therefore, the light-field microscopy technique is not suitable for our imaging system.

      (5) The fluorescence images of cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs) stained with Rhodamine phalloidin, as presented in Figure 1(E), exhibit suboptimal quality. This may hinder the effective use of the image for biological research. It is imperative that the authors address and explain this aspect, shedding light on the limitations and potential implications of the research findings. 

      We acknowledge the reviewer’s concern regarding the suboptimal quality of the fluorescence image. Upon further examination, we recognized that the resolution and clarity of the image could potentially limit its utility for detailed biological analysis. To address this, we have re-examined the image size and quality to enhance its presentation in Fig. 2C-E in the revised manuscript, which allows for finer structures to be recognized within the large image size.

      Regarding the effective use of the image for biological research, the results shown in the images indicated the capability of observing subcellular structures, such as myofibrils, in cell sheets with a large area, such as myocardial sheets. This would enable us to simultaneously investigate micro-level structures (orientation and density of myofibrils) and macro-level multicellular dynamics (performance of myocardial sheet). We added the above explanation in the manuscript (Line 146). We hope this revision clarifies the quality and utility of the presented image.

      (6) The imaging quality difference between the two techniques shown in Figure 1F, G is relatively small, and the signal distribution difference shown in Figure H is significant, unlike the effects expected from an improvement in resolution. 

      We acknowledge the reviewer's concern regarding the minimal apparent difference in imaging quality between the two images. Upon re-evaluation, we recognized that the original presentation may not have clearly demonstrated the improvements intended by the different techniques. Figure 1H, which showed the line profile of Figs. 1F and G, may have been impacted by the resolution and compression settings of the image file, leading to a less pronounced distinction between the two techniques. To address this, we have enlarged Figs 1F and 1G

      (renumbered as Fig. 2D and 2E in the revised manuscript) and carefully reviewed the resolution and compression ratio to ensure that the differences are more clearly visible. 

      (7) The chart in Figure 2(C) lacks axis titles and numerical labels, making it challenging for readers to comprehend. To enhance reader convenience, it is recommended that the authors incorporate axis titles and numerical labels, providing a clearer context for interpreting the chart. 

      We appreciate the reviewer’s observation regarding the lack of axis titles and numerical labels in the figure. The vertical axis represents fluorescence intensity, which we initially omitted, assuming it was self-evident. However, as the reviewer correctly pointed out, it is crucial to ensure that figures are clear and accessible to readers from diverse backgrounds. In response, we have added the vertical axis title to Fig. 2C (renumbered as Fig. 3C in the revised manuscript) to enhance clarity, while the numerical labels remain omitted as the unit is arbitrary (a.u.). We have also reviewed all other figures in the manuscript to ensure that no similar errors are present.

      (8) In Figures 2(D) and (E), where the authors present the point spread function for quantifying the lateral and axial resolution of the system, I would recommend increasing the number of fluorescent microspheres to more than 10 for statistical averaging. This adjustment would strengthen the persuasiveness of the data and contribute to a more robust analysis. 

      We appreciate the reviewer’s recommendation to increase the number of fluorescent microspheres for statistical averaging in Figs. 2D and E (renumbered as Fig. 3D-E in the revised manuscript). In response, we have revised the graphs to present the point spread function with the statistical mean and standard deviation (SD) of fluorescent images obtained from a large sample size (N = 100), and accordingly revised the main text to mention the statistics (Line 118, Line 132). We also recognized that a similar adjustment was necessary for Figs 1C and D (renumbered as Fig. 2A-B in the revised manuscript), and have accordingly made the same modifications to those figures as well. We believe these changes enhance the robustness and persuasiveness of our data.

      (9) Figure 4(C) visually represents the characteristic 3D structures of several regions. However, discerning the 3D structural information in the images poses a challenge. To address this issue, I recommend that the authors optimize the 3D visualization to improve clarity and facilitate a more effective interpretation of the depicted structures. 

      We appreciate the reviewer’s suggestion regarding the challenges in discerning the 3D structural information in Fig. 4C. To address this, we have added representative images from the xy-plane and xz-plane of the cortex, medial habenula, and choroid plexus (Fig. 5G-I) in the revised manuscript. These additions provide a clearer visualization of the 3D distribution in each region, making it easier for readers to interpret the structures. Additionally, we have overlaid the results of deep-learning based cell detection on these images, further enhancing the visibility of the cells. This adjustment also aligns with our response to Reviewer #1's second comment.

      Minor comments: 

      (1) The labelling of ROI is missing in Figure 1(e). 

      We appreciate the reviewer’s observation regarding the missing labeling of the ROI in Fig. 1E. Upon review, we confirmed that the ROI was indeed labeled with a white square in the previous manuscript; however, it was difficult to discern due to its small size and the black-and-white contrast. To improve visibility, we have recolored the square in magenta, ensuring that it stands out more clearly in the figure (Fig. 2C in the revised manuscript).

      (2) The subfigure order and labeling in Fig. 1 and Fig. 2 are not consistent.

      We appreciate the reviewer’s attention to the subfigure order and labeling in Fig. 1 and 2 (Fig. 1-3 in the revised manuscript). To accommodate subfigures of varying sizes without leaving gaps, we arranged the subfigures in a non-sequential order. However, we have ensured that the text refers to the figures in the correct order. We acknowledge the importance of consistency and will work with the editorial team to explore the best way to present the figures while maintaining clarity and alignment with standard practices.

      (3) Figure 1B reappears in Figure 2.  

      We appreciate the reviewer’s observation regarding the repetition of Figure 1B in Figure 2. While the central part of the optical system (custom lens system) is common to both figures, the illumination system, pinhole array disk, and detection optics for the confocal set up differ. To provide a complete understanding of the optical system, we opted to include the full diagram in Fig. 2B (renumbered as Fig. 3B in the revised manuscript). We considered highlighting only the different components, but we felt that doing so might complicate the reader’s comprehension of the overall system. Therefore, we chose to include the common elements twice to ensure clarity.

    1. eLife Assessment

      Wang et al. presented visual (dot) motion and/or the sound of a walking person and found solid evidence that EEG activity tracks the step rhythm, as well as the gait (2-step cycle) rhythm, with some demonstration that the gait rhythm is tracked superadditively (power for A+V condition is higher than the sum of the A-only and V-only condition). The valuable findings will be of wide interest to those examining biological motion perception and oscillatory processes more broadly. Some of the theoretical interpretations concerning entrainment must remain speculative when the authors cannot dissociate evoked responses from entrained oscillatory effects

    2. Reviewer #1 (Public review):

      Summary:

      Shen et al. conducted three experiments to study the cortical tracking of the natural rhythms involved in biological motion (BM), and whether these involve audiovisual integration (AVI). They presented participants with visual (dot) motion and/or the sound of a walking person. They found that EEG activity tracks the step rhythm, as well as the gait (2-step cycle) rhythm. The gait rhythm specifically is tracked superadditively (power for A+V condition is higher than the sum of the A-only and V-only condition, Experiments 1a/b), which is independent of the specific step frequency (Experiment 1b). Furthermore, audiovisual integration during tracking of gait was specific to BM, as it was absent (that is, the audiovisual congruency effect) when the walking dot motion was vertically inverted (Experiment 2). Finally, the study shows that an individual's autistic traits are negatively correlated with the BM-AVI congruency effect.

      Strengths:

      The three experiments are well designed and the various conditions are well controlled. The rationale of the study is clear, and the manuscript is pleasant to read. The analysis choices are easy to follow, and mostly appropriate.

      Weaknesses:

      There is a concern of double-dipping in one of the tests (Experiment 2, Figure 3: interaction of Upright/Inverted X Congruent/Incongruent). I raised this concern on the original submission, and it has not been resolved properly. The follow-up statistical test (after channel selection using the interaction contrast permutation test) still is geared towards that same contrast, even though the latter is now being tested differently. (Perhaps not explicitly testing the interaction, but in essence still testing the same.) A very simple solution would be to remove the post-hoc statistical tests and simply acknowledge that you're comparing simple means, while the statistical assessment was already taken care of using the permutation test. (In other words: the data appear compelling because of the cluster test, but NOT because of the subsequent t-tests.)

    3. Reviewer #2 (Public review):

      Summary:

      The authors evaluate spectral changes in electroencephalography (EEG) data as a function of the congruency of audio and visual information associated with biological motion (BM) or non-biological motion. The results show supra-additive power gains in the neural response to gait dynamics, with trials in which audio and visual information was presented simultaneously producing higher average amplitude than the combined average power for auditory and visual conditions alone. Further analyses suggest that such supra-additivity is specific to BM and emerges from temporoparietal areas. The authors also find that the BM-specific supra-additivity is negatively correlated with autism traits.

      Strengths:

      The manuscript is well-written, with a concise and clear writing style. The visual presentation is largely clear. The study involves multiple experiments with different participant groups. Each experiment involves specific considered changes to the experimental paradigm that both replicate the previous experiment's finding yet extend it in a relevant manner.

      Weaknesses:

      In the revised version of the paper, the manuscript better relays the results and anticipates analyses, and this version adequately resolves some concerns I had about analysis details. Still, it is my view that the findings of the study are basic neural correlate results that do not provide insights into neural mechanisms or the causal relevance of neural effects towards behavior and cognition. The presence of an inversion effect suggests that the supra-additivity is related to cognition, but that leaves open whether any detected neural pattern is actually consequential for multi-sensory integration (i.e., correlation is not causation). In other words, the fact that frequency-specific neural responses to the [audio & visual] condition are stronger than those to [audio] and [visual] combined does not mean this has implications for behavioral performance. While the correlation to autism traits could suggest some relation to behavior and is interesting in its own right, this correlation is a highly indirect way of assessing behavioral relevance. It would be helpful to test the relevance of supra-additive cortical tracking on a behavioral task directly related to the processing of biological motion to justify the claim that inputs are being integrated in the service of behavior. Under either framework, cortical tracking or entrainment, the causal relevance of neural findings toward cognition is lacking.

      Overall, I believe this study finds neural correlates of biological motion, and it is possible that such neural correlates relate to behaviorally relevant neural mechanisms, but based on the current task and associated analyses this has not been shown.

    4. Author response:

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

      Reviewer #1 (Public Review):

      Strengths:

      The three experiments are well designed and the various conditions are well controlled. The rationale of the study is clear, and the manuscript is pleasant to read. The analysis choices are easy to follow, and mostly appropriate.

      We are grateful to the reviewer’s thoughtful comments.

      Weaknesses:

      I only have one potential worry. The analysis for gait tracking (1 Hz) in Experiment 2 (Figures 3a/b) starts by computing a congruency effect (A/V stimulation congruent (same frequency) versus A/V incongruent (V at 1 Hz, A at either 0.6 or 1.4 Hz), separately for the Upright and Inverted conditions. Then, this congruency effect is contrasted between Upright and Inverted, in essence computing an interaction score (Congruent/Incongruent X Upright/Inverted). Then, the channels in which this interaction score is significant (by cluster-based permutation test; Figure 3a) are subselected for further analysis. This further analysis is shown in Figure 3b and described in lines 195-202. Critically, the further analysis exactly mirrors the selection criteria, i.e. it is aimed at testing the effect of Congruent/Incongruent and Upright/Inverted. This is colloquially known as "double dipping", the same contrast is used for selection (of channels, in this case) as for later statistical testing. This should be avoided, since in this case even random noise might result in a significant effect. To strengthen the evidence, either the authors could use a selection contrast that is orthogonal to the subsequent statistical test, or they could skip either the preselection step or the subsequent test. (It could be argued that the test in Figure 3b and related text is not needed to make the point - that same point is already made by the cluster-based permutation test.)

      Thanks for the helpful suggestions. In Experiment 2, to investigate whether the multisensory integration effect was specialized for biological motion perception, we contrasted the congruency effect between the upright and inverted conditions to search for clusters showing a significant interaction effect. We performed further analyses based on neural responses from this cluster to examine whether the congruency effect was significant in the upright and the inverted conditions, respectively, following the logic of post hoc comparisons after identifying an interaction effect. However, we agree with the reviewer that comparing the congruency effects between the upright and inverted conditions again based on data from this cluster was redundant and resulted in doubledipping. Therefore, we have removed this comparison from the main text and optimized the way to present our results in the revised Fig. 3).

      Related to the above: the test for the three-way interaction (lines 211-216) is reported as "marginally significant", with a p-value of 0.087. This is not very strong evidence.

      As shown in Fig.3b & e, the magnitude of amplitude differs between the gaitcycle frequency (mean = 0.008, SD = 0.038) and the step-cycle frequency (mean = 0.052; SD =0.056), which might influence the statistical results of the interaction effect. To reduce such influence, we converted the amplitude data at each frequency condition into Z-scores, separately. The repeated-measures ANOVA analysis on these normalized amplitude data revealed a significant three-way interaction (F (1,23) = 7.501, p = 0.012, ƞ<sub>p</sub><sup>2</sup> \= 0.246). We have updated the results in the revised manuscript (lines 218-225).

      Reviewer #1 (Recommendations For The Authors):

      -  Which variable caused one data point to be classified as outlier? (line 221).

      The outlier is a participant whose audiovisual congruency effect (Upright – Inverted) in neural responses at the frequency of interest exceeds 3 SD from the group mean. It is marked by a red diamond in Author response 2. Before removing the data, the correlation between the AQ score and the congruency effect is r \= -0.396, p \= 0.055. For comparison, the results after removing the outlier are shown in Fig. 3c of the revised manuscript. We have added more information about the variable causing the outlier in the revised manuscript (lines 231-232).

      Author response image 1.

      The correlation between AQ score and congruency effect

      -  The authors cite Maris & Oostenveld (2007) in line 415 as the main reference for the FieldTrip toolbox, but the correct reference here is different, see https://www.fieldtriptoolbox.org/faq/how_should_i_refer_to_fieldtrip_in_my_p ublication/

      Thank you for pointing out this issue. Citation corrected.

      -  The authors could consider giving some more background on the additive vs superadditive distinction in the Introduction, which may increase the impact; as it stands the reader might not know why this is particularly interesting. Summarize some of the takeaways of the Stevenson et al. (2014) review in this respect.

      Thanks for the suggestion and we have added the following relevant information in the Introduction (lines 80-90):

      “Moreover, we adopted an additive model to classify multisensory integration based on the AV vs A+V comparison. This model assumes independence between inputs from each sensory modality and distinguishes among sub-additive (AV < A+V), additive (AV = A+V), and super-additive (AV > A+V) response modes (see a review by Stevenson et al., 2014). The additive mode represents a linear combination between two modalities. In contrast, the super-additive and subadditive modes indicate non-linear interaction processing, either with potentiated neural activation to facilitate the perception or detection of nearthreshold signals (super-additive) or a deactivation mechanism to minimize the processing of redundant information cross-modally (sub-additive) (Laurienti et al., 2005; Metzger et al., 2020; Stanford et al., 2005; Wright et al., 2003).”

      Reviewer #2 (Public Review):

      Strengths:

      The manuscript is well-written, with a concise and clear writing style. The visual presentation is largely clear. The study involves multiple experiments with different participant groups. Each experiment involves specific considered changes to the experimental paradigm that both replicate the previous experiment's finding yet extend it in a relevant manner.

      We thank the reviewer for the valuable feedback.

      Weaknesses:

      The manuscript interprets the neural findings using mechanistic and cognitive claims that are not justified by the presented analyses and results.

      First, entrainment and cortical tracking are both invoked in this manuscript, sometimes interchangeably so, but it is becoming the standard of the field to recognize their separate evidential requirements. Namely, step and gate cycles are striking perceptual or cognitive events that are expected to produce event-related potentials (ERPs). The regular presentation of these events in the paradigm will naturally evoke a series of ERPs that leave a trace in the power spectrum at stimulation rates even if no oscillations are at play. Thus, the findings should not be interpreted from an entrainment framework except if it is contextualized as speculation, or if additional analyses or experiments are carried out to support the assumption that oscillations are present. Even if oscillations are shown to be present, it is then a further question whether the oscillations are causally relevant toward the integration of biological motion and for the orchestration of cognitive processes.

      Second, if only a cortical tracking account is adopted, it is not clear why the demonstration of supra-additivity in spectral amplitude is cognitively or behaviorally relevant. Namely, the fact that frequency-specific neural responses to the [audio & visual] condition are stronger than those to [audio] and [visual] combined does not mean this has implications for behavioral performance. While the correlation to autism traits could suggest some relation to behavior and is interesting in its own right, this correlation is a highly indirect way of assessing behavioral relevance. It would be helpful to test the relevance of supra-additive cortical tracking on a behavioral task directly related to the processing of biological motion to justify the claim that inputs are being integrated with the service of behavior. Under either framework, cortical tracking or entrainment, the causal relevance of neural findings toward cognition is lacking.

      Overall, I believe this study finds neural correlates of biological motion, and it is possible that such neural correlates relate to behaviorally relevant neural mechanisms, but based on the current task and associated analyses this has not been shown.

      Thanks for raising the important concerns regarding the interpretation of our results within the entrainment or the cortical tracking frame. A strict neural entrainment account emphasizes the alignment of endogenous neural oscillations with external rhythms, rather than a mere regular repetition of stimulus-evoked responses. However, it is challenging to fully dissociate these components, given that rhythmic stimulation can shape intrinsic neural oscillations, resulting in an intricate interplay between endogenous neural oscillations and stimulus-evoked responses (Duecker et al., 2024; Herrmann et al., 2016; Hosseinian et al., 2021). Therefore, some research, including the current study, use the term “entrainment” to refer to the alignment of brain activity to rhythmic stimulation in a broader context, without isolating the intrinsic oscillations and evoked responses (e.g., Ding et al., 2016; Nozaradan et al., 2012; Obleser & Kayser, 2019). Nevertheless, we agree with the reviewer that since the current results did not examine or provide direct evidence for endogenous oscillations, it is better to contextualize the oscillation view as speculations. Hence, we have replaced most of the expressions about “entrainment” with a more general term “tracking” in the revised manuscript (as well as in the title of the manuscript). We only briefly mentioned the entrainment account in the Discussion to facilitate comparison with the literature (lines 307-312).

      Regarding the relevance between neural findings and cognition or behavioral performance, the first supporting evidence comes from the inversion effect in Experiment 2. For the neural responses at gait-cycle frequency, we observed a significantly enhanced audiovisual congruency effect in the upright condition compared with the inverted condition. Inversion disrupts the distinctive kinematic features of biological motion (e.g., gravity-compatible ballistic movements) and significantly impairs biological motion processing, but it does not change the basic visual properties of the stimuli, including the rhythmic signals generated by low-level motion cues. Therefore, the inversion effect has long been regarded as an indicator of the specificity of biological motion processing in numerous behavioral and neuroimaging studies (Bardi et al., 2014; Grossman & Blake, 2001; Shen, Lu, Yuan, et al., 2023; Simion et al., 2008; Troje & Westhoff, 2006; Vallortigara & Regolin, 2006; Wang et al., 2014; Wang & Jiang, 2012; Wang et al., 2022). Here, our finding of the cortical tracking of higher-order rhythmic structures (gait cycles) present in the upright but not in the inverted condition suggests that this cortical tracking effect can not be explained by ERPs evoked by regular onsets of rhythmic events. Rather, it is closely linked with the specialized cognitive processing of biological motion. Furthermore, we found that the BM-specific cortical tracking effect at gait-cycle frequency (rather than the non-selective tracking effect at step-cycle frequency) correlates with observers’ autistic traits, indicating its functional relevance to social cognition. These findings convergingly suggest that the cortical tracking effect that we currently observed engages cognitively relevant neural mechanisms. In addition, our recent behavioral study showed that listening to frequency-congruent footstep sounds, compared with incongruent sounds, enhanced the visual search for human walkers but not for non-biological motion stimuli containing the same rhythmic signals (Shen, Lu, Wang, et al., 2023). These results suggest that audiovisual correspondence specifically enhances the perceptual and attentional processing of biological motion. Future research could examine whether the cortical tracking of rhythmic structures plays a functional role in this process, which may shed more light on the behavioral relevance of the cortical tracking effect to biological motion perception. We have incorporated the above information into the Discussion (lines 268-293).

      Reviewer #2 (Recommendations For The Authors):

      In Figure 1c, it could be helpful to add the word "static" in the illustration for the auditory condition so that readers understand without reading the subtext that it is a static image without biological motion.

      Suggestion taken.

      In the Discussion, I believe it is important to justify an oscillation and entrainment account, or if it cannot be justified based on the current results and analyses (which is my opinion), it could be helpful to explicitly frame it as speculation.

      We agree with the reviewer. For more clarification, please refer to our response to the public review.

      L335, I did not understand this sentence - a reformulation would be helpful.

      The point-light stimuli were created by capturing the motion of a walking actor (Vanrie & Verfaillie, 2004). The global motion of the walking sequences was eliminated so that the point-light walker looks like walking on a treadmill without translational motion. We have reformulated the sentence as follows: “The point-light walker was presented at the center of the screen without translational motion.”

      The results in Figure 2a and 2d are derived by performing a t-test between the amplitude at the frequency of gait and step cycles and zero. Comparison against amplitude of zero is too liberal; the possibility for a Type-I error is inflated because even EEG data with only noise will not have amplitudes of zero at all frequencies. A better baseline (H0) is either the 1/frequency trend in the power spectrum derived using methods like FOOOF (https://fooof-tools.github.io/fooof/) or by performing non-parametric shuffling based methods (https://doi.org/10.1016/j.jneumeth.2007.03.024).

      In our data analysis, instead of performing the t-test between raw amplitude with zero, we compared the normalized amplitude at each frequency bin (by subtracting the average amplitude measured at the neighboring frequency bins from the original amplitude data) against zero. Such analysis is equal to contrasting the raw amplitude to its neighboring frequency bins, allowing us to test whether the neural response in each frequency bin showed a significant enhancement compared with its neighbors. The multiple comparisons on each frequency bin were controlled by false discovery rate (FDR) correction, reducing the Type-I error. Such analysis procedures help reduce (though not totally remove) the influence of the 1/f trend and have been widely used in this field (Cirelli et al., 2016; Henry & Obleser, 2012; Lenc et al., 2018; Nozaradan et al., 2012; Peter et al., 2023).

      To further verify our findings, we adopted the reviewer’s suggestion and created a baseline by performing a non-parametric shuffling-based analysis. More specifically, to establish the statistical significance of amplitude peaks, we carried out a surrogate analysis on each condition. For each participant, a single control surrogate dataset was derived from their actual dataset by jittering the onset of each step-cycle relative to the actual original onset by a randomly selected integer value ranging between − 490–490 ms. This procedure removed the consistent relationship between the EEG signal and the stimuli while preserving each epoch’s general timing within the exposure period. Then, epochs were extracted based on surrogate stimuli onset, and amplitude was computed across frequencies through FFT under a null model of non-entrainment (Moreau et al., 2022). This entire procedure was performed 100 times, producing a surrogate amplitude distribution of 100 group-averaged values for each condition. If the observed amplitude values at the frequency of interest exceeded the value corresponding to the 95th percentile of the surrogate distribution (p < .05) within a given condition (e.g., AV), the amplitude peak was considered significant (Batterink, 2020). As shown in Author response image 2, the statistical results from these analyses are similar to those reported in the manuscript, confirming the significant amplitude peaks at the frequencies of interest.

      Author response image 2.

      Non-parametric analysis for spectral peak. The dotted lines represent the random data based on shuffling analysis. The solid lines represent the observed data in measured EEG signals. All conditions induced significant peaks at step-cycle frequency and its harmonic, while only the AV condition induced a significant peak at gait-cycle frequency.

      Reviewer #3 (Public Review):

      Strengths:

      The main strengths of the paper relate to the conceptualization of BM and the way it is operationalized in the experimental design and analyses. The use of entrainment, and the tracking of different, nested aspects of BM result in seemingly clean data that demonstrate the basic pattern. The first experiments essentially provide the basic utility of the methodological innovation and the second experiment further hones in on the relevant interpretation of the findings by the inclusion of better control stimuli sets.

      Another strength of the work is that it includes at a conceptual level two replications.

      We appreciate the reviewer for the comprehensive review and positive comments.

      Weaknesses:

      The statistical analysis is misleading and inadequate at times. The inclusion of the autism trait is not foreshadowed and adequately motivated and is likely underpowered. Finally, a broader discussion over other nested frequencies that might reside in the point-light walker stimuli would also be important to fully interpret the different peaks in the spectra.

      (1) Regarding the nested frequency peaks in the spectra, we did observe multiple significant amplitude peaks at 1f (1/0.83 Hz), 2f (2/1.67 Hz), and 4f (4/3.33 Hz) relative to the gait-cycle frequency (Fig. 2 a&d). To further test the functional roles of the neural activity at different frequencies, we analyzed the audiovisual integration modes at each frequency. Note that we collapsed the data from Experiments 1a & 1b in the analysis as they yielded similar results. Overall, results show a similar additive audiovisual integration mode at 2f and 4f and a super-additive integration mode only at 1f (Figure S1), suggesting that the cortical tracking effects at 2f and 4f may be functionally linked but independent of that at 1f. We have reported the detailed results in the Supplementary Information.

      (2) For the reviewer’s other concerns about statistical analysis and autism traits, please refer to our responses below to the Recommendations for the authors.

      Reviewer #3 (Recommendations For The Authors):

      The description of the analyses performed for experiment 2 comes across as double dipping. Congruency effects for BM and non-BM motion (inverted) were compared using cluster-based statistics. Then identified clusters informed an averaging of signals which then were subjected to a paired comparison. At this point, it is no surprise that these paired comparisons are highly significant seeing that the channels were selected based on a cluster analysis of the same exact contrast. This approach should be avoided.

      In the analysis of the repeated measures ANOVA reporting a trend as marginally significant is misleading. Reporting the statistical results whilst indicating that those do not reach significance is the appropriate way to communicate this finding. Other statistics can be used in order to provide the likelihood of those findings supporting H1 or H0 if the authors would like to state something more precise (Bayesian).

      Thanks for the comments. We have addressed these two points in our response to the public review of Reviewer #1.

      The authors perform a correlation along "autistic trait" scores in an individual differences approach. Individual differences are typically investigated in larger samples (>n=40). In addition, the range of AQ scores seems limited to mostly average or lower-than-average AQs (barring a couple). These points make the conclusions on the possible role of BM in the autistic phenotype very tentative. I would recommend acknowledging this.

      An alternative analysis approach that might better suit the smaller sample size is a comparison between high and low AQ participants, defined based on a median split.

      Many thanks for the suggestion. We agree with the reviewer that the sample size (n = 24) in the current study is not large for exploring the correlation between BM and autistic traits. The narrow range of AQ scores was due to the fact that all participants were non-clinical populations and we did not pre-select participants by AQ scores. To further confirm our findings, we adopted your suggestion to compare the BM-specific cortical tracking effect (i.e., audiovisual congruency effect (Upright - Inverted)) between high and low AQ participants split by the median AQ score (20) of this sample. Similar to correlation analysis, one outlier, whose audiovisual congruency effect (Upright – Inverted) in neural responses at 1 Hz exceeds 3 SD from the group mean, was removed from the following analysis. As shown in Figure S3, at 1 Hz, participants with low AQ showed a greater cortical tracking effect compared with high AQ participants (t (21) = 2.127, p \= 0.045). At 2 Hz, low and high AQ participants showed comparable neural responses (t (22) = 0.946, p \= 0.354). These results are in line with the correlation analysis, providing further support to the functional relevance between social cognition and cortical tracking of biological motion as well as its dissociation at the two temporal scales. We have added these results to the main text (lines 238-244) and the supplementary information.

      Writing

      The narrative could be better unfolded and studies better motivated. The transition from basic science research on BM to possibly delineating a mechanistic understanding of autism was a surprise at the end of the intro. Once the authors consider the suggestions and comments above it would be good to have this detail and motivation more obviously foreshadowed in the text.

      Thanks for the great suggestion and we have provided an introduction about how audiovisual BM processing links with social cognition and ASD in the first paragraph of the revised manuscript (lines 46-56). In particular, integrating multisensory BM cues is foundational for perceiving and attending to other people and developing further social interaction. However, such ability is usually compromised in people with social deficits, such as individuals with autism spectrum disorder (ASD) (Feldman et al., 2018), and even in non-clinical populations with high autistic traits (Ujiie et al., 2015). These behavioral findings underline the close relationship between multisensory BM processing and one’s social cognitive capability, motivating us to further explore this issue at the neural level in the current study. We have also modified the relevant content in the last paragraph of the Introduction (lines 100-108), briefly mentioning the methods that we used to investigate this issue.

      The use of terminology related to neural oscillations which are entraining to the BM seems to suggest that the rhythmic tracking inevitably stems from the shaping of existing intrinsic dynamics of the brain. I am not sure this is necessarily the case. I would therefore adopt a more concrete jargon for the description of the entrainment seen in this study. If a discussion over internal dynamics shaped by external stimuli should be invoked, it should be done explicitly with appropriate references (but in my opinion, it isn't quite required).

      Please refer to our response to a similar point raised in the public review of Reviewer #2.

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    1. eLife Assessment

      In this manuscript, Griesius et al analyze the dendritic integration properties of NDNF and OLM interneurons, and suggest that the supralinear NMDA receptor-dependent synaptic integration may be associated with dendritic calcium transients only in NDNF interneurons. These findings are important because they suggest there might be functional heterogeneities in the mechanisms underlying synaptic integration in different classes of interneurons of the mouse neocortex and hippocampus. The revised work remains incomplete due to remaining concerns about experimental methodology, cell health, and lack of dendritic Na-spikes which have been recorded in previous works.

    2. Reviewer #2 (Public review):

      Summary:

      Griesius et al. investigate the dendritic integration properties of two types of inhibitory interneurons in the hippocampus: those that express NDNF+ and those that express somatostatin. They found that both neurons showed supralinear synaptic integration in the dendrites, blocked by NMDA receptor blockers but not by blockers of Na+ channels. These experiments are critically overdue and very important because knowing how inhibitory neurons are engaged by excitatory synaptic input has important implications for all theories involving these inhibitory neurons.

      Comments on revisions:

      The authors have addressed the reviewers' comments, but haven't resolved most of the key issues.

      Specifically, performing only a single uncaging experiment at a single dendritic location per cell prevents a detailed biophysical analysis of NDNF and OLM cell integration properties. A more extended exploration would have potentially addressed several of the reviewers' questions. It is particularly worrying that the authors cite cell health, dendritic blebbing, and changes in input resistance as the reason for terminating experiments after a single uncaging event. This suggests that the uncaging laser may be damaging the dendrite, potentially affecting the membrane potential directly, and overall cell health, beyond simply uncaging glutamate.

      While the authors' qualitative conclusions about supra-linear integration and NMDA receptor dependency seem plausible, the limited data and potential methodological issues weaken any quantitative interpretations and comparisons between the two cell types.

      Similarly, the absence of dendritic Na-spikes remains unexplained, despite reports of strong dendritic Na-currents in these cells.

    3. Reviewer #3 (Public review):

      Summary:

      The authors study temporal summation of caged EPSPs in dendrite-targeting hippocampal CA1 interneurons. The data indicate non-linear summation, which is larger in dendrites of NDNF-expressing neurogliaform cells versus OLM cells. However, the underlying mechanisms are largely unclear.

      Strengths:

      Synaptic integration in dendrites of cortical GABAergic interneurons is important and still poorly investigated. Focal 2-photon uncaging of glutamate is a nice and detailed method to study temporal summation of small potentials in dendritic segments. 2P calcium imaging is a powerful method to potentially disentangle dendritic signal processing in interneuron dendrites.

      Weaknesses:

      Due to several experimental limitations of the study including a relatively low number of recorded dendrites, lack of voltage-clamp recordings, lack of NMDA-dependent calcium signals in OLM cells and lack of wash-out during pharmacological experiments (AP5-application), the mechanistic insights are limited.

      (1) NMDA-receptor signalling in NDNF-IN. The authors nicely show that temporal summation in dendrites of NDNF-INs is to a certain extent non-linear. Pharmacology with AP5 hints towards contribution of NMDA receptors. However, the authors report that the non-linearity in not significantly dependent on EPSP amplitude (Fig. S2), which should be the case if NMDA-receptors are involved. Unfortunately, there are no voltage-clamp data showing NMDA and AMPA currents, potentially providing a mechanistic explanation for the non-linear summation.

      (2) Recovery of drug effect. Pharmacological application of AP5 is the only argument for the involvement of NMDA receptors. However, as long-lasting experiments were apparently difficult to obtain, there is no washout-data presented - only drug effect versus baseline. For all the other drugs (TTX, Nimodipine, CPA) recordings were even shorter, lacking a baseline recording. Thus, it remains open to what extent the AP5-effect might be affected by rundown of receptors or channels during whole-cell recordings or beginning phototoxicity.

      (3) Nonlinear EPSP summation in OLM-IN. The authors do similar experiments in dendrite-targeting OLM-INs and show that the non-linear summation is smaller than in NDNF cells. The reason for this remains unclear. The diameter of proximal dendrites in OLM cells is larger than the diameter in NDNF cells. However, there is probably also an important role of synapse density and glutamate receptor density, which was shown to be very low in proximal dendrites of OLM cells and strongly increase with distance (Guirado et al. 2014, Cerebral Cortex 24:3014-24, Gramuntell et al. 2021, Front Aging Neurosci 13:782737). Therefore, it would have been helpful to see experiments quantifying synapse density (counting spines, PSD95-puncta, ...) and show how this density compares with non-linearity in the analyzed NDNF and OLM dendrites.

      (4) NMDA in OLM-IN. Similar to the NDNF cells, the authors argue for an involvement of NMDA receptors in OLM cells, based on bath-application of AP5 (Fig. 8). Again, there seems to be no significant dependence on EPSP amplitude (Fig. S3). Even more remarkable, the authors claim that there is no dendritic calcium increase after activation of NMDA receptors without showing data. Therefore, it remains unclear whether the calcium signals are just below detection threshold, or whether the non-linearity depends on other calcium-impermeable channels and receptors. To understand this phenomenon different calcium sensors, different Ca2+/Mg2+ concentrations or voltage-clamp data would have helped.

    4. Author response:

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

      Public Reviews:

      Reviewer #1 (Public Review):

      The manuscript by Griesius et al. addresses the dendritic integration of synaptic input in cortical GABAergic interneurons (INs). Dendritic properties, passive and active, of principal cells have been extensively characterized, but much less is known about the dendrites of INs. The limited information is particularly relevant in view of the high morphological and physiological diversity of IN types. The few studies that investigated IN dendrites focused on parvalbumin-expressing INs. In fact, in a previous study, the authors examined dendritic properties of PV INs, and found supralinear dendritic integration in basal, but not in apical dendrites (Cornford et al., 2019 eLife).

      In the present study, complementary to the prior work, the authors investigate whether dendrite-targeting IN types, NDNF-expressing neurogliaform cells, and somatostatin(SOM)-expressing O-LM neurons, display similar active integrative properties by combining clustered glutamate-uncaging and pharmacological manipulations with electrophysiological recording and calcium imaging from genetically identified IN types in mouse acute hippocampal slices.

      The main findings are that NDNF IN dendrites show strong supralinear summation of spatially- and temporally-clustered EPSPs, which is changed into sublinear behavior by bath application of NMDA receptor antagonists, but not by Na+-channel blockers. L-type calcium channel blockers abolished the supralinear behavior associated calcium transients but had no or only weak effect on EPSP summation. SOM IN dendrites showed similar, albeit weaker NMDA-dependent supralinear summation, but no supralinear calcium transients were detected in these INs. In summary, the study demonstrates that different IN types are endowed with active dendritic integrative mechanisms, but show qualitative and quantitative divergence in these mechanisms.

      While the research is conceptionally not novel, it constitutes an important incremental gain in our understanding of the functional diversity of GABAergic INs. In view of the central roles of IN types in network dynamics and information processing in the cortex, results and conclusions are of interest to the broader neuroscience community.

      The experiments are well designed, and closely follow the approach from the previous publication in parts, enabling direct comparison of the results obtained from the different IN types. The data is convincing and the conclusions are well-supported, and the manuscript is very well-written.

      I see only a few open questions and some inconsistencies in the presentation of the data in the figures (see details below).

      We thank the reviewer for the evaluation and address the detailed points below.

      Reviewer #2 (Public review):

      Summary:

      Griesius et al. investigate the dendritic integration properties of two types of inhibitory interneurons in the hippocampus: those that express NDNF+ and those that express somatostatin. They found that both neurons showed supralinear synaptic integration in the dendrites, blocked by NMDA receptor blockers but not by blockers of Na+ channels. These experiments are critically overdue and very important because knowing how inhibitory neurons are engaged by excitatory synaptic input has important implications for all theories involving these inhibitory neurons.

      Strengths:

      (1) Determined the dendritic integration properties of two fundamental types of inhibitory interneurons.

      (2) Convincing demonstration that supra-threshold integration in both cell types depends on NMDA receptors but not on Na+ channels.

      Weaknesses:

      It is unknown whether highly clustered synaptic input, as used in this study (and several previous studies), occurs physiologically.

      We are grateful to the reviewer for the critique. Indeed, the degree to which clustered inputs belonging to a functional neuronal assembly occur on interneuron dendrites is an open question. However, Chen et al (2013, Nature 499:295-300) reported that dendritic domains of PV-positive interneurons in visual cortex, unlike their somata, exhibit calcium transients in vivo which are highly tuned to stimulus orientation. This suggests that clustered inputs to dendritic segments may well belong to functional assemblies, much as in principal cells (e.g. Wilson et al, 2016, Nature Neuroscience 19:1003–1009; Iacaruso et al, 2017, Nature 547;449–452). In our earlier work reporting NMDAR-dependent supralinear summation of glutamate uncaging-evoked responses at a subset of dendrites on PV-positive interneurons, we demonstrated how this arrangement in an oscillating feedback circuit could be exploited to stabilise neuronal assemblies.

      Reviewer #3 (Public review):

      Summary:

      The authors study the temporal summation of caged EPSPs in dendrite-targeting hippocampal CA1 interneurons. There are some descriptive data presented, indicating non-linear summation, which seems to be larger in dendrites of NDNF expressing neurogliaform cells versus OLM cells. However, the underlying mechanisms are largely unclear.

      Strengths:

      Focal 2-photon uncaging of glutamate is a nice and detailed method to study temporal summation of small potentials in dendritic segments.

      Weaknesses:

      (1) NMDA-receptor signaling in NDNF-IN. The authors nicely show that temporal summation in dendrites of NDNF-INs is to a certain extent non-linear. However, this non-linearity varies massively from cell to cell (or dendrite to dendrite) from 0% up to 400% (Figure S2). The reason for this variability is totally unclear. Pharmacology with AP5 hints towards a contribution of NMDA receptors. However, the authors claim that the non-linearity is not dependent on EPSP amplitude (Figure S2), which should be the case if NMDA-receptors are involved. Unfortunately, there are no voltage-clamp data of NMDA currents similar to the previous study. This would help to see whether NMDA-receptor contribution varies from synapse to synapse to generate the observed variability? Furthermore, the NMDA- and AMPA-currents would help to compare NDNF with the previously characterized PV cells and would help to contribute to our understanding of interneuron function.

      We thank the reviewer for the helpful comments.

      We did not actually claim that EPSP amplitude has no role in determining the magnitude of non-linearity: “Among possible sources of variability for voltage supralinearity, we did not observe a systematic dependence on the average amplitude of individual uEPSPs […] (Fig. S2)”. Whilst we fully agree that, at first sight, a positive dependence of supralinearity on uEPSP amplitude might be expected simply from the voltage-dependent kinetics of NMDARs, there are two main reasons why this could have been obscured. First, the expected relationship is non-monotonic, because with large local depolarizations the driving force collapses, as seen in the overall sigmoid shape of the average relationship between the scaled observed response and arithmetic sum (e.g. Figs 2a & c; 4c & e). Therefore, we would arguably expect a parabolic relationship rather than a simple positive slope relating the degree of supralinearity to the average amplitude of individual uEPSPs. Second, given that the uncaging distance varied substantially, the average amplitudes of the individual uEPSPs recorded at the soma would have undergone different degrees of electrotonic attenuation and further distortion by active conductances before they were measured. Ultimately, the plots in Fig. S2 show too much scatter to be able to exclude a positive or parabolic relationship of nonlinearity to uEPSP amplitude. To avoid misunderstanding, we have changed the sentence in the Results that refers to Fig. S2 to: “Among possible sources of variability for voltage supralinearity, we did not observe a significant monotonic dependence on the average amplitude of individual uEPSPs, distance from the uncaging location along the dendrite to the soma, [or] the dendrite order (Fig. S2)”.

      As for the relative contributions of NMDARs and AMPARs, voltage clamp recordings from both neurogliaform and OLM interneurons have already been reported, with the conclusion that neurogliaform cells exhibit relatively larger NMDAR-mediated currents (e.g. Chittajallu et al. 2017; Booker et al. 2021; Mercier et al. 2022), entirely in keeping with the conclusions of our study. Repeating these measurements would add little to the study. Furthermore, because the mean baseline uEPSP amplitude was <0.5 mV (Fig S2), it would be difficult to obtain reliable meaurements of isolated NMDAR-mediated uEPSCs.

      Turning to the high variability of supralinearity, indeed, the 95% confidence interval for the data in Fig. 2d is 73%, 213%. This degree of variability is consistent with the wide range of NMDAR/AMPAR ratios reported by Chittajallu et al. 2017 (their Fig. 1g), compounded by the expected non-monotonic relationship alluded to above.

      (2) Sublinear summation in NDNF-INs. In the presence of AP5, the temporal summation of caged EPSPs is sublinear. That is potentially interesting. The authors claim that this might be dependent on the diameter of dendrites. Many voltage-gated channels can mediate such things as well. To conclude the contribution of dendritic diameter, it would be helpful to at least plot the extent of sublinearity in single NDNF dendrites versus the dendritic diameter. Otherwise, this statement should be deleted.

      We have plotted the degree of nonlinearity against dendritic diameter for neurogliaform cells (under baseline conditions and in D-AP5) in Fig S2h-k. We did not observe any significant linear correlations, other than between amplitude nonlinearity and dendrite diameter post D-AP5. This does not negate the possibility that the significant difference in average dendritic diameters between neurogliaform and OLM cells contributes to differences in impedance (which we have rephrased as “Among possible explanations is that the local dendritic impedance is greater in neurogliaform cells, lowering the threshold for recruitment of regenerative currents”).

      (3) Nonlinear EPSP summation in OLM-IN. The authors do similar experiments in dendrite-targeting OLM-INs and show that the non-linear summation is smaller than in NDNF cells. The reason for this remains unclear. The authors claim that this is due to the larger dendritic diameter in OLM cells. However, there is no analysis. The minimum would be to correlate non-linearity with dendritic diameter in OLM-cells. Very likely there is an important role of synapse density and glutamate receptor density, which was shown to be very low in proximal dendrites of OLM cells and strongly increase with distance (Guirado et al. 2014, Cerebral Cortex 24:3014-24, Gramuntell et al. 2021, Front Aging Neurosci 13:782737). Therefore, the authors should perform a set of experiments in more distal dendrites of OLM cells with diameters similar to the diameters of the NDNF cells. Even better would be if the authors would quantify synapse density by counting spines and show how this density compares with non-linearity in the analyzed NDNF and OLM dendrites.

      The difference in average dendritic diameters between OLM and neurogliaform cells is highly significant (Fig. 8q, P<0.001). We do not claim that dendritic diameter (and by implication local impedance) is the only determinant of the degree of non-linearity. The suggestion that a gradient of glutamate receptor density contributes is interesting. However, the results of uncaging experiments targeting more distal OLM dendrites of similar diameter as neurogliaform dendrites would be subject to numerous confounds, not least the very different electrotonic attenuation, likely differences in various active conductances, and the presence of spines in OLM dendrites (which are generally sparse and were not reliably imaged in our experiments). Moreover, the cell would have to remain patched for longer in order for the fluorescent dyes to invade the distal dendrites. This alone could potentially result in systematic biases among groups. We now cite Guirrado et al (2014) and Gramuntell et al (2021) to highlight that factors other than dendritic diameter per se, such as inhomogeneity in spine and NMDA receptor density may also contribute to the heterogeneity of nonlinear summation in OLM cells.

      (4) NMDA in OLM. Similar to the NDNF cells, the authors claim the involvement of NMDA receptors in OLM cells. Again there seems to be no dependence on EPSP amplitude, which is not understandable at this point (Figure S3). Even more remarkable is the fact that the authors claim that there is no dendritic calcium increase after activation of NMDA receptors. Similar to NDNF-cell analysis there are no NMDA currents in OLMs. Unfortunately, even no calcium imaging experiments were shown. Why? Are there calcium-impermeable NNDA receptors in OLM cells? To understand this phenomenon the minimum is to show some physiological signature of NMDA-receptors, for example, voltage-clamp currents. Furthermore, it would be helpful to systematically vary stimulus intensity to see some calcium signals with larger stimulation. In case there is still no calcium signal, it would be helpful to measure reversal potentials with different ion compositions to characterize the potentially 'Ca2+ impermeable' voltage-dependent NMDA receptors in OLM cells.

      The same response to point 1) above applies to OLM cells. As with neurogliaform cells, mean OLM baseline asynchronous (separate response) amplitudes were <0.5 mV, making it very difficult to record an isolated NMDAR-mediated uEPSC. Having said that, NMDARs do contribute to EPSCs elicited by stimulation of multiple afferents (e.g. Booker et al, 2021). We do not claim that dendritic calcium transients cannot be elicited following activation of NMDARs in OLM cells. We simply reported that the evoked uEPSPs, designed to approximate individual synaptic signals, were sub-threshold for detectable dendritic calcium signals under conditions that were suprathreshold in neurogliaform cells. The statement has been amended to specify that there were no detectable signals under our recording conditions. There is no evidence presented in the manuscript to suggest that OLM NMDARs are calcium impermeable and indeed no such claim was made.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      There is a large variability in the observed dendritic nonlinearity, in NDNF IN dendrites e.g. the uEPSP amplitude nonlinearity measure varies from as low as 10-20% to over 200%. As only single dendrites were recorded from each IN, it is unclear if this variability is among the cells or between individual dendrites. While the authors analyzed some potential factors, such as distance along the dendrites, branch order, or response magnitude (amplitude and integral), they did not find any substantial correlation. It remains open if different dendrites of NDNF INs, located in the str. moleculare vs. those in or projecting towards str. radiatum, have divergent properties. Similarly, for SOM INs an important question is if axon-carrying dendrites show distinct properties.

      In this context, it would be interesting to see not only values for the mean nonlinearity but also the maximal nonlinearity and its distribution.

      Nonlinearity as defined in the manuscript is a cumulative measurement. The final value per dendritic segment is therefore the sum of nonlinearities at 1 to 12 near-synchronous uncaging locations. The data for the individual dendritic segments are shown in the slopegraphs as in Fig 2b, with their distribution visible. The averages referred to in the results correspond to the paired mean difference plots, which are the group summaries. The method section has been amended to clarify the analysis method. We did not address specifically whether dendrites projecting in different directions behaved differently. This is an interesting question beyond the scope of this study. Nor did we compare axon-carrying OLM dendrites to other dendrites.

      Figures:

      Figure 1: The gray line in plots g and h is not explained. While it looks like an identity line, the legend in plot i ("asynchronous") interferes.

      In plots g and h the gray line is the line of identity. In plot i it is an estimate of the linear summation. In plot i it is not the line of identity as it does not start at the origin with a slope of 1. The figure legend has been amended to clarify.

      In the same panels (Figure 1g,h, and subsequent figures) consider changing the title from "soma (voltage)" to uEPSP.

      The titles have been amended.

      In panel Figure 1i note the missing "(" in the title.

      Title amended.

      In panel Figure 1h: Shouldn't the X-axis label and legend text read "Arithmetic sum of (EPSP) integrals" instead of "Integral of arithmetic sum").

      The wording more accurately reflects the analytical operations. The asynchronous (separate) responses were summed arithmetically first, and then the integral was taken of each cumulative sum. We have therefore left the axis title and legend unchanged.

      Figure 2a,c: Could you please describe how the scaling was performed for the two axes?

      Method section amended.

      In the same panels (Figure 2a,c, and subsequent figures), the legend seems to be misleading: the plot is NS Amplitude/Integral vs Arithmetic sum, and the black line is the identity line (or scaled interpolation of the arithmetic sum, which is essentially the same).

      The scaled arithmetic sums (uEPSP amplitude, integral) represent linear summation and so overlap with the line of identity. The interpolation estimate of the asynchronous (separate) calcium transient response does not overlap with the line of identity as this estimate does not start at the origin with a slope of 1. The legends throughout the manuscript have been amended to clarify this.

      Figure 2b,d,f (and subsequent figures) slope plots: Please indicate that this is the average amplitude supralinearity for the individual recorded dendrites. Note here that the Results text mentions only the average amplitude supralinearity, but not the slop plots, paired mean difference, or Gardner-Altman estimation, illustrated in the figures.

      Nonlinearity as defined in the manuscript is a cumulative measurement. The final value per dendritic segment is therefore the sum of nonlinearities at 1 to 12 near-synchronous uncaging locations. The data for the individual dendritic segments are shown in the slopegraphs as in fig 2b, with their distribution visible. The averages referred to in the results correspond to the paired mean difference plots, which are the group summaries. The method section has been amended to clarify.

      Fig 2e: The legend (both text and figure, also in the following figures) is confusing, as the gray line and diamonds are defined as separate 12(?) responses, but it seems to represent a linear interpolation of the scaled arithmetic sums (ultimately nothing else but an identity line).

      The grey line shows the linear interpolation output between the calcium transient measurements at 1 uncaging location and at 12 uncaging locations. The 12th uncaging location is indicated in the key as “separate 12”. The linear interpolation in these plots does represent linear summation but is not the line of identity as it does not begin at the origin and does not have a slope of 1.

      Reviewer #2 (Recommendations for the authors):

      This study is well-developed and technically executed. I only have minor comments for the authors:

      (1) To target NDNF+ neurons, the authors use the NDNF-Cre mouse line and a Cre-dependent AAV using the mDLX promotor. Why the mDLX promotor? Would it have been sufficient to use any Cre-dependent fluorophore?

      Pilot experiments revealed leaky expression when a virus driving flexed ChR2 under a non-specific promoter (EF1a) was injected in the neocortex of Ndnf-Cre mice (Author response image 1). In our hands, and in line with Dimidschtein et al (2016),  the use of the mDLX enhancer reduced off-target expression.

      Author response image 1.

      A. AAV2/5-EF1a-DIO-hChR2(H134R)-mCherry injected into superficial neocortex of Ndnf-Cre mice led to expression in a few pyramidal neurons in addition to layer 1 neurogliaform cells. B. Patch-clamp recording from a non-labelled pyramidal cell showed that an optogenetically evoked glutamatergic current remained after blockade of GABAA and GABAB receptors, further confirming limited specificity of expression of ChR2. (Data from M Muller, M Mercier and V Magloire, Kullmann lab.)

      (2) The distance of the uncaring sites from the soma plays a key role. The authors should indicate the mean distance of the cluster and its variance.

      Uncaging distance from soma is indicated for both NGF and OLM interneurons in the supplementary figures S2 and S3 respectively.

      (3) Martina et al., in Science 2000, showed high levels of Na+ channels in the dendrites of OLM cells and hinted that spikes could occur in them. The authors should discuss this possible discrepancy.

      Discussion amended.

      (4) Looking at Figure 1d, the EPSPs look exceptionally long-lasting, longer than those observed by stimulating axonal inputs. Could this indicate spill-over excitation? If so, how could this affect the outcome of this study?

      The asynchronous (separate responses) decay to baseline within 100 ms, similar to the neurogliaform EPSPs evoked by electrical stimulation of axons in the SLM in Mercier et al. 2022. We observed clear plateau potentials in a minority of cells (e.g. Fig. S1b). Such plateau potentials can be generated by dendritic calcium channels and we do not consider that glutamate spillover needs to be invoked to account for them.

      (5) In the legend of Figure 2: "n=11 dendrites in 11 cells from 9 animals". Why do the authors only study 11 dendrites from 11 cells? Isn't it possible to repeatedly stimulate clusters of synaptic inputs onto the same cells? In principle, could one test many dendrites of the same cell at different distances from the soma? It is also remarkable that there were very few cells per animal.

      The goal always was to record from as many dendrites as possible from the same cells whilst maintaining high standards of cell health. When cell health indicators such as blebbing, input resistance change or resting voltage change were detected, no further dendritic location could be tested with reasonable confidence. In a given 400 um slice there would be relatively few healthy candidate cells at a suitable depth to attempt to patch-clamp.

    1. eLife assessment

      This manuscript provides valuable information about the genesis of CPSF6 condensates due to HIV-1 infection. However, the evidence is incomplete as it is missing more functional assays. Furthermore, some data on the fusion between CPSF6 Aggregates and SC35 speckles are not novel.

    2. Reviewer #1 (Public review):

      In recent years, our understanding of the nuclear steps of the HIV-1 life cycle has made significant advances. It has emerged that HIV-1 completes reverse transcription in the nucleus and that the host factor CPSF6 forms condensates around the viral capsid. The precise function of these CPSF6 condensates is under investigation, but it is clear that the HIV-1 capsid protein is required for their formation. This study by Tomasini et al. investigates the genesis of the CPSF6 condensates induced by HIV-1 capsid, what other co-factors may be required, and their relationship with nuclear speckels (NS). The authors show that disruption of the condensates by the drug PF74, added post-nuclear entry, blocks HIV-1 infection, which supports their functional role. They generated CPSF6 KO THP-1 cell lines, in which they expressed exogenous CPSF6 constructs to map by microscopy and pull down assays of the regions critical for the formation of condensates. This approach revealed that the LCR region of CPSF6 is required for capsid binding but not for condensates whereas the FG region is essential for both. Using SON and SRRM2 as markers of NS, the authors show that CPSF6 condensates precede their merging with NS but that depletion of SRRM2, or SRRM2 lacking the IDR domain, delays the genesis of condensates, which are also smaller.

      The study is interesting and well conducted and defines some characteristics of the CPSF6-HIV-1 condensates. Their results on the NS are valuable. The data presented are convincing.

      I have two main concerns. Firstly, the functional outcome of the various protein mutants and KOs is not evaluated. Although Figure 1 shows that disruption of the CPSF6 puncta by PF74 impairs HIV-1 infection, it is not clear if HIV-1 infection is at all affected by expression of the mutant CPSF6 forms (and SRRM2 mutants) or KO/KD of the various host factors. The cell lines are available, so it should be possible to measure HIV-1 infection and reverse transcription. Secondly, the authors have not assessed if the effects observed on the NS impact HIV-1 gene expression, which would be interesting to know given that NS are sites of highly active gene transcription. With the reagents at hand, it should be possible to investigate this too.

    3. Reviewer #2 (Public review):

      Summary:

      HIV-1 infection induces CPSF6 aggregates in the nucleus that contain the viral protein CA. The study of the functions and composition of these nuclear aggregates have raised considerable interest in the field, and they have emerged as sites in which reverse transcription is completed and in the proximity of which viral DNA becomes integrated. In this work, the authors have mutated several regions of the CPSF6 protein to identify the domains important for nuclear aggregation, in addition to the already-known FG region; they have characterized the kinetics of fusion between CPSF6 aggregates and SC35 nuclear speckles and have determined the role of two nuclear speckle components in this process (SRRM2, SUN2).

      Strengths:

      The work examines systematically the domains of CPSF6 of importance for nuclear aggregate formation in an elegant manner in which these mutants complement an otherwise CPSF6-KO cell line. In addition, this work evidences a novel role for the protein SRRM2 in HIV-induced aggregate formation, overall advancing our comprehension of the components required for their formation and regulation.

      Weaknesses:

      Some of the results presented in this manuscript, in particular the kinetics of fusion between CPSF6-aggregates and SC35 speckles have been published before (PMID: 32665593; 32997983).

      The observations of the different effects of CPSF6 mutants, as well as SRRM2/SUN2 silencing experiments are not complemented by infection data which would have linked morphological changes in nuclear aggregates to function during viral infection. More importantly, these functional data could have helped stratify otherwise similar morphological appearances in CPSF6 aggregates.

      Overall, the results could be presented in a more concise and ordered manner to help focus the attention of the reader on the most important issues. Most of the figures extend to 3-4 different pages and some information could be clearly either aggregated or moved to supplementary data.

    4. Reviewer #3 (Public review):

      In this study, the authors investigate the requirements for the formation of CPSF6 puncta induced by HIV-1 under a high multiplicity of infection conditions. Not surprisingly, they observe that mutation of the Phe-Gly (FG) repeat responsible for CPSF6 binding to the incoming HIV-1 capsid abrogates CPSF6 punctum formation. Perhaps more interestingly, they show that the removal of other domains of CPSF6, including the mixed-charge domain (MCD), does not affect the formation of HIV-1-induced CPSF6 puncta. The authors also present data suggesting that CPSF6 puncta form individual before fusing with nuclear speckles (NSs) and that the fusion of CPSF6 puncta to NSs requires the intrinsically disordered region (IDR) of the NS component SRRM2. While the study presents some interesting findings, there are some technical issues that need to be addressed and the amount of new information is somewhat limited. Also, the authors' finding that deletion of the CPSF6 MCD does not affect the formation of HIV-1-induced CPSF6 puncta contradicts recent findings of Jang et al. (https://doi.org/10.1093/nar/gkae769).

    5. Author response:

      We would like to extend our sincere thanks to you and reviewers at eLife for their thoughtful handling of our manuscript and their valuable feedback, which will greatly improve our study.

      We are committed to performing the additional experiments as recommended by the reviewers. However, we would like to clarify our study's focus. 

      The novelty of our study lies in the highlights of our manuscript:

      • The formation of HIV-induced CPSF6 puncta is critical for restoring HIV-1 nuclear reverse transcription (RT).

      • CPSF6 protein lacking the FG peptide cannot bind to the viral core, thereby failing to form HIVinduced CPSF6 puncta.

      • The FG peptide, rather than low-complexity regions (LCRs) or the mixed charge domains (MCDs) of the CPSF6 protein, drives the formation of HIV-induced CPSF6 puncta.

      • HIV-induced CPSF6 puncta form individually and later fuse with nuclear speckles (NS) via the intrinsically disordered region (IDR) of SRRM2.

      By focusing on these processes, we believe our study provides a critical perspective on the molecular interactions that mediate the formation of HIV-induced CPSF6 puncta and broadens the understanding of how HIV manipulates host nuclear architecture.

      Public Reviews: 

      Reviewer #1 (Public review): 

      In recent years, our understanding of the nuclear steps of the HIV-1 life cycle has made significant advances. It has emerged that HIV-1 completes reverse transcription in the nucleus and that the host factor CPSF6 forms condensates around the viral capsid. The precise function of these CPSF6 condensates is under investigation, but it is clear that the HIV-1 capsid protein is required for their formation. This study by Tomasini et al. investigates the genesis of the CPSF6 condensates induced by HIV-1 capsid, what other co-factors may be required, and their relationship with nuclear speckels (NS). The authors show that disruption of the condensates by the drug PF74, added post-nuclear entry, blocks HIV-1 infection, which supports their functional role. They generated CPSF6 KO THP-1 cell lines, in which they expressed exogenous CPSF6 constructs to map by microscopy and pull down assays of the regions critical for the formation of condensates. This approach revealed that the LCR region of CPSF6 is required for capsid binding but not for condensates whereas the FG region is essential for both. Using SON and SRRM2 as markers of NS, the authors show that CPSF6 condensates precede their merging with NS but that depletion of SRRM2, or SRRM2 lacking the IDR domain, delays the genesis of condensates, which are also smaller. 

      The study is interesting and well conducted and defines some characteristics of the CPSF6-HIV-1 condensates. Their results on the NS are valuable. The data presented are convincing. 

      I have two main concerns. Firstly, the functional outcome of the various protein mutants and KOs is not evaluated. Although Figure 1 shows that disruption of the CPSF6 puncta by PF74 impairs HIV-1 infection, it is not clear if HIV-1 infection is at all affected by expression of the mutant CPSF6 forms (and SRRM2 mutants) or KO/KD of the various host factors. The cell lines are available, so it should be possible to measure HIV-1 infection and reverse transcription. Secondly, the authors have not assessed if the effects observed on the NS impact HIV-1 gene expression, which would be interesting to know given that NS are sites of highly active gene transcription. With the reagents at hand, it should be possible to investigate this too. 

      We thank the reviewer for her/his valuable feedback on our manuscript. We are pleased to see her/his appreciation of our results, and we will do our utmost to address the highlighted points to further improve our work.

      Reviewer #2 (Public review): 

      Summary: 

      HIV-1 infection induces CPSF6 aggregates in the nucleus that contain the viral protein CA. The study of the functions and composition of these nuclear aggregates have raised considerable interest in the field, and they have emerged as sites in which reverse transcription is completed and in the proximity of which viral DNA becomes integrated. In this work, the authors have mutated several regions of the CPSF6 protein to identify the domains important for nuclear aggregation, in addition to the alreadyknown FG region; they have characterized the kinetics of fusion between CPSF6 aggregates and SC35 nuclear speckles and have determined the role of two nuclear speckle components in this process (SRRM2, SUN2). 

      Strengths: 

      The work examines systematically the domains of CPSF6 of importance for nuclear aggregate formation in an elegant manner in which these mutants complement an otherwise CPSF6-KO cell line. In addition, this work evidences a novel role for the protein SRRM2 in HIV-induced aggregate formation, overall advancing our comprehension of the components required for their formation and regulation. 

      Weaknesses: 

      Some of the results presented in this manuscript, in particular the kinetics of fusion between CPSF6aggregates and SC35 speckles have been published before (PMID: 32665593; 32997983). 

      The observations of the different effects of CPSF6 mutants, as well as SRRM2/SUN2 silencing experiments are not complemented by infection data which would have linked morphological changes in nuclear aggregates to function during viral infection. More importantly, these functional data could have helped stratify otherwise similar morphological appearances in CPSF6 aggregates. 

      Overall, the results could be presented in a more concise and ordered manner to help focus the attention of the reader on the most important issues. Most of the figures extend to 3-4 different pages and some information could be clearly either aggregated or moved to supplementary data. 

      First, we thank the reviewer for her/his appreciation of our study and to give to us the opportunity to better explain our results and to improve our manuscript. We appreciate the reviewer’s positive feedback on our study, and we will do our best to address her/his concerns. In the meantime, we would like to clarify the focus of our study. Our research does not aim to demonstrate an association between CPSF6 condensates (we use the term "condensates" rather than "aggregates," as aggregates are generally non-dynamic (Alberti & Hyman, 2021; Banani et al., 2017), and our work specifically examines the dynamic behavior of CPSF6 during infection, as shown in Scoca et al., JMCB 2022) and SC35 nuclear speckles. This association has already been established in previous studies, as noted in the manuscript.

      About the point highlighted by the reviewer: "Kinetics of fusion between CPSF6-aggregates and SC35 speckles have been published before (PMID: 32665593; 32997983)."

      Our study differs from prior work PMID 32665593 because we utilize a full-length HIV genome and we did not follow the integrase (IN) fluorescence in trans and its association with CPSF6 but we specifically assess if CPSF6 clusters form in the nucleus independently of NS factors and next to fuse with them. In the current study we evaluated the dynamics of formation of CPSF6/NS puncta, which it has not been explored before. Given this focus, we believe that our work offers a novel perspective on the molecular interactions that facilitate HIV / CPSF6-NS fusion.

      For better clarity, we would like to specify that our study focuses on the role of SON, a scaffold factor of nuclear speckles, rather than SUN2 (SUN domain-containing protein 2), which is a component of the LINC (Linker of Nucleoskeleton and Cytoskeleton) complex.

      As suggested by the reviewer, we will keep key information in the main figure and move additional details to the supplementary material.

      Reviewer #3 (Public review): 

      In this study, the authors investigate the requirements for the formation of CPSF6 puncta induced by HIV-1 under a high multiplicity of infection conditions. Not surprisingly, they observe that mutation of the Phe-Gly (FG) repeat responsible for CPSF6 binding to the incoming HIV-1 capsid abrogates CPSF6 punctum formation. Perhaps more interestingly, they show that the removal of other domains of CPSF6, including the mixed-charge domain (MCD), does not affect the formation of HIV-1-induced CPSF6 puncta. The authors also present data suggesting that CPSF6 puncta form individual before fusing with nuclear speckles (NSs) and that the fusion of CPSF6 puncta to NSs requires the intrinsically disordered region (IDR) of the NS component SRRM2. While the study presents some interesting findings, there are some technical issues that need to be addressed and the amount of new information is somewhat limited. Also, the authors' finding that deletion of the CPSF6 MCD does not affect the formation of HIV-1-induced CPSF6 puncta contradicts recent findings of Jang et al. (doi.org/10.1093/nar/gkae769). 

      We thank the reviewer for her/his thoughtful feedback and the opportunity to elaborate on why our findings provide a distinct perspective compared to those of Jang et al. (doi.org/10.1093/nar/gkae769), while aligning with the results of Rohlfes et al. (doi.org/10.1101/2024.06.20.599834).

      One potential reason for the differences between our findings and those of Jang et al. could be the choice of experimental systems. Jang et al. conducted their study in HEK293T cells with CPSF6 knockouts, as described in Sowd et al., 2016 (doi.org/10.1073/pnas.1524213113). In contrast, our work focused on macrophage-like THP-1 cells, which share closer characteristics with HIV-1’s natural target cells. 

      Our approach utilized a complete CPSF6 knockout in THP-1 cells, enabling us to reintroduce untagged versions of CPSF6, such as wild-type and deletion mutants, to avoid potential artifacts from tagging. Jang et al. employed HA-tagged CPSF6 constructs, which may lead to subtle differences in experimental outcomes due to the presence of the tag.

      Finally, our investigation into the IDR of SRRM2 relied on CRISPR-PAINT to generate targeted deletions directly in the endogenous gene (Lester et al., 2021, DOI: 10.1016/j.neuron.2021.03.026). This approach provided a native context for studying SRRM2’s role.

      We will incorporate these clarifications into the discussion section of the revised manuscript.

    1. eLife Assessment

      This fundamental work demonstrates that compartmentalized cellular metabolism is a dominant input into cell size control in a variety of mammalian cell types and in Drosophila. The authors show that increased pyruvate import into the mitochondria in liver-like cells and in primary hepatocytes drives gluconeogenesis but reduces cellular amino acid production, suppressing protein synthesis. The evidence supporting the conclusions is compelling, with a variety of genetic and pharmacologic assays rigorously testing each step of the proposed mechanism. This work will be of interest to cell biologists, physiologists, and researchers interested in cell metabolism, and is significant because stem cells and many cancers exhibit metabolic rewiring of pyruvate metabolism.

    2. Reviewer #1 (Public review):

      Summary:

      The study examines how pyruvate, a key product of glycolysis that influences TCA metabolism and gluconeogenesis, impacts cellular metabolism and cell size. It primarily utilizes the Drosophila liver-like fat body, which is composed of large post-mitotic cells that are metabolically very active. The study focuses on the key observations that over-expression of the pyruvate importer MPC complex (which imports pyruvate from the cytoplasm into mitochondria) can reduce cell size in a cell-autonomous manner. They find this is by metabolic rewiring that shunts pyruvate away from TCA metabolism and into gluconeogenesis. Surprisingly, mTORC and Myc pathways are also hyper-active in this background, despite the decreased cell size, suggesting a non-canonical cell size regulation signaling pathway. They also show a similar cell size reduction in HepG2 organoids. Metabolic analysis reveals that enhanced gluconeogenesis suppresses protein synthesis. Their working model is that elevated pyruvate mitochondrial import drives oxaloacetate production and fuels gluconeogenesis during late larval development, thus reducing amino acid production and thus reducing protein synthesis.

      Strengths:

      The study is significant because stem cells and many cancers exhibit metabolic rewiring of pyruvate metabolism. It provides new insights into how the fate of pyruvate can be tuned to influence Drosophila biomass accrual, and how pyruvate pools can influence the balance between carbohydrate and protein biosynthesis. Strengths include its rigorous dissection of metabolic rewiring and use of Drosophila and mammalian cell systems to dissect carbohydrate:protein crosstalk.

      Weaknesses:

      However, questions on how these two pathways crosstalk, and how this interfaces with canonical Myc and mTORC machinery remain. There are also questions related to how this protein:carbohydrate crosstalk interfaces with lipid biosynthesis. Addressing these will increase the overall impact of the study.

    3. Reviewer #2 (Public review):

      In this manuscript, the authors leverage multiple cellular models including the drosophila fat body and cultured hepatocytes to investigate the metabolic programs governing cell size. By profiling gene programs in the larval fat body during the third instar stage - in which cells cease proliferation and initiate a period of cell growth - the authors uncover a coordinated downregulation of genes involved in mitochondrial pyruvate import and metabolism. Enforced expression of the mitochondrial pyruvate carrier restrains cell size, despite active signaling of mTORC1 and other pathways viewed as traditional determinants of cell size. Mechanistically, the authors find that mitochondrial pyruvate import restrains cell size by fueling gluconeogenesis through the combined action of pyruvate carboxylase and phosphoenolpyruvate carboxykinase. Pyruvate conversion to oxaloacetate and use as a gluconeogenic substrate restrains cell growth by siphoning oxaloacetate away from aspartate and other amino acid biosynthesis, revealing a tradeoff between gluconeogenesis and provision of amino acids required to sustain protein biosynthesis. Overall, this manuscript is extremely rigorous, with each point interrogated through a variety of genetic and pharmacologic assays. The major conceptual advance is uncovering the regulation of cell size as a consequence of compartmentalized metabolism, which is dominant even over traditional signaling inputs. The work has implications for understanding cell size control in cell types that engage in gluconeogenesis but more broadly raise the possibility that metabolic tradeoffs determine cell size control in a variety of contexts.

    4. Reviewer #3 (Public review):

      Summary:

      In this article, Toshniwal et al. investigate the role of pyruvate metabolism in controlling cell growth. They find that elevated expression of the mitochondrial pyruvate carrier (MPC) leads to decreased cell size in the Drosophila fat body, a transformed human hepatocyte cell line (HepG2), and primary rat hepatocytes. Using genetic approaches and metabolic assays, the authors find that elevated pyruvate import into cells with forced expression of MPC increases the cellular NADH/NAD+ ratio, which drives the production of oxaloacetate via pyruvate carboxylase. Genetic, pharmacological, and metabolic approaches suggest that oxaloacetate is used to support gluconeogenesis rather than amino acid synthesis in cells over-expressing MPC. The reduction in cellular amino acids impairs protein synthesis, leading to impaired cell growth.

      Strengths:

      This study shows that the metabolic program of a cell, and especially its NADH/NAD+ ratio, can play a dominant role in regulating cell growth.

      The combination of complementary approaches, ranging from Drosophila genetics to metabolic flux measurements in mammalian cells, strengthens the findings of the paper and shows a conservation of MPC effects across evolution.

      Weaknesses:

      In general, the strengths of this paper outweigh its weaknesses. However, some areas of inconsistency and rigor deserve further attention.

      The authors comment that MPC overrides hormonal controls on gluconeogenesis and cell size (Discussion, paragraph 3). Such a claim cannot be made for mammalian experiments that are conducted with immortalized cell lines or primary hepatocytes.

      Nuclear size looks to be decreased in fat body cells with elevated MPC levels, consistent with reduced endoreplication, a process that drives growth in these cells. However, acute, ex vivo EdU labeling and measures of tissue DNA content are equivalent in wild-type and MPC+ fat body cells. This is surprising - how do the authors interpret these apparently contradictory phenotypes?

      In Figure 4d, oxygen consumption rates are measured in control cells and those over-expressing MPC. Values are normalized to protein levels, but protein is reduced in MPC+ cells. Is oxygen consumption changed by MPC expression on a per-cell basis?

      Trehalose is the main circulating sugar in Drosophila and should be measured in addition to hemolymph glucose. Additionally, the units in Figure 4h should be related to hemolymph volume - it is not clear that they are.

      Measurements of NADH/NAD ratios in conditions where these are manipulated genetically and pharmacologically (Figure 5) would strengthen the findings of the paper. Along the same lines, expression of manipulated genes - whether by RT-qPCR or Western blotting - would be helpful to assess the degree of knockdown/knockout in a cell population (for example, Got2 manipulations in Figures 6 and S8).

    5. Author response:

      Reviewer #1 (Public review):

      The study examines how pyruvate, a key product of glycolysis that influences TCA metabolism and gluconeogenesis, impacts cellular metabolism and cell size. It primarily utilizes the Drosophila liver-like fat body, which is composed of large post-mitotic cells that are metabolically very active. The study focuses on the key observations that over-expression of the pyruvate importer MPC complex (which imports pyruvate from the cytoplasm into mitochondria) can reduce cell size in a cell-autonomous manner. They find this is by metabolic rewiring that shunts pyruvate away from TCA metabolism and into gluconeogenesis. Surprisingly, mTORC and Myc pathways are also hyper-active in this background, despite the decreased cell size, suggesting a non-canonical cell size regulation signaling pathway. They also show a similar cell size reduction in HepG2 organoids. Metabolic analysis reveals that enhanced gluconeogenesis suppresses protein synthesis. Their working model is that elevated pyruvate mitochondrial import drives oxaloacetate production and fuels gluconeogenesis during late larval development, thus reducing amino acid production and thus reducing protein synthesis.

      Strengths:

      The study is significant because stem cells and many cancers exhibit metabolic rewiring of pyruvate metabolism. It provides new insights into how the fate of pyruvate can be tuned to influence Drosophila biomass accrual, and how pyruvate pools can influence the balance between carbohydrate and protein biosynthesis. Strengths include its rigorous dissection of metabolic rewiring and use of Drosophila and mammalian cell systems to dissect carbohydrate:protein crosstalk.

      Weaknesses:

      However, questions on how these two pathways crosstalk, and how this interfaces with canonical Myc and mTORC machinery remain. There are also questions related to how this protein:carbohydrate crosstalk interfaces with lipid biosynthesis. Addressing these will increase the overall impact of the study.

      We thank the reviewer for recognizing the significance of our work and for providing constructive feedback. Our findings indicate that elevated pyruvate transport into mitochondria acts independently of canonical pathways, such as mTORC1 or Myc signaling, to regulate cell size. To investigate these pathways, we utilized immunofluorescence with well-validated surrogate measures (p-S6 and p-4EBP1) in clonal analyses of MPC expression, as well as RNA-seq analyses in whole fat body tissues expressing MPC. These methods revealed hyperactivation of mTORC1 and Myc signaling in fat body cells expressing MPC in Drosophila, which are dramatically smaller than control cells. One explanation of these seemingly contradictory observations could be an excess of nutrients that activate mTORC1 or Myc pathways. However, our data is inconsistent with a nutrient surplus that could explain this hyperactivation. Instead, we observed reduced amino acid abundance upon MPC expression, which is very surprising given the observed hyperactivation of mTORC1. This led us to hypothesize the existence of a feedback mechanism that senses inappropriate reductions in cell size and activates signaling pathways to promote cell growth. The best characterized “sizer” pathway for mammalian cells is the CycD/CDK4 complex which has been well studied in the context of cell size regulation of the cell cycle (PMID 10970848, 34022133). However, the mechanisms that sense cell size in post-mitotic cells, such as fat body cells and hepatocytes, remain poorly understood. Investigating the hypothesized size-sensing mechanisms at play here is a fascinating direction for future research.

      For the current study, we conducted epistatic analyses with mTOR pathway members by overexpressing PI3K and knocking down the TORC1 inhibitor Tuberous Sclerosis Complex 1 (Tsc1). These manipulations increased the size of control fat body cells but not those over-expressing the MPC (Supplementary Fig. 3c, 3d). Regarding Myc, its overexpression increased the size of both control and MPC+ clones (Supplementary Fig. 3e), but Myc knockdown had no additional effect on cell size in MPC+ clones (Supplementary Fig. 3f). These results suggest that neither mTORC1, PI3K, nor Myc are epistatic to the cell size effects of MPC expression. Consequently, we shifted our focus to metabolic mechanisms regulating biomass production and cell size.

      When analyzing cellular biomolecules contributing to biomass, we observed a significant impact on protein levels in Drosophila fat body cells and mammalian MPC-expressing HepG2 spheroids. TAG abundance in MPC-expressing HepG2 spheroids and whole fat body cells showed a statistically insignificant decrease compared to controls. Furthermore, lipid droplets in fat body cells were comparable in MPC-expressing clones when normalized to cell size.

      Interestingly, RNA-seq analysis revealed increased expression of fatty acid and cholesterol biosynthesis pathways in MPC-expressing fat body cells. Upregulated genes included major SREBP targets, such as ATPCL (2.08-fold), FASN1 (1.15-fold), FASN2 (1.07-fold), and ACC (1.26-fold). Since mTOR promotes SREBP activation and MPC-expressing cells showed elevated mTOR activity and upregulation of SREBP targets, we hypothesize that SREBP is activated in these cells. Nonetheless, our data on amino acid abundance and its impact on protein synthesis activity suggest that protein abundance, rather than lipids, is likely to play a larger causal role in regulating cell size in response to increased pyruvate transport into mitochondria.

      Reviewer #2 (Public review):

      In this manuscript, the authors leverage multiple cellular models including the drosophila fat body and cultured hepatocytes to investigate the metabolic programs governing cell size. By profiling gene programs in the larval fat body during the third instar stage - in which cells cease proliferation and initiate a period of cell growth - the authors uncover a coordinated downregulation of genes involved in mitochondrial pyruvate import and metabolism. Enforced expression of the mitochondrial pyruvate carrier restrains cell size, despite active signaling of mTORC1 and other pathways viewed as traditional determinants of cell size. Mechanistically, the authors find that mitochondrial pyruvate import restrains cell size by fueling gluconeogenesis through the combined action of pyruvate carboxylase and phosphoenolpyruvate carboxykinase. Pyruvate conversion to oxaloacetate and use as a gluconeogenic substrate restrains cell growth by siphoning oxaloacetate away from aspartate and other amino acid biosynthesis, revealing a tradeoff between gluconeogenesis and provision of amino acids required to sustain protein biosynthesis. Overall, this manuscript is extremely rigorous, with each point interrogated through a variety of genetic and pharmacologic assays. The major conceptual advance is uncovering the regulation of cell size as a consequence of compartmentalized metabolism, which is dominant even over traditional signaling inputs. The work has implications for understanding cell size control in cell types that engage in gluconeogenesis but more broadly raise the possibility that metabolic tradeoffs determine cell size control in a variety of contexts.

      We thank the reviewer for their thoughtful recognition of our efforts, and we are honored by the enthusiasm the reviewer expressed for the findings and the significance of our research. We share the reviewer’s opinion that our work might help to unravel metabolic mechanisms that regulate biomass gain independent of the well-known signaling pathways.

      Reviewer #3 (Public review):

      Summary:

      In this article, Toshniwal et al. investigate the role of pyruvate metabolism in controlling cell growth. They find that elevated expression of the mitochondrial pyruvate carrier (MPC) leads to decreased cell size in the Drosophila fat body, a transformed human hepatocyte cell line (HepG2), and primary rat hepatocytes. Using genetic approaches and metabolic assays, the authors find that elevated pyruvate import into cells with forced expression of MPC increases the cellular NADH/NAD+ ratio, which drives the production of oxaloacetate via pyruvate carboxylase. Genetic, pharmacological, and metabolic approaches suggest that oxaloacetate is used to support gluconeogenesis rather than amino acid synthesis in cells over-expressing MPC. The reduction in cellular amino acids impairs protein synthesis, leading to impaired cell growth.

      Strengths:

      This study shows that the metabolic program of a cell, and especially its NADH/NAD+ ratio, can play a dominant role in regulating cell growth.

      The combination of complementary approaches, ranging from Drosophila genetics to metabolic flux measurements in mammalian cells, strengthens the findings of the paper and shows a conservation of MPC effects across evolution.

      Weaknesses:

      In general, the strengths of this paper outweigh its weaknesses. However, some areas of inconsistency and rigor deserve further attention.

      Thank you for reviewing our manuscript and offering constructive feedback. We appreciate your recognition of the significance of our work and your acknowledgment of the compelling evidence we have presented. We will carefully revise the manuscript in line with the reviewers' recommendations.

      The authors comment that MPC overrides hormonal controls on gluconeogenesis and cell size (Discussion, paragraph 3). Such a claim cannot be made for mammalian experiments that are conducted with immortalized cell lines or primary hepatocytes.

      We appreciate the reviewer’s insightful comment. Pyruvate is a primary substrate for gluconeogenesis, and our findings suggest that increased pyruvate transport into mitochondria increases the NADH-to-NAD+ ratio, and thereby elevates gluconeogenesis. Notably, we did not observe any changes in the expression of key glucagon targets, such as PC, PEPCK2, and G6PC, suggesting that the glucagon response is not activated upon MPC expression. By the statement referenced by the reviewer, we intended to highlight that excess pyruvate import into mitochondria drives gluconeogenesis independently of hormonal and physiological regulation.

      It seems the reviewer might also have been expressing the sentiment that our in vitro models may not fully reflect the in vivo situation, and we completely agree.  Moving forward, we plan to perform similar analyses in mammalian models to test the in vivo relevance of this mechanism. For now, we will refine the language in the manuscript to clarify this point.

      Nuclear size looks to be decreased in fat body cells with elevated MPC levels, consistent with reduced endoreplication, a process that drives growth in these cells. However, acute, ex vivo EdU labeling and measures of tissue DNA content are equivalent in wild-type and MPC+ fat body cells. This is surprising - how do the authors interpret these apparently contradictory phenotypes?

      We thank the reviewer for raising this important issue. The size of the nucleus is regulated by DNA content and various factors, including the physical properties of DNA, chromatin condensation, the nuclear lamina, and other structural components (PMID 32997613). Additionally, cytoplasmic and cellular volume also impacts nuclear size, as extensively documented during development (PMID 17998401, PMID 32473090).

      In MPC-expressing cells, it is plausible that the reduced cellular volume impacts chromatin condensation or the nuclear lamina in a way that slightly decreases nuclear size without altering DNA content. Specifically, in our whole fat body experiments using CG-Gal4 (as shown in Supplementary Figure 2a-c), we noted that after 12 hours of MPC expression, cell size was significantly reduced (Supplementary Figure 2c and Author response image 1A). However, the reduction in nuclear size became significant only after 36 hours of MPC expression (Author response image 1B), suggesting that the reduction in cell size is a more acute response to MPC expression, followed only later by effects on nuclear size.

      In clonal analyses, this relationship was further clarified. MPC-expressing cells with a size greater than 1000 µm² displayed nuclear sizes comparable to control cells, whereas those with a drastic reduction in cell size (less than 1000 µm²) exhibited smaller nuclei (Author response image 1C and D). These observations collectively suggest that changes in nuclear size are more likely to be downstream rather than upstream of cell size reduction. Given that DNA content remains unaffected, we focused on investigating the rate of protein synthesis. Our findings suggest that protein synthesis might play a causal role in regulating cell size, thereby reinforcing the connection between cellular and nuclear size in this context.

      Author response image 1.

      Cell Size vs. Nuclear Size in MPC-Expressing Fat Body Cells. A. Cell size comparison between control (blue, ay-GFP) and MPC+ (red, ay-MPC) fat body cells over time, measured in hours after MPC expression induction. B. Nuclear area measurements from the same fat body cells in ay-GFP and ay-MPC groups. C. Scatter plot of nuclear area vs. cell area for control (ay-GFP) cells, including the corresponding R<sup>²</sup> value. D. Scatter plot of nuclear area vs. cell area for MPC-expressing (ay-MPC) cells, with the respective R<sup>²</sup> value.

      This image highlights the relationship between nuclear and cell size in MPC-expressing fat body cells, emphasizing the distinct cellular responses observed following MPC induction.

      In Figure 4d, oxygen consumption rates are measured in control cells and those over-expressing MPC. Values are normalized to protein levels, but protein is reduced in MPC+ cells. Is oxygen consumption changed by MPC expression on a per-cell basis?

      As described in the manuscript, MPC-expressing cells are smaller in size. In this context, we felt that it was most appropriate to normalize oxygen consumption rates (OCR) to cellular mass to enable an accurate interpretation of metabolic activity. Therefore, we normalized OCR with protein content to account for variations in cellular size and (probably) mitochondrial mass.

      Trehalose is the main circulating sugar in Drosophila and should be measured in addition to hemolymph glucose. Additionally, the units in Figure 4h should be related to hemolymph volume - it is not clear that they are.

      We appreciate this valuable suggestion. In the revised manuscript, we will quantify trehalose abundance in circulation and within fat bodies. As described in the Methods section, following the approach outlined in Ugrankar-Banerjee et al., 2023, we bled 10 larvae (either control or MPC-expressing) using forceps onto parafilm. From this, 2 microliters of hemolymph were collected for glucose measurement. We will apply this methodology to include the trehalose measurements as part of our updated analysis.

      Measurements of NADH/NAD ratios in conditions where these are manipulated genetically and pharmacologically (Figure 5) would strengthen the findings of the paper. Along the same lines, expression of manipulated genes - whether by RT-qPCR or Western blotting - would be helpful to assess the degree of knockdown/knockout in a cell population (for example, Got2 manipulations in Figures 6 and S8).

      We appreciate this suggestion, which will provide additional rigor to our study. We have already quantified NADH/NAD+ ratios in HepG2 cells under UK5099, NMN, and Asp supplementation, as presented in Figure 6k. As suggested, we will quantify the expression of Got2 manipulations mentioned in Figure 6j using RT-qPCR and validate the corresponding data in Supplementary Figure 8f through western blot analysis.

      Additionally, we will assess the efficiency of pcb, pdha, dlat, pepck2, and Got2 manipulations used to modulate the expression of these genes. These validations will ensure the robustness of our findings and strengthen the conclusions of our study.

    1. eLife Assessment

      This work is of fundamental significance and has a compelling level of evidence for the role of mutant p53 in regulation of tumorigenesis using an in vivo mouse model. The study is well-conducted and will be of interest to a broad audience including those interested in p53, transcription factors and cancer biology.

    2. Reviewer #1 (Public review):

      Summary:

      This manuscript by Toledo and colleagues describes the generation and characterization of Y220C mice (Y217C in the mouse allele). The authors make notable findings: Y217C mice that have been backcrossed to C57Bl/6 for five generations show decreased female pup births due to exencephaly, a known defect in p53 -/- mice, and they show a correlation with decreased Xist expression, as well increased female neonatal death. They also noted similar tumor formation in Y217C/+ and p53 +/- mice, suggesting that Y217C may not function as a dominant negative. Notably, the authors find that homozygous Y217C mice die faster than p53 -/- mice and that the lymphomas in the Y217C mice were more aggressive and invasive. The authors then perform RNA seq on thymi of Y217C homozygotes compared to p53 -/-, and they suggest that these differentially expressed genes may explain the increased tumorigenesis in Y217C mice.

      Strengths:

      Overall, the study is well controlled and quite well done and will be of interest to a broad audience, particularly given the high frequency of the Y220C mutation in cancer (1% of all cancers, 4% of ovarian cancer).

      Weaknesses:

      No weaknesses were noted by this reviewer.

    3. Reviewer #2 (Public review):

      Summary:

      Jaber et al. describe the generation and characterization of a knock-in mouse strain expressing the p53 Y217C hot-spot mutation. While the homozygous mutant cells and mice reflect the typical loss-of-p53 functions, as expected, the Y217C mutation also appears to display gain-of-function (GOF) properties, exemplified by elevated metastasis in the homozygous context (as noted with several hot-spot mutations). Interestingly, this mutation does not appear to exhibit any dominant-negative effects associated with most hot-spot p53 mutations, as determined by the absence of differences in overall survival and tumor predisposition of the heterozygous mice, as well as target gene activation upon nutlin treatment.

      In addition, the authors noted a severe reduction in the female 217/217 homozygous progeny, significantly more than that observed with the p53 null mice, due to exencephaly, leading them to conclude that the Y217C mutation also has additional, non-cancer-related GOFs. Though this property has been well described and attributed to p53 functional impairment, the authors conclude that the Y217C has additional properties in accelerating the phenotype.

      Transcriptomic analyses of thymi found additional gene signature differences between the p53 null and the Y217C strains, indicative of novel target gene activation, associated with inflammation.

      Strengths:

      Overall, the characterisation of the mice highlights the expected typical outcomes associated with most hot-spot p53 mutations published earlier. The quality of the work presented is well done and good, and the conclusions and reasonably well justified.

      Weaknesses:

      The manuscript would benefit from the provision of additional data to strengthen the claims made, as follows:

      (1) Oncogenic GOF - the main data shown for GOF are the survival curve and enhanced metastasis. Often, GOF is exemplified at the cellular level as enhanced migration and invasion, which are standard assays to support the GOF. As such, the authors should perform these assays using either tumor cells derived from the mice or transformed fibroblasts from these mice. This will provide important and confirmatory evidence for GOF for Y217C.

      (2) Novel target gene activation - while a set of novel targets appears to be increased in the Y217C cells compared to the p53 null cells, it is unclear how they are induced. The authors should examine if mutant p53 can bind to their promoters through CHIP assays, and, if these targets are specific to Y217C and not the other hot-spot mutations. This will strengthen the validity of the Y217C's ability to promote GOF.

      (3) Dominant negative effect - the authors' claim of lack of DN effect needs to be strengthened further, as most p53 hot-spot mutations do exhibit DN effect. At the minimum, the authors should perform additional treatment with nutlin and gamma irradiation (or cytotoxic/damaging agents) and examine a set of canonical p53 target genes by qRT-PCR to strengthen their claim.

    1. eLife Assessment

      This manuscript provides potentially important findings examining in 2D and 3D models in MYC liver cancer cells changes in DNA repair genes and programs in response to hypoxia. The authors use convincing methodology in most cases, but there is some concern that the analysis is incomplete.

    2. Reviewer #1 (Public review):

      Summary:

      In this report, the authors made use of a murine cell life derived from a MYC-driven liver cancer to investigate the gene expression changes that accompany the switch from normoxic to hypoxia conditions during 2D growth and the switch from 2D monolayer to 3D organoid growth under normoxic conditions. They find a significant (ca. 40-50%) overlap among the genes that are dysregulated in response to hypoxia in 2D cultures and in response to spheroid formation. Unsurprisingly, hypoxia-related genes were among the most prominently deregulated under both sets of conditions. Many other pathways pertaining to metabolism, splicing, mitochondrial electron transport chain structure and function, DNA damage recognition/repair, and lipid biosynthesis were also identified.

      Major comments:

      (1) Lines 239-240: The authors state that genes involved in DNA repair were identified as being necessary to maintain survival of both 2D and 3D cultures (Figure S6A). Hypoxia is a strong inducer of ROS. Thus, the ROS-specific DNA damage/recognition/repair pathways might be particularly important. The authors should look more carefully at the various subgroups of the many genes that are involved in DNA repair. They should also obtain at least a qualitative assessment of ROS and ROS-mediated DNA damage by staining for total and mitochondrial-specific ROS using dyes such as CM-H2-DCFDA and MitoSox. Actual direct oxidative damage could be assessed by immunostaining for 8-oxo-dG and related to the sub-types of DNA damage-repair genes that are induced. The centrality of DNA damage genes also raises the question as to whether the previously noted prominence of the TP53 pathway (see point 5 below) might represent a response to ROS-induced DNA damage.

      (2) Because most of the pathway differences that distinguish the various cell states from one another are described only in terms of their transcriptome variations, it is not always possible to understand what the functional consequences of these changes actually are. For example, the authors report that hypoxia alters the expression of genes involved in PDH regulation but this is quite vague and not backed up with any functional or empirical analyses. PDH activity is complex and regulated primarily via phosphorylation/dephosphorylation (usually mediated by PDK1 and PDP2, respectively), which in turn are regulated by prevailing levels of ATP and ADP. Functionally, one might expect that hypoxia would lead to the down-regulation of PDH activity (i.e. increased PDH-pSer392) as respiration changes from oxidative to non-oxidative. This would not be appreciated simply by looking at PDH transcript levels. This notion could be tested by looking at total and phospho-PDH by western blotting and/or by measuring actual PDH activity as it converts pyruvate to AcCoA.

      (3) Line 439: Related to the above point: the authors state: "It is likely that blockade of acetyl-CoA production by PDH knockout may force cells to use alternative energy sources under hypoxic and 3D conditions, averting the Warburg effect and promoting cell survival under limited oxygen and nutrient availability in 3D spheroids." This could easily be tested by determining whether exogenous fatty acids are more readily oxidized by hypoxic 2D cultures or spheroids than occurs in normoxic 2D cultures.

      (4) Line 472: "Hypoxia induces high expression of Acaca and Fasn in NEJF10 cells indicating that hypoxia promotes saturated fatty acid synthesis...The beneficial effect of Fasn and Acaca KO to NEJF10 under hypoxia is probably due to reduction of saturated fatty acid synthesis, and this hypothesis needs to be tested in the future.". As with the preceding comment, this supposition could readily be supported directly by, for example, performing westerns blots for these enzymes and by showing that incubation of hypoxic 2D cells or spheroids converted more AcCoA into lipid.

      (5) In Supplementary Figure 2B&C, the central hub of the 2D normoxic cultures is Myc (as it should well be) whereas, in the normoxic 3D, the central hub is TP53 and Myc is not even present. The authors should comment on this. One would assume that Myc levels should still be quite high given that Myc is driven by an exogenous promoter. Does the centrality of TP53 indicate that the cells within the spheroids are growth-arrested, being subjected to DNA damage and/or undergoing apoptosis?

      (6) In the Materials and Methods section (lines 711-720), the description of how spheroid formation was achieved is unclear. Why were the cells first plated into non-adherent 96 well plates and then into non-adherent T75 flasks? Did the authors actually utilize and expand the cells from 144 T75 flasks and did the cells continue to proliferate after forming spheroids? Many cancer cell types will initially form monolayers when plated onto non-adherent surfaces such as plastic Petri dishes and will form spheroid-like structures only after several days. Other cells will only aggregate on the "non-adherent" surface and form spheroid-like structures but will not actually detach from the plate's surface. Have the authors actually documented the formation of true, non-adherent spheroids at 2 days and did they retain uniform size and shape throughout the collection period? The single photo in Supplementary Figure 1 does not explain when this was taken. The authors include a schematic in Figure 2A of the various conditions that were studied. A similar cartoon should be included to better explain precisely how the spheroids were generated and clarify the rationale for 96 well plating. Overall, a clearer and more concise description of how spheroids were actually generated and their appearance at different stages of formation needs to be provided.

      (7) The authors maintained 2D cultures in either normoxic or hypoxic (1% O2) states during the course of their experiments. On the other hand, 3D cultures were maintained under normoxic conditions, with the assumption that the interiors of the spheroids resemble the hypoxic interiors of tumors. However, the actual documentation of intra-spheroid hypoxia is never presented. It would be a good idea for the authors to compare the degree of hypoxia achieved by 2D (1% O2) and 3D cultures by staining with a hypoxia-detecting dye such as Image-iT Green. Comparing the fluorescence intensities in 2D cultures at various O2 concentrations might even allow for the construction of a "standard curve" that could serve to approximate the actual internal O2 concentration of spheroids. This would allow the authors to correlate the relative levels of hypoxia between 2D and 3D cultures.

      (8) Related to the previous 2 points, the authors performed RNAseq on spheroids only 48 hours after initiating 3D growth. I am concerned that this might not have been a sufficiently long enough time for the cells to respond fully to their hypoxic state, especially given my concerns in Point 6. Might the results have been even more robust had the authors waited longer to perform RNA seq? Why was this short time used?

      (9) What happens to the gene expression pattern if spheroids are re-plated into standard tissue culture plates after having been maintained as spheroids? Do they resume 2D growth and does the gene expression pattern change back?

      (10) Overall, the paper is quite descriptive in that it lists many gene sets that are altered in response to hypoxia and the formation of spheroids without really delving into the actual functional implications and/or prioritizing the sets. Some of these genes are shown by CRISPR screening to be essential for maintaining viability although in very few cases are these findings ever translated into functional studies (for example, see points 1-4 above). The list of genes and gene pathways could benefit from a better explanation and prioritization of which gene sets the authors believe to be most important for survival in response to hypoxia and for spheroid formation.

      (11) The authors used a single MYC-driven tumor cell line for their studies. However, in their original paper (Fang, et al. Nat Commun 2023, 14: 4003.) numerous independent cell lines were described. It would help to know whether RNAseq studies performed on several other similar cell lines gave similar results in terms of up & down-regulated transcripts (i.e. representative of the other cell lines are NEJF10 cells).

    3. Reviewer #2 (Public review):

      Summary:

      The manuscript by Fang et al., provides a tour-de-force study uncovering cancer cell's varied dependencies on several gene programs for their survival under different biological contexts. The authors addressed genomic differences in 2D vs 3D cultures and how hypoxia affects gene expression. They used a Myc-driven murine liver cancer model grown in 2D monolayer culture in normoxia and hypoxia as well as cells grown as 3D spheroids and performed CRISPR-based genome-wide KO screen to identify genes that play important roles in cell fitness. Some context-specific gene effects were further validated by in-vitro and in-vivo gene KO experiments.

      Strengths:

      The key findings in this manuscript are:

      (1) Close to 50% of differentially expressed genes were common between 2D Hypoxia and 3D spheroids conditions but they had differences in chromatin accessibility.<br /> (2) VHL-HIF1a pathway had differential cell fitness outcomes under 2D normoxia vs 2D hypoxia and 3D spheroids.<br /> (3) Individual components of the mitochondrial respiratory chain complex had contrasting effects on cell fitness under hypoxia.<br /> (4) Knockout of organogenesis or developmental pathway genes led to better cell growth specifically in the context of 3D spheroids and knockout of epigenetic modifiers had varied effects between 2D and 3D conditions.<br /> (5) Another key program that leads to cells fitness outcomes in normoxia vs hypoxia is the lipid and fatty acid metabolism.<br /> (6) Prmt5 is a key essential gene under all growth conditions, but in the context of 3D spheroids even partial loss of Prmt5 has a synthetic lethal effect with Mtap deletion and Mtap is epigenetically silenced specifically in the 3D spheroids.

      Issues to address:

      (1) The authors should clarify the link between the findings of the enrichment of TGFb-SMAD signaling REACTOME pathway to the findings that knocking out TGFb-SMAD pathway leads to better cell fitness outcomes for cells in the 3D growth conditions.

      (2) Supplementary Figure 4C has been cited in the text but doesn't exist in the supplementary figures section.

      (3) A small figure explaining this ABC-Myc driven liver cancer model in Supplementary Figure 1 would be helpful to provide context.

      (4) The method for spheroids formation is not found in the method section.

      (5) In Supplementary Figure 1b, the comparisons should be stated the opposite way - 3D vs 2D normoxia and 2D-Hypoxia vs 2D-Normoxia.

      (6) There are typos in the legend for Supplementary Figure 10.

      (7) Consider putting Supplementary Figure 1b into the main Figure 1.

      (8) Please explain only one timepoint (endpoint) for 3D spheroids was performed for the CRISPR KO screen experiment, while several timepoints were done for 2D conditions? Was this for technical convenience?

      (9) In line 372, it is indicated that Bcor KO (Fig 5e) had growth advantage - this was observed in only one of the gRNA -- same with Kmt2d KO in the same figure where there was an opposite effect. Please justify the use of only one gRNA.

      (10) Why was CRISPR based KO strategy not used for the PRMT5 gene but rather than the use of shRNA.? Note that one of the shRNA for PRMT5 had almost no KO (PRMT5-shRNA2 Figure 7B) but still showed phenotype (Figure 7D) - please explain.

      (11) In Figure 7D, which samples (which shRNA group) were being compared to do the t-test?

      (12) In line 240, it is stated that oxphos gene set is essential for NEJF10 cell survival in both normoxia and hypoxia conditions. But shouldn't oxphos be non-essential in hypoxia as cells move away from oxphos and become glycolytic?

      (13) In line 485 it is mentioned that Pmvk and Mvd genes which are involved in cholesterol synthesis when knocked out had a positive effect on cell growth in 3D conditions and since cholesterol synthesis is essential for cell growth how does this not matter much in the context of 3D - please explain.

    4. Reviewer #3 (Public review):

      Summary:

      In this study, Fang et al. systematically investigate the effects of culture conditions on gene expression, genome architecture, and gene dependency. To do this, they cultivate the murine HCC line NEJF10 under standard culture conditions (2D), then under similar conditions but under hypoxia (1% oxygen, 2D hypoxia) and under normoxia as spheroids (3D). NEJF10 was isolated from a marine HCC model that relies exclusively on MYC as a driver oncogene. In principle, (1) RNA-seq, (2) ATAC-seq and (3) genetic screens were then performed in this isogenic system and the results were systematically compared in the three cultivation methods. In particular, genome-wide screens with the CRISPR library Brie were performed very carefully. For example, in the 2D conditions, many different time points were harvested to control the selection process kinetically. The authors note differential dependencies for metabolic processes (not surprisingly, hypoxia signaling is affected) such as the regulation and activity of mitochondria, but also organogenesis signaling and epigenetic regulation.

      Strengths:

      The topic is interesting and relevant and the experimental set-up is carefully chosen and meaningful. The paper is well written. While the study does not reveal any major surprises, the results represent an important resource for the scientific community.

      Weaknesses:

      However, this presupposes that the statistical analysis and processing are carried out very carefully, and this is where my main suggestions for revision begin. Firstly, I cannot find any information on the number of replicates in RNA- and ATAC-seq. This should be clearly stated in the results section and figure legends and cut-offs, statistical procedures, p-values, etc. should be mentioned as well. In principle, all NGS experiments (here ATAC- and RNA-seq) should be performed in replicates (at least duplicates, better triplicates) or the results should be validated by RT-PCR in independent biological triplicates. Secondly, the quantification of the analyses shown in the figures and especially in the legends is not sufficiently careful. Units are often not mentioned. Example Figure 4a: The legend says: 'gRNA reads' but how can the read count be -1? I would guess these are FC, log2FC, or Z-values. All figure legends need careful revision.

      Furthermore, I would find a comparison of the sgRNA abundances at the earliest harvesting time with the distribution in the library interesting, to see whether and to what extent selection has already taken place before the three culture conditions were established (minor point).

    1. eLife Assessment

      Overall, this fundamental study identified a novel role of NOLC1 in regulating p53 nuclear transcriptional activity and p53-mediated ferroptosis in gastric cancer. The evidence supporting the conclusions is solid, although some new evidence is needed to make it more robust. The work will be of broad interest to cancer biologists and oncologists.

    2. Reviewer #1 (Public review):

      Summary:

      In this manuscript, the authors identified that NOLC1 was upregulated in gastric cancer samples, which promoted cancer progression and cisplatin resistance. They further found that NOLC1 could bind to p53 and decrease its nuclear transcriptional activity, then inhibit p53-mediated ferroptosis. There are several major concerns regarding the conclusions.

      Strengths:

      This study identified that NOLC1 could bind to p53 and decrease its nuclear transcriptional activity, then inhibit p53-mediated ferroptosis in gastric cancer.

      Weaknesses:

      The major conclusions were not sufficiently supported by the results. The experiments were not conducted in a comprehensive manner.

    3. Reviewer #2 (Public review):

      Summary:

      Shengsheng Zhao et al. investigated the role of nucleolar and coiled-body phosphoprotein 1 (NOLC1) in relegating gastric cancer (GC) development and cisplatin-induced drug resistance in GC. They found a significant correlation between high NOLC1 expression and the poor prognosis of GC. Meanwhile, upregulation of NOLC1 was associated with cis-resistant GC. Experimentally, the authors demonstrate that knocking down NOLC1 increased GC sensitivity to Cis possibly by regulating ferroptosis. Mechanistically, they found NOLC1 suppressed ferroptosis by blocking the translocation of P53 from the cytoplasm to the nucleus and promoting its degradation. In addition, The authors also evaluated the effect of combinational treatment of anti-PD-1 and cisplatin in NOLC1 -knockdown tumor cells, revealing a potential role of NOLC1 in the targeted therapy for GC.

      Strengths:

      Chemoresistance is considered a major reason causing failure of tumor treatment and death of cancer patients. This paper explored the role of NOLC1 in the regulation of Cis-mediated resistance, which involves a regulated cell death named ferroptosis. These findings provide more evidence highlighting the study of regulated cell death to overcome drug resistance in cancer treatment, which could give us more potential strategies or targets for combating cancer.

      Weaknesses:

      More evidence supporting the regulation of ferroptosis induced by Cisplatin by NOLC1 should be added. Particularly, the role of ferroptosis in the cisplatin-resistance should be verified and whether NOLC1 regulates ferroptosis induced by additional FINs should be explored. Besides, the experiments to verify the regulation of ferroptosis sensitivity by NOLC1 are sort of superficial. The role of MDM2/p53 in ferroptosis or cisplatin resistance mediated by NOLC1 should be further studied by genetic manipulation of p53, which is the key evidence to confirm its contribution to NOLC1 regulation of GC and relative cell death.

    4. Reviewer #3 (Public review):

      Summary:

      The authors have put forth a compelling argument that NOLC1 is indispensable for gastric cancer resistance in both in vivo and in vitro models. They have further elucidated that NOLC1 silencing augments cisplatin-induced ferroptosis in gastric cancer cells. The mechanistic underpinning of their findings suggests that NOLC1 modulates the p53 nuclear/plasma ratio by engaging with the p53 DNA Binding Domain, which in turn impedes p53-mediated transcriptional regulation of ferroptosis. Additionally, the authors have shown that NOLC1 knockdown triggers the release of ferroptosis-induced damage-associated molecular patterns (DAMPs), which activate the tumor microenvironment (TME) and enhance the efficacy of the anti-PD-1 and cisplatin combination therapy.

      Strengths:

      The manuscript presents a robust dataset that substantiates the authors' conclusion. They have identified NOLC1 as a potential oncogene that confers resistance to immuno-chemotherapy in gastric cancer through the mediation of ferroptosis and subsequent TME reprogramming. This discovery positions NOLC1 as a promising therapeutic target for gastric cancer treatment. The authors have delineated a novel mechanistic pathway whereby NOLC1 suppresses p53 transcriptional functions by reducing its nuclear/plasma ratio, underscoring the significance of p53 nuclear levels in tumor suppression over total protein levels.

      Weaknesses:

      While the overall findings are commendable, there are specific areas that could benefit from further refinement. The authors have posited that NOLC1 suppresses p53-mediated ferroptosis; however, the mRNA levels of ferroptosis genes regulated by p53 have not been quantified, which is a critical gap in the current study. In Figure 4A, transmission electron microscopy (TEM) results are reported solely for the MGC-803 cell line. It would be beneficial to include TEM data for the MKN-45 cell line to strengthen the findings. The authors have proposed a link between NOLC1-mediated reduction in the p53 nuclear/plasma ratio and gastric cancer resistance, yet the correlation between this ratio and patient prognosis remains unexplored, which is a significant limitation in the context of clinical relevance.

    1. eLife Assessment

      This important work advances our understanding of how the SARS-CoV-2 Nsp16 protein is regulated by host E3 ligases to promote viral mRNA capping. However, support for the overall claims is incomplete as the authors need to demonstrate Nsp16 ubiquitination and the role of E3 ligases in a more biologically relevant context (ie. infection). This work will be of interest to those working in host-viral interactions and the role of the ubiquitin-proteasome system in viral replication.

    2. Reviewer #1 (Public review):

      Summary:

      In this study, Tiang et al. explore the role of ubiquitination of non-structural protein 16 (nsp16) in the SARS-CoV-2 life cycle. nsp16, in conjunction with nsp10, performs the final step of viral mRNA capping through its 2'-O-methylase activity. This modification allows the virus to evade host immune responses and protects its mRNA from degradation. The authors demonstrate that nsp16 undergoes ubiquitination and subsequent degradation by the host E3 ubiquitin ligases UBR5 and MARCHF7 via the ubiquitin-proteasome system (UPS). Specifically, UBR5 and MARCHF7 mediate nsp16 degradation through K48- and K27-linked ubiquitination, respectively. Notably, degradation of nsp16 by either UBR5 or MARCHF7 operates independently, with both mechanisms effectively inhibiting SARS-CoV-2 replication in vitro and in vivo. Furthermore, UBR5 and MARCHF7 exhibit broad-spectrum antiviral activity by targeting nsp16 variants from various SARS-CoV-2 strains. This research advances our understanding of how nsp16 ubiquitination impacts viral replication and highlights potential targets for developing broadly effective antiviral therapies.

      Strengths:

      The proposed study is of significant interest to the virology community because it aims to elucidate the biological role of ubiquitination in coronavirus proteins and its impact on the viral life cycle. Understanding these mechanisms will address broadly applicable questions about coronavirus biology and enhance our overall knowledge of ubiquitination's diverse functions in cell biology. Employing in vivo studies is a strength.

      Weaknesses:

      While the conclusions are generally well-supported by the data, additional work is needed to confirm that NSP16 is ubiquitinated in a biologically relevant context and to better define the roles of the reported E3 ligases. Clarifications regarding aspects of data acquisition, data analysis, and text editing could notably strengthen the manuscript and its conclusions.

    3. Reviewer #2 (Public review):

      Summary:

      This study provides a novel understanding of CoV-host interaction, leading potential therapeutics for SARS-CoV2 infection. Tian et al. identified and demonstrated that the two E3 ligases UBR5 and MARCHF7 both interact with and catalyze the ubiquitination of NSP16 protein of SARS-CoV2, thereby leading to its degradation by the ubiquitin-proteasome system (UPS) and inhibiting SARS-CoV-2 replication. It is interesting to see that the two E3 ligases perform their functions on the same target independently.

      Strengths:

      Overall, the topic and initial discoveries appear interesting. The experimental designs of this study were rigorous and logical, most of the work has been carefully done, and the conclusions drawn from this study are relatively convincing and reliable.

      Weaknesses:

      The quality of the presentation could be improved with better organization, a more conservative interpretation of the data, and further clarity in the writing.

    4. Reviewer #3 (Public review):

      Summary:

      The manuscript "SARS-CoV-2 nsp16 is regulated by host E3 ubiquitin ligases, UBR5 and MARCHF7" is an interesting work by Tian et al. describing the degradation/ stability of NSP16 of SARS CoV2 via K48 and K27-linked Ubiquitination and proteasomal degradation. The authors have demonstrated that UBR5 and MARCHF7, an E3 ubiquitin ligase bring about the ubiquitination of NSP16. The concept, and experimental approach to prove the hypothesis looks ok. The in vivo data looks ok with the controls. Overall, the manuscript is good. However, several major and minor changes/points need to be addressed.

      Strengths:

      The study identified important E3 ligases (MARCHF7 and UBR5) that can ubiquitinate NSP16, an important viral factor.

      Weaknesses:

      Most of the in vitro experiments (IP, overexpression) lack appropriate controls. The summary figure in actual terms does not show/correlate to the experimental findings.

    1. eLife Assessment

      In the field of early detection of disease and recurrence and monitoring of treatment efficacy by cfDNA analysis, this study presents a useful finding that HPV cfDNA level monitoring provides advantages over serum levels of squamous cell carcinoma antigen (SCC-Ag), specifically for HPV+ cervical cancer. The data were collected and analysed using solid and validated methodology but the sample number was limited.

    2. Reviewer #1 (Public review):

      Summary:

      The study "Monitoring of Cell-free Human Papillomavirus DNA in Metastatic or Recurrent Cervical Cancer: Clinical Significance and Treatment Implications" by Zhuomin Yin and colleagues focuses on the relationship between cell-free HPV (cfHPV) DNA and metastatic or recurrent cervical cancer patients. It expands the application of cfHPV DNA in tracking disease progression and evaluating treatment response in cervical cancer patients. The study is overall well-designed, including appropriate analyses.

      Strengths:

      The findings provide valuable reference points for monitoring drug efficacy and guiding treatment strategies in patients with recurrent and metastatic cervical cancer. The concordance between HPV cfDNA fluctuations and changes in disease status suggests that cfDNA could play a crucial role in precision oncology, allowing for more timely interventions. As with similar studies, the authors used Droplet Digital PCR to measure cfDNA copy numbers, a technique that offers ultrasensitive nucleic acid detection and absolute quantification, lending credibility to the conclusions.

      Weaknesses:

      Despite including 28 clinical cases, only 7 involved recurrent cervical cancer, which may not be sufficient to support some of the authors' conclusions fully. Future studies on larger cohorts could solidify HPV cfDNA's role as a standard in the personalized treatment of recurrent cervical cancer patients.

    3. Reviewer #2 (Public review):

      Summary:

      The authors conducted a study to evaluate the potential of circulating HPV cell-free DNA (cfDNA) as a biomarker for monitoring recurrent or metastatic HPV+ cervical cancer. They analyzed serum samples from 28 patients, measuring HPV cfDNA levels via digital droplet PCR and comparing these to squamous cell carcinoma antigen (SCC-Ag) levels in 26 SCC patients, while also testing the association between HPV cfDNA levels and clinical outcomes. The main hypothesis that the authors set out to test was whether circulating HPV cfDNA levels correlated with metastatic patterns and/or treatment response in HPV+ CC.

      The main claims put forward by the paper are that:

      (1) HPV cfDNA was detected in all 28 CC patients enrolled in the study and levels of HPV cfDNA varied over a median 2-month monitoring period.<br /> (2) 'Median baseline' HPV cfDNA varied according to 'metastatic pattern' in individual patients.<br /> (3) Positivity rate for HPV cfDNA was more consistent than SCC-Ag.<br /> (4) In 20 SCC patients monitored longitudinally, concordance with changes in disease status was 90% for HPV cfDNA.

      This study highlights HPV cfDNA as a promising biomarker with advantages over SCC-Ag, underscoring its potential for real-time disease surveillance and individualized treatment guidance in HPV-associated cervical cancer.

      Strengths:

      This study presents valuable insights into HPV+ cervical cancer with potential translational significance for management and guiding therapeutic strategies. The focus on a non-invasive approach is particularly relevant for women's cancers, and the study exemplifies the promising role of HPV cfDNA as a biomarker that could aid personalized treatment strategies.

      Weaknesses:

      While the authors acknowledge the study's small cohort and variability in sequential sampling protocols as a limitation, several revisions should be made to ensure that (1) the findings are presented in a way that aligns more closely with the data without overstatement and (2) that the statistical support for these findings is made more clear. Specific suggestions are outlined below.

      (1) The authors should provide source data for Figures 2, 3, and 4 as supplementary material.

      (2) Description of results in Figure 2: Figure 2 would benefit from clearer annotations regarding HPV virus subtypes. For example, does the color-coding in Figure 2B imply that all samples in the LR subgroup are of type HPV16? If that is the case, is it possible that detection variations are due to differences in subtype detection efficiency rather than cfDNA levels? The authors should clarify these aspects. Annotation of Figure 2B suggests that the p-value comes from comparing the LR and LN+H+DSM groups. This should be clarified in the legend. If this p-value comes from comparing HPV cfDNA copies for the (LR, LNM, HM) and (LN+HM, LN+HM+DSM) groups, did the authors carry out post-hoc pairwise comparisons? It would be helpful to include acronyms for these groups in the legend also.

      (3) Interpretation of results in Figure 2 and elsewhere: Significant differences detected in Figure 2B could imply potential associations between HPV cfDNA levels (or subtypes) and recurrence/metastasis patterns. Figure 2C shows that there is a difference in cfDNA levels between the groups compared, suggesting an association but this would not necessarily be a direct "correlation". Overall, interpretation of statistical findings would benefit from more precise language throughout the text and overstatement should be avoided.

      (4) The authors state that six patients showed cfDNA elevation with clinically progressive disease, yet only three are represented in Figure 3B1 under "Patients whose disease progressed during treatment." What is the expected baseline variability in cfDNA for patients? If we look at data from patients with early-stage cancer would we see similar fluctuations? And does the degree of variability vary for different HPV subtypes? Without understanding the normal fluctuations in cfDNA levels, interpreting these changes as progression indicators may be premature.

      (5) It would be helpful if where p-values are given, the test used to derive these values was also stated within parentheses e.g. (P < 0.05, permutation test with Benjamini-Hochberg procedure).

    1. eLife Assessment

      This work presents a valuable self-supervised method for the segmentation of 3D cells in microscopy images, alongside an implementation as a Napari plugin and an annotated dataset. While the Napari plugin is readily applicable and promises to eliminate time consuming data labeling to speed up quantitative analysis, there is incomplete evidence to support the claim that the segmentation method generalizes to other light-sheet microscopy image datasets beyond the four specific ones used here.

    2. Reviewer #1 (Public review):

      This work presents a self-supervised method for the segmentation of 3D cells in microscopy images, an annotated dataset, as well as a napari plugin. While the napari plugin is potentially useful, there is insufficient evidence in the manuscript to support the claim that the proposed method is able to segment cells in other light-sheet microscopy image datasets than the four specific ones used here.

      I acknowledge that the revision is now more upfront about the scope of this work. However, my main point still stands: even with the slight modifications to the title, this paper suggests to present a general method for self-supervised 3D cell segmentation in light-sheet microscopy data. This claim is simply not backed up.

      I still think the authors should spell out the assumptions that underlie their method early on (cells need to be well separated and clearly distinguishable from background). A subordinate clause like "often in cleared neural tissue" does not serve this purpose. First, it implies that the method is also suitable for non-cleared tissue (which would have to be shown). Second, this statement does not convey the crucial assumptions of well separated cells and clear foreground/background differences that the method is presumably relying on.

      It does appear that the proposed method works very well on the four investigated datasets, compared to other pre-trained or fine-tuned models. However, it still remains unclear whether this is because of the proposed method or the properties of those specific datasets (namely: well isolated cells that are easily distinguished from the background). I disagree with the authors that a comparison to non-learning methods "is unnecessary and beyond the scope of this work". In my opinion, this is exactly what is needed to proof that CellSeg3D's performance can not be matched with simple image processing.

      As I mentioned in the original review, it appears that thresholding followed by connected component analysis already produces competitive segmentations. I am confused about the authors' reply stating that "[this] is not the case, as all the other leading methods we fairly benchmark cannot solve the task without deep learning". The methods against which CellSeg3D is compared are CellPose and StarDist, both are deep-learning based methods. That those methods do not perform well on this dataset does not imply that a simpler method (like thresholding) would not lead to competitive results. Again, I strongly suggest the authors include a simple, non-learning based baseline method in their analysis, e.g.:<br /> * comparison to thresholding (with the same post-processing as the proposed method)<br /> * comparison to a normalized cut segmentation (with the same post-processing as the proposed method)

      Regarding my feedback about the napari plugin, I apologize if I was not clear. The plugin "works" as far as I tested it (i.e., it can be installed and used without errors). However, I was not able to recreate a segmentation on the provided dataset using the plugin alone (see my comments in the original review). I used the current master as available at the time of the original review and default settings in the plugin.

    3. Reviewer #1 (Public review):

      This work presents a self-supervised method for the segmentation of 3D cells in microscopy images, an annotated dataset, as well as a napari plugin. While the napari plugin is potentially useful, there is insufficient evidence in the manuscript to support the claim that the proposed method is able to segment cells in other light-sheet microscopy image datasets than the four specific ones used here.

      I acknowledge that the revision is now more upfront about the scope of this work. However, my main point still stands: even with the slight modifications to the title, this paper suggests to present a general method for self-supervised 3D cell segmentation in light-sheet microscopy data. This claim is simply not backed up.

      I still think the authors should spell out the assumptions that underlie their method early on (cells need to be well separated and clearly distinguishable from background). A subordinate clause like "often in cleared neural tissue" does not serve this purpose. First, it implies that the method is also suitable for non-cleared tissue (which would have to be shown). Second, this statement does not convey the crucial assumptions of well separated cells and clear foreground/background differences that the method is presumably relying on.

      It does appear that the proposed method works very well on the four investigated datasets, compared to other pre-trained or fine-tuned models. However, it still remains unclear whether this is because of the proposed method or the properties of those specific datasets (namely: well isolated cells that are easily distinguished from the background). I disagree with the authors that a comparison to non-learning methods "is unnecessary and beyond the scope of this work". In my opinion, this is exactly what is needed to proof that CellSeg3D's performance can not be matched with simple image processing.

      As I mentioned in the original review, it appears that thresholding followed by connected component analysis already produces competitive segmentations. I am confused about the authors' reply stating that "[this] is not the case, as all the other leading methods we fairly benchmark cannot solve the task without deep learning". The methods against which CellSeg3D is compared are CellPose and StarDist, both are deep-learning based methods. That those methods do not perform well on this dataset does not imply that a simpler method (like thresholding) would not lead to competitive results. Again, I strongly suggest the authors include a simple, non-learning based baseline method in their analysis, e.g.:<br /> * comparison to thresholding (with the same post-processing as the proposed method)<br /> * comparison to a normalized cut segmentation (with the same post-processing as the proposed method)

      Regarding my feedback about the napari plugin, I apologize if I was not clear. The plugin "works" as far as I tested it (i.e., it can be installed and used without errors). However, I was not able to recreate a segmentation on the provided dataset using the plugin alone (see my comments in the original review). I used the current master as available at the time of the original review and default settings in the plugin.

    4. Author response:

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

      Public Reviews:

      Reviewer #1 (Public Review):

      This work makes several contributions: (1) a method for the self-supervised segmentation of cells in 3D microscopy images, (2) an cell-segmented dataset comprising six volumes from a mesoSPIM sample of a mouse brain, and (3) a napari plugin to apply and train the proposed method.

      First, thanks for acknowledging our contributions of a new tool, new dataset, and new software.

      (1) Method

      This work presents itself as a generalizable method contribution with a wide scope: self-supervised 3D cell segmentation in microscopy images. My main critique is that there is almost no evidence for the proposed method to have that wide of a scope. Instead, the paper is more akin to a case report that shows that a particular self-supervised method is good enough to segment cells in two datasets with specific properties.

      First, thanks for acknowledging our contributions of a new tool, new dataset, and new software. We agree we focus on lightsheet microscopy data, therefore to narrow the scope we have changed the title to “CellSeg3D: self-supervised 3D cell segmentation for light-sheet microscopy”.

      To support the claim that their method "address[es] the inherent complexity of quantifying cells in 3D volumes", the method should be evaluated in a comprehensive study including different kinds of light and electron microscopy images, different markers, and resolutions to cover the diversity of microscopy images that both title and abstract are alluding to.

      You have selectively dropped the last part of that sentence that is key: “.... 3D volumes, often in cleared neural tissue” – which is what we tackle. The next sentence goes on to say: “We offer a new 3D mesoSPIM dataset and show that CellSeg3D can match state-of-the-art supervised methods.” Thus, we literally make it clear our claims are on MesoSPIM and cleared data.

      The main dataset used here (a mesoSPIM dataset of a whole mouse brain) features well-isolated cells that are easily distinguishable from the background. Otsu thresholding followed by a connected component analysis already segments most of those cells correctly.

      This is not the case, as all the other leading methods we fairly benchmark cannot solve the task without deep learning (i.e., no method is at an F1-Score of 1).

      The proposed method relies on an intensity-based segmentation method (a soft version of a normalized cut) and has at least five free parameters (radius, intensity, and spatial sigma for SoftNCut, as well as a morphological closing radius, and a merge threshold for touching cells in the post-processing). Given the benefit of tweaking parameters (like thresholds, morphological operation radii, and expected object sizes), it would be illuminating to know how other non-learning-based methods will compare on this dataset, especially if given the same treatment of segmentation post-processing that the proposed method receives. After inspecting the WNet3D predictions (using the napari plugin) on the used datasets I find them almost identical to the raw intensity values, casting doubt as to whether the high segmentation accuracy is really due to the self-supervised learning or instead a function of the post-processing pipeline after thresholding.

      First, thanks for testing our tool, and glad it works for you. The deep learning methods we use cannot “solve” this dataset, and we also have a F1-Score (dice) of ~0.8 with our self-supervised method. We don’t see the value in applying non-learning methods; this is unnecessary and beyond the scope of this work.

      I suggest the following baselines be included to better understand how much of the segmentation accuracy is due to parameter tweaking on the considered datasets versus a novel method contribution:

      *  comparison to thresholding (with the same post-processing as the proposed method) * comparison to a normalized cut segmentation (with the same post-processing as the proposed method)

      *  comparison to references 8 and 9.

      Ref 8 and 9 don’t have readily usable (https://github.com/LiangHann/USAR) or even shared code (https://github.com/Kaiseem/AD-GAN), so re-implementing this work is well beyond the bounds of this paper. We benchmarked Cellpose, StartDist, SegResNets, and a transformer – SwinURNet. Moreover, models in the MONAI package can be used. Note, to our knowledge the transformer results also are a new contribution that the Reviewer does not acknowledge.

      I further strongly encourage the authors to discuss the limitations of their method. From what I understand, the proposed method works only on well-separated objects (due to the semantic segmentation bottleneck), is based on contrastive FG/BG intensity values (due to the SoftNCut loss), and requires tuning of a few parameters (which might be challenging if no ground-truth is available).

      We added text on limitations. Thanks for this suggestion.

      (2) Dataset

      I commend the authors for providing ground-truth labels for more than 2500 cells. I would appreciate it if the Methods section could mention how exactly the cells were labelled. I found a good overlap between the ground truth and Otsu thresholding of the intensity images. Was the ground truth generated by proofreading an initial automatic segmentation, or entirely done by hand? If the former, which method was used to generate the initial segmentation, and are there any concerns that the ground truth might be biased towards a given segmentation method?

      In the already submitted version, we have a 5-page DataSet card that fully answers your questions. They are ALL labeled by hand, without any semi-automatic process.

      In our main text we even stated “Using whole-brain data from mice we cropped small regions and human annotated in 3D 2,632 neurons that were endogenously labeled by TPH2-tdTomato” - clearly mentioning it is human-annotated.

      (3) Napari plugin

      The plugin is well-documented and works by following the installation instructions.

      Great, thanks for the positive feedback.

      However, I was not able to recreate the segmentations reported in the paper with the default settings for the pre-trained WNet3D: segments are generally too large and there are a lot of false positives. Both the prediction and the final instance segmentation also show substantial border artifacts, possibly due to a block-wise processing scheme.

      Your review here does not match your comments above; above you said it was working well, such that you doubt the GT is real and the data is too easy as it was perfectly easy to threshold with non-learning methods.

      You would need to share more details on what you tried. We suggest following our code; namely, we provide the full experimental code and processing for every figure, as was noted in our original submission: https://github.com/C-Achard/cellseg3d-figures.

      Reviewer #2 (Public Review):

      Summary:

      The authors propose a new method for self-supervised learning of 3d semantic segmentation for fluorescence microscopy. It is based on a WNet architecture (Encoder / Decoder using a UNet for each of these components) that reconstructs the image data after binarization in the bottleneck with a soft n-cuts clustering. They annotate a new dataset for nucleus segmentation in mesoSPIM imaging and train their model on this dataset. They create a napari plugin that provides access to this model and provides additional functionality for training of own models (both supervised and self-supervised), data labeling, and instance segmentation via post-processing of the semantic model predictions. This plugin also provides access to models trained on the contributed dataset in a supervised fashion.

      Strengths:

      (1) The idea behind the self-supervised learning loss is interesting.

      (2) The paper addresses an important challenge. Data annotation is very time-consuming for 3d microscopy data, so a self-supervised method that yields similar results to supervised segmentation would provide massive benefits.

      Thank you for highlighting the strengths of our work and new contributions.

      Weaknesses:

      The experiments presented by the authors do not adequately support the claims made in the paper. There are several shortcomings in the design of the experiment, presentation of the results, and reproducibility.

      We address your concerns and misunderstandings below.

      Major weaknesses:

      (1) The main experiments are conducted on the new mesoSPIM dataset, which contains quite small nuclei, much smaller than the pretraining datasets of CellPose and StarDist. I assume that this is one of the main reasons why these well-established methods don't work for this dataset.

      StarDist is not pretrained, we trained it from scratch as we did for WNet3D. We retrained Cellpose and reported the results both with their pretrained model and our best-retrained model. This is documented in Figure 1 and Suppl. Figure 1. We also want to push back and say that they both work very well on this data. In fact, our main claim is not that we beat them, it is that we can match them with a self-supervised method.

      Limiting method comparison to only this dataset may create a misleading impression that CellSeg3D is superior for all kinds of 3D nucleus segmentation tasks, whereas this might only hold for small nuclei.

      The GT dataset we labeled has nuclei that are normal brain-cell sized. Moreover in Figure 2 we show very different samples with both dense and noisy (c-FOS) labeling.

      We also clearly do not claim this is superior for all tasks, from our text: “First, we benchmark our methods against Cellpose and StarDist, two leading supervised cell segmentation packages with user-friendly workflows, and show our methods match or outperform them in 3D instance segmentation on mesoSPIM-acquired volumes" – we explicitly do NOT claim beyond the scope of the benchmark. Moreover we state: "We found that WNet3D could be as good or better than the fully supervised models, especially in the low data regime, on this dataset at semantic and instance segmentation" – again noting on this dataset. Again, we only claimed we can be as good as these methods with an unsupervised approach, and in the low-GT data regime we can excel.

      Further, additional preprocessing of the mesoSPIM images may improve results for StarDist and CellPose (see the first point in minor weaknesses). Note: having a method that works better for small nuclei would be an important contribution. But I doubt that the claims hold for larger and or more crowded nuclei as the current version of the paper implies.

      Figure 2 benchmarks our method on larger and denser nuclei, but we do not intend to claim this is a universal tool. It was specifically designed for light-sheet (brain) data, and we have adjusted the title to be more clear. But we also show in Figure 2 it works well on more dense and noisy samples, hinting that it could be a promising approach. But we agree, as-is, it’s unlikely to be good for extremely dense samples like in electron microscopy, which we never claim it would be.

      With regards to preprocessing, we respectfully disagree. We trained StarDist (and asked the main developer of StarDist, Martin Weigert, to check our work and he is acknowledged in the paper) and it does very well. Cellpose we also retrained and optimized and we show it works as-well-as leading transformer and CNN-based approaches. Again, we only claimed we can be as good as these methods with an unsupervised approach.

      The contribution of the paper would be much stronger if a **fair** comparison with StarDist / CellPose was also done on the additional datasets from Figure 2.

      We appreciate that more datasets would be ideal, but we always feel it’s best for the authors of tools to benchmark their own tools on data. We only compared others in Figure 1 to the new dataset we provide so people get a sense of the quality of the data too; there we did extensive searches for best parameters for those tools. So while we think it would be nice, we will leave it to those authors to be most fair. We also narrowed the scope of our claims to mesoSPIM data (added light-sheet to the title), which none of the other examples in Figure 2 are.

      (2) The experimental setup for the additional datasets seems to be unrealistic. In general, the description of these experiments is quite short and so the exact strategy is unclear from the text. However, you write the following: "The channel containing the foreground was then thresholded and the Voronoi-Otsu algorithm used to generate instance labels (for Platynereis data), with hyperparameters based on the Dice metric with the ground truth." I.e., the hyperparameters for the post-processing are found based on the ground truth. From the description it is unclear whether this is done a) on the part of the data that is then also used to compute metrics or b) on a separate validation split that is not used to compute metrics. If a) this is not a valid experimental setup and amounts to training on your test set. If b) this is ok from an experimental point of view, but likely still significantly overestimates the quality of predictions that can be achieved by manual tuning of these hyperparameters by a user that is not themselves a developer of this plugin or an absolute expert in classical image analysis, see also 3.

      We apologize for this confusion; we have now expanded the methods to clarify the setup is now b; you can see what we exactly did as well in the figure notebook: https://c-achard.github.io/cellseg3d-figures/fig2-b-c-extra-datasets/self-supervised-ext ra.html#threshold-predictions.

      For clarity, we additionally link each individual notebook now in the Methods.

      (3) I cannot reproduce any of the results using the plugin. I tried to reproduce some of the results from the paper qualitatively: First I downloaded one of the volumes from the mesoSPIM dataset (c5image) and applied the WNet3D to it. The prediction looks ok, however the value range is quite close (Average BG intensity ~0.4, FG intensity 0.6-0.7). I try to apply the instance segmentation using "Convert to instance labels" from "Utilities". Using "Voronoi-Otsu" does not work due to an error in pyClesperanto ("clGetPlatformIDs failed: PLATFORM_NOT_FOUND_KHR"). Segmentation via "Connected Components" and "Watershed" requires extensive manual tuning to get a somewhat decent result, which is still far from perfect.

      We are sorry to hear of the installation issue; pyClesperanto is a dependency that would be required to reproduce the images (sounds like you had this issue; https://forum.image.sc/t/pyclesperanto-prototype-doesnt-work/45724 ) We added to our docs now explicitly the fix:https://github.com/AdaptiveMotorControlLab/CellSeg3D/pull/90. We recommend checking the reproduction notebooks (which were linked in initial submission): https://c-achard.github.io/cellseg3d-figures/intro.html.

      Then I tried to reproduce the results for the Mouse Skull Nuclei Dataset from EmbedSeg. The results look like a denoised version of the input image, not a semantic segmentation. I was skeptical from the beginning that the method would transfer without retraining, due to the very different morphology of nuclei (much larger and elongated). None of the available segmentation methods yield a good result, the best I can achieve is a strong over-segmentation with watersheds.

      We are surprised to hear this; did you follow the following notebook which directly produces the steps to create this figure? (This was linked in preprint): https://c-achard.github.io/cellseg3d-figures/fig2-c-extra-datasets/self-supervised-extra .html

      We also expanded the methods to include the exact values from the notebook into the text.

      Minor weaknesses:

      (1) CellPose can work better if images are resized so that the median object size in new images matches the training data. For CellPose the cyto2 model should do this automatically. It would be important to report if this was done, and if not would be advisable to check if this can improve results.

      We reported this value in Figure 1 and found it to work poorly, that is why we retrained Cellpose and found good performance results (also reported in Figure 1). Resizing GB to TB volumes for mesoSPIM data is otherwise not practical, so simply retraining seems the preferable option, which is what we did.

      (2) It is a bit confusing that F1-Score and Dice Score are used interchangeably to evaluate results. The dice score only evaluates semantic predictions, whereas F1-Score evaluates the actual instance segmentation results. I would advise to only use F1-Score, which is the more appropriate metric. For Figure 1f either the mean F1 score over thresholds or F1 @ 0.5 could be reported. Furthermore, I would advise adopting the recommendations on metric reporting from https://www.nature.com/articles/s41592-023-01942-8.

      We are using the common metrics in the field for instance and semantic segmentation, and report them in the methods. In Figure 2f we actually report the “Dice” as defined in StarDist (as we stated in the Methods). Note, their implementation is functionally equivalent to F1-Score of an IoU >= 0, so we simply changed this label in the figure now for clarity. We agree this clarifies for the expert readers what was done, and we expanded the methods to be more clear about metrics.

      We added a link to the paper you mention as well.

      (3) A more conceptual limitation is that the (self-supervised) method is limited to intensity-based segmentation, and so will not be able to work for cases where structures cannot be distinguished based on intensity only. It is further unclear how well it can separate crowded nuclei. While some object separation can be achieved by morphological operations this is generally limited for crowded segmentation tasks and the main motivation behind the segmentation objective used in StarDist, CellPose, and other instance segmentation methods. This limitation is only superficially acknowledged in "Note that WNet3D uses brightness to detect objects [...]" but should be discussed in more depth. Note: this limitation does not mean at all that the underlying contribution is not significant, but I think it is important to address this in more detail so that potential users know where the method is applicable and where it isn't.

      We agree, and we added a new section specifically on limitations. Thanks for raising this good point. Thus, while self-supervision comes at the saving of hundreds of manual labor, it comes at the cost of more limited regimes it can work on. Hence why we don’t claim this should replace excellent methods like Cellpose or Stardist, but rather complement them and can be used on mesoSPIM samples, as we show here.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) One of the listed contributions is "adding the SoftNCuts loss". This is not true, reference 10 already introduced that loss.

      “Our changes include a conversion to a fully 3D architecture and adding the SoftNCuts loss” - we dropped the common and added the word “AND” to note that we added the 3D version of the SoftNCuts loss TO the 3D architecture, which 10 did not do.

      (2) "Typically, these methods use a multi-step approach" to segment 3D from 2D: this is only true for CellPose, StarDist does real 3D.

      That is why we preface with “typically” which implies not always.

      (3) "see Methods, Figure 1c, c)" is missing an opening in parentheses.

      (4) K is not introduced in equation (1) (presumably the number of classes, which seems to be 2 for all experiments considered).

      k actually was introduced just below equation 1 as the number of classes. We added the note that k was set to 2.

      (5) X is not introduced in equation (2) (presumably the spatial position of a voxel).

      Sorry for this oversight. We add that $X$ is the spatial position of the voxel.

      Reviewer #2 (Recommendations For The Authors):

      To improve the paper the weaknesses mentioned above should be addressed:

      (1) Compare to StarDist and/or CellPose on further datasets, esp. using pre-trained CellPose, to see if the claims of competitive performance with state-of-the-art approaches hold up for the case of different nucleus morphologies. The EmbedSeg datasets from Figure 2 c are well suited for this. In the current form, the claims are too broad and not supported if thorough experiments are performed on a single dataset with a very specific morphology. Note: even if the method is not fully competitive with CellPose / StarDist on these Datasets it holds merit since a segmentation method that works for small nuclei as in the mesoSPIM dataset and works self-supervised is very valuable.

      (2) Clarify how the best instance segmentation hyperparameters are found. If you indeed optimize these on the same part of the dataset used for evaluating metrics then the current experimental set-up is invalid. If this is not the case I would still rethink if this is a good way to report the results since it does not seem to reflect user experience. I found it not possible to find good hyperparameters for either of the two segmentation approaches I tried (see also next point) so I think these numbers are too optimistic.

      (3) Improve the instance segmentation part of the plugin: either provide troubleshooting for how to install pyClesperanto correctly to use the voronoi-based instance segmentation or implement it based on more standard functionality like skimage / scipy. Provide more guidance for finding good hyperparameters for the segmentation task.

      (4) Make sure image resizing is done correctly when using pre-trained CellPose models and report on this.

      (5) Report F1 Scores only (unless there is a compelling reason to also report Dice).

      (6) Address the limitations of the method in more detail.

      On a positive note: all data and code are available and easy to download/install. A minor comment: it would be very helpful to have line numbers for reviewing a revised version.

      All comments are also addressed in the public reviews.

    1. eLife Assessment

      This important study uses optogenetics in combination with single cell recordings to selectively activate sensory input channels within the olfactory bulb, providing direct evidence for activity-dependent and distance-independent enhancement of stimulus-evoked gamma oscillations via lateral interactions between input channels, most likely via granule cells. The article presents solid evidence to support the main conclusions.

    2. Reviewer #1 (Public review):

      Summary:

      Dalal and Haddad investigated how neurons in the olfactory bulb are synchronized in oscillatory rhythms at gamma frequency. Temporal coordination of action potentials fired by projection neurons can facilitate information transmission to downstream areas. In a previous paper (Dalal and Haddad 2022, https://doi.org/10.1016/j.celrep.2022.110693), the authors showed that gamma frequency synchronization of mitral/tufted cells (MTCs) in the olfactory bulb enhances the response in the piriform cortex. The present study builds on these findings and takes a closer look at how gamma synchronization is restricted to a specific subset of MTCs in the olfactory bulb. They combined odor and optogenetic stimulations in anesthetized mice with extracellular recordings.

      The main findings are that lateral synchronization of MTCs at gamma frequency is mediated by granule cells (GCs), independent of the spatial distance, and strongest for MTCs with firing rates close to 40 Hz. The authors conclude that this reveals a simple mechanism by which spatially distributed neurons can form a synchronized ensemble. In contrast to lateral synchronization, they found no evidence for the involvement of GCs in lateral inhibition of nearby MTCs.

      Strengths:

      Investigating the mechanisms of rhythmic synchronization in vivo is difficult because of experimental limitations for the readout and manipulation of neuronal populations at fast timescales. Using spatially patterned light stimulation of opsin-expressing neurons in combination with extracellular recordings is an elegant approach. The paper provides evidence for an activity-dependent synchronization of MTCs in gamma frequency that is mediated by GCs.

      Weaknesses:

      The study provides several results showing the firing of MTCs in gamma frequency range, however, direct evidence for the synchronization of MTCs in gamma frequency is missing.

    3. Reviewer #2 (Public review):

      Summary

      This study provides a detailed analysis and dissociation between two effects of activation of lateral inhibitory circuits in the olfactory bulb on ongoing single mitral/tufted cell (MTC) spiking activity, namely enhanced synchronization in the gamma frequency range or lateral inhibition of firing rate.

      The authors use a clever combination of single cell recordings, optogenetics with variable spatial stimulation of MTCs and sensory stimulation in vivo, and established mathematical methods, to describe changes in autocorrelation/synchronization of a single MTC's spiking activity upon activation of other, lateral glomerular MTC ensembles. This assay is rounded off by a gain of function experiment in which the authors enhance granule cell (GC) excitation to establish a causal relation between GC activation and enhanced synchronization of a single MTC's spiking to the gamma rhythm. They had used the same optogenetic manipulation in their previous paper Dalal & Haddad 2022, but use a smaller illumination spot here for spatially restricted activation.

      Strengths

      This study is of high interest for olfactory processing since it shows directly that interactions between only two selected active receptor channels are sufficient to enhance synchronization of single neurons to gamma in one receptor channel and thus by inference most likely in both. Such synchronization across co-active receptor channels in turn would enable upstream neurons in olfactory cortices to read out odour identity.

      The authors find that these interactions are distance-independent over many 100s of µms and thus can allow for non-topographical inhibitory action across the bulb, in contrast to the center-surround lateral inhibition known from other sensory modalities. In my view, analogies between vision and olfaction might have been overemphasized so far, since the combinatorial encoding of olfactory stimuli across the glomerular map might require different mechanisms of lateral interaction versus vision. This result is indicative of such a major difference.

      Such enhanced local synchronization to gamma in one channel was observed in a subset of activated channel pairs; in addition, the authors report another type of lateral interaction that does involve reduction of firing rates, drops off with distance and most likely is caused by a different circuit mediated by PV+ neurons (PVN). The evidence for the latter is more circumstantial since no manipulations of PVNs were performed.

      Weaknesses/Room for improvement

      This study is an impressive proof of concept that however does not yet allow for broad generalization. Thus the framing of results should be slightly more careful IMHO. While the claims in the initial version of this preprint have been toned down quite substantially, the authors do not provide direct hard evidence for synchronization across channels. Admittedly, this would be hard to achieve since it would require paired recordings from MTCs in different locations in vivo. Therefore, the term „lateral synchronization" as it is used in the abstract is still problematic, as well as the title which should rather say „can enable" instead of „enables". That being said, this study definitely provides important evidence regarding the concept of "lateral synchronization".

      The other comments and recommendations have been well taken care of in the new version.

    4. Author response:

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

      eLife Assessment

      This valuable study provides in vivo evidence for the synchronization of projection neurons in the olfactory bulb at gamma frequency in an activity-dependent manner. This study uses optogenetics in combination with single-cell recordings to selectively activate sensory input channels within the olfactory bulb. The data are thoughtfully analyzed and presented; the evidence is solid, although some of the conclusions are only partially supported.

      We deeply thank all the reviewers for their time, effort, and insightful comments. Their revision led to a significant improvement of the paper.

      The reviewers suggested toning down our claim that we found a mechanism that synchronizes all odor-evoked MTC activities, as we do not directly show that. We concur and address this in our revised version to ensure a precise interpretation of our findings. In short, we state that we revealed a synchronization mechanism between two groups of active mitral and tufted cells (MTCs) and show that this synchronization is activity-dependent and distance-independent. This mechanism can enable the synchronization of all odor-activated MTCs.

      Another issue raised is the interpretation of the results obtained under Ketamine anesthesia. Ketamine is an NMDA receptor antagonist that plays a crucial role in the  MTC-GC reciprocal synapse. To address this, we include new analyses demonstrating that optogenetic activation of granule cells (GCs) can inhibit the recorded MTCs during baseline activity but does not substantially affect odor-evoked MTC firing rates. We show that this is correct in both Ketamine-induced anesthesia and awake mice (Dalal & Haddad, 2022). This indicates that GC-MTC connections are functional even under Ketamine anesthesia, however, they do not exert substantial suppression on odor-evoked MTC responses. We added a paragraph to the discussion section on the potential influence of Ketamine anesthesia on GC-MTC synapses and its implications on our findings.

      Finally, we discuss several recent studies that are particularly relevant to our research and expand the discussion on our hypothesis that parvalbumin-positive cells in the olfactory bulb may serve as key mediators of the activity- and distance-dependent lateral inhibition observed in our findings.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      Dalal and Haddad investigated how neurons in the olfactory bulb are synchronized in oscillatory rhythms at gamma frequency. Temporal coordination of action potentials fired by projection neurons can facilitate information transmission to downstream areas. In a previous paper (Dalal and Haddad 2022, https://doi.org/10.1016/j.celrep.2022.110693), the authors showed that gamma frequency synchronization of mitral/tufted cells (MTCs) in the olfactory bulb enhances the response in the piriform cortex. The present study builds on these findings and takes a closer look at how gamma synchronization is restricted to a specific subset of MTCs in the olfactory bulb. They combined odor and optogenetic stimulations in anesthetized mice with extracellular recordings.<br /> The main findings are that lateral synchronization of MTCs at gamma frequency is mediated by granule cells (GCs), independent of the spatial distance, and strongest for MTCs with firing rates close to 40 Hz. The authors conclude that this reveals a simple mechanism by which spatially distributed neurons can form a synchronized ensemble. In contrast to lateral synchronization, they found no evidence for the involvement of GCs in lateral inhibition of nearby MTCs.

      Strengths:

      Investigating the mechanisms of rhythmic synchronization in vivo is difficult because of experimental limitations for the readout and manipulation of neuronal populations at fast timescales. Using spatially patterned light stimulation of opsin-expressing neurons in combination with extracellular recordings is a nice approach. The paper provides evidence for an activity-dependent synchronization of MTCs in gamma frequency that is mediated by GCs.

      Weaknesses:

      An important weakness of the study is the lack of direct evidence for the main conclusion - the synchronization of MTCs in gamma frequency. The data shows that paired optogenetic stimulation of MTCs in different parts of the olfactory bulb increases the rhythmicity of individual MTCs (Figure 1) and that combined odor stimulation and GC stimulation increases rhythmicity and gamma phase locking of individual MTCs (Figure 4). However, a direct comparison of the firing of different MTCs is missing. This could be addressed with extracellular recordings at two different locations in the olfactory bulb. The minimum requirement to support this conclusion would be to show that the MTCs lock to the same phase of the gamma cycle. Also, showing the evoked gamma oscillations would help to interpret the data.

      We agree with the reviewer that direct evidence of mutual synchronization between multiple recorded MTCs has not been shown in our study. Our study only shows a mechanism that can enable this synchronization. We now state this clearly in the manuscript. We based this on previous studies that tested MTC spike synchronization. Specifically, Schoppa 2006, reported that electrical OSN stimulation evokes MTC spikes synchronization in the gamma range, in-vitro. Kashiwadni et al., 1999 and Doucette et al., 2011 showed that odor-evoked MTC spike times are synchronized, in-vivo. Given these studies, we asked what is the underlying mechanism that can support such a synchronization. Our study demonstrates that activating a group of MTCs can entrain another MTC in an activity-dependent and distance-independent manner. We claim this could be the underlying mechanism for the odor-evoked synchronization as demonstrated by these previous studies.

      To make sure this is clearly stated in the manuscript we changed the title to “Activity-dependent lateral inhibition enables the synchronization of active olfactory bulb projection neurons”, and rephrased a sentence in the abstract to “This lateral synchronization was particularly effective when the recorded MTC fired at the gamma rhythm”. To further clarify this point, we made several other changes throughout the results and the discussion section.

      Another weakness is that all experiments are performed under anesthesia with ketamine/medetomidine. Ketamine is an antagonist of NMDA receptors and NMDA receptors are critically involved in the interactions of MTCs and GCs at the reciprocal synapses (see for example Lage-Rupprecht et al. 2020, https://doi.org/10.7554/eLife.63737; Egger and Kuner 2021, https://doi.org/10.1007/s00441-020-03402-7). This should be considered for the interpretation of the presented data.

      This issue has been raised by reviewers #1 and #2. We think, as also reviewer #2 acknowledged, that this issue does not compromise our results. However, to address this important point we added the below section to the Discussion:

      “Our experiments were performed under Ketamine anesthesia, an NMDA receptor antagonist that affects the reciprocal dendro-dendritic synapses between MTCs and GCs (Egger and Kuner, 2021; Lage-Rupprecht et al., 2020). Consistent with that, recent studies reported lower excitability of GC activity under anesthesia (Cazakoff et al., 2014; Kato et al., 2012).  This raises the concern that our result might not be valid in the awake state. We argue that this is unlikely. First, (Fukunaga et al., 2014) reported that GCs baseline activity in anesthetized and awake mice is similar, suggesting that MTC-GC synapses are functioning. Second, we show that light activation of GCL neurons strongly inhibits the MTC baseline activity (Figure 5) and increases MTC odor-evoked spike-LFP coupling in the gamma range (Figure 4). These experiments validate that GCL neurons can exert inhibition over MTCs in our experimental setup. Third, we have shown that light-activating all accessible GCL neurons has a minor effect on the MTC odor-evoked firing rates in an awake state (Dalal and Haddad, 2022), corroborating the finding that GCL neurons are unlikely to provide strong suppression to MTCs. Fourth, and most importantly, we showed that optogenetic stimulation of MTCs entrains other MTC spike times, which is achieved via the GCL neurons. This suggests that the lack of lateral suppression following MTC or GCL neuron opto-activation is not due to MTC-GC synapse blockage. That said, we cannot exclude the unlikely possibility that NMDA receptor blockage under anesthesia impairs MTC-to-MTC suppressive interactions but not the MTC-to-MTC mediated spike entrainment.”

      Figure 1A and D from Dalal & Haddad 2022 show the effect of GCL neurons opto-activation during odor stimulation on MTC firing rates in awake and anesthetized mice.

      Furthermore, the direct effect of optogenetic stimulation on GCs activity is not shown. This is particularly important because they use Gad2-cre mice with virus injection in the olfactory bulb and expression might not be restricted to granule cells and might not target all subtypes of granule cells (Wachowiak et al., 2013, https://doi.org/10.1523/JNEUROSCI.4824-12.2013). This should be considered for the interpretation of the data, particularly for the absence of an effect of GC stimulation on lateral inhibition.

      In this study we used Gad2-cre mice, and the protocol for viral transfection of GCL neurons reported in Fukunaga et al., 2014. They reported that: ‘more than 90% of Cre-expressing neurons in the GCL also expressed fluorescently tagged ArchT’. Consistently, when Fukunaga et al. expressed ChR2 in the GCL using the same viral infection as we used, they reported that: ”Light presentation in vivo resulted in rapid and strong depolarization of, and action potential (AP) discharges in, GCs (Fig. 3b), which in

      turn consistently and strongly hyperpolarized M/TCs (9 of 9 cells showed 100% AP suppression; Fig. 3c,d)”. This study shows clearly that this infection protocol is robust. Moreover, in new panels we added to the manuscript (Figure 5a-b), we show that optogenetic activation of GCL neurons strongly suppressed MTC activity during baseline conditions but not odor-evoked responses MTCs. This is consistent with the reports by Fukunaga et al, and indicates that GCL neurons are functional as they can suppress MTC baseline activity.

      Finally, since virus injection to the granule cell layer can target other GCL neuron types, we changed the reference in the text to GCL neurons (as was done in Gschwend et al., 2015) instead of ‘GCs’ when referring to GC. We replaced the image in Figure 4A, to show the expression of ChR2 is restricted to GCL neurons. That said, it is still possible that our protocol did not infect all GC subtypes. To address this, we added this line to the Discussion: “We also note that our viral transfection protocol in Gad2-Cre mice might not transfect all subtypes of GCs”

      Several conclusions are only supported by data from example neurons. The paper would benefit from a more detailed description of the analysis and the display of some additional analysis at the population level:

      - What were the criteria based on which the spots for light-activation were chosen from the receptive field map?

      In order to make this point clearer, we extended the explanation in the Methods on the selection criteria: “Spots were selected either randomly or manually. In the manual selection case, we selected spots that caused either significant or mild but insignificant inhibitory effect on the recorded MTC (e.g., local cold spots in the receptive-field map; see example in Figure 2a of example spots that were selected manually)”. We also add a reference in the text to the Methods: “see Methods for spots selection criteria”.

      - The absence of an effect on firing rate for paired stimulations is only shown for one example (Figure 1c). A quantification of the population level would be interesting.

      - Only one example neuron is shown to support the conclusion that "two different neural circuits mediate suppression and entrainment" in Figure 3. A population analysis would provide more evidence.

      Thank you very much for these comments. We added a population analysis in Figure 3. This analysis shows a dissociation between firing rate suppression and the entrainment groups (Figure 3c-d). This suggests that two different circuits mediate suppression and entrainment.

      - Only one example neuron is shown to illustrate the effect of GC stimulation on gamma rhythmicity of MTCs in Figures 4 f,g.

      In this figure, we show that the activation of subsets of GCL neurons elevated odor-evoked spike synchronization to the gamma rhythm. We thought it would be beneficial to demonstrate the change in spike entrainment following GCL neurons optogenetic activation regardless of the ongoing OB gamma oscillations, using the method presented by Fukunaga et al., 2014. However, this analysis requires that the neuron has a relatively high firing rate. As we describe in the figure legend of this panel, this neuron is probably a tufted cell based on the findings shown in Fukunaga et al., 2014 and Burton & Urban, 2021. Most of our recorded cells had a lower firing rate, which coincides with our typical recording depth, targeting mitral cells rather than tufted cells (~400µm deep). Since this analysis is shown only over a single neuron, we moved it to Supplementary Figure 4.

      - In Figure 5 and the corresponding text, "proximal" and "distal" GC activation are not clearly defined.

      We agree. Initially, we used these terms to refer to GC columns that include the recorded MTC (proximal) and columns that are away from it (distal). We decided that instead of using a coarse division, we would show the whole range of distances. We updated the analysis in Figure 5d to show the effect of GC optogenetic activation on MTC odor-evoked responses as a function of the distance from the recorded MTC.

      Reviewer #2 (Public Review):

      Summary

      This study provides a detailed analysis and dissociation between two effects of activation of lateral inhibitory circuits in the olfactory bulb on ongoing single mitral/tufted cell (MTC) spiking activity, namely enhanced synchronization in the gamma frequency range or lateral inhibition of firing rate.

      The authors use a clever combination of single-cell recordings, optogenetics with variable spatial stimulation of MTCs and sensory stimulation in vivo, and established mathematical methods to describe changes in autocorrelation/synchronization of a single MTC's spiking activity upon activation of lateral glomerular MTC ensembles. This assay is rounded off by a gain-of-function experiment in which the authors enhance granule cell (GC) excitation to establish a causal relation between GC activation and enhanced synchronization to gamma (they had used this manipulation in their previous paper Dalal & Haddad 2022, but use a smaller illumination spot here for spatially restricted activation).

      Strengths

      This study is of high interest for olfactory processing - since it shows directly that interactions between only two selected active receptor channels are sufficient to enhance the synchronization of single neurons to gamma in one channel (and thus by inference most likely in both). These interactions are distance-independent over many 100s of µms and thus can allow for non-topographical inhibitory action across the bulb, in contrast to the center-surround lateral inhibition known from other sensory modalities.

      In my view, parallels between vision and olfaction might have been overemphasized so far, since the combinatorial encoding of olfactory stimuli across the glomerular map might require different mechanisms of lateral interaction versus vision. This result is indicative of such a major difference.

      Such enhanced local synchronization was observed in a subset of activated channel pairs; in addition, the authors report another type of lateral interaction that does involve the reduction of firing rates, drops off with distance and most likely is caused by a different circuit-mediated by PV+ neurons (PVN; the evidence for which is circumstantial).

      Weaknesses/Room for improvement

      Thus this study is an impressive proof of concept that however does not yet allow for broad generalization. Therefore the framing of results should be slightly more careful in my opinion.

      We agree with the reviewer. We copy here our response to reviewer #1, who raised the same issue.

      We agree that direct evidence of mutual synchronization between multiple recorded MTCs has not been shown in our study. Our study only shows a mechanism that can enable this synchronization. We now state this clearly in the manuscript. We relayed previous studies that tested MTC spike synchronization. Specifically, Schoppa 2006, reported that electrical OSN stimulation evokes MTC spikes synchronization in the gamma range, in-vitro. Kashiwadni et al., 1999 and Doucette et al., showed that odor-evoked MTC spike times are synchronized, in-vivo. Given these studies, we asked what is the underlying mechanism that can support such a synchronization. Our study demonstrates that activating a group of MTCs can entrain another MTC in an activity-dependent and distance-independent manner. We claim this could be the underlying mechanism for the odor-evoked synchronization as demonstrated by these previous studies.

      To make sure this is clearly stated in the manuscript we changed the title to “Activity-dependent lateral inhibition enables the synchronization of active olfactory bulb projection neurons”, and rephrased a sentence in the abstract to “This lateral synchronization was particularly effective when the recorded MTC fired at the gamma rhythm”. To further clarify this point, we made several other changes throughout the results and the discussion section.

      Along this line, the conclusions regarding two different circuits underlying lateral inhibition vs enhanced synchronization are not quite justified by the data, e.g.

      (1) The authors mention that their granule cell stimulation results in a local cold spot (l. 527 ff) - how can they then said to be not involved in the inhibition of firing rate (bullet point in Highlights)? Please elaborate further. In l.406 they also state that GCs can inhibit MTCs under certain conditions. The argument, that this stimulation is not physiological, makes sense, but still does not rule out anything. You might want to cite Aghvami et al 2022 on the very small amplitude of GC-mediated IPSPs, also McIntyre and Cleland 2015.

      We apologize for the lack of clarity. We reported that we found a local cold spot in the context of an additional experiment not presented in the manuscript and only described in the Methods section. Following the revision, we decided to add the analysis of this experiment to Figure 5. This experiment validated that optogenetic activation of GCs is potent and can affect the recorded MTC firing rates. This is particularly important as we performed all experiments under Ketamine anesthesia, which is a NMDA receptor antagonist. In this experiment, we recorded the activity of MTCs at baseline conditions (without odor presentation) under optogenetic activation of GCs. We divided the OB surface into a grid and optogenetically activated GC columns at a random order, one light spot in each trial, using light patches of size of size 330um2. We used the same light intensity as in the optogenetic GC activation during odor stimulation (reported in Figures 4-5). We show that the recorded MTC was strongly inhibited by GC light activation, mostly when activating GCs in its vicinity (within its column, i.e., local cold spot). This experiment validates that in our experimental setup, GCs can exert inhibition over MTCs at baseline conditions.

      (2) Even from the shown data, it appears that laterally increased synchronization might co-occur with lateral suppression (See also comment on Figures 1d,e and Figure S1c)

      We kindly note that the panels you referred to do not quantify the firing rate but the rhythmicity of MTC light-evoked responses. We should have explained these graphs better in the main text and not only in the Methods section. We added a panel to Supplementary Figure 1, which describes our analysis: In each of these examples, we performed a time-frequency Wavelet analysis over the average response of the neurons across trials (computed using a sliding Gaussian with a std of 2ms). The results of the Wavelet analysis allowed us to visually capture the enhanced spike alignment across trials under paired activation as a function of the stimulus duration (as, for example, in Figure 1c, middle panel). The response amplitude to light stimulation did not change in this example (shown in Figure 1c lower panel), and the spikes entrainment increased following paired activation of MTCs.

      To address the relations between lateral suppression and synchronization at the population level, we added additional analyses to Figure 3c-d.

      (3) There are no manipulations of PVN activity in this study, thus there is no direct evidence for the substrate of the second circuit.

      We completely agree with the reviewer. Using the current data, we can only claim that optogenetic activation of GCL neurons did not affect the MTC odor-evoked response. This finding is consistent with the loss-of-function experiment reported by Fukunaga et al., 2014, where GC suppression did not change odor-evoke responses in both anesthetized and awake mice. Therefore, we speculated that PVN might be a candidate OB interneuron to mediate lateral inhibition between MTCs. This hypothesis is based on their higher likelihood of interconnecting two MTCs compared with GCs (Burton, 2017). We elaborated on this in the discussion and made sure it is clearly stated as a hypothesis.

      (4) The manipulation of GC activity was performed in a transgenic line with viral transfection, which might result in a lower permeation of the population compared to the line used for optogenetic stimulation of MTCs.

      We used a previously validated protocol for optogenetic manipulation of GCs from Fukunaga et al., 2014 in order to minimize this caveat. As we cited previously from their paper, following the expression of ChR2 in the GCL, ‘Light presentation in vivo resulted in rapid and strong depolarization of, and action potential (AP) discharges in, GCs (Fig. 3b), which in turn consistently and strongly hyperpolarized M/TCs (9 of 9 cells showed 100% AP suppression; Fig. 3c,d)’. These results are consistent with the additional experiment we added to the manuscript, where optogenetic activation of GCL neurons strongly suppressed MTC activity during baseline conditions (without odor presentation). The high similarity between these two reports, in which, in the case of Fukunaga et al., GC activation was directly measured, suggests that lack of opsin expression or insufficient light intensity is unlikely to explain the lack of GCL neuron activation effect on lateral inhibition. Moreover, GCL neurons' optogenetic activation during odor stimulation increased MTC spike-LFP coupling in the gamma range. Therefore, the dissociation between the effects of GCL neurons on spike entrainment and lateral inhibition suggests that the lack of lateral inhibition following GC activation is unlikely due to low expression rates.

      In some instances, the authors tend to cite older literature - which was not yet aware of the prominent contribution of EPL neurons including PVN to recurrent and lateral inhibition of MT cells - as if roles that then were ascribed to granule cells for lack of better knowledge can still be unequivocally linked to granule cells now. For example, they should discuss Arevian et al (2006), Galan et al 2006, Giridhar et al., Yokoi et al. 1995, etc in the light of PVN action.

      Therefore it is also not quite justified to state that their result regarding the role of GCs specifically for synchronization, not suppression, is "in contrast to the field" (e.g. l.70 f.,, l.365, l. 400 ff).

      We changed several sentences in the discussion and introduction to explain that previous studies attributed lateral suppression to GC because they were not aware of the prominent contribution of EPL neurons as has been demonstrated by more recent studies (Burton 2024, Huang et al., 2016,  Kato et al., 2013, and more).

      We also toned down the statement that these findings are in contrast to the field. Instead, we state that our findings support the claim that GCs are not involved in affecting MTC odor-evoked firing rate.

      Why did the authors choose to use the term "lateral suppression", often interchangeably with lateral inhibition? If this term is intended to specifically reflect reductions of firing rates, it might be useful to clearly define it at first use (and cite earlier literature on it) and then use it consistently throughout.

      We agree and have changed the manuscript accordingly. We added the following in the introduction: “We use this phrase here to refer to a process that suppresses the firing rate of the post-synaptic neuron.”

      A discussion of anesthesia effects is missing - e.g. GC activity is known to be reportedly stronger in awake mice (Kato et al). This is not a contentious point at all since the authors themselves show that additional excitation of GCs enhances synchrony, but it should be mentioned.

      We completely agree and added a paragraph to the Discussion in this regard. Please see also the response to reviewer #1, who made a similar suggestion.

      Some citations should be added, in particular relevant recent preprints - e.g. Peace et al. BioRxiv 2024, Burton et al. BioRxiv 2024 and the direct evidence for a glutamate-dependent release of GABA from GCs (Lage-Rupprecht et al. 2020).

      We thank the reviewer for noting us these relevant recent manuscripts. We have now cited Peace et al., when discussing the spatial range of inhibition and gamma synchronization in the OB, Lage-Rupprecht et al in the context of the involvement of NMDA receptor in MTC-GC reciprocal synapse and Burton et al. when discussing PV neurons potential function.

      The introduction on the role of gamma oscillations in sensory systems (in particular vision) could be more elaborated.

      In our previous paper (Dalal & Haddad 2022) we had an elaborated introduction on the role of gamma oscillations in sensory processing, since we focused in this study in the effect of gamma synchronization on information transmission between brain regions. In the current study we looked at gamma rhythms as a mechanism that can facilitate ensemble synchronization.

      Reviewer #3 (Public Review):

      Summary:

      This study by Dalal and Haddad analyzes two facets of cooperative recruitment of M/TCs as discerned through direct, ChR2-mediated spot stimulations:

      (1) mutual inhibition and

      (2) entrainment of action potential timing within the gamma frequency range.

      This investigation is conducted by contrasting the evoked activity elicited by a "central" stimulus spot, which induces an excitatory response alone, with that elicited when paired with stimulations of surrounding areas. Additionally, the effect of Gad2-expressing granule cells is examined.

      Based on the observed distance dependence and the impact of GC stimulations, the authors infer that mutual inhibition and gamma entrainment are mediated by distinct mechanisms.

      Strengths:

      The results presented in this study offer a nice in vivo validation of the significant in vitro findings previously reported by Arevian, Kapoor, and Urban in 2008. Additionally, the distance-dependent analysis provides some mechanistic insights.

      We thank the reviewer for his comments. Indeed, the current study provides in-vivo replication of the results reported in Arevian et al., 2008 in-vitro, and adds further insights by showing that lateral inhibition is distant-dependent. However, this is not the main focus of the current study. Following the findings reported by Dalal & Haddad 2022, the motivation for this study was to test the mechanism that allows co-activated MTCs to entrain their spike timing. By light-activating pairs of MTCs at varying distances, we detected a subset of pairs in which paired light-activation evoked activity-dependent lateral inhibition, as was reported by Arevian et al., 2008. Moreover, we think it is highly important to know that a previous result in an in-vitro study is fully reproducible in-vivo.

      Weaknesses:

      The results largely reproduce previously reported findings, including those from the authors' own work, such as Dalal and Haddad (2022), where a key highlight was "Modulating GC activities dissociates MTCs odor-evoked gamma synchrony from firing rates." Some interpretations, particularly the claim regarding the distance independence of the entrainment effect, may be considered over-interpretations.

      We kindly disagree with the reviewer. We think the current study extends rather than reproduces the findings reported in Dalal & Haddad 2022. The 2022 study mainly focused on the effect of OB gamma synchronization on odor representation in the Piriform cortex. We bidirectionally modulated the level of MTC gamma synchronization and found that it had bidirectional effects on odor representation in one of their downstream targets, the anterior piriform cortex. The current study, however, focuses on the question of how spatially distributed odor-activated MTCs can synchronize their spiking activity. Our current main finding is that paired activation of MTCs can enhance the spikes entrainment of the recorded MTC in an activity-dependent and spatially independent manner. We suggest that this mechanism is mediated by GCL neurons.

      The reviewer did not explain why he\she thinks that the distance independence of the entrainment effects is an over-interpretation. However, to make our claim more precise we added the following sentence to the corresponding results section:” Furthermore, within the distance range that we were able to measure, the increased phase-locking did not significantly correlate with the distance from the MTC”

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Minor comments:

      (1) Line 17f: "This lateral synchronization was particularly effective when both MTCs fired at the gamma rhythm, ..."

      This sentence implies a direct comparison of the simultaneously recorded firing of MTCs but I could not find evidence for this in this manuscript. I would suggest to change this.

      We thank the reviewer. The sentence was changed to “This lateral synchronization was particularly effective when the recorded MTC fired at the gamma rhythm”.

      (2) Line 43f: A brief description of what glomeruli are could help to avoid confusion for readers less familiar with the OB. The phrasing of "activated glomeruli" and "each glomerulus innervates" are somewhat misleading given that they do not contain the cell bodies of the projection neurons.

      We edited this part of the introduction so it briefly describes what glomeruli are: ‘Olfactory processing starts with the activity of odorant-activated olfactory sensory neurons. The axons of these sensory neurons terminate in one or two anatomical structures called glomeruli located on the surface of the olfactory bulb (OB). Each glomerulus is innervated by several mitral and tufted cells (MTCs), which then project the odor information to several cortical regions. ‘

      (3) Line 78ff: The text sounds as if glomeruli are activated by the light stimulation but ChR2 is expressed in MTCs, the postsynaptic component of the glomeruli. It would be clearer to refer to the stimulation as light activation of MTCs.

      We corrected this sentence to: ‘We first mapped each recorded cell's receptive field, i.e., the set of MTCs on the dorsal OB that affect its firing rates when they are light-stimulated.’

      (4) Line 90: It would be great to mention somewhere in this paragraph that you are analyzing single-unit data sorted from extracellular recordings with tungsten electrodes.

      We added that to the description of the experimental setup: ‘To investigate how MTCs interact, we expressed the light-gated channel rhodopsin (ChR2) exclusively in MTCs by crossing the Tbet-Cre and Ai32 mouse lines (Grobman et al., 2018; Haddad et al., 2013), and extracellularly recorded the spiking activity of MTCs in anesthetized mice during optogenetic stimulation using tungsten electrodes.’

      (5) Line 97: The term "delta entrainment" could be easily confused with the entrainment of MTCs to respiration in the delta frequency band. Maybe better to use a different term or stick to "change in entrainment" also used in the text.

      We completely agree. The term was changed to “change in entrainment” throughout the manuscript and figures.

      (6) Line 121f: "Light stimulation did not affect ..." . Should this be "Paired light stimulation did not affect ..."?

      Corrected, thank you.

      (7) Supplementary Figure 1a: The example is not very convincing. It looks a bit like a rhythmic bursting neuron mildly depending on the stimulation.

      This panel serves to present our light stimulation method. The potency of the light stimulation protocol can be seen in the receptive field maps.

      (8) Supplementary Figure 1c: Why is there no confidence interval for 'Paired'?

      This panel shows the power spectrum density of the average neuron response across trials computed over the entire stimulus window (100ms). We decided to remove this panel, as panel Figure 1d shows the evolution of the entrainment in time and, therefore, provides better insight into the effect.

      (9) Line 166f: "... across any light intensities". Maybe better "... for the four light intensities tested"?

      We agree, we changed the text in accordance.

      (10) Figure 2f: It would be more intuitive to have the x-axis in the same orientation as in 2e.

      Corrected, thank you.

      (11) Figure 4a: The image in this panel is identical to Figure 1a in Dalal and Haddad 2022 in Cell reports just with a different intensity. The reuse of items and data from previous publications should be indicated somewhere but I could not find it.

      We apologize for this replication. We replaced it with a photo showing a larger portion of the OB, demonstrating the restricted viral expression within the GCL.

      (12) Line 408ff: A brief explanation for the hypothesis of EPL parvalbumin interneurons as the ones mediating lateral inhibition would be great.

      We agree. We added the following paragraph to the discussion section: “We speculate that MTC-to-MTC suppression is mediated by EPL neurons, most likely the Parvalbumin neuron (PV). This hypothesis is based on their activity and connectivity properties with MTCs(Burton, 2017; Kato et al., 2013; Miyamichi et al., 2013; Burton, 2024). More studies are required to reveal how PV neurons affect MTC activity.”

      (13) Line 425ff: You show that only activity of high firing rate neurons is suppressed by lateral inhibition, whereas "low and noise MTC responses" are not affected. Wouldn't this rather support the conclusion that lateral inhibition prevents excess activity from the OB?

      We found lateral inhibition was mainly effective when the postsynaptic neurons fired at ~30-80Hz in response to light stimulation. That is, it affects MTC firing in this “intermediate” rate, and to a lesser extent when the MTC have low and very high firing rates. To prevent excess activity, one would expect a mechanism that affects more high firing rates than medium ones. This was demonstrated in Kato 2013 for PV-MTC inhibition

      (14) Line 387: "..., only ~20% of the tested MTC pairs exhibited significant lateral inhibition." This is higher than the 16% of neurons you reported to have lateral entrainment (line 100). Why do you consider the lateral inhibition as 'sparse' but the lateral entrainment as relevant?

      We apologize for this unclear statement. The papers we cited in this regard (Fantana et al., 2008; Lehmann et al., 2016; Pressler and Strowbridge, 2017) have tested lateral inhibition when the recorded MTC was not active, which resulted in a sparse MTC-MTC inhibition. We validated and replicated these findings in our setup, by systematically projecting light spots over the dorsal OB without simultaneous activation of the recorded MTC and found similar rates of largely scarce inhibition (data not shown). In this study, using spike-triggered average light stimulation protocol and paired activation of MTCs, we found higher rates of lateral inhibition, consistent with the reports by Isaacson and Strowbridge, 1998, Urban and Sakmann, 2002. We changed this paragraph to the following:

      “We found that in only ~20% of the tested MTC pairs exhibited significant lateral suppression. This rate is consistent with previous in-vitro studies that found lateral suppression between 10-20% of heterotypic MTC pairs (Isaacson and Strowbridge, 1998; Urban and Sakmann, 2002), and is higher compared to a case where the recorded MTC is not active (Lehmann et al., 2016).”

      Reviewer #2 (Recommendations For The Authors):

      Figure-by-figure comments:

      (1) Figures 1d,e: both these examples seem to show that the firing rate is decreased in the paired condition? From maxima at 110 to 58 Hz in d and 100 to 48 Hz in e. Please explain (see also comment on Figure S1c).

      Please see the response in the Public Review section, reviewer #2, bullet (2). We also added a panel to Supplementary Figure 1 to better explain this.

      (2) Figure 1 f The means and SEMs are hard to see. Why is the SEM bar plotted horizontally? Since this is a major finding of the paper, will there be a table provided that shows the distribution of ∆ shifts across animals?

      We apologize for the mistake. The horizontal bar was the marking of the mean. Since the SEM is small, we corrected the graph for better visualization of the SEM.

      (3) Figure 1g Showing the running average of data where there is almost none or no data points (beyond 50 Hz) seems not ideal. Is the enhanced entrainment around 40Hz significant? Perhaps the moving average should be replaced by binned data with indicated n?

      We prefer to show all data points instead of binning the data so the reader can see it all. We agree that such a wide range on the x-axis is unnecessary. We shorten this graph only to include the firing rate range in which the data points ranged.

      (4) Figure 1h Impressive result!

      Thank you!

      (5) Figure S1a: since the authors show the respiratory pattern here and there obviously was no alignment of light stimulation with inspiration, was there any correlation between the respiratory phase and efficiency of light stimulation with respect to lateral interactions?

      This is an interesting idea. In Haddad et al., 2013, figure 7, the authors performed a similar analysis, and showed that optogenetic activation of MTCs had a more pronounced effect on firing rate in the respiration phases where the neuron was less firing. However, we haven’t quantified the impact of lateral interactions with respect to the respiration phase. That being said, the data will be publicly available to test this question.

      (6) Figure S1c: Here the shift towards a lower firing rate seems to be obvious (see comment in Figures 1 d and e). Please also show the plot for Figure 1e.

      This panel shows the power spectrum density of the average neuron's response across trials computed over the entire stimulus window (100ms). We decided to remove this panel, as panel Figure 1d shows the evolution of the entrainment in time and, therefore, provides better insight into the effect.

      (7) Figure 2b: show the same plot also for pair 2? Why is it stated that there is no lateral suppression for lateral stimulation alone, if the MTC did not spike spontaneously in the first place and thus inhibition cannot be demonstrated?

      We use Figure 2b to demonstrate the effect of lateral inhibition, and in Figure 2c we detail the responses under each light intensity for both pairs. We think that showing the mean and SEM for one example is enough to give a sense of the effect, as in Figure 2c we show the average response across time together with significant assessment for each pair (panels without a p-value have no significant difference between the conditions).

      However, we agree with the comment on this specific example and therefore deleted this sentence. However, at the population level we found no inhibition when activating the lateral spots, regardless of their firing rates (shown in Supplementary Figure 2a).

      (8) Figure 2d: why is there no distance-dependent color coding for the significant data points? Or, alternatively, since the distance plot is shown in 2e, perhaps drop this information altogether? Again, the moving average is problematic.

      Distance-dependent color coding is applied to all data points in this panel. Significant data points are shown in full circles and have distance-dependent color coding, which is mainly restricted to the lower part of the distance scale (cold colors).

      We used a moving average to relate to the similar result reported in Arevian 2008.In Figure 2e, the actual distance for each data point is indicated on the x-axis.

      (9) Figure 2f: the diagonal averaging method seems to neglect a lot of the data in Figure S2b, why not use radial coordinates for averaging?

      Thank you for the great suggestion. We indeed performed radial coordinates for the averaging, and the results are more robust and better summarize the entire data.

      (10) Figure 3: These are interesting observations, but are there cumulative data on such types of pairs? Please describe and show, otherwise this can only be a supplemental observation. Regarding 3b was it always the lower light intensity that resulted in suppression and the higher in sync? Since Burton et al. 2024 have just shown that PVNs require very little input to fire!

      This figure shows several examples of entrainment and inhibition properties. As suggested, we added population analysis (Figure 3c-d). This analysis compares the firing rate changes in pairs that evoked significant suppression or entrainment. First, we found only a few pairs in which paired activation evoked both spikes entrainment and suppression. Second, the mean of firing rate changes of pairs that evoked significant entrainment (N=50, shown in Figure 1f in full circles) is significantly different from the mean of the pairs that evoked significant lateral inhibition (N=51, shown in Figure 2d in full circles).

      (11) Figure 4: This Figure and the corresponding section should be entitled "Additional GC activation... ", otherwise it might be confusing for the reader. A loss of function manipulation (local GC silencing) would be also great to have! You did this in the previous paper, why not here? Raw LFP data are not shown. In Figure 4e the reported odor response firing rate ranges only up to 40Hz, but the example in g shows a much higher frequency. Is the maximum in 4e significant? (same issue as for Figure 1g).

      We changed the phrase to ‘optogenetic GCL neurons activation’. Unfortunately, we haven’t performed experiments where we suppress GC columns. In the previous paper, we suppressed the activity of all accessible GCs, which resulted in reduced spike synchronization to the OB gamma oscillations. Silencing only the GC column is, we think, unlikely to have a substantial effect, especially if the GCs have low activity (but this needs to be tested). Furthermore, we added examples of raw LFP data for odor stimulation and odor combined with GCL column activation (see Supplementary Figure 4a).

      The instantaneous firing rate is high (~80Hz), however the firing rate values we report in Figure 4e is the average within a window of 2 seconds (the odor duration is 1.5 seconds and we extend the window to account for responses with late return to baseline). The average firing rate of this example neuron in this window was 28Hz.

      (12) Fig 5: what does "proximal" mean - does this mean stimulation of the GCs below the recorded MTC, that might actually belong to the same glomerular unit?

      Yes, by “proximal” we mean the activation of the GC in the column of the recorded MTC. However, we decided that instead of coarsely dividing the data into proximal and distal optogenetic activation of GCL neurons, we will show the data continuously to show that GC had no significant effect on MTC odor-evoked firing rates regardless of their location (Figure 5d).

      A comment on the title:

      Please tone it down: "Ensemble synchronization" is a hypothesis at this point, not directly shown in the paper. Also, the paper does not show lateral interactions between odor-activated neurons.

      We agree and have rephrased it to “Activity-dependent lateral inhibition enables the synchronization of active olfactory bulb projection neurons ”

      (1) Figure 1a, 2a scale bar missing.

      Corrected, thank you.

      (2) Figure 1 c is the "rebound" in the lateral stim trace (green) real or not significant?

      The activity during this rebound is not significantly different than the baseline activity before light stimulation.

      (3) Figure 2b legend: "lateral alone" instead of lateral?

      We appreciate the suggestion. For simplicity, we will keep it as “lateral”.

      (4) Figure 2c: some of the data plots seem to be breaking off, e.g. the blue line in the bottom third one.

      This line breaking is due to the lack of spikes in this period. The PSTHs used in all analyses result from the convolution of the spike train with a Gaussian window with a standard deviation of 50ms.

      (5) Figure 2f: Why is the x axis flopped vs 2d,e?

      This panel was mistakenly plotted that way, and was corrected.

      Comments on the text:

      Abstract - we had indicated suggestions by strike-throughs and color which are lost in the online submission system, please compare with your original text:

      Information in the brain is represented by the activity of neuronal ensembles. These ensembles are adaptive and dynamic, formed and truncated based on the animal`s experience. One mechanism by which spatially distributed neurons form an ensemble is via synchronization of their spiking activity in response to a sensory event. In the olfactory bulb, odor stimulation evokes rhythmic gamma activity in spatially distributed mitral and tufted cells (MTCs). This rhythmic activity is thought to enhance the relay of odor information to the downstream olfactory targets. However, how only specifically the odor-activated MTCs are synchronized is unknown. Here, we demonstrate that light optogenetic activation of activating one set of MTCs can gamma-entrain the spiking activity of another set. This lateral synchronization was particularly effective when both MTCs fired at the gamma rhythm, facilitating the synchronization of only the odor-activated MTCs. Furthermore, we show that lateral synchronization did not depend on the distance between the MTCs and is mediated by granule cells. In contrast, lateral inhibition between MTCs that reduced their firing rates was spatially restricted to adjacent MTCs and was not mediated by granule cells. Our findings reveal lead us to propose ? a simple yet robust mechanism by which spatially distributed neurons entrain each other's spiking activity to form an ensemble.

      Thank you. We adopted most of the changes and edited the abstract to reflect the reported results better.

      "both MTCs fired at the gamma rhythm"/this is at this point unwarranted since the mutual entrainment is not shown - tone down or present as hypothesis?

      We completely agree. This sentence was changed to “This lateral synchronization was particularly effective when the recorded MTC fired at the gamma rhythm, facilitating the synchronization of the active MTC”.

      l. 28: distance-independent instead of "spatially independent"?

      Corrected

      l. 46: are there inhibitory neurons in the ONL? Or which 6 layers are you referring to here?

      Corrected to “spanning all OB layers”.

      l. 49: "is mediated" => "likely to be mediated". Schoppa's work is in vitro and did not account for PVNs, see comment in Public Review.

      Corrected. Indeed Schoppa`s work was performed in-vitro. We cite it here since it showed that the synchronized firing of two MTC pairs depends on granule cells.

      l.52: "method"? rather "mechanism"? "specifically" instread of "only"?

      Corrected.

      l.52: perhaps more precise: a recent hypothesis is that GCs enable synchronization solely between odor-activated MTCs via an activity-dependent mechanism for GABA-release (Lage Rupprecht et al. 2020 - please cite the experimental paper here). Again. Galan has no direct evidence for GCs vs PVNs, see comment in Public Review.

      Thank you, we updated this sentence here and in the discussion and added the relevant citation.

      l. 66: spike timings instead of spike's timing?

      Corrected to spike timings

      l. 67 -71: this part could be dropped.

      We appreciate the suggestion; however, we think that it is convenient to briefly read the main results before the results section.

      l. 76 mouse instead of mice.

      Corrected.

      l. 77: for clarification: " a single MTC"?

      In some cases, we recorded more than one cell simultaneously.

      l. 89: just use "hotspot".

      Corrected

      l. 97 instead of "change", "positive change" or "increase"?

      We left the word change, since we wanted to report that the change between hotspot alone and paired stimulation was significantly higher than zero.

      l. 104: the postsyn MTC's firing rate.

      Corrected to MTC instead of MTCs

      l.108: "distributed on the OB surface" sounds misleading, perhaps "across the glomerular map"?

      Corrected.

      l. 254: "which the MTCs form with each other"- perhaps "which interconnect MTCs".

      Corrected.

      l. 270 Additional GC activation.

      Corrected to ‘optogenetic activation of GCL neurons’

      l. 284 somewhat unclear - please expand.

      Corrected to ‘This measure minimizes the bias of the neuron's firing rate on the spike-LFP synchrony value’.

      l. 371: no odors in Schoppa et al.

      Corrected to ‘It has been shown that two active MTCs can synchronize their stimulus-evoked and odor-evoked spike timings’

      l. 406 ff. good point - but where is the transition? How does this observation rule out that GCs can mediate lateral suppression?

      It is an important question. We tested two setups of GCs optogenetic activation, either column activation (in this paper) or the activation of all accessible GCs of the dorsal OB (Dalal & Haddad, 2022). Although the latter manipulation results in significant firing rate suppression, the effect of MTC suppression was relatively small in anesthetized mice and even smaller in awake mice. Optogenetically activating GCs at baseline conditions resulted in a strong suppression of only the adjacent MTCs. Taken together, we think that GCs are capable of strongly inhibit MTCs, but it is not their main function in natural olfactory sensation.

      l. 422 ff: again, this is a hypothesis, please frame accordingly.

      Corrected to ‘Activity-dependent synchronization can enables the synchronization of odor-activated MTCs that are dispersed across the glomerular map’

      l. 551 typo.

      Corrected.

      l 556 ff: Figure 2 does not show odor responses.

      Corrected.

      l 582: Mix up of above/below and low/high?

      Corrected to ‘The values in the STA map that were above or below these high and low percentile thresholds’

      Reviewer #3 (Recommendations For The Authors):

      Line 76: "Ai39" should be corrected to "Ai32".

      Corrected. Thank you.

      Figure Legends: The legends should describe the results rather than interpret the data. For instance, the legends for Figures 1f, g, and h contain interpretations. The authors should review all legends and revise them accordingly.

      We appreciate the comment. However, we kindly disagree. We don’t see these opening sentences as interpretations but as guidance to the reader. For example, ‘Paired stimulation increases spikes’ temporal precision’ is not an interpretation; instead, it describes the finding presented in this panel. We think that legends that only repeat what can already be deduced from the graph are not helpful and, in many cases, obsolete. Explaining what we think this graph shows is common, and we prefer it as it helps the reader.

      For Figures 1d and e, it may be beneficial to add the spectrograms for the second stimulation alone.

      We show the stimulation of the hotspot alone and when we stimulate both.<br /> The spectrogram of the lateral alone does not show anything of importance.

      Figures 1a and 2a: Please add color bars so that readers can understand the meaning of the colors plotted.

      Color bars were added.

      Figure 3: The purpose of this figure is unclear. Why does the baseline firing rate for the paired activation differ? Is this an isolated observation, or is it observed in other units as well?

      This issue has been raised also by reviewer #2. Attached here is our response to reviewer #2

      This figure shows several examples of entrainment and inhibition properties. As suggested, we added population analysis (Figure 3c-d). This analysis compares the firing rate changes in pairs that evoked significant suppression or entrainment. First, we found only a few pairs in which paired activation evoked both spikes entrainment and suppression. Second, the mean of firing rate changes of pairs that evoked significant entrainment (N=50, shown in Figure 1f in full circles) is significantly different from the mean of the pairs that evoked significant lateral inhibition (N=51, shown in Figure 2d in full circles).

      Figures 4 and 5 data seems to come from the same dataset as in Dalal and Haddad (2022) DOI: https://doi.org/10.1016/j.celrep.2022.110693. For example, the fluorescence image looks identical. If this is the case, the authors may want to state that that the image and and some of the data and analyses are reproduced.

      The recorded data shown in these figures are not reproduced from Dalal & Haddad 2022. We collected this data, using GC-columns activation instead of light activating the entire OB dorsal surface as was done in the 2022 paper.

      However, the histology image is the same and we now replaced it with a new image, which shows that the expression is restricted to the GCL.

      Figure 4d: the authors use the data plotted here to argue that the gamma entrainment is distance-independent. But there is a clear decrease over distance (e.g., delta PPC1 over 0.01 is not seen for distance beyond 1000 m). The claim of distance independence may be an over-interpretation of the data. Peace et al. (2024) also claimed that coupling via gamma oscillations occurs over a large spatial extent.

      From a statistical point of view, we can’t state that there is a dependency on distance as the correlation is insignificant (P = 0.86). PPC1 of value 0.01 can be found at 0, 500, and 700 microns. Lower values are found at far distances, but this can result from a smaller number of points. The reduced level of synchrony observed at distances above one mm could be the result of the reduced density of lateral interactions at these distances. That said, we rephrase the sentence to a more careful statement. Please see the rephrased sentence at the Public review section.

    1. eLife Assessment

      The findings of this study are potentially valuable, offering insights into the neural representation of reversal probability in decision-making tasks, with potential implications for understanding flexible behavior in changing environments. The evidence presented is incomplete, with interesting comparisons between neural data and models, but the analyses do not yet provide clear evidence against line attractor dynamics for the accumulation of evidence of a reversal in this probabilistic reversal learning task.

    2. Reviewer #1 (Public review):

      The authors aimed to investigate how the probability of a reversal in a decision-making task is represented in cortical neurons. They analyzed neural activity in the prefrontal cortex of monkeys and units in recurrent neural networks (RNNs) trained on a similar task. Their goal was to understand how the dynamical systems that implement computation perform a probabilistic reversal learning task in RNNs and nonhuman primates.

      Major strengths and weaknesses:

      Strengths:

      (1) Integrative Approach: The study exemplifies a modern approach by combining empirical data from monkey experiments with computational modeling using RNNs. This integration allows for a more comprehensive understanding of the dynamical systems that implement computation in both biological and artificial neural networks.

      (2) The focus on using perturbations to identify causal relationships in dynamical systems is a good goal. This approach aims to go beyond correlational observations.

      Weaknesses:

      (1) The description of the RNN training procedure and task structure lacks detail, making it difficult to fully evaluate the methodology.

      (2) The conclusion that the representation is better described by separable dynamic trajectories rather than fixed points on a line attractor may be premature.

      (3) The use of targeted dimensionality reduction (TDR) to identify the axis determining reversal probability may not necessarily isolate the dimension along which the RNN computes reversal probability.

      Appraisal of aims and conclusions:

      The authors claim that substantial dynamics associated with intervening behaviors provide evidence against a line attractor. The conclusion that this representation is better described by separable dynamic trajectories rather than fixed points on a line attractor may be premature. The authors found that the state was translated systematically in response to whether outcomes were rewarded, and this translation accumulated across trials. This is consistent with a line attractor, where reward input bumps the state along a line. The observed dynamics could still be consistent with a curved line attractor, with faster timescale dynamics superimposed on this structure.

      Likely impact and utility:

      This work contributes to our understanding of how probabilistic information is represented in neural circuits and how it influences decision-making. The methods used, particularly the combination of empirical data and RNN modeling, provide a valuable approach for investigating neural computations. However, the impact may be limited by some of the methodological concerns raised.

      The data and methods could be useful to the community, especially if the authors provide more detailed descriptions of their RNN training procedures and task structure. However, reverse engineering of the network dynamics was minimal. Most analyses didn't take advantage of the full access to the RNN's update equations.

    3. Reviewer #2 (Public review):

      Summary:

      In this work, the authors trained RNN to perform a reversal task also performed by animals while PFC activity is recorded. The authors devised a new method to train RNN on this type of reversal task, which in principle ensures that the behavior of the RNN matches the behavior of the animal. They then performed some analysis of neural activity, both RNN and PFC recording, focusing on the neural representation of the reversal probability and its evolution across trials. Given the analysis presented, it has been difficult for me to assess at which point RNN can reasonably be compared to PFC recordings.

      Strengths:

      Focusing on a reversal task, the authors address a challenge in RNN training, as they do not use a standard supervised learning procedure where the desired output is available for each trial. They propose a new way of doing that.

      They attempt to confront RNN and neural recordings in behaving animals.

      Weaknesses:

      The design of the task for the RNN does not seem well suited to support the claim of the paper: no action is required to be performed by neurons in the RNN, instead, the choice of the animal is determined by applying a non-linearity to the RNN's readout (equation 7), no intervening behavior is thus performed by neurons on which the analysis is performed throughout the paper. 
Instead, it would have been nice to mimic more closely the task structure of the experiments on monkeys, with a fixation period where the read-out is asked to be at a zero value, and then asked to reach a target value (not just taking its sign), depending on the expected choice after a cue presentation period.

      The comparison between RNN and neural data focuses on very specific features of neural activity. It would have been nice to see how individual units in the RNN behave over the course of the trial, do all units show oscillatory behavior like the readout shown in Figure 1B?

      It would be nice to justify why it has been chosen to take a network of inhibitory neurons and to know whether the analysis can also be performed with excitatory neurons.
 All the analysis relies on the dimensionality reduction. It would have been nice to have some other analysis confirming the claim of the absence of a line attractor in the neural data. Or at least to better characterize this dimensionality reduction procedure, e.g. how much of the variance is explained by this analysis for instance?

      It is thus difficult to grasp, besides the fact that reversal behavior is similar, to what extent the RNN is comparable to PFC functioning and to what extent we learn anything about the latter.

      Other computational works (e.g. [1,2]) have developed procedures to train RNN on reversal-like tasks, it would have been nice to compare the procedure presented here with these other works.

      [1] H Francis Song & Xiao-Jing Wang. Reward-based training of recurrent neural networks for cognitive and value-based tasks. eLife doi:10.7554/elife.21492.001.

      [2] Molano-Mazón, M. et al. Recurrent networks endowed with structural priors explain suboptimal animal behavior. Current Biology 33, 622-638.e7 (2023).

    4. Reviewer #3 (Public review):

      Summary:

      Kim et al. present a study of the neural dynamics underlying reversal learning in monkey PFC and neural networks. The concept of studying neural dynamics throughout the task (including intervening behaviour) is interesting, and the data provides some insights into the neural dynamics driving reversal learning. The modelling seems to support the analyses, but both the modelling and analyses also leave several open questions.

      Strengths:

      The paper addresses an interesting topic of the neural dynamics underlying reversal learning in PFC, using a combination of biological and simulated data. Reversal learning has been studied extensively in neuroscience, but this paper takes a step further by analysing neural dynamics throughout the trials instead of focusing on just the evidence integration epoch.

      The authors show some close parallels between the experimental data and RNN simulations, both in terms of behaviour and neural dynamics. The analyses of how rewarded and unrewarded trials differentially affect dynamics throughout the trials in RNNs and PFC were particularly interesting. This work has the potential to provide new insights into the neural underpinnings of reversal learning.

      Weaknesses:

      Conceptual:

      A substantial focus of the paper is on the within-trial dynamics associated with "intervening behaviour", but it is not clear whether that is well-modelled by the RNN. In particular, since there is little description of the experimental task, and the RNN does not have to do any explicit computation during the non-feedback parts of the trial, it is unclear whether the RNN 'non-feedback' dynamics can be expected to reasonably model the experimental data.

      Data analyses:

      While the basic analyses seem mostly sound, it seems like a potential confound that they are all aligned to the inferred reversal trial rather than the true experimental reversal trial. For example, the analyses showing that 'x_rev' decays strongly after the reversal trial, irrespective of the reward outcome, seem like they are true essentially by design. The choice to align to the inferred reversal trial also makes this trial seem 'special' (e.g. in Figure 2, Figure 5A), but it is unclear whether this is a real feature of the data or an artifact of effectively conditioning on a change in behaviour. It would be useful to investigate whether any of these analyses differ when aligned to the true reversal trial. It is also unsurprising that x_rev increases before the reversal and decreases after the reversal (it is hard to imagine a system where this is not the case), yet all of Figure 5 and much of Figure 4 is devoted to this point.

      Most of the analyses focus on the dynamics specifically in the x_rev subspace, but a major point of the paper is to say that biological (and artificial) networks may also have to do other things at different times in the trial. If that is the case, it would be interesting to also ask what happens in other subspaces of neural activity, that are not specifically related to evidence integration or choice - are there other subspaces that explain substantial variance? Do they relate to any meaningful features of the experiment?

      On a related note, descriptions of the task itself, the behaviour of the animal(s?), and the neural recordings are largely absent, making it difficult to know what we should expect from neural dynamics throughout a trial. In fact, we are not even told how many monkeys were used for the paper or which part of PFC the recordings are from.

      Modelling:

      There are a number of surprising and non-standard modelling choices made in this paper. For example, the choice to only use inhibitory neurons is non-conventional and not consistent with prior work. The authors cite van Vreeswijk & Sompolinsky's balanced network paper, but this and most other balanced networks use a combination of excitatory and inhibitory neurons.

      It also seems like the inputs are provided without any learnable input weights (and the form of the inputs is not described in any detail). This makes it hard to interpret the input-driven dynamics during the different phases of a trial, despite these dynamics being a central topic of the paper.

      It is surprising that the RNN is "trained to flip its preferred choice a few trials after the inferred scheduled reversal trial", with the reversal trial inferred by an ideal Bayesian observer. A more natural approach would be to directly train the RNN to solve the task (by predicting the optimal choice) and then investigate the emergent behaviour & dynamics. If the authors prefer their imitation learning approach (which should at least be motivated), it is also surprising that the network is trained to predict the reversal trial inferred using Bayesian smoothing instead of Bayesian filtering.

    5. Author response:

      We appreciate Reviewer 1’s observation that our findings (i.e., separable dynamic trajectories are systematically translated in response to whether outcomes are rewarded, and this translation is accumulated across trials) are consistent with a line attractor model. We agree with this assessment and, in the revised manuscript, will reframe our findings about the dynamic trajectories to address its consistency with a line attractor.

      However, we would like to emphasize that a line attractor model does not account for the dynamic nature of reversal probability activity observed in the neural data. Line attractor, regardless of whether it is curved or straight, implies that the activity is fixed when no reward information is presented. The focus of our work is to highlight this dynamic nature of reversal probability activity and its incompatibility with the line attractor model.

      This leads to the question of how we could reconcile the line attractor-like properties and the dynamic nature of reversal probability activity. In the revised manuscript, we will provide evidence for an augmented model that has an attractor state at the beginning of each trial, followed by dynamic activity during the trial. Such a model is an example of superposition of initial attractor states with fast within-trial dynamics, as pointed out by Reviewer 1.

      We also thank Reviewer 2 and Reviewer 3 for their comments on how the manuscript could be improved. In the revised manuscript, we will provide detailed explanations to clarify the choice of network model, data analysis methods and experiment and model setups.

      In addition, we would like to take this opportunity to point out potentially misleading statements in the reviews by Reviewer 2 and Reviewer 3. Reviewer 2 stated that “no action is required to be performed by neurons in the RNN, …, no intervening behavior is thus performed by neurons”. Reviewer 3 stated that “the RNN does not have to do any explicit computation during the non-feedback parts of the trial…”. These statements convey the message that the trained RNN does not perform any computation. In fact, the RNN is trained to make a choice during non-feedback period in response to feedback. This is the (and the only) computation RNN performs. “Intervening behavior” refers to the choice the RNN makes across trials until reversing its initially preferred choice. We think that this confusion might have happened because the meaning of the term “intervening behavior” was unclear. We will clarify this point in the revised manuscript.

      Again, thank you for the insightful comments. We will provide a more detailed response to the reviews and revise the manuscript accordingly.

    1. eLife Assessment

      This important work examines how microexons contribute to brain activity, structure, and behavior. The authors find that loss of microexon sequences generally has subtle impacts on these metrics in larval zebrafish, with few exceptions. The evidence is still partially incomplete and needs to be strengthened by key experiments or more precise data descriptions. Overall, this work will be of interest to neuroscientists and generate further studies of interest to the field.

    2. Reviewer #1 (Public review):

      Summary:

      The authors use high-throughput gene editing technology in larval zebrafish to address whether microexons play important roles in the development and functional output of larval circuits. They find that individual microexon deletions rarely impact behavior, brain morphology, or activity, and raise the possibility that behavioral dysregulation occurs only with more global loss of microexon splicing regulation. Other possibilities exist: perhaps microexon splicing is more critical for later stages of brain development, perhaps microexon splicing is more critical in mammals, or perhaps the behavioral phenotypes observed when microexon splicing is lost are associated with loss of splicing in only a few genes.

      A few questions remain:

      (1) What is the behavioral consequence for loss of srrm4 and/or loss-of-function mutations in other genes encoding microexon splicing machinery in zebrafish?

      (2) What is the consequence of loss-of-function in microexon splicing genes on splicing of the genes studied (especially those for which phenotypes were observed).

      (3) For the microexons whose loss is associated with substantial behavioral, morphological, or activity changes, are the same changes observed in loss-of-function mutants for these genes?

      (4) Do "microexon mutations" presented here result in the precise loss of those microexons from the mRNA sequence? E.g. are there other impacts on mRNA sequence or abundance?

      (5) Microexons with a "canonical layout" (containing TGC / UC repeats) were selected based on the likelihood that they are regulated by srrm4. Are there other parallel pathways important for regulating the inclusion of microexons? Is it possible to speculate on whether they might be more important in zebrafish or in the case of early brain development?

      Strengths:

      (1) The authors provide a qualitative analysis of splicing plasticity for microexons during early zebrafish development.

      (2) The authors provide comprehensive phenotyping of microexon mutants, addressing the role of individual microexons in the regulation of brain morphology, activity, and behavior.

      Weaknesses:

      (1) It is difficult to interpret the largely negative findings reported in this paper without knowing how the loss of srrm4 affects brain activity, morphology, and behavior in zebrafish.

      (2) The authors do not present experiments directly testing the effects of their mutations on RNA splicing/abundance.

      (3) A comparison between loss-of-function phenotypes and loss-of-microexon splicing phenotypes could help interpret the findings from positive hits.

    3. Reviewer #2 (Public review):

      Summary:

      The manuscript from Calhoun et al. uses a well-established screening protocol to investigate the functions of microexons in zebrafish neurodevelopment. Microexons have gained prominence recently due to their enriched expression in neural tissues and misregulation in autism spectrum disease. However, screening of microexon functionality has thus far been limited in scope. The authors address this lack of knowledge by establishing zebrafish microexon CRISPR deletion lines for 45 microexons chosen in genes likely to play a role in CNS development. Using their high throughput protocol to test larval behaviour, brain activity, and brain structure, a modest group of 9 deletion lines was revealed to have neurodevelopmental functions, including 2 previously known to be functionally important.

      Strengths:

      (1) This work advances the state of knowledge in the microexon field and represents a starting point for future detailed investigations of the function of 7 microexons.

      (2) The phenotypic analysis using high-throughput approaches is sound and provides invaluable data.

      Weaknesses:

      (1) There is not enough information on the exact nature of the deletion for each microexon.

      (2) Only one deletion is phenotypically analysed, leaving space for the phenotype observed to be due to sequence modifications independent of the microexon itself.

    4. Reviewer #3 (Public review):

      Summary:

      This paper sought to understand how microexons influence early brain function. By selectively deleting a large number of conserved microexons and then phenotyping the mutants with behavior and brain activity assays, the authors find that most microexons have minimal effects on the global brain activity and broad behaviors of the larval fish-- although a few do have phenotypes.

      Strengths:

      The work takes full advantage of the scale that is afforded in zebrafish, generating a large mutant collection that is missing microexons and systematically phenotyping them with high throughput behaviour and brain activity assays. The work lays an important foundation for future studies that seek to uncover the likely subtle roles that single microexons will play in shaping development and behavior.

      Weaknesses:

      The work does not make it clear enough what deleting the microexon means, i.e. is it a clean removal of the microexon only, or are large pieces of the intron being removed as well-- and if so how much? Similarly, for the microexon deletions that do yield phenotypes, it will be important to demonstrate that the full-length transcript levels are unaffected by the deletion. For example, deleting the microexon might have unexpected effects on splicing or expression levels of the rest of the transcript that are the actual cause of some of these phenotypes.

    5. Author response:

      Reviewer #1 (Public review):

      Summary:

      The authors use high-throughput gene editing technology in larval zebrafish to address whether microexons play important roles in the development and functional output of larval circuits. They find that individual microexon deletions rarely impact behavior, brain morphology, or activity, and raise the possibility that behavioral dysregulation occurs only with more global loss of microexon splicing regulation. Other possibilities exist: perhaps microexon splicing is more critical for later stages of brain development, perhaps microexon splicing is more critical in mammals, or perhaps the behavioral phenotypes observed when microexon splicing is lost are associated with loss of splicing in only a few genes.

      A few questions remain:

      (1) What is the behavioral consequence for loss of srrm4 and/or loss-of-function mutations in other genes encoding microexon splicing machinery in zebrafish?

      It is established that srrm4 mutants have no overt morphological phenotypes and are not visually impaired (Ciampi et al., 2022).

      We chose not to generate and characterize the behavior and brain activity of srrm4 mutants for two reasons: 1) we were aware of two other labs in the zebrafish community that had generated srrm4 mutants (Ciampi et al., 2022 and Gupta et al., 2024, https://doi.org/10.1101/2024.11.29.626094; Lopez-Blanch et al., 2024, https://doi.org/10.1101/2024.10.23.619860), and 2) we were far more interested in determining the importance of individual microexons to protein function, rather than loss of the entire splicing program. Microexon inclusion can be controlled by different splicing regulators, such as srrm3 (Ciampi et al., 2022) and possibly other unknown factors. Genetic compensation in srrm4 mutants could also result in microexons still being included through actions of other splicing regulators, complicating the analysis of these regulators. We mention srrm4 in the manuscript to point out that some selected microexons are adjacent to regulatory elements expected of this pathway. We did not, however, choose microexons to mutate based on whether they were regulated by srrm4, making the characterization of srrm4 mutants disconnected from our overarching project goal.

      We are coordinating our publication with Lopez-Blanch et al. (https://doi.org/10.1101/2024.10.23.619860), which shows that srrm4 mutants also have minimal behavioral phenotypes.

      (2) What is the consequence of loss-of-function in microexon splicing genes on splicing of the genes studied (especially those for which phenotypes were observed).

      We acknowledge that unexpected changes to the mRNA could occur following microexon removal. In particular, all regulatory elements should be removed from the region surrounding the microexon, as any remaining elements could drive the inclusion of unexpected exons that result in premature stop codons.

      First, we will clarify our generated mutant alleles by adding a figure that details the location of the gRNA cut sites in relation to the microexon, its predicted regulatory elements, and its neighboring exons.

      Second, we will experimentally determine whether the mRNA was modified as expected for a subset of mutants with phenotypes.

      Third, we will further emphasize in the manuscript that these observed phenotypes are extremely mild compared to those observed in over one hundred protein-truncating mutations we have assessed in previous and ongoing work. We currently show one mutant, tcf7l2, which we consider to have strong neural phenotypes, and we will expand this comparison in the revision. In our study of 132 genes linked to schizophrenia (Thyme et al., 2019), we established a signal cut-off for whether a mutant would be designated as having a neural phenotype, and we classify this set of microexon mutants in this context. Far stronger phenotypes are expected of loss-of-function alleles for microexon-containing genes, as we showed in Figure S1 of this manuscript in addition to our published work.

      (3) For the microexons whose loss is associated with substantial behavioral, morphological, or activity changes, are the same changes observed in loss-of-function mutants for these genes?

      We had already included two explicit comparisons of microexon loss with a standard loss-of-function allele, one with a phenotype and one without, in Figure S1 of this manuscript. We will make the conclusions and data in this figure more obvious in the main text.

      Beyond the two pairs we had included, Lopez-Blanch et al. (https://doi.org/10.1101/2024.10.23.619860) describes mild behavioral phenotypes for a microexon removal for kif1b, and we already show developmental abnormalities for the kif1b loss-of-function allele (Figure S1).

      Additionally, we can draw expected conclusions from the literature, as some genes with our microexon mutations have been studied as typical mutants in zebrafish or mice. We will modify our manuscript to include a discussion of these mutants.

      (4) Do "microexon mutations" presented here result in the precise loss of those microexons from the mRNA sequence? E.g. are there other impacts on mRNA sequence or abundance?

      See response to point 2. We will experimentally determine whether the mRNA was modified as expected for a subset of mutants with phenotypes.

      (5) Microexons with a "canonical layout" (containing TGC / UC repeats) were selected based on the likelihood that they are regulated by srrm4. Are there other parallel pathways important for regulating the inclusion of microexons? Is it possible to speculate on whether they might be more important in zebrafish or in the case of early brain development?

      The microexons were not selected based on the likelihood that they were regulated by srrm4. We will clarify the manuscript regarding this point. There are parallel pathways that can control the inclusion of microexons, such as srrm3 (Ciampi et al., 2022). It is well-known that loss of srrm3 has stronger impacts on zebrafish development than srrm4 (Ciampi et al., 2022). The goal of our work was not to investigate these splicing regulators, but instead was to determine the individual importance of these highly conserved protein changes.

      Strengths:

      (1) The authors provide a qualitative analysis of splicing plasticity for microexons during early zebrafish development.

      (2) The authors provide comprehensive phenotyping of microexon mutants, addressing the role of individual microexons in the regulation of brain morphology, activity, and behavior.

      We thank the reviewer for their support. The pErk brain activity mapping method is highly sensitive, significantly minimizing the likelihood that the field has simply not looked hard enough for a neural phenotype in these microexon mutants. In our published work (Thyme et al., 2019), we show that brain activity can be drastically impacted without manifesting in differences in those behaviors assessed in a typical larval screen (e.g., tcf4, cnnm2, and more).

      Weaknesses:

      (1) It is difficult to interpret the largely negative findings reported in this paper without knowing how the loss of srrm4 affects brain activity, morphology, and behavior in zebrafish.

      See response to point 1.

      (2) The authors do not present experiments directly testing the effects of their mutations on RNA splicing/abundance.

      See response to point 3.

      (3) A comparison between loss-of-function phenotypes and loss-of-microexon splicing phenotypes could help interpret the findings from positive hits.

      See response to point 2.

      Reviewer #2 (Public review):

      Summary:

      The manuscript from Calhoun et al. uses a well-established screening protocol to investigate the functions of microexons in zebrafish neurodevelopment. Microexons have gained prominence recently due to their enriched expression in neural tissues and misregulation in autism spectrum disease. However, screening of microexon functionality has thus far been limited in scope. The authors address this lack of knowledge by establishing zebrafish microexon CRISPR deletion lines for 45 microexons chosen in genes likely to play a role in CNS development. Using their high throughput protocol to test larval behaviour, brain activity, and brain structure, a modest group of 9 deletion lines was revealed to have neurodevelopmental functions, including 2 previously known to be functionally important.

      Strengths:

      (1) This work advances the state of knowledge in the microexon field and represents a starting point for future detailed investigations of the function of 7 microexons.

      (2) The phenotypic analysis using high-throughput approaches is sound and provides invaluable data.

      We thank the reviewer for their support.

      Weaknesses:

      (1) There is not enough information on the exact nature of the deletion for each microexon.

      To clarify the nature of our mutant alleles, we will add a figure that details the location of the gRNA cut sites in relation to the microexon, its predicted regulatory elements, and its neighboring exons.

      (2) Only one deletion is phenotypically analysed, leaving space for the phenotype observed to be due to sequence modifications independent of the microexon itself.

      We will experimentally determine whether the mRNA is impacted in unanticipated ways for a subset of mutants with mild phenotypes (see the point 2 response to reviewer 1). We also have already compared the microexon removal to a loss-of-function mutant for two lines (Figure S1), and we will make that outcome more obvious as well as increasing the discussion of the expected phenotypes from typical loss-of-function mutants (see point 3 response to reviewer 1).

      In addition, our findings for three microexon mutants (ap1g1, vav2, and vti1a) are corroborated by Lopez-Blanch et al. (https://doi.org/10.1101/2024.10.23.619860).

      Unlike protein-coding truncations, clean removal of the microexon and its regulatory elements is unlikely to yield different phenotypic outcomes if independent lines are generated (with the exception of genetic background effects). When generating a protein-truncating allele, the premature stop codon can have different locations and a varied impact on genetic compensation. In previous work (Capps et al., 2024), we have observed different amounts of nonsense-mediated decay-induced genetic compensation (El-Brolosy, et al., 2019) depending on the location of the mutation. As they lack variable premature stop codons (the expectation of a clean removal), two mutants for the same microexons should have equivalent impacts on the mRNA.

      Reviewer #3 (Public review):

      Summary:

      This paper sought to understand how microexons influence early brain function. By selectively deleting a large number of conserved microexons and then phenotyping the mutants with behavior and brain activity assays, the authors find that most microexons have minimal effects on the global brain activity and broad behaviors of the larval fish-- although a few do have phenotypes.

      Strengths:

      The work takes full advantage of the scale that is afforded in zebrafish, generating a large mutant collection that is missing microexons and systematically phenotyping them with high throughput behaviour and brain activity assays. The work lays an important foundation for future studies that seek to uncover the likely subtle roles that single microexons will play in shaping development and behavior.

      We thank the reviewer for their support.

      Weaknesses:

      The work does not make it clear enough what deleting the microexon means, i.e. is it a clean removal of the microexon only, or are large pieces of the intron being removed as well-- and if so how much? Similarly, for the microexon deletions that do yield phenotypes, it will be important to demonstrate that the full-length transcript levels are unaffected by the deletion. For example, deleting the microexon might have unexpected effects on splicing or expression levels of the rest of the transcript that are the actual cause of some of these phenotypes.

      To clarify the nature of our mutant alleles, we will add a figure that details the location of the gRNA cut sites in relation to the microexon, its predicted regulatory elements, and its neighboring exons.

      We will experimentally determine whether the mRNA is impacted in unanticipated ways for a subset of mutants with mild phenotypes (see the point 2 response to reviewer 1).

    1. eLife Assessment

      This study demonstrates the potential role of 17α-estradiol in modulating neuronal gene expression in the aged hypothalamus of male rats, identifying key pathways and neuron subtypes affected by the drug. While the findings are useful and provide a foundation for future research, the strength of supporting evidence is incomplete due to the lack of female comparison, a young male control group, unclear link to 17α-estradiol lifespan extension in rats, and insufficient analysis of glial cells and cellular stress in CRH neurons.

    2. Reviewer #1 (Public review):

      Summary:

      Previous studies have shown that treatment with 17α-estradiol (a stereoisomer of the 17β-estradiol) extends lifespan in male mice but not in females. The current study by Li et al, aimed to identify cell-specific clusters and populations in the hypothalamus of aged male rats treated with 17α-estradiol (treated for 6 months). This study identifies genes and pathways affected by 17α-estradiol in the aged hypothalamus.

      Strengths:

      Using single-nucleus transcriptomic sequencing (snRNA-seq) on hypothalamus from aged male rats treated with 17α-estradiol they show that 17α-estradiol significantly attenuated age-related increases in cellular metabolism, stress, and decreased synaptic activity in neurons.<br /> Moreover, sc-analysis identified GnRH as one of the key mediators of 17α-estradiol's effects on energy homeostasis. Furthermore, they show that CRH neurons exhibited a senescent phenotype, suggesting a potential side effect of the 17α-estradiol. These conclusions are supported by supervised clustering by neuropeptides, hormones, and their receptors.

      Weaknesses:

      However, the study has several limitations that reduce the strength of the key claims in the manuscript. In particular:

      (1) The study focused only on males and did not include comparisons with females. However, previous studies have shown that 17α-estradiol extends lifespan in a sex-specific manner in mice, affecting males but not females. Without the comparison with the female data, it's difficult to assess its relevance to the lifespan.

      (2) It's not known whether 17α-estradiol leads to lifespan extension in male rats similar to male mice. Therefore, it is not possible to conclude that the observed effects in the hypothalamus, are linked to the lifespan extension.

      (3) The effect of 17α-estradiol on non-neuronal cells such as microglia and astrocytes is not well described (Fig.1). Previous studies demonstrated that 17α-estradiol reduces microgliosis and astrogliosis in the hypothalamus of aged male mice. Current data suggest that the proportion of oligo, and microglia were increased by the drug treatment, while the proportions of astrocytes were decreased. These data might suggest possible species differences, differences in the treatment regimen, or differences in drug efficiency. This has to be discussed.

      A more detailed analysis of glial cell types within the hypothalamus in response to drug should be provided.

      (4) The conclusion that CRH neurons are going into senescence is not clearly supported by the data. A more detailed analysis of the hypothalamus such as histological examination to assess cellular senescence markers in CRH neurons, is needed to support this claim.

      Comments on revisions:

      Some of the concerns were addressed in this revised version, and the authors responded and addressed study design limitations in both sexes/ages.

      However, there are still some concerns that were not sufficiently addressed:

      While the term "senescent" was changed to "stressed," some histological/ cellular validation of this phenotype is still needed.

      Some discussion on the sex-specific effects of 17α-estradiol in the hypothalamus is still required. Previous studies in mice demonstrated that 17α-estradiol reduced hypothalamic microgliosis and astrogliosis in male but not female UM-HET3 mice.

      Additionally, the provided analysis on astrocytes and microglia is superficial.

    3. Reviewer #2 (Public review):

      Summary:

      Li et al. investigated the potential anti-ageing role of 17α-Estradiol on the hypothalamus of aged rats. To achieve this, they employed a very sophisticated method for single-cell genomic analysis that allowed them to analyze effects on various groups of neurons and non-neuronal cells. They were able to sub-categorize neurons according to their capacity to produce specific neurotransmitters, receptors, or hormones. They found that 17α-Estradiol treatment led to an improvement in several factors related to metabolism and synaptic transmission by bringing the expression levels of many of the genes of these pathways closer or to the same levels to those of young rats, reversing the ageing effect. Interestingly, among all neuronal groups, the proportion of Oxytocin-expressing neurons seems to be the one most significantly changing after treatment with 17α-Estradiol, suggesting an important role of these neurons on mediating its anti-ageing effects. This was also supported by an increase in circulating levels of oxytocin. It was also found that gene expression of corticotropin-releasing hormone neurons was significantly impacted by 17α-Estradiol even though it was not different between aged and young rats, suggesting that these neurons could be responsible for side effects related to this treatment. This article revealed some potential targets that should be further investigated in future studies regarding the role of 17α-Estradiol treatment in aged males.

      Strengths:

      • The single nucleus mRNA sequencing is a very powerful method for gene expression analysis and clustering. The supervised clustering of neurons was very helpful in revealing otherwise invisible differences between neuronal groups and helped identify specific neuronal populations as targets.<br /> • There is a variety of functions used that allowed the differential analysis of a very complex type of data. This led to a better comparison between the different groups in many levels.<br /> • There were some physiological parameters measured such as circulating hormone levels that helped the interpretation of the effects of the changes in hypothalamic gene expression.

      Weaknesses:

      • One main control group is missing from the study, the young males treated with 17α-Estradiol.<br /> • Even though the technical approach is a sophisticated one, analyzing the whole rat hypothalamus instead of specific nuclei or subregions makes the study weaker.<br /> • Although the authors claim to have several findings, the data fail to support these claims.<br /> • The study is about improving ageing but no physiological data from the study demonstrated such claim with the exception of the testes histology which was not properly analyzed and was not even significantly different between the groups.<br /> • Overall, the study remains descriptive with no physiological data to demonstrate that any of the effects on hypothalamic gene expression is related to metabolic, synaptic or other function.

      Comments on revisions:

      The authors revised part of the manuscript to address some of the reviewers' comments This improved the language and the text flow to a certain extent. They also added an additional analysis including glial cells. However, they failed to address the main weaknesses brought up by the reviewers and did not add any experimental demonstration of their claims on lifespan expansion induced by 17α-estradiol in rats. In addition, they insisted i keeping parts in the discussion that are not directly linked to any of the papers' findings.

    4. Author response:

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

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      Previous studies have shown that treatment with 17α-estradiol (a stereoisomer of the 17β-estradiol) extends lifespan in male mice but not in females. The current study by Li et al, aimed to identify cell-specific clusters and populations in the hypothalamus of aged male rats treated with 17α-estradiol (treated for 6 months). This study identifies genes and pathways affected by 17α-estradiol in the aged hypothalamus.

      Strengths:

      Using single-nucleus transcriptomic sequencing (snRNA-seq) on the hypothalamus from aged male rats treated with 17α-estradiol they show that 17α-estradiol significantly attenuated age-related increases in cellular metabolism, stress, and decreased synaptic activity in neurons.

      Thanks.

      Moreover, sc-analysis identified GnRH as one of the key mediators of 17α-estradiol's effects on energy homeostasis. Furthermore, they show that CRH neurons exhibited a senescent phenotype, suggesting a potential side effect of the 17α-estradiol. These conclusions are supported by supervised clustering by neuropeptides, hormones, and their receptors.

      Thanks.

      Weaknesses:

      However, the study has several limitations that reduce the strength of the key claims in the manuscript. In particular:

      (1) The study focused only on males and did not include comparisons with females. However, previous studies have shown that 17α-estradiol extends lifespan in a sex-specific manner in mice, affecting males but not females. Without the comparison with the female data, it's difficult to assess its relevance to the lifespan.

      This study was originally designed based on previous findings indicating that lifespan extension is only effective in males, leading to the exclusion of females from the analysis. The primary focus of our research was on the transcriptional changes and serum endocrine alterations induced by 17α-estradiol in aged males compared to untreated aged males. We believe that even in the absence of female subjects, the significant effects of 17α-estradiol on metabolism in the hypothalamus, synapses, and endocrine system remain evident, particularly regarding the expression levels of GnRH and testosterone. Notably, lower overall metabolism, increased synaptic activity, and elevated levels of GnRH and testosterone are strong indicators of health and well-being in males, supporting the validity of our primary conclusions. However, including female controls would enhance the depth of our findings. If female controls were incorporated, we propose redesigning the sample groups to include aged male control, aged female control, aged female treated, aged male treated, as well as young male control, young male treated, young female control, and young female treated. We regret that we cannot provide this data in the short term. Nevertheless, we believe this presents a valuable avenue for future research on this topic. In this study, we emphasize the role of 17α-estradiol in overall metabolism, synaptic function, GnRH, and testosterone in aged males and underscore the importance of supervised clustering of neuropeptide-secreting neurons in the hypothalamus.

      (2) It is not known whether 17α-estradiol leads to lifespan extension in male rats similar to male mice. Therefore, it is not possible to conclude that the observed effects in the hypothalamus, are linked to the lifespan extension.

      Thanks for the reminding. 17α-estradiol was reported to extend lifespan in male rats similar to male mice (PMID: 33289482). We have added the valuable reference to introduction in the new version.  

      (3) The effect of 17α-estradiol on non-neuronal cells such as microglia and astrocytes is not well-described (Figure 1). Previous studies demonstrated that 17α-estradiol reduces microgliosis and astrogliosis in the hypothalamus of aged male mice. Current data suggest that the proportion of oligo, and microglia were increased by the drug treatment, while the proportions of astrocytes were decreased. These data might suggest possible species differences, differences in the treatment regimen, or differences in drug efficiency. This has to be discussed.

      We have reviewed reports describing changes in cell numbers following 17α-estradiol treatment in the brain, using the keywords "17α-estradiol," "17alpha-estradiol," and "microglia" or "astrocyte." Only a limited amount of data was obtained. We found one article indicating that 17α-estradiol treatment in Tg (AβPP(swe)/PS1(ΔE9)) model mice resulted in a decreased microglial cell number compared to the placebo (AβPP(swe)/PS1(ΔE9) mice), but this change was not significant when compared to the non-transgenic control (PMID: 21157032). The transgenic AβPP(swe)/PS1(ΔE9) mouse model may differ from our wild-type aging rat model in this context.

      Moreover, the calculation of cell numbers was based on visual observation under a microscope across several brain tissue slices. This traditional method often yields controversial results. For example, oligodendrocytes in the corpus callosum, fornix, and spinal cord have been reported to be 20-40% more numerous in males than in females based on microscopic observations (PMID: 16452667). In contrast, another study found no significant difference in the number of oligodendrocytes between sexes when using immunohistochemistry staining (PMID: 18709647). Such discrepancies arising from traditional observational methods are inevitable.

      We believe the data presented in this article are reliable because the cell number and cell ratio data were derived from high-throughput cell counting of the entire hypothalamus using single-cell suspension and droplet wrapping (10x Genomics).

      (4) A more detailed analysis of glial cell types within the hypothalamus in response to drugs should be provided.

      We provided more enrichment analysis data of differentially expressed genes between Y, O, and O.T in microglia and astrocytes in Figure 2—figure supplement 3. In this supplemental data, we found unlike that in neurons, Micro displayed lower levels of synapse-related cellular processes in O.T. compared to O.

      (5) The conclusion that CRH neurons are going into senescence is not clearly supported by the data. A more detailed analysis of the hypothalamus such as histological examination to assess cellular senescence markers in CRH neurons, is needed to support this claim.

      We also noticed the inappropriate claim and we have changed "senescent phenotype" to "stressed phenotype" and "abnormal phenotype" in abstract and in results.

      Reviewer #2 (Public Review):

      Summary:

      Li et al. investigated the potential anti-ageing role of 17α-Estradiol on the hypothalamus of aged rats. To achieve this, they employed a very sophisticated method for single-cell genomic analysis that allowed them to analyze effects on various groups of neurons and non-neuronal cells. They were able to sub-categorize neurons according to their capacity to produce specific neurotransmitters, receptors, or hormones. They found that 17α-Estradiol treatment led to an improvement in several factors related to metabolism and synaptic transmission by bringing the expression levels of many of the genes of these pathways closer or to the same levels as those of young rats, reversing the ageing effect. Interestingly, among all neuronal groups, the proportion of Oxytocin-expressing neurons seems to be the one most significantly changing after treatment with 17α-Estradiol, suggesting an important role of these neurons in mediating its anti-ageing effects. This was also supported by an increase in circulating levels of oxytocin. It was also found that gene expression of corticotropin-releasing hormone neurons was significantly impacted by 17α-Estradiol even though it was not different between aged and young rats, suggesting that these neurons could be responsible for side effects related to this treatment. This article revealed some potential targets that should be further investigated in future studies regarding the role of 17α-Estradiol treatment in aged males.

      Strengths:

      (1) Single-nucleus mRNA sequencing is a very powerful method for gene expression analysis and clustering. The supervised clustering of neurons was very helpful in revealing otherwise invisible differences between neuronal groups and helped identify specific neuronal populations as targets.

      Thanks.

      (2) There is a variety of functions used that allow the differential analysis of a very complex type of data. This led to a better comparison between the different groups on many levels.

      Thanks.

      (3) There were some physiological parameters measured such as circulating hormone levels that helped the interpretation of the effects of the changes in hypothalamic gene expression.

      Thanks.

      Weaknesses

      (1) One main control group is missing from the study, the young males treated with 17α-Estradiol.

      Given that the treatment period lasts six months, which extends beyond the young male rats' age range, we aimed to investigate the perturbation of 17α-Estradiol on the normal aging process. Including data from young males could potentially obscure the treatment's effects in aged males due to age effects, though similar effects between young and aged animals may exist. Long-term treatment of hormone may exert more developmental effects on the young than the old. Consequently, we decided to exclude this group from our initial sample design. We apologize for this omission.

      (2) Even though the technical approach is a sophisticated one, analyzing the whole rat hypothalamus instead of specific nuclei or subregions makes the study weaker.

      The precise targets of 17α-Estradiol within the hypothalamus remain unresolved. Selecting a specific nucleus for study is challenging. The supervised clustering method described in this manuscript allows us to identify the more sensitive neuron subtypes influenced by 17α-Estradiol and aging across the entire hypothalamus, without the need to isolate specific nuclei in a disturbed hypothalamic environment.

      (3) Although the authors claim to have several findings, the data fail to support these claims. You may mean the claim as the senescent phenotype in Crh neuron induced by 17a-estradiol.

      Thanks. We have changed the "senescent phenotype" to "stressed phenotype"  or "abnormal phenotype" in the abstract and results to avoid such claim.

      (4) The study is about improving ageing but no physiological data from the study demonstrated such a claim with the exception of the testes histology which was not properly analyzed and was not even significantly different between the groups.

      The primary objective of this study is to elucidate the effects of 17α-Estradiol on the endocrine system in the aging hypothalamus; exploring anti-aging effects is not the main focus. From the characteristics of the aging hypothalamus, we know that down-regulated GnRH and testosterone levels, along with elevated mTOR signaling, are indicators of aging in these organs (PMID: 37886966, PMID: 37048056, PMID: 22884327). The contrasting signaling networks related to metabolism and synaptic processes significantly differentiate young and aging hypothalami, and 17α-Estradiol helps rebalance these networks, suggesting its potential anti-aging effects.

      (5) Overall, the study remains descriptive with no physiological data to demonstrate that any of the effects on hypothalamic gene expression are related to metabolic, synaptic, or other functions.

      The study focuses on investigating cellular responses and endocrine changes in the aging hypothalamus induced by 17α-estradiol, utilizing single-nucleus RNA sequencing (snRNA-seq) and a novel data mining methodology to analyze various neuron subtypes. It is important to note that this study does not mainly aim to explore the anti-aging effects. Consequently, we have revised the claim in the abstract from “the effects of 17α-estradiol in anti-aging in neurons” to “the effects of 17α-estradiol on aging neurons.” We observed that the lower overall metabolism and increased expression levels of cellular processes in the synapses align with findings previously reported regarding 17α-estradiol. To address the lack of physiological data and the challenges in measuring multiple endocrine factors due to their volatile nature, we employed several bidirectional Mendelian analyses of various genome-wide association study (GWAS) data related to these serum endocrine factors to identify their mutual causal effects.

      Reviewing Editor Comment:

      Based on the Public Reviews and Recommendations for Authors, the Reviewers strongly recommend that revisions include an experimental demonstration of the physiological effects of the treatment on ageing in rats as well as the CRH-senescence link. Additional analysis of the glia would greatly strengthen the study, as would inclusion of females and young male controls. The important point was also raised that the work linking 17a-estradiol was performed in mice, and the link with lifespan in rats is not known. Discussion of this point is recommended.

      We acknowledge that 17α-estradiol has been reported to extend lifespan in male rats, similar to findings in male mice (PMID: 33289482), and we have noted this in the Introduction. We apologize for not conducting further experiments to validate this point.

      Additionally, we have revised the description of the phenotype of senescent CRH neurons to “stressed phenotype” without carrying out further experiments to confirm the senescent phenotype. To provide more clarity on the performance of glial cells during treatment, we have included additional enrichment analysis data of differentially expressed genes among young (Y), old (O), and old treated (O.T) microglia and astrocytes in Figure 2—figure supplement 3. Notably, the behavior of microglia contrasts with that of total neurons concerning synapse-related cellular processes. We apologize for being unable to include female and young controls in this study.

      Reviewer #2 (Recommendations For The Authors)

      General comments:

      (1) The manuscript is very hard to read. Proofreading and editing by software or a professional seems necessary. The words "enhanced", "extensive" etc. are not always used in the right way.

      Thanks for the suggestion. We have revised the proofreading and editing. The words "enhanced" and "extensive" were also revised in most sentences.

      (2) The numbers of animals and samples are not well explained. Is it 9 rats overall or per group? If there are 8 testes samples per group, should we assume that there were 4 rats per group? The pooling of the hypothalamic how was it done? Were all the hypothalamic from each group pooled together? A small table with the animals per group and the samples would help.

      We appreciate your reminder regarding the initial mistake in our manuscript preparation. In the preliminary submission, we reported 9 rats based solely on sequencing data and data mining. The revised version (v1) now includes additional experimental data, with an effective total of 12 animals (4 per group). Unfortunately, we overlooked updating this information in the v1 submission. We have since added detailed information in the Materials and Methods sections: Animals, Treatment and Tissues, and snRNA-seq Data Processing, Batch Effect Correction, and Cell Subset Annotation.

      (3) The Clustering is wrong. There are genes in there that do not fall into any of the 3 categories: Neurotransmitters, Receptors, Hormones.

      We have changed the description to “Vast majority of these subtypes were clustered by neuropeptides, hormones, and their receptors within all the neurons”.

      (4) The coloring of groups in the graphs is inconsistent. It must be more homogeneous to make it easier to identify.

      We have changed the colors of groups in Fig. 1D to make the color of cell clusters consistent in Fig. 1A-D.

      (5) The groups c1-c4 are not well explained. How did the authors come up with these?

      We have added more descriptions of c1-c4 in materials and methods in the new version.

      (6) In most cases it's not clear if the authors are talking about cell numbers that express a certain mRNA, the level of expression of a certain mRNA, or both. They need to do a better job using more precise descriptions instead of using general terms such as "signatures", "expression profiles", "affected neurons" etc. It is very hard to understand if the number of neurons is compared between the groups or the gene expression.

      We have changed the "signatures" to "gene signatures" to make it more accurate in meaning. The "affected neurons" were also changed to "sensitive neurons". But sorry that we were not able to find better alternatives to the "expression profiles".

      (7) Sometimes there are claims made without justification or a reference. For example, the claim about the senescence of CRH neurons due to the upregulation of mitochondrial genes and downregulation of adherence junction genes (lines 326-328) should be supported by a reference or own findings.

      The "senescence" here is not appropriate. We have changed it to "stressed phenotype" or "aberrant changes" in abstract and results.

      (8) Young males treated with Estradiol as a control group is necessary and it is missing.

      Your suggestion is appreciated; however, the treatment duration for aged mice (O.T) was set at 6 months, while the young mice were only 4 months old. This disparity makes it challenging to align treatment timelines for the young animals. The primary aim of this study is to investigate the perturbation of 17α-estradiol on the aging process, and any distinct effects due to age effect observed in young males might complicate our understanding of its role in aged males, though similar endocrine effects may exist in the young animals. Long-term treatment of hormone may exert more developmental effects on the young than the old. Therefore, we made the decision to exclude the young samples in our initial study design. We apologize for any confusion this may have caused.

      Specific Comments:

      Line 28: "elevated stresses and decreased synaptic activity": Please make this clearer. Can't claim changes in synaptic activity by gene expression.

      We have changed it to "the expression level of pathways involved in synapse".

      Line 32: "increased Oxytocin": serum Oxytocin.

      We have added the “serum”.

      Line 52 - 54: Any studies from rats?

      Thanks. In rats there is also reported that 17α-estradiol has similar metabolic roles as that in mice (PMID: 33289482) and we have added it to the refences. It’s very useful for this manuscript.

      Line 62 - 65: It wasn't investigated thoroughly in this paper so why was it suggested in the introduction?

      We have deleted this sentence as being suggested.

      Line 70: "synaptic activity" Same as line 28.

      We have changed it to "pathways involved in synaptic activity".

      Line 79: Why were aged rats caged alone and young by two? Could that introduce hypothalamic gene expression effects?

      The young males were bred together in peace. But the aged males will fight and should be kept alone.

      Lines 78, 99, 109-110: It is not clear how many animals per group were used and how many samples per group were used separately and/or grouped. Please be more specific.

      We have added these information to Materials and methods/Animals, treatment and tissues and Materials and methods/snRNA-seq data processing, batch effect correction, and cell subset annotation.

      Line 205: "in O" please add "versus young.".

      We have changed accordingly.

      Line 207: replace "were" with "was" .

      We have alternatively changed the "proportion" to "proportions".

      Line 208: replace "that" with "compared to" and after "in O.T." add "compared to?"

      We have changed accordingly.

      Line 223: "O.T." compared to what? Figure?

      We have changed it accordingly.

      Line 227: Figure?

      We have added (Figure 1E) accordingly.

      Line 229: "synaptic activity" Same as line 28.

      We have revised it.

      Line 235: "synaptic activity" and "neuropeptide secretion" Same as line 28.

      We have revised it.

      Line 256:" interfered" please revise.

      We changed to "exerted".

      Line 263: "on the contrary" please revise.

      We have changed "on the contrary" to "opposite".

      Line 270: "conversed" did you mean "conserved"?

      We have changed "conversed" to "inversed".

      Line 296-298: Please explain. Why would these be side effects?

      It’s hard to explain, therefore, we deleted the words "side effects".

      Line 308: "synaptic activity" Same as line 28.

      We have changed it to "expression levels of synapse-related cellular processes".

      Line 314: "and sex hormone secretion and signaling"Isn't this expected?

      Yes, it is expected. We have added it to the sentence "and, as expected, sex hormone secretion and signaling".

      Line 325-328: Why is this senescence? Reference?

      We have added “potent” to it.

      Line 360-361: This doesn't show elevated synaptic activity.

      "elevated synaptic activity" was changed to "The elevated expression of synapse-related pathways"

      Line 363-364: "Unfortunately" is not a scientific expression and show bias.

      We have changed it to "Notably".

      Line 376: Similar as above.

      Yes, we have change it to "in contrast".

      Lines 382-385: This is speculation. Please move to discussion.

      Sorry for that. We think the causal effects derived from MR result is evidence. As such, we have not changed it.

      Line 389: Please revise "hormone expressing".

      We have changed it accordingly.

      Line 401: Isn't this effect expected due to feedback inhibition of the biochemical pathway? Please comment.

      The binding capability of 17alpha-estradiol to estrogen receptors and its role in transcriptional activation remain core questions surrounded by controversy. Earlier studies suggest that 17alpha-estradiol exhibits at least 200 times less activity than 17beta-estradiol (PMID: 2249627, PMID: 16024755). However, recent data indicate that 17alpha-estradiol shows comparable genomic binding and transcriptional activation through estrogen receptor α (Esr1) to that of 17beta-estradiol (PMID: 33289482). Additionally, there is evidence that 17alpha-estradiol has anti-estrogenic effects in rats (PMID: 16042770). These findings imply possible feedback inhibition via estrogen receptors. Furthermore, 17alpha-estradiol likely differs from 17beta-estradiol due to its unique metabolic consequences and its potential to slow aging in males, an effect not attributed to 17beta-estradiol. For instance, neurons are also targets of 17alpha-estradiol, with Esr1 not being the sole target (PMID: 38776045). Nevertheless, the precise effective targets of 17alpha-estradiol are still unresolved.

      Line 409: This conclusion cannot be made because the effect is not statistically significant. Can say "trend" etc.

      Thanks for the recommendation. We have added "potential" in front of the conclusion.

      Line 426: "suggesting" please revise.

      sorry, it’s a verb.

      Lines 426-428: This is speculation. Please move to discussion.

      The elevated GnRH levels in O.T., observed through EIA analysis, suggest a deduction regarding the direct causal effects of 17alpha-estradiol on various endocrine factors related to feeding, energy homeostasis, reproduction, osmotic regulation, stress response, and neuronal plasticity through MR analysis. Thus, we have not amended our position. We apologize for any confusion.

      Lines 431-432: improved compared to what?

      The statement have been revised as " The most striking role of 17α-estradiol treatment revealed in this study showed that HPG axis was substantially improved in the levels of serum Gnrh and testosterone".

      Line 435: " Estrogen Receptor Antagonists". Please revise.

      Thanks for the recommendation. We have changed it to "estrogen receptor antagonists".

      Line 438" "Secrete". Please revise.

      Sorry, it is "secret".

      Lines 439-449: None of this has been demonstrated. Please remove these conclusions.

      These are not conclusions but rather intriguing topics for discussion. Given the role of 17alpha-estradiol in promoting testosterone and reducing estradiol levels in males, we believe it is worthwhile to explore the potential application of 17alpha-estradiol in increasing testosterone levels in aged males, particularly those with hypogonadism.

      Lines 450-457: No females were included in this study. Why? Also, why is this discussed? It is relevant but doesn't belong in this manuscript since it was not studied here.

      Testosterone levels are crucial for male health, while estradiol levels are essential for the health and fertility of females. Previous studies have demonstrated that 17α-estradiol does not contribute to lifespan extension in females. Given the effects of 17α-estradiol on males—specifically, its role in promoting testosterone and reducing estradiol levels—we believe it is important to discuss the potential sex-biased effects of 17α-estradiol, as this could inform future investigations. Therefore, we have chosen not to make changes to this section.

      Lines 458-459: This was not demonstrated in this article. Please remove.

      We have restricted the claim to "expression level of energy metabolism in hypothalamic neurons".

      Line 464: "Promoted lifespan extension" Not demonstrated. Please remove.

      At the end of the sentence it was revised as "which may be a contributing factor in promoting lifespan extension".

      Line 466: "Showed" No.

      The whole sentence was deleted in the new version.

      Line 483: "the sex-based effects". Not studied here.

      Since the changes in testosterone levels are significant in this dataset and this hormone has a sex-biased nature, we find it worthwhile to suggest this as a topic for future investigation. We have added "which needs further verification in the future" at the end of this sentence.

    1. eLife Assessment

      This valuable study suggests that Naa10, an N-α-acetyltransferase with known mutations that disrupt neurodevelopment, acetylates Btbd3, which has been implicated in neurite outgrowth and obsessive-compulsive disorder, in a manner that regulates F-actin dynamics to facilitate neurite outgrowth. While the study provides promising insights and biochemical, co-immunoprecipitation, and proteomic data that enhance our understanding of protein N-acetylation in neuronal development, the evidence supporting larger claims is incomplete. Nonetheless, the implications of these findings are noteworthy, particularly regarding neurodevelopmental and psychiatric conditions tied to altered expression of Naa10 or Btbd3.

    2. Reviewer #1 (Public review):

      The manuscript examines the role of Naa10 in cKO animals, in immortalized neurons, and in primary neurons. Given that Naa10 mutations in humans produce defects in nervous system function, the authors used various strategies to try to find a relevant neuronal phenotype and its potential molecular mechanism.

      This work contains valuable findings that suggest that the depletion of Naa10 from CA1 neurons in mice exacerbates anxiety-like behaviors. Using neuronal-derived cell lines authors establish a link between N-acetylase activity, Btbd3 binding to CapZb, and F-actin, ultimately impinging on neurite extension. The evidence demonstrating this is in most cases incomplete, since some key controls are missing and clearly described or simply because claims are not supported by the data. The manuscript also contains biochemical, co-immunoprecipitation, and proteomic data that will certainly be of value to our knowledge of the effects of protein N--acetylation in neuronal development and function.

    3. Reviewer #2 (Public review):

      In this study, the authors sought to elucidate the neural mechanisms underlying the role of Naa10 in neurodevelopmental disruptions with a focus on its role in the hippocampus. The authors use an impressive array of techniques to identify a chain of events that occurs in the signaling pathway starting from Naa10 acetylating Btbd3 to regulation of F-actin dynamics that are fundamental to neurite outgrowth. They provide convincing evidence that Naa10 acetylates Btbd3, that Btbd3 facilitates CapZb binding to F-actin in a Naa10 acetylation-dependent manner, and that this CapZb binding to F-actin is key to neurite outgrowth. Besides establishing this signaling pathway, the authors contribute novel lists of Naa10 and Btbd3 interacting partners, which will be useful for future investigations into other mechanisms of action of Naa10 or Btbd3 through alternative cell signaling pathways. The evidence presented for an anxiety-like behavioral phenotype as a result of Naa10 dysfunction is mixed and tenuous, and assays for the primary behaviors known to be altered by Naa10 mutations in humans were not tested. As such, behavioral findings and their translational implications should be interpreted with caution. Finally, while not central to the main cell signaling pathway delineated, the characterization of brain region-specific and cell maturity of Naa10 expression patterns was presented in few to single animals and not quantified, and as such should also be interpreted with caution. On a broader level, these findings have implications for neurodevelopment and potentially, although not tested here, synaptic plasticity in adulthood, which means this novel pathway may be fundamental for brain health.

      Summarized list of minor concerns

      (1) The early claims of the manuscript are supported by very small sample sizes (often 1-3) and/or lack of quantification, particularly in Figures S1 and 1.

      (2) Evidence is insufficient for CA1-specific knockdown of Naa10.

      (3) The relationship between the behaviors measured, which centered around mood, and Ogden syndrome, was not clear, and likely other behavioral measures would be more translationally relevant for this study. Furthermore, the evidence for an anxiety-like phenotype was mixed.

      (4) Btbd3 is characterized by the authors as an OCD risk gene, but its status as such is not well supported by the most recent, better-powered genome-wide association studies than the one that originally implicated Btbd3. However, there is evidence that Btbd3 expression, including selectively in the hippocampus, is implicated in OCD-relevant behaviors in mice.

      (5) The reporting of the statistics lacks sufficient detail for the reader to deduce how experimental replicates were defined.

    4. Author response:

      eLife Assessment<br /> This valuable study suggests that Naa10, an N-α-acetyltransferase with known mutations that disrupt neurodevelopment, acetylates Btbd3, which has been implicated in neurite outgrowth and obsessive-compulsive disorder, in a manner that regulates F-actin dynamics to facilitate neurite outgrowth. While the study provides promising insights and biochemical, co-immunoprecipitation, and proteomic data that enhance our understanding of protein N-acetylation in neuronal development, the evidence supporting larger claims is incomplete. Nonetheless, the implications of these findings are noteworthy, particularly regarding neurodevelopmental and psychiatric conditions tied to altered expression of Naa10 or Btbd3.

      Thank you very much for recognizing our study, carefully reviewing our work, and providing insightful comments and constructive criticism!

      Public Reviews:

      Reviewer #1 (Public review):

      The manuscript examines the role of Naa10 in cKO animals, in immortalized neurons, and in primary neurons. Given that Naa10 mutations in humans produce defects in nervous system function, the authors used various strategies to try to find a relevant neuronal phenotype and its potential molecular mechanism.

      This work contains valuable findings that suggest that the depletion of Naa10 from CA1 neurons in mice exacerbates anxiety-like behaviors. Using neuronal-derived cell lines authors establish a link between N-acetylase activity, Btbd3 binding to CapZb, and F-actin, ultimately impinging on neurite extension. The evidence demonstrating this is in most cases incomplete, since some key controls are missing and clearly described or simply because claims are not supported by the data. The manuscript also contains biochemical, co-immunoprecipitation, and proteomic data that will certainly be of value to our knowledge of the effects of protein N--acetylation in neuronal development and function.

      Thanks! It would be appreciated if the Reviewer could point out in the public review which experiment lacks a control group.

      Reviewer #2 (Public review):

      In this study, the authors sought to elucidate the neural mechanisms underlying the role of Naa10 in neurodevelopmental disruptions with a focus on its role in the hippocampus. The authors use an impressive array of techniques to identify a chain of events that occurs in the signaling pathway starting from Naa10 acetylating Btbd3 to regulation of F-actin dynamics that are fundamental to neurite outgrowth. They provide convincing evidence that Naa10 acetylates Btbd3, that Btbd3 facilitates CapZb binding to F-actin in a Naa10 acetylation-dependent manner, and that this CapZb binding to F-actin is key to neurite outgrowth. Besides establishing this signaling pathway, the authors contribute novel lists of Naa10 and Btbd3 interacting partners, which will be useful for future investigations into other mechanisms of action of Naa10 or Btbd3 through alternative cell signaling pathways.

      Thank you very much for recognizing our study!

      The evidence presented for an anxiety-like behavioral phenotype as a result of Naa10 dysfunction is mixed and tenuous, and assays for the primary behaviors known to be altered by Naa10 mutations in humans were not tested. As such, behavioral findings and their translational implications should be interpreted with caution.

      (1) For the anxiety-like behavioral phenotype, we provided a paragraph titled “Naa10 and stress-induced anxiety” in the Discussion section of the text: “Our investigations revealed that hippocampal CA1-KO of Naa10 did not exhibit significant differences in the open field test (Figure S1K) but led to anxiety-like behavior in mice in the elevated plus maze (EPM) test (Figure 1A). This disparity might be attributed to the specific design of the EPM test, which is tailored to elicit a conflict between an animal's inclination to explore and its fear of open spaces and elevated areas. This distinction implies that Naa10 might play a role in stress responses within the emotional regulation circuitry, particularly in navigating potentially threatening and anxiety-provoking environments.” The open field test offers a less challenging, open environment that primarily promotes exploratory behavior. We agree that additional assays, such as the light-dark box test, would be helpful in clarifying the issue.

      (2) We agree that the behavioral findings and their translational implications should be interpreted with caution. The primary neurological behaviors known to be altered by Naa10 mutations in humans include intellectual disability and autism-like syndrome with defective emotional control. These behaviors are influenced by many factors, including defects in the hippocampal CA1. Thus, we tested hippocampal CA1 Naa10-KO mice using the Y-maze, tail suspension test, open field test, and elevated plus maze (EPM). However, only the EPM results were affected, while the other tests showed no significant changes. It should be noted that our study employed a postnatal, CA1-specific Naa10 conditional knockout (cKO) model driven by Camk2a-Cre, which selectively depletes Naa10 from hippocampal CA1 neurons after birth. In contrast, Naa10 mutations in human patients involve global effects and impact multiple brain regions from the embryonic stage, leading to a broader spectrum of phenotypes. The limited disruption in our model likely explains the absence of learning and memory deficits and the incomplete recapitulation of the full range of patient phenotypes. Furthermore, Naa10 knockout may not produce the same effects as Naa10 mutations. Our current study is primarily intended to explore the physiological function of Naa10 in hippocampal function.

      (3) We will replace all instances of “anxiety behavior” with “anxiety-like behavior.”

      Finally, while not central to the main cell signaling pathway delineated, the characterization of brain region-specific and cell maturity of Naa10 expression patterns was presented in few to single animals and not quantified, and as such should also be interpreted with caution.

      We agree that we should provide additional Naa10 immunostaining data from more than three WT and hippocampal CA1 Naa10-KO mouse brains, as well as quantify data such as the silver staining and Light Sheet Fluorescence Microscopy results presented in Figures 1C and 1D, respectively. Nevertheless, the current report presents consistent results across different mice used for various assays. For example, Figures 1B-D, with three different assays, each demonstrate that Naa10-cKO reduces neurite complexity in vivo.

      On a broader level, these findings have implications for neurodevelopment and potentially, although not tested here, synaptic plasticity in adulthood, which means this novel pathway may be fundamental for brain health.

      Thank you very much again for recognizing our study!

      Summarized list of minor concerns

      (1) The early claims of the manuscript are supported by very small sample sizes (often 1-3) and/or lack of quantification, particularly in Figures S1 and 1.

      We agree that we should provide additional Naa10 immunostaining data from more than three WT and hippocampal CA1 Naa10-KO mouse brains, as well as quantify data such as the silver staining and Light Sheet Fluorescence Microscopy results presented in Figures 1C and 1D, respectively. Nevertheless, the current report presents consistent results across different mice used for various assays. For example, Figures 1B-D, with three different assays, each demonstrate that Naa10-cKO reduces neurite complexity in vivo.

      (2) Evidence is insufficient for CA1-specific knockdown of Naa10.

      The Camk2a-Cre mice used in this study were derived from Dr. Susumu Tonegawa’s laboratory. According to the referenced paper, this strain restricts Cre/loxP recombination to the forebrain, with particularly high efficiency in the hippocampal CA1. Consistently, our data show that Naa10 was almost completely absent in the CA1 but partially depleted in the DG of the Naa10-cKO mice (Figure S1F in the text). Similar results were observed in a different pair of

      (3) The relationship between the behaviors measured, which centered around mood, and Ogden syndrome, was not clear, and likely other behavioral measures would be more translationally relevant for this study. Furthermore, the evidence for an anxiety-like phenotype was mixed.

      (1) For the anxiety-like behavioral phenotype, we provided a paragraph titled “Naa10 and stress-induced anxiety” in the Discussion section of the text: “Our investigations revealed that hippocampal CA1-KO of Naa10 did not exhibit significant differences in the open field test (Figure S1K) but led to anxiety-like behavior in mice in the elevated plus maze (EPM) test (Figure 1A). This disparity might be attributed to the specific design of the EPM test, which is tailored to elicit a conflict between an animal's inclination to explore and its fear of open spaces and elevated areas. This distinction implies that Naa10 might play a role in stress responses within the emotional regulation circuitry, particularly in navigating potentially threatening and anxiety-provoking environments.” The open field test offers a less challenging, open environment that primarily promotes exploratory behavior. We agree that additional assays, such as the light-dark box test, would be helpful in clarifying the issue.

      (2) We agree that the behavioral findings and their translational implications should be interpreted with caution. The primary neurological behaviors known to be altered by Naa10 mutations in humans include intellectual disability and autism-like syndrome with defective emotional control. These behaviors are influenced by many factors, including defects in the hippocampal CA1. Thus, we tested hippocampal CA1 Naa10-KO mice using the Y-maze, tail suspension test, open field test, and elevated plus maze (EPM). However, only the EPM results were affected, while the other tests showed no significant changes. It should be noted that our study employed a postnatal, CA1-specific Naa10 conditional knockout (cKO) model driven by Camk2a-Cre, which selectively depletes Naa10 from hippocampal CA1 neurons after birth. In contrast, Naa10 mutations in human patients involve global effects and impact multiple brain regions from the embryonic stage, leading to a broader spectrum of phenotypes. The limited disruption in our model likely explains the absence of learning and memory deficits and the incomplete recapitulation of the full range of patient phenotypes. Furthermore, Naa10 knockout may not produce the same effects as Naa10 mutations. Our current study is primarily intended to explore the physiological function of Naa10 in hippocampal function.

      (3) We will replace all instances of “anxiety behavior” with “anxiety-like behavior.”

      (4) Btbd3 is characterized by the authors as an OCD risk gene, but its status as such is not well supported by the most recent, better-powered genome-wide association studies than the one that originally implicated Btbd3. However, there is evidence that Btbd3 expression, including selectively in the hippocampus, is implicated in OCD-relevant behaviors in mice.

      Thanks for clarifying the issue!

      (5) The reporting of the statistics lacks sufficient detail for the reader to deduce how experimental replicates were defined.

      We believe we have provided sufficient detail for readers to deduce how experimental replicates were defined in each corresponding figure legend. It would be appreciated if the Reviewer could point out which specific figures lack sufficient details.

    1. eLife Assessment

      This study uncovers and characterizes a role for Pfdn5 in stabilizing axonal microtubules and synaptic morphology in the Drosophila peripheral nervous system. Although the mechanisms remain unresolved, the phenotypic characterization is an important contribution with solid evidence. The work also aims to address a potential interaction between Pfdn5/6 and Tau-mediated mechanisms of neurodegeneration; here, the evidence is partially incomplete.

    2. Reviewer #1 (Public review):

      Summary:

      In this manuscript, Bisht et al address the hypothesis that protein folding chaperones may be implicated in aggregopathies and in particular Tau aggregation, as a means to identify novel therapeutic routes for these largely neurodegenerative conditions.

      The authors conducted a genetic screen in the Drosophila eye, which facilitates the identification of mutations that either enhance or suppress a visible disturbance in the nearly crystalline organization of the compound eye. They screened by RNA interference all 64 known Drosophila chaperones and revealed that mutations in 20 of them exaggerate the Tau-dependent phenotype, while 15 ameliorated it. The enhancer of the degeneration group included 2 subunits of the typically heterohexameric prefoldin complex and other co-translational chaperones.

      The authors characterized in depth one of the prefoldin subunits, Pfdn5, and convincingly demonstrated that this protein functions in the regulation of microtubule organization, likely due to its regulation of proper folding of tubulin monomers. They demonstrate convincingly using both immunohistochemistry in larval motor neurons and microtubule binding assays that Pfdn5 is a bona fide microtubule-associated protein contributing to the stability of the axonal microtubule cytoskeleton, which is significantly disrupted in the mutants.

      Similar phenotypes were observed in larvae expressing Frontotemporal dementia with Parkinsonism on chromosome 17-associated mutations of the human Tau gene V377M and R406W. On the strength of the phenotypic evidence and the enhancement of the TauV377M-induced eye degeneration, they demonstrate that loss of Pfdn5 exaggerates the synaptic deficits upon expression of the Tau mutants. Conversely, the overexpression of Pfdn5 or Pfdn6 ameliorates the synaptic phenotypes in the larvae, the vacuolization phenotypes in the adult, and even memory defects upon TauV377M expression.

      Strengths:

      The phenotypic analyses of the mutant and its interactions with TauV377M at the cell biological, histological, and behavioral levels are precise, extensive, and convincing and achieve the aims of characterization of a novel function of Pfdn5.

      Regarding this memory defect upon V377M tau expression. Kosmidis et al (2010) pmid: 20071510, demonstrated that pan-neuronal expression of TauV377M disrupts the organization of the mushroom bodies, the seat of long-term memory in odor/shock and odor/reward conditioning. If the novel memory assay the authors use depends on the adult brain structures, then the memory deficit can be explained in this manner.

      If the mushroom bodies are defective upon TauV377M expression does overexpression of Pfdn5 or 6 reverse this deficit? This would argue strongly in favor of the microtubule stabilization explanation.

      The discovery that Pfdn5 (and 6 most likely) affect tauV377M toxicity is indeed a novel and important discovery for the Tauopathies field. It is important to determine whether this interaction affects only the FTDP-17-linked mutations, or also WT Tau isoforms, which are linked to the rest of the Tauopathies. Also, insights on the mode(s) that Pfdn5/6 affect Tau toxicity, such as some of the suggestions above are aiming at, will likely be helpful towards therapeutic interventions.

      Weaknesses:

      What is unclear however is how Pfdn5 loss or even overexpression affects the pathological Tau phenotypes.

      Does Pfdn5 (or 6) interact directly with TauV377M? Colocalization within tissues is a start, but immunoprecipitations would provide additional independent evidence that this is so.

      Does Pfdn5 loss exacerbate TauV377M phenotypes because it destabilizes microtubules, which are already at least partially destabilized by Tau expression?<br /> Rescue of the phenotypes by overexpression of Pfdn5 agrees with this notion.

      However, Cowan et al (2010) pmid: 20617325 demonstrated that wild-type Tau accumulation in larval motor neurons indeed destabilizes microtubules in a Tau phosphorylation-dependent manner.

      So, is TauV377M hyperphosphorylated in the larvae?? What happens to TauV377M phosphorylation when Pfdn5 is missing and presumably more Tau is soluble and subject to hyperphosphorylation as predicted by the above?

      Expression of WT human Tau (which is associated with most common Tauopathies other than FTDP-17) as Cowan et al suggest has significant effects on microtubule stability, but such Tau-expressing larvae are largely viable. Will one mutant copy of the Pfdn5 knockout enhance the phenotype of these larvae?? Will it result in lethality? Such data will serve to generalize the effects of Pfdn5 beyond the two FDTP-17 mutations utilized.

      Does the loss of Pfdn5 affect TauV377M (and WTTau) levels?? Could the loss of Pfdn5 simply result in increased Tau levels? And conversely, does overexpression of Pfdn5 or 6 reduce Tau levels?? This would explain the enhancement and suppression of TauV377M (and possibly WT Tau) phenotypes. It is an easily addressed, trivial explanation at the observational level, which if true begs for a distinct mechanistic approach.

      Finally, the authors argue that TauV377M forms aggregates in the larval brain based on large puncta observed especially upon loss of Pfdn5. This may be so, but protocols are available to validate this molecularly the presence of insoluble Tau aggregates (for example, pmid: 36868851) or soluble Tau oligomers as these apparently differentially affect Tau toxicity. Does Pfdn5 loss exaggerate the toxic oligomers and overexpression promotes the more benign large aggregates??

    3. Reviewer #2 (Public review):

      Bisht et al detail a novel interaction between the chaperone, Prefoldin 5, microtubules, and tau-mediated neurodegeneration, with potential relevance for Alzheimer's disease and other tauopathies. Using Drosophila, the study shows that Pfdn5 is a microtubule-associated protein, which regulates tubulin monomer levels and can stabilize microtubule filaments in the axons of peripheral nerves. The work further suggests that Pfdn5/6 may antagonize Tau aggregation and neurotoxicity. While the overall findings may be of interest to those investigating the axonal and synaptic cytoskeleton, the detailed mechanisms for the observed phenotypes remain unresolved and the translational relevance for tauopathy pathogenesis is yet to be established. Further, a number of key controls and important experiments are missing that are needed to fully interpret the findings.

      The strength of this study is the data showing that Pfdn5 localizes to axonal microtubules and the loss-of-function phenotypic analysis revealing disrupted synaptic bouton morphology. The major weakness relates to the experiments and claims of interactions with Tau-mediated neurodegeneration. In particular, it is unclear whether knockdown of Pfdn5 may cause eye phenotypes independent of Tau. Further, the GMR>tau phenotype appears to have been incorrectly utilized to examine age-dependent, neurodegeneration.

      This manuscript argues that its findings may be relevant to thinking about mechanisms and therapies applicable to tauopathies; however, this is premature given that many questions remain about the interactions from Drosophila, the detailed mechanisms remain unresolved, and absent evidence that tau and Pfdn may similarly interact in the mammalian neuronal context. Therefore, this work would be strongly enhanced by experiments in human or murine neuronal culture or supportive evidence from analyses of human data.

    4. Author response:

      Reviewer #1:

      Summary:<br /> In this manuscript, Bisht et al address the hypothesis that protein folding chaperones may be implicated in aggregopathies and in particular Tau aggregation, as a means to identify novel therapeutic routes for these largely neurodegenerative conditions.

      The authors conducted a genetic screen in the Drosophila eye, which facilitates the identification of mutations that either enhance or suppress a visible disturbance in the nearly crystalline organization of the compound eye. They screened by RNA interference all 64 known Drosophila chaperones and revealed that mutations in 20 of them exaggerate the Tau-dependent phenotype, while 15 ameliorated it. The enhancer of the degeneration group included 2 subunits of the typically heterohexameric prefoldin complex and other co-translational chaperones.

      In a previous paper, we identified 95 Drosophila chaperones (Raut et al., 2017). We request that “all 64 known Drosophila chaperones” be replaced with “64 out of 95 known Drosophila chaperones” to make it factually correct.

      Strengths:

      Regarding this memory defect upon V377M tau expression. Kosmidis et al (2010) pmid: 20071510, demonstrated that pan-neuronal expression of TauV377M disrupts the organization of the mushroom bodies, the seat of long-term memory in odor/shock and odor/reward conditioning. If the novel memory assay the authors use depends on the adult brain structures, then the memory deficit can be explained in this manner.

      If the mushroom bodies are defective upon TauV377M expression does overexpression of Pfdn5 or 6 reverse this deficit? This would argue strongly in favor of the microtubule stabilization explanation.

      We agree that the disruptive organization of the mushroom body may cause memory deficits upon hTauV337M expression and that expression of Pfdn5 or Pfdn6 could reverse the deficits. One possible mechanism by which overexpression of Pfdn5/6 could rescue the Tau-induced memory deficits may be due to the stabilization of microtubules in the mushroom bodies.

      Proposed revision: We will assess if Tau-induced mushroom body disruption can be rescued with the overexpression of Pfdn5 or Pfdn6.

      Weakness:

      What is unclear however is how Pfdn5 loss or even overexpression affects the pathological Tau phenotypes. Does Pfdn5 (or 6) interact directly with TauV377M? Colocalization within tissues is a start, but immunoprecipitations would provide additional independent evidence that this is so.

      Our data suggests that Pfdn5 stabilizes neuronal microtubules by directly associating with it, and loss of Pfdn5 exacerbates Tau-phenotypes by destabilizing microtubules. However, as the reviewer notes, analysis of direct interaction between Pfdn5 and hTau<sup>V337M</sup> might provide further insights into the mechanism of Pfdn5 and Tau-aggregation.

      Proposed revision: We will perform colocalization analysis and coimmunoprecipitation to ask if Pfdn5 colocalizes and directly interacts with Tau.

      Does Pfdn5 loss exacerbate TauV377M phenotypes because it destabilizes microtubules, which are already at least partially destabilized by Tau expression? Rescue of the phenotypes by overexpression of Pfdn5 agrees with this notion.

      However, Cowan et al (2010) pmid: 20617325 demonstrated that wild-type Tau accumulation in larval motor neurons indeed destabilizes microtubules in a Tau phosphorylation-dependent manner. So, is TauV377M hyperphosphorylated in the larvae?? What happens to TauV377M phosphorylation when Pfdn5 is missing and presumably more Tau is soluble and subject to hyperphosphorylation as predicted by the above?

      Proposed revisions: We will overexpress Pfdn5 or Pfdn6 with hTau<sup>V337M</sup> and ask if microtubule disruption caused by hTau<sup>V337M</sup> is rescued. Further, we will analyze the phospho-Tau levels in controls and Pfdn5 mutant background.

      Expression of WT human Tau (which is associated with most common Tauopathies other than FTDP-17) as Cowan et al suggest has significant effects on microtubule stability, but such Tau-expressing larvae are largely viable. Will one mutant copy of the Pfdn5 knockout enhance the phenotype of these larvae?? Will it result in lethality? Such data will serve to generalize the effects of Pfdn5 beyond the two FDTP-17 mutations utilized.

      Proposed revision: We will incorporate data about the effect of heterozygous mutation of Pfdn5 on the lethality and synaptic phenotypes associated with the hTau<sup>WT</sup> and hTau<sup>V337M</sup> in the revised manuscript.

      Does the loss of Pfdn5 affect TauV377M (and WTTau) levels?? Could the loss of Pfdn5 simply result in increased Tau levels? And conversely, does overexpression of Pfdn5 or 6 reduce Tau levels?? This would explain the enhancement and suppression of TauV377M (and possibly WT Tau) phenotypes. It is an easily addressed, trivial explanation at the observational level, which if true begs for a distinct mechanistic approach.

      We thank the reviewer for suggesting an alternate model for the Pfdn5 function. We will perform the Western blot analysis to assess Tau<sup>WT</sup> and Tau<sup>V337M</sup> levels in the absence of Pfdn5 or animals coexpressing Tau and Pfdn5. We will incorporate these data and conclusions in the revised manuscript.

      Finally, the authors argue that TauV377M forms aggregates in the larval brain based on large puncta observed especially upon loss of Pfdn5. This may be so, but protocols are available to validate this molecularly the presence of insoluble Tau aggregates (for example, pmid: 36868851) or soluble Tau oligomers as these apparently differentially affect Tau toxicity. Does Pfdn5 loss exaggerate the toxic oligomers and overexpression promotes the more benign large aggregates??

      We will perform the Tau solubility assay in control, in the absence of Pfdn5 or animals coexpressing Tau and Pfdn5. Moreover, we will also ask if the large Tau puncta formed in the absence of Pfdn5 are soluble oligomers or stable aggregates. We have found that the coexpression of Tau and Pfdn5 does not result in the formation of  Tau aggregates. We will incorporate these and other relevant data in the revised manuscript.

      Reviewer #2 (Public review):

      Bisht et al detail a novel interaction between the chaperone, Prefoldin 5, microtubules, and tau-mediated neurodegeneration, with potential relevance for Alzheimer's disease and other tauopathies. Using Drosophila, the study shows that Pfdn5 is a microtubule-associated protein, which regulates tubulin monomer levels and can stabilize microtubule filaments in the axons of peripheral nerves. The work further suggests that Pfdn5/6 may antagonize Tau aggregation and neurotoxicity. While the overall findings may be of interest to those investigating the axonal and synaptic cytoskeleton, the detailed mechanisms for the observed phenotypes remain unresolved and the translational relevance for tauopathy pathogenesis is yet to be established. Further, a number of key controls and important experiments are missing that are needed to fully interpret the findings.The major weakness relates to the experiments and claims of interactions with Tau-mediated neurodegeneration. In particular, it is unclear whether knockdown of Pfdn5 may cause eye phenotypes independent of Tau. Further, the GMR>tau phenotype appears to have been incorrectly utilized to examine age-dependent, neurodegeneration.

      We have consistently found the progression of eye degeneration in the population of animals expressing Tau<sup>V337M</sup>, measured as the number of fused ommatidia/total number of ommatidia, with age. A few other studies have also shown age-dependent progressive degeneration in Drosophila retinal axons or lamina (Iijima-Ando et al., 2012; Sakakibara et al., 2018). We appreciate other studies that have proposed hTau-induced eye degeneration as a developmental defect (Malmanche et al., 2017; Sakakibara et al., 2023).

      Proposed revision: a) We will analyze the age-dependent neurodegeneration in the adult brain to further support our main conclusion that Pfdn5 ameliorates hTauV337M-induced progressive neurodegeneration.

      b) We have used three independent Pfdn5 RNAi lines (the RNAi's target different regions of Pfdn5) – all of which enhance the Tau phenotypes. The knockdown of any of these RNAi lines with GMR-Gal4 does not give detectable eye phenotypes. We will include these data in the revised manuscript.

      This manuscript argues that its findings may be relevant to thinking about mechanisms and therapies applicable to tauopathies; however, this is premature given that many questions remain about the interactions from Drosophila, the detailed mechanisms remain unresolved, and absent evidence that tau and Pfdn may similarly interact in the mammalian neuronal context. Therefore, this work would be strongly enhanced by experiments in human or murine neuronal culture or supportive evidence from analyses of human data.

      Proteome analysis of Alzheimer's brain tissue shows that the Pfdn5 level is reduced in patients (Askenazi et al., 2023; Tao et al., 2020). Moreover, the Pfdn5 expression level was found to be reduced in the blood samples from AD patients (Ji et al., 2022). Another study further validates the age-dependent reduction of Pfdn5 in the tauopathy transgenic murine model (Kadoyama et al., 2019). Together, these reports highlight a potential link between Pfdn5 levels and tauopathies. We will revise the manuscript to reflect these findings in more detail.

      References

      Askenazi, M., Kavanagh, T., Pires, G., Ueberheide, B., Wisniewski, T., and Drummond, E. (2023). Compilation of reported protein changes in the brain in Alzheimer's disease. Nat Commun 14, 4466. 10.1038/s41467-023-40208-x.

      Iijima-Ando, K., Sekiya, M., Maruko-Otake, A., Ohtake, Y., Suzuki, E., Lu, B., and Iijima, K.M. (2012). Loss of axonal mitochondria promotes tau-mediated neurodegeneration and Alzheimer's disease-related tau phosphorylation via PAR-1. PLoS Genet 8, e1002918. 10.1371/journal.pgen.1002918.

      Ji, W., An, K., Wang, C., and Wang, S. (2022). Bioinformatics analysis of diagnostic biomarkers for Alzheimer's disease in peripheral blood based on sex differences and support vector machine algorithm. Hereditas 159, 38. 10.1186/s41065-022-00252-x.

      Kadoyama, K., Matsuura, K., Takano, M., Maekura, K., Inoue, Y., and Matsuyama, S. (2019). Changes in the expression of prefoldin subunit 5 depending on synaptic plasticity in the mouse hippocampus. Neurosci Lett 712, 134484. 10.1016/j.neulet.2019.134484.

      Malmanche, N., Dourlen, P., Gistelinck, M., Demiautte, F., Link, N., Dupont, C., Vanden Broeck, L., Werkmeister, E., Amouyel, P., Bongiovanni, A., et al. (2017). Developmental Expression of 4-Repeat-Tau Induces Neuronal Aneuploidy in Drosophila Tauopathy Models. Sci Rep 7, 40764. 10.1038/srep40764.

      Raut, S., Mallik, B., Parichha, A., Amrutha, V., Sahi, C., and Kumar, V. (2017). RNAi-Mediated Reverse Genetic Screen Identified Drosophila Chaperones Regulating Eye and Neuromuscular Junction Morphology. G3 (Bethesda) 7, 2023-2038. 10.1534/g3.117.041632.

      Sakakibara, Y., Sekiya, M., Fujisaki, N., Quan, X., and Iijima, K.M. (2018). Knockdown of wfs1, a fly homolog of Wolfram syndrome 1, in the nervous system increases susceptibility to age- and stress-induced neuronal dysfunction and degeneration in Drosophila. PLoS Genet 14, e1007196. 10.1371/journal.pgen.1007196.

      Sakakibara, Y., Yamashiro, R., Chikamatsu, S., Hirota, Y., Tsubokawa, Y., Nishijima, R., Takei, K., Sekiya, M., and Iijima, K.M. (2023). Drosophila Toll-9 is induced by aging and neurodegeneration to modulate stress signaling and its deficiency exacerbates tau-mediated neurodegeneration. iScience 26, 105968. 10.1016/j.isci.2023.105968.

      Tao, Y., Han, Y., Yu, L., Wang, Q., Leng, S.X., and Zhang, H. (2020). The Predicted Key Molecules, Functions, and Pathways That Bridge Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD). Front Neurol 11, 233. 10.3389/fneur.2020.00233.

    1. eLife Assessment

      This valuable study explores the role of spatial genome organization in oncogenic transformation, addressing an ambitious and significant topic. The authors have assembled comprehensive datasets from various subtypes of localized and lung-metastatic breast cancer cells, as well as from healthy and cancerous lung cells. They identified switching patterns in the 3D genome organization of lung-metastatic breast cancer cells, revealing a reconfiguration of genome architecture that resembles that of lung cells. If validated, this study could be critical for the field; however, at this stage, it is incomplete, as the main claims are only partially substantiated.

    2. Reviewer #1 (Public review):

      Summary:

      This study utilized publicly available Hi-C data to ensemble a comprehensive set of breast cancer cell lines (luminal, Her2+, TNBC) with varying metastatic features to answer whether breast cancer cells would acquire organ-specific features at the 3D genome level to metastasize to that specific organ. The authors focused on lung metastasis and included several controls as the comparison including normal mammary lines, normal lung epithelial lines, and lung cancer cell lines. Due to the lower resolution at 250KB binning size, the authors only addressed the compartments (A for active compartment and B for inactive compartment) not the other 3D organization of the genome. They started by performing clustering and PCA analysis for the compartment identity and discovered that this panel of cell lines could be well separated based on Her2 and epithelial-mesenchymal features according to the compartment identity. While correlating with the transcriptomic changes, the authors noticed the existence of concordance and divergence between the compartment changes and transcriptomic changes. The authors then switched gears to tackle the core question of metastatic organotropism to the lung. They discovered a set of "lung permissive compartment changes" and concluded that "lung metastatic breast cancer cell lines acquire lung-like genome architecture" and "organotropic 3D genome changes match target organ more than an unrelated organ". To prove the latter point, the authors enlisted an additional non-breast cancer cell line (prostate cancer) in the setting of brain metastasis. This is a piece of pure dry computational work without wet bench experiments.

      Strengths:

      The authors embarked on an ambitious journey to seek the answer regarding 3D genome changes predisposing to metastatic organotropism. The authors succeeded in the assembly of a comprehensive panel of breast cancer cell lines and the aggregation of the 3D genome structure data to conduct a hypothesis-driven computation analysis. The authors also achieved in including proper controls representing normal non-cancerous epithelium and the end organ of interest. The authors did well in the citation of relevant references in 3D genome organization and EMT.

      Weaknesses:

      (1) The authors should clearly indicate how they determine the patterns of spread of the breast cancer cell lines being utilized in this manuscript. How did the authors arrive at the conclusion that certain cell lines would be determined as "localized spread" and "metastatic tropism to the lung"? This definition is crucial, and I will explain why.

      Todd Golub's team from the Broad Institute of MIT and Harvard published "A metastasis map of human cancer cell lines" to exhaustively create a first-generation metastasis map (MetMap) that reveals organ-specific patterns of metastasis. (By the way, this work was not cited in the reference in this manuscript.) The MetMap Explorer (https://depmap.org/metmap/vis-app/index.html) is a public resource that could be openly accessed to visualize the metastatic potential of each cell line as determined by the in vivo barcoding approach as described in the MetMap paper in the format of petal plots. 5 organs were tested in the MetMap paper, including brain, lung, liver, kidney, and bone. The authors would discover that some of the organ-specific metastasis patterns defined in the MetMap Explorer would be different from the authors' classification. For example, the authors defined MCF7 as a line as lung metastatic, and rightly so the MetMap charted a signal towards lung with low penetrance and low metastatic potential. The authors defined ZR751 as a line with localized spread, however, the MetMap charted a signal towards the kidney with low penetrance and low metastatic potential, the signal strength similar to the lung metastasis in MCF7. A similar argument could be made for T47D. The TNBC line MDA-MB-231 is indeed highly metastatic, however, in MetMap data, its metastasis is not only specific to the lung but towards all 5 organs with high penetrance and metastatic potential. The 2 lung cancer cell lines mentioned in this study, A549 and H460, the authors defined them as localized spread to the lung. However, the MetMap data clearly indicated that A549 and H460 are highly metastatic to all 5 organs with high penetrance and high metastatic potential.

      Since results will vary among different experimental models testing metastatic organotropism, (intra-cardiac injection was the metastasis model being adopted in the MetMap), the authors should state more clearly which experimental model system served as the basis for their definition of organ-specific metastasis. In my opinion, this is the most crucial first step for this entire study to be sound and solid.

      (2) Figure 1b: The authors found that "MDA-MB-231 cells were grouped with the lung carcinoma cells. This implies that the genome organization of this cell line is closer to that of lung cells than to other breast epithelial cell lines.". In fact, another TNBC line BT549 was also clustered under the same clade. So this clade consisted of normal-like and highly metastatic lines. Therefore, the authors should be mindful of the fact that the compartment features might not directly link to metastasis (or even metastatic organotropism).

      (3) Figure 3: In the text, the authors stated, "To further investigate this result, we examined the transcription status of genes that changed compartment across the EMT spectrum and, conversely, the compartment status of genes that changed transcription (Fig. 3b, c, and d)". However, it was not apparent in the figure that the cell lines were arranged according to an EMT spectrum. Also, the clustering heatmaps did not provide sufficient information regarding the genes with concordant/divergent compartments vs transcription changes. It would be more informative if the authors could spend more effort in annotating these genes/pathways.

      (4) Figure 4: The title of the subheading of this section was 'Lung metastatic breast cancer cell lines acquire lung-like genome architecture". Echoing my comments in point 1, I am a bit hesitant to term it as "lung metastatic" but rather "metastatic' in general since cell lines such as MDA-MD-231 do metastasize to other organs as well. However, I do get the point that the definition of "lung metastasis" is derived from the common metastasis features among the cell lines here (MCF7, T47D, SKBR3, MDA-MB-231).

      There might be another argument about whether the "lung" carcinoma cell lines can be considered "localized" since they are also capable of metastasizing to other organs. In a way, what the authors probably were trying to leverage here is the "tissue" identity of that organ. Having said this, in addition to showing the "lung permissive changes", the authors should show the "breast identity conservation" as well. Because this section started to deal with the concept of "tissue/lineage identify", the authors should also clarify whether these breast cancer cell lines capable of making lung metastasis are also preserving their original tissue identity from the compartment features (which would most likely be the case).

      (5) Rest of the sections: The authors started to claim that the organ-specific metastasis permissive compartmental features mimic the destinated end organ. The authors utilized additional non-breast cancer cell lines (prostate cancer cell lines LNCaP as localized and DU145 as brain metastatic) in brain metastasis to strengthen this claim. (DU145 in MetMap again is highly metastatic to lung, brain, and kidney). However, this makes one wonder that for cell lines that are capable of metastasizing to multiple organ sites (eg. MDA-MB-231, DU145, A459, H460), does it mean that they all acquire the permissive features for all these organs? This scenario is clinically relevant in Stage 4 patients who often present with not only one metastatic lesion in one single organ but multiple metastatic lesions in more than one organ (eg. concomitant liver and lung metastasis). Do the authors think that there might be different clones having different tropism-permissive 3D genome features or there might be evolutionary trajectory in this?

      In my opinion, to further prove this point, the authors might need to consider doing in vivo experiments to collect paired primary and organ-specific metastatic samples to look at the 3D genome changes.

      (6) Technically, the study utilized public Hi-C data without generating new Hi-C data. The resolution of the Hi-C data for compartments was set at 250KB as the binning size indicating that the Hi-C data was at lower resolution so it might not be ideal to address other 3D genome architecture changes such as TADs or long-range loops. It is therefore unknown whether there might be permissive TAD/loop changes associated with organotropism and this is the limitation of this study.

      (7) In the final sentence of the discussion the authors stated "Overall, our results suggest that genome spatial compartment changes can help encode a cell state that favors metastasis (EMT)". The "metastasis (EMT)" was in fact not clearly linked inside the manuscript. The authors did not provide a strong link between metastasis and EMT in their result description. It is also unclear whether the EMT-associated compartment identity would also correlate with the organotropic compartment identity.

    3. Reviewer #2 (Public review):

      Summary:

      This work addresses an important question of chromosome architecture changes associated with organotopic metastatic traits, showing important trends in genome reorganization. The most important observation is that 3D genome changes consistent with adaptations for new microenvironments, including lung metastatic breast cells exhibiting signatures of the genome architecture typical to a lung cell-like conformation and brain metastatic prostate cancer cells showing compartment shifts toward a brain-like state.

      Strengths:

      This work presents interesting original results, which will be important for future studies and biomedical implications of epigenetic regulation in norm and pathology.

      Weaknesses:

      The authors used publicly available data for 15 cell types. They should show how many different sources the data were obtained from and demonstrate that obtained results are consistent if the data from different sources were used.

    4. Author response:

      We appreciate the constructive feedback from the reviewers and will work to address many of these concerns in a revised version.  Here, we provide initial responses to a few key points that the reviewers raised:

      (1) The reviewers rightly pointed out that it is very important to clearly define and explain what qualifies as metastatic potential to particular organs in our system.  We acknowledge the valuable contributions of animal models in metastatic cancer studies, but here we intentionally limited our scope to metastasis that had occurred within the human system only.  For example, we use data from cancer cells that model human organotropism from the breast to the lung, since the cells originated from infiltrative ductal carcinoma (human breast) but were collected from pleural effusions (human lung). We propose that in this case a comparison with a human lung cancer-derived cell line that was itself purified from a pleural effusion could reveal factors essential for lung metastasis, without adding the confounder of an animal microenvironment.  The MetMap Explorer contains valuable information, but the “metastatic potential of each cell line” is measured in a mouse environment.  Knowing that a particular cell line, which originated from a human lung metastasis, can further metastasize to other organs in a mouse does not necessarily mean that those cells could do so in humans.  The microenvironment responses to metastatic colonization can differ among species.  Further, the changes a cell needs to make to adapt to a new organ system in a mouse could be confounded by the changes needed to adapt to mouse conditions in general.  Finally, migration from a site of ectopic injection may not mimic migration from an initial tumor site.  We agree that the very best data would come from matched primary and metastatic tumors in the same human patient, but those data do not currently exist and generating them would require future work beyond the scope of this study.   In our revision, we will ensure that  we more clearly explain how and why we chose the cell lines we did and what the advantages and limitations of this choice are.

      (2) The reviewers are correct that our unsupervised Principal component analysis (PCA) does not precisely stratify cells according to epithelial-mesenchymal status.  In a high dimensional, complex system, it is expected than an unsupervised analysis such as this will not capture just one biological feature in the first principal component. Therefore, when we performed PCA on the compartmental organization profiles of different healthy and cancerous cell lines, instead of finding the largest variation (PC1) following exactly EMT state, it captured an ordering that includes influences from epithelial-mesenchymal state, disease condition, nuclear geometry, and other cellular properties.  However, it was striking that this completely unsupervised analysis did match previous annotations of EMT state so well (as seen in supp fig 1b).  Therefore, we conclude that the most prominent variations in A/B compartment signature strongly relate to EMT state.   In the revision, we will more clearly present the caveats of this interpretation.

      (3) Our decision to focus on A/B compartmentalization rather than TAD or loop structure in this analysis was intentional and biologically motivated, rather than solely being a reflection of data resolution.  Both compartments and topologically associated domains (TADs) are key parts of genome organization and disruption of these structures has the potential to alter downstream gene regulation, as shown by numerous studies. But, compartments have been found, more so than TADs, to be strongly associated with cell type and cell fate.  Therefore,  in this manuscript, we decided to focus only on the compartment organization changes between different healthy and cancerous cells as they are more likely to represent the stable alterations of the genome organization malignant transformations.

    1. eLife Assessment

      This study presents the state-dependent role of serotonin for the protein and sugar intake of Drosophila by expressing a dominant-negative serotonin transporter in subsets of serotoninergic neurons. This paper is valuable for neuroscientists working on neuromodulation and the effects of internal states such as hunger, however the characterization of behavioral and neuroanatomical data is incomplete.

    2. Reviewer #1 (Public review):

      Summary:

      Dorn et al. investigate the role of specific serotonergic cell types in fed appetite and starved hunger. They show that neurons labeled by the Sert3-GAL4 line modulate sucrose appetite and that neurons labeled by R50H05-GAL4 and Tph-GAL4 modulate yeast hunger, by expressing a non-functioning serotonin transporter. Similarly, activating these neurons leads to the same effects - a decrease in sucrose appetite and an increase in yeast hunger, respectively. Manipulation of the serotonin transporter in Sert3 neurons impairs appetitive sugar-odor conditioning, however aversive shock-odor conditioning is intact. The authors further tested the role of insulin signaling in this paradigm and the Sert3 neurons. Expressing either constitutively active or non-function insulin receptor impaired sucrose appetite. The expression of the different modulated insulin receptors affects the anatomy of the cells and the distribution of serotonin transporters. It seems that overexpression of the serotonin transporter can rescue the sugar appetite phenotype caused by the constitutively active insulin receptor. Additional experiments reveal that CG9911 and CG10029 RNAi - genes potentially involved in the insulin-serotonin pathway - knockdown does not affect sugar appetite, however Sec24AB RNAi - required for proper serotonin transporter localization - knockdown also leads to sugar appetite reduction. Finally, the authors show that IR60b taste receptor neurons potentially get modulated by Sert 3 and thereby influence sucrose appetite.

      Strengths:

      The authors provide a more detailed description of the multiple roles that serotonin neurons can take on. Manipulating specific subsets of serotonergic cells, they can distinguish cells that are involved in sucrose feeding in fed animals, whereas other cells are involved in regulating yeast hunger in starved animals. Thus, further cell-type specific dissections and manipulations are required to understand the full functional repertoire of different serotonergic neurons in the brain. The authors further describe that insulin seems to modulate serotonergic neurons and starts to elucidate the underlying complex neuromodulatory mechanisms.

      Weaknesses:

      Even though the authors provide evidence for behavioral phenotypes due to manipulations of serotonin and insulin cells, the evidence for the required molecular mechanism and connectivity is not convincing and requires further investigation. The authors expand their findings to play a role in sugar conditioning, however, according to the authors flies were starved for these experiments - thus these results rather contradict the innate phenotype.

    3. Reviewer #2 (Public review):

      Summary:

      This study by Dorn et al. from Dr. Henrike Scholz's group investigates the function of serotonin signaling in state-dependent feeding control for protein and sugar intake. Using a dominant-negative serotonin transporter to block serotonin reuptake and optogenetics to activate serotoninergic neurons, the authors identified that serotonin released from a small group of Sert3-expressing neurons specifically reduces sucrose consumption of the fed files but not in the starved flies. Conversely, blocking serotonin reuptake in broad serotonergic neurons increases yeast consumption only in starved flies but does not affect fed flies. These results suggest prolonged serotonin signals may suppress sucrose appetite in fed flies while promoting protein intake in starved flies.

      Although the phenotypes presented are intriguing and fundamental to animal fitness, the data in its current form is insufficient to support the proposed mechanisms underlying the state-dependent diet control by serotonin signals. Specifically, the authors should carefully analyze the requirement of serotonin by showing the efficiency of the serotonin reuptake blockade caused by the dominant-negative serotonin and validating the requirement of serotonin in the optogenetic activation of Sert3-expressing neurons. Additionally, the conclusions based on the overexpressed Sert3::gfp transgene should be retrieved as the overexpression affects sucrose consumption. Therefore, I recommend some alternative interpretations and approaches below for authors to verify the current form of conclusions.

      Strengths:

      The authors identified the state-dependent diet control for sucrose and yeast intake regulated by a restricted population of serotonin neurons expressing Sert3.

      Weaknesses:

      The data only partially supports most conclusions. Specifically, findings based on the use of the transgene Sert3::GFP lack sufficient rigor, as the authors overlooked potential overexpression effects.

      Major issues

      (1) The authors try to distinguish the motivation to feed on sucrose or protein in fed or starved conditions using "sucrose appetite" and "protein hunger", respectively. However, appetite and hunger should be synonymous in the current context. When specifying protein hunger, readers will expect the craving for protein in the protein-deprived situation. In the current study, starved flies were prepared by starvation on wet tissues so the flies are supposed to be hungry for sugar and protein. To avoid confusion, "sucrose appetite in fed flies" and "protein appetite in starved flies" are better descriptions.

      (2) In Figure 1A-1I (lines 141-142), it remains unclear whether additional serotonergic neurons are required or if the serotonergic neurons labeled exclusively by R50H05-Gal4 and Tph-Gal4 are necessary to regulate yeast consumption in starved flies. The overlapping expressions of these two drivers with the Sert3-Gal4 make it hard to distinguish these two possibilities.

      (3) The data in Figure 1L-1M suggests that the serotonin-dependent regulation in yeast consumption of starved flies is suppressed by sucrose supplementation. However, the neurons required for yeast consumption remain undefined due to the overlapping expression. This result implies that the neurons labeled by R50H05-Gal4 and Tph-Gal4 influence both sucrose and yeast consumption but not specific to yeast.

      (4) The regulatory relationship between insulin receptors and serotonin signaling in sucrose appetite remains unclear. How do the authors interpret the result that both the constitutively active and dominant-negative forms of the insulin receptor (InR) reduce sucrose appetite in Figure 4? One possibility is that insulin receptors are involved in two parallel pathways to regulate sucrose consumption that converge to the same phenotype. However, the insulin receptor (InR) pathways can still be independent of the serotonin signaling pathway despite showing a comparable reduction of sucrose consumption in fed flies. This issue should be discussed further following lines 229-231.

      (5) The quantification of Figure 5 should be revised. First, as the transgene Sert3::GFP affects sucrose consumption, quantifying the transgene signals may not explain its endogenous function. Second, the quantification lacks a Gal4 expression control using an untagged fluorescent marker, preferably a different color so that the authors can quantify it in the same individual as the comparison. Lastly, it is hard to be convinced that the distance between two layers represents the broad expression of Sert3::GFP in response to insulin receptor alterations. Quantifying the area size of each layer with fixed imaging conditions such as the intervals of brain sections and the laser intensity may be a better alternative approach.

      (6) The conclusions drawn based on the Sert3::GFP transgene failed to explain the endogenous function of the serotonin transporter Sert3 in regulating sucrose consumption. Expressing the constitutive-active form of the insulin receptor in Sert3-expressing neurons reduces the total sucrose consumption of fed flies in Figure 4A, which appears inconsistent with the fly line with an additional Sert3::GFP expression shown in Figures 6F, where the suppression of sucrose consumption is not shown for the normalized sucrose intake. This inconsistency suggests that Sert3::GFP transgene itself affects sucrose consumption.

      (7) In lines 324-326, the authors should investigate whether IR60b neurons are indeed the downstream of serotoninergic neurons SE1 to regulate sucrose consumption in fed flies. First, synaptic connections could be confirmed by additional approaches. Following this, the authors could demonstrate that the knockdown of serotonin receptors in IR60b neurons eliminates the suppression in sucrose consumption induced by the activation of Sert3-expressing neurons or by the expression of the dominant-negative serotonin transporter in fed flies.

    1. eLife Assessment

      This study reports important findings about the nature of feedback to primary visual cortex (V1) during object recognition. The state-of-the-art functional MRI evidence for the main claims is solid, although currently alternative explanations of the findings cannot be fully ruled out. The findings presented here are relevant to a number of scientific fields such as object recognition, categorisation and predictive coding.

    2. Reviewer #1 (Public review):

      This study investigates spatial and temporal aspects of feedback information in the brain during categorization tasks. The authors found that feedback to V1 contained low-level features and was present in the deep layers of V1 originating presumably from occipito-temporal brain regions. High-level category feedback was found in the deep and the superficial layers and was directed to V1 from occipitotemporal and parietal cortices. This study raises a timely question in the fields of object categorization and predictive coding about the granularity of feedback and its separability by cortical depth and time course.

      Here are a couple of concerns and questions:

      The authors argue that low-level features in a feedback format could be decoded only from deep layers of V1 (and not superficial layers) during a perceptual categorization task. However, previous studies (Bergman et al., 2024; Iamshchinina et al., 2021) demonstrated that low-level features in the form of feedback can be decoded from both superficial and deep layers. While this result could be due to perceptual task or highly predictable orientation feature (orientation was kept the same throughout the experimental block), an alternative explanation is a weaker representation of orientation in the feedback (even before splitting by layers there is only a trend towards significance; also granger causality for orientation information in MEG part is lower than that for category in peripheral categorization task), because it is orthogonal to the task demand. It would be helpful if the authors added a statistical comparison of the strength of category and orientation representations in each layer and across the layers.

      The authors argue that category feedback is not driven by low-level confounding features embedded in the stimuli. They demonstrate the ability to decode orientations, particularly well represented by V1, in the absence of category discrimination. However, the orientation is not a category-discriminating feature in this task. It could be that the category-discriminating features cannot be as well decoded from V1 activity patterns as orientations. Also, there are a number of these category discriminating features and it is unclear if it is a variation in their representational strength or merely the absence of the task-driven enhancement that preempts category decoding in V1 during the foveal task. In other words, I am not sure whether, if orientation was a category-specific feature (sharpies are always horizontal and smoothies are vertical), there would still be no category decoding.

    3. Reviewer #2 (Public review):

      Summary:

      This manuscript reports high-resolution functional MRI data and MEG data revealing additional mechanistic information about an established paradigm studying how foveal regions of the primary visual cortex (V1) are involved in processing peripheral visual stimuli. Because of the retinotopic organization of V1, peripheral stimuli should not evoke responses in the regions of V1 that represent stimuli in the center of the visual field (the fovea). However, functional MRI responses in foveal regions do reflect the characteristics of peripheral visual stimuli - this is a surprising finding first reported in 2008. The present study uses fMRI data with sub-millimeter resolution to study how responses at different depths in the foveal gray matter do or don't reflect peripheral object characteristics during 2 different tasks: one in which observers needed to make detailed judgments about object identity, and one in which observers needed to make more coarse judgments about object orientation. FMRI results reveal interesting and informative patterns in these two conditions. A follow-on MEG study yields information about the timing of these responses. Put together, the findings settle some questions in the field and add new information about the nature of visual feedback to V1.

      Strengths:

      (1) Rigorous and appropriate use of "laminar fMRI" techniques.

      (2) The introduction does an excellent job of contextualizing the work.

      (3) Control experiments and analyses are designed and implemented well

      Weaknesses:

      (1) While not necessarily a weakness, I do not fully agree with the description of the 2 kinds of feedback information as "low-order" and "high-order". I understand the motivation to do this - orientation is typically considered a low-level visual feature. But when it's the orientation of an entire object, not a single edge, orientation can only be defined after the elements of the object are grouped. Also, the discrimination between spikies and smoothies requires detecting the orientations of particular edges that form the identifying features. To my mind, it would make more sense to refer to discrimination of object orientation as "coarse" feature discrimination, and orientation of object identity as "fine" feature discrimination. Thus, the sentence on line 83, for example, would read "Interestingly, feedback with fine and coarse feature information exhibits different laminar profiles.".

      (2) Figure 2 and text on lines 185, and 186: it is difficult to interpret/understand the findings in foveal ROIs for the foveal control task without knowing how big the ROI was. Foveal regions of V1 are grossly expanded by cortical magnification, such that the central half-degree can occupy several centimeters across the cortical surface. Without information on the spatial extent of the foveal ROI compared to the object size, we can't know whether the ROI included voxels whose population receptive fields were expected to include the edges of the objects.

      (3) Line 143 and ROI section of the methods: in order for the reader to understand how robust the responses and analyses are, voxel counts should be provided for the ROIs that were defined, as well as for the number (fraction) of voxels excluded due to either high beta weights or low signal intensity (lines 505-511).

      (4) I wasn't able to find mention of how multiple-comparisons corrections were performed for either the MEG or fMRI data (except for one Holm-Bonferonni correction in Figure S1), so it's unclear whether the reported p-values are corrected.

    1. eLife Assessment

      This valuable study relating brain anatomy to reading ability in children studied longitudinally finds that a difference in sulcal anatomy is more predictive of reading ability than cognitive measures. The evidence that this anatomical difference is predictive and confers some benefit in the connectivity between brain areas is based on careful analyses and is solid. The findings would be of interest to researchers studying brain and cognitive development.

    2. Reviewer #1 (Public review):

      Summary:

      There is prior literature showing a robust relationship between sulcal interruptions in the posterior occipital temporal sulcus (pOTS) and reading ability. The goals of this study were to extend these findings to children examined longitudinally as they become better readers, and to examine the underlying white matter properties in individuals with and without pOTS sulcal interruptions. To do this, the authors collected longitudinal structural, diffusion, and behavioral data in 51 children (TP1 age 5.5, TP3 age 8.2 years).

      First, the authors found that the gyral gap was consistent across time within the subject. This is expected, as they state in the introduction that sulcal patterns are typically established in utero. Next, they found that children with an interrupted pOTS have higher reading scores (across a variety of measures) at timepoint (TP) 3 than children with continuous pOTS, and this was specific to the pOTS, as no associations emerged for the anterior OTS or MFS; this is again expected from prior literature. They then found that the binary presence of this gap, but not anterior OTS or MFS predicted T3 reading performance. Further, they found that a subsample of the lowest readers at TP1 did not have differences in reading score by gyral gap, but that this difference emerged at TP3. Additionally, the gyral gap at TP1 is similar to variance TOWRE 3 reading skills as some behavioral measures at TP1. Examining underlying white matter in a smaller subset of children, the authors found higher MD in children with an interrupted pOTS vs. those with a continuous pOTS, which was contrary to their hypothesis, and higher local connectivity for interrupted, aligning with their hypothesis, but this difference was no longer present when accounting for TP3 reading scores. The authors conclude that structural properties, in this case, the gyral gap, may guide neural plasticity for reading.

      Strengths:

      This paper has an interesting set of longitudinal data to examine the perhaps changing relationship between sulcal interruptions in the pOTS with reading scores. I commend the authors on data collection and attention to detail in the anatomical analyses.

      Weaknesses:

      However, my enthusiasm was somewhat dampened after finding numerous prior publications on this very topic and I'm unclear as to how much more this paper adds to the current literature. Would we expect the existence of sulcal interruptions to be aligned with reading skills in older kids but not younger kids? Is the point to see if the interruptions exist prior to reading (but these children are not really prereaders)? What is the alternative- why would these interruptions not exist? After all, this anatomy is determined prenatally. Children who have pOTS interruptions at T1 should also have these interruptions at T3 (and indeed that is what the authors find). So how can this be the mechanism that drives plasticity? The authors also talk about the neuronal recycling hypothesis but their data cannot speak to this because they do not have fMRI data nor does their sample include only prereaders with no reading experience. The conclusions are overall overstated and not supported by the results. I think this paper could add interesting knowledge for the specific subfield of reading and the brain. However, the current state of the results, especially with the inclusion of so many trending results and the comparison of so many different processing pipelines and models, in addition to a conclusion that is not motivated by the work makes it difficult to appreciate the paper.

    3. Reviewer #2 (Public review):

      Summary:

      This manuscript examined the impact of sulcal morphology on reading development. A very specific feature on the ventral surface of the brain was identified, namely the presence of an interruption in the posterior portion of the left occipitotemporal sulcus (pOTS). Compared to children with a continuous pOTS, children with an interruption at age 5 years had better reading ability at age 8. This was a large effect measured in 43 children. Surprisingly, this morphological feature was a better predictor of reading ability than measures of pre-literacy cognitive skills, such as phonological awareness. The effect was tested and reproduced across several different measures of reading ability. The authors hypothesised that the mechanism underlying this benefit related to greater local connectivity, which confers a computational advantage. This was demonstrated using analysis of diffusion-weighted imaging data in 29 of the children obtained at age 8.

      Strengths:

      The novelty of the manuscript is threefold: (i) the measure was made in children who were pre-literate (previous work was in older children and adults); (ii) longitudinal brain imaging and behavioural data were analysed; and (iii) diffusion data were analysed to test a hypothesis about the underlying mechanism.

      The manuscript is exceptionally well written. The methods are detailed and easily reproduced. The approach is thoughtful and meticulous. All possible alternatives appear to have been considered. Where possible, further analyses have been done to address these alternatives. For example, the testing of the specificity of the sulcal interruption to left pOTS was an important addition. None predicted reading skills.

      Weaknesses:

      The correlation of the interruption with all kinds of literacy measures and in particular reading comprehension and then PIQ suggest this interruption might confer a more general cognitive advantage rather than specifically a reading one.

      It would be interesting to know if the anatomical difference predicts any other cognitive ability or if there might be any cognitive cost (a negative correlation) of this sulcal interruption.<br /> The location of the interruption in the sulcus is quite variable and in some cases, there is more than one interruption. The sample size is probably not big enough to compare these different patterns or to evaluate the influence of the location of the sulcal interruption.

      The sample is quite high-functioning and the generalisability of the findings outside of this specific population is inevitably limited.

    1. eLife Assessment

      This valuable study combines evolution experiments with molecular and genetic techniques to study how a genetic lesion in MreB that causes rod-shape cells to become spherical, with concomitant deleterious fitness effects, can be rescued by natural selection. The results are convincing, although further improvement of the statistical analyses and figure presentation, and further clarification of the concrete contribution of the paper and how it relates to previous literature, would be welcome.

    2. Reviewer #1 (Public review):

      Summary:

      The authors performed experimental evolution of MreB mutants that have a slow growing round phenotype and studied the subsequent evolutionary trajectory using analysis tool from molecular biology. It was remarkable and interesting that they found that the original phenotype was not restored (most common in these studies) but that the round phenotype was maintained.

      Strengths:

      The finding that the round phenotype was maintained during evolution rather than that the original phenotype, rod shape cells, was recovered is interesting. The paper extensively investigates what happens during adaptation with various different techniques. Also the extensive discussion of the findings at the end of the paper is well thought through and insightful.

      Weaknesses:

      I find there are three general weaknesses<br /> (1) Although the paper states in the abstract that it emphasizes "new knowledge to be gained" it remains unclear what this concretely is. At page 4 they state 3 three research questions, these could be more extensively discussed in the abstract. Also these questions read more like genetics questions while the paper is a lot about cell biological findings.<br /> (2) It is not clear to me from the text what we already know about restoration of MreB loss from suppressors studies (in the literature). Are there supressor screens in the literature and which part of the findings is consistent with suppressor screens and which parts are new knowledge?<br /> (3) The clarity of the figures, captions and data quantification need to be improved.

    3. Reviewer #3 (Public review):

      This paper addresses a long-standing problem in microbiology: the evolution of bacterial cell shape. Bacterial cells can take a range of forms, among the most common being rods and spheres. The consensus view is that rods are the ancestral form and spheres the derived form. The molecular machinery governing these different shapes is fairly well understood but the evolutionary drivers responsible for the transition between rods and spheres is not. Enter Yulo et al.'s work. The authors start by noting that deletion of a highly conserved gene called MreB in the Gram-negative bacterium Pseudomonas fluorescens reduces fitness but does not kill the cell (as happens in other species like E. coli and B. subtilis) and causes cells to become spherical rather than their normal rod shape. They then ask whether evolution for 1000 generations restores the rod shape of these cells when propagated in a rich, benign medium.

      The answer is no. The evolved lineages recovered fitness by the end of the experiment, growing just as well as the unevolved rod-shaped ancestor, but remained spherical. The authors provide an impressively detailed investigation of the genetic and molecular changes that evolved. Their leading results are:

      (1) the loss of fitness associated with MreB deletion causes high variation in cell volume among sibling cells after cell division;<br /> (2) fitness recovery is largely driven by a single, loss-of-function point mutation that evolves within the first ~250 generations that reduces the variability in cell volume among siblings;<br /> (3) the main route to restoring fitness and reducing variability involves loss of function mutations causing a reduction of TPase and peptidoglycan cross-linking, leading to a disorganized cell wall architecture characteristic of spherical cells.

      The inferences made in this paper are on the whole well supported by the data. The authors provide a uniquely comprehensive account of how a key genetic change leads to gains in fitness and the spectrum of phenotypes that are impacted and provide insight into the molecular mechanisms underlying models of cell shape.

      Suggested improvements and clarifications include:<br /> (1) A schematic of the molecular interactions governing cell wall formation could be useful in the introduction to help orient readers less familiar with the current state of knowledge and key molecular players;<br /> (2) It remains unclear whether corrections for multiple comparisons are needed when more than one construct or strain is compared to the common ancestor, as in Supp Fig 19A (relative PG density of different constructs versus the SBW25 ancestor). The author's response did not clarify matters: was data for the WT obtained independently alongside each each strain/construct (justifying a paired t-test) or was a single set of data for the WT obtained and used to compare against all other strains/constructs (which would demand a correction for multiple comparisons)?<br /> (3) The authors refrain from making strong claims about the nature of selection on cell shape, perhaps because their main interest is the molecular mechanisms responsible. They identify sources of stabilizing selection favouring an intermediate cell size (lack of DNA in small cells and disorganized DNA in large cells). Their interpretation of stabilizing selection in the review is correct and entirely consistent with the mechanistic causes identified here. I think this is valuable and interesting, although I recognize it is not the focus of the paper.

      Comments on revisions:

      Please further clarify the experimental design and replication for the contrast between mutants and WT to address the issue of multiple comparisons.

    4. Author response:

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

      Public Reviews: 

      Reviewer #1 (Public Review): 

      Summary: 

      The authors performed experimental evolution of MreB mutants that have a slow-growing round phenotype and studied the subsequent evolutionary trajectory using analysis tools from molecular biology. It was remarkable and interesting that they found that the original phenotype was not restored (most common in these studies) but that the round phenotype was maintained. 

      Strengths: 

      The finding that the round phenotype was maintained during evolution rather than that the original phenotype, rod-shaped cells, was recovered is interesting. The paper extensively investigates what happens during adaptation with various different techniques. Also, the extensive discussion of the findings at the end of the paper is well thought through and insighXul. 

      Weaknesses: 

      I find there are three general weaknesses: 

      (1) Although the paper states in the abstract that it emphasizes "new knowledge to be gained" it remains unclear what this concretely is. On page 4 they state 3 three research questions, these could be more extensively discussed in the abstract. Also, these questions read more like genetics questions while the paper is a lot about cell biological findings. 

      Thank you for drawing attention to the unnecessary and gratuitous nature of the last sentence of the Abstract. We are in agreement. It has been modified, and we have taken  advantage of additional word space to draw attention to the importance of the two competing (testable) hypotheses laid out in the Discussion. 

      As to new knowledge, please see the Results and particularly the Discussion. But beyond this, and as recognised by others, there is real value for cell biology in seeing how (and whether) selection can compensate for effects that are deleterious to fitness. The results will very o_en depart from those delivered from, for example, suppressor analyses, or bottom up engineering. 

      In the work recounted in our paper, we chose to focus – by way of proof-of principle – on the most commonly observed mutations, namely, those within pbp1A.  But beyond this gene, we detected mutations  in other components of the cell shape / division machinery whose connections are not yet understood and which are the focus of on-going investigation.  

      As to the three questions posed at the end of the Introduction, the first concerns whether selection can compensate for deleterious effects of deleting mreB (a question that pertains to evolutionary aspects); the second seeks understanding of genetic factors; the third aims to shed light on the genotype-to-phenotype map (which is where the cell biology comes into play).  Given space restrictions, we cannot see how we could usefully expand, let alone discuss, the three questions raised at the end of the Introduction in restrictive space available in the Abstract.   

      (2) It is not clear to me from the text what we already know about the restoration of MreB loss from suppressors studies (in the literature). Are there suppressor screens in the literature and which part of the findings is consistent with suppressor screens and which parts are new knowledge?  

      As stated in the Introduction, a previous study with B. subtilis (which harbours three MreB isoforms and where the isoform named “MreB” is essential for growth under normal conditions), suppressors of MreB lethality were found to occur in ponA, a class A penicillin binding protein (Kawai et al., 2009). This led to recognition that MreB plays a role in recruiting Pbp1A to the lateral cell wall. On the other hand, Patel et al. (2020) have shown that deletion of classA PBPs leads to an up-regulation of rod complex activity. Although there is a connection between rod complex and class A PBPs, a further study has shown that the two systems work semi-autonomously (Cho et al., 2016). 

      Our work confirms a connection between MreB and Pbp1A, and has shed new light on how this interaction is established by means of natural selection, which targets the integrity of cell wall. Indeed, the Rod complex and class A PBPs have complementary activities in the building of the cell wall with each of the two systems able to compensate for the other in order to maintain cell wall integrity. Please see the major part of the Discussion. In terms of specifics, the connection between mreB and pbp1A (shown by Kawai et al (2009)) is indirect because it is based on extragenic transposon insertions. In our study, the genetic connection is mechanistically demonstrated.  In addition, we capture that the evolutionary dynamics is rapid and we finally enriched understanding of the genotype-to-phenotype map.

      (3) The clarity of the figures, captions, and data quantification need to be improved.  

      Modifications have been implemented. Please see responses to specific queries listed below.

      Reviewer #2 (Public Review): 

      Yulo et al. show that deletion of MreB causes reduced fitness in P. fluorescens SBW25 and that this reduction in fitness may be primarily caused by alterations in cell volume. To understand the effect of cell volume on proliferation, they performed an evolution experiment through which they predominantly obtained mutations in pbp1A that decreased cell volume and increased viability. Furthermore, they provide evidence to propose that the pbp1A mutants may have decreased PG cross-linking which might have helped in restoring the fitness by rectifying the disorganised PG synthesis caused by the absence of MreB. Overall this is an interesting study. 

      Queries: 

      Do the small cells of mreB null background indeed have have no DNA? It is not apparent from the DAPI images presented in Supplementary Figure 17. A more detailed analysis will help to support this claim. 

      It is entirely possible that small cells have no DNA, because if cell division is aberrant then division can occur prior to DNA segregation resulting in cells with no DNA. It is clear from microscopic observation that both small and large cells do not divide. It is, however, true, that we are unable to state – given our measures of DNA content – that small cells have no DNA. We have made this clear on page 13, paragraph 2.

      What happens to viability and cell morphology when pbp1A is removed in the mreB null background? If it is actually a decrease in pbp1A activity that leads to the rescue, then pbp1A- mreB- cells should have better viability, reduced cell volume and organised PG synthesis. Especially as the PG cross-linking is almost at the same level as the T362 or D484 mutant.  

      Please see fitness data in Supp. Fig. 13. Fitness of ∆mreBpbp1A is no different to that caused by a point mutation. Cells remain round.  

      What is the status of PG cross-linking in ΔmreB Δpflu4921-4925 (Line 7)? 

      This was not analysed as the focus of this experiment was PBPs. A priori, there is no obvious reason to suspect that ∆4921-25 (which lacks oprD) would be affected in PBP activity.

      What is the morphology of the cells in Line 2 and Line 5? It may be interesting to see if PG cross-linking and cell wall synthesis is also altered in the cells from these lines. 

      The focus of investigation was restricted to L1, L4 and L7. Indeed, it would be interesting to look at the mutants harbouring mutations in :sZ, but this is beyond scope of the present investigation (but is on-going). The morphology of L2 and L5 are shown in Supp. Fig. 9.

      The data presented in 4B should be quantified with appropriate input controls. 

      Band intensity has now been quantified (see new Supp. Fig .20). The controls are SBW25, SBW25∆pbp1A, SBW25 ∆mreB and SBW25 ∆mreBpbp1A as explained in the paper.

      What are the statistical analyses used in 4A and what is the significance value? 

      Our oversight. These were reported in Supp. Fig. 19, but should also have been presented in Fig. 4A. Data are means of three biological replicates. The statistical tests are comparisons between each mutant and SBW25, and assessed by paired t-tests.  

      A more rigorous statistical analysis indicating the number of replicates should be done throughout. 

      We have checked and made additions where necessary and where previously lacking. In particular, details are provided in Fig. 1E, Fig. 4A and Fig. 4B. For Fig. 4C we have produced quantitative measures of heterogeneity in new cell wall insertion. These are reported in Supp. Fig. 21 (and referred to in the text and figure caption) and show that patterns of cell wall insertion in ∆mreB are highly heterogeneous.

      Reviewer #3 (Public Review): 

      This paper addresses an understudied problem in microbiology: the evolution of bacterial cell shape. Bacterial cells can take a range of forms, among the most common being rods and spheres. The consensus view is that rods are the ancestral form and spheres the derived form. The molecular machinery governing these different shapes is fairly well understood but the evolutionary drivers responsible for the transition between rods and spheres are not. Enter Yulo et al.'s work. The authors start by noting that deletion of a highly conserved gene called MreB in the Gram-negative bacterium Pseudomonas fluorescens reduces fitness but does not kill the cell (as happens in other species like E. coli and B. subtilis) and causes cells to become spherical rather than their normal rod shape. They then ask whether evolution for 1000 generations restores the rod shape of these cells when propagated in a rich, benign medium. 

      The answer is no. The evolved lineages recovered fitness by the end of the experiment, growing just as well as the unevolved rod-shaped ancestor, but remained spherical. The authors provide an impressively detailed investigation of the genetic and molecular changes that evolved. Their leading results are: 

      (1) The loss of fitness associated with MreB deletion causes high variation in cell volume among sibling cells a_er cell division. 

      (2) Fitness recovery is largely driven by a single, loss-of-function point mutation that evolves within the first ~250 generations that reduces the variability in cell volume among siblings. 

      (3) The main route to restoring fitness and reducing variability involves loss of function mutations causing a reduction of TPase and peptidoglycan cross-linking, leading to a disorganized cell wall architecture characteristic of spherical cells. 

      The inferences made in this paper are on the whole well supported by the data. The authors provide a uniquely comprehensive account of how a key genetic change leads to gains in fitness and the spectrum of phenotypes that are impacted and provide insight into the molecular mechanisms underlying models of cell shape. 

      Suggested improvements and clarifications include: 

      (1) A schematic of the molecular interactions governing cell wall formation could be useful in the introduction to help orient readers less familiar with the current state of knowledge and key molecular players. 

      We understand that this would be desirable, but there are numerous recent reviews with detailed schematics that we think the interested reader would be better consulting. These are referenced in the text.

      (2) More detail on the bioinformatics approaches to assembling genomes and identifying the key compensatory mutations are needed, particularly in the methods section. This whole subject remains something of an art, with many different tools used. Specifying these tools, and the parameter sesngs used, will improve transparency and reproducibility, should it be needed. 

      We overlooked providing this detail, which has now been corrected by provision of more information in the Materials and Methods. In short we used Breseq, the clonal option, with default parameters. Additional analyses were conducted using Genieous. The BreSeq output files are provided https://doi.org/10.17617/3.CU5SX1 (which include all read data).

      (3) Corrections for multiple comparisons should be used and reported whenever more than one construct or strain is compared to the common ancestor, as in Supplementary Figure 19A (relative PG density of different constructs versus the SBW25 ancestor). 

      The data presented in Supp Fig 19A (and Fig 4A) do not involve multiple comparisons. In each instance the comparison is between SBW25 and each of the different mutants. A paired t-test is thus appropriate.

      (4) The authors refrain from making strong claims about the nature of selection on cell shape, perhaps because their main interest is the molecular mechanisms responsible. However, I think more can be said on the evolutionary side, along two lines. First, they have good evidence that cell volume is a trait under strong stabilizing selection, with cells of intermediate volume having the highest fitness. This is notable because there are rather few examples of stabilizing selection where the underlying mechanisms responsible are so well characterized. Second, this paper succeeds in providing an explanation for how spherical cells can readily evolve from a rod-shaped ancestor but leaves open how rods evolved in the first place. Can the authors speculate as to how the complex, coordinated system leading to rods first evolved? Or why not all cells have lost rod shape and become spherical, if it is so easy to achieve? These are important evolutionary questions that remain unaddressed. The manuscript could be improved by at least flagging these as unanswered questions deserving of further attention. 

      These are interesting points, but our capacity to comment is entirely speculative. Nonetheless, we have added an additional paragraph to the Discussion that expresses an opinion that has yet to receive attention:

      “Given the complexity of the cell wall synthesis machinery that defines rod-shape in bacteria, it is hard to imagine how rods could have evolved prior to cocci. However, the cylindrical shape offers a number of advantages. For a given biomass (or cell volume), shape determines surface area of the cell envelope, which is the smallest surface area associated with the spherical shape. As shape sets the surface/volume ratio, it also determines the ratio between supply (proportional to the surface) and demand (proportional to cell volume). From this point of view, it is more efficient to be cylindrical (Young 2006). This also holds for surface attachment and biofilm formation (Young 2006). But above all, for growing cells, the ratio between supply and demand is constant in rod shaped bacteria, whereas it decreases for cocci. This requires that spherical cells evolve complex regulatory networks capable of maintaining the correct concentration of cellular proteins despite changes in surface/volume ratio. From this point of view, rod-shaped bacteria offer opportunities to develop unsophisticated regulatory networks.”

      why not all cells have lost rod shape and become spherical.

      Please see Kevin Young’s 2006 review on the adaptive significance of cell shape

      The value of this paper stems both from the insight it provides on the underlying molecular model for cell shape and from what it reveals about some key features of the evolutionary process. The paper, as it currently stands, provides more on which to chew for the molecular side than the evolutionary side. It provides valuable insights into the molecular architecture of how cells grow and what governs their shape. The evolutionary phenomena emphasized by the authors - the importance of loss-of-function mutations in driving rapid compensatory fitness gains and that multiple genetic and molecular routes to high fitness are o_en available, even in the relatively short time frame of a few hundred generations - are wellunderstood phenomena and so arguably of less broad interest. The more compelling evolutionary questions concern the nature and cause of stabilizing selection (in this case cell volume) and the evolution of complexity. The paper misses an opportunity to highlight the former and, while claiming to shed light on the latter, provides rather little useful insight. 

      Thank you for these thoughts and comments. However, we disagree that the experimental results are an overlooked opportunity to discuss stabilising selection. Stabilising selection occurs when selection favours a particular phenotype causing a reduction in underpinning population-level genetic diversity. This is not happening when selection acts on SBW25 ∆mreB leading to a restoration of fitness. Driving the response are biophysical factors, primarily the critical need to balance elongation rate with rate of septation. This occurs without any change in underlying genetic diversity.  

      Recommendations for the authors:  

      Reviewer 1 (Recommendations for the Authors): 

      Hereby my suggestion for improvement of the quantification of the data, the figures, and the text. 

      -  p 14, what is the unit of elongation rate?  

      At first mention we have made clear that the unit is given in minutes^-1

      -  p 14, please give an error bar for both p=0.85 and f=0.77, to be able to conclude they are different 

      Error on the probability p is estimated at the 95% confidence interval by the formula:1.96 , where N is the total number of cells. This has been added in the paragraph p »probability » of the Image Analysis section in the Material and Methods. 

      We also added errors on p measurement in the main text.

      -  p 14, all the % differences need an errorbar 

      The error bars and means are given in Fig 3C and 3D.

      -  Figure 1B adds units to compactness, and what does it represent? Is the cell size the estimated volume (that is mentioned in the caption)? Shouldn't the datapoints have error bars? 

      Compactness is defined in the “Image Analysis” section of the Material and Methods. It is a dimensionless parameter. The distribution of individual cell shapes / sizes are depicted in Fig 1B. Error does arise from segmentation, but the degree of variance (few pixels) is much smaller than the representations of individual cells shown.

      -  Figure 1C caption, are the 50.000 cells? 

      Correct. Figure caption has been altered.

      -  Figure 1D, first the elongation rate is described as a volume per minute, but now, looking at the units it is a rate, how is it normalized? 

      Elongation rate is explained in the Materials and Methods (see the image analysis section) and is not volume per minute. It is dV/dt = r*V (the unit of r is min^-1). Page 9 includes specific mention of the unit of r.

      -  Figure 1E, how many cells (n) per replicate? 

      Our apologies. We have corrected the figure caption that now reads:

      “Proportion of live cells in ancestral SBW25 (black bar) and ΔmreB (grey bar) based on LIVE/DEAD BacLight Bacterial Viability Kit protocol. Cells were pelleted at 2,000 x g for 2 minutes to preserve ΔmreB cell integrity. Error bars are means and standard deviation of three biological replicates (n>100).”

      -  Figure 1G, how does this compare to the wildtype 

      The volume for wild type SBW25 is 3.27µm^3 (within the “white zone”). This is mentioned in the text.

      -  Figure 2B, is this really volume, not size? And can you add microscopy images? 

      The x-axis is volume (see Materials and Methods, subsection image analysis). Images are available in Supp. Fig. 9.

      -  Figure 3A what does L1, L4 and L7 refer too? Is it correct that these same lines are picked for WT and delta_mreB 

      Thank you for pointing this out. This was an earlier nomenclature. It was shorthand for the mutants that are specified everywhere else by genotype and has now been corrected. 

      -  Figure 3c: either way write out p, so which probability, or you need a simple cartoon that is plotted. 

      The value p is the probability to proceed to the next generation and is explained in Materials and Methods  subsection image analysis.  We feel this is intuitive and does not require a cartoon. We nonetheless added a sentence to the Materials and Methods to aid clarity.

      -  Figure 4B can you add a ladder to the gel? 

      No ladder was included, but the controls provide all the necessary information. The band corresponding to PBP1A is defined by presence in SBW25, but absence in SBW25 ∆pbp1A.

      -  Figure 4c, can you improve the quantification of these images? How were these selected and how well do they represent the community? 

      We apologise for the lack of quantitative description for data presented in Fig 4C. This has now been corrected. In brief, we measured the intensity of fluorescent signal from between 10 and 14 cells and computed the mean and standard deviation of pixel intensity for each cell. To rule out possible artifacts associated with variation of the mean intensity, we calculated the ratio of the standard deviation divided by the square root of the mean. These data reveal heterogeneity in cell wall synthesis and provide strong statistical support for the claim that cell wall synthesis in ∆mreB is significantly more heterogeneous than the control. The data are provided in new Supp. Fig. 21. 

      Minor comments: 

      -  It would be interesting if the findings of this experimental evolution study could be related to comparative studies (if these have ever been executed).  

      Little is possible, but Hendrickson and Yulo published a portion of the originally posted preprint separately. We include a citation to that paper. 

      -  p 13, halfway through the page, the second paragraph lacks a conclusion, why do we care about DNA content? 

      It is a minor observation that was included by way of providing a complete description of cell phenotype.  

      -  p 17, "suggesting that ... loss-of-function", I do no not understand what this is based upon. 

      We show that the fitness of a pbp1A deletion is indistinguishable from the fitness of one of the pbp1A point mutants. This fact establishes that the point mutation had the same effects as a gene deletion thus supporting the claim that the point mutations identified during the course of the selection experiment decrease (or destroy) PBP1A function.

      -  p 25, at the top of the page: do you have a reference for the statement that a disorganized cell wall architecture is suited to the topology of spherical cells? 

      The statement is a conclusion that comes from our reasoning. It stems from the fact that it is impossible to entirely map the surface of a sphere with parallel strands.

    1. eLife Assessment

      Gil Ávila et al. evaluated the aperiodic component in the medial prefrontal cortex using resting-state EEG recordings from 149 individuals with chronic pain and 115 healthy participants. The authors present compelling evidence that the aperiodic component of the EEG does not differentiate between those with chronic pain and healthy individuals. The study was well-designed and rigorously conducted, and the clear and conclusive results provide important insights that can guide future research in the field of pain neuroscience.

    2. Reviewer #1 (Public review):

      Summary:

      In this study, Avila et al. tested the hypothesis that chronic pain states are associated with changes in excitability of the medial prefrontal cortex (mPFC). The authors used the slope of the aperiodic component of the EEG power spectrum (= the aperiodic exponent) as a novel, non-invasive proxy for the cortical excitation-inhibition ratio. They performed source localization to estimate the EEG signals generated specifically by the mPFC. By pooling resting-state EEG recordings from three existing datasets, the authors were able to compare the aperiodic exponent in the mPFC and across the whole brain (at all modeled cortical sources) between 149 chronic pain patients and 115 healthy controls. Additionally, they assessed the relationship between the aperiodic exponent and pain intensity reported by the patients. To account for heterogeneity in pain etiology, the analysis was also performed separately for two patient subgroups with different chronic pain conditions (chronic back pain and chronic widespread pain). The study found robust evidence against differences in the aperiodic exponent in the mPFC between people with chronic pain and healthy participants, and no correlation was observed between the aperiodic exponent and pain intensity. These findings were consistent across different patient subgroups and were corroborated by the whole-brain analysis.

      Strengths:

      The study is based on sound scientific reasoning and rigorously employs suitable methods to test the hypothesis. It follows a pre-registered protocol, which greatly increases the transparency and, consequently, the credibility of the reported results. In addition to the planned steps, the authors used a multiverse analysis to ensure the robustness of the results across different methodological choices. I find this particularly interesting, as the EEG aperiodic exponent has only recently been linked to network excitability, and the most appropriate methods for its extraction and analysis are still being determined. The methods are clearly and comprehensively described, making this paper very useful for researchers planning similar studies. The results are convincing, supported by informative figures, and the lack of the expected difference in mPFC excitability between the tested groups is thoroughly and constructively discussed.

      Weaknesses:

      Firstly, to augment the sample size, the authors pooled data recorded by different researchers using different experimental protocols. This inevitably increases sample variability and may limit the availability of certain measures, as was the case here with the reports of pain intensity in the patient group. Secondly, the analysis heavily relies on the estimation of cortical sources, an approach that may yield imprecise results, especially when default conduction models, source models, and electrode coordinates are used (as was the case here).

      Comments on revisions:

      The authors satisfactorily revised the manuscript and responded to previous questions and suggestions. I have no further comments.

    3. Reviewer #2 (Public review):

      Summary:

      This study evaluated the aperiodic component in the medial prefrontal cortex (mPFC) using resting-state EEG recordings from 149 individuals with chronic pain and 115 healthy participants. The findings showed no significant differences in the aperiodic component of the mPFC between the two groups, nor was there any correlation between the aperiodic component and pain intensity. These results were consistent across various chronic pain subtypes and were corroborated by whole-brain analyses. The study's robustness was further reinforced by preregistration and multiverse analyses, which accounted for a wide range of methodological choices.

      Strengths:

      This study was rigorously conducted, yielding clear and conclusive results. Furthermore, it adhered to stringent open and reproducible science practices, including preregistration, blinded data analysis, and Bayesian hypothesis testing. All data and code have been made openly available, underscoring the study's commitment to transparency and reproducibility.

      Weaknesses:

      The aperiodic exponent of the EEG power spectrum is often regarded as an indicator of the excitatory/inhibitory (E/I) balance. However, this measure may not be the most accurate or optimal for quantifying E/I balance, a limitation that the authors might consider addressing in the future.

      Comments on revisions:

      All my comments have been well addressed.

    4. Author response:

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

      Public Reviews

      Reviewer #1: 

      Summary:

      In this study, Avila et al. tested the hypothesis that chronic pain states are associated with changes in the excitability of the medial prefrontal cortex (mPFC). The authors used the slope of the aperiodic component of the EEG power spectrum (= the aperiodic exponent) as a novel, non-invasive proxy for the cortical excitation-inhibition ratio. They performed source localization to estimate the EEG signals generated specifically by the mPFC. By pooling resting-state EEG recordings from three existing datasets, the authors were able to compare the aperiodic exponent in the mPFC and across the whole brain (at all modeled cortical sources) between 149 chronic pain patients and 115 healthy controls. Additionally, they assessed the relationship between the aperiodic exponent and pain intensity reported by the patients. To account for heterogeneity in pain etiology, the analysis was also performed separately for two patient subgroups with different chronic pain conditions (chronic back pain and chronic widespread pain). The study found robust evidence against differences in the aperiodic exponent in the mPFC between people with chronic pain and healthy participants, and no correlation was observed between the aperiodic exponent and pain intensity. These findings were consistent across different patient subgroups and were corroborated by the whole-brain analysis.

      Strengths:

      The study is based on sound scientific reasoning and rigorously employs suitable methods to test the hypothesis. It follows a pre-registered protocol, which greatly increases the transparency and, consequently, the credibility of the reported results. In addition to the planned steps, the authors used a multiverse analysis to ensure the robustness of the results across different methodological choices. I find this particularly interesting, as the EEG aperiodic exponent has only recently been linked to network excitability, and the most appropriate methods for its extraction and analysis are still being determined. The methods are clearly and comprehensively described, making this paper very useful for researchers planning similar studies. The results are convincing, and supported by informative figures, and the lack of the expected difference in mPFC excitability between the tested groups is thoroughly and constructively discussed.

      We are grateful for the appreciation of the strengths of our study.  

      Weaknesses:

      Firstly, although I appreciate the relatively large sample size, pooling data recorded by different researchers using different experimental protocols inevitably increases sample variability and may limit the availability of certain measures, as was the case here with the reports of pain intensity in the patient group. Secondly, the analysis heavily relies on the estimation of cortical sources, an approach that offers many advantages but may yield imprecise results, especially when default conduction models, source models, and electrode coordinates are used. In my opinion, this point should be discussed as well.

      We agree that the heterogeneous sample of people with chronic pain increases variability and limits the availability of clinical measures. We further agree on the limitations of source space analysis. Therefore, we have added these limitations to the discussion section.

      Reviewer #2: 

      Summary:

      This study evaluated the aperiodic component in the medial prefrontal cortex (mPFC) using restingstate EEG recordings from 149 individuals with chronic pain and 115 healthy participants. The findings showed no significant differences in the aperiodic component of the mPFC between the two groups, nor was there any correlation between the aperiodic component and pain intensity. These results were consistent across various chronic pain subtypes and were corroborated by whole-brain analyses. The study's robustness was further reinforced by preregistration and multiverse analyses, which accounted for a wide range of methodological choices.

      Strengths:

      This study was rigorously conducted, yielding clear and conclusive results. Furthermore, it adhered to stringent open and reproducible science practices, including preregistration, blinded data analysis, and Bayesian hypothesis testing. All data and code have been made openly available, underscoring the study's commitment to transparency and reproducibility.

      We appreciate the appraisal of the strengths of our study, highlighting our efforts in open and reproducible science practices.

      Weaknesses:

      The aperiodic exponent of the EEG power spectrum is often regarded as an indicator of the excitatory/inhibitory (E/I) balance. However, this measure may not be the most accurate or optimal for quantifying E/I balance, a limitation that the authors might consider addressing in the future.

      We are grateful for this suggestion and fully agree that the aperiodic component of the power spectrum is not necessarily the most optimal and accurate measure for quantifying E/I balance. We have now included this limitation in the discussion section.

      Recommendations for the authors

      Reviewer #1: 

      (1) In the Results section, it might be helpful to provide the mean values of the aperiodic exponent (before age correction) for all tested groups and subgroups. As this measure is still not widely used, providing these values would allow readers to better understand the normal range of the aperiodic exponent.

      We have added the mean values of the aperiodic exponent and their standard deviation (before age correction) to the manuscript's results section (page 6 and 11).

      (2) When reporting the aperiodic exponent across all cortical sources (Q3), I think it would be useful to include the raw values in Figure 6 in the main text rather than in the Supplementary Materials. At a glance, these plots seem to suggest that the aperiodic exponent differs between groups in the occipital and parietal regions, even though no tests were significant after correcting for multiple comparisons. Maybe this observation also deserves a mention in the text and possibly in the Discussion..?

      We have moved the report on the aperiodic exponent across all cortical sources from the Supplementary Material to the main text. It is now Fig. 7 of the main manuscript. Moreover, we agree that the plots suggest group differences in certain brain regions. However, according to our rigorous open and reproducible science practices and pre-registration, we prefer not to speculate on these non-significant findings. 

      (3) In the Methods section, when describing the participants, the authors state that "Gender was balanced across both groups...". It might be better to avoid referring to the datasets as "balanced," considering that the sample includes almost twice as many females as males.

      We have replaced the misleading statement with the more precise statement that ”the gender ratio of both groups was similar.”

      (4) In the Methods section, when describing the source localization, I find it slightly confusing that the authors first mention the anterior cingulate cortex as a possible label included in the mPFC cortical parcels but then state that the version of the cortical atlas used did not contain such a label. It might be simpler not to mention the cingulate cortex at all.

      We have deleted the misleading sentence from the manuscript.  

      Reviewer #2: 

      (1) The aperiodic exponent of the EEG power spectrum is often considered an indicator of the excitatory/inhibitory (E/I) balance, but this measure can be susceptible to artifacts. It is important to acknowledge this limitation and consider exploring alternative measures to quantify the E/I ratio in future studies.

      We are grateful for this suggestion and fully agree that the aperiodic component of the power spectrum is not necessarily the most optimal and accurate measure for quantifying E/I balance. We have now included this limitation in the discussion section.

      (2) The study assumed a linear relationship between the E/I ratio (represented by the aperiodic exponent of the EEG power spectrum) and chronic pain. However, this assumption may not hold true in all cases, and this point could be discussed in the study.

      We fully agree that the relationship between the E/I ratio and chronic pain might not be a linear one and have added this point to the discussion section.

      (3) The aperiodic component was characterized in eyes-closed resting-state EEG recordings, although EEG data were collected in both eyes-closed and eyes-open conditions. The authors could also consider assessing the aperiodic component from EEG data with eyes open.

      We thank the reviewer for this suggestion. We have focused our analysis on eyes-closed recordings since these recordings are usually less contaminated by artifacts than eyes-open recordings. Moreover, in our current datasets, some participants were missing eyes-open recordings. We agree that performing similar analyses for the eyes-open recordings would also be interesting. However, adding these analyses would double the amount of data included in the manuscript, which would likely overload it. We have, therefore, now included a statement to the discussion that future studies should also analyze eyes-open EEG recordings.  

      (4) The EEG power spectrum was calculated from signals after source reconstruction, a crucial step for targeting specific brain regions. However, this process can introduce potential signal distortions, such as variations in source waveforms depending on different regularization parameters. To ensure the robustness of the results, the authors could perform the same analysis at the sensor level, for example, using signals recorded at Fz.

      We agree on the potential shortcomings and limitations of source space analysis and have added this limitation to the discussion section.

      (5) It would be beneficial to present the raw EEG power spectrum averaged across subjects for each condition, along with the scalp distribution of the aperiodic exponent. This would enhance readers' understanding of the study and help demonstrate the quality of the data.

      We are grateful for this suggestion and added the power spectrum for each condition and the scalp distribution of the aperiodic exponent to the Supplementary Material.

      (6) Linear regression models were used to control for the influence of age on aperiodic exponents and pain intensity ratings. However, it is unclear why other relevant variables, such as gender and medication use, were not considered.

      We agree that the aperiodic exponent might be influenced by gender and medication. As these analyses had not been included in our pre-registered analysis plan, we have not performed them. Moreover, although we agree that gender might have an impact, we have not found any evidence for this so far. Regarding medication, we fully agree that medication can influence the measure. However, medication was very heterogeneous, including drugs with fundamentally different mechanisms of action. Thus, we do not see a robust way to appropriately analyze these effects with sufficient statistical power. We have now added this important point to the discussion section.

      (7) The authors may consider addressing or discussing the impact of inter-individual variability on the negative results, particularly given that the data were derived from multiple experiments.

      We agree that the heterogeneous sample of people with chronic pain increases variability and limits the availability of clinical measures. We have added this limitation to the discussion.

    1. eLife Assessment

      This important study enhances our understanding of the foraging behaviour of aerial insectivorous birds. Using solid methodology, the authors have collected extensive data on bird movements and prey availability, which in turn provide support for the main claim of the study. The work will be of broad interest to behavioural ecologists.

    2. Reviewer #1 (Public review):

      This study tests whether Little Swifts exhibit optimal foraging, which the data seem to indicate is the case. This is unsurprising as most animals would be expected to optimize the energy income : expenditure ratio, however it hasn't been explicitly quantified before the way it was in this manuscript.

      The major strength of this work is the sheer volume of tracking data and the accuracy of those data. The ATLAS tracking system really enhanced this study and allowed for pinpoint monitoring of the tracked birds. These data could be used to ask and answer many questions beyond just the one tested here.

      The major weakness of this work lies in the sampling of insect prey abundance at a single point on the landscape, 6.5 km from the colony. This sampling then requires the authors to work under the assumption that prey abundance is simultaneously even across the study region. It may be fair to say that prey populations might be correlated over space but are not equal. It is uncertain whether other aspects of the prey data are problematic. For example, the radar only samples insects at 50m or higher from the ground - how often do Little Swifts forage under 50m high?

      The finding that Little Swifts forage optimally is indeed supported by the data, notwithstanding some of the shortcomings in the prey abundance data. The authors achieved their aims and the results support their conclusions.

      At its centre, this work adds to our understanding of Little Swift foraging and extends to a greater understanding of aerial insectivores in general. While unsurprising that Little Swifts act as optimal foragers, it is good to have quantified this and show that the population declines observed in so many aerial insectivores are not necessarily a function of inflexible foraging habits. Further, the methods used in this research have great potential for other work. For example, the ATLAS system poses some real advantages and an exciting challenge to existing systems, like MOTUS. The radar that was used to quantify prey abundance also presents exciting possibilities if multiple units could be deployed to get a more spatially-explicit view.

      To improve the context of this work, it is worth noting that this research goes into much further depth than any previous studies on a similar topic in several flycatcher and swallow species. A further justification is posited that this research is needed due to dramatic insect population declines, however, the magnitude and extent of such declines are fiercely debated in the literature.

    3. Reviewer #2 (Public review):

      Summary:

      Bloch et al. studied the relationships between aerial foragers (lesser swifts) tracked using an automated radio telemetry system (Atlas) and their prey (flying insects) monitored using a small vertical-looking radar (BirdScan MR1). The aim of the study was to check whether swifts optimise their foraging according to the abundance of their prey. The results provide evidence that small swifts can increase their foraging rate when aerial insect abundance is high, but found no correlation between insect abundance and flight energy expenditure.

      Key points:

      This study fills gaps in fundamental knowledge of prey-predator dynamics in the air. It describes the coincidence between the abundance of flying insects and the characteristics derived from monitoring individual swifts.

      Weaknesses:

      The paper uses assumptions largely derived from optimal foraging theory, but mixes up the form of natural selection: parental energy, parental survival (predation risk), nestling foraging and reproductive success. The results are partly inconsistent, and confounding factors (e.g., the brooding phase versus the nestling phase) remained ignored. In conclusion, the analyses performed are insufficient to rigorously assess whether lesser swifts are optimising their foraging beyond making shorter foraging trips.<br /> The filters applied to the monitoring data are necessary but may strongly influence the characteristics derived based on maximum or mean values. Sensitivity tests or the use of characteristics that are less dependent on extreme values could provide more robust results.

    4. Author response:

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

      eLife Assessment

      This valuable work advances our understanding of the foraging behaviour of aerial insectivorous birds. Its major strength is the large volume of tracking data and the accuracy of those data. However, the evidence supporting the main claim of optimal foraging is incomplete.

      We deeply appreciate the thoughtful review provided by the reviewers, including their valuable insights and meticulous attention to detail. Each comment has been thoroughly evaluated, leading to substantial improvements in the manuscript. Your constructive critique has been instrumental in refining our research and rectifying any oversights. We are confident that the revised article will make a substantial contribution to ecological research, particularly in advancing our understanding of foraging theories and the behaviors of aerial insectivores.

      Public Reviews:

      Reviewer #1 (Public Review):

      This study tests whether Little Swifts exhibit optimal foraging, which the data seem to indicate is the case. This is unsurprising as most animals would be expected to optimize the energy income: expenditure ratio; however, it hasn't been explicitly quantified before the way it was in this manuscript.

      The major strength of this work is the sheer volume of tracking data and the accuracy of those data. The ATLAS tracking system really enhanced this study and allowed for pinpoint monitoring of the tracked birds. These data could be used to ask and answer many questions beyond just the one tested here.

      The major weakness of this work lies in the sampling of insect prey abundance at a single point on the landscape, 6.5 km from the colony. This sampling then requires the authors to work under the assumption that prey abundance is simultaneously even across the study region - an assumption that is certainly untrue. The authors recognize this problem and say that sampling in a spatially explicit way was beyond their scope, which I understand, but then at other times try to present this assumption as not being a problem, which it very much is.

      Further, it is uncertain whether other aspects of the prey data are problematic. For example, the radar only samples insects at 50 m or higher from the ground - how often do Little Swifts forage under 50 m high?

      Another example might be that the phrases "high abundance" and "low abundance" are often used in the manuscript, but never defined.

      It may be fair to say that prey populations might be correlated over space but are not equal. It is this unknown degree of spatial correlation that lends confidence to the findings in the Results. As such, the finding that Little Swifts forage optimally is indeed supported by the data, notwithstanding some of the shortcomings in the prey abundance data. The authors achieved their aims and the results support their conclusions.

      Thanks for this comment.

      The basic assumption of this paper is that the abundance of insects bioflow in the airspace is correlated in space and varies over time. This has been demonstrated by different studies, see for example Bell et al. (Bell, J. R., Aralimarad, P., Lim, K. S., & Chapman, J. W. (2013). Predicting insect migration density and speed in the daytime convective boundary layer. PloS one, 8(1), e54202) in which positive correlation in insect bioflow is demonstrated between different sites that are more than 100 km away in Southern England. Given the much closer proximity of the colony and the radar site, as well as the large foraging distance of the swifts that often forage in the vicinity of the radar and beyond it, it is reasonable to assume that the radar was able to successfully capture between-day variation in the abundance of flying insects in the airspace, which is highly relevant for the foraging swifts. This is likely because meteorological variables such as temperature and wind, which tend to vary over a synoptic-system scale of several hundred kilometers, significantly influence the abundance of aerial insects. Furthermore, the direction of insect flight that has been recorded by the radar points to an overall south-north directionality of the insects during the period of the study (Werber et al. Under Review: Werber, Y., Chapman, J. W., Reynolds, D. R. and Sapir, N. Active navigation and meteorological selectivity drive patterns of mass intercontinental insect migration through the Levant). Hence, it is reasonable to assume that since the colony is positioned approximately 6.5 km south of the radar site, the radar is able to reliable estimate the between-day variation in aerial insect abundance experienced by the foraging swifts. Importantly, this between-day variation is very high, and detailed information regarding this variation is provided in the paper.  We thank the reviewer for the comments on the wording and have corrected it accordingly so that it is explicitly stated that the spatial distribution of the flying insects is indeed not uniform, but is expected to be simultaneously affected by environmental variables creating spatially correlated bioflow of aerial insects.

      The term "high abundance" or "low abundance" is relative to the variable being examined but throughout the manuscript we did not use these terms to describe an absolute amount or a certain threshold but rather to describe the ecological circumstances experienced by the birds on different days that substantially varied in abundance of insect recorded by the radar. However, we have improved the wording of the text so that it is now clear that we refer to relative  and not to absolute values.

      At its centre, this work adds to our understanding of Little Swift foraging and extends to a greater understanding of aerial insectivores in general. While unsurprising that Little Swifts act as optimal foragers, it is good to have quantified this and show that the population declines observed in so many aerial insectivores are not necessarily a function of inflexible foraging habits. Further, the methods used in this research have great potential for other work. For example, the ATLAS system poses some real advantages and an exciting challenge to existing systems, like MOTUS. The radar that was used to quantify prey abundance also presents exciting possibilities if multiple units could be deployed to get a more spatially-explicit view.

      To improve the context of this work, it is worth noting that the authors suggest that this work is important because it has never been done before for an aerial insectivore; however, that justification is untrue as it has been assessed in several flycatcher and swallow species. A further justification is that this research is needed due to dramatic insect population declines, but the magnitude and extent of such declines are fiercely debated in the literature. Perhaps these justifications are unnecessary, and the work can more simply be couched as just a test of optimality theory.

      We appreciate the reviewer's helpful comment. A flycatcher is indeed an aerial insect eater, but its foraging strategy is very different from that of swifts. A comparison with the foraging strategy of the swallow is much more relevant. However, the methods used to quantify bird movement in the airspace in previous articles limited the ability to examine the optimal foraging theory in detail. Following the comment, we revised the text to better describe the uniqueness of our research. Further, since we studied insectivores, it is important to provide a broad context to potentially significant threats to the birds, albeit being debatable

      Reviewer #2 (Public Review):

      Summary:

      Bloch et al. investigate the relationships between aerial foragers (little swifts) tracked with an automated radio-telemetry system (Atlas) and their prey (flying insects) monitored with a small-scale vertical-looking radar device (BirdScan MR1). The aim of the study was to test whether little swifts optimise their foraging with the abundance of their prey. However, the results provided little evidence of optimal foraging behaviour.

      Strengths:

      This study addresses fundamental knowledge gaps on the prey-predator dynamics in the airspace. It describes the coincidence between the abundance of flying insects and features derived from tracking individual swifts.

      Weaknesses:

      The article uses hypotheses broadly derived from optimal foraging theory, but mixes the form of natural selection: parental energetics, parental survival (predation risks), nestling foraging, and breeding success.

      While this study explores additional behavioral theories alongside optimal foraging theory, its findings unequivocally support the latter. The highly statistically significant observed reduction in flight distance from the breeding colony in elation to increasing insect abundance (supporting predictions 1 and 2) coupled with an increased rate of colony visits (supporting prediction 5) demonstrate the Little Swifts' adeptness at optimizing their aerial foraging behavior. This behavior manifests in an enhanced frequency of visits to the breeding colony, underscoring their food provisioning maximization.

      Results are partly incoherent (e.g., "Thus, even when the birds foraged close to the colony under optimal conditions, the shorter traveling distance is not thought to not confer lower flight-related energetic expenditure because more return trips were made.", L285-287),

      Thanks for the comment. We have corrected this sentence.

      and confounding factors (e.g., brooding vs. nestling phase) are ignored.

      The breeding stage may indeed affect food provisioning properties but this factor is not confounded since insect abundance, and the consequent changes in bird foraging properties, fluctuated between sequential days while brooding and nestling phases take place over a period of several weeks, each. Further, despite the possible influence of breeding stages on bird behavior, variability in reproductive stages is expected among pairs in a breeding colony occupying dozens of pairs, despite some coordination in nesting initiation. Practically, the narrow and concealed nest openings hindered direct observation of the nests, posing challenges in determining the precise reproductive stage of each pair. Anyway, we added a short description of the dense colony structure to the Methods section.

      Some limits are clearly recognised by the authors (L329 and ff).

      See above the response about the distribution of insects in space.

      To illustrate potential confounding effects, the daily flight duration (Prediction 4) should decrease with prey abundance, but how far does the daily flight duration coincide with departure and arrival at sunrise and sunset (note that day length increases between March and May), respectively, and how much do parents vary in the duration of nest attendance during the day across chick ages?

      We added the following explanation to the Methods section:

      To standardize the effect of day length on daily foraging duration, we calculated and subtracted the day length from the total daily foraging time (Day duration - Daily foraging duration = Net foraging duration). The resulting data represent the daily foraging duration in relation to sunrise and sunset, independent of day length.

      To conclude, insufficient analyses are performed to rigorously assess whether little swifts optimize their foraging.

      We disagree. See our responses above.

      Filters applied on tracking data are necessary but may strongly influence derived features based on maximum or mean values. Providing sensitivity tests or using features less dependent on extreme values may provide more robust results.

      Thank you for highlighting the importance of considering the impact of data filtering on derived features. In our analysis, we employed rigorous filtering methods to emphasize central data tendencies while mitigating the influence of extreme values. These methods, validated through consultation with experts in tracking data analysis, follow established practices in the literature. Detailed descriptions of our filtering procedures can be found in the Methods section, with citations to relevant published studies.

      Radar insect monitoring is incomplete and strongly size-dependent. What is the favourite prey size of swifts? How does it match with BirdScan MR1 monitoring capability?

      We added an explanation to the Methods section to address this comment:

      The Radar Cross Section (RCS) quantifies the reflectivity of a target, serving as a proxy for size by representing the cross-sectional area of a sphere with identical reflectivity to water, whose diameter equals the target's body length. Recent findings indicate that the BirdScan MR1 radar can detect insects with an RCS as low as 3 mm², enabling the detection of insects with body lengths as small as 2 mm. These capabilities make the radar suitable for locating the primary prey of swifts, which typically range in size from 1 to 16 mm.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Lines 53-59 - major run-on sentence

      Thanks for the comment. Done.

      Line 133 - describe better. Attached where? Were feathers clipped or removed?

      Thanks for the comment. Done.

      Line 153 - shouldn't be a new paragraph

      Done.

      Line 157 - justify choosing four 

      To ensure a robust analysis of swifts' behavior relative to food abundance across multiple individuals simultaneously, we opted to exclude data from instances where only 3 tags were active. This decision was motivated by the fact that these instances accounted for only 2.9% of the data, and their exclusion minimally impacted overall data volume while enhancing data quality. In contrast, instances with 4 tags, comprising 16.2% of the data, provided substantial insights. Omitting these instances would have resulted in significant data loss. Thus, setting a threshold of 4 simultaneous tags represents a balance between maintaining adequate data quantity and ensuring high data quality for meaningful analysis.

      It took me a long time to determine whether the average and maximum flight distance was actual or Euclidean. It was only in the Results that I grasped it was actual. Define up front in the Methods.

      Thanks for the comment. Done.

      In my public review, I mention that optimal foraging has been assessed in other aerial insectivores. Here are some of the papers I was referring to:

      • Davies (1977) Prey selection and the search strategy of the spotted flycatcher (Muscicapa striata): A field study on optimal foraging. Animal Behaviour 25: 1016-1022.

      • Lifjeld & Slagsvold (1988) Effects of energy costs on the optimal diet: an experiment with pied flycatchers Ficedula hypoleuca feeding nestlings. Ornis Scandinavica 19: 111-118.

      • Quinney & Ankney (1985) Prey size selection by tree swallows. Auk 102: 245-250.

      • Turner (1982) Optimal foraging by the swallow (Hirundo rustica, L): Prey size selection. Animal Behaviour 30:862-872.

      Lastly, in terms of the work not being spatially-explicit, I do note that in lines 323-324 you acknowledge that prey populations can be patchy, then ten lines later, you provide citations to say that patchiness is not a problem because of spatial correlations. This is a bit overly dismissive, in my view, and to suggest (lines 336-337) that "patches of high insect concentration...might not exist at all" is certainly incorrect (and misleading). I do note the valiant attempt to address the spatial shortcoming in the remainder of the paragraph - although addressing it does not make the problem go away.

      Thanks for the comment.

      We revised the text to make it more coherent.

      Reviewer #2 (Recommendations For The Authors):

      L161: typo > missing space in 'meanof'

      Corrected.

      L192-193: Did the authors use the timing of sunrise and sunset to determine daytime?

      Yes. The daytime was calculated in relation to sunrise and sunset.

      Did the authors calculate the MTR from sunrise to sunset, or averaging the hourly MTR?

      If using hourly MTR, specify the criteria to assign an hourly MTR to daytime when sunset/sunrise is happening during that hour.

      A simplified terminology for "Average daily insect MTR" might be useful, in particular for the result section (insect MTR).

      Average daily insect MTR is calculated for a fixed period from 5 am to 8 pm local time. An explanation has been added to the Methods section, and the terminology in the text has been simplified as suggested

      Note that the 'M' of MTR stands for migration, which may not be appropriate in this context, and simply using "insect traffic rate" may be a better terminology.

      Thanks for the comment. The 'M' of MTR can also stand for movement, as the insects detected by the radar move in the airspace. This is how this term has been defined in the paper (e.g. in line 23 of the Summary section). Therefore, we did not change the terminology to “insect traffic rate”, which is a term not used in other studies.

      Considering the large number of predictions (10!), it would be appropriate to list them in the results (e.g., "on the daily average flight distance from the breeding colony (Prediction 3)").

      We added prediction numbers to the Results and the Discussion.

      Note that the terminology varies; e.g., in the introduction "overall daily flight distance" (L75), in the results "average length of the daily flight route" (L236), and further confusion with "daily average flight distance from the breeding colony" (L232).

      Thanks for the comment. fixed.

      The terminology - average daily 'air/flight' distance (L74-76) - needs clarification.

      Done.

      Results: Use only a relevant and consistent number of decimals to report on the effect size and p-values.

      Done.

      The authors are citing non-peer-reviewed publications:

      21. Bloch I, Troupin D, Sapir N. Movement and parental care characteristics during the nesting season of 468 the Little Swift (Apus affinis) [Poster presentation]. 12th European Ornithologists' Union Congress. Cluj Napoca, Romania. 2019.

      62. Zaugg S, Schmid B, Liechti F. Ensemble approach for automated classification of radar echoes into functional bird sub-types. In: Radar Aeroecology. 2017. p. 1. doi:10.13140/RG.2.2.23354.80326

      It is acceptable to cite non-peer-reviewed sources if they have a significant contribution to the background of the article without a critical impact on the core of the research.

    1. eLife Assessment

      This important study describes two findings: first, that TEAD is subject to turnover by the ubiquitin-proteasome system involving RNF146 and Parylation, and second, the development of a pan-TEAD heterobifunctional degrader that is used to inhibit growth of a YAP-dependent cancer cell line and to characterize TEAD binding sites in the genome. Convincing evidence supports the development and specificity of the degrader. This article will be of relevance to cancer biologists and scientists interested in proteostasis, cellular signaling, and post-translation modification of proteins.

    2. Reviewer #1 (Public review):

      Summary:

      In the first half of this study, Pham et al. investigate the regulation of TEAD via ubiquitination and PARylation, identifying an E3 ubiquitin ligase, RNF146, as a negative regulator of TEAD activity through an siRNA screen of ubiquitin-related genes in MCF7 cells. The study also finds that depletion of PARP1 reduced TEAD4 ubiquitination levels, suggesting a certain relationship between TEAD4 PARylation and ubiquitination which was also explored through an interesting D70A mutation. Pham et al. subsequently tested this regulation in D. melanogaster by introducing Hpo loss-of-function mutations and rescuing the overgrowth phenotype through RNF146 overexpression.

      In the second half of this study, Pham et al. designed and assayed several potential TEAD degraders with a heterobifunctional design, which they term TEAD-CIDE. Compounds D and E were found to effectively degrade pan-TEAD, an effect which could be disrupted by treatment with TEAD lipid pocket binders, proteasome inhibitors, or E1 inhibitors, demonstrating that the TEAD-CIDEs operate in a proteasome-dependent manner. These TEAD-CIDEs could reduce cell proliferation in OVCAR-8, a YAP deficient cell line, but not SK-N-FI, a Hippo pathway independent cell line. Finally, this study also utilizes ATAC-seq on Compound D to identify reductions in chromatin accessibility at the regions enriched for TEAD DNA binding motifs.

      Strengths:

      The study provides compelling evidence that the E3 ubiquitin ligase RNF146 is a novel negative regulator of TEAD activity. The authors convincingly delineate the mechanism through multiple techniques and approaches. The authors also describe the development of heterobifunctional pan-degraders of TEAD, that could serve as valuable reagents to more deeply study TEAD biology.

      Weaknesses:

      The scope of this study is extremely broad. The first half of the paper highlights the mechanisms underlying TEAD degradation; however, the connection to the second half of the paper on small molecule degraders of TEAD is jarring, and it seems as though two separate stories were combined into this single massive study. In my opinion, the study would be stronger if it chose to focus on only one of these topics and instead went deeper.

      Additionally, the figure clarity needs to be substantially improved, as readability and interpretation was difficult in many panels. Lastly, there are numerous typos and poor grammar throughout the text that need to be addressed.

      Comments on revisions:

      The authors have addressed most of our critiques. The manuscript has improved significantly, particularly in the clarity of the figures and the flow of the text. The findings of this study contribute valuable insights into TEAD biology in cancer and provide useful resources for further research into TEAD.

      However, as noted by other reviewers, the manuscript still feels somewhat disjointed, despite the attempt to connect the two parts on RNF146-mediated TEAD degradation and the development of TEAD degraders. Certain data inconsistencies and technical limitations may have made some aspects of the data hard to interpret accurately and could benefit from further clarification.

    3. Author response:

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

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      In the first half of this study, Pham et al. investigate the regulation of TEAD via ubiquitination and PARylation, identifying an E3 ubiquitin ligase, RNF146, as a negative regulator of TEAD activity through an siRNA screen of ubiquitin-related genes in MCF7 cells. The study also finds that depletion of PARP1 reduced TEAD4 ubiquitination levels, suggesting a certain relationship between TEAD4 PARylation and ubiquitination which was also explored through an interesting D70A mutation. Pham et al. subsequently tested this regulation in D. melanogaster by introducing Hpo loss-of-function mutations and rescuing the overgrowth phenotype through RNF146 overexpression.

      In the second half of this study, Pham et al. designed and assayed several potential TEAD degraders with a heterobifunctional design, which they term TEAD-CIDE. Compounds D and E were found to effectively degrade pan-TEAD, an effect which could be disrupted by treatment with TEAD lipid pocket binders, proteasome inhibitors, or E1 inhibitors, demonstrating that the TEAD-CIDEs operate in a proteasome-dependent manner. These TEAD-CIDEs could reduce cell proliferation in OVCAR-8, a YAP-deficient cell line, but not SK-N-FI, a Hippo pathway independent cell line. Finally, this study also utilizes ATAC-seq on Compound D to identify reductions in chromatin accessibility at the regions enriched for TEAD DNA binding motifs.

      Strengths:

      The study provides compelling evidence that the E3 ubiquitin ligase RNF146 is a novel negative regulator of TEAD activity. The authors convincingly delineate the mechanism through multiple techniques and approaches. The authors also describe the development of heterobifunctional pan-degraders of TEAD, which could serve as valuable reagents to more deeply study TEAD biology.

      Weaknesses:

      The scope of this study is extremely broad. The first half of the paper highlights the mechanisms underlying TEAD degradation; however, the connection to the second half of the paper on small molecule degraders of TEAD is jarring, and it seems as though two separate stories were combined into this single massive study. In my opinion, the study would be stronger if it chose to focus on only one of these topics and instead went deeper.

      We thank the reviewer for the thoughtful feedback. In our mind, the two parts of the paper are inherently related as they both focus on proteasome-mediated degradation of TEADs. We first demonstrated that TEAD can be turned over by the ubiquitin proteasome system under endogenous conditions and identified a PARylation-dependent E3 ligase RNF146 as a major regulator of TEAD stability. Intriguingly, we observed that the four TEAD paralogs show different levels of polyubiquitination with some of them being highly stable in cells. These observations raised the question of whether the activity of the ubiquitin-proteasome system could be further enhanced pharmacologically to effectively target TEADs. We then tackled this question by providing a proof-of-concept demonstration of engineered heterobifunctional protein degraders can effectively degrade TEADs in cells and can be exploited as a therapeutic strategy for treating Hippo-dependent cancers.

      Additionally, the figure clarity needs to be substantially improved, as readability and interpretation were difficult in many panels. Lastly, there are numerous typos and poor grammar throughout the text that need to be addressed.

      We appreciate the suggestions from the reviewer and have updated the figures with high resolution images. We also corrected typos and grammatical errors in the text.

      Reviewer #2 (Public Review):

      The paper is made of two parts. One deals with RNF146, the other with the development of compounds that may cause TEAD degradation. The two parts are rather unrelated to each other.

      The main limit of this work is the lack of evidence that TEAD factors are in fact regulated by the proteasome and ubiquitylation under endogenous conditions. Also lacking is the demonstration that TEADs are labile proteins to the extent that such quantitative regulation at the level of stability can impact on YAP-TAZ biology. Without these two elements, the relevance and physiological significance of all these data is lacking.

      As for the development of new inhibitors of TEAD, this is potentially very interesting but underdeveloped in this manuscript. Irrespectively, if TEAD is stable, these molecules are likely lead compounds of interest. If TEAD is unstable, as entertained in the first part of the paper, then these molecules are likely marginal.

      We thank the reviewer for evaluating our manuscript. As the reviewer pointed out, the paper aimed to address 1) whether TEAD is being regulated by the proteasome and ubiquitination under endogenous conditions, and 2) whether TEAD can be inhibited through pharmacologically-induced degradation. First, we demonstrated that TEAD is ubiquitinated in cells and mapped the lysine residues that are poly-ubiquitinated (Fig. 1). Next, we identified RNF146 as a major E3 ligase that ubiquitinates TEADs and reduces their stability. Third, we show that RNF146-mediated TEAD ubiquitination is functionally important: RNF146 suppresses TEAD activity, and RNF146 genetically interacts with Hippo pathway components in fruit flies. Furthermore, as we showed in Fig. S2H, RNF-146 does not affect TEAD1 and TEAD4 to the same extent. Across all four cell lines evaluated, TEAD1 is more stable than TEAD4, raising the question of whether more consistent degradation of different TEAD paralogues could be achieved. To this end, we demonstrated that while the TEAD family of proteins is labile under endogenous conditions, more complete degradation of the TEAD proteins could be achieved using a heterobifunctional CRBN degrader. We further characterized these TEAD degraders in a series of cellular and genomic assays to demonstrate their cellular activity, selectivity, and inhibitory effects against YAP/TAZ target genes. We believe these degrader compounds would be of great interest to the Hippo community. We have revised the main text to clarify these points.

      Here are a few other specific observations:

      (1) The effect of MG is shown in a convoluted way, by MS. What about endogenous TEAD protein stability?

      We thank the reviewer for the question. The MS experiment shown in Figure 1 is a standard KGG experiment, where we used MS to map ubiquitination sites on TEADs. The graphical representation of the process is included in Fig. 1C, and the details of the procedure are included in the Methods section. Fig. 1D shows the different KGG peptides detected with or without MG-132 treatment. Fig. 1E shows the quantified abundance of each of the peptides across the four conditions indicated at the bottom of the plot. Regarding endogenous TEAD stability, ​​we conducted cycloheximide chase experiments to assess the stability of endogenously expressed TEAD isoforms upon RNF146 knockdown (Fig. S2G and S2H). Using isoform-specific antibodies, we demonstrated that siRNF146 significantly stabilized TEAD4 in multiple cell lines, including H226, PATU-8902, Detroit-562, and OVCAR-8 (Fig. S2G, S2H, and S2I), supporting the notion that RNF146 is a negative regulator of TEAD stability. Notably, the effect of siRNF146 on TEAD1 stability was less pronounced, and TEAD1 is more stable than TEAD4 across all four cell lines. These results are consistent with the lower level of ubiquitination of TEAD1 (Fig. 1A) and are corroborated by various biochemical, molecular, and genetic characterizations (Fig. 3A-C and S3E).

      (2) The relevance of siRNF on YAP target genes of Fig.2D is not statistically significant.

      We thank the reviewer for this comment. We have now removed the statistically significant claim.

      (3) All assays are with protein overexpression and Ub-laddering

      We thank the reviewer for the comment. To examine the ubiquitination level of TEAD proteins, we adopted an in vivo ubiquitination assay as described in our Materials and Methods section. To our knowledge, this assay is very standard in the ubiquitination field. Furthermore, as mentioned above, we have included in our revised manuscript cycloheximide chase experiments to assess the stability of endogenously expressed TEAD isoforms upon RNF146 knockdown (Fig. S2G and S2H). In addition to the overexpression system, we also assessed endogenously expressed TEAD using isoform-specific antibodies. We demonstrated that siRNF146 firmly stabilized TEAD4 in multiple cell lines, including H226, PATU-8902, Detroit-562, and OVCAR-8 (Fig. S2G with quantification and t-test), supporting the notion that RNF146 is a negative regulator of TEAD stability.

      (4) An inconsistency exists on the only biological validation (only by overexpression) on the fly eye size. RNF gain in Fig4C is doing the opposite of what is expected from what is portrayed here as a YAP/TEAD inhibitor: RNF gain is shown to INCREASE eye size, phenocopying a Hippo loss of function phenotype. According to the model proposed, RNF addition should reduce eye size. The authors stated that " This is in contrast to the anti-growth effect of RNF-146 in the Hpo loss-of-function background and indicates RNF146 may regulate other genes/pathways controlling eye sizes besides its role as a negative regulator of Sd/yki activity". This raises questions on what the authors are really studying: why, according to the authors, these caveats should occur on the controls, and not when they study Hpo mutants?

      We thank the reviewer for the comment. We acknowledge the complexity of the fly phenotype compared to tumor growth. TEAD (Sd) isn’t the only substrate of RNF146 in the fly. For instance, RNF146 is known to positively regulate Wnt signaling by degrading Axin. Previous studies have shown that activation of the Wnt signaling pathway by removal of the negative regulator Axin from clones of cells results in an overgrowth phenotype (Legent and Treisman, 2008). The overgrowth phenotype that we observed with overexpressing RNF146 only, therefore, likely is due to the role of RNF146 in regulating other signaling pathways. Importantly, we showed that upon Hippo loss of function, overexpression of RNF146 can rescue the Hippo overgrowth phenotype (Fig 4B). This differential outcome of RNF146 expression in wildtype versus Hippo-deficient flies indicates that the genetic interactions between RNF146 and Hippo pathway components altered the phenotypic outcome, and the phenotype we get with RNF146 overexpression in a Hippo loss of function background is not simply due to additive effects of functional loss of either component alone.

      Complementary to these overexpression data, we showed that knockdown of RNF146 increased the eye size further (Fig. S4A, B) in Hippo loss of function background, further supporting the role of RNF146 as a negative regulator of the overall pro-growth signals induced by yki upon Hippo loss of function.

      (5) The role of TEAD inactivation on YAP function is already well known. Disappointingly, no prior literature is cited. In any case, this is a mere control.

      We thank the reviewer for the suggestion. We have cited several published reviews that touch upon this aspect of the TEAD-YAP function, including Calses et al., 2019; Dey et al., 2020; Halder and Johnson, 2011; Wang et al., 2018. We are open to your suggestions on additional citations.

      (6) The second part of the paper on the Development and Screening of pan-TEAD lipid pocket degraders is interesting but unconnected to the above. The degradation pathway it involves has nothing to do with the enzyme described in the first figures.

      We thank the reviewer for the comment. We acknowledge that our paper broadly covers two aspects. We believe that they are inherently connected as they both address ubiquitin/proteasome-mediated TEAD degradation and the functional consequences of TEAD degradation. Given the increasing interest in targeting TEAD/YAP/TAZ in cancers, we think the pharmacological approaches to enhance TEAD degradation using orthogonal E3 ligases provide an important toolbox to understand how this pathway can be regulated under both physiological and pathological conditions. While RNF146 appears to be a major E3 ligase responsible for TEAD turnover under physiological conditions, we showed that the four TEAD paralogs have different poly-ubiquitination levels (Fig. 1A), and are differentially labile in cells (Fig. S2G-I). These observations raised the question of whether the activity of the ubiquitination-proteasome system could be further enhanced to allow more complete removal of TEADs. To this end, we demonstrated that E3 ligases that do not regulate TEAD under endogenous conditions can be leveraged pharmacologically to achieve deep TEAD degradation, thus providing a proof of concept that TEADs can be targeted simultaneously using such approaches. Finally, in addition to establishing the basic biological concept linking RNF146 to TEAD degradation, the compounds we engineered will serve as valuable chemical tools for future studies of TEAD biology and the Hippo pathway in cancers and beyond.

      (7) The role of CIDE on YAP accessibility to Chromatin is superficially executed. Key controls are missing along with the connection with mechanisms and prior knowledge of TEAD, YAP, chromatin, and other TEAD inhibitors, just to mention a few.

      We used ATAC-seq to assess chromatin accessibility comparing cells treated with DMSO and two different concentrations of compound D. We acknowledge there are small molecule inhibitors of TEADs that can modulate accessibility of YAP binding sites. Potential mechanistic differences between TEAD degraders versus TEAD small molecule inhibitions will be a future area of investigation.

      (8) The physiological relevance and the mechanistic interpretation of what should be in the ATAC seq in ovcar cells is missing.

      We showed in Fig. 7A-D the dose response of OVCAR cells to the TEAD degraders. As evident from those experiments, TEAD degraders inhibit the proliferation of OVCAR cells as expected from their dependencies on the TEAD/YAP/TAZ transcription complex. In the ATAC-seq experiment, we showed that the canonical TEAD/YAP/TAZ target genes ANKRD1 and CCN1 have reduced chromatin accessibility at their promoter/enhancer regions (Fig. 8C). By unbiased motif and pathway analyses, we show that TEAD binding sites and YAP signatures are most significantly downregulated in OVCAR-8 cells (Fig. 8D-E). These results are incorporated into the results section of the manuscript.

      Reviewer #3 (Public Review):

      Summary

      Pham, Pahuja, Hagenbeek, et al. have conducted a comprehensive range of assays to biochemically and genetically determine TEAD degradation through RNF146 ubiquitination. Additionally, they designed a PROTAC protein degrader system to regulate the Hippo pathway through TEAD degradation. Overall, the data appears robust. However, the manuscript lacks detailed methodological descriptions, which should be addressed and improved before publication. For instance, the methods used to analyze the K48 ubiquitination site on TEAD and the gene expression analysis of Hippo Signaling are unclear. Furthermore, the multiple proteomics, RNA-seq, and ATAC-seq data must be made publicly available upon publication to ensure reproducibility. Most of the main figures are of low resolution, which needs addressing.

      We thank the reviewer for evaluating our manuscript. All of the data will be uploaded to public databases. We apologize for the low figure resolution and have updated the figures in the revised manuscript. We also expanded the methods section with more details.

      Strengths:

      - A broad range of assays was used to robustly determine the role of RNF146 in TEAD degradation.

      - Development of novel PROTAC for degrading TEAD.

      Weaknesses:

      - An orthogonal approach is needed (e.g., PARP1 inhibitor) to demonstrate PARP1's dependency in TEAD ubiquitination.

      We thank the reviewer for the suggestion. We had attempted to assess the effect of PARP inhibitors (including veliparib and olaparib) on TEAD ubiquitination, but the data is relatively complex to interpret. Besides inhibiting PARP1/2 catalytic activities, these PARP inhibitors also trap PARP on chromatin. Hence, these inhibitors could induce other cellular changes in addition to inhibiting the catalytic activities of PARP1/2. Given these potential pitfalls, we decided not to include these inconclusive data. Even though the experiments with PARP inhibitors were inconclusive, our study supports that TEAD2 and TEAD4 are PARylated in cells using an anti-PAR antibody (Fig. 3B). Furthermore, we show that mutation of the D70 PARsylation site to alanine greatly abolished TEAD4 ubiquitination in cells, suggesting PARylation is important for TEAD4 ubiquitination. In addition, PARP1 depletion by siRNA and CRISPR guide RNA reduced TEAD2 and TEAD4 ubiquitination levels, indicating PARP1 is one of the PARPs responsible for TEAD PARylation in cells.

      - The data from Table 2 is unclear in illustrating the association of identified K48 ubiquitination with TEAD4, especially since the experiments were presumably to be conducted on whole cell lysates with KGG enrichment. This raises the possibility that the K48 ubiquitination could originate from other proteins. Alternatively, if the authors performed immunoprecipitation on TEAD followed by mass spectrometry, this should be explicitly described in the text and materials and methods section.

      We thank the reviewer for this question. The experiment was an IP-mass spectrometry study in a TEAD4 amplified cell line model (PATU-8902) after IP with a pan-TEAD antibody. Here, we observed K48 ubiquitin and other ubiquitin linkages as shown in the Supplementary Table S2 of the original submission. Although it is possible that the IP wash steps could be more stringent, we did enrich for TEAD protein prior to mass spectrometry. While the ubiquitin linkage signals may come mainly from TEAD protein (mainly TEAD4), we recognized that some signals may come from other proteins. Given the caveat, we have now removed the table from our paper and updated the text accordingly.

      - Figure 2D: The methodology for measuring the Hippo signature is unclear, as is the case for Figures 7E and F regarding the analysis of Hippo target genes.

      We apologize for the lack of clarification. In short, we previously developed the Hippo signature using machine learning and chemogenomics as described previously (Pham et al. Cancer Discovery 2021). In the revised version of the manuscript, we added the methodology for measuring the Hippo signature and cited our previous publication where we developed the Hippo signature.

      - Figure S3F requires quantification with additional replicates for validation.

      We thank the reviewer for the suggestion. We added the quantification for the blot and indicated the replication in the figure legend. Note that Figure S3F is now S3G.

      - There is a misleading claim in the discussion stating "TEAD PARylation by PAR-family members (Figure 3)"; however, the demonstration is only for PARP1, which should be corrected.

      We apologize for the statement. We observed both PARP1 and PARP9 in our TEAD IP-mass spec (now Figure S3E), which suggest both PARP-family members could be invovled. Nonetheless, we primarily focus on PARP1, which is widely expressed aross cell line models and present in higher abundance. Thus, our study only experimentally validated PARP1's role in regulating TEAD.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      General comments:

      (1) Please provide a smoother transition and well-defined connection between the first and second parts of the manuscript. The manuscript reads as two papers that were combined into one, without much attempt to disguise the fact.

      We thank the reviewer for the suggestion. We have added a transition paragraph to smoothen the transition. We acknowledge that our paper broadly covers two aspects. However, they both touch upon TEAD ubiquitination and degradation. In the first part of the manuscript, we described TEAD biology and showed that TEADs are post-translationally modified and subsequently regulated through PARylation-dependent RNF146-mediated ubiquitination. In the second part, we highlighted our abilities to leverage the PROTAC system for degrading such labile oncogenic proteins like TEADs. In addition to the biological concept, the compounds we engineered will serve as valuable chemical tools for future studies of TEAD biology and the Hippo pathway in cancers and beyond.

      (2) To confirm the proteasome mechanism of action, viability assays should be conducted with a CRBN KO.

      We thank the reviewer for the comment. In Figure 6E, we measured TEAD protein levels under CRBN knockdown and observed an expected change in TEAD stability. This observation and the other data presented in Figure 6 suggest that TEAD proteins are targeted for proteasomal degradation under compound D treatment.

      (3) As a control, sgPARP1 or PARP1 inhibitors should be used to confirm TEAD PARylation reduction.

      We thank the reviewer for the suggestion. We had attempted to assess the effect of PARP inhibitors (including veliparib and olaparib) on TEAD ubiquitination, but the data is relatively complex to interpret. Besides inhibiting PARP1/2 catalytic activities, PARP inhibitors also trap PARP on chromatin. Hence, these inhibitors could induce other cellular changes in addition to inhibit the catalytic activities of PARP1/2. Given these pitfalls, we decided not to include these inconclusive data. Even though the experiments with PARP inhibitors were inconclusive, our study supports that TEAD2 and TEAD4 are PARylated in cells using an anti-PAR antibody (Fig. 3B). Furthermore, we show that mutation of the D70 PARsylation site to alanine greatly abolished TEAD4 ubiquitination in cells, suggesting PARylation is important for TEAD4 ubiquitination. In addition, PARP1 depletion by siRNA and CRISPR guide RNA reduced TEAD2 and TEAD4 ubiquitination levels, indicating PARP1 is one of the PARPs responsible for TEAD PARylation in cells.

      (4) MS data looks convincing but an FDR of 1% should be applied - this is the accepted standard in the proteomics field. Please research the data with the more stringent filter.

      We thank the reviewer for the suggestion. Our IP-MS experiment comparing siNTC versus siYAP1/WWTR1 in Patu-8902 cells did not have replicates and FDR could not be derived. Therefore, we listed the raw data in Supplemental Table 3 without showing statistics. To validate the putative interactions identified by IP-MS, we performed IP-Western experiments to confirm that TEAD4 interacts with PARP1 (Figure 3A). It is important to note that in addition to our report, the interaction between PARP1 and TEADs has been observed in other publications (Calses et al., 2023; Yang et al., 2017). We have included more details of the IP-MS experiment reported in Supplemental Table 3 in the revised manuscript and cited previous work reporting TEAD-PARP1 interaction.

      (5) Proofread the manuscript more thoroughly for typos and grammatical errors.

      We thank the reviewer for raising this issue and have addressed it in the revision.

      (6) Improve figure clarity (e.g., clearly labeling graph axes).

      We apologize for the oversight. The revised manuscript contains high resolution figures.

      Specific points:

      Generally, the manuscript could use additional proofreading for grammar and clarity. It would not be practical to list all, but some representative examples are listed below:

      Run-on: "They act through an event-driven mechanism instead of conventional occupancy-driven pharmacology, in addition, target protein degradation removes all functions of the target protein and may also lead to destabilization of entire multidomain protein complexes."

      Typo: "Compound D exhibits significant inhibition of cell proliferation and downstream signaling compared to compound A, a reversible TEAD lipid pocket binder that lack the ubiquitin ligase binding moiety."

      Typo: "Thus, we sought to deplete TEAD proteins by directly target them for ubiquitination and proteasomal degradation via pharmacologically inducing interactions between TEAD and other abundantly expressed and PARylation-independent E3 ligases."

      Typo: "Compound A is a close in analog of Compound B as described previously (Holden et al., 2020)."

      We have revised the manuscript and corrected the typos and grammatical errors listed above and beyond.

      Specific comments on the figures are listed below:

      Figure 2:

      • Figures 2B and 2C should be separated into separate panels for clarity.

      We have updated the Figures 2B and 2C as suggested.

      • Figure 2C - "To further assess the function of RNF146, we depleted RNF146 by either sgRNA or siRNA." This should say either CRISPR-Cas9 KO or siRNA-mediated knockdown.

      We thank the reviewer for the suggestion. We revised the text to address this issue.

      • Figure 2D - y-axis is not labeled well/clearly. Additionally, there are different resolutions for the p-values on the graph (the top p-value is slightly clearer than the other two, suggesting either a different font was used or the value was pasted on top of a picture of the graph at a different resolution).

      We updated the figures according to the suggestions.

      • Figure S2A - "We identified three ubiquitin ligases - RNF146, TRAF3, and PH5A - as potential negative regulators for the Hippos pathway from the primary screen using the luciferase reporter." However, the siPHF5A data appears to decrease luciferase levels whereas siRNF146 and siTRAF3 increase it.

      We thank the reviewer for catching this error. We removed PH5A from this list.

      Figure 3:

      • Figure 3A - label more clearly. Is this an endogenous TEAD4 co-IP?

      We thank the reviewer for the suggestion. The experiment was an IP-mass spectrometry study in a TEAD4 amplified cell line model (PATU-8902) with pan-TEAD antibody. We have included the details to in the figure legends. Figure 3A is now Figure S3E in the revised manuscript.

      • Figure 3C - why are the dark and light exposures not matching/corresponding? In the dark exposure, there are two particularly dark bands, the darkest of which is at the top of the gel. However, this darkest band disappears in the light exposure gel. Additionally, the last lane is marked as +TEAD2 and +TEAD4. Not sure if this is a typo, and meant to be only +TEAD4? Seems a bit strange to have a double TEAD lane.

      We thank the reviewer for this comment and apologize for the oversight. There was a typo in the label. The light exposure image was from a replicate run instead of the same run, therefore the lanes didn’t all match up. We have removed the light exposure panel to resolve the confusion. (Figure 3B).

      Figure 5:

      • Figure 5B - why is shTEAD1-4/Sucrose a much higher tumor volume than shNTC/Sucrose negative control? Additionally, should the legend say "sNTC/Sucrose" as it does or "shNTC/Sucrose"?

      The labels for shTEAD1-4/Sucrose and shNTC/Sucrose are correct. We do not understand why there is a slight increase in tumor volume for shTEAD1-4/Sucrose and suspect that is due to the considerable variation in the experiment. This slight change, however, doesn’t influence our observation of tumor regression in shTEAD1-4 under the Doxycycline treatment.

      "sNTC/Sucrose" is a typo. We apologize for the oversight and have revised the figure.

      • Figure 5E - cited in text after Figures 6 and 7.

      We have updated the text accordingly.

      Figure 6:

      • Figure 6B - it is very interesting how this clearly shows the Hook effect for Compound D, but it's a bit harder to see for compound E that the compound degrades pan-TEAD. Would it be possible to quantify the blots to reinforce claims about protein degradation here?

      We thank the reviewer for the question. There may seem to be some hook effect across the three concentrations of compound D treatment in Fig. 6B.  However, in Fig. 6C-E, we observed pretty consistent TEAD degradation levels across a variety of concentrations. In addition, these experiments have been repeated in multiple cell lines with consistent results. We respectfully argue that more detailed investigation of the hook effect is beyond the scope of our study.

      Figure 7:

      • Figure 7F - this heat map is extremely difficult to interpret. Are there any interesting clusters? What are the darker/lighter bands for Compound D compared to DMSO control?

      We thank the reviewer for the comment and apologize for the lack of information on the figure. These are genes from a Hippo signature derived from our earlier work (Pham et al. Cancer Discovery). As a result of degrading TEAD when treating the cells with Compound D, we observed an expected downregulation of most of these genes compared to compound A.

      Figure 8:

      • Figure 8B - these two pie charts are also difficult to interpret. Perhaps try to present the data in a form other than encircling pie charts?

      We thank the reviewer for the suggestion. However, this is a very descriptive pie chart, we used this format to save space.

      • Figure 8C - what is GNE-6915? Is this Compound D?

      Yes, this is compound D. The text is updated accordingly.

      Reviewer #3 (Recommendations For The Authors):

      Figure 3A would benefit from explicitly stating the conditions within the figure, rather than referring to the legend. This clarity is also needed for Figure 8C, indicating whether the treatment was with compound D or GNE-6915.

      We thank the reviewer for the suggestion. We have added the details to the figures and made the suggested edits.

      Standardize the terms "ubiquitination" and "ubiquitylation" throughout the paper for consistency.

      We now use the term “ubiquitination” throughout the manuscript.

      The statement "In this study, we show that the activity of TEAD transcription factors can be post-transcriptionally regulated via the ubiquitin/proteasome system" should be corrected to "post-translationally regulated."

      We have update the manuscript accordingly.

      There is an additional exclamation mark above Figure 5E that should be removed.

      We have revised Figure 5E.

    1. eLife Assessment

      This study presents a useful model of genetic drift by incorporating variance in reproductive success, claiming to address several paradoxes in molecular evolution. However, some of the claimed "paradoxes" seem to be overstatements, as previous literature has pointed out the limitations of the standard model and proposed more advanced models to address those limitations. While the proposed new model presented in this paper yields some intriguing theoretical predictions, the analysis and simulations presented are incomplete to support the authors' strong claims, and it is unclear how much the model helps explain empirical observations.

    2. Reviewer #1 (Public review):

      The revision by Ruan et al clarifies several aspects of the original manuscript that were difficult to understand, and I think it presents some useful and interesting ideas. I understand that the authors are distinguishing their model from the standard Wright-Fisher model in that the population size is not imposed externally, but is instead a consequence of the stochastic reproduction scheme. Here, the authors chose a branching process but in principle any Markov chain can probably be used. Within this framework, the authors are particularly interested in cases where the variance in reproductive success changes through time, as explored by the DDH model, for example. They argue with some experimental results that there is a reason to believe that the variance in reproductive success does change over time.

      One of the key aspects of the original manuscript that I want to engage with is the DDH model. As the authors point out, their equations 5 and 6 are assumptions, and not derived from any principles. In essence, the authors are positing that that the variance in reproductive success, given by 6, changes as a function of the current population size. There is nothing "inherent" to a negative binomial branching mechanism that results in this: in fact, the the variance in offspring number could in principle be the same for all time. As relates to models that exist in the literature, I believe that this is the key difference: unlike Cannings models, the authors allow for a changing variance in reproduction through time.

      This is, of course, an interesting thing to consider, and I think that the situation the authors point out, in which drift is lower at small population sizes and larger at large population sizes, is not appreciated in the literature. However, I am not so sure that there is anything that needs to be resolved in Paradox 1. A very strong prediction of that model is that Ne and N could be inversely related, as shown by the blue line in Fig 3b. This suggests that you could see something very strange if you, for example, infer a population size history using a Wright-Fisher framework, because you would infer a population *decline* when there is in fact a population *expansion*. However, as far as I know there are very few "surprising population declines" found in empirical data. An obvious case where we know there is very rapid population growth is human populations; I don't think I've ever seen an inference of recent human demographic history from genetic data that suggests anything other than a massive population expansion. While I appreciate the authors empirical data supporting their claim of Paradox 1 (more on the empirical data later), it's not clear to me that there's a "paradox" in the literature that needs explaining so much as this is a "words of caution about interpreting inferred effective population sizes". To be clear, I think those words of caution are important, and I had never considered that you might be so fundamentally misled as to infer decline when there is growth, but calling it a "paradox" seems to suggest that this is an outstanding problem in the literature, when in fact I think the authors are raising a *new* and important problem. Perhaps an interesting thing for the authors to do to raise the salience of this point would be to perform simulations under this model and then infer effective population sizes using e.g. dadi or psmc and show that you could identify a situation in which the true history is one of growth, but the best fit would be one of decline

      The authors also highlight that their approach reflects a case where the population size is determined by the population dynamics themselves, as opposed to being imposed externally as is typical in Cannings models. I agree with the authors that this aspect of population regulation is understudied. Nonetheless, several manuscripts have dealt with the case of population genetic dynamics in populations of stochastically fluctuating size. For example, Kaj and Krone (2003) show that under pretty general conditions you get something very much like a standard coalescent; for example, combining their theorem 1 with their arguments on page 36 and 37, they find that exchangeable populations with stochastic population dynamics where the variance does not change with time still converge to exactly the coalescent you would expect from Cannings models. This is strongly suggestive that the authors key result isn't about stochastic population dynamics per se, but instead related to arguing that variance in reproductive success could change through time. In fact, I believe that the result of Kaj and Krone (2003) is substantially more general than the models considered in this manuscript. That being said, I believe that the authors of this manuscript do a much better job of making the implications for evolutionary processes clear than Kaj and Krone, which is important---it's very difficult to understand from Kaj and Krone the conditions under which effective population sizes will be substantially impacted by stochastic population dynamics.

      I also find the authors exposition on Paradox 3 to be somewhat strange. First of all, I'm not sure there's a paradox there at all? The authors claim that the lack of dependence of the fixation probability on Ne is a paradox, but this is ultimately not surprising---fixation of a positively selected allele depends mostly on escaping the boundary layer, which doesn't really depend on the population size (see Gillespie's book "The Causes of Molecular Evolution" for great exposition on boundary layer effects). Moreover, the authors *use a Cannings-style argument* to get gain a good approximation of how the fixation probability changes when there is non-Poisson reproduction. So it's not clear that the WFH model is really doing a lot of work here. I suppose they raise the interesting point that the particularly simple form of p(fix) = 2s is due to the assumption that variance in offspring is equal to 1.

      In addition, I raised some concerns about the analysis of empirical results on reproductive variance in my original review, and I don't believe that the authors responded to it at all. I'm not super worried about that analysis, but I think that the authors should probably respond to me.

      Overall, I feel like I now have a better understanding of this manuscript. However, I think it still presents its results too strongly: Paradox 1 contains important words of caution that reflect what I am confident is an under appreciated possibility, and Paradox 3 is, as far as I'm concerned, not a paradox at all. I have not addressed Paradox 2 very much because I think that another reviewer had solid and interesting comments on that front and I am leaving it to them. That being said, I do think Paradox 2 actually presents a deep problem in the literature and that the authors' argument may actually represent a path toward a solution.

      This manuscript can be a useful contribution to the literature, but as it's presented at the moment, I think most of it is worded too strongly and it continues to not engage appropriately with the literature. Theoretical advances are undoubtedly important, and I think the manuscript presents some interesting things to think about but ultimately needs to be better situated and several of the claims strongly toned down.

      References:<br /> Kaj, I., & Krone, S. M. (2003). The coalescent process in a population with stochastically varying size. Journal of Applied Probability, 40(1), 33-48.

    3. Reviewer #2 (Public review):

      Summary:

      This theoretical paper examines genetic drift in scenarios deviating from the standard Wright-Fisher model. The authors discuss Haldane's branching process model, highlighting that the variance in reproductive success equates to genetic drift. By integrating the Wright-Fisher model with the Haldane model, the authors derive theoretical results that resolve paradoxes related to effective population size.

      Strengths:

      The most significant and compelling result from this paper is perhaps that the probability of fixing a new beneficial mutation is 2s/V(K). This is an intriguing and potentially generalizable discovery that could be applied to many different study systems.

      The authors also made a lot of effort to connect theory with various real-world examples, such as genetic diversity in sex chromosomes and reproductive variance across different species.

      Comments on revisions:

      The author has addressed some of the concerns in my review, and I think the revised manuscript is more clear. I like the discussion about the caveats of the WFH model.

      I hope the authors could also discuss the conditions needed for V(K)/Ne to be a reasonable approximation. It is currently unclear how the framework should be adopted in general.

      The idea about estimating male-female V(K) ratios from population genetic data is interesting. Unfortunately, the results fell short. The accuracy of their estimators (derived using approximation Ne/V(K) approximation, and certain choice of theta, and then theta estimated with Watterson's estimator) should be tested with simulated results before applying to real data. The reliability of their estimator and their results from real data are unclear.

      Arguments made in this paper sometimes lack precision (perhaps the authors want to emphasize intuition, but it seems more confusing than otherwise). For example: The authors stated that "This independence from N seems intuitively obvious: when an advantageous mutation increases to say, 100 copies in determining a population (depending mainly on s), its fixation would be almost certain, regardless of N.". Assuming large Ne, and with approximation, one could assume the probability of loss is e^(-2sn), but the writing about "100 copies" and "almost certain" is very imprecise, in fact, a mutation with s=0.001 segregating at 100 copies in a large Ne population is most probably lost. Whereas in a small population, it will be fixed. Yet the following sentence states "regardless of N. This may be a most direct argument against equating genetic drift, certainly no less important than 1/ N . with N, or Ne (which is supposed to be a function of N's)." I find this new paragraph misleading.

      Some of the statements/wordings in this paper still seem too strong to me.

    4. Reviewer #3 (Public review):

      Summary:

      Ruan and colleagues consider a branching process model (in their terminology the "Haldane model") and the most basic Wright-Fisher model. They convincingly show that offspring distributions are usually non-Poissonian (as opposed to what's assumed in the Wright-Fisher model), and can depend on short-term ecological dynamics (e.g., variance in offspring number may be smaller during exponential growth). The authors discuss branching processes and the Wright-Fisher model in the context of 3 "paradoxes" --- 1) how Ne depends on N might depend on population dynamics; 2) how Ne is different on the X chromosome, the Y chromosome, and the autosomes, and these differences do match the expectations base on simple counts of the number of chromosomes in the populations; 3) how genetic drift interacts with selection. The authors provide some theoretical explanations for the role of variance in the offspring distribution in each of these three paradoxes. They also perform some experiments to directly measure the variance in offspring number, as well as perform some analyses of published data.

      Strengths:

      - The theoretical results are well-described and easy to follow.<br /> - The analyses of different variances in offspring number (both experimentally and analyzing public data) are convincing that non-Poissonian offspring distributions are the norm.<br /> - The point that this variance can change as the population size (or population dynamics) change is also very interesting and important to keep in mind.<br /> - I enjoyed the Density-Dependent Haldane model. It was a nice example of the decoupling of census size and effective size.<br /> - Equation (10) is a nice result (but see below)

      Weaknesses:

      - I am not convinced that these types of effects cannot just be absorbed into some time-varying Ne and still be well-modeled by the Wright-Fisher process. As a concrete example, Mohle and Sagitov 2001 show that a "coalescent Ne" for the WF model should be (N-1)/Var(K). This resolves the exponentially growing bacteria "paradox" raised in the present paper --- when the bacteria are growing Var(K) ~ 0, and hence there should be very little drift. This exactly resolves the "paradox" raised by the authors. Instead, it merely underscores that Ne does not need to be equal to (or even positively correlated!) with N. I absolutely do not see this as a failure of the WF model. Whether one finds branching processes or the WF model more biologically intuitive is a matter of taste, but to say that WF models cannot explain this "paradox" is false, when a well-known paper from more than 20 years ago does just that.<br /> - Along these lines, the result that Ne in the Wright-Fisher process might not be related to N in any straightforward (or even positively correlated) way are well-known (e.g., Neher and Hallatschek 2012; Spence, Kamm, and Song 2016; Matuszewski, Hildebrandt, Achaz, and Jensen 2018; Rice, Novembre, and Desai 2018; the work of Lounès Chikhi on how Ne can be affected by population structure; etc...)<br /> - I was also missing some discussion of the relationship between the branching process and the Wright-Fisher model (or more generally Cannings' Exchangeable Models) when conditioning on the total population size. In particular, if the offspring distribution is Poisson, then conditioned on the total population size, the branching process is identical to the Wright-Fisher model.<br /> - Given that Cannings' exchangeable models decouple N and Ne, it would not surprise me if something like equation (10) could be derived under such a model. I have not seen such a derivation, and the authors' result is nice, but I do not see it as proof that WF-type models (i.e., Cannings' models) are irreparably broken.

    5. Author response:

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

      eLife Assessment

      This study presents a useful modification of a standard model of genetic drift by incorporating variance in offspring numbers, claiming to address several paradoxes in molecular evolution. It is unfortunate that the study fails to engage prior literature that has extensively examined the impact of variance in offspring number, implying that some of the paradoxes presented might be resolved within existing frameworks.

      The prior literature the reviewers referred to are all "modified WF models". In the original submission, we lumped the standard and modified WF models together as the "generalized WF models". As the lumping causes confusions, their distinctions are now made clear.  That said, the Haldane model in our proposal is not a modification of the standard WF model because, conceptually, the two models are very different. WF is based on sampling whereas the Haldane model is based on gene transmission.

      While the "modified WF models" often incorporate V(K) [variance in progeny number], the modification is still based on the WF model of population sampling. The modification is mathematically feasible but biologically untenable, as explained explicitly in the revised text. Most important, all four paradoxes are as incompatible with the modified WF models as with the standard model. Note that the Haldane model does not have the sampling step, which is absorbed into the V(K) term. In the integrated WF-Haldane model, these paradoxes are resolved (see the new sections of Discussion, quoted below).

      If readers do not have time to ponder on all four paradoxes, they may simply read the first one, as follows. When the population size (N) is growing exponentially, such as in a bacteria culture, drift is nearly absent when N is small and becomes stronger as N increases, especially when approaching the carrying capacity.  Such common observations are exactly opposite of the WF model's central prediction. Any model based on sampling cannot escape the constraint of "greater drift, smaller N".

      Revision - The following text is a reproduction of the last 7 paragraphs of Discussion.

      “The standard WF model has been extended in several directions (overlapping generations, multiple alleles, ploidy, etc.). The modification most relevant to our studies here is the introduction of V(K) into the model, thus permitting V(K) ≠ E(K). While the modifications are mathematically valid, they are often biologically untenable. Kimura and Crow (1963) may be the first to offer a biological mechanism for V(K) ≠ E(K), effectively imposing the Haldane model on the WF model. Other models (Kimura and Crow 1963; Lynch, et al. 1995; Sjodin, et al. 2005; Der, et al. 2011; Cannings 2016) indeed model mathematically the imposition of the branching process on the population, followed by the WF sampling. The constructions of such models are biologically dubious but, more importantly, still unable to resolve the paradoxes. It would seem more logical to use the Haldane model in the first place by having two parameters, E(K) and V(K). 

      Even if we permit V(K) ≠ E(K) under the WF sampling, the models would face other difficulties. For example, a field biologist needs to delineate a Mendelian population and determine its size, N or Ne. In all WF models, one cannot know what the actual population being studied is. Is it the fly population in an orchard being sampled, in the geographical region, or in the entire species range? It is unsatisfactory when a population biologist cannot identify the population being studied. The Haldane model is an individual-output model (Chen, et al. 2017), which does not require the delineation of a Mendelian population.

      We shall now review the paradoxes specifically in relation to the modified WF models, starting with the multi-copy gene systems such as viruses and rRNA genes covered in the companion study (Wang, et al. 2024). These systems evolve both within and between hosts. Given the small number of virions transmitted between hosts, drift is strong in both stages as shown by the Haldane model (Ruan, Luo, et al. 2021; Ruan, Wen, et al. 2021; Hou, et al. 2023). Therefore, it does not seem possible to have a single effective population size in the WF models to account for the genetic drift in two stages. The inability to deal with multi-copy gene systems may explain the difficulties in accounting for the SARS-CoV-2 evolution (Deng, et al. 2022; Pan, Liu, et al. 2022; Ruan, Wen, et al. 2022; Hou, et al. 2023; Ruan, et al. 2023).

      We now discuss the first paradox of this study, which is about the regulation of N. In the general WF models, N is imposed from outside of the model, rather than self-generating within the model. When N is increasing exponentially as in bacterial or yeast cultures, there is almost no drift when N is very low and drift becomes intense as N grows to near the carrying capacity. As far as we know, no modifications of the WF model can account for this phenomenon that is opposite of its central tenet. In the general WF models, N is really the carrying capacity, not population size. 

      The second paradox of sex chromosomes is rooted in V(K) ≠ E(K). As E(K) is the same between sexes but V(K) is different, clearly V(K) = E(K) would not be feasible. The mathematical solution of defining separate Ne's for males and females (Kimura and Crow 1963; Lynch, et al. 1995; Sjodin, et al. 2005; Der, et al. 2011; Cannings 2016) unfortunately obscures the interesting biology. As shown in Wang et al. (2024; MBE), the kurtosis of the distribution of K indicates the presence of super-breeder males. While the Haldane model can incorporate the kurtosis, the modified WF models are able to absorb only up to the variance term, i.e., the second moment of the distribution. The third paradox of genetic drift is manifested in the fixation probability of an advantageous mutation, 2_s_/V(K). As explained above, the fixation probability is determined by the probability of reaching a low threshold that is independent of N itself. Hence, the key parameter of drift in the WF model, N (or Ne), is missing. This paradox supports the assertion that genetic drift is fundamentally about V(K) with N being a scaling factor. 

      As the domain of evolutionary biology expands, many new systems do not fit into the WF models, resulting in the lack of a genetic drift component in their evolutionary trajectories. Multi-copy gene systems are obvious examples. Others include domestications of animals and plants that are processes of rapid evolution  (Diamond 2002; Larson and Fuller 2014; Purugganan 2019; Chen, Yang, et al. 2022; Pan, Zhang, et al. 2022; Wang, et al. 2022). Due to the very large V(K) in domestication, drift must have played a large role. Somatic cell evolution is another example with “undefinable” genetic drift (Wu, et al. 2016; Chen, et al. 2017; Chen, et al. 2019; Ruan, et al. 2020; Chen, Wu, et al. 2022). The Haldane (or WFH) model, as an "individual output" model, can handle these general cases of genetic drift.

      The Haldane model and the WF model are fundamentally different approaches to random forces of evolution. While the WF models encounter many biological contradictions, they have provided approximate mathematical solutions to more realistic scenarios. In systems such as in viral evolution (Ruan, Hou, et al. 2022; Hou, et al. 2023) or somatic cell evolution (Chen, Wu, et al. 2022; Zhai, et al. 2022) whereby the WF solution is absent, further development of the WFH model will be necessary.”

      In addition, while the modified model yields intriguing theoretical predictions, the simulations and empirical analyses are incomplete to support the authors' claims.

      This point is addressed in the responses to reviewers' comments. Since they are quite technical, they do not fit in the overview here.

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      The authors present a theoretical treatment of what they term the "Wright-Fisher-Haldane" model, a claimed modification of the standard model of genetic drift that accounts for variability in offspring number, and argue that it resolves a number of paradoxes in molecular evolution. Ultimately, I found this manuscript quite strange.

      The notion of effective population size as inversely related to the variance in offspring number is well known in the literature, and not exclusive to Haldane's branching process treatment. However, I found the authors' point about variance in offspring changing over the course of, e.g. exponential growth fairly interesting, and I'm not sure I'd seen that pointed out before.

      Weaknesses:

      I have several outstanding issues. First of all, the authors really do not engage with the literature regarding different notions of an effective population. Most strikingly, the authors don't talk about Cannings models at all, which are a broad class of models with non-Poisson offspring distributions that nonetheless converge to the standard Wright-Fisher diffusion under many circumstances, and to "jumpy" diffusions/coalescents otherwise (see e.g. Mohle 1998, Sagitov (2003), Der et al (2011), etc.). Moreover, there is extensive literature on effective population sizes in populations whose sizes vary with time, such as Sano et al (2004) and Sjodin et al (2005).

      Of course in many cases here the discussion is under neutrality, but it seems like the authors really need to engage with this literature more.

      The reviewer's summary and weakness statement reflects the general criticism summarized by the editors. The reply and revision to these criticisms have been presented in the long reply to elife assessment above.

      We hence re-emphasize only the key points here.

      (1) The literature that the reviewers fault us for not citing is about the modifications of the standard WF model. We now cite them as well as a few others in that vein. However, the WF-Haldane model we propose is conceptually very different from the modified WF models. This WFH model is in essence the Haldane model which may use the results of the WF models as the starting point to find the exact solutions.

      (2) The check of the power of the modified WF models is whether they can resolve the paradoxes. None of them can. The arguments apply to neutral cases as well as selection effects. Hence, our central point is that the modifications of the standard WF model [e.g., by incorporating V(K)] do not help the WF model in resolving the paradoxes.  Besides, the incorporation of V(K) is mathematically feasible but biologically untenable as presented in the new sections of Discussion.

      Nonetheless, I don't think the authors' modeling, simulations, or empirical data analysis are sufficient to justify their claims.

      The most interesting part of the manuscript, I think, is the discussion of the Density Dependent Haldane model (DDH). However, I feel like I did not fully understand some of the derivation presented in this section, …… - this is the whole notion of exchangeability, also neglected in this manuscript). As such, I don't believe that their analysis of the empirical data supports their claim. [Since the comments above are highly technical and fairly long, they are not copied verbatim.]

      We thank this reviewer for the detailed comments with respect to the potential confusion in the discussion of the Density Dependent Haldane (DDH) model.

      First, the reviewer appears to ask how Eqs (5-6) are derived. We should clarify that both Eq (5) and (6) are assumptions rather than derived results. Both equations are assumptions based on population ecology. Eq (7) is then derived by substituting the assumptions in Eq (5) and (6) into Eq (3).

      The definition in Equation (5) allows the growth rate of the population size to be dependent on N itself, such that growth rate E(K) (average offspring number per generation) is greater than 1 when N < Ck and less than 1 when N > Ck. The parameter z is introduced to adjust the sensitivity of E(K) to changes in population size (as shown in Fig. 3a).

      Second, we appreciate the comments regarding the use of individual-based simulations and the apparent lack of interaction between individuals. In our simulations, there is indeed an interaction among individuals, which is represented by Eq (5). This equation reflects how the competition between two alleles affects the expected growth rate 𝐸(𝐾), which decreases as the population size increases. Furthermore, once 𝐸(𝐾) for the entire population is determined, the offspring numbers of the alleles are independent.

      We believe that the primary purpose of our simulations was not clearly stated. This lack of clarity may be the root of the criticisms. We now note that the simulations are aimed at testing the accuracy of Equation (10).

      Note that Eq. (10) is a textbook result and quite important in our study. This equation shows that the strength of genetic drift, as given by Pf (the fixation probability of an advantageous mutation), is not a function of N at all. This approximate solution has been obtained using the WF model by Kimura.  The Haldane model solution that can explain Paradox 1 is based on Equation (7) as shown below

      Since the fixation probability of Equation (10) cannot be easily obtained using Eq. (7), we conducted simulations to confirm the accuracy of Eq. (10) when applied to the Haldane model.

      We have revised the relevant sections of the manuscript to clarify these points and to better distinguish between assumptions and results. 

      Revision - Details of the DDH model are given in the Supplementary Information. A synopsis is given here: We consider a non-overlapping haploid population with two neutral alleles. The population size at time t is Nt. We assume that expected growth rate E(K) is greater than 1 when N < Ck and less than 1 when N > Ck, as defined by Eq. (5) below:

      The slope of E(K) vs. N (i.e., the sensitive of growth rate to changes in population size), as shown in Fig 3a, depends on z. To determine the variance V(K), we assume that K follows the negative binomial distribution whereby parents would suffer reproduction-arresting injury with a probability of pt at each birthing (Supplementary Information). Accordingly, V(K) can then be expressed as

      By Eq. (6), the ratio of V(K)/E(K) could be constant, decrease or increase with the increase of population size. With E(K) and V(K) defined, we could obtain the effective population size by substituting Eq. (5) and Eq. (6) into Eq. (3).

      Eq. (7) presents the relationship between effective population size (Ne) and the population size (N) as shown in Fig. 3. The density-dependent E(K) could regulate N with different strength (Fig. 3a). The steeper the slope in Fig. 3a, the stronger the regulation.

      Simulation of genetic drift in the Haldane model and the Wright-Fisher (WF) model. In both models, interactions between individuals are implicitly included through the dependency of the average number of offspring on population size, as defined by Eq. (5). This dependency leads to the logistic population growth, reflecting the density-dependent interactions.

      Thus, while I think there are some interesting ideas in this manuscript, I believe it has some fundamental issues:

      first, it fails to engage thoroughly with the literature on a very important topic that has been studied extensively. Second, I do not believe their simulations are appropriate to show what they want to show. And finally, I don't think their empirical analysis shows what they want to show.

      References omitted

      The comments are the summary of previous ones, which have been addressed in detail in the preceding sections.

      Reviewer #2 (Public Review):

      Summary:

      This theoretical paper examines genetic drift in scenarios deviating from the standard Wright-Fisher model. The authors discuss Haldane's branching process model, highlighting that the variance in reproductive success equates to genetic drift. By integrating the Wright-Fisher model with the Haldane model, the authors derive theoretical results that resolve paradoxes related to effective population size [Ne]

      Thanks.  The issue of Ne will be addressed below where the reviewer returns to this issue. The strength of the integrated WFH model is that N (or Ne) is generated by the model itself, rather than externally imposed as in WF models.

      Strengths:

      The most significant and compelling result from this paper is perhaps that the probability of fixing a new beneficial mutation is 2s/V(K). This is an intriguing and potentially generalizable discovery that could be applied to many different study systems.

      The authors also made a lot of effort to connect theory with various real-world examples, such as genetic diversity in sex chromosomes and reproductive variance across different species.

      Thanks. 

      Weaknesses:

      One way to define effective population size is by the inverse of the coalescent rate. This is where the geometric mean of Ne comes from. If Ne is defined this way, many of the paradoxes mentioned seem to resolve naturally. If we take this approach, one could easily show that a large N population can still have a low coalescent rate depending on the reproduction model. However, the authors did not discuss Ne in light of the coalescent theory. This is surprising given that Eldon and Wakeley's 2006 paper is cited in the introduction, and the multiple mergers coalescent was introduced to explain the discrepancy between census size and effective population size, superspreaders, and reproduction variance - that said, there is no explicit discussion or introduction of the multiple mergers coalescent.

      The Haldane model treats N’s very differently from the WF models.  In the WF models, N’s are imposed externally (say, constant N, exponentially growing N, temporally fluctuating N’s and so on; all provided from outside of the model). Ne and coalescence are all derived from these given N’s.  In order to account for the first paradox (see the next paragraph), N needs to be regulated but the WF models cannot regulate N’s. The density-dependent Haldane model that Reviewer 1 inquired above is a model that regulates N internally. It can thus account for the paradox.

      Paradox 1 -  When the population size (N) is growing exponentially, such as in a bacteria culture, drift is nearly absent when N is small and is much stronger as N increases, especially when approaching the carrying capacity.  Such a pattern is a common observation and is exactly opposite of the WF model's central prediction. In short, a model that does not regulate N cannot explain the paradox

      Ne is a fix of the WF model in order to account for the missing components of genetic drift. The paradoxes presented in this one and the companion study show that the fix is rather inadequate.  In contrast, by the WFH model, N is regulated within the model itself as E(K) and V(K) are both functions of N.

      The Wright-Fisher model is often treated as a special case of the Cannings 1974 model, which incorporates the variance in reproductive success. This model should be discussed. It is unclear to me whether the results here have to be explained by the newly introduced WFH model, or could have been explained by the existing Cannings model. The abstract makes it difficult to discern the main focus of the paper. It spends most of the space introducing "paradoxes".

      We appreciate greatly the illuminating advice.  Nevertheless, we should explain, or should have explained, more clearly that these four paradoxes presented are central to this pair of eLife papers. The WF and Haldane models are very different conceptual ideas altogether. The choice should not be based on mathematical grounds but on how they help us understand biological evolution. We are using four paradoxes to highlight the differences.  We have said in the papers that the origin and evolution of COVID-19 caused a lot of confusions partly because the WF models cannot handle multi-copy gene systems, including viruses that evolve both within- and between- hosts.

      The standard Wright-Fisher model makes several assumptions, including hermaphroditism, non-overlapping generations, random mating, and no selection. It will be more helpful to clarify which assumptions are being violated in each tested scenario, as V(K) is often not the only assumption being violated. For example, the logistic growth model assumes no cell death at the exponential growth phase, so it also violates the assumption about non-overlapping generations.

      We appreciate the question which has two aspects.  First, why do we think the WF models are insufficient? After all, for each assumption of the WF model (as given in the reviewer’s examples), there is often a solution by modifying Ne which relaxes the assumption. In this sense, there is only one grand assumption made by the WF models. That is, however complex the biology is, it is possible to find Ne that can make the WF model work. Our argument is that Ne is a cumbersome fix of the WF model and it does not work in many situations. That is how we replied about the importance of the paradoxes above.  We shall again use the first paradox as an example whereby drift is stronger as N becomes larger, the fix has to make Ne negatively correlated with N. In reality, it does not appear possible to resolve this paradox. Another paradox is the evolution of multi-copy gene systems. In short, it seems clear that Ne is not a useful or usable fix.

      The second aspect is that “why, among the many modifications the WF models make, do we only emphasize the inclusion of V(K)?” This is the essence of the two papers of ours.  Although V(K) is a modification of the WF models, it does not enable the WF models to resolve the paradoxes. In contrast, the Haldane model has incorporate E(K) and V(K) in the model. In presenting paradox 3, it was stated that

      This equation shows that the strength of genetic drift, as given by Pf (the fixation probability of an advantageous mutation), is not a function of N at all. It supports the view that the essence of genetic drift is V(K) with N as a scaling factor. Note that, if V(K) = 0, there is no genetic drift regardless of N. As V(K) is not an add-on to the Haldane model (unlike in WF models), the Haldane model can resolve the paradoxes.

      The theory and data regarding sex chromosomes do not align. The fact that \hat{alpha'} can be negative does not make sense. The authors claim that a negative \hat{alpha'} is equivalent to infinity, but why is that? It is also unclear how theta is defined. It seems to me that one should take the first principle approach e.g., define theta as pairwise genetic diversity, and start with deriving the expected pair-wise coalescence time under the MMC model, rather than starting with assuming theta = 4Neu. Overall, the theory in this section is not well supported by the data, and the explanation is insufficient.

      a' can be negative for the same reason that a (the male/female ratio in mutation rate) can be negative (Miyata, et al. 1987; Li, et al. 2002; Makova and Li 2002). Clearly, this has not been a problem in the large literature on a becoming negative.  In fact, in many reports, a is negative, which is read as a approaching infinity.  Imagine that our equation is a'^2 = 0.25, then a' can be 0.5 or -0.5, although the latter solution is not biologically meaningful.

      As for theta, the reviewer asked why we do not use the pairwise genetic diversity (or theta[pi]) as the first-principle approach to estimating theta. While theta(pi) is the first estimator of theta used, the general principle is that every bin of the frequency spectrum can be used for estimating theta since the expected value is theta/i where i is the occurrence of the mutation in the sample.  (If the sample size is 100, then i is between 1 and 99.)  Hence, the issue is which part of the spectrum has the best statistical properties for the questions at hand.  The pairwise measure is theta(pi) [which the reviewer recommends]. While theta(pi) and theta(w) are most commonly used, there are in fact numerous ways to estimate theta.  ((Fu 2022) presents an excellent review.) For our purpose, we need a theta estimate least affected by selection and we choose the lowest frequency bin of the spectrum, which is theta(1) based on the singletons. Theta(1), least affected by selection, is the basis of the Fu and Li test. 

      Reviewer #3 (Public Review):

      Summary:

      Ruan and colleagues consider a branching process model (in their terminology the "Haldane model") and the most basic Wright-Fisher model. They convincingly show that offspring distributions are usually non-Poissonian (as opposed to what's assumed in the Wright-Fisher model), and can depend on short-term ecological dynamics (e.g., variance in offspring number may be smaller during exponential growth). The authors discuss branching processes and the Wright-Fisher model in the context of 3 "paradoxes": (1) how Ne depends on N might depend on population dynamics; (2) how Ne is different on the X chromosome, the Y chromosome, and the autosomes, and these differences do match the expectations base on simple counts of the number of chromosomes in the populations; (3) how genetic drift interacts with selection. The authors provide some theoretical explanations for the role of variance in the offspring distribution in each of these three paradoxes. They also perform some experiments to directly measure the variance in offspring number, as well as perform some analyses of published data.

      Strengths:

      (1) The theoretical results are well-described and easy to follow.

      (2) The analyses of different variances in offspring number (both experimentally and analyzing public data) are convincing that non-Poissonian offspring distributions are the norm.

      (3) The point that this variance can change as the population size (or population dynamics) change is also very interesting and important to keep in mind.

      (4) I enjoyed the Density-Dependent Haldane model. It was a nice example of the decoupling of census size and effective size.

      Thanks.

      Weaknesses:

      (1) I am not convinced that these types of effects cannot just be absorbed into some time-varying Ne and still be well-modeled by the Wright-Fisher process.

      Please allow us to refer to, again, two of the four paradoxes.  We believe that that no modification of the WF model can resolve the paradoxes.

      (1) When the population size (N) is growing exponentially, such as in a bacteria culture, drift is nearly absent when N is small and is much stronger as N increases, especially when approaching the carrying capacity.  Such common observations are exactly opposite of the WF model's key prediction. It is not possible for a model that does not regulate N to explain the paradox.

      (2) There is no way the WF models can formulate Ne for, say viruses or ribosomal RNA genes that have two levels of populations – the within-host populations as well as the host population itself.

      The fact that there are numerous Ne's suggests that Ne is a collection of cumbersome fixes of the WF model. By the WF-Haldane model, all factors are absorbed into V(K) resulting in a simpler model in the end. V(K) is often a measurable quantity. Note that, even if V(K) is incorporated into the WF model, the paradoxes remain unresolvable.

      (2) Along these lines, there is well-established literature showing that a broad class of processes (a large subset of Cannings' Exchangeable Models) converge to the Wright-Fisher diffusion, even those with non-Poissonian offspring distributions (e.g., Mohle and Sagitov 2001). E.g., equation (4) in Mohle and Sagitov 2001 shows that in such cases the "coalescent Ne" should be (N-1) / Var(K), essentially matching equation (3) in the present paper.

      The criticism of lack of engagement with well-established literature has been responded extensively above.  Briefly, the literature is about modifications of the WF model which share the same feature of population sampling. With that feature, the paradoxes are unresolvable.  For example, however Ne is defined, the fixation probability of an advantageous mutation does not depend on N or Ne. This is the third paradox of the WF models.

      (3) Beyond this, I would imagine that branching processes with heavy-tailed offspring distributions could result in deviations that are not well captured by the authors' WFH model. In this case, the processes are known to converge (backward-in-time) to Lambda or Xi coalescents (e.g., Eldon and Wakely 2006 or again in Mohle and Sagitov 2001 and subsequent papers), which have well-defined forward-in-time processes.

      We admire the learned understanding of the literature expressed by the review, which raise two points.  First, our model may not be able to handle the heavy-tailed progeny distribution (i.e., the kurtosis of the distribution of k). Second, the Xi coalescence models (cited above) can do that.  Below are our clarifications.

      First, the WFH model is based on the general distribution of K, which includes flexible and realistic representations of offspring number distributions. In fact, we have used various forms of K distribution in our publications on the evolution of SARS-CoV-2 (see the Ruan et al publications in the bibliography). Power-law distribution is particularly useful as the K-distribution in viral transmission is highly kurtotic. This is reflected in the super-spreader hypothesis. In short, the branching process on which the WFH model is based in is mainly about the distribution of K. Nevertheless, the variance V(K) can often yield good approximations when the kurtosis is modest.

      Second, we would like to comment on the models of Eldon and Wakely 2006. or Mohle and Sagitov 2001 and subsequent papers. These papers are based on the Moran model by considering a highly skewed distribution of offspring numbers. Fundamentally, the Moran models generally behave like WF models (standard or modified) and hence have the same problems with the paradoxes that are central to our studies. In fact, the reservations about introducing V(K) into the WF models apply as well to the Moran models.  The introduction of V(K) is mathematically valid but biologically untenable. Essentially, the WF models incorporate the Haldane model as a first step in the generation transition. The introduction of V(K) into the Moran model is even less biologically sensible. Furthermore, the model allows K to take only three discrete values: 0, 2, and Nψ (see Eq. (7) in Eldon and Wakely). Their model also assumes a constant population size, which contrasts with our model's flexibility in handling varying population sizes and more complex distributions for K.

      In short, the modifications of the WF (and Moran) models are unnecessarily complicated, biologically untenable but still fail to account for the paradoxes. The WFH model can rectify these problems. 

      (4) These results that Ne in the Wright-Fisher process might not be related to N in any straightforward (or even one-to-one) way are well-known (e.g., Neher and Hallatschek 2012; Spence, Kamm, and Song 2016; Matuszewski, Hildebrandt, Achaz, and Jensen 2018; Rice, Novembre, and Desai 2018; the work of Lounès Chikhi on how Ne can be affected by population structure; etc...)

      The reviewer is correct in pointing out the inexact correlation between N and Ne. Nevertheless, it should still be true that the WF models predict qualitatively weaker drift as N increases. The first paradox is as stated:

      When the population size (N) is growing exponentially, such as in a bacteria culture, drift is nearly absent when N is small and is much stronger as N increases, especially when approaching the carrying capacity.  Such common observations are exactly opposite of the WF model's key prediction.

      (5) I was also missing some discussion of the relationship between the branching process and the Wright-Fisher model (or more generally Cannings' Exchangeable Models) when conditioning on the total population size. In particular, if the offspring distribution is Poisson, then conditioned on the total population size, the branching process is identical to the Wright-Fisher model.

      We thank the reviewer for this important comment. The main difference is that N is imposed from outside the WF models but can be generated from within the Haldane model (see the density-dependent Haldane model). In nature, N of the next generation is the sum of K’s among members of the population. It is how the Haldane model determines N(t+1) from N(t). In the WF models, N is imposed from outside the model and, hence the given N determines the distribution of K.  For this reason, N regulation is not possible in the WF models, thus resulting in the paradoxes.

      (6) In the discussion, it is claimed that the last glacial maximum could have caused the bottleneck observed in human populations currently residing outside of Africa. Compelling evidence has been amassed that this bottleneck is due to serial founder events associated with the out-of-Africa migration (see e.g., Henn, Cavalli-Sforza, and Feldman 2012 for an older review - subsequent work has only strengthened this view). For me, a more compelling example of changes in carrying capacity would be the advent of agriculture ~11kya and other more recent technological advances.

      We thank the reviewer and have used this more convincing case as suggested by the reviewer.

      Recommendations for the authors:

      General replies - We thank the editors and reviewers again.  The points below are re-iterations of the comments received above and have since been replied in detail. Specific instructions about wording and notations have also been rectified. Again, we are grateful for the inputs from which we learned a great deal.

      Reviewing Editor Comments:

      The reviewers recognize the value of this model and some of the findings, particularly results from the density-dependent Haldane model. However, they expressed considerable concerns with the model and overall framing of this manuscript.

      First, all reviewers pointed out that the manuscript does not sufficiently engage with the extensive literature on various models of effective population size and genetic drift, notably lacking discussion on Cannings models and related works.

      We have addressed this issue in the beginning of Introduction and Discussion, pointing to the long section in the new second half of Discussion. The essence is that the literature is all about the modified WF models.  The WF-Haldane model is conceptually and operationally distinct from the WF models, either standard or modified ones,

      Second, there is a disproportionate discussion on the paradoxes, yet some of the paradoxes might already be resolved within current theoretical frameworks. All three reviewers found the modeling and simulation of the yeast growth experiment hard to follow or lacking justification for certain choices. The analysis approach of sex chromosomes is also questioned.

      This criticism is addressed together with the next one as they make the same point.

      The reviewers recommend a more thorough review of relevant prior literature to better contextualize their findings. The authors need to clarify and/or modify their derivations and simulations of the yeast growth experiment to address the identified caveats and ensure robustness. Additionally, the empirical analysis of the sex chromosome should be revisited, considering alternative scenarios rather than relying solely on the MSE, which only provides a superficial solution. Furthermore, the manuscript's overall framing should be adjusted to emphasize the conclusions drawn from the WFH model, rather than focusing on the "unresolved paradoxes", as some of these may be more readily explained by existing frameworks. Please see the reviewers' overall assessment and specific comments.

      Many thanks.  We have carefully reframed and presented the WF-Haldane model to make it clear and logically consistent. Whether a new model (i.e., the WF-Haldane model) deserves to be introduced depends on whether it makes any contribution for understanding nature. That is why we emphasize the four paradoxes. 

      A most important disagreement between the reviewers and the authors is about the nature of the paradoxes. While the reviewers suggest that they "may" be resolvable by the conventional WF model (standard or modified), they did not offer the possible resolutions.  To use the analogy in our provisional response: the WF vs. Haldane models are compared to gas cars vs electric vehicles.  We can say confidently that the internal combustion engine cannot resolve the conflicting demands of transportation and zero emission. Its design has limited its capability. 

      Reviewer #2 (Recommendations For The Authors):

      Many thanks.  We have incorporated all these suggestions.  When the incorporation is not straightforward, we have carefully revised the text to minimize mis-communications.

      In the introduction -- "Genetic drift is simply V(K)" -- this is a very strong statement. You can say it is inversely proportional to V(K), but drift is often defined based on changes in allele frequency.

      We change the word “simply” to “essentially”. This wording is supported by the fixation probability of advantageous mutations, 2s/(V(k). We have shown in the text that N does not matter here because the fixation is nearly deterministic when the copy number reaches, say, 100, regardless of whether N is 10^4 or 10^8,

      Page 3 line 86. "sexes is a sufficient explanation."--> "sex could be a sufficient explanation"

      The strongest line of new results is about 2s/V(K). Perhaps, the paper could put more emphasis on this part and demonstrate the generality of this result with a different example.

      The math notations in the supplement are not intuitive. e.g., using i_k and j_k as probabilities. I also recommend using E[X] and V[X]for expectation and variance rather than \italic{E(X)} to improve the readability of many equations.

      Thank you for your careful reading. Regarding the use of i_k and j_k  as probabilities, we initially considered using 𝑝 or 𝑞 to represent probabilities. However, since 𝑝 and 𝑞 are already used in the main text, we opted for 𝑖 and 𝑗 to avoid potential confusion potential confusion. As for your recommendation to use

      E[X] and V[X] for expectation and variance, we would like to clarify that we follow the standard practice of italicizing these symbols to represent variables.

      Eq A6, A7, While I manage to follow, P_{10}(t) and P_{10} are not defined anywhere in the text.<br /> Supplement page 7, the term "probability of fixation" is confusing in a branching model.

      Thank you for your observation. We have carefully revised the supplement to provide clarity on these points.<br /> Revision - In population genetics, the fixation of M allele means that the population consist entirely of the M allele, with no W alleles remaining. We define the fixation probability of M allele by generation t as follows:

      Given that M and W allele reproduce independently, this can be factored as:

      As t approaches infinity, the ultimate fixation probability of M allele can be derived as follows:

      E.q. A 28. It is unclear eq. A.1 could be used here directly. Some justification would be nice.

      We appreciate your careful review, and we will ensure this connection between the two equations is made clearer in the supplement. 

      Revision - Note we would like to clarify that Eq. (A1) and Eq. (A28) are essentially the same, with the only difference being the subscript 𝑡, which indicates the time dependence in the dynamic process.

      Supplement page 17. "the biological meaning of negative..". There is no clear justification for this claim. As a reader, I don't have any intuition as to why that is the case.

      Thank you for raising this concern. We have addressed this issue earlier.

    1. eLife Assessment

      In this important study, the authors employed three types of theoretical/computational models (coarse-grained molecular dynamics, analytical theory and field-theoretical simulations) to analyze the impact of salt on protein liquid-liquid phase separation. These different models reinforce each other and together provide convincing evidence to explain distinct salt effects on ATP mediated phase separation of different variants of caprin1. The insights and general approach are broadly applicable to the analysis of protein phase separation. Still, modeling at the coarse-grained level misses key effects that have been revealed by all-atom simulations, including salt-backbone coordination and strengthening of pi-type interactions by salt.

    2. Reviewer #1 (Public review):

      Summary:

      The authors used multiple approaches to study salt effects in liquid-liquid phase separation (LLPS). Results on both wild-type Caprin1 and mutants and on different types of salts contribute to a comprehensive understanding.

      Strengths:

      The main strength of this work is the thoroughness of investigation. This aspect is highlighted by the multiple approaches used in the study, and reinforced by the multiple protein variants and different salts studied.

      Weaknesses:

      (1) The multiple computational approaches are a strength, but they're cruder than explicit-solvent all-atom molecular dynamics (MD) simulations and may miss subtle effects of salts. In particular, all-atom MD simulations demonstrate that high salt strengthens pi-types of interactions (ref. 42 and MacAinsh et al, https://www.biorxiv.org/content/10.1101/2024.05.26.596000v3).<br /> (2) The paper can be improved by distilling the various results into a simple set of conclusions. By example, based on salt effects revealed by all-atom MD simulations, MacAinsh et al. presented a sequence-based predictor for classes of salt dependence. Wild-type Caprin1 fits right into the "high net charge" class, with a high net charge and a high aromatic content, showing no LLPS at 0 NaCl and an increasing tendency of LLPS with increasing NaCl. In contrast, pY-Caprin1 belongs to the "screening" class, with a high level of charged residues and showing a decreasing tendency of LLLPS.<br /> (3) Mechanistic interpretations can be further simplified or clarified. (i) Reentrant salt effects (e.g., Fig. 4a) are reported but no simple explanation seems to have been provided. Fig. 4a,b look very similar to what has been reported as strong-attraction promotor and weak-attraction suppressor, respectively (ref. 50; see also PMC5928213 Fig. 2d,b). According to the latter two studies, the "reentrant" behavior of a strong-attraction promotor, CL- in the present case, is due to Cl-mediated attraction at low to medium [NaCl] and repulsion between Cl- ions at high salt. Do the authors agree with this explanation? If not, could they provide another simple physical explanation? (ii) The authors attributed the promotional effect of Cl- to counterion-bridged interchain contacts, based on a single instance. There is another simple explanation, i.e., neutralization of the net charge on Caprin1. The authors should analyze their simulation results to distinguish net charge neutralization and interchain bridging; see MacAinsh et al.<br /> (4) The authors presented ATP-Mg both as a single ion and as two separate ions; there is no explanation of which of the two versions reflects reality. When presenting ATP-Mg as a single ion, it's as though it forms a salt with Na+. I assume NaCl, ATP, and MgCl2 were used in the experiment. Why is Cl- not considered? Related to this point, it looks ATP is just another salt ion studied and much of the Results section is on NaCl, so the emphasis of ATP ("Diverse Roles of ATP" in the title is somewhat misleading.

      Comments on revisions:

      This revision addressed all my previous comments.

    3. Reviewer #2 (Public review):

      Summary:

      In this paper, Lin and colleagues aim to understand the role of different salts on the phase behavior of a model protein of significant biological interest, Caprin1, and its phosphorylated variant, pY-Caprin1. To achieve this, the authors employed a variety of methods to complement experimental studies and obtain a molecular-level understanding of ion partitioning inside biomolecular condensates. A simple theory based on rG-RPA is shown to capture the different salt dependencies of Caprin1 and pY-Caprin1 phase separation, demonstrating excellent agreement with experimental results. The application of this theory to multivalent ions reveals many interesting features with the help of multicomponent phase diagrams. Additionally, the use of CG model-based MD simulations and FTS provides further clarity on how counterions can stabilize condensed phases.

      Strengths:

      The greatest strength of this study lies in the integration of various methods to obtain complementary information on thermodynamic phase diagrams and the molecular details of the phase separation process. The authors have also extended their previously proposed theoretical approaches, which should be of significant interest to other researchers. Some of the findings reported in this paper, such as bridging interactions, are likely to inspire new studies using higher-resolution atomistic MD simulations.

    4. Reviewer #3 (Public review):

      Authors first use rG-RPA to reproduce two observed trends. Caprin1 does not phase separate at very low salt but then undergoes LLPS with added salt while further addition of salt reduces its propensity to LLPS. On the other hand pY-Caprin1 exhibits a monotonic trend where the propensity to phase separate decreases with the addition of salt. This distinction is captured by a two component model and also when salt ions are explicitly modeled as a separate species with a ternary phase diagram. The predicted ternary diagrams (when co and counter ions are explicitly accounted for) also predict the tendency of ions to co-condense or exclude proteins in the dense phase. Predicted trends are generally in line with the measurement for Cparin1. Next, the authors seek to explain the observed difference in phase separation when Arginines are replaced by Lysines creating different variants. In the current rG-RPA type models both Arginine (R) and Lysine (K) are treated equally since non-electrostatic effects are only modeled in a mean-field manner that can be fitted but not predicted. For this reason, coarse grain MD simulation is suitable. Moreover, MD simulation affords structural features of the condensates. They used a force field that is capable of discriminating R and K. The MD predicted degrees of LLPS of these variants again is consistent with the measurement. One additional insight emerges from MD simulations that a negative ion can form a bridge between two positively charged residues on the chain. These insights are not possible to derive from rG-RPA. Both rG-RPA and MD simulation become cumbersome when considering multiple types of ions such as Na, Cl, [ATP] and [ATP-Mg] all present at the same time. FTS is well suited to handle this complexity. FTS also provides insights into the co-localization of ions and proteins that is consistent with NMR. By using different combinations of ions they confirm the robustness of the prediction that Caprin1 shows salt-dependent reentrant behavior, adding further support that the differential behavior of Caprin1, and pY-Caprin1 is likely to be mediated by charge-charge interactions.

      Comments on revisions:

      The authors addressed my comments and it is ready for publication.

    5. Author response:

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

      Reviewer #1 (Public Review):

      Comments on revisions:

      This revision addressed all my previous comments.

      Reviewer #3 (Public Review):

      Comments on revisions:

      The authors addressed my comments and it is ready for publication.

      We are grateful for the reviewers’ effort and are encouraged by their generally positive assessment of our manuscript.

      Reviewer #1 (Recommendations For The Authors):

      This revision addressed all my previous comments. The only new issue concerns the authors’ response to the following comment of reviewer 3:

      (2) Authors note ”monovalent positive salt ions such as Na+ can be attracted, somewhat counterintuitively, into biomolecular condensates scaffolded by positively-charged polyelectrolytic IDRs in the presence of divalent counterions”. This may be due to the fact that the divalent negative counterions present in the dense phase (as seen in the ternary phase diagrams) also recruit a small amount of Na+.

      Author reply: The reviewer’s comment is valid, as a physical explanation for this prediction is called for. Accordingly, the following sentence is added to p. 10, lines 27-29: ...

      Here are my comments on this issue. Most IDPs with a net positive charge still have negatively charged residues, which in theory can bind cations. In fact, Caprin1 has 3 negatively charged residues (same as A1-LCD). All-atom simulations of MacAinsh et al (ref 72) have shown that these negatively charged residues bind Na+; I assume this effect can be captured by the coarsegrained models in the present study. Moreover, all-atom simulations showed that Na+ has a strong tendency to be coordinated by backbone carbonyls, which of course are present on all residues. Suggestions:

      (a) The authors may want to analyze the binding partners of Na+. Are they predominantly the3 negatively charged residues, or divalent counterions, or both?

      (b) The authors may want to discuss the potential underestimation of Na+ inside Caprin1 condensates due to the lack of explicit backbone carbonyls that can coordinate Na+ in their models. A similar problem applies to backbone amides that can coordinate anions, but to a lesser extent (see Fig. 3A of ref 72).

      The reviewer’s comments are well taken. Regarding the statement in the revised manuscript “This phenomenon arises because the positively charge monovalent salt ions are attracted to the negatively charged divalent counterions in the protein-condensed phase.”, it should be first noted that the statement was inferred from the model observation that Na+ is depleted in condensed Caprin1 (Fig. 2a) when the counterion is monovalent (an observation that was stated almost immediately preceding the quoted statement). To make this logical connection clearer as well as to address the reviewer’s point about the presence of negatively charged residues in Caprin1, we have modified this statement in the Version of Record (VOR) as follows:

      “This phenomenon most likely arises from the attraction of the positively charge monovalent salt ions to the negatively charged divalent counterions in the proteincondensed phase because although the three negatively charged D residues in Caprin1 can attract Na+, it is notable that Na+ is depleted in condensed Caprin1 when the counterion is monovalent (Fig. 2a).”

      The reviewer’s suggestion (a) of collecting statistics of Na+ interactions in the Caprin1 condensate is valuable and should be attempted in future studies since it is beyond the scope of the present work. Thus far, our coarse-grained molecular dynamics has considered only monovalent Cl− counterions. We do not have simulation data for divalent counterions.

      Following the reviewer’s suggestion (b), we have now added the following sentence in Discussion under the subheading “Effects of salt on biomolecular LLPS”:

      “In this regard, it should be noted that positively and negatively charged salt ions can also coordinate with backbone carbonyls and amides, respectively, in addition to coordinating with charged amino acid sidechains (MacAinsh et al., eLife 2024). The impact of such effects, which are not considered in the present coarse-grained models, should be ascertained by further investigations using atomic simulations (MacAinsh et al., eLife 2024; Rauscher & Pom`es, eLife 2017; Zheng et al., J Phys Chem B 2020).”

      Here we have added a reference to Rauscher & Pom`es, eLife 2017 to more accurately reflect progress made in atomic simulations of biomolecular condensates.

      More generally, regarding the reviewer’s comments on the merits of coarse-grained versus atomic approaches, we re-emphasize, as stated in our paper, that these approaches are complementary. Atomic approaches undoubtedly afford structurally and energetically high-resolution information. However, as it stands, simulations of the assembly-disassembly process of biomolecular condensate are nonideal because of difficulties in achieving equilibration even for a small model system with < 10 protein chains (MacAinsh et al., eLife 2024) although well-equilibrated simulations are possible for a reasonably-sized system with ∼ 30 chains when the main focus is on the condensed phase (Rauscher & Pom`es, eLife 2017). In this context, coarse-grained models are valuable for assessing the energetic role of salt ions in the thermodynamic stability of biomolecular condensates of physically reasonable sizes under equilibrium conditions.

      In addition to the above minor additions, we have also added citations in the VOR to two highly relevant recent papers: Posey et al., J Am Chem Soc 2024 for salt-dependent biomolecular condensation (mentioned in Dicussion under subheadings “Tielines in protein-salt phase diagrams” and “Counterion valency” together with added references to Hribar et al., J Am Chem Soc 2002 and Nostro & Ninham, Chem Rev 2012 for the Hofmeister phenomena discussed by Posey et al.) and Zhu et al., J Mol Cell Biol 2024 for ATP-modulated reentrant behavior (mentioned in Introduction). We have also added back a reference to our previous work Lin et al., J Mol Liq 2017 to provide more background information for our formulation.

      Reviewer #2 (Recommendations For The Authors):

      The authors have done a great job addressing previous comments.

      We thank this reviewer for his/her effort and are encouraged by the positive assessment of our revised manuscript.

      ---

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

      Reviewer #1 (Public Review):

      Summary:

      The authors used multiple approaches to study salt effects in liquid-liquid phase separation (LLPS). Results on both wild-type Caprin1 and mutants and on different types of salts contribute to a comprehensive understanding.

      Strengths:

      The main strength of this work is the thoroughness of investigation. This aspect is highlighted by the multiple approaches used in the study, and reinforced by the multiple protein variants and different salts studied.

      We are encouraged by this positive overall assessment.

      Weaknesses: (1) The multiple computational approaches are a strength, but they’re cruder than explicit-solvent all-atom molecular dynamics (MD) simulations and may miss subtle effects of salts. In particular, all-atom MD simulations demonstrate that high salt strengthens pi-types of interactions (ref. 42 and MacAinsh et al, https://www.biorxiv.org/content/10.1101/2024.05.26.596000v3).

      The relative strengths and limitations of coarse-grained vs all-atom simulation are now more prominently discussed beginning at the bottom of p. 5 through the first 8 lines of p. 6 of the revised manuscript (page numbers throughout this letter refer to those in the submitted pdf file of the revised manuscript), with MacAinsh et al. included in this added discussion (cited as ref. 72 in the revised manuscript). The fact that coarse-grained simulation may not provide insights into more subtle structural and energetic effects afforded by all-atom simulations with regard to π-related interaction is now further emphasized on p. 11 (lines 23–30), with reference to MacAinsh et al. as well as original ref. 42 (Krainer et al., now ref. 50 in the revised manuscript).

      (2) The paper can be improved by distilling the various results into a simple set of conclusions. By example, based on salt effects revealed by all-atom MD simulations, MacAinsh et al. presented a sequence-based predictor for classes of salt dependence. Wild-type Caprin1 fits right into the “high net charg”e class, with a high net charge and a high aromatic content, showing no LLPS at 0 NaCl and an increasing tendency of LLPS with increasing NaCl. In contrast, pY-Caprin1 belongs to the “screening” class, with a high level of charged residues and showing a decreasing tendency of LLPS.

      This is a helpful suggestion. We have now added a subsection with heading “Overview of key observations from complementary approaches” at the beginning of the “Results” section on p. 6 (lines 18–37) and the first line of p. 7. In the same vein, a few concise sentences to summarize our key results are added to the first paragraph of “Discussion” (p. 18, lines 23– 26). In particular, the relationship of Caprin1 and pY-Caprin1 with the recent classification by MacAinsh et al. (ref. 72) in terms of “high net charge” and “screening” classes is now also stated, as suggested by this reviewer, on p. 18 under “Discussion” (lines 26–30).

      (3) Mechanistic interpretations can be further simplified or clarified. (i) Reentrant salt effects (e.g., Fig. 4a) are reported but no simple explanation seems to have been provided. Fig. 4a,b look very similar to what has been reported as strong-attraction promotor and weak-attraction suppressor, respectively (ref. 50; see also PMC5928213 Fig. 2d,b). According to the latter two studies, the “reentrant” behavior of a strong-attraction promotor, CL- in the present case, is due to Cl-mediated attraction at low to medium [NaCl] and repulsion between Cl- ions at high salt. Do the authors agree with this explanation? If not, could they provide another simple physical explanation? (ii) The authors attributed the promotional effect of Cl- to counterionbridged interchain contacts, based on a single instance. There is another simple explanation, i.e., neutralization of the net charge on Caprin1. The authors should analyze their simulation results to distinguish net charge neutralization and interchain bridging; see MacAinsh et al.

      The relationship of Cl− in bridging and neutralizing configurations, respectively, with the classification of “strong-attraction promoter” and “weak-attraction suppressor” by Zhou and coworkers is now stated on p. 13 (lines 29–31), with reference to original ref. 50 by Ghosh, Mazarakos & Zhou (now ref. 59 in the revised manuscript) as well as the earlier patchy particle model study PMC5928213 by Nguemaha & Zhou, now cited as ref. 58 in the revised manuscript. After receiving this referee report, we have conducted an extensive survey of our coarse-grained MD data to provide a quantitative description of the prevalence of counterion (Cl−) bridging interactions linking positively charged arginines (Arg+s) on different Caprin1 chains in the condensed phase (using the [Na+] = 0 case as an example). The newly compiled data is reported under a new subsection heading “Explicit-ion MD offers insights into counterion-mediated interchain bridging interactions among condensed Caprin1 molecules” on p. 12 (last five lines)–p. 14 (first 10 lines) [∼ 1_._5 additional page] as well as a new Fig. 6 to depict the statistics of various Arg+–Cl−–Arg+ configurations, with the conclusion that a vast majority (at least 87%) of Cl− counterions in the Caprin1-condensed phase engage in favorable condensation-driving interchain bridging interactions.

      (4) The authors presented ATP-Mg both as a single ion and as two separate ions; there is no explanation of which of the two versions reflects reality. When presenting ATP-Mg as a single ion, it’s as though it forms a salt with Na+. I assume NaCl, ATP, and MgCl2 were used in the experiment. Why is Cl- not considered? Related to this point, it looks like ATP is just another salt ion studied and much of the Results section is on NaCl, so the emphasis of ATP (“Diverse Roles of ATP” in the title is somewhat misleading.

      We model ATP and ATP-Mg both as single-bead ions (in rG-RPA) and also as structurally more realistic short multiple-bead polymers (in field-theoretic simulation, FTS). We have now added discussions to clarify our modeling rationale in using and comparing different models for ATP and ATP-Mg, as follows:

      p. 8 (lines 19–36):

      “The complementary nature of our multiple methodologies allows us to focus sharply on the electrostatic aspects of hydrolysis-independent role of ATP in biomolecular condensation by comparing ATP’s effects with those of simple salt. Here, Caprin1 and pY-Caprin1 are modeled minimally as heteropolymers of charged and neutral beads in rG-RPA and FTS. ATP and ATP-Mg are modeled as simple salts (singlebead ions) in rG-RPA whereas they are modeled with more structural complexity as short charged polymers (multiple-bead chains) in FTS, though the latter models are still highly coarse-grained. Despite this modeling difference, rG-RPA and FTS both rationalize experimentally observed ATP- and NaCl-modulated reentrant LLPS of Caprin1 and a lack of a similar reentrance for pY-Caprin1 as well as a prominent colocalization of ATP with the Caprin1 condensate. Consistently, the same contrasting trends in the effect of NaCl on Caprin1 and pY-Caprin1 are also seen in our coarse-grained MD simulations, though polymer field theories tend to overestimate LLPS propensity [99]. The robustness of the theoretical trends across different modeling platforms underscores electrostatics as a significant component in the diverse roles of ATP in the context of its well-documented ability to modulate biomolecular LLPS via hydrophobic and π-related effects [63, 65, 67].”

      Here, the last sentence quoted above addresses this reviewer’s question about our intended meaning in referring to “diverse roles of ATP” in the title of our paper. To make this point even clearer, we have also added the following sentence to the Abstract (p. 2, lines 12–13):

      “... The electrostatic nature of these features complements ATP’s involvement in π-related interactions and as an amphiphilic hydrotrope, ...”

      Moreover, to enhance readability, we have now added pointers in the rG-RPA part of our paper to anticipate the structurally more complex ATP and ATP-Mg models to be introduced subsequently in the FTS part, as follows:

      p. 9 (lines 13–15):

      “As mentioned above, in the present rG-RPA formulation, (ATP-Mg)<sup>2−</sup> and ATP<sup>4−</sup> are modeled minimally as a single-bead ion. They are represented by charged polymer models with more structural complexity in the FTS models below.”

      p. 11 (lines 8–11):

      These observations from analytical theory will be corroborated by FTS below with the introduction of structurally more realistic models of (ATP-Mg) <sup>2−</sup>, ATP<sup>4−</sup> together with the possibility of simultaneous inclusion of Na<sup>+</sup>, Cl−, and Mg<sup>2+</sup> in the FTS models of Caprin1/pY-Caprin1 LLPS systems.

      Reviewer #2 (Public Review):

      Summary:

      In this paper, Lin and colleagues aim to understand the role of different salts on the phase behavior of a model protein of significant biological interest, Caprin1, and its phosphorylated variant, pY-Caprin1. To achieve this, the authors employed a variety of methods to complement experimental studies and obtain a molecular-level understanding of ion partitioning inside biomolecular condensates. A simple theory based on rG-RPA is shown to capture the different salt dependencies of Caprin1 and pY-Caprin1 phase separation, demonstrating excellent agreement with experimental results. The application of this theory to multivalent ions reveals many interesting features with the help of multicomponent phase diagrams. Additionally, the use of CG model-based MD simulations and FTS provides further clarity on how counterions can stabilize condensed phases.

      Strengths:

      The greatest strength of this study lies in the integration of various methods to obtain complementary information on thermodynamic phase diagrams and the molecular details of the phase separation process. The authors have also extended their previously proposed theoretical approaches, which should be of significant interest to other researchers. Some of the findings reported in this paper, such as bridging interactions, are likely to inspire new studies using higher-resolution atomistic MD simulations.

      Weaknesses:

      The paper does not have any major issues.

      We are very encouraged by this reviewer’s positive assessment of our work.

      Reviewer #3 (Public Review):

      Authors first use rG-RPA to reproduce two observed trends. Caprin1 does not phase separate at very low salt but then undergoes LLPS with added salt while further addition of salt reduces its propensity to LLPS. On the other hand pY-Caprin1 exhibits a monotonic trend where the propensity to phase separate decreases with the addition of salt. This distinction is captured by a two component model and also when salt ions are explicitly modeled as a separate species with a ternary phase diagram. The predicted ternary diagrams (when co and counter ions are explicitly accounted for) also predict the tendency of ions to co-condense or exclude proteins in the dense phase. Predicted trends are generally in line with the measurement for Cparin1 [sic]. Next, the authors seek to explain the observed difference in phase separation when Arginines are replaced by Lysines creating different variants. In the current rG-RPA type models both Arginine (R) and Lysine (K) are treated equally since non-electrostatic effects are only modeled in a meanfield manner that can be fitted but not predicted. For this reason, coarse grain MD simulation is suitable. Moreover, MD simulation affords structural features of the condensates. They used a force field that is capable of discriminating R and K. The MD predicted degrees of LLPS of these variants again is consistent with the measurement. One additional insight emerges from MD simulations that a negative ion can form a bridge between two positively charged residues on the chain. These insights are not possible to derive from rG-RPA. Both rG-RPA and MD simulation become cumbersome when considering multiple types of ions such as Na, Cl, [ATP] and [ATP-Mg] all present at the same time. FTS is well suited to handle this complexity. FTS also provides insights into the co-localization of ions and proteins that is consistent with NMR. By using different combinations of ions they confirm the robustness of the prediction that Caprin1 shows salt-dependent reentrant behavior, adding further support that the differential behavior of Caprin1, and pY-Caprin1 is likely to be mediated by charge-charge interactions.

      We are encouraged by this reviewer’s positive assessment of our manuscript.

      Reviewer #1 (Recommendations For The Authors):

      Analysis:

      Analyze the simulation results to distinguish net charge neutralization and interchain bridging; see MacAinsh et al.

      Please see response above to points (3) and (4) under “Weaknesses” in this reviewer’s public review. We have now added a 1.5-page subsection starting from the bottom of p. 12 to the top of p. 14 to discuss a new extensive analysis of Arg<sup>+</sup>–Cl<sup>−</sup>–Arg<sup>+</sup> configurations to identify bridging interactions, with key results reported in a new Fig. 6 (p. 42). Recent results from MacAinsh, Dey & Zhou (cited now as ref. 72) are included in the added discussion. Relevant advances made in MacAinsh et al., including clarification and classification of salt-mediated interactions in the phase separation of A1-LCD are now mentioned multiple times in the revised manuscript (p. 5, lines 19–20; p. 6, lines 2–5; p. 11, line 30; p. 14, line 10; p. 18, lines 28–29; and p. 20, line 4).

      Writing and presentation

      (1) Cite subtle effects that may be missed by the coarser approaches in this study

      Please see response above to point (1) under “Weaknesses” in this reviewer’s public review.

      (2) Try to distill the findings into a simple set of conclusions

      Please see response above to point (2) under “Weaknesses” in this reviewer’s public review.

      (3) Clarify and simplify physical interpretations

      Please see response above to point (2) under “Weaknesses” in this reviewer’s public review.

      (4) Explain the treatment of ATP-Mg as either a single ion or two separate ions; reconsider modifying the reference to ATP in the title

      Please see response above to point (4) under “Weaknesses” in this reviewer’s public review.

      (5) Minor points:

      p. 4, citation of ref 56: this work shows ATP is a driver of LLPS, not merely a regulator (promotor or suppressor)

      This citation to original ref. 56 (now ref. 63) on p. 4 is now corrected (bottom line of p. 4).

      p. 7 and throughout: “using bulk [Caprin1]” – I assume this is the initial overall Caprin1 concentration. It would avoid confusion to state such concentrations as “initial” or “initial overall”

      We have now added “initial overall concentration” in parentheses on p. 8 (line 4) to clarify the meaning of “bulk concentration”.

      p. 7 and throughout: both mM (also uM) and mg/ml have been used as units of protein concentration and that can cause confusion. Indeed, the authors seem to have confused themselves on p. 9, where 400 (750) mM is probably 400 (750) mg/ml. The same with the use of mM and M for salt concentrations (400 mM Mg2+ but 0.1 and 1.0 M Na+)

      Concentrations are now given in both molarity and mass density in Fig. 1 (p. 37), Fig. 2 (p. 38), Fig. 4 (p. 40), and Fig. 7 (p. 43), as noted in the text on p. 8 (lines 4–5). Inconsistencies and errors in quoting concentrations are now corrected (p. 10, line 18, and p. 11, line 2).

      p. 7, “LCST-like”: isn’t this more like a case of a closed coexistence curve that contains both UCST and LCST?

      The discussion on p. 8 around this observation from Fig. 1d is now expanded, including alluding to the theoretical possibility of a closed co-existence curve mentioned by this reviewer, as follows:

      “Interestingly, the decrease in some of the condensed-phase [pY-Caprin1]s with decreasing T (orange and green symbols for ≲ 20◦C in Fig. 1d trending toward slightly lower [pY-Caprin1]) may suggest a hydrophobicity-driven lower critical solution temperature (LCST)-like reduction of LLPS propensity as temperature approaches ∼ 0◦C as in cold denaturation of globular proteins [7,23] though the hypothetical LCST is below 0◦C and therefore not experimentally accessible. If that is the case, the LLPS region would resemble those with both an UCST and a LCST [4]. As far as simple modeling is concerned, such a feature may be captured by a FH model wherein interchain contacts are favored by entropy at intermediate to low temperatures and by enthalpy at high temperatures, thus entailing a heat capacity contribution in χ(T), with [7,109,110] beyond the temperature-independent ϵ<sub>h</sub> and ϵ<sub>s</sub> used in Fig. 1c,d and Fig. 2. Alternatively, a reduction in overall condensed-phase concentration can also be caused by formation of heterogeneous locally organized structures with large voids at low temperatures even when interchain interactions are purely enthalpic (Fig. 4 of ref. [111]).”

      p. 8 “Caprin1 can undergo LLPS without the monovalent salt (Na+) ions (LLPS regions extend to [Na+] = 0 in Fig. 2e,f”: I don’t quite understand what’s going on here. Is the effect caused by a small amount of counterion (ATP-Mg) that’s calculated according to eq 1 (with z s set to 0)?

      The discussion of this result in Fig. 2e,f is now clarified as follows (p. 10, lines 8–14 in the revised manuscript):

      “The corresponding rG-RPA results (Fig. 2e–h) indicate that, in the present of divalent counterions (needed for overall electric neutrality of the Caprin1 solution), Caprin1 can undergo LLPS without the monvalent salt (Na+) ions (LLPS regions extend to [Na+] = 0 in Fig. 2e,f; i.e., ρs \= 0, ρc > 0 in Eq. (1)), because the configurational entropic cost of concentrating counterions in the Caprin1 condensed phase is lesser for divalent (zc \= 2) than for monovalent (zc \= 1) counterions as only half of the former are needed for approximate electric neutrality in the condensed phase.”

      p. 9 “Despite the tendency for polymer field theories to overestimate LLPS propensity and condensed-phase concentrations”: these limitations should be mentioned earlier, along with the very high concentrations (e.g., 1200 mg/ml) in Fig. 2

      This sentence (now on p. 11, lines 11–18) is now modified to clarify the intended meaning as suggested by this reviewer:

      “Despite the tendency for polymer field theories to overestimate LLPS propensity and condensed-phase concentrations quantitatively because they do not account for ion condensation [99]—which can be severe for small ions with more than ±1 charge valencies as in the case of condensed [Caprin1] ≳ 120 mM in Fig. 2i–l, our present rG-RPA-predicted semi-quantitative trends are consistent with experiments indicating “

      In addition, this limitation of polymer field theories is also mentioned earlier in the text on p. 6, lines 30–31.

      Reviewer #2 (Recommendations For The Authors):

      (1) he current version of the paper goes through many different methodologies, but how these methods complement or overlap in terms of their applicability to the problem at hand may not be so clear. This can be especially difficult for readers not well-versed in these methods. I suggest the authors summarize this somewhere in the paper.

      As mentioned above in response to Reviewer #1, we have now added a subsection with heading “Overview of key observations from complementary approaches” at the beginning of the “Results” section on p. 6 (lines 18–37) and the first line of p. 7 to make our paper more accessible to readers who might not be well-versed in the various theoretical and computational techniques. A few sentences to summarize our key results are added as well to the first paragraph of “Discussion” (p. 18, lines 23–26).

      (2) It wasn’t clear if the authors obtained LCST-type behavior in Figure 1d or if another phenomenon is responsible for the non-monotonic change in dense phase concentrations. At the very least, the authors should comment on the possibility of observing LCST behavior using the rG-RPA model and if modifications are needed to make the theory more appropriate for capturing LCST.

      As mentioned above in response to Reviewer #1, the discussion regarding possible LCSTtype behanvior in Fig. 1d is now expanded to include two possible physical origins: (i) hydrophobicity-like temperature-dependent effective interactions, and (ii) formation of heterogeneous, more open structures in the condensed phase at low temperatures. Three additional references [109, 110, 111] (from the Dill, Chan, and Panagiotopoulos group respectively) are now included to support the expanded discussion. Again, the modified discussion is as follows:

      “Interestingly, the decrease in some of the condensed-phase [pY-Caprin1]s with decreasing T (orange and green symbols for ≲ 20◦C in Fig. 1d trending toward slightly lower [pY-Caprin1]) may suggest a hydrophobicity-driven lower critical solution temperature (LCST)-like reduction of LLPS propensity as temperature approaches ∼ 0◦C as in cold denaturation of globular proteins [7,23] though the hypothetical LCST is below 0◦C and therefore not experimentally accessible. If that is the case, the LLPS region would resemble those with both an UCST and a LCST [4]. As far as simple modeling is concerned, such a feature may be captured by a FH model wherein interchain contacts are favored by entropy at intermediate to low temperatures and by enthalpy at high temperatures, thus entailing a heat capacity contribution in χ(T), with [7,109,110] beyond the temperature-independent ϵ<sub>h</sub> and ϵ<sub>s</sub> used in Fig. 1c,d and Fig. 2. Alternatively, a reduction in overall condensed-phase concentration can also be caused by formation of heterogeneous locally organized structures with large voids at low temperatures even when interchain interactions are purely enthalpic (Fig. 4 of ref. [111]).”

      (3) In Figures 4c and 4d, ionic density profiles could be shown as a separate zoomed-in version to make it easier to see the results.

      This is an excellent suggestion. Two such panels are now added to Fig. 4 (p. 40) as parts (g) and (h).

      Reviewer #3 (Recommendations For The Authors):

      I would suggest authors make some minor edits as noted here.

      (1) Please note down the chi values that were used when fitting experimental phase diagrams with rG-RPA theory in Figure 2a,b. At present there aren’t too many such values available in the literature and reporting these would help to get an estimate of effective chi values when electrostatics is appropriately modeled using rG-RPA.

      The χ(T) values and their enthalpic and entropic components ϵh and ϵs used to fit the experimental data in Fig. 1c,d are now stated in the caption for Fig. 1 (p. 37). Same fitted χ(T) values are used in Fig. 2 (p. 38) as it is now stated in the revised caption for Fig. 2. Please note that for clarity we have now changed the notation from ∆h and ∆s in our originally submitted manuscript to ϵh and ϵs in the revised text (p. 7, last line) as well as in the revised figure captions to conform to the notation in our previous works [18, 71].

      (2) Authors note “monovalent positive salt ions such as Na+ can be attracted, somewhat counterintuitively, into biomolecular condensates scaffolded by positively-charged polyelectrolytic IDRs in the presence of divalent counterions”. This may be due to the fact that the divalent negative counterions present in the dense phase (as seen in the ternary phase diagrams) also recruit a small amount of Na+.

      The reviewer’s comment is valid, as a physical explanation for this prediction is called for. Accordingly, the following sentence is added to p. 10, lines 27–29:

      “This phenomenon arises because the positively charge monovalent salt ions are attracted to the negatively charged divalent counterions in the protein-condensed phase.”

      (3) In the discussion where authors contrast the LLPS propensity of Caprin1 against FUS, TDP43, Brd4, etc, they correctly note majority of these other proteins have low net charge and possibly higher non-electrostatic interaction that can promote LLPS at room temperature even in the absence of salt. It is also worth noting if some of these proteins were forced to undergo LLPS with crowding which is sometimes typical. A quick literature search will make this clear.

      A careful reading of the work in question (Krainer et al., ref. 50) does not suggest that crowders were used to promote LLPS for the proteins the authors studied. Nonetheless, the reviewer’s point regarding the potential importance of crowder effects is well taken. Accordingly, crowder effects are now mentioned briefly in the Introduction (p. 4, line 13), with three additional references on the impact of crowding on LLPS added [30–32] (from the Spruijt, Mukherjee, and Rakshit groups respectively). In this connection, to provide a broader historical context to the introductory discussion of electrostatics effects in biomolecular processes in general, two additional influential reviews (from the Honig and Zhou groups respectively) are now cited as well [15, 16].

    1. eLife Assessment

      This manuscript aims to identify the pacemaker cells in the lymphatic collecting vessels - the cells that initiate the autonomous action potentials and contractions needed to drive lymphatic pumping. Through the exemplary use of existing approaches (genetic deletions and cytosolic calcium detection in multiple cell types), the authors convincingly determine that lymphatic muscle cells are the origin of the action potential that triggers lymphatic contraction. The inclusion of scRNAseq and membrane potential data enhances a tremendous study. This fundamental discovery establishes a new standard for the field of lymphatic physiology.

    2. Reviewer #1 (Public review):

      Summary:

      This manuscript explores the multiple cell types present in the wall of murine collecting lymphatic vessels with the goal of identifying cells that initiate the autonomous action potentials and contractions needed to drive lymphatic pumping. Through the use of genetic models to delete individual genes or detect cytosolic calcium in specific cell types, the authors convincingly determine that lymphatic muscle cells are the origin of the action potential that triggers lymphatic contraction.

      Strengths:

      The experiments are rigorously performed, the data justify the conclusions and the limitations of the study are appropriately discussed.

      There is a need to identify therapeutic targets to improve lymphatic contraction and this work helps identify lymphatic muscle cells as potential cellular targets for intervention.

    3. Reviewer #2 (Public review):

      Summary:

      This is a well written manuscript describing studies directed at identifying the cell type responsible for pacemaking in murine collecting lymphatics. Using state-of-the-art approaches, the authors identified a number of different cell types in the wall of these lymphatics and then using targeted expression of Channel Rhodopsin and GCaMP, the authors convincingly demonstrate that only activation of lymphatic muscle cells produces coordinated lymphatic contraction and that only lymphatic muscle cells display pressure-dependent Ca2+ transients as would be expected of a pacemaker in these lymphatics.

      Strengths:

      The use of targeted expression of channel rhodopsin and GCaMP to test the hypothesis that lymphatic muscle cells serve as the pacemakers in musing lymphatic collecting vessels.

      Weaknesses:

      The only significant weakness was the lack of quantitative analysis of most of the imaging data shown in Figures 1-11. In particular, the colonization analysis should be extended to show cells not expected to demonstrate colocalization as a negative control for the colocalization analysis that the authors present. These weaknesses have been resolved by revision and addition of new and novel RNAseq data, additional colocalization data and membrane potential measurements.

    4. Reviewer #3 (Public review):

      Summary:

      Zawieja et al. aimed to identify the pacemaker cells in the lymphatic collecting vessels. Authors have used various Cre-based expression systems and optogentic tools to identify these cells. Their findings suggest these cells are lymphatic muscle cells that drive the pacemaker activity in the lymphatic collecting vessels.

      Strengths:

      The authors have used multiple approaches to test their hypothesis. Some findings are presented as qualitative images, while some quantitative measurements are provided.

      Weaknesses:

      - More quantitative measurements.<br /> - Possible mechanisms associated with the pacemaker activity.<br /> - Membrane potential measurements.

      Comments on revisions:

      The authors have answered my comments with additional experiments, data and manuscript edits.

    5. Author response:

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

      Public Reviews: 

      Reviewer #1 (Public Review): 

      Summary: 

      This manuscript explores the multiple cell types present in the wall of murine-collecting lymphatic vessels with the goal of identifying cells that initiate the autonomous action potentials and contractions needed to drive lymphatic pumping. Through the use of genetic models to delete individual genes or detect cytosolic calcium in specific cell types, the authors convincingly determine that lymphatic muscle cells are the origin of the action potential that triggers lymphatic contraction. 

      Strengths: 

      The experiments are rigorously performed, the data justify the conclusions, and the limitations of the study are appropriately discussed. 

      There is a need to identify therapeutic targets to improve lymphatic contraction and this work helps identify lymphatic muscle cells as potential cellular targets for intervention. 

      Weaknesses: 

      My only major comment would be that the manuscript provides a lot of rich information describing the cellular components of the muscular lymphatic vessel wall and that these data are not well represented by the title. The title (while currently accurate) could be tweaked to better represent all that is in this manuscript. Maybe something like

      "Characterization/Interrogation of the cellular components of murine collecting lymphatic vessels reveals that lymphatic muscle cells are the innate pacemaker cells regulating lymphatic contractions" or "Discovery/Confirmation of lymphatic muscle cells as innate pacemaker cells of lymphatic contraction through characterization of the cellular components of murine collecting lymphatic vessels". Potentially a cartoon summary figure of the components that make up the collecting lymphatic vessel wall could also be included. In my opinion, these changes will make this manuscript of more interest to a broader group of scientists. I have a few additional comments for consideration to improve the clarity and enhance the discussion of this work. 

      We agree with the reviewer that our original manuscript, and our resubmission even more so with the addition of the scRNAseq data, provides a significant amount of information regarding the composition of the lymphatic collecting vessel wall. We have changed our title to match one suggestion of the reviewer: “Characterization of the cellular components of murine collecting lymphatic vessels reveals that lymphatic muscle cells are the innate pacemaker cells regulating lymphatic contractions".

      Reviewer #2 (Public Review): 

      Summary: 

      This is a well-written manuscript describing studies directed at identifying the cell type responsible for pacemaking in murine-collecting lymphatics. Using state-of-the-art approaches, the authors identified a number of different cell types in the wall of these lymphatics and then using targeted expression of Channel Rhodopsin and GCaMP, the authors convincingly demonstrate that only activation of lymphatic muscle cells produces coordinated lymphatic contraction and that only lymphatic muscle cells display pressure-dependent Ca2+ transients as would be expected of a pacemaker in these lymphatics. 

      Strengths: 

      The use of a targeted expression of channel rhodopsin and GCaMP to test the hypothesis that lymphatic muscle cells serve as the pacemakers in musing lymphatic collecting vessels. 

      Weaknesses: 

      The only significant weakness was the lack of quantitative analysis of most of the imaging data shown in Figures 1-11. In particular, the colonization analysis should be extended to show cells not expected to demonstrate colocalization as a negative control for the colocalization analysis that the authors present. 

      We understand the reviewer’s concern regarding the lack of a control for the colocalization analysis and that the colocalization analysis was limited to just one set of cell markers. We have now provided a colocalization analysis of Myh11 and PDGFRα, to serve as a co-localization negative control based on our RT-PCR and scRNASeq findings, which is incorporated into the current Supplemental figure 1. In regard to the staining pattern of other various marker combinations, the results were often quite clear with the representative images that two separate cell populations were being stained such as the case with labeling endothelial cells with CD31, macrophage labeling with the MacGreen mice, or hematopoietic cells with CD45. 

      During our lengthy rebuttal process we completed a single cell RNA sequence analysis using our isolated and cleaned mouse inguinal axillary lymphatic collecting vessels to aid in our characterization of the vessel wall and to more thoroughly answer these questions regarding colocalization in arguably a robust manner. The generation of our scRNAseq dataset, derived from isolated and cleaned mouse inguinal axillary collecting vessels from 10 mice, 5 male and 5 females, allowed us to profile over 2200 of the adventitial fibroblast like cells (AdvCs) we had identified in our original submission. Using this dataset, we were able to confirm co-expression of Cd34 and Pdgfrα in AdvCs and assess the co-expression of other genes of interest from our RT-PCR experiments and immunofluorescence experiments. This approach will also allow other lymphatic investigators to assess their genes of interest as our dataset is uploaded to the NIH Gene Omnibus and will be uploaded to the Broad Institute Single Cell Portal upon publication.

      Here we show that the vast majority of non-muscle fibroblast like cells referred to as AdvCs were double positive for both CD34 and PDGFRα. We also show that the AdvCs that express commonly used pericyte markers Pdgfrb and Cspg4 also co-expressed Pdgfrα. Critically, this data also shows that the AdvCs that express genes linked with lymphatic contractile dysfunction (Ano1, Gjc1 or connexin 45, and Cacna1c “Cav1.2”) co-express Pdgfrα and would render these genes susceptible to Cre-mediated recombination using our Pdgfrα-CreER<sup>TM</sup> model.  

      Reviewer #3 (Public Review): 

      Summary: 

      Zawieja et al. aimed to identify the pacemaker cells in the lymphatic collecting vessels. Authors have used various Cre-based expression systems and optogenetic tools to identify these cells. Their findings suggest these cells are lymphatic muscle cells that drive the pacemaker activity in the lymphatic collecting vessels. 

      Strengths: 

      The authors have used multiple approaches to test their hypothesis. Some findings are presented as qualitative images, while some quantitative measurements are provided.   

      Weaknesses: 

      -  More quantitative measurements. 

      -  Possible mechanisms associated with the pacemaker activity. 

      -  Membrane potential measurements. 

      We thank the reviewers for their concerns and have addressed them in the following manner. 

      - We added novel single cell RNA sequencing of isolated and cleaned inguinal axillary vessels from 10 mice (5 males and 5 females). This allowed us to quantify the number of AdvCs that coexpress CD34 and Pdgfrα as well as the number of cells co-expressing Pdgfrα and other markers.

      - We have added a negative control with quantification for the co-localization analysis assessing Myh11 and Pdgfrα. We have added a negative control with quantification for the ChR2-photo stimulated contraction experiments using Myh11CreERT2-ChR2 mice that were not injected with tamoxifen. 

      - We also used Biocytin-AF488 in our intracellular Vm electrodes to map the specific cells in which we recorded action potentials and in neighboring cells since Biocytin-AF488 is under 1KDa and can pass through gap junctions. This approach independently labeled lymphatic muscle cells and their direct neighbors for 3 IALVs from 3 separate mice. 

      - We performed membrane potential recordings in isolated, pressurized (under isobaric conditions), and spontaneously contracting inguinal axillary lymphatic collecting vessels at different pressures. 

      - We also show that the pressure-frequency relationship is dependent on the slope of the diastolic depolarization as no other parameter was significantly altered in our study and the diastolic depolarization slope was highly correlated with contraction frequency. 

      We believe the addition of these novel data, controls, experiments, and quantifications have improved the manuscript in line with the reviewers’ suggestions.

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors): 

      Lines 149-162: The authors rule out the methylene blue staining cells in the cLV wall as pacemakers because they don't form continuous longitudinal connections to drive propagation. Is it possible for a pacemaker cell to only initiate the contraction and then have the LMCs make the axial electrical connections to propagate the electrical wave? I am not trying to suggest the methylene blue cells are pacemakers, but I am not sure the lack of longitudinal (or radial) connectivity is sufficient evidence to rule out the possibility. This comment also is relevant to the 3 criteria for a pacemaker cell listed in the Discussion (Lines 413-417). 

      We agree with the reviewer’s broader point that a pacemaker cell may not require direct contact with other ‘pacemaker’ cells within the tissue as long as they are still within the same electrical syncytium. However, we do expect a continuous presence of a pacemaker cell type throughout the vessel wall length to account for the persistence of spontaneous contractile behavior despite vessel length, and the ability for contraction initiation to shift (Akl et al 2011, Castorena et al 2018 and Castorena et al 2022) and the occurrence of spontaneous action potentials. In Dirk van Helden’s seminal work in 1993 on lymphatic pacemaking, a major finding was that “SM of small lymphangions or that of short segments, cut from lymphangions of any length, behaved similarly”. We have adjusted our phrase regarding the requirement of a contiguous network and instead suggest a continuous presence along the vessel network and integrated into the electrical syncytium. 

      Methylene blue is an alkaline stain that will stain acidic structures and historically methylene blue is noted to stain Interstitial cells of Cajal in the gastrointestinal tract which typically exist as network of cells(Huizinga et al 1993 and Berezin 1988). No such network was readily apparent in our methylene blue staining nor did the stained cells have a similar morphology to the ICCs of the gastrointestinal tract. Further, methylene blue is staining is not limited to ICCs or pacemaker cells at large as it has been used to kill cancer cells. Within the small intestine methylene blue was noted to also stain macrophage like cells (Mikkelsen et al 1988), and we too draw parallels between the macrophage morphology observed with Macgreen mice and methylene-blue stained cells. The specific structure for the ICC affinity for methylene blue is not well described and while the innate cytotoxicity of methylene blue and light has been used to kill ICCs and impair slow wave generation, the lack of specificity of this method leaves much to be desired. What is clear is that the ICC network highlighted by methylene blue in the gut is absent in lymphatic collecting vessels.

      In Figure 15/Video12, is it possible that the cells that are showing intracellular Ca2+ in diastole are the cells that reach a threshold membrane potential that then trigger the rest of the LMCs? As the authors have shown heterogeneity in the LMCs surface markers, is it possible that the cells with Ca2+ activity during diastole are identifiable by a distinct molecular phenotype? Or is the thought that these cells are randomly active in diastole? Some discussion/speculation about this seems appropriate. 

      We are in agreement with the reviewer’s conclusion that there is heterogeneity in the LMCs as it pertains to the calcium oscillations in diastole, either under normal buffer conditions or when L-type channels are inhibited with nifedipine. We also note significant heterogeneity in the gene expression noted within the four LMC subclusters (0-3), though we did not see significant differences in either in Ip3R1 or Ano1 expression. However, subcluster “0” had increased expression of Itprid2, also known as KRas-induced actin-interacting protein (KRAP) which is thought to tether, and thus immobilize, IP3 receptors to the actin cortex beneath the cell membrane. KRAP has been recently proposed to be a critical player in IP3 receptor “licensing” which allows IP3 receptors to release calcium (Vorontsova et al., 2022).  However, whether similar requirement of IP3R licensing is necessitated in all cells or specifically in LMCs is unknown it is quite clear there are specific release sites within the cell and this topic is currently under further investigation for a separate manuscript. We would like to note that there is yet to be a clear consensus on whether IP3R licensing is required as much of these studies are performed in cultured cells and this mechanism has only recently been described. 

      Healthy lymphatic collecting vessels typically have a single pacemaker driving a coordinated propagated contraction in ex vivo isobaric myograph studies (Castorena-Gonzalez et al., 2018), which is typically at either end of the cannulated vessel. We believe that this is due to the lack of a bordering cell in one direction and allows charge to accumulate and voltage to reach threshold at these sites preferentially. We have tried to image calcium at the pacemaking pole of the vessel to observe the specific Ca<sup>2+</sup> transients at these sites though invariably the act of imaging GCaMP6f results in the pacemaker activity initiating from the other pole of the vessel. It is our opinion that the fact that LMCs are heterogenous in their Ca<sup>2+</sup> transients is a feature to the system as it permits a wider range of depolarization signals, and thus allows finer control of the pacing as different physical/pressure or signaling stimuli is encountered. Likely, the cells with the higher propensity of Ca<sup>2+</sup> transients act as the contraction initiation site in vivo, though it must also be noted that the LMC density decreases around lymphatic valve sites. In fact, in guinea pig collecting vessels there are very few LMCs at the valves which can render them electrically uncoupled or poorly coupled (Van Helden, 1993). Thus, valve sites in which there is greater electrical resistance due to lower LMC-LMC coupling may allow for charge accumulation in the LMCs at the valve site, similar to the artificial condition achieved in our myograph preparations with two cut ends, and allow them to reach threshold first and drive coordination at the valve sties.

      An additional description of what the PTCL analysis is meant to represent physiologically would be helpful for readers. 

      We have better described the conversion of the calcium signals into “particles” for analysis at first mention in the methods and results section and have included the requisite reference to this specific methodology in Line 429-30. 

      A description of how DMAX is experimentally determined is needed. 

      We have adjusted our methods section to describe DMAX in line 774-775.

      “with Ca<sup>2+</sup>-free Krebs buffer (3mM EGTA) and diameter at each pressure recorded under passive conditions (DMAX).”

      I think the vessels referred to as popliteal lymphatic vessels are actually saphenous lymphatic vessels (afferent to the popliteal lymph node). Please clarify. 

      Indeed, some of the vessels used in this study are the afferents to the single popliteal node. They travel with the caudal branch of the saphenous vein, but have routinely been described as popliteal vessels, as opposed to saphenous lymphatic vessels, by the lymphatic field at large (Tilney 1971 PMCID: PMC1270981, Liao 2015 PMID: 25512945). To move away from this nomenclature would likely add to confusion although we agree that the lymphatic field may need to improve or correct the vessel naming paradigm to match the vascular pairs they follow.

      Reviewer #2 (Recommendations For The Authors): 

      Lines 214-215 - can you cite a reference for the observation that rhythmic contractions don't require the presence of valves? 

      We have added the reference. In Dr. Van Helden’s seminal work on the topic in 1993, “Vessel segments were then cut from selected small lymphangions (length 300-500 um) by cutting at the valves.” Additionally, work by Dr Anatoliy Gashev utilized sections of lymphatic vessels that lacked valves to study orthograde and retrograde shear sensitivity (Gashev et al., 2002).

      Lines 224-230 - It would have been nice to see colocalization analysis for all cell types so that "negative" results could be compared with the "positives" that you report. This would help bolster evidence of your ability to separate cell types. 

      We understand the reviewer’s sentiment and agree. We have now added a “negative control” colocalization staining and analysis for PDGFR and Myh11 which has been added to the current SuppFigure 1. We stained 3 IALVs from 3 separate mice with PDGFRα and Myh11 and performed confocal microscopy. We ran the FIJI BIOP-JACOP colocalization plugin as before and observed very little colocalization of the two signals. Additionally, we have also added a coexpression assessment for CD34 and PDGFRα and other genes using our scRNAseq dataset.  

      line 293 - Should read "Cx45 in..." 

      This has been corrected. 

      “The expression of the genes critically involved in cLV function—Cav1.2, Ano1, and Cx45—in the PdgfrαCreER<sup>TM</sup>-ROSA26mTmG purified cells and scRNAseq data prompted us to generate PdgfrαCreER<sup>TM</sup>-Ano1<sup>fl/fl</sup>, PdgfrαCreER<sup>TM</sup>-Cx45<sup>fl/fl</sup>, and PdgfrαCreER<sup>TM</sup>-Cav1.2<sup>fl/fl</sup> mice for contractile tests.”

      lines 470-473 - A reference for this statement should be cited. 

      We have added the reference. In Dr. Van Helden’s seminal work on the topic in 1993, “Vessel segments were then cut from selected small lymphangions (length 300-500 um) by cutting at the valves.” Additionally, work by Dr Anatoliy Gashev utilized sections of lymphatic vessels that lacked valves to study orthograde and retrograde shear sensitivity (Gashev et al., 2002).

      Lines 483-487 - References should be cited for these statements. 

      We have narrowed and clarified this statement and supported it with the necessary citations. 

      “Of course, mesenchymal stromal cells (Andrzejewska et al., 2019) and fibroblasts (Muhl et al., 2020; Buechler et al., 2021; Forte et al., 2022) are present, and it remains controversial to what extent telocytes are distinct from or are components/subtypes of either cell type (Clayton et al., 2022). Telocytes are not monolithic in their expression patterns, displaying both organ directed transcriptional patterns as well as intra-organ heterogeneity (Lendahl et al., 2022) as readily demonstrated by recent single cell RNA sequencing studies that provided immense detail about the subtypes and activation spectrum within these cells and their plasticity (Luo et al., 2022).”

      Lines 584-585 - Missing a reference citation. 

      Thank you for catching this error, the correct citation was for Boedtkjer et al 2013 and is now properly cited. 

      Line 638 - "these this" should read "this" 

      Thank you for catching this error. This particular sentence was removed in light of the addition of the scRNAseq data.

      Reviewer #3 (Recommendations For The Authors): 

      This manuscript from Zawieja et al. explored an interesting hypothesis about the pacemaker cells in lymphatic collecting vessels. Many aspects of lymphatic collecting vessels are still under investigation; hence this work provides timely knowledge about the lymphatic muscle cells as a pacemaker. Although it is an important topic of the investigation, the data provided do not support the overall goal of the manuscript. Many figures (Figure 1-5) provide quantitative estimation and the description provided in the results section might only be useful for a restricted audience, but not to the broader audience. Some of the figures are very condensed with multiple imaging panels and it is hard to follow the differences in qualitative analysis. Overall, this manuscript can be improved by more streamlined description/writing and figure arrangements (some of the figures/panels can be moved to the supplementary figures). 

      We disagree with the notion that the original data provided did not support the goal of the manuscript- to identify and test putative pacemaker cell types. Nonetheless we believe we have also added ample novel data to the manuscript, including membrane potential recordings and scRNAseq to highlight and to add further support to our conclusion that the pacemaker cell is an LMC. We believe the scRNAseq data will also greatly enhance the appeal of the manuscript to a broader audience and have renamed the manuscript in line with the wealth of data we have collected on the components of the vessel wall as we tested for putative pacemaker cells.

      As requested, we have moved many figures to the supplement to allow readers to focus more on the more critical experiments.

      A few other points that need to be addressed: 

      (1) Authors used immunofluorescence-based differences in various cell types in the collecting vessels. Initially, they chose ICLC, pericytes, and lymphatic muscle cells. But then they started following adventitial cells and endothelial cells. It is not clear from the description, why these other cells could be possibly involved in the pacemaker activity. It will be easier to follow if authors provide a graphical abstract or summary figure about their hypothesis and what is known from their and others' work. 

      We would like to clarify that we used the endothelial cells as controls to ensure what we observed via immunofluorescence and FACs RT-PCR were a separate cell type from either lymphatic muscle or lymphatic endothelial cells on the vessel wall. Staining for the endothelium also allowed us to assess where these PDGFRα+CD34+ cells reside in the vessel wall.  We started with a wide range of markers that are conventionally used for targeting specific cell types, but as expected those markers are not always 100% specific. Specifically, we focused on CD34, Kit, and Vimentin as those were the markers for the non-muscle cells observed in the lymphatic collecting vessel wall previously. What we found was that CD34 and PDGFRα labeled the same cell type. As there was not a CD34Cre mouse available at the time we instead utilized the inducible PDGFRαCreERTM. We are unsure how well an abstract figure will condense the conclusions from the experiments listed here but if absolutely required for publication we can attempt to highlight the representative cell populations identified on the vessel wall.

      (2) Authors used many acronyms in the manuscript without defining them (when they appeared for the first time). Please follow the convention. 

      We have checked the manuscript and made several corrections regarding the use of abbreviations.

      (3) How specific PDGFR-alpha as a marker of the pericytes? It can also label the mesenchymal cells. Why did the author choose PDGFR-alpha over beta for their Cre-based expression approach? 

      We tried to assess if there were a pericyte like cell present in or along the wall using PDGFRbeta (Pdgfrβ). Pdgfrβ is commonly used to identify pericytes (Winkler et al., 2010), while in contrast Pdgfrα is a known fibroblast marker (Lendahl et al., 2022). Pdgfrβ CreERT2 resulted in recombination in both LMCs and AdvCs, preventing it from being a discriminating marker for our study where as Myh11CreER<sup>T2</sup> and PDGFRαCreER<sup>TM</sup> were specific at least to cell type based on our FACSs-RT-PCR and staining. As you can tell from the scRNAseq data in Figure 5, there was no cell cluster that Pdgfrβ was specific for in contrast to PDGFRα and Myh11.  In Figure 6 we show the expression of another commonly used pericyte marker NG2 (Cspg4) in our scRNAseq dataset which was observed in both LMCs and AdvCs as well. Lastly, MCAM (Figure 6) can also be a marker for pericytes though we see only expression in the LMCs and LECs for this marker. Notably, almost all of the AdvCs express PDGFRα rendering the PDGFRαCreER<sup>TM</sup> a powerful tool to study this population of cells on the vessel wall including those that were PDGFRα+Cspg4+ or PDGFRα+ Pdgfrβ+.

      We were reliant on PDGFRαCreER<sup>TM</sup> as that was the only available PDGFRα Cre model at the time. Note we used PdgfrβCreER<sup>T2</sup> and Ng2Cre in our study but found that both Cre models recombined both LMCs and AdvCs.

      (4) Please include appropriate references for all the labeling markers (PDGFR-alpha, beta, and myc11 etc.) that are used in this manuscript. 

      We have added multiple references to the manuscript to support the use of these common cell “specific” markers as of course each marker is limited in some capacity to fully or specifically label a single population of cells (Muhl et al., 2020).

      (5) One of the criteria for the pacemaker cells is depolarization-induced propagated contractions. Authors have used optogenetics-induced depolarization to test this phenomenon. Please include negative controls for these experiments. 

      We have now added negative controls to this experiment which were non-induced (no tamoxifen) Myh11CreER<sup>T2</sup>-Chr2 popliteal vessels. This data has been added to the Figure 8.  

      (6) What are the resting membrane potentials of Lymphatic muscle cells? The authors should provide some details about this in the manuscript. 

      We agree with the reviewer and have added membrane potential recordings (Figure 13) at different pressures and filled our recording electrode with the cell labeling molecule BiocytinAF488 to highlight the action potential exhibiting cells, which were the LMCs. Lymphatic resting membrane potential is dynamic in pressurized vessels, which appears to be a critical difference in this approach as compared to pinned out vessels or those on wire myographs likely due to improper stretch or damage to the vessel wall. In mesenteric lymphatic vessels isolated from rats the minimum membrane potential achieved during repolarization ranges from -45 to 50mV typically while IALVs from mice are typically around -40mV, though IALVs have a notably higher contraction frequency. Critically, we have also added novel membrane potential recordings to this manuscript in IALVs at different pressures and show that the diastolic depolarization rate is the critical factor driving the pressure-dependent frequency.

      (7) In the discussion, the authors discussed SR Ca2+ cycling in Pacemaking, but the relevant data are not included in this manuscript, but a manuscript from JGP (in revision) is cross-referenced. 

      As discussed above, we have recently published our work where studied IALVs from Myh11CreERT2-Ip3R1fl/fl (Ip3r1ismKO) and Myh1CreERT2-Ip3r1fl/fl-Ip3r2fl/fl-Ip3r3fl/fl mice (Zawieja et al., 2023). Deletion of Ip3r1 from LMCs recapitulated the dramatic reduction in frequency we previously published in Myh11CreERT2-Ano1fl/fl mice and the loss of pressure dependent chronotropy. Furthermore, in this manuscript we also showed that the diastolic calcium transients are nearly completely lost in ILAVs from Myh11CreERT2-Ip3R1fl/fl knockout mice. There was no difference in the contractile function between IALVs from single Ip3r1 knockout and the triple Ip3r1-3 knockout mice suggesting that it is Ip3r1 that is required for the diastolic calcium oscillations. Further, in the presence of 1uM nifedipine there were still no calcium oscillations in the Myh11CreERT2-Ip3r1fl/fl LMCs. These findings provide further support for our interpretation that the pacemaking is of myogenic origin.

      Andrzejewska, A., B. Lukomska, and M. Janowski. 2019. Concise Review: Mesenchymal Stem Cells: From Roots to Boost. Stem Cells. 37:855-864.

      Buechler, M.B., R.N. Pradhan, A.T. Krishnamurty, C. Cox, A.K. Calviello, A.W. Wang, Y.A. Yang, L.

      Tam, R. Caothien, M. Roose-Girma, Z. Modrusan, J.R. Arron, R. Bourgon, S. Muller, and S.J. Turley. 2021. Cross-tissue organization of the fibroblast lineage. Nature. 593:575579.

      Castorena-Gonzalez, J.A., S.D. Zawieja, M. Li, R.S. Srinivasan, A.M. Simon, C. de Wit, R. de la Torre, L.A. Martinez-Lemus, G.W. Hennig, and M.J. Davis. 2018. Mechanisms of Connexin-Related Lymphedema. Circ Res. 123:964-985.

      Clayton, D.R., W.G. Ruiz, M.G. Dalghi, N. Montalbetti, M.D. Carattino, and G. Apodaca. 2022. Studies of ultrastructure, gene expression, and marker analysis reveal that mouse bladder PDGFRA(+) interstitial cells are fibroblasts. Am J Physiol Renal Physiol. 323:F299F321.

      Forte, E., M. Ramialison, H.T. Nim, M. Mara, J.Y. Li, R. Cohn, S.L. Daigle, S. Boyd, E.G. Stanley, A.G. Elefanty, J.T. Hinson, M.W. Costa, N.A. Rosenthal, and M.B. Furtado. 2022. Adult mouse fibroblasts retain organ-specific transcriptomic identity. Elife. 11.

      Gashev, A.A., M.J. Davis, and D.C. Zawieja. 2002. Inhibition of the active lymph pump by flow in rat mesenteric lymphatics and thoracic duct. J Physiol. 540:1023-1037.

      Lendahl, U., L. Muhl, and C. Betsholtz. 2022. Identification, discrimination and heterogeneity of fibroblasts. Nat Commun. 13:3409.

      Luo, H., X. Xia, L.B. Huang, H. An, M. Cao, G.D. Kim, H.N. Chen, W.H. Zhang, Y. Shu, X. Kong, Z.

      Ren, P.H. Li, Y. Liu, H. Tang, R. Sun, C. Li, B. Bai, W. Jia, Y. Liu, W. Zhang, L. Yang, Y. Peng, L. Dai, H. Hu, Y. Jiang, Y. Hu, J. Zhu, H. Jiang, Z. Li, C. Caulin, J. Park, and H. Xu. 2022. Pancancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment. Nat Commun. 13:6619.

      Muhl, L., G. Genove, S. Leptidis, J. Liu, L. He, G. Mocci, Y. Sun, S. Gustafsson, B. Buyandelger, I.V.

      Chivukula, A. Segerstolpe, E. Raschperger, E.M. Hansson, J.L.M. Bjorkegren, X.R. Peng, M. Vanlandewijck, U. Lendahl, and C. Betsholtz. 2020. Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination. Nat Commun. 11:3953.

      Van Helden, D.F. 1993. Pacemaker potentials in lymphatic smooth muscle of the guinea-pig mesentery. J Physiol. 471:465-479.

      Vorontsova, I., J.T. Lock, and I. Parker. 2022. KRAP is required for diffuse and punctate IP(3)mediated Ca(2+) liberation and determines the number of functional IP(3)R channels within clusters. Cell Calcium. 107:102638.

      Winkler, E.A., R.D. Bell, and B.V. Zlokovic. 2010. Pericyte-specific expression of PDGF beta receptor in mouse models with normal and deficient PDGF beta receptor signaling. Mol Neurodegener. 5:32.

      Zawieja, S.D., G.A. Pea, S.E. Broyhill, A. Patro, K.H. Bromert, M. Li, C.E. Norton, J.A. CastorenaGonzalez, E.J. Hancock, C.D. Bertram, and M.J. Davis. 2023. IP3R1 underlies diastolic ANO1 activation and pressure-dependent chronotropy in lymphatic collecting vessels. J Gen Physiol. 155.

    1. eLife Assessment

      This valuable study presents new observations on white matter organisation at the micron scale, using a combination of synchrotron imaging and diffusion MRI across two species. Notably, the authors provide solid evidence for the fasciculation of axons within major fibre bundles into laminar structures, though these structures are not consistently observed across modalities or species. The study will be of general interest to neuroanatomists and those interested in white matter imaging.

    2. Reviewer #1 (Public Review):

      This study presents valuable observations of white matter organisation from diffusion MRI and two types of synchrotron imaging in both monkeys and mice. Cross-modality comparisons are interesting as the different methods are able to probe anatomical structures at different length scales, from single axons in high-resolution synchrotron (ESRF) imaging, to clusters of axons in lower-resolution synchrotron (DEXY) data, to axon populations at the mm-scale in diffusion MRI. By acquiring all modalities in monkey and mouse ex vivo samples, the authors can observe principles of fibre organisation, and characterise how fibre characteristics, such as tortuosity and micro-dispersion, vary across select brain regions and in healthy tissue versus a demyelination model.

      One very interesting result is the observation of apparent laminar organisation of fibres in ex vivo monkey white matter samples. DESY data from the corpus callosum shows fibres with two dominant orientations (one L-R, one slightly inclined), clustered in laminar structures within this major fibre bundle. Thanks to the authors providing open data, I was able to look through the raw DESY volume and observe regions with different "textures" (different orientations) in the described laminar arrangement. That this organisation can be observed by eye, as well as by structure tensor, is fairly convincing.

    3. Reviewer #2 (Public Review):

      Summary:

      In this work, the authors combine diffusion MRI and high-resolution x-ray synchrotron phase-contrast imaging in monkey and mouse brains to investigate the 3D organization of brain white matter across different scales and species. The work is at the forefront of the anatomical investigation of the human connectome and aligns with several current efforts to bridge the resolution gap between what we can see in vivo at the millimeter scale and the complexity of the human brain at the sub-micron scale. The authors compare the 3D white matter organization across modalities within 2 small regions in one monkey brain (body of the corpus callosum, centrum semiovale) and within one region (splenium of the corpus callosum) in healthy mice and in one murine model of focal demyelination. The study compares measures of tissue anisotropy and fiber orientations across modalities, performs a qualitative comparison of fasciculi trajectories across brain regions and tissue conditions using streamlined tractography based on the structure tensor, and attempts to quantify the shape of fasciculi trajectories by measuring the tortuosity index and the maximum deviation for each reconstructed streamline. Results show measures of anisotropy and fiber orientations largely agree across modalities, especially for larger FOV data. The high-resolution data allows us to explore the fiber trajectories in relation to tissue complexity and pathology. The authors claim the study reveals new common organization principles of white matter fibers across species and scales, for which axonal fasciculi arrange into sheet-like laminar structures.

      Strengths:

      The aim of the study is of central importance within present efforts to bridge the gap between macroscopic structures observable in vivo in humans using conventional diffusion MRI and the microscopic organization of white matter tissue. Results obtained from this type of study are important to interpret data obtained in vivo, inform the development of novel methodologies, and expand our knowledge of the structural and thus functional organization of brain circuits.

      Multi-scale data acquired across modalities within the same sample constitute extremely valuable data that is often hard to acquire and represent a precious resource for validation of both diffusion MRI tractography and microstructure methods.

      The inclusion of multi-species data adds value to the study, allowing the exploration of common organization principles across species.

      The addition of data from a murine cuprizone model of focal demyelination adds interesting opportunities to study the underlying biological changes that follow demyelination and how these impact tissue anisotropy and fiber trajectories. These data can inform the interpretation and development of diffusion MRI microstructure models.

      [Editors' note: The Reviewing Editor considers that the authors addressed the reviewers' questions adequately. The original reviews are here: https://elifesciences.org/reviewed-preprints/94917/reviews]

    4. Author response:

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

      Reviewer #1 (Public Review):

      This study presents valuable observations of white matter organisation from diffusion MRI and two types of synchrotron imaging in both monkeys and mice. Cross-modality comparisons are interesting as the different methods are able to probe anatomical structures at different length scales, from single axons in high-resolution synchrotron (ESRF) imaging, to clusters of axons in lower-resolution synchrotron (DEXY) data, to axon populations at the mm-scale in diffusion MRI. By acquiring all modalities in monkey and mouse ex vivo samples, the authors can observe principles of fibre organisation, and characterise how fibre characteristics, such as tortuosity and micro-dispersion, vary across select brain regions and in healthy tissue versus a demyelination model. The results are solid, though some statements (in the abstract/discussion) do not appear to be fully supported, and statistical tests would help confirm whether tissue characteristics are similar/different between different conditions.

      R1.1: Thank you for the kind feedback. We have included statistical tests in the paper for tissue characteristics where appropriate.

      Due to the very high number of sample points (one per voxel) within the 3D synchrotron volumes, testing for statistical significance is challenging for the structure tensor-based tissue fractional anisotropy (FA) metric. This causes any standard statistical test to have sufficient power to evaluate even minute differences between the volumes as statistically significant with high confidence. In other words, the null hypothesis (H0) will always be rejected with p = 0, regardless of the practical significance of the difference. Therefore, we have not added statistical analysis for FA results.

      For the tractography based metrics, the number of sample points (one per streamline) is not as high as that for the structure tensor FA, thus making it more reasonable to test for statistical significance. The statistical analyses performed included tests for equality of distributions (Two-sample Kolmogorov-Smirnov tests), equality of medians (Two-sided Wilcoxon rank sum tests), and equality of variance (Brown-Forsythe tests). The results are described in relation to Figure 5(B, D), Figure 8(CF), and detailed in the Methods section.

      One very interesting result is the observation of apparent laminar organisation of fibres in ex vivo monkey white matter samples. DESY data from the corpus callosum shows fibres with two dominant orientations (one L-R, one slightly inclined), clustered in laminar structures within this major fibre bundle. Thanks to the authors providing open data, I was able to look through the raw DESY volume and observe regions with different "textures" (different orientations) in the described laminar arrangement. That this organisation can be observed by eye, as well as by structure tensor, is fairly convincing. As not all readers will download the data themselves, the manuscript could benefit from additional figures/videos to demonstrate (1) the quality of the DESY data and (2) a more 3D visualisation of the laminar structures (where the coronal plane shows convincing columnar structure or stripes). Similarly in Figure 5A, though this nicely depicts two populations with different orientations, it is somewhat difficult to see the laminar structure in the current image.

      ESRF data of the centrum semiovale (CS) contributes evidence for similar laminar structures in a crossing fibre region, where primarily AP fibres are shown to cluster in 3 laminar structures. As above, further visualisations of the ESRF volume in the CS (as shown in Figure 4E) would be of value (e.g. showing consistency across the 4 volumes, 2D images showing stripey/columnar patterns along different axes, etc).

      R1.2: Conveying complex 3D geometry through 2D still images is indeed challenging, and we greatly appreciate the reviewer’s comments and suggestions. To better communicate the understanding of the 3D anatomical environments, we have taken the following actions:

      (1) To enhance insights into the tractography results in Figures 5A and 5D, we have rendered and added animations of the tractography scenes as supplemental material.

      (2) To visually support 3D insights concerning the consistency of the laminar organisation of the callosal fibres, we have replaced the 2D slice views in Figures 3A and 3B with 3D renderings similar to the one in Figure 4E.

      (3) An animation of Figure 4E was created to display the colour-coded structure tensor directions of all four stacked scans. This animation visually supports the complexity of the fibre orientation and the layered structural laminar organisation of the CS sample.

      A key limitation of this result is that, though the DESY data from the CC seems convincing, the same structures were not observed in high-resolution synchrotron (ESRF) data of the same tissue sample in the corpus callosum. This seems surprising and the manuscript does not provide a convincing explanation for this inconsistency. The authors argue that this is due to the limited FOV of the ESRF data (~200x200x800 microns). However, the observed laminar structures in DESY are ~40 microns thick, and ERSF data from the CST suggests laminar thicknesses in the range of 5-40 microns with a similar FOV. This suggests the ERSF FOV would be sufficient to capture at least a partial description of the laminar organisation. Further, the DESY data from the CC shows columnar variations along the LR axis, which we might expect to be observed along the long axis of the ESFR volume of the same sample. Additional analyses or explanations to reconcile these apparently conflicting observations would be of value. For example, the authors could consider down-sampling the ESRF data in an appropriate manner to make it more similar to the DESY data, and running the same analysis, to see if the observed differences are related to resolution (i.e. the thinner laminar structures cluster in ways that they look like a thicker laminar structure at lower resolution), or crop the DESY data to the size of the ESRF volume, to test whether the observed differences can be explained by differences in FOV. Laminar structures were not observed in mouse data, though it is unclear if this is due to anatomical differences or somewhat related to differences in data quality across species.

      R1.3: We have clarified and expanded upon the results regarding the laminar organisation observed in the monkey CC DESY data. As noted in R1.2, we replaced the 2D images in Figures 3A (DESY) and 3B (ESRF) with 3D renderings to better display the spatial outline of the laminar organisation in the volumes. The reviewer is correct that, although the smaller field of view (FOV) of the ESRF data should allow us to at least partially capture parts of the laminar organisation observed in the larger FOV of the DESY data, this is not guaranteed. It depends on how the smaller FOV is positioned relative to the structural organisation, and since we lack co-registration, we do not know this. It should now be visually evident that the ESRF FOV can be placed such that it does not cover the observed laminae, a point which is now also emphasised in the Discussion. 

      Secondly, it is important to emphasise that the voxel colouring using the primary structure tensor direction is just a visualisation technique, which has limitations when it comes to assessing laminar organisation. Mapping 3D directions to RGB colours is inherently difficult and will always have ambiguities. If we had used the standard R-G-B to LR-AP-IS colouring in Figure 3, the laminar organisation would not be evident. Additionally, the laminae will only be visible when there are clear angular differences. There can still be a layered organisation even if we don’t observe it, which is the case for the mouse. The primary direction differences of these layers could be very low (i.e., parallel layers), and consequently not visually evident. This point has been clarified in both the Results and Discussion sections.

      Finally, in response to R1.6, we have added analyses regarding the shape of the FOD, specifically estimating the Orientation Dispersion Index (ODI) and Dispersion Anisotropy (DA). This provides further context to the reviewer’s comments about the discrepancies in laminar organisation. We have reflected on the relationship between DA and the visually observed laminar organisation, and this has been integrated into the relevant parts of the Results and Discussion sections.

      The changes to manuscript reflecting the statements above are listed here: 

      The Discussion section (page 21): “In the monkey CC DESY data, which has a field of view (FOV) comparable to a dMRI voxel, a columnar laminar organisation at a macroscopic level was visually revealed from the structure tensor (ST) direction colouring. However, this laminar organisation was not visible in the higher-resolution ESRF data for the same tissue sample. Although the two samples were not co-registered, the size of a single ESRF FOV within the DESY sample is illustrated in Fig. 3A. This demonstrates the possibility of placing the ESRF sample where the observed laminar structure is absent. Consequently, knowledge of the tissue structural organisation and its orientation is important to fully benefit from the stacked FOV of the ESRF sample and when choosing appropriate minimal FOV sizes in future experiments.

      Interestingly, when characterising FODs with measures like ODI and DA as indicators of fibre organisation, rather than relying on visualisation, results from large- and small-FOV data show no discrepancies. This statistical approach discards the spatial context (visually perceived as laminae), highlighting the need to combine both methods.” 

      The Results section (page 8): “The mid-level DA values suggest some anisotropic spread of the directions, reflecting the angled laminar organisation observed in the DESY sample. Interestingly, the DA value for the ESRF sample is almost identical, despite the laminar bands being less visually apparent.”

      The Results section (page 17): “Nevertheless, visualisation of orientations did not reveal any axonal organisation in the mouse CC due to the lack of local angular contrast, unlike the clear laminar structures seen in the monkey sample (Fig. 3A). Any parallel organisation in tissue remains undetectable because our visual contrast relies on angular differences.”

      The Discussion section (page 22): “In the monkey CC (mid-body), we observed laminar organisation indicated by clear spatial angular differences in the ST directions in the sample (Fig. 3A). Quantifications of the FOD shape showed DA indices of 0.55 and 0.59 for the DESY and ESRF samples, respectively. In contrast, the mouse CC (splenium) did not visually reveal a similar angled laminar organisation (Fig. 7C), and the DA indices were lower, at 0.49 and 0.32, respectively. Two possible explanations exist. First, the within-pathway laminar organisation may not be identical across the entire CC. Consequently, more scans from other CC regions would be required to confirm. Second, the different species might account for the differences. Larger brains like the monkey might foster a different level of within-pathway axon organisation compared to the smaller mouse. Although we could not visually detect laminar organisation from the colour coding of the ST direction in the mouse, the non-zero DA values suggest some level of organisation. This is supported by our streamline tractography, which indicates a vertical layered organisation (Fig. 8A, B). It further aligns with studies using histological tracer mapping that shows a stacked parallel organisation of callosal projections in mice, between cortex regions M1 and S1 (Zhou et al. 2013). Nevertheless, we cannot rely solely on voxel-wise ST directions to fully describe axonal organisation, as this method does not contrast almost parallel fasciculi (inclination angles approaching 0 degrees). Analysing patterns in tractography streamlines would be an interesting future direction for this purpose.”

      The authors further quantify various other characteristics of the white matter, such as micro-dispersion, tortuosity, and maximum displacement. Notably, the microscopic FA calculated via structure tensor is fairly consistent across regions, though not modalities. When fibre orientations are combined across the sample, they are shown to produce similar FODs to dMRI acquired in the same tissue, which is reassuring. As noted in the text, the estimates of tortuosity and max displacement are dependent on the FOV over which they are calculated. Calculating these metrics over the same FOV, or making them otherwise invariant to FOV, could facilitate more meaningful comparisons across samples and/or modalities.

      R1.4: This raises an interesting point about the necessity of normalising the FOV to obtain invariant, tractography-based metrics of tortuosity and maximum deviation across different samples and modalities. In general, achieving this is challenging, and in this study, it is practically not possible. Between species, we encounter significant differences in brain volume ratios, which complicates the establishment of a common reference FOV due to the distinct anatomical organisation of monkey and mouse brains (see our response to R1.8). Within species, we would encounter challenges due to missing contrast—such as issues with staining—and the lack of perfect co-registration.

      The Discussion section (page 28) has been extended to reflect this: ”Within the same species, assuming perfect co-registration of samples, it would be possible to perform correlative imaging and analysis. This would allow validation of whether tractography streamlines could be reproduced at different image resolutions within the same normalised FOV. Although this was not possible with the current data and experimental setup, it would be an interesting point to pursue in future work.”

      Though the results seem solid, some statements, particularly in the abstract and discussion, do not seem to be fully supported by the data. For example, the abstract states "Our findings revealed common principles of fibre organisation in the two species; small axonal fasciculi and major bundles formed laminar structures with varying angles, according to the characteristics of major pathways.", though the results show "no strong indication within the mouse CC of the axonal laminar organisation observed in the monkey". Similarly, the introduction states: "By these means, we demonstrated a new organisational principle of white matter that persists across anatomical length scales and species, which governs the arrangement of axons and axonal fasciculi into sheet-like laminar structures." Further comments on the text are provided below.

      R1.5: We understand that it can be misunderstood that the laminar organisation is identical in monkeys and mice, which is not the case. For example, we show that in the corpus callosum, pathways are parallel in the mouse but not in the monkey. We have clarified that while the principle of layered laminar organisation of pathways is shared between monkeys and mice, species-specific differences do exist.

      We have made the following clarifying changes to the manuscript:

      The Abstract (page 2): “Our findings revealed common principles of fibre organisation that apply despite the varying patterns observed across species” 

      The Introduction (page 4-5): “Through these methods, we demonstrated organisational principles of white matter that persists across anatomical length scales and species. These principles govern the organisation of axonal fasciculi into sheet-like laminar shapes (structures with a predominant planar arrangement). Interestingly, while these principles remain consistent, they result in varied structural organisations in different species.” 

      The Discussion (page 21): “despite species differences”.

      One observation not notably discussed in the paper is that the spherical histograms of Figure 3E/H appear to have an anisotropic spread of the white points about 0,0. It would be interesting if the authors could comment on whether this could be interpreted as the FOD having asymmetric dispersion and if so, whether the axis of dispersion relates to the fibre orientations of the laminar structures.

      R1.6: That is a good point, and to address it, we have fitted spherical Bingham distributions to the FODs, allowing us to quantify their shapes. From each Bingham distribution, we derived two wellknown indices from the diffusion MRI community: the Orientation Dispersion Index (ODI) and Dispersion Anisotropy (DA) index. The ODI explains the dispersion of fibres for a single bundle FOD, whereas DA expresses the shape of the FOD on the unit sphere surface, i.e., the degree of anisotropy. We have integrated the Bingham-based analysis into the Methods, Discussion, and Results sections concerning Figures 3 and 7, but not Figure 4, which contains multiple fibre bundles that we cannot separate on a voxel level. The analysis does not impact the overall message and conclusion but adds interesting context to the discussion around laminar organisation.

      A limitation of the study is that it considers only small ex vivo tissue samples from two locations in a single postmortem monkey brain and slightly larger regions of mouse brain tissue. Consequently, further evidence from additional brain regions and subjects would be required to support more generalised statements about white matter organisation across the brain.

      R1.7: Collecting more samples from various locations in the brain would provide valuable insights into the consistency of white matter organisation across anatomical length scales, as well as the structuretensor based anisotropy and tortuosity metrics. However, being awarded beamtime at two different synchrotron facilities to scan the same sample with different imaging setups is practically challenging. At the ESRF, we have gathered additional image volumes from other white matter regions of the monkey brain that support all our findings, which will be published separately. X-ray synchrotron imaging technology is advancing rapidly, with faster acquisition times enabling more image volumes to be stitched together. This extends the FOV and allows for a more robust statistical description of the anatomy. Consequently, future studies with an extended FOV and varying image resolutions could utilise a single synchrotron facility to collect additional samples, further supporting our findings.

      The Discussion section (page 27) has been extended to reflect this: “Increasing the number of samples across both species and examining laminar organisation at various length scales in more regions would strengthen our findings. However, securing beamtime at two different synchrotron facilities to scan the same sample with varying image resolutions is a limiting factor. Beamline development for multiresolution experimental setups, along with faster acquisition methods, is a rapidly advancing field. For instance, the Hierarchical Phase-Contrast Tomography (HiP-CT) imaging beamline at ID-18 at the ESRF, enables multi-resolution imaging within a single session to address this challenge, though it is currently limited to a resolution of 2.5 μm (Walsh et al. 2021).”

      Given the monkey results, the mouse study (section 2.5 onwards) lacks some motivation. In particular, it is unclear why a demyelination model was studied and if/how this would link to the laminar structure observed in the monkey data. Further, it is unclear how comparable tortuosity/max deviation values are across species, considering the differences in data quality and relative resolution, given that the presented results show these values are very modality-dependent.

      R1.8: We have clarified the motivation for including the mouse part of the study in both the Introduction and the Results sections.

      The Introduction section (page 5): “Furthermore, using a mouse model of focal demyelination induced by cuprizone (CPZ) treatment, we investigate the inflammation-related influence on axonal organisation. This is achieved through the same structure tensor-derived micro-anisotropy and tractography streamline metrics.”

      The Results section (page 15): “Finally, we investigated the organisation of fasciculi in both healthy mouse brains and a murine model of focal demyelination induced by five weeks of cuprizone (CPZ) treatment. This allowed for the exploration of the disease-related influence on axonal organisation, particularly under inflammation-like conditions with high glial cell density at the demyelination site (He et al. 2021). The experimental setup for DESY and ESRF is similar to that described for the monkey, with the exception that we did not perform dMRI and synchrotron imaging on the same brains, and only collected MRI data for healthy mouse brains. This approach allowed us to apply the same structure tensor and tractography streamline analysis used previously, but in a healthy versus disease comparison, demonstrating the methodology’s ability to provide insights into pathological conditions.”

      Across species, the comparison of tortuosity and maximum deviation must be approached with caution. On one hand, we observe a comparable influence of the extra-axonal environment in both the monkey and mice, as discussed in the section “Sources to the non-straight trajectories of axon fasciculi.” On the other hand, the anatomical scale and relative image resolution are significant factors, as correctly pointed out. In the mouse, for instance, the measures are influenced by white matter pathway macroscopic effects, making cross-species comparison challenging to perform in a normalised way.

      The limitations section of the Discussion (page 28) has been updated to reflect this: ”A limiting consequence of having samples imaged at differing anatomical scales is that certain measures become inherently hard to compare in a normalised way. The tractography-based metrics—tortuosity and maximum deviation—serve as good examples of this resolution and FOV dependence. In the ESRF samples, the anatomical scale was at the level of individual axons, and the streamline metrics primarily reflect micro-scale effects from the extra-axonal environment, such as the influence of cells and blood vessels. In comparison, the larger anatomical scale in the DESY samples represents the level of fasciculi and above, with metrics influenced by macroscopic effects, such as the bending of the CC pathway. Both scales are interesting and can provide valuable insights in their own right, but caution is required when comparing the numbers, especially for cross-species studies where there is a significant difference in brain volume ratios.”

      The paper introduces a new method of "scale-space" parameters for structure tensors. Since, to my understanding, this is the first description of the method, some simple validation of the method would be welcomed. Further, the same scale parameters are not used across monkeys and mice, with a larger kernel used in mice (Table 2) which is surprising given their smaller brain size. Some explanation would be helpful.

      R1.9: We have expanded the description of the scale-space structure tensor approach in the Methods section. Specifically, we have elaborated on the empirical process used to select the scale-space parameters shown in Table 2 and explained why multiple scales were applied only to the monkey samples scanned at ESRF (see Table 2, sample IDs 2 and 3) but not to the other datasets. Additionally, we have added a supplementary figure to assist in illustrating the concept.

      Reviewer #2 (Public Review):

      Summary:

      In this work, the authors combine diffusion MRI and high-resolution x-ray synchrotron phase-contrast imaging in monkey and mouse brains to investigate the 3D organization of brain white matter across different scales and species. The work is at the forefront of the anatomical investigation of the human connectome and aligns with several current efforts to bridge the resolution gap between what we can see in vivo at the millimeter scale and the complexity of the human brain at the sub-micron scale. The authors compare the 3D white matter organization across modalities within 2 small regions in one monkey brain (body of the corpus callosum, centrum semiovale) and within one region (splenium of the corpus callosum) in healthy mice and in one murine model of focal demyelination. The study compares measures of tissue anisotropy and fiber orientations across modalities, performs a qualitative comparison of fasciculi trajectories across brain regions and tissue conditions using streamlined tractography based on the structure tensor, and attempts to quantify the shape of fasciculi trajectories by measuring the tortuosity index and the maximum deviation for each reconstructed streamline. Results show measures of anisotropy and fiber orientations largely agree across modalities, especially for larger FOV data. The high-resolution data allows us to explore the fiber trajectories in relation to tissue complexity and pathology. The authors claim the study reveals new common organization principles of white matter fibers across species and scales, for which axonal fasciculi arrange into sheet-like laminar structures.

      Strengths:

      The aim of the study is of central importance within present efforts to bridge the gap between macroscopic structures observable in vivo in humans using conventional diffusion MRI and the microscopic organization of white matter tissue. Results obtained from this type of study are important to interpret data obtained in vivo, inform the development of novel methodologies, and expand our knowledge of the structural and thus functional organization of brain circuits.

      Multi-scale data acquired across modalities within the same sample constitute extremely valuable data that is often hard to acquire and represent a precious resource for validation of both diffusion MRI tractography and microstructure methods.

      The inclusion of multi-species data adds value to the study, allowing the exploration of common organization principles across species.

      The addition of data from a murine cuprizone model of focal demyelination adds interesting opportunities to study the underlying biological changes that follow demyelination and how these impact tissue anisotropy and fiber trajectories. These data can inform the interpretation and development of diffusion MRI microstructure models.

      Weaknesses:

      The main claim of a newly discovered laminar organization principle that is consistent across scales and species is not supported strongly enough by the data. The main evidence in support of the claim comes from the larger FOV data obtained from the body of the corpus callosum in the monkey brain. A laminar organization principle is partially shown in the centrum semiovale in the monkey brain and it is not shown in mice data. Additionally, the methods lack details to help the correct interpretation of these findings (e.g., how were these fasciculi defined?; how well do they represent different axonal populations?; what is the effect of blood vessels on the structure tensor reconstruction?; how was laminar separation quantified?) and the discussion does not provide a biological background for this organization. The corpus callosum sample suggests axons within a bundle of fibers are organized in a sheet-like fashion, while data from the centrum semiovale suggest fibers belonging to different fiber bundles are organized in a sheet-like arrangement. While I acknowledge the challenges in acquiring such high-resolution data, additional samples from different regions in the same animals and from different animals would help strengthen this claim.

      R2.1 

      -  how were these fasciculi defined?

      In the introduction (page 3), we have clarified our definition of an axon fasciculus: “A fasciculus is a bundle of axons that travel together over short or long distances. Its size and shape can vary depending on its internal organisation and its relationship to neighbouring fasciculi.”

      Additionally, we emphasise in the Results section (page 12) that the centroid streamlines are not guaranteed to be actual fasciculi, but rather representations of them. The paragraph now states: “To ease visualisation and quantification, we used QuickBundle clustering(Garyfallidis et al. 2012) to group neighbouring streamlines with similar trajectories into a centroid streamline. This centroid streamline serves as an approximation of the actual trajectory of a fasciculus.”

      - what is the effect of blood vessels on the structure tensor reconstruction?

      Fair point, that was not clear from our description. The clarification contains two parts. First, the estimation of the structure tensor occurs in all voxels, and in that sense, the blood vessels respond very similarly to axons. Second, when it comes to sample statistics derived from the structure tensor analysis (FA histograms and the FODs), they will have an influence, albeit a small one, given the low volume percentage of the blood vessels within the FOVs. In the monkey samples, segmenting the blood vessels was achievable with little effort, allowing us to exclude their contribution from FA statistics and FODs. To make this clear, we have added a paragraph to the Methods section (page 34) titled “Structure tensor-based quantifications,” reflecting this clarification. Additionally, we have restructured the entire structure tensor methods description (starting on page 32) as part of the reviewer comments in R1.6 and R1.9.

      - how was laminar separation quantified?

      We have added a clarification in Results section (page 7): “The laminar thickness was determined by manual measurements on laminae visually identified in the 3D volume”.

      - discussion does not provide a biological background for this organization.

      A good point. Including the biological background is relevant as it supports the laminar organisation of white matter pathways observed in our findings and those of others.

      We have added a section on this background in the Discussion (page 24): “We believe our observed topological rule of white matter laminar organisation can be explained by a biological principle known from studies of nervous tissue development. The first axons to reach their destination, guided by their growth cones, are known as “pioneering” axons. “Follower” axons use the shaft of the pioneering axon for guidance to efficiently reach the target region (Breau and Trembleau 2023). Axons can form a fasciculus by fasciculating or defasciculating along their trajectory through a zippering or unzipping mechanism, controlled by chemical, mechanical, and geometrical parameters. Zippering “glues” the axons together, while unzipping allows them to defasciculate at a low angle (Šmít et al. 2017). Although speculative, the zippering mechanism may be responsible for forming the laminar topology observed across length scales. The defasciculation effect can explain our results in the corpus callosum (CC) of monkeys, with laminar structures at low angles (~35 degrees) also observed by (Innocenti et al. 2019; Caminiti et al. 2009), as well as in other major pathways (Sarubbo et al. 2019). In contrast, a fasciculation mechanism may be observed in the mouse CC (0 degrees). If the geometrical angle between two axons is high, i.e., toward 90 degrees, the zippering mechanism will not occur, and the two axons (fasciculi) will cross (Šmít et al. 2017). This supports our and other findings that crossing fasciculi or pathways occur at high angles toward 90 degrees in the fully matured brain (Wedeen et al. 2012). Once myelination begins, the zippering mechanism is lost (Šmít et al. 2017), suggesting that laminar topology is established at the earliest stages of brain maturation.”

      - additional samples from different regions in the same animals and from different animals would help strengthen this claim

      Reviewer #1 also pointed to the inclusion of additional samples, and this is now discussed as part of the study limitations on page 27 (see also R1.7).

      The main goal of the study is to bridge the organization of white matter across anatomical length scales and species. However, given the substantial difference in FOVs between the two imaging modalities used, and the absence of intermediate-resolution data, it remains difficult to effectively understand how these results can be used to inform conventional diffusion MRI. In this sense, the introduction does not do a good enough job of building a strong motivation for the scientific questions the authors are trying to answer with these experiments and for the specific methodology used.

      R2.2: Indeed, this is an essential point now emphasised in the introduction, page 3, which now states: ”Despite the limited resolution of dMRI, the water diffusion process can reveal microstructural geometrical features, such as axons and cell bodies, though these features are compounded at the voxel level. Consequently, estimating microstructural characteristics depends on biophysical modelling assumptions, which can often be simplistic due to limited knowledge of the 3D morphology of cells and axons and their intermediate-level topological organisation within a voxel. Thus, complementary highresolution imaging techniques that directly capture axon morphology and fasciculi organisation in 3D across different length scales within an MRI voxel are essential for understanding anatomy and improving the accuracy of dMRI-based models(Alexander et al. 2019).”

      Additionally, in the introduction, page 4, we have made the following changes to strengthen the link across modalities, such that it now states: “In the x-ray synchrotron data, we applied a scale-space structure tensor analysis, which allowed for the quantification of structure tensor-derived tissue anisotropy and FOD in the same anatomical regime indirectly detected by dMRI.”

      The cuprizone data represent a unique opportunity to explore the effect of demyelination on white matter tissue. However, this specific part of the study is not well motivated in the introduction and seems to represent a missed opportunity for further exploration of the qualitative and quantitative relationship between diffusion MRI and sub-micron tissue information (although unfortunately not within the same brain sample). This is especially true considering the diffusion MRI protocol for mice would allow extrapolation of advanced measures from different tissue compartments.

      R2.3: A similar point was raised by Reviewer 1 (R1.8), and we have clarified the motivation for including the healthy mice and the demyelination samples.  

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Many thanks to the authors for providing open data. This was very helpful when reviewing the manuscript and is a valuable resource for the community.

      R1.10: We are happy to share our data with the community. Understanding anatomy in 3D is hard to achieve through still images and animations, so the ability to explore it on your own is quite important. The link to the data repository has been added in the Methods section in the following paragraph: “Due to the size of the data selected, processed image volumes, masks and results are available at https://zenodo.org/records/10458911. Other datasets can be shared on request.“

      One confusing element of the paper is that orientations (or axes) do not seem to be consistent across samples/modalities. For example, the green tensors in Figures 3 C and D are tilted up/down in opposite directions and the streamlines in Figure 5A seem opposite (SL) from what we would expect from Figure 2A (SR). Having consistent orientations across modalities and images would help the reader. When colouring tensors (e.g. in Figure 3), the authors could consider a 3D colour scheme (similar to that used by diffusion MRI) rather than colouring by only inclination, as this would provide useful information on whether different laminae have similar orientations, as implied by the tractography in Figure 4.

      R1.11: Thank you for spotting the suboptimal consistency between Figures 2, 3, and 5. Figure 2 has been corrected and updated. The left-right direction in the coronal views was not correctly displayed. Additionally, the glyph directions have been updated in Figures 2 and 3.

      By default, we use the “standard” RGB colour scheme used in dMRI. However, for the monkey CC— essentially Figure 3—this did not effectively illustrate our findings. We decided to use a different directional colour encoding scheme, which captures the angular deviation from the L-R axis. This was to assist in the visualisation of the inclination angle between the laminars. We have used the same colour scheme for the tensors in Figure 3 to avoid confusion.

      On a general note, the standard colour scheme has uniform “colour contrast” in all directions, but when there is only a single dominant direction in the sample, it can make sense to concentrate the colour contrast in that axis.

      Results: "even higher FA anisotropy in the micro-tensor domain of 0.997, i.e., the micro (μ)FA (20, 21)." I understand these references lead to a definition of μFA that is based on multiple diffusion tensor encodings which is quite different from that suggested by Kaden. It may be preferable to reference Kaden directly (since I understand this is the method used) to avoid confusion.

      R1.12: Correctly spotted, and we now reference the method from Kaden et al. and use the other references elsewhere when relevant.

      "and scanned the mouse brain in a whole." - typo?

      R1.13: Thank you for spotting the typo. The mouse brain was kept in the skull during MRI scanning, which has been clarified in the Methods section.

      The crossing fibre region appears to be sometimes referred to as the centrum semiovale, and other times as the CST. CS seems the better description and keeping this naming consistent would avoid confusion to the reader.

      R1.14: Well spotted, thank you. We have replaced the usage of Corticospinal Tract (CST) with centrum semiovale (CS) where relevant.

      Direct comments on the text:

      Abstract: "Individual axon fasciculi exhibited tortuous paths .... in a manner independent of fibre complexity and demyelination"

      Do statistical comparisons of the various distributions support this? The data shows somewhat increased tortuosity in the CST compared to the CC, and somewhat lower tortuosity in CPZ tissue.

      R1.15: The intention of the text was not to point to the comparison of tortuosity, but rather to highlight the maximum deviation. We observe a high probability density of maximum deviations at approximately 5-10 microns in all samples, which corresponds to the size of structures in the extraaxonal environment, such as blood vessels and cells.

      Additionally, we understand that the original statement might imply an expectation of a statistical analysis demonstrating independence, which is not the case. To clarify, we have reformulated the sentence in the Abstract (page 2) to address these points: “Fasciculi exhibited non-straight paths around obstacles like blood vessels, comparable across the samples of varying fibre complexity and demyelination.”

      Abstract: "A quantitative analysis of tissue anisotropies and fibre orientation distributions gave consistent results for different anatomical length scales and modalities, while being dependent on the field-of-view."

      To my understanding, the FODs here from different modalities are calculated over different FOVs (in monkeys at least), and FODs are only presented for a single FOV for each modality, meaning it is difficult to separate the effects of modality from FOV. The microscopic anisotropy is also noticeably different across modalities (DESY < ESRF < dMRI).

      R1.16: That is a fair point. Our statement was trying to capture too much condensed content to be correctly interpretable. We have reformulated the sentence to state: “Quantifications of fibre orientation distributions were consistent across anatomical length scales and modalities, whereas tissue anisotropy had a more complex relationship, both dependent on the field-of-view”.

      While it is true that we only present the ST-derived quantifications – FOD and FA statistics – for a single FOV per modality and sample, the results shown for the ESRF monkey samples (Figures 3 and 4) are a merge of four individually processed volumes. The quantifications of each individual subFOV have now been added as a supplementary figure (Figure S3) to highlight the consistency of the methodology and the effect of shifting the FOV position. In the case of the mouse, we have two volumes from different mice, which also display similar FOD and FA statistics.

      Abstract: "Our study emphasises the need to balance field-of-view and voxel size when characterising white matter features across anatomical length scales."

      This point does not seem very well explored in the paper, rather it is an observation of the limitations of the different imaging modalities. For example, there aren't analyses to compare metrics from highresolution data at different FOVs (i.e. by taking neighbourhoods of different sizes), nor are metrics compared from data at different resolutions and the same FOV.

      R1.17: The question is related to R1.16, R1.4, and R1.8, and we have addressed this point in our responses to those comments.

      Figure 7 - Taking into account the eigenvalues can be helpful when interpreting the secondary and tertiary eigenvectors of tensors (V2 and V3). It would be interesting to know whether the eigenvalues L2 ~= L3 are approximately equal (suggesting isotropic diffusion about V1, where the definition of V2 versus V3 isn't very meaningful), or if L2 is noticeably larger than L3 (suggesting anisotropic diffusion about V1, potentially similar to the anisotropic dispersion discussed above).

      R1.18: It would be interesting to explore the eigenvalues of the structure tensor in more detail, as has been done for the diffusion tensor. However, we believe this belongs to future work, as such additional detailed methodological analysis would complicate the already complex story. As mentioned in response to R1.10, most processed data has been made publicly available, and the rest can be requested (due to the storage size of the data sets) to perform such additional analysis.

      Discussion: "Importantly, our findings revealed common principles of fibre organisation in both monkeys and mice; small axonal fasciculi and major bundles formed sheet-like laminar structures," See above regarding the lack of evidence for laminar structures in mouse data.

      R1.19: We have reformulated the text for clarification as part of R1.3. Additionally, we added FOD quantifications to support why we do not observe an apparent laminar organisation in the mouse CC— please see our response to R1.6.

      Discussion: "Interestingly, the dispersion magnitude is indicative of fasciculi that skirt around obstacles in the white matter such as cells and blood vessels, and the results are largely independent of both white matter complexity (straight vs crossing fibre region) and pathology." Again, do statistical tests of the various distributions support this?

      R1.20: As part of R1.1, we have added statistical tests of significance for the quantifications of how max deviation changes when bending around objects. Indeed, the distributions are not statistically the same, and we do not wish to convey that sentiment, but they are comparable in the object sizes that they detect. As done in the abstract, we have reformulated the sentence to avoid misunderstanding and have replaced “largely independent” with “observed across.”

      Discussion: "Tax et al. have demonstrated the calculation of a sheet probability index from diffusion MRI data, which suggested the presence of sheet-like features in the CC"

      My understanding was that this was observed in crossing fibre regions, such as where fibres projecting with the CC cross the CST, but not the main body of the CC itself. Tax defines sheet structure as "composed of two tracts that cross each other on the same surface in certain regions along their trajectories." Is this a different phenomenon to the laminar structures observed here (where we observe fibres within a single tract being locally organised into laminar structures)?

      R1.21: Thank you for pointing our attention to this. We have corrected the section in the Discussion (page 23), so it now states: “Additionally, Tax et al. have demonstrated the calculation of a gridcrossing sheet probability index from diffusion MRI data, which suggested the presence of sheet-like features in a crossing fibre region (Tax et al. 2016), which is in line with our findings in the synchrotron data. Note that the method by Tax et al. only detects sheet-like structures crossing on a grid and does not reveal laminar structures with lower inclination angles, as we observed in the monkey CC.”

      Discussion: "We found that FODs were consistent across image resolutions and modalities, but only given that the FOV is the same." See above.

      R1.22: As part of our response to R1.6, we quantified the FODs using the ODI and DA indices, which should help support our statement. Nevertheless, we have toned down the statement and reformulated the text as follows: “We found that FODs were comparable across image resolutions and modalities. The observed discrepancies can be attributed to the fact that the FOVs are not exactly matched.”

      Discussion: "microscopic FA were highly correlated across modalities."

      The data shows FA is considerably lower in DESY to ESRF; within modality FA is quite consistent irrespective of tissue region; and differences between the CC and CG shown in ESRF data in mice are not repeated in DESY. It is unclear from the current data if this would lead to a high correlation across modalities. Some evidence would be helpful.

      R1.23: This is a fair point; we have not performed a correlation analysis. However, the pattern we observe for the synchrotron samples is as follows: When the anatomical length scale increases (becomes more macroscopic), the FA distribution shifts to lower values. This reflects the scale of information captured with the ST analysis (see also R1.9). Therefore, the most interesting comparison of FA statistics occurs when the resolution and anatomical length scale are approximately the same.  The sentence in question has been reformulated to the following: ”Estimates of structure tensor derived microscopic FA show a clear pattern across modalities.”

      Discussion: "If so, the (inclination angle) information might serve to form rules for low-resolution diffusion MRI based tractography about how best to project through bottleneck regions, which is currently a source of false-positives trajectories (6)."

      This is an interesting idea but it is unclear to me how this inclination information would help track through bottlenecks where, by definition, fibres are passing through with the same orientation. Some further explanation would be helpful.

      R1.24: We have elaborated on the section in the Discussion (page 23), explaining how this can be used to improve tractography tracing through complex regions: “The reason is that standard tractography methods do not "remember" or follow anatomical organisation rules as they trace through complex regions. Our findings on pathway lamination and inclination angles—low for parallel-like trajectories and high for crossing-like trajectories—can help incorporate trajectory memory into these methods, reducing the risk of false trajectories”.

      Reviewer #2 (Recommendations For The Authors):

      Below I report comments that if addressed I believe would improve the clarity and readability of the manuscript.

      -  Figures 1 and 2 would be more meaningful if combined into one figure. This would allow for a direct visual comparison of the two modalities. If space is needed, I believe the second row of Figure 1 (coronal views of CC) does not add much information. It is often hard to navigate the different orientations of the tissue in the images; thus any effort in trying to help the reader visually clarify would improve readability.

      R2.4: We considered the reviewer’s suggestion to merge Figures 2 and 3. However, this made both the figures and the main text additionally complex, so we chose to retain the original figure layout. Secondly, Figure 3 utilises a non-standard directional colormap. Keeping the colormap consistent within each figure is a feature we wish to preserve. In response to R1.11, the figures have been updated to have more consistent orientations for the monkey samples.

      In Figure 2, the second row, showing a coronal view of the CC, is essential for comparison with human data in Figure S1. It highlights where we observed the columnar laminar organisation and their inclination angle, as also detected by DTI.

      -  Figure 4 shows synchrotron data revealing an anterior-posterior component within the centrum semiovale that is not necessarily seen in the dMRI data. Could the authors comment on this?

      R2.5: Thank you for pointing this out. We have now addressed this in the Results section (page 10), where we describe the observation in detail: “Interestingly, visual inspection of the colour-coded structure tensor directions in Fig. 4E shows the existence of voxels whose primary direction is along the A-P axis. However, this represents a small enough portion of the volume that it does not appear as a distinct peak on the FOD.“

      -  The authors claim they observed several purple axons crossing orthogonally in Figure 5c. However, that is not necessarily clear in the figure.

      R2.6: We appreciate the feedback. We have now coloured the streamlines of the crossing fasciculi in Figure 5C in red.

      -  Figure 5 would benefit from adding the color encoding scheme for Figure 5d, as sometimes this is not necessarily consistent.

      R2.7: We appreciate the feedback. We have added an indication of the standard directional colour coding to Figure 5D.

      -  Figure 5d shows interesting data from the complex region. However, it is hard to visualize and it looks like there are not many streamlines traveling entirely I-S? Maybe a different orientation of the sample would help visualization.

      R2.8: A similar point was raised by Reviewer 1 (see R1.2). We have added an animation of the scene to assist in the interpretation of the 3D organisation within this complex sample.

      -  The concept of axon fasciculi is not necessarily immediately clear. Adding an explanation for what the authors refer to when using this term would improve clarity.

      R2.9: In the introduction, we now state our conceptual definition of an axon fasciculus as a number of axons that follow each other (see also R2.1).

      -  The methods do not provide details on how structure tensor FA is measured.

      R2.10: Thank you for pointing this out. We have restructured and expanded the structure tensor description in the Methods section (see also R1.9 and R2.1), which now includes the definition of FA.

      -  Why didn't the authors select the same cc region for both mice and monkeys? It seems this would have increased the strength of the comparison.

      R2.11: We agree. The reason lies in the chronology of experiments and the fact that we cannot control where demyelination takes place. We have added a clarifying description in the Methods section (page 31): “Note that several separate beamline experiments were conducted to collect the volumes listed in Table 1. In the first two experiments, samples from the monkey brain were scanned at ESRF and DESY, respectively. The samples from the mouse brain were imaged in two subsequent experiments. Consequently, the location of the identified demyelinating lesion in the cuprizone mice, which cannot be precisely controlled, did not match the location of the CC biopsies in the monkey.”

      -  While it is mentioned in the results, the methods do not explain how vessel segmentations or cell segmentation in mice was performed and for which datasets it was performed.

      R2.12: For the small ROI shown in Figure 6, the labelling was a manual process using the software ITK-SNAP, which has now been clarified in the corresponding figure caption. The generation of ROI masks and blood vessel segmentations involved a combination of intensity thresholding, morphological operations, and manual labelling in ITK-SNAP. This has been clarified in the restructured and expanded description of structure tensor analysis in the Methods section (starting on page 32).

      -  From the methods it is hard to understand (1) how many mice were used; (2) why dMRI was done on a different sample; (3) whether the same selenium region was selected for both healthy and CPZ animals; (4) how the registration across samples was performed.

      R2.13: We appreciate the feedback and have inserted clarifying statements in the relevant parts of the Methods section. (1) The total number of mice included was three: one normal, one cuprizone, and one normal for MRI scanning. (2) The quality of the collected dMRI on the mouse was too poor to use, and it could not be redone as the brain had already been sliced and prepared for synchrotron experiments. (3) The same splenium section was selected for both healthy and cuprizone mice. (4) A paragraph on image registration has been added.

      -  Diffusion MRI method sections would benefit from additional details on the protocols used.

      R2.14: Thank you for pointing this out. We have added more details about the diffusion MRI protocols, including the b-value, gradient strength, and other relevant parameters.

    1. eLife Assessment

      This valuable study extends the previous interesting work of this group to address the potentially different control of movement and posture. Through experiments in which stroke participants used a robotic manipulandum, the authors provide solid evidence supporting a lack of a relation between the resting force postural bias they measure (closely related to the flexor synergy in stroke) and kinematic deficits during movement. Based on these results, the authors propose a conceptual framework that differentially weights the two main descending pathways (corticospinal tract and reticulospinal tract) for neurologically intact and stroke patients. Discussing the potential impact of differences on muscle/spinal circuit state and their responses between holding a posture and movement, as well as the assumptions of their statistical comparisons, would further improve the paper.

    2. Reviewer #1 (Public review):

      This study extends the previous interesting work of this group to address the potentially differential control of movement and posture. Their earlier work explored a broad range of data to make the case for a downstream neural integrator hypothesized to convert descending velocity movement commands into postural holding commands. Included in that data were observations from people with hemiparesis due to stroke. The current study uses similar data, but pushes into a different, but closely related direction, suggesting that these data may address the independence of these two fundamental components of motor control. I find the logic laid out in the second sentence of the abstract ("The paretic arm after stroke is notable for abnormalities both at rest and during movement, thus it provides an opportunity to address the relationships between control of reaching, stopping, and stabilizing") less then compelling, but the study does make some interesting observations. Foremost among them, is the relation between the resting force postural bias and the effect of force perturbations during the target hold periods, but not during movement. While this interesting observation is consistent with the central mechanism the authors suggest, it seems hard to me to rule out other mechanisms, including peripheral ones. These limitations should should be discussed.

    3. Reviewer #2 (Public review):

      Summary:

      Here the authors address the idea that postural and movement control are differentially impacted with stroke. Specifically, they examined whether resting postural forces influenced several metrics of sensorimotor control (e.g., initial reach angle, maximum lateral hand deviation following a perturbation, etc.) during movement or posture. The authors found that resting postural forces influenced control only following the posture perturbation for the paretic arm of stroke patients, but not during movement. They also found that resting postural forces were greater when the arm was unsupported, which correlated with abnormal synergies (as assessed by the Fugl-Meyer). The authors suggest that these findings can be explained by the idea that the neural circuitry associated with posture is relatively more impacted by stroke than the neural circuitry associated with movement. They also propose a conceptual model that differentially weights the reticulospinal tract (RST) and corticospinal tract (CST) to explain greater relative impairments with posture control relative to movement control, due to abnormal synergies, in those with stroke.

      Comments on revisions:

      The authors should be commended for being very responsive to comments and providing several further requested analyses, which have improved the paper. However, there is still some outstanding issues that make it difficult to fully support the provided interpretation.

      The authors say within the response, "We would also like to stress that these perturbations were not designed so that responses are directly compared to each other ***(though of course there is an *indirect* comparison in the sense that we show influence of biases in one type of perturbation but not the other)***." They then state in the first paragraph of the discussion that "Remarkably, these resting postural force biases did not seem to have a detectable effect upon any component of active reaching but only emerged during the control of holding still after the movement ended. The results suggest a dissociation between the control of movement and posture." The main issue here is relying on indirect comparisons (i.e., significant in one situation but not the other), instead of relying on direct comparisons. Using well-known example, just because one group / condition might display a significant linear relationship (i.e., slope_1 > 0) and another group / condition does not (slope_2 = 0), does not necessarily mean that the two groups / conditions are statistically different from one another [see Figure 1 in Makin, T. R., & Orban de Xivry, J. J. (2019). Ten common statistical mistakes to watch out for when writing or reviewing a manuscript. eLife, 8, e48175.].

      The authors have provided reasonable rationale of why they chose certain perturbation waveforms for different. Yet it still holds that these different waveforms would likely yield very different muscular responses making it difficult to interpret the results and this remains a limitation. From the paper it is unknown how these different perturbations would differentially influence a variety of classic neuromuscular responses, including short-range stiffness and stretch reflexes, which would be at play here.

      Much of the results can be interpreted when one considers classic neuromuscular physiology. In Experiment 1, differences in resting postural bias in supported versus unsupported conditions can readily be explained since there is greater muscle activity in the unsupported condition that leads to greater muscle stiffness to resist mechanical perturbations (Rack, P. M., & Westbury, D. R. (1974). The short-range stiffness of active mammalian muscle and its effect on mechanical properties. The Journal of physiology, 240(2), 331-350.). Likewise muscle stiffness would scale with changes in muscle contraction with synergies. Importantly for experiment 2, muscle stiffness is reduced during movement (Rack and Westbury, 1974) which may explain why resting postural biases do not seem to be impacting movement. Likewise, muscle spindle activity is shown to scale with extrafusal muscle fiber activity and forces acting through the tendon (Blum, K. P., Campbell, K. S., Horslen, B. C., Nardelli, P., Housley, S. N., Cope, T. C., & Ting, L. H. (2020). Diverse and complex muscle spindle afferent firing properties emerge from multiscale muscle mechanics. eLife, 9, e55177.). The concern here is that the authors have not sufficiently considered muscle neurophysiology, how that might relate to their findings, and how that might impact their interpretation. Given the differences in perturbations and muscle states at different phases, the concern is that it is not possible to disentangle whether the results are due to classic neurophysiology, the hypothesis they propose, or both. Can the authors please comment.

      The authors should provide a limitations paragraph. They should address 1) how they used different perturbation force profiles, 2) the muscles were in different states which would change neuromuscular responses between trial phase / condition, 3) discuss a lack of direct statistical comparisons that support their hypothesis, and 4) provide a couple of paragraphs on classic neurophysiology, such as muscle stiffness and stretch reflexes, and how these various factors could influence the findings (i.e., whether they can disentangle whether the reported results are due to classic neurophysiology, the hypothesis they propose, or both).

    4. Author response:

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

      Public Reviews:

      Reviewer #1 (Public Review):

      This study extends the previous interesting work of this group to address the potentially differential control of movement and posture. Their earlier work explored a broad range of data to make the case for a downstream neural integrator hypothesized to convert descending velocity movement commands into postural holding commands. Included in that data were observations from people with hemiparesis due to stroke. The current study uses similar data but pushes into a different, but closely related direction, suggesting that these data may address the independence of these two fundamental components of motor control. I find the logic laid out in the second sentence of the abstract ("The paretic arm after stroke is notable for abnormalities both at rest and during movement, thus it provides an opportunity to address the relationships between control of reaching, stopping, and stabilizing") less than compelling, but the study does make some interesting observations. Foremost among them, is the relation between the resting force postural bias and the effect of force perturbations during the target hold periods, but not during movement. While this interesting observation is consistent with the central mechanism the authors suggest, it seems hard to me to rule out other mechanisms, including peripheral ones. 

      Response 1.1. Thank you for your comments, which we address in detail below and in our response to Recommendations to the authors (see pp. 15-19 of this letter). We would first like to clarify the motivation behind our use of a stroke population to understand the interactions between the control of reaching in and holding. We agree that this idea can be laid out in a more compelling way.

      The fact that stroke patients usually display issues with their control of both reaching and holding, allows for within-individual comparisons of those two modes of control. Further, the magnitude of abnormalities is relatively large, making it easier to measure, compare and investigate effects. And, importantly, these two modes of control can be differentially affected after stroke (also pointed out by Reviewer 2, point 4 in Comments to the Authors). Finally, this kind of work – examining interactions between positive signs of stroke (such as abnormal posture or synergy) vs. negative signs (such as loss of motor control) – needs to be done in humans, as positive signs are relatively absent even in primates (Tower, 1940).

      We have changed our abstract (changes shown below in red), and our intro (expanding the second paragraph, lines 75-76), to lay out our motivation more clearly.

      From the abstract:

      “The paretic arm after stroke exhibits different abnormalities during rest vs. movement, providing an opportunity to ask whether control of these behaviors is independently affected in stroke. “

      On the other hand, the relation between force bias and the well-recognized flexor synergy seems rather self-evident, and I don't see that these results add much to that story.

      Response 1.2. While it seems natural that these biases would be the resting expression of abnormal flexor synergies (given their directionality towards the body, as shown in Figures 2-3, and the other similarities we demonstrate in Figure 8), we do not believe it is self-evident. These biases are measured at rest, with the patient passively moved and held still, whereas abnormal synergies emerge when the patient actively tries to move. The lack of relationship we find between these resting force biases and active movement underlines that the relation between force bias and flexor synergy should not be taken as self-evident, making it worthwhile to examine it (as we motivate in lines 589-596 and show in Figure 8).

      The paradox here is that, in spite of a relationship between force bias and flexor synergy (itself manifesting during attempted movement), there seems to be no relationship between force bias and direct measures of active movement (Figures 5,6). This is the paradox that inspired our conceptual model (Figure 9) and inspires to further investigate the factors under which these two systems are intermingled or kept separate. We thus find it to be a helpful element in the story.

      I am also struck by what seems to be a contradiction between the conclusions of the current and former studies: "These findings in stroke suggest that moving and holding still are functionally separable modes of control" and "the commands that hold the arm and finger at a target location depend on the mathematical integration of the commands that moved the limb to that location." The former study is mentioned here only in passing, in a single phrase in the discussion, with no consideration of the relation between the two studies. This is odd and should be addressed. 

      Response 1.3. While these two sets of findings are not contradictory, we understand how they can appear as such without providing context. We now discuss the relationship between our present study and the previous one more directly (lines 66-70 and 663-669 of the revised manuscript).

      The previous study examined how the control of movement informs the control of holding after the movement was over; the current study examines whether abnormalities in holding measured at rest with the movement leading to the rest position being passive. There are thus two important distinctions:

      First, directionality of potential effects: here we examine the effect of (abnormalities in) holding control upon movement, but the 2020 study (Albert et al., 2020) examines the effects of movement upon holding control. Stroke patient data in the 2020 study showed that, under CST damage, while the reach controller is disrupted, the hold controller can continue to integrate the malformed reach commands faithfully. In line with this, we proposed a model where the postural controller system sits downstream of the moving controller (Figure 7G in the 2020 paper). We thus did not claim, in 2020, that integration of movement commands is the only way to do determine posture control, as we stated explicitly back then, e.g. (emphasis ours):

      “Equations (1) and (2) describe how the integration of move activity may relate to changes in hold commands, but does not specify the hold command at the target.”

      In short, finding no effect of holding abnormalities upon movement (present finding) does not mean there is no potential effect of movement upon holding (2020 finding). This is something we had alluded to in the Discussion but not clarified, which we do now (see edits at the end of our response to this point).

      Second, active vs. passive movement: here, we measure holding control at rest (Experiment 1). The 2020 study shows that endpoint forces reflect the integration of learned dynamics exerted during active movement that led to the endpoint position. However, in Experiment 1, there is no active reaching to integrate, as the robot passively moves the arm to the held position. Thus, resting postural forces measured in Experiment 1 could not reflect the integration of reach commands that led to each rest position.  

      Thus, the two sets of findings are not contradictory. Taking our current and 2020 findings together suggests that active holding control would comprise would reflect both the integration of movement control that led to assuming the held position, plus the force biases measured at rest.

      Hence our decision to describe these two systems as functionally separable: while these systems can interact, the effects of post-stroke malfunctions in each can be independent depending on the function and conditions at hand. This does not make this a limited finding: being able to dissociate post-stroke impairment based on each of these two modes of control may inform rehabilitation, and also importantly, understanding the conditions in which these two modes of control become separable can substantially advance our understanding of both how different stroke signs interact with each other and how motor control is assembled in the healthy motor system. Figure 9 illustrates our conceptual model behind this and may serve as a blueprint to further dissect these circuits in the future.

      We discuss these issues briefly in lines 663-669 in our Discussion section, reproduced below for convenience:

      “It should be noted, however, that having distinct neural circuits for reaching and holding does not rule out interactions between them. For example, we recently demonstrated how arm holding control reflects the integration of motor commands driving the preceding active movement that led to the hold position, in both healthy participants and patients with hemiparesis (Albert et al., 2020). However, in that paper, we did not claim that this integration is the only source of holding control. Indeed, in Experiment 1 of the current study, we used passive movement to bring the arm to each probed position, which means that the postural biases could not be the result of integration of motor commands.” 

      And, we have adjusted our Introduction to provide pertinent context regarding our 2020 work (first paragraph, lines 66-70 of the updated manuscript).

      A minor wording concern I had is that the term "holding still" is frequently hard to parse. A couple of examples: "These findings in stroke suggest that moving and holding still are functionally separable modes of control." This example is easily read, "moving and holding [continue to be] functionally separable". Another: "...active reaching and holding still in the same workspace, " could be "...active reaching and holding [are] still in the same workspace." Simply "holding", "posture" or "posture maintenance" would all be better options.

      Response 1.4. Thank you for your suggestion. Following your comment, we have abbreviated this term to simply “holding”, both on the title and throughout the text.

      Reviewer #2 (Public Review):

      Summary: 

      Here the authors address the idea that postural and movement control are differentially impacted with stroke. Specifically, they examined whether resting postural forces influenced several metrics of sensorimotor control (e.g., initial reach angle, maximum lateral hand deviation following a perturbation, etc.) during movement or posture. The authors found that resting postural forces influenced control only following the posture perturbation for the paretic arm of stroke patients, but not during movement. They also found that resting postural forces were greater when the arm was unsupported, which correlated with abnormal synergies (as assessed by the Fugl-Meyer). The authors suggest that these findings can be explained by the idea that the neural circuitry associated with posture is relatively more impacted by stroke than the neural circuitry associated with movement. They also propose a conceptual model that differentially weights the reticulospinal tract (RST) and corticospinal tract (CST) to explain greater relative impairments with posture control relative to movement control, due to abnormal synergies, in those with stroke.

      Strengths: 

      The strength of the paper is that they clearly demonstrate with the posture task (i.e., active holding against a load) that the resting postural forces influence subsequent control (i.e., the path to stabilize, time to stabilize, max. deviation) following a sudden perturbation (i.e., suddenly removal of the load). Further, they can explain their findings with a conceptual model, which is depicted in Figure 9. 

      Weaknesses: 

      Current weaknesses and potential concerns relate to i) not displaying or reporting the results of healthy controls and non-paretic arm in Experiment 2 and ii) large differences in force perturbation waveforms between movement (sudden onset) and posture (sudden release), which could potentially influence the results and or interpretation. 

      Response 2.0. Thank you for your assessment, and for pointing out ways to improve our paper. We address the weakness and potential concerns in detail below.

      Larger concerns

      (1) Additional analyses to further support the interpretation. In Experiment 1 the authors present the results for the paretic arm, non-paretic arm, and controls. However, in Experiment 2 for several key analyses, they only report summary statistics for the paretic arm (Figure 5D-I; Figure 6D-E; Figure 7F). It is understood that the controls have much smaller resting postural force biases, but they are still present (Figure 3B). It would strengthen the position of the paper to show that controls and the non-paretic arm are not influenced by resting postural force biases during movement and particularly during posture, while acknowledging the caveat that the resting positional forces are smaller in these groups. It is recommended that the authors report and display the results shown in Figure 5D-I; Figure 6D-E; Figure 7F for the controls and non-paretic arm. If these results are all null, the authors could alternatively place these results in an additional supplementary. 

      Response 2.1a. Thank you for your recommendations. We agree both on the value of these analyses and the caveat associated with them: these resting postural force biases are substantially smaller for the non-paretic and control data (for example, the magnitude of resting biases in the supported condition is 2.8±0.4N for the paretic data, but only 1.8±0.4N and 1.3±0.2N for the non-paretic and control data, respectively; the difference is even greater in the unsupported condition, though this is not the one being compared to Experiment 2).

      We now conduct a comprehensive series of supplementary analyses, including the examination of non-paretic and control data for all three components of Experiment 2 (unperturbed reaches; pulse perturbations; and active holding control). These are mentioned in the Results (lines 422-424, 512513, and 574-574 of the revised manuscript) and illustrated in the supplementary materials: Supplementary Figures S5-1, S6-1, and S7-1 contain the main analyses (comparisons of instances with the most extreme resting biases for each individual) for the unperturbed reach analysis, pulse perturbation analysis, and active holding control analysis, respectively.

      We find that non-paretic and control data do not display effects of resting biases upon unperturbed reaching control (Figure S5-1) or control against a pulse perturbation early during movement (Figure S6-1) – as is the case with the paretic data. Non-paretic and control data do not display evidence of influence of their resting force biases upon active holding control either (Figure S7-1), unlike the paretic data. For the non-paretic data, however, these influences are nominally towards the same direction as in the paretic data. Given that resting biases are substantially weaker for the non-paretic case, it is possible a similar relationship exists but requires increased statistical power to discern. Moreover, it is possible that the effect of resting biases is non-linear, with small biases effectively kept under check so that their impact upon active holding control is even less than a linearly scaled version of the impact of the stronger, paretic-side biases. This can be the subject of future work.

      Please also note that, following your recommendation (Recommendations to the Authors, point 2.1), we have conducted secondary analyses which estimate sensitivity to resting bias using all datapoints, validating our main analyses; these analyses were also performed for control and non-paretic data, with similar results (Response 2.A.1).

      Further, the results could be further boosted by reporting/displaying additional analyses. In Figure 6D the authors performed a correlation analysis. Can they also display the same analysis for initial deviation and endpoint deviation for the data shown in Figure 5D-F & 5G-I, as well for 7F for the path to stabilization, time to stabilization, and max deviation? This will also create consistency in the analyses performed for each dependent variable across the paper.

      Response 2.1b. Here, we set to test whether resting biases affect movement. It is best to do this using a within-individual comparison design, rather than using across-individual correlations: while correlation analyses can in general be informative, they obscure within-individual effects which are the main comparisons of interest in our study. Consider a participant with strong resting bias towards one direction, tested on opposing perturbations; averaging these responses for each individual would mostly cancel out any effects of resting biases. Even if we were to align responses to the direction of the perturbation before averaging, the power of correlation analyses may be diluted by inter-individual differences in other factors, such as overall stiffness.

      Thus, our analysis design was instead focused on examining the differential effects of resting posture biases within each individual’s data. We compared the most extreme opposing/aligned or clockwise/counter-clockwise instances within each individual, specifically to assess these differential effects. In our revised version, we have further reinforced these analyses to include all data rather than the most extreme instances (see response 2.A.1.a to the Reviewer’s recommendation to the authors) where we performed correlations of within-individual resting posture vs. the corresponding dependent variables and compared the resulting slopes. 

      The across-individual correlation analyses add little to that for the reasons we outlined above. At the same time, it is possible they can be helpful in e.g. illustrating across-individual variability. We thus now include across-individual correlation analyses for all dependent variables, but, given their limited value, only in the supplementary material. This also means that, for consistency, we moved the correlation analysis in Figure 6 to the corresponding supplementary figure as well (Figure S6-3).

      In addition, following the Reviewer’s comment about consistency in the analyses performed for each dependent variable across the paper, we added within-individual comparisons for settling time following the pulse perturbations (Figure 6D, right).

      (2) Inconsistency in perturbations that would differentially impact muscle and limb states during movement and posture. It is well known that differences in muscle state (activation / preloaded, muscle fiber length and velocity) and limb state (position and velocity) impact sensorimotor control (Pruszynski, J. A., & Scott, S. H. (2012). Experimental brain research, 218, 341-359.). Of course, it is appreciated that it is not possible to completely control all states when comparing movement and posture (i.e., muscle and limb velocity). However, using different perturbations differentially impacts muscle and limb states. Within this paper, the authors used very different force waveforms for movement perturbations (i.e., 12 N peak, bell-shaped, 0.7ms duration -> sudden force onset to push the limb; Figure 6A) and posture perturbations (i.e., 6N, 2s ramp up -> 3s hold -> sudden force release that resulted in limb movement; Figure 4) that would differentially impact muscle (and limb) states. Preloaded muscle (as in the posture perturbation) has a very different response compared to muscle that has little preload (as in the movement perturbations, where muscles that would resist a sudden lateral perturbation would likely be less activated since they are not contributing to the forward movement). Would the results hold if the same perturbation had been used for both posture and movement (e.g., 12 N pulse for both experiments)? It is recommended that the authors comment and discuss in the paper why they chose different perturbations and how that might impact the results. 

      Response 2.2a. We agree that it can be impossible to completely control all states when comparing movement and posture. We would also like to stress that these perturbations were not designed so that responses are directly compared to each other (though of course there is an indirect comparison in the sense that we show influence of biases in one type of perturbation but not the other). Instead, Experiment 2 tried to implement a probe optimized for each motor control modality (moving vs. holding). However, the Reviewer has a point that the potential impact of differences between the perturbations is important to discuss in the paper.

      The Reviewer points out two potentially interesting differences between the two perturbations. First, the magnitude (6N for the posture perturbation vs. 12N for the pulse perturbation); second, the presence of background load in the posture perturbation, in contrast to the pulse perturbation.

      For the movement perturbation, we used a 12-N, 70ms pulse. This perturbation and scaled versions have been tested before in both control and patient populations (Smith et al., 2000; Fine and Thoroughman, 2006). For the holding perturbation, we used a background load to ensure that active holding control is engaged, and the duration of the probe (holding for about 5s) made using a stronger perturbation impractical –maintaining a background load at, say, 12N for that long could lead to increased fatigue.

      The question raised by the Reviewer, whether the findings would be the same if the same, 12-N pulse were used to probe both moving and holding control, is interesting to investigate. We would expect the same qualitative findings (i.e. there would still be a connection between resting posture and active holding control when the latter were probed with a 12N pulse). Recent work provides more specific insight into what to expect. Our posture perturbation task is similar to the Unload Task in (Lowrey et al., 2019), whereby a background torque is released, whereas our pulse perturbation is more similar to their Load Task, whereby a torque is imposed against no background load (though it is a step perturbation rather than a pulse). Lowrey et al., 2019 find that their Unload task is harder than the Load task, with 2x the fraction of patient trials classified as failed (with failure defined as task performance being outside of the 95% confidence interval for controls), though there are still clear effects for the Load task. 

      This suggests that the potential effects of using a pulse-like perturbation to probe posture control would likely be weaker in magnitude, all other things being equal. At the same time, however, the Load and Unload tasks in Lowrey et al., 2019 were perturbations of the same magnitude; it is thus also likely that the reduction in effect would be mitigated, or reversed, by the fact that we would be using a 12N instead of a 6N perturbation.

      A relevant consequence of the Lowrey et al., 2019 findings is that the Unload paradigm is superior in its ability to detect impairment in static, posture perturbations, and thus provides a better signal to detect potential relationships with resting posture biases. This is not surprising, as a background load further engages the control of active holding, which what we were trying to probe in the first place.

      But then why not use the same paradigm (preloading and release) for movement? There are two main reasons. First, requiring a background load throughout the experiment is unfeasible due to fatigue. Second, for the holding perturbation, we wanted to ensure that the postural control system is meaningfully engaged when the perturbation hits, hence we picked the background load. Were we to impose the same during moving – i.e. impose a lateral background load on the movement - we could be engaging posture control on top of movement control. This preloading would reduce the degree to which the pulse probe isolates movement control, and lead to intrusion of the posture control system in the movement task by design. This relates to what the Reviewer proposes in the comment below: preloading may result in postural biases i.e. engage posture control; see below where we argue this interpretation is within the scope of our conceptual model rather a counter to it.

      We now explain the rationale behind our perturbation design in the Methods section (lines 211-220).

      Relatedly, an alternative interpretation of the results is that preloading muscle for stroke patients, whether by supporting the weight of one's arm (experiment 1) or statically resisting a load prior to force release (experiment 2), leads to a greater postural force bias that can subsequently influence control. It is recommended that the authors comment on this. 

      Response 2.2b. We find this interpretation valid, but we do not see how it meaningfully differs from the framework we propose. We already state that the RST may be tailored for both posture/holding control and the production of large forces (which would include muscle preloading):

      “Thus, the accumulated evidence suggests that the RST could control posture and large force production in the upper limb.“ (lines 698-699 in the current version)

      “the RST, in contrast, is weighted more towards slower postural control and generation of large isometric forces” (lines 724-726 in the current version)

      And, we discuss other conditions where the RST is involved in large force production, such as power grip, and how these interact with the role of the RST in posture/holding control (lines 758-768 in the current version).

      To better explain our model, we now provide the two examples mentioned by the reviewer along with our description of the proposed role for the RST (lines 726-727):

      “…the RST, in contrast, is weighted more towards slower postural control and generation of large isometric forces (such as vertical forces for arm support, or horizontal forces for holding the arm still against a background load like in our posture/release perturbation trials).”

      We note, however, that we find resting posture abnormalities even in the presence of arm support, suggesting the involvement of the RST in holding control even when the forces involved (and the need to preload the muscle) are small.

      Reviewer #3 (Public Review): 

      The authors attempt to dissociate differences in resting vs active vs perturbed movement biases in people with motor deficits resulting from stroke. The analysis of movement utilizes techniques that are similar to previous motor control in both humans and non-human primates, to assess impairments related to sensorimotor injuries. In this regard, the authors provide additional support to the extensive literature describing movement abnormalities in patients with hemiparesis both at rest and during active movement. The authors describe their intention to separate out the contribution of holding still at a position vs active movement as a demonstration that these two aspects of motor control are controlled by two separate control regimes.

      Strengths: 

      (1) The authors utilize a device that is the same or similar to devices previously used to investigate motor control of movement in normal and impaired conditions in humans and non-human primates. This allows comparisons to existing motor control studies. 

      (2) Experiment 1 demonstrates resting flexion biases both in supported and unsupported forelimb conditions. These biases show a correlated relationship with FM-UE scores, suggesting that the degree of motor impairment and the degree of resting bias are related.

      (3) The stroke patient participant population had a wide range of both levels of impairment and time since stroke, including both sub-acute and chronic cases allowing the results to be compared across impairment levels.

      The authors describe several results from their study: 1. Postural biases were systematically toward the body (flexion) and increased with distance from the body (when the arm was more extended) and were stronger when the arm was unsupported. 2. These postural biases were correlated with FM-UE score. 3. They found no evidence of postural biases impacting movement, even when that movement was perturbed. 4. When holding a position at the end of a movement, if the position was perturbed opposite of the direction of bias, movement back to the target was improved compared to the perturbation in the direction of bias. Taken together, the authors suggest that there are at least two separate motor controls for tasks at rest versus with motion. Further, the authors propose that these results indicate that there is an imbalance between cortical control of movement (through the corticospinal tracts) and postural control (through the reticulospinal tract).

      Response 3.1. Thank you for pointing out some of the strengths of our work and summarizing our findings. A minor clarification we would like to make, related to (3), is that, while our study did enroll two patients towards the end of the subacute stage (2-3 months), the rest of the population were at the chronic stage, at one year and beyond. We thus find it very unlikely that time after stroke was the primary driver of differences in impairment in the population we studied.

      There are several weaknesses related to the interpretation of the results:

      In Experiment 1, the participants are instructed to keep their limbs in a passive position after being moved. The authors show that, in the impaired limb, these resting biases are significantly higher when the limb is unsupported and increase when the arm is moved to a more extended position.

      When supported by the air sled, the arm is in a purely passive position, not requiring the same antigravity response so will have less RST but also less CST involvement. While the unsupported task invokes more involvement of the reticulospinal tract (RST), it likely also has significantly higher CST involvement due to the increased difficulty and novelty of the task.

      If there were an imbalance in CST regulating RST as proposed by the authors, the bias should be higher in the supported condition as there should be relatively less CST activation/involvement/ modulation leading to less moderating input onto the RST and introducing postural biases. In the unsupported condition, there is likely more CST involvement, potentially leading to an increased modulatory effect on RST. If the proportion of CST involvement significantly outweighs the RST activation in the unsupported task, then it isn't obvious that there is a clear differentiation of motor control. As the degree of resting force bias and FM-UE score are correlated, an argument could be made that they are both measuring the impairment of the CST unrelated to any RST output. If it is purely the balance of CST integrity compared to RST, then the degree of bias should have been the same in both conditions. In this idea of controller vs modulator, it is unclear when this switch occurs or how to weigh individual contributions of CST vs. extrapyramidal tracts. Further, it isn't clear why less modulation on the RST would lead only to abnormal flexion.

      Response 3.2. Our model posits two mechanisms by which CST impairment would lead to increased RST involvement. The first – which is the one discussed by the Reviewer here - is a direct one, whereby weaker modulation of the RST by the CST leads to increased RST involvement. The second is an indirect one, whereby the incapacity of CST to drive sufficient motor output to deal with tasks eventually leads to increased RST drive.

      The reviewer suggests it is likely that the unsupported task demands increased activation through both the CST and the RST. If that were the case, however, it would exaggerate the effects of CST/RST imbalance after stroke compared to healthy motor control: if task conditions (lack of support) required higher CST involvement, then CST damage would have an even larger effect. In turn, this would lead to even higher RST involvement and further diminishing the ability of CST to moderate RST. Thus, RST-driven biases would be higher in the unsupported condition.

      And, given that the CST itself is damaged and has to deal with an even-increased RST activation, we would not expect that the proportion of CST involvement would outweigh RST activation, but the opposite. In fact, a series of relatively recent findings suggest just this. For example,

      • Zaaimi et al., 2012  showed that unilateral CST lesions in monkeys lead to significant increases in the excitability of the contralesional RST (Zaaimi et al., 2012). Interestingly, this effect was present in flexors but not extensors, potentially explaining why less modulation and/or overactivation of the RST would primarily lead to abnormal flexion. 

      • McPherson et al. (further discussed in point 2.A.23, by Reviewer 2 – Recommendations to the Authors) showed that, after stroke, contralesional activity (which would include the ipsilateral RST) increases relative to ipsilesional activity (which would include the contralateral CST)

      (McPherson et al., 2018). The same study also provides evidence that FM-UE may primarily reflect RST-driven impairment. The ipsilateral(RST)/contralateral(CST) balance, expressed as a laterality index, correlated with FM-UE, with lower FM-UE for indices indicating higher RST involvement. (Interestingly, the slope of this relationship was steeper when the laterality of brain activation patterns was examined under tasks with less arm support, mirroring the steeper FM-UE vs resting bias slope when arm support is absent, as shown in our Figure 8).

      • Wilkins et al., 2020 (Wilkins et al., 2020) found that providing less support (i.e. requiring increased shoulder abduction) increases ipsilateral activation (representing RST) relative to contralateral activation (representing CST).

      This resting bias could be explained by an imbalance in the activation of flexors vs extensors which follows the results that this bias is larger as the arm is extended further, and/or in a disconnect in sensory integration that is overcome during active movement. Neither would necessitate separate motor control for holding vs active movement. 

      Response 3.3. We do not think that either of these points necessarily argue against our model. First, the resting biases we observe are clearly pointed towards increased flexion, and can thus be seen as the outcome of an imbalance in the activation of flexors vs. extensors at rest. This imbalance between flexors/extensors can also be explained by the CST/RST imbalance posited by our conceptual model: in their study of CST lesions in the monkey, Zaaimi et al., 2012 found increased RST activation for flexors but not extensors, suggesting that RST over-involvement may specifically lead to flexor abnormalities (Zaaimi et al., 2012). Second, overcoming a disconnect in sensory integration may be one way the motor system switches between separate controllers; how this switch happens is not examined by our conceptual model.

      In Experiment 2, the participants are actively moving to and holding at targets for all trials while being supported by the air sled. Even with the support, the paretic participants all showed start- and endpoint force biases around the movement despite not showing systematic deviations in force direction during active movement start or stop. There could be several factors that limit systematic deviations in force direction. The most obvious is that the measured biases are significantly higher when the limb is unsupported and by testing with a supported limb the authors are artificially limiting any effect of the bias.

      Response 3.4. We do expect, in line with what the reviewer suggests, that any potential effects would be stronger in the unsupported condition. The decision to test active motor control with arm support was done as running the same Experiment 2 would pose challenges, particularly with our most impaired patients, given the duration of Experiment 2 (~2 hours, about 1 hour with each arm) and the expected fatigue that would ensue.

      However, a key characteristic of our comparisons is that we are comparing Experiment 2 active control data under arm support, against Experiment 1 resting bias data also under arm support. While Experiment 1 measured biases without arm support as well, these are not used for this comparison. And, while resting biases are weaker with arm support, they are still clear and significant; yet they do not lead to detectable changes in active movement.

      At the same time, we do not rule out that, if we were to repeat Experiment 2 without arm support, we could find some systematic deviation in the direction of resting bias in movement control. Our conceptual model, in fact, suggests that this may be the case, as we described in lines 618-620 of our original manuscript. The idea here is that, when arm support is not provided, the increased strength requirements lead to increased drive through the RST, to the point that posture control (and its abnormalities) spills into movement control (Figure 9). We now better clarify this position in our Discussion (lines 744-750):

      “The interesting implication of this conceptual model is that synergies are in fact postural abnormalities that spill over into active movement when the CST can no longer modulate the increased RST activation that occurs when weight support is removed (i.e. resting biases may influence active reaching in absence of weight support). Supporting this idea, a study found increased ipsilateral activity (which primarily represents activation via the descending ipsilateral RST (Zaaimi et al., 2012)) when the paretic arm had reduced support compared to full support (McPherson et al., 2018).”

      It is also possible that significant adaptation or plasticity with the CST or rubrospinal tracts could give rise to motor output that already accounts for any intrinsic resting bias.  

      Response 3.5. This kind of adaptation – regardless of the tracts potentially involved – is an issue we examined in our experiment. As we talk about in our Results (lines 458-460 in the updated manuscript), with most of our patient population in the chronic stage, it could be likely that their motor system adapted to those biases to the point that movement planning took them into account, thereby limiting their effect. This motivated us to examine responses to unpredictable perturbations during movement (Figure 6) where we still find lack of an obvious effect of resting biases upon reaching control. We thus believe that our findings are not explained by this kind of adaptation, though we agree it would be of great interest for future work to compare resting biases and reaching control in acute vs. chronic stroke populations to examine the degree to which stroke patients adapt to these biases as they recover.

      In any case, the results from the reaching phase of Experiment 2 do not definitively show that directional biases are not present during active reaching, just that the authors were unable to detect them with their design. The authors do acknowledge the limitations in this design (a 2D constrained task) in explaining motor impairment in 3D unconstrained tasks. 

      Response 3.6. It is, of course, an inherent limitation of a negative finding is that it cannot be proven. What we show here is that, there is no hint of intrusion of resting posture abnormalities upon active movement in spite of these resting posture abnormalities being substantial and clearly demonstrated even under arm support. To allow for the maximum bandwidth to detect any such effects, we specifically chose to compare the most extreme instances (resting bias-wise) for each individual, and yet we did not find any relationship between biases and active reaching.

      This suggests that, even if these biases could be in some form present during active movement, their effect would be minimal and thus limited in meaningfully explaining post-stroke impairment in active movement under arm support.

      Note that, as we already discuss, our conceptual model (Figure 9) suggests that the degree to which directional biases would be present in active reaching may be influenced by arm support (or the specific movements examined – hence our limitation in not examining 3D movement). Thus we do not claim that this independence is absolute. Examples include the last line of the passage quoted right above, and the summary statement of our Discussion quoted below (lines 639-641):

      “…which raises the possibility that the observed dissociation of movement and posture control for planar weight-supported movements may break down for unsupported 3D arm movements.”

      Finally, we now more explicitly acknowledge that abnormal resting biases may influence active movement in the absence of arm support (see Response 3.4).

      It would have been useful, in Experiment 2, to use FM-UE scores (and time from injury) as a factor to determine the relationship between movement and rest biases. Using a GLMM would have allowed a similar comparison to Experiment 1 of how impairment level is related to static perturbation responses. While not a surrogate for imaging tractography data showing a degree of CST involvement in stroke, FM-UE may serve as an appropriate proxy so that this perturbation at hold responses may be put into context relative to impairment.

      Response 3.7. Here the Reviewer suggests we use FM-UE scores as a proxy for CST integrity. We do not think this analysis would be particularly helpful in our case for a number of reasons:

      First, while FM-UE is a general measure of post-stroke impairment, it was designed to track - among other things - the emergence and resolution of abnormal synergies, a sign assumed to result from abnormally high RST outflow (McPherson et al., 2018; McPherson and Dewald, 2022). In line with this, the FM-UE scales with EMG-based measures of synergy abnormality (Bourbonnais et al., 1989). Impairments in dexterity, a sign associated with damage to the CST (Lawrence and Kuypers, 1968; Porter and Lemon, 1995; Duque et al., 2003), dissociate with synergy abnormalities when compared under arm support as we do here (Levin, 1996; Hadjiosif et al., 2022). This means that FM-UE would be a stronger proxy for RST activity and thus not a direct proxy for CST integrity particularly when one wants to dissociate RST-specific vs. CST-specific abnormalities. In fact, as we discuss in Response 3.2 above, there is a number of studies supporting this idea: for example, Zaaimi et al., 2012 show that relative RST activation – the balance between ipsilateral excitability, primarily reflecting RST, and contralateral excitability, primarily reflecting the CST, scales with FM-UE (Zaaimi et al., 2012).

      Second, this kind of analysis would obscure within-individual effects, since FM-UE scores are, of course, assigned to each individual. This is the same issue as doing across-individual correlation analyses in general (see response 2.1b).Strong resting force bias would have opposite effects on opposing perturbations, averaging across subjects would occlude these effects.

      Third, while FM-UE is a good measure of synergy abnormality, weakness alone could also give an abnormal FM-UE (Avni et al., 2024).

      The Reviewer also suggests we use time from injury for this analysis. Time from injury can indeed potentially be an important factor. However, this analysis would not be appropriate for our dataset, since the effective variation in recovery stage within our population is limited: our sample is essentially chronic (only two patients were examined within the subacute stage – at 2 and 3 months after stroke - with everybody else examined more than a year after stroke) with the “positive” elements of their phenotype (and FM-UE itself) essentially plateaued (Twitchell, 1951; Cortes et al., 2017). We thus would not expect to see any meaningful effects of time from injury within our population. It would be an excellent question for future work to investigate both resting biases and their relationship to reaching in acute/subacute patients, and examine whether the trajectory of resting biases (both emergence and abatement due to recovery) follows the one for abnormal synergies.

      It is not clear that even in the static perturbation trials that the hold (and subsequent move from perturbation) is being driven by reticulospinal projections. Given a task where ~20% of the trials are going to be perturbed, there is likely a significant amount of anticipatory or preparatory signaling from the CST. How does this balance with any proposed contribution that the RST may have with increased grip?

      Response 3.8. We included our response to this as part of Response 3.2. In brief, while we cannot rule out that these tasks may recruit increased CST signaling, this would tend to increase, rather than reduce, the effects of post-stroke impairment: the requirement for increased signaling from a CST that is damaged would magnify the effects of this damage, in turn leading to increased recruitment of other tracts, such as the RST.

      In general, the weakness of the interpretation of the results with respect to the CST/RST framework is that it is necessary to ascribe relative contributions of different tracts to different phases of movement and hold using limited or indirect measures. Barring any quantification of this data during these tasks, different investigators are likely to assess these contributions in different ways and proportions limiting the framework's utility.

      Response 3.9. We believe that our Reponses 3.2-3.6 put our findings in fair perspective, and the edits undertaken based on the Reviewer’s comments have clarified our position as to how the dissociation between holding and moving control may break down. We do agree, however, that our framework would be strengthened by the use of direct measures of CST/RST connectivity in future research. We present our conceptual model as a comprehensive explanation of our findings and how they blend with current hypotheses regarding the role of these two tracts in motor control after stroke.  As such, it provides a blueprint towards future research that more directly measures or modulates CST and RST involvement, using tools such as tractography or non-invasive brain stimulation.

      Recommendations for the authors:   

      Reviewer #1 (Recommendations For The Authors):

      L226 “…of this issue, we repeated the analysis of Figure 7F (a) by excluding these four patients…”.  Should this be three, based on the previous sentence? 

      Response 1.A.1. Thank you for pointing this typo, which is now corrected. The analysis in question (Figure S1 in the original submission, now re-numbered as Figure S7-4), excluded the three patients mentioned in the previous sentence.

      L254 “…the hand was held in a more distal position. The postural force biases were strongest when…”  Could this be "extended" rather than distal? See my later comment about the inadequate description of targets.

      Response 1.A.2. The reviewer is correct that, the arm will tend to be more extended in the distal targets. However, since these positions were defined in extrinsic coordinates, we think the terms distal/proximal are also appropriate. In either case, we now clarify these definitions in the text (see Response 1.A.3 below).

      L263 “…contained both distal and proximal targets, and, importantly, they were also the movement…”.  Distal/proximal targets were never described as part of the task. 

      Response 1.A.3. We improved our description by (i) changing the wording above to “represented positions both distal and proximal to the body,”, (ii) doing the same in our Methods (line 175) and (iii) indicating distal/proximal targets in Figure 3A (bottom right of panel A).

      L378 “…the pulse perturbation. We hypothesized that, should resting postural forces play a role, they…”  L379 “…would tend to reduce the effect of the pulse if they were in the opposite direction, and…”  Not really obvious why. A reduction in the displacement caused by a force pulse might be caused by different stiffness or viscosity, but not by a linear, time-invariant force bias. This situation is different from that of "moving the arm through a high-postural bias area vs. a low-postural bias area" where it would encounter time- (actually spatially) varying forces and varying amounts of displacement. Clarify the logic if this is a critical point.

      Response 1.A.4. We thank the Reviewer for highlighting this point of potential confusion. We now clarify that these postural bias forces are neuromuscular in origin (Kanade-Mehta et al., 2023), and likely result from an expression of abnormal synergy, at least under static conditions. In this case, we hypothesized that force pulses acting against the gradient of the postural bias field would act to stretch the already active muscles, which would lead to a further increase in postural resistance due to inherent length-tension properties of active muscle. By contrast, force pulses acting along the gradient of the postural bias field would act to shorten the same active muscles, which would lead to a reduction in postural resistance. The data did not support this in the case of force pulses imposed during movement. We note, however, that similar effects would affect responses to static perturbations as well, wherein we do find an effect of resting biases. We now better explain this reasoning (lines 479482).

      L466 “resting postural force). In short, our perturbations revealed that resting flexor biases switched  467 on after movement was over, providing evidence for separate control between moving” and 

      L468 “holding still.”

      I do not think the authors have presented clear evidence that forces, "switch on", implying the switch to a different controller which they posit. This could as easily be a nonlinear or time-varying property of a single controller (admittedly, the latter possibility overlaps broadly with their idea of distinct, interacting controllers). An example that the authors are certainly aware of is that of muscle "thixotropy" a purely peripheral mechanism due to the dynamics of crossbridge cycling that causes resting muscle to be stiffer than moving muscle, changing with a time constant of ~1-2 seconds. Neither this particular example nor changing levels of contraction (more likely during the unpredictable force perturbations) would be in the direction to explain the main observation here -- a point perhaps worth making, together with the stretch reflex comments. 

      Response 1.A.5. Thank you for this perspective. Indeed, it might be that “switching on” represents a shift along a nonlinear property of the same controller: in the extreme, if this nonlinearity is a step (on/off) function, this single controller would be functionally identical to two separate controllers. We thus cannot tell if these controllers are distinct in the strict sense. What we argue here is that, no matter the underlying controller architecture - two distinct controllers or two distinct modes of the same controller - is that the control of reaching vs. holding can be functionally separable even after stroke. In line with this idea, we used a more nuanced phrasing (e.g. “separable functional modes for moving vs. holding”) throughout our manuscript, and we have now edited out a mention of “separate controllers” to be consistent with this.

      Moreover, thank you for pointing out the example of thixotropy, showing how peripheral mechanisms could interact with central control. As you point out, this effect would not explain the main observation here: in fact, if stiffness were substantially higher during rest or holding (instead of moving) that would reduce the impact of the static perturbation, making it harder to detect any effects of resting biases compared to the moving perturbation case.

      L480 “…during movement (Sukal et al., 2007). Yet, Experiment 2 found no relationship between resting…” L481”… postural force biases and active movement control. To further investigate this apparent…”  The methods of the two studies seem fairly similar, but this question warrants a more careful comparison. How did the size of the two workspaces compare? What about the magnitude of the exerted forces? The movement condition in this study was done with the limb entirely supported. Under that condition, the Sukal study also found fairly small effects of the range of motion.

      Response 1.A.6. Sukal et al., 2007 did not directly measure exerted forces, but instead compared the active range of motion under different loading conditions. They used the extent of reach area to quantify the effect of abnormal synergies, with a more extended active range of motion signifying reduced effect of abnormal synergies. As the Reviewer points out, Sukal et al. found fairly small effects of synergies upon the range of motion when arm support was provided (the reach area for the paretic side was found to be about 85% of the nonparetic side under full arm support, though they were statistically significantly different, Figure 5 of their paper). They found increasing effect of synergies as arm support was reduced: on average, the reach area when participants had to fully support the arm was less than 50% the reach area when full arm support was given (comparing the 0% vs. 100% active support conditions [i.e. 100% vs. 0% external support] in their Figure 5). As we discuss in our paper, this effect of arm support upon synergy mirrors the one we found for resting postures.

      To compare our workspace with the one in Sukal et al., we overlaid our workspace (the array of positions for which the posture biases were measured, for a typical participant from Experiment 1) on the one they used as shown in their Figure 4. Note that their figure only shows an example participant, and thus our ability to compare is limited by the fact that each participant can vary widely in terms of their impairment, and assumptions had to be made to prepare this overlay (e.g. that (0,0) represents the position of the right acromion point). 

      For this example, and our assumptions, our workspace was smaller, with the main points of interest (red dots, the movement start/end points used for Experiment 2) within the Sukal et al. workspace. That our workspace is smaller is not surprising, given that the area in Sukal et al. represents the limit of what can be reached, and thus motor control *has* to be examined in a subset of that area.

      Author response image 1.

      Comparing the two study methodologies, however, suggests an advantage of measuring resting biases in terms of sensitivity and granularity: first, resting biases can be clearly detected even under arm support (something we point out in our Discussion, lines 715-717); second, they can measure abnormalities at any point in the workspace, rather than a binary within/without the reach area. The resting bias approach may thus be a more potent tool to probe the shared bias/synergy mechanisms we propose here.

      Figure 2 

      Needs color code. 

      The red dots could be bigger.

      Response 1.A.7. We have increased the size of the red dots and added a color code to explain the levels illustrated by the contours. We also expanded our caption to better explain this illustration.

      Figure 3

      Labeling is confusing. Drop the colored words (from both A and B), and stick to the color legend. Consider using open and filled symbols (and bars) to represent arm support or lack thereof. The different colored ovals are very hard to distinguish.

      Response 1.A.8. We find these recommendations improve the readability of Figure 3 and we have thus adopted them - see updated Figure 3.

      Figure 4

      Not terribly necessary.  

      Response 1.A.9. While this figure is indeed redundant based our descriptions in the text, we kept it as we believe it can be useful in clarifying the different stages of movement we examine.

      Figure 5 

      Tiny blue and green arrows are impossible to distinguish. 

      Although the general idea is clear, E and H are not terribly intuitive.  Add distance scale bars for D-I. 

      Response 1.A.10. For improved contrast, we now use red and blue (also in line with comment below regarding Figure 7), and switched to brighter colors in general. To make E and H more intuitive and easier to follow, we expanded the on-panel legend. Thank you for pointing out that distance scale bars are missing; we have now added them (panels EFHI).

      Figure 6 

      Panel E inset is too small. 

      Response 1.A.11. We have now moved the inset to the right and enlarged it.

      Figure 7 

      Green and blue colors are not good. 

      Response 1.A.12. For improved contrast, we now use red and blue.

      Figure 8 

      Delete or move to supplement? 

      Response 1.A.13. We respectfully disagree. While the relationships on these data are also captured by the ANOVA, we believe these scatter plots offer a better overview of the relationships between force biases and FM-UE across different conditions.

      Really minor

      L113 “…participants' lower arm was supported using a custom-made air-sled (Figure 1C). Above the  participant's…” 

      Response 1.A.14. We put the apostrophe after the s so to refer to participants in general (plural).

      L117 ”…subject-produced forces on the handle were recorder using a 6-axis force transducer.”  recorded 

      Response 1.A.14. Thank you for pointing out this error which we have now corrected.

      L136 “…2013), Experiment 1 assessed resting postural forces by passively moving participants to>…”  The experiment did not move the participant. 

      Response 1.A.15. We now fix this issue: “by having the robot passively move…”

      L248 “…experiment blocks: two with each arm, with or without arm weight support (provided by an air experimental…”

      Response 1.A.16. We have now corrected this.

      L364 “…responses to mid-movement perturbations. In 1/3 of randomly selected reaching movements…”  Obviously, you mean 1/3 of all movements: "One-third of the reaching movements were chosen randomly"  

      Response 1.A.17. We now clarify: “In 1/3 of reaching movements in Experiment 2, chosen randomly”. Also please note our response to Reviewer 2, point 10: we now report the exact number of trials for which each kind of perturbation was present.

      L609 “Damage to the CST after stroke reduces its moderating influence upon the RST (Figure 9,…”  "its" refers to the subject, "Damage", not "CST".

      Response 1.A.18. We have changed this to “Post-stroke damage to the CST reduces the moderating influence the CST has upon the RST”.

      Reviewer #2 (Recommendations For The Authors):

      (1) Throughout, the authors cleverly selected the most opposed and most aligned resting postural force biases to perform a within-subject analysis. However, this approach excludes a lot of data. The authors could perform an additional within-subject analysis. For each participant they could correlate lateral resting posture force bias to each dependent variable, utilizing all the trials of a participant. 

      Response 2.A.1a. Thank you for your appreciating our analysis design, and suggesting additional analyses. We focused our within-subject analysis design on the most extreme instances, as we believe that this approach would offer the best opportunity to detect any potential effects of resting biases. We reasoned that, since resting biases tend to be relatively small for most locations in the workspace, taking all biases into account would inject a disproportionate amount of noise in our analysis, which would in turn diminish our ability to detect any potential relationships. This could be because small biases lead to small effects but also small biases may themselves be more likely to reflect measurement noise in the first place. Note that our study talks about separability of active reaching from resting abnormalities based on lack of relationships between the two. While one cannot definitely prove a negative, it is also important to take the approach that maximizes the ability to detect any such relationship if there were one. We believe taking the most extreme instances fulfills that role.

      However, as the Reviewer points out, this approach also excludes a substantial amount of data. We agree that our findings could be further strengthened by exploring additional within-subject analyses that utilize all trials. Thus, following the reviewer’s suggestion, we estimated the sensitivity of each dependent variable to lateral resting posture force bias. Specifically, we estimated the slope of this relationship for each individual (separately for paretic and non-paretic data) using linear regression, and assessed whether the average slope is significant for each group (paretic data, non-paretic data, and control data).

      This secondary analysis replicated our main findings: lack of relationship between posture biases and active reaching control (both for unperturbed and perturbed movement), and a significant relationship between posture biases and active holding control. In addition, in line with main point 2.1 by the reviewer, we performed the same analyses for non-paretic and control data. While there are no definitive conclusions to be made for these cases (as was likely, given that the resting force biases are smaller, as also pointed out by the Reviewer in 2.1) these data are worthy of discussion, with potentially interesting insights (for example, there are hints that the connection between resting biases and active holding control is present in the non-paretic arm as well, and may be explored in future research).

      We have included these analyses in the supplementary materials, and we point to them in the main text. Specifically:

      First, in line with our main analyses in Figure 5, we find no effect (the average slope is insignificant) for start and endpoint biases upon the corresponding reaching angles. This is now mentioned in lines 425-434 of the Results, and illustrated in Figure S5-2. There was a lack of effect for the non-paretic and control data as well.

      Second, in line with our main analyses in Figure 6, we find no effect of start biases upon responses to the pulse (Figure S6-2, mentioned in lines 513-517 of the Results). As above, there was no effect of non-paretic or control data either.

      And, finally, in line with our main analysis in Figure 7, we find an effect of resting biases upon performance for the static perturbation (Figure S7-2, mentioned in lines 578-586 of the Results). Interestingly, there is a suggestion that resting biases may affect static perturbation responses in the non-paretic data as well based on the relationship between posture bias and maximum deviation, but not the other two metrics. Given the lack of consistency of resting bias effects for all three different dependent variables examined, however, our current data are thus unable to give a definite answer as to whether there is the connection between resting biases and active holding control is also present in the non-paretic side. Our hypothesis is that, since resting abnormalities and their effects are the pathological over-manifestations of mechanisms inherent in the motor system in general, then such a relationship would exist. Answering this question, however, would require an experiment design better tailored to detect relationships in the non-paretic arm, where resting biases are weaker.

      We thank the Reviewer for their suggestions and believe that these additional analyses provide a more complete picture of the data, and their consistency with our main results reinforces the message of the paper.

      Then, they can report the percentage of participants that display significant correlations separately for the paretic, nonparetic, and control arms. 

      Response 2.A.1b. We note that, even in cases where the average slope (across individuals) is significant, the individual slopes themselves are usually not significant, likely due to the large amount of noise for datapoints corresponding to weak resting biases. To further examine this, we performed additional analyses whereby we examined slopes by (a) pooling all participant data together (centered separately for each individual), and then (b) took a further step to normalize each participant’s data not only by centering but by also adjusting by each individual’s variability along each axis (i.e. assess the slope between z-scores of resting bias vs. z-scores of each dependent variable). These two analyses confirmed our finding that resting biases interacted with active motor control, with significant slopes between resting biases and outcome variables. (a) Pooling all data together: path to stabilization: p = 0.032; time to stabilization: p = 1.4x10-5; maximum deviation: p = 0.021. (b) Pooling and normalizing: path to stabilization: p = 0.0013; time to stabilization: p = 8.6x10-6; maximum deviation: p = 0.00056. The latter analysis showed even stronger connection between resting bias and active holding control, probably due to better accounting for differences in the range of resting biases across participants). For simplicity, however, we only provide the across-individual slope comparisons in the paper.

      (2) An important aspect of all the analyses is that they rely heavily on estimates of the resting postural force bias. How stable are these resting postural force biases at the individual level? The authors could assess this by reporting within-subject variance for both the magnitude and direction of the resting postural force bias.

      Response 2.A.2. Thank you for your suggestion. We now assess the individual-level variance in error across measurements for patients’ paretic data using an ANOVA: the variance that remains after all other factors (same probe location; same arm support condition; same participant) are taken into account. We found that individual level measurement variance explained a mere 9.0% of total variance for resting bias magnitude. (We note that the same figure was 20.2% for the non-paretic data, in line with the weaker average biases which would be more susceptible to noise). We now note this in the Methods, as part of the new subsection “Stability of resting posture bias measurements in Experiment 1” (lines 266-273).

      (3) Does resting postural force bias influence hand movement immediately following force release from the postural perturbation? This could be assessed before any volitional responses by examining the velocity of the hand during the first 50 ms following the postural perturbation.

      Response 2.A.3. The influence seems fairly rapid, within the first 100ms as shown to the right. Here we plot hand deviation in the direction of the perturbation for the most-opposed (red) vs. most-aligned (blue) instances to examine when these curves become different. The bottom plots show the difference between these two, whereas shading indicates SEM (note that these curves are referenced to the average deviation in the last 0.5 s before force release). The rightmost plots zoom in to make it easier to see how responses to the most opposed vs. most aligned instances diverge.

      To detect the earliest post-perturbation timepoint for which this effect was significant, we performed paired t-tests at each timestep, and found that the two responses were systematically statistically different 95ms after perturbation onset onwards. For reference, the same method detected a response at 25ms for the most aligned instances and 40ms for the most opposed instances.

      We have now added Supplementary Figure S7-4 with short commentary in the Supplementary Materials.

      (4) Abstract. lines 7-9. At a glance (and when reading the manuscript linearly) this sentence is unclear. If the paretic arm is compromised across rest and movement, how does that afford the opportunity to address the relationship between reaching, stopping, and stabilizing when all could be impacted? It might be useful to specify that these factors may impacted differently relative to one another with stroke, providing an opportunity to better understand the differences between movement and postural control. 

      Response 2.A.4. Thank you for pointing out this issue (also related to Reviewer 1’s point – Response 1.1). We have changed this to more clearly reflect our reasoning and highlight that the issue is that stroke can differentially impact reaching vs. holding, copied below:

      “The paretic arm after stroke exhibits different abnormalities during rest vs. movement, providing an opportunity to ask whether control of these behaviors is independently affected in stroke.”

      (5) Line 27. It is perhaps more appropriate to say conceptual model than simply 'model'.  

      Response 2.A.5. Thank you for your suggestion, which we have adopted throughout the manuscript.

      (6) Line 122-125. Figure 1A caption. The authors should specify that resting posture force biases occur when the limb or hand is physically constrained in a specific position. 

      Response 2.A.6. Thank you for pointing this out – we have clarified the caption:

      “If one were to physically constrain the hand in a position away from the resting posture, the torques involved in each component of the abnormal resting posture translate to a force on the hand (blue arrow);”

      (7) Line 147. Why was the order not randomized or counterbalanced? 

      Response 2.A.7. We prioritized paretic data, as the primary analyses and comparisons in our paper involved resting posture biases and active movement with the paretic arm. We note that our primary analyses, which rely on paretic-paretic comparisons, would not be affected by paretic vs. non-paretic ordering effects. However, ordering effects could potentially affect comparisons between paretic and non-paretic data. We now note the reasoning behind the absence of counterbalancing, and mention the potential limitation in interpreting paretic to non-paretic comparisons in lines 124-129 of the Methods.

      (8) Line 172. 12N is the peak force of the pulse?

      Response 2.A.8. The reviewer is correct; we have clarified our description (line 463 in the updated manuscript):

      “a 70 ms bell-shaped force pulse which was 12N at its peak”

      (9) Line 175. What is a clockwise pulse? Was the force vector rotating in direction over time so that it was always acting orthogonally to the movement, or did it always act leftwards or rightwards?

      Response 2.A.9. The force vector was not rotating in direction over time. Here, we used clockwise/counterclockwise to indicate rightwards/leftwards with respect to the ideal movement direction – the line from start position to target (which is what we understand the Reviewer means by “always act rightwards or leftwards”). We have clarified the text to indicate this (lines 193-195):

      …was applied by the robot lateral to the ideal movement direction (i.e. the direction formed between the center of the start position and the center of the target) after participants reached 2cm away from the starting position (Smith and Shadmehr, 2005; Fine and Thoroughman, 2006).

      (10) Lines 177-182. It might be useful to explicitly mention the frequency of each of the perturbations, just for ease of the reader. 

      Response 2.A.10. We have added this information to our Methods (lines 206-210):

      Thus, in summary, each 96-movement block consisted of 64 unperturbed movements and 32 movements perturbed with a force pulse (16 clockwise, and 16 counter-clockwise). For 20 out of the 96 movements in each block, the hold period was extended to test the hold perturbation (4 trials for each of the 5 target locations, each one of the 4 trials testing one perturbation direction as shown in Figure 7C).

      (11) Line 191. Lines 188-190. It would be useful to see a sample of several of these force traces over time (0-5s) that were used to make the average for a position. That would give insight into the stability of the forces of a participant for one of the postures. These traces could be shown in Figure 2.

      Response 2.A.11. Thank you for your suggestion. We have added these panels to Figure 1, (as Figure 2 was already large). Each panel illustrates the three measurements taken at similar positions (closest to midline, distal from the body) and the same condition (paretic arm, with arm support given) for one participant (same participants as in Figure 2). Solid lines indicate the force on the x-axis (positive values indicate forces towards the left), whereas dashed lines indicate the force on the y-axis (positive values indicate forces towards the body). The shaded area indicates the part averaged in order to estimate the resting bias, illustrating how resting biases were relatively stable by the 2s mark. Note that these examples include one trial (blue traces in the third panel) which was rejected following visual inspection as described in Materials and Methods – Data Exclusion Criteria (“trials where forces appeared unstable and/or there was movement during the robot hold period”). We find this helpful as this illustrates (and motivates) one component of our methodology. 

      (12) Line 196. Figure 1D (not 1E).  

      Response 2.A.12. Thank you for catching this error, which we have now corrected.

      (13) Line 215: The authors mentioned similar results. Were there any different results that impacted interpretation? Some evidence of this, similar to and in addition to Supplementary 1, would be helpful. 

      Response 2.A.13. We repeated our analyses without these exclusion criteria, with no impact to the interpretation. We now include versions of the main outcome panels from Figures 5, 6, and 7 in the supplementary materials calculated without this outlier exclusion (Figures S5-E, S6-E, and S7-E, respectively). 

      (14) Line 231: Perhaps better to explicitly state the furthest three positions are being across as the distal targets for the ANOVA. 

      Response 2.A.14. Thank you for your suggestion. We now explicitly clarify this in line 276:

      “distal targets [furthest three positions] vs. proximal targets [closest two positions]”

      (15) Figure 3B, lines 265. Clearly, these are different, but the authors should report statistics. 

      Response 2.A.15. We now report these numbers (lines 339-346 of the revised manuscript, which also include statistics related to bias direction as described in 2.A.17 below).

      (16) Figure 2 should have a heat map scale.  

      Response 2.A.16. We have now added this (also Response 1.A.7), including an explanation of what the heat map represents in the caption.

      (17) Figure 3C: It would be useful to quantify and plot the direction of the resting force bias vector. 

      Response 2.A.17. Thank you for your suggestion. We have expanded Figure 3 to include the average direction of the resting force bias vector (note the readjustment of colors following Reviewer 1’s comment: striped bars indicate No Support data, and full bars indicate Support data, with the colors being the same). The direction of the force bias vector, however, may not be very informative in cases where the magnitude is small (and the signal-to-noise ratio is small), whereas averaging the direction of the force bias vector across different positions for one participant may average out systematic variations in this direction across different locations. Nevertheless, the average direction appears generally towards the body (around -90°, or 6 o’clock) even in the non-paretic and control data (though the noise – as suggested by the size of the errorbars – is much higher in the latter cases, especially when the arm is supported). This is a (weak) suggestion that these resting biases may be present, though much subdued, in the nonparetic limb and healthy individuals; further work will be needed to elucidate this.

      (18) Line 428. It is not significantly longer compared to controls. Can the authors slightly revise this sentence?

      Response 2.A.18. We have revised this sentence (lines 529-532):

      Patients showed impaired capacity to resist and recover from this perturbation (the abrupt release of the imposed force). The time to stabilization for the paretic side (0.94±0.05s) was longer compared to the non-paretic side (0.79±0.03s, p = 0.024) and controls (0.78±0.06s, though this was statistically marginal, p = 0.061) as shown in Figure 7E, left.

      (19) Line 541. It is unclear how these data support the idea of three distinct controllers. Can the authors please clarify? 

      Response 2.A.19. Here, we compared our findings to previous ideas about distinct controllers, and discuss a potential fusion of these ideas with ours. Specifically, we find that holding is distinct from both initial reaching and coming to a stop. Previous work argues that initial reaching and coming to a stop are themselves distinct (Ghez et al., 2007; Jayasinghe et al., 2022). Combining these two sets of arguments, we arrive at the possibility of three distinct controllers. 

      (20) It would be useful if the authors provided a definition of synergy, as well as distinguishing between muscle and movement synergies. 

      Response 2.A.20. We now provide this in lines 591-594:

      Here, “synergies” refer to abnormal co-activation patterns across joints that manifest as the patient tries to move – for example, the elbow involuntarily flexing as the patient tries to abduct their shoulder (Twitchell, 1951; Brunnstrom, 1966). 

      (21) Line 592-593. The wording of this sentence could be improved. 

      Response 2.A.21. We have switched this sentence to active voice for more clarity:

      Thus, while full weight support reduces both resting flexor biases and movement-related flexor synergies, this reduction seems more complete for synergies rather than resting biases.

      (22) Figure 9. In the left column, it should read normal synergies and normal resting posture.  

      Response 2.A.22. We intentionally used the same terminology, as the idea behind our conceptual model is that these patterns, which manifest as well-recognized abnormal synergies and abnormal resting postures in stroke, may be present in the healthy motor system as well, but kept in check by CST moderating the RST. At the same time, we recognize that, by definition, synergies and posture in controls are the “normal” reference point against which “abnormal” synergies and posture are defined after stroke. To clarify this issue, we thus decided to forgo the use of the terms “abnormal” in the figure, and instead refer to “synergistic movement ” and “synergistic resting posture”.

      (23) Figure 9. With stroke, is RST upregulated, a decreased influence of CST, or both? All seem plausible.

      Response 2.A.23a. We believe both can be happening. From previous work (e.g. McPherson et al., 2018) it seems safe to say that RST upregulation is the case, whereas one would also expect a decreased CST influence due to its damage due to the stroke. The relative weight of these influences would be interesting to elucidate in future work.

      I have not read the paper, but did McPherson et al., 2018 test these different hypotheses?  

      Response 2.A.23b. The main point of McPherson et al., 2018 is that increased synergy expression is due to increased RST involvement, rather than reduced CST influence. However, McPherson et al. do not show separate increases/reductions in RST/CST activity; they show that contralesional activity relative to ipsilesional activity is increased (using a laterality index). While it does seem that RST is upregulated in this case, this does not exclude the possibility that CST influence is reduced as well.

      We also noticed that the citation itself, while mentioned in the text, was missing from the bibliography. This is now fixed.

      For Figure 9, McPherson is cited as they provide evidence for the idea that RST involvement increases when arm support is decreased. This evidence is both direct (e.g. in their Figure 3 where they show that “Stroke participants exhibited increased activity in the contralesional (R) hemisphere as SABD loading increased” [i.e. arm support was reduced]) and indirect: they connect synergies to RST involvement, and also show increased synergies with reduced arm support (also shown multiple times previously). Both these arguments suggest that arm support reduces RST involvement. We have clarified the relevant sentence:

      The interesting implication of this conceptual model is that synergies are in fact postural abnormalities that spill over into active movement when the CST can no longer modulate the increased RST activation that occurs when weight support is removed. Supporting this idea, McPherson et al. found increased ipsilateral activity (which primarily represents activation via the descending RST (Zaaimi et al., 2012)) when the paretic arm had reduced support compared to full support (McPherson et al., 2018).

      Reviewer #3 (Recommendations For The Authors):

      For Experiment 2, it is not immediately clear how the within-subject values are being pooled and compared across the different conditions. For instance, in the static perturbation trials, there are four blocks with 20 perturbation trials per block per arm (80 total per arm) with each location and direction once per block. For each participant, the comparison is between the location/direction that was most opposed (although this doesn't look accurately represented in Fig 7F). Therefore, the within-subject comparison is 4 trials per participant? Were these values averaged or pooled? It is a little odd that the SD for all the within-subjects trials are identical or nearly identical across conditions especially when looking at the example patient data in 7B and 7F.  

      Response 3.A.1. For static perturbation trials, the within-subject comparison involves 8 trials per participant: 4 trials corresponding to the perturbation direction/position combination with resting bias most opposed to the perturbation, and 4 trials corresponding to the perturbation direction/position combination with resting bias most aligned with the perturbation. These values were averaged for each individual. We have expanded our methods to make this part of our data analysis clear (lines 284-296) for all types of comparisons (unperturbed movement, pulse perturbation, static perturbations – now referred to as “release perturbation”).

      The across-subject SDs for the average resting forces for each one of these two conditions, shown in Figure 7F are indeed identical. This is due to how these two instances (most aligned vs. most resistive) were selected: because the perturbation directions come in pairs that exactly oppose each other (Figure 7B), if one were to select the position with the most opposing resting bias, that would mean that the combination with same position and the oppositely-directed perturbation would be the one with the most assistive resting bias. Hence the resting biases selected for the most opposing/assistive instances would be equal in magnitude and opposite to each other for each participant, as illustrated in Figure 7F, whereby the most-opposed bias for each individual is exactly opposite to the corresponding most-aligned bias for the same individual. We have added a brief commentary about this on the caption (lines 551-554), reproduced below:

      Note how the most-opposed resting bias for each patient is equal and opposite to the their mostaligned resting bias. This is because the same resting bias, when projected along the direction of two oppositely-directed perturbations (illustrated in C), it would oppose one with the same magnitude it would align with the other.

      Importantly, following suggestions by Reviewer 2 (see point 2.A.1), we now provide supplementary analyses that use the entirety of the relevant data, rather than the most extreme instances, which provide evidence supporting our main findings (Figures S5-2, S6-2, and S7-2).

      The printed colors in Figure 3 are very muddled and hard to read/interpret, especially in panel A. 

      Response 3.A.2. Thank you for pointing out this issue, also raised by Reviewer 1. We have adjusted the colors to be more distinct from each other and look clear both in print and on-screen, making use of dashed lines and stripes rather than different shades.

      I think it would improve readability and interpretation if Figure 8 and the results related to FM-UE were contained within the description of results for Experiment 1.

      Response 3.A.3. Thank you for this suggestion. This is actually a debate we had among ourselves earlier, and we can see merits to either ordering. It is very arguable that moving Figure 8 and the FMUE results within the rest of Experiment 1 may improve readability somewhat. However, we believe that presenting these results at the end better serves to illustrate the apparent paradox between the lack of direct connection between resting biases and active movement on one hand, and the relationship between resting biases and abnormal synergies on the other. We believe that this better sets the stage to present our conceptual model, which explains this paradox based on the role arm support plays in modulating the expression of both resting biases and abnormal synergies.

      Additional changes/corrections not outlined above

      Figure 1D displayed a right arm, but showed a target array (red dots) for a left arm paradigm. We now flip the target array shown for consistency.

      We corrected Figure 6C, which accidentally used an earlier definition of settling time which was based on lateral stabilization throughout the entire movement, rather focus on the period immediately following the pulse. The intended definition of settling time (as we had described in the Methods, lines 204-206 of original submission) focuses on lateral corrections specific to the pulse (rather than corrections when the participant approaches the endpoint) and better matches the one for settling time for the release (static) perturbation trials. Note that this change did not affect the (lack of) relationship between settling time and resting force bias, both across individuals (correlation plots now in Figure S6-1) and within individuals (now shown in the right part of panel 6D). Also in panel C, an error in the scaling for the maximum lateral deviation in the pulse direction (right side of the panel) is also now corrected.

      In addition, we made minor edits throughout the text to improve readability.

      References

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    1. eLife Assessment

      This study provides important insights into the regulation of a retained intron in the mRNA coding for OGT, a process known to be regulated by the O-GlcNAc cycling system, and highlights the functional role of the splicing regulator SFSWAP. The evidence supporting the claims of the authors is convincing: the authors performed an elegant state-of-the-art CRISPR knockout strategy and sophisticated bioinformatic analysis to identify SFSWAP as a negative regulator of alternative splicing. The work will be of interest to researchers in the fields of splicing and glycobiology.

    2. Reviewer #1 (Public review):

      Summary:

      Govindan and Conrad use a genome-wide CRISPR screen to identify genes regulating retention of intron 4 in OGT, leveraging an intron retention reporter system previously described (PMID: 35895270). Their OGT intron 4 reporter reliably responds to O-GlcNAc levels, mirroring the endogenous splicing event. Through a genome-wide CRISPR knockout library, they uncover a range of splicing-related genes, including multiple core spliceosome components, acting as negative regulators of OGT intron 4 retention. They choose to follow up on SFSWAP, a largely understudied splicing regulator shown to undergo rapid phosphorylation in response to O-GlcNAc level changes (PMID: 32329777). RNA-sequencing reveals that SFSWAP depletion not only promotes OGT intron 4 splicing but also broadly induces exon inclusion and intron splicing, affecting decoy exon usage. While this study offers interesting insights into intron retention and O-GlcNAc signaling regulation, the RNA sequencing experiments lack the essential controls needed to provide full confidence to the authors' conclusions.

      Strengths:

      (1) This study presents an elegant genetic screening approach to identify regulators of intron retention, uncovering core spliceosome genes as unexpected positive regulators of intron retention.

      (2) The work proposes a novel functional role for SFSWAP in splicing regulation, suggesting that it acts as a negative regulator of splicing and cassette exon inclusion, which contrasts with expected SR-related protein functions.

      (3) The authors suggest an intriguing model where SFSWAP, along with other spliceosome proteins, promotes intron retention by associating with decoy exons.

      Weaknesses:

      (1) The conclusions on SFSWAP impact on alternative splicing are based on cells treated with two pooled siRNAs for five days. This extended incubation time without independent siRNA treatments raises concerns about off-target effects and indirect effects from secondary gene expression changes, potentially limiting confidence in direct SFSWAP-dependent splicing regulation. Rescue experiments and shorter siRNA-treatment incubation times could address these issues.

      (2) The mechanistic role of SFSWAP in splicing would benefit from further exploration. Key questions remain, such as whether SFSWAP directly binds RNA, specifically the introns and exons (including the decoy exons) it appears to regulate. Furthermore, given that SFSWAP phosphorylation is influenced by changes in O-GlcNAc signaling, it would be interesting to investigate this relationship further. While generating specific phosphomutants may not yield definitive insights due to redundancy and also beyond the scope of the study, the authors could examine whether distinct SFSWAP domains, such as the SR and SURP domains, which likely overlap with phosphorylation sites, are necessary for regulating OGT intron 4 splicing.

      (3) Data presentation could be improved (specific suggestions are included in the recommendations section). Furthermore, Excel tables with gene expression and splicing analysis results should be provided as supplementary datasheets. Finally, a more detailed explanation of statistical analyses is necessary in certain sections.

    3. Reviewer #2 (Public review):

      Summary:

      The paper describes an effort to identify the factors responsible for intron retention and alternate exon splicing in a complex system known to be regulated by the O-GlcNAc cycling system. The CRISPR/Cas9 system was used to identify potential factors. The bioinformatic analysis is sophisticated and compelling. The conclusions are of general interest and advance the field significantly.

      Strengths:

      (1) Exhaustive analysis of potential splicing factors in an unbiased screen.

      (2) Extensive genome wide bioinformatic analysis.

      (3) Thoughtful discussion and literature survey.

      Weaknesses:

      (1) No firm evidence linking SFSWA to an O-GlcNAc specific mechanism.

      (2) Resulting model leaves many unanswered questions.

    4. Reviewer #3 (Public review):

      Summary:

      The major novel finding in this study is that SFSWAP, a splicing factor containing an RS domain but no canonical RNA binding domain, functions as a negative regulator of splicing. More specifically, it promotes retention of specific introns in a wide variety of transcripts including transcripts from the OGT gene previously studied by the Conrad lab. The balance between OGT intron retention and OGT complete splicing is an important regulator of O-GlcNAc expression levels in cells.

      Strengths:

      An elegant CRISPR knockout screen employed a GFP reporter, in which GFP is efficiently expressed only when the OGT retained intron is removed (so that the transcript will be exported from the nucleus to allow for translation of GFP). Factors whose CRISPR knockdown causes decreased intron retention therefore increase GFP, and can be identified by sequencing RNA of GFP-sorted cells. SFSWAP was thus convincingly identified as a negative regulator of OGT retained intron splicing. More focused studies of OGT intron retention indicate that it may function by regulating a decoy exon previously identified in the intron, and that this may extend to other transcripts with decoy exons.

      Weaknesses:

      The mechanism by which SFSWAP represses retained introns is unclear, although some data suggests it can operate (in OGT) at the level of a recently reported decoy exon within that intron. Interesting/appropriate speculation about possible mechanisms are provided and will likely be the subject of future studies.

      Overall the study is well done and carefully described but some figures and some experiments should be described in more detail.

    1. eLife Assessment

      This study provides useful findings about the effects of heterozygosity for Trio variants linked to neurodevelopmental and psychiatric disorders in mice. However, the strength of the evidence is limited and incomplete mainly because the experimental flow is difficult to follow, raising concerns about the conclusions' robustness. Clearer connections between variables, such as sex, age, behavior, brain regions, and synaptic measures, and more methodological detail on breeding strategies, test timelines, electrophysiology, and analysis, are needed to support their claims.

    2. Reviewer #1 (Public review):

      Summary:

      This study explores how heterozygosity for specific neurodevelopmental disorder-associated Trio variants affects mouse behavior, brain structure, and synaptic function, revealing distinct impacts on motor, social, and cognitive behaviors linked to clinical phenotypes. Findings demonstrate that Trio variants yield unique changes in synaptic plasticity and glutamate release, highlighting Trio's critical role in presynaptic function and the importance of examining variant heterozygosity in vivo.

      Strengths:

      This study generated multiple mouse lines to model each Trio variant, reflecting point mutations observed in human patients with developmental disorders. The authors employed various approaches to evaluate the resulting behavioral, neuronal morphology, synaptic function, and proteomic phenotypes.

      Weaknesses:

      While the authors present extensive results, the flow of experiments is challenging to follow, raising concerns about the strength of the experimental conclusions. Additionally, the connection between sex, age, behavioral data, brain regions, synaptic transmission, and plasticity lacks clarity, making it difficult to understand the rationale behind each experiment. Clearer explanations of the purpose and connections between experiments are recommended. Furthermore, the methodology requires more detail, particularly regarding mouse breeding strategies, timelines for behavioral tests, electrophysiology conditions, and data analysis procedures.

    3. Reviewer #2 (Public review):

      Summary:

      The authors generated three mouse lines harboring ASD, Schizophrenia, and Bipolar-associated variants in the TRIO gene. Anatomical, behavioral, physiological, and biochemical assays were deployed to compare and contrast the impact of these mutations in these animals. In this undertaking, the authors sought to identify and characterize the cellular and molecular mechanisms responsible for ASD, Schizophrenia, and Bipolar disorder development.

      Strengths:

      The establishment of TRIO dysfunction in the development of ASD, Schizophrenia, and Bipolar disorder is very recent and of great interest. Disorder-specific variants have been identified in the TRIO gene, and this study is the first to compare and contrast the impact of these variants in vivo in preclinical models. The impact of these mutations was carefully examined using an impressive host of methods. The authors achieved their goal of identifying behavioral, physiological, and molecular alterations that are disorder/variant specific. The impact of this work is extremely high given the growing appreciation of TRIO dysfunction in a large number of brain-related disorders. This work is very interesting in that it begins to identify the unique and subtle ways brain function is altered in ASD, Schizophrenia, and Bipolar disorder.

      Weaknesses:

      (1) Most assays were performed in older animals and perhaps only capture alterations that result from homeostatic changes resulting from prodromal pathology that may look very different.

      (2) Identification of upregulated (potentially compensating) genes in response to these disorder-specific Trio variants is extremely interesting. However, a functional demonstration of compensation is not provided.

      (3) There are instances where data is not shown in the manuscript. See "data not shown". All data collected should be provided even if significant differences are not observed.

      I consider weaknesses 1 and 2 minor. While they would very interesting to explore, these experiments might be more appropriate for a follow-up study. I would recommend that the missing data in 3 should be provided in the supplemental material.

    4. Author response:

      eLife Assessment

      This study provides useful findings about the effects of heterozygosity for Trio variants linked to neurodevelopmental and psychiatric disorders in mice. However, the strength of the evidence is limited and incomplete mainly because the experimental flow is difficult to follow, raising concerns about the conclusions' robustness. Clearer connections between variables, such as sex, age, behavior, brain regions, and synaptic measures, and more methodological detail on breeding strategies, test timelines, electrophysiology, and analysis, are needed to support their claims.

      We appreciate the opportunity to address the constructive feedback provided by eLife and the reviewers. Below, we respond to the overall assessment and individual reviewers' comments, clarifying our experimental approach, addressing concerns, and providing additional details where necessary.

      We thank the editors for highlighting the significance of our findings regarding the effects of Trio variant heterozygosity in mice. We acknowledge the feedback concerning the experimental flow and agree that clarity is paramount. To address these concerns:

      (1) Connections between variables: We will revise the manuscript to explicitly outline and extend explanations and the relationships between sex, age, behavior, brain regions, and synaptic measures, ensuring that the rationale for each experiment and its relevance to the overall conclusions are improved.

      (2) Methodological details: Our paper Methods section was formatted to be short with additional details provided in the Supplemental Methods section.  We will merge all into an extended section to improve clarity. We will also expand on our breeding strategies, test timelines, electrophysiological protocols, and data analysis methods in the revised Methods section. These additions aim to enhance the transparency and reproducibility of our study and to ensure full support of our conclusions.

      (3) Experimental flow: We will revise and extend our results, methods, and discussion sections to clarify the rationale and experimental design to guide readers through the experimental sequence and rationale.

      We are confident these revisions address the concerns raised and enhance the robustness and coherence of our findings.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This study explores how heterozygosity for specific neurodevelopmental disorder-associated Trio variants affects mouse behavior, brain structure, and synaptic function, revealing distinct impacts on motor, social, and cognitive behaviors linked to clinical phenotypes. Findings demonstrate that Trio variants yield unique changes in synaptic plasticity and glutamate release, highlighting Trio's critical role in presynaptic function and the importance of examining variant heterozygosity in vivo.

      Strengths:

      This study generated multiple mouse lines to model each Trio variant, reflecting point mutations observed in human patients with developmental disorders. The authors employed various approaches to evaluate the resulting behavioral, neuronal morphology, synaptic function, and proteomic phenotypes.

      Weaknesses:

      While the authors present extensive results, the flow of experiments is challenging to follow, raising concerns about the strength of the experimental conclusions. Additionally, the connection between sex, age, behavioral data, brain regions, synaptic transmission, and plasticity lacks clarity, making it difficult to understand the rationale behind each experiment. Clearer explanations of the purpose and connections between experiments are recommended. Furthermore, the methodology requires more detail, particularly regarding mouse breeding strategies, timelines for behavioral tests, electrophysiology conditions, and data analysis procedures.

      We appreciate the reviewer’s recognition of the novelty and comprehensiveness of our approach, particularly the generation of multiple mouse lines and our efforts to model Trio variant effects in vivo.

      Weaknesses

      (1) Experimental flow and rationale and connection between variables: We will expand on the connections between behavioral data, neuronal morphology, synaptic function, and proteomics in the Results and Discussion sections to clarify how each experiment informs the reasoning and the conclusions and to highlight the relationships between sex, age, behavior, and synaptic measures.

      (2) Methodological details: Our paper Methods section was formatted to be short to fulfill word limits on the submitted version, with additional details provided in the Supplemental Methods section. We will merge our Methods and Supplemental Methods sections and expand on our breeding strategies, test timelines, electrophysiological protocols, and data analysis methods in the revised Methods section.  These additions aim to enhance the transparency and reproducibility of our study and to ensure full support of our conclusions.

      Reviewer #2 (Public review):

      Summary:

      The authors generated three mouse lines harboring ASD, Schizophrenia, and Bipolar-associated variants in the TRIO gene. Anatomical, behavioral, physiological, and biochemical assays were deployed to compare and contrast the impact of these mutations in these animals. In this undertaking, the authors sought to identify and characterize the cellular and molecular mechanisms responsible for ASD, Schizophrenia, and Bipolar disorder development.

      Strengths:

      The establishment of TRIO dysfunction in the development of ASD, Schizophrenia, and Bipolar disorder is very recent and of great interest. Disorder-specific variants have been identified in the TRIO gene, and this study is the first to compare and contrast the impact of these variants in vivo in preclinical models. The impact of these mutations was carefully examined using an impressive host of methods. The authors achieved their goal of identifying behavioral, physiological, and molecular alterations that are disorder/variant specific. The impact of this work is extremely high given the growing appreciation of TRIO dysfunction in a large number of brain-related disorders. This work is very interesting in that it begins to identify the unique and subtle ways brain function is altered in ASD, Schizophrenia, and Bipolar disorder.

      Weaknesses:

      (1) Most assays were performed in older animals and perhaps only capture alterations that result from homeostatic changes resulting from prodromal pathology that may look very different.

      (2) Identification of upregulated (potentially compensating) genes in response to these disorder-specific Trio variants is extremely interesting. However, a functional demonstration of compensation is not provided.

      (3) There are instances where data is not shown in the manuscript. See "data not shown". All data collected should be provided even if significant differences are not observed.

      I consider weaknesses 1 and 2 minor. While they would very interesting to explore, these experiments might be more appropriate for a follow-up study. I would recommend that the missing data in 3 should be provided in the supplemental material.

      We are grateful for the reviewer’s recognition of our study’s significance and methodological rigor. The acknowledgment of Trio dysfunction as a novel and impactful area of research is deeply appreciated.

      Weaknesses: 

      We agree that focusing on older animals may limit insights into early-stage pathophysiology. However, given the goal of this study was to examine the functional impacts of Trio heterozygosity at an adolescent stage and to reveal the ultimate impact of these alleles on synaptic function, we believe the choice of animal age aligns with our objectives. We agree that future studies of earlier developmental stages will be beneficial and complement these findings.

      Functional compensation: In this study, we tested functional compensation through rescue experiments in +/K1431M brain slices using a Rac1-specific inhibitor, NSC, which prevents its activation by Trio or Tiam1. Our findings strongly suggest that increased Rac1 activity, attributed to the proposed compensation, drives the deficiency in neurotransmitter release. Furthermore, this deficiency can be normalized by direct Rac1 inhibition.

      Data not shown: We will incorporate all previously shown data into the Supplemental Materials, even when results are nonsignificant. We agree that this ensures full transparency and facilitates a more comprehensive evaluation of our findings.

    1. eLife Assessment

      This study investigates the fundamental role of polyunsaturated fatty acids (PUFAs) in membrane biology, using a unique model to perform a thorough genetic screen that highlights that PUFA synthesis defects cannot be compensated for by mutations in other pathways. While the data are solid and generally support the claims, additional experimental validation or more detailed descriptions of their results would strengthen the broader conclusions. This study will appeal to researchers in membrane biology, lipid metabolism, and C. elegans genetics.

    2. Reviewer #1 (Public review):

      Summary:<br /> This study addresses the roles of polyunsaturated fatty acids (PUFAs) in animal physiology and membrane function. A C. elegans strain carrying the fat-2(wa17) mutation possess a very limited ability to synthesize PUFAs and there is no dietary input because the E. coli diet consumed by lab grown C. elegans does not contain any PUFAs. The fat-2 mutant strain was characterized to confirm that the worms grow slowly, have rigid membranes, and have a constitutive mitochondrial stress response. The authors showed that chemical treatments or mutations known to increase membrane fluidity did not rescue growth defects. A thorough genetic screen was performed to identify genetic changes to compensate for the lack of PUFAs. The newly isolated suppressor mutations that compensated for FAT-2 growth defects included intergenic suppressors in the fat-2 gene, as well as constitutive mutations in the hypoxia sensing pathway components EGL-9 and HIF-1, and loss of function mutations in ftn-2, a gene encoding the iron storage protein ferritin. Taken together, these mutations lead to the model that increased intracellular iron, an essential cofactor for fatty acid desaturases, allows the minimally functional FAT-2(wa17) enzyme to be more active, resulting in increased desaturation and increased PUFA synthesis.

      Strengths:<br /> (1) This study provides new information further characterizing fat-2 mutants. The authors measured increased rigidity of membranes compared to wild type worms, however this rigidity is not able to be rescued with other fluidity treatments such as detergent or mutants. Rescue was only achieved with polyunsaturated fatty acid supplementation.<br /> (2) A very thorough genetic suppressor screen was performed. In addition to some internal fat-2 compensatory mutations, the only changes in pathways identified that are capable of compensating for deficient PUFA synthesis was the hypoxia pathway and the iron storage protein ferritin. Suppressor mutations included an egl-9 mutation that constitutively activates HIF-1, and Gain of function mutations in hif-1 that are dominant. This increased activity of HIF conferred by specific egl-9 and hif-1 mutations lead to decreased expression of ftn-2. Indeed, loss of ftn-2 leads to higher intracellular iron. The increased iron apparently makes the FAT-2 fatty acid desaturase enzyme more active, allowing for the production of more PUFAs.<br /> (3) The mutations isolated in the suppressor screen show that the only mutations able to compensate for lack of PUFAs were ones that increased PUFA synthesis by the defective FAT-2 desaturase, thus demonstrating the essential need for PUFAs that cannot be overcome by changes in other pathways. This is a very novel study, taking advantage of genetic analysis of C. elegans, and it confirms the observations in humans that certain essential PUFAs are required for growth and development.<br /> (4) Overall, the paper is well written, and the experiments were carried out carefully and thoroughly. The conclusions are well supported by the results.

      Weaknesses:<br /> Overall, there are not many weaknesses. The main one I noticed is that the lipidomic analysis shown in Figs 3C, 7C, S1 and S3. Whie these data are an essential part of the analysis and provide strong evidence for the conclusions of the study, it is unfortunate that the methods used did not enable the distinction between two 18:1 isomers. These two isomers of 18:1 are important in C. elegans biology, because one is a substrate for FAT-2 (18:1n-9, oleic acid) and the other is not (18:1n-7, cis vaccenic acid). Although rarer in mammals, cis-vaccenic acid is the most abundant fatty acid in C. elegans and is likely the most important structural MUFA. The measurement of these two isomers is not essential for the conclusions of the study, but the manuscript should include a comment about the abundance of oleic vs vaccenic acid in C. elegans (authors can find this information, even in the fat-2 mutant, in other publications of C. elegans fatty acid composition). Otherwise, readers who are not familiar with C. elegans might assume the 18:1 that is reported is likely to be mainly oleic acid, as is common in mammals.

      Other suggestions to authors to improve the paper:<br /> (1) The title could be less specific; it might be confusing to readers to include the allele name in the title.<br /> (2) There are two errors in the pathway depicted in Figure 1A. The16:0-16:1 desaturation can be performed by FAT-5, FAT-6, and FAT-7. The 18:0-18:1 desaturation can only be performed by FAT-6 and FAT-7

    3. Reviewer #2 (Public review):

      Summary:<br /> The authors use a genetic screen in C. elegans to investigate the physiological roles of polyunsaturated fatty acids (PUFAs). They screen for mutations that rescue fat-2 mutants, which have strong reductions in PUFAs. As a result, either mutations in fat-2 itself, or mutations in genes involved in the HIF-1 pathway, were found to rescue fat-2 mutants.

      Strengths:<br /> As C. elegans can produce PUFAs de novo as essential lipids, the genetic model is well suited to study the fundamental roles of PUFAs, and the results are very interesting. The genetic screen finds mutations in convergent pathways, suggesting that it has reached near-saturation. The link between the HIF-1 pathway and lipid unsaturation is very interesting. As many of the mutations found to rescue fat-2 mutants are of gain-of-function, it is unlikely that similar discoveries could have been made with other approaches like genome-wide CRISPR screenings, making the current study distinctive.

      Weaknesses:<br /> The authors make very important statements, but some are not sufficiently supported by data. In page 5, they conclude that membrane rigidity is a minor cause of fat-2 mutant defects, which is a relevant observation regarding why PUFAs are important. However, they use treatments that have rescued fluidity in another mutant (paqr-2), but do not test if they have the same fluidifying effects in fat-2 mutants.

      The screening results seem to converge into the HIF-1 pathway, which is hypothetically correct according to the literature. However, the authors do not validate this hypothesis, which is a critical limitation, especially because many of the mutations they obtained seem to be of gain-of-function. Therefore, without experimental testing, it cannot be concluded that the mutations have the expected effect on the HIF-1 pathway.

      In some of the mutants, the rescues in lipid compositions seem to be weak, and it is arguable whether phenotypic rescues are really via a restoration in lipid compositions.

      The hypothesis linking iron homeostasis and the rescue of fat-2 mutants is interesting, but the data of rescue by iron repletion seem to be against it. The results might be due to the inefficiency in iron repletion, as the authors suggest, but this has not been formally addressed.

      Therefore, the authors propose multiple very interesting and important hypotheses, but experimental validations remain limited.

    4. Author response:

      We thank the editors at eLife and the reviewers for the care with which our mansucript has been reviewed and the constructive feedback that we have received. Both reviewers viewed the manuscript positively and in particular praised the merits of the forward genetic screen that led to the discovery of a new link between the HIF-1 pathway and fatty acid desaturation.

      We agree with all points by Reviewer #1. We will modify our manuscript to clarify that two types of C18:1 fatty acids are present in our lipidomics, and that the majority is likely vaccenic acid that is not a FAT-2 substrate. The title will be modified and Fig. 1A corrected.

      All points raised by Reviewer #2 are also valid and we will try to address most of them experimentally, though not always as suggested. In particular, we plan to use FRAP to verify that membrane-fluidizing treatments are effective in the fat-2 mutant. We also plan to use qPCR to test whether the novel egl-9(lof) and hif-1(gof) alleles lead to the expected downregulation of ftn-2. We note that the pathway connecting EGL-9, HIF-1 and FTN-2 is well supported by published work and that the alleles isolated in our screen are consistent with it, with the addition that FAT-2 is likely a regulated outcome of FTN-2 inhibition/mutation. We also plan to monitor FAT-2 protein levels using Western blots and thus provide more clarity about the mechanism of action of the novel fat-2(wa17) suppressors. The manuscript will be modified to tone down interpretations not directly supported by experiments.

    1. eLife Assessment

      This paper provides a valuable contribution to our understanding of how adenosine acts as a signal of nutrient insufficiency and extends this idea to suggest that adenosine is released by metabolically active cells in proportion to the activity of methylation events. Convincing data support this idea. The authors use metabolic tracing approaches to identify the biochemical pathways that contribute to the regulation of adenosine levels and the S-adenosylmethionine cycle in Drosophila larval hemocytes in response to wasp egg infection.

    2. Reviewer #1 (Public review):

      Summary:

      In this article, Nedbalova et al. investigate the biochemical pathway that acts in circulating immune cells to generate adenosine, a systemic signal that directs nutrients toward the immune response, and S-adenosylmethionine (SAM), a methyl donor for lipid, DNA, RNA, and protein synthetic reactions. They find that SAM is largely generated through the uptake of extracellular methionine, but that recycling of adenosine to form ATP contributes a small but important quantity of SAM in immune cells during the immune response. The authors propose that adenosine serves as a sensor of cell activity and nutrient supply, with adenosine secretion dominating in response to increased cellular activity. Their findings of impaired immune action but rescued larval developmental delay when the enzyme Ahcy is knocked down in hemocytes are interpreted as due to effects on methylation processes in hemocytes and reduced production of adenosine to regulate systemic metabolism and development, respectively. Overall this is a strong paper that uses sophisticated metabolic techniques to map the biochemical regulation of an important systemic mediator, highlighting the importance of maintaining appropriate metabolite levels in driving immune cell biology.

      Strengths:

      The authors deploy metabolic tracing - no easy feat in Drosophila hemocytes - to assess flux into pools of the SAM cycle. This is complemented by mass spectrometry analysis of total levels of SAM cycle metabolites to provide a clear picture of this metabolic pathway in resting and activated immune cells.

      The experiments show that the recycling of adenosine to ATP, and ultimately SAM, contributes meaningfully to the ability of immune cells to control infection with wasp eggs.

      This is a well-written paper, with very nice figures showing metabolic pathways under investigation. In particular, the italicized annotations, for example, "must be kept low", in Figure 1 illustrate a key point in metabolism - that cells must control levels of various intermediates to keep metabolic pathways moving in a beneficial direction.

      Experiments are conducted and controlled well, reagents are tested, and findings are robust and support most of the authors' claims.

      Weaknesses:

      The authors posit that adenosine acts as a sensor of cellular activity, with increased release indicating active cellular metabolism and insufficient nutrient supply. It is unclear how generalizable they think this may be across different cell types or organs.

      The authors extrapolate the findings in Figure 3 of decreased extracellular adenosine in ex vivo cultures of hemocytes with knockdown of Ahcy (panel B) to the in vivo findings of a rescue of larval developmental delay in wasp egg-infected larvae with hemocyte-specific Ahcy RNAi (panel C). This conclusion (discussed in lines 545-547) should be somewhat tempered, as a number of additional metabolic abnormalities characterize Ahcy-knockdown hemocytes, and the in vivo situation may not mimic the ex vivo situation. If adenosine (or inosine) measurements were possible in hemolymph, this would help bolster this idea. However, adenosine at least has a very short half-life.

    3. Reviewer #2 (Public review):

      Summary:

      In this work, the authors wish to explore the metabolic support mechanisms enabling lamellocyte encapsulation, a critical antiparasitic immune response of insects. They show that S-adenosylmethionine metabolism is specifically important in this process through a combination of measurements of metabolite levels and genetic manipulations of this metabolic process.

      Strengths:

      The metabolite measurements and the functional analyses are generally very strong and clearly show that the metabolic process under study is important in lamellocyte immune function.

      Weaknesses:

      The gene expression data are a potential weakness. Not enough is explained about how the RNAseq experiments in Figures 2 and 4 were done, and the representation of the data is unclear. The paper would also be strengthened by the inclusion of some measure of encapsulation effectiveness: the authors show that manipulation of the S-adenosylmethionine pathway in lamellocytes affects the ability of the host to survive infection, but they do not show direct effects on the ability of the host to encapsulate wasp eggs.

    4. Reviewer #3 (Public review):

      Summary:

      The authors of this study provide evidence that Drosophila immune cells show upregulated SAM transmethylation pathway and adenosine recycling upon wasp infection. Blocking this pathway compromises the lamellocyte formation, developmental delay, and host survival, suggesting its physiological relevance.

      Strengths:

      Snapshot quantification of the metabolite pool does not provide evidence that the metabolic pathway is active or not. The authors use an ex vivo isotope labelling to precisely monitor the SAM and adenosine metabolism. During infection, the methionine metabolism and adenosine recycling are upregulated, which is necessary to support the immune reaction. By combining the genetic experiment, they successfully show that the pathway is activated in immune cells.

      Weaknesses:

      The authors knocked down Ahcy to prove the importance of SAM methylation pathway. However, Ahcy-RNAi produces a massive accumulation of SAH, in addition to blocking adenosine production. To further validate the phenotypic causality, it is necessary to manipulate other enzymes in the pathway, such as Sam-S, Cbs, SamDC, etc. The authors do not demonstrate how infection stimulates the metabolic pathway given the gene expression of metabolic enzymes is not upregulated by infection stimulus.

    5. Author response:

      We would like to thank the editors and reviewers for reviewing our work, for finding it valuable supported by convincing data, which we greatly appreciate, but also for identifying the weaknesses of the manuscript. We plan to address these weaknesses in the revised version, briefly as follows:

      (1) In the Discussion, we will elaborate more on a possible generalization of our results, while being aware of the limited space in this experimental paper and therefore intend to address this in more detail and comprehensively in a subsequent perspective article.

      (2) In the Discussion, we will more clearly address the limitations of our work, in particular the difference between the measurement of extracellular adenosine production ex vivo and the actual production in vivo, where the measurement is indeed very challenging, and also the limitations of manipulating the SAM pathway only at the Ahcy level.

      (3) We will describe in detail and complement the supplementary RNAseq data. The RNAseq data have already been described in detail in our previous paper (doi.org/10.1371/journal.pbio.3002299), but we agree with the reviewers that we should describe the necessary details again here.

      (4) We will fill in the missing data on encapsulation efficiency; we agree that it was unfortunate to omit them.

      (5) We will supplement the data with methyltransferase expressions and better describe the changes in expression of some SAM pathway genes, which, especially with methyltransferase expressions, also support stimulation of this pathway by changes in expression. Although the goal of this work was to test by 13C-labeling whether SAM pathway activity is upregulated, not to analyze how the activity is regulated, we certainly agree that an explanation of possible regulation, especially in the context of the enzyme expressions we show, should be included in our work.

    1. eLife Assessment

      This valuable study investigates the neural basis of causal inference of illness, suggesting that it relies on semantic networks specific to living things in the absence of a generalized representation of causal inference across domains. However, the evidence remains incomplete due to some unjustified design and analysis choices. Moreover, the authors do not fully exploit the potential of multivariate fMRI analyses to rigorously test their main hypothesis.

    2. Reviewer #1 (Public review):

      Summary:

      In this study, the authors aim to understand the neural basis of implicit causal inference, specifically how people infer causes of illness. They use fMRI to explore whether these inferences rely on content-specific semantic networks or broader, domain-general neurocognitive mechanisms. The study explores two key hypotheses: first, that causal inferences about illness rely on semantic networks specific to living things, such as the 'animacy network,' given that illnesses affect only animate beings; and second, that there might be a common brain network supporting causal inferences across various domains, including illness, mental states, and mechanical failures. By examining these hypotheses, the authors aim to determine whether causal inferences are supported by specialized or generalized neural systems.

      The authors observed that inferring illness causes selectively engaged a portion of the precuneus (PC) associated with the semantic representation of animate entities, such as people and animals. They found no cortical areas that responded to causal inferences across different domains, including illness and mechanical failures. Based on these findings, the authors concluded that implicit causal inferences are supported by content-specific semantic networks, rather than a domain-general neural system, indicating that the neural basis of causal inference is closely tied to the semantic representation of the specific content involved.

      Strengths:

      (1) The inclusion of the four conditions in the design is well thought out, allowing for the examination of the unique contribution of causal inference of illness compared to either a different type of causal inference (mechanical) or non-causal conditions. This design also has the potential to identify regions involved in a shared representation of inference across general domains.

      (2) The presence of the three localizers for language, logic, and mentalizing, along with the selection of specific regions of interest (ROIs), such as the precuneus and anterior ventral occipitotemporal cortex (antVOTC), is a strong feature that supports a hypothesis-driven approach (although see below for a critical point related to the ROI selection).

      (3) The univariate analysis pipeline is solid and well-developed.

      (4) The statistical analyses are a particularly strong aspect of the paper.

      Weaknesses:

      Based on the current analyses, it is not yet possible to rule out the hypothesis that inferring illness causes relies on neurocognitive mechanisms that support causal inferences irrespective of their content, neither in the precuneus nor in other parts of the brain.

      (1) The authors, particularly in the multivariate analyses, do not thoroughly examine the similarity between the two conditions (illness-causal and mechanical-causal), as they are more focused on highlighting the differences between them. For instance, in the searchlight MVPA analysis, an interesting decoding analysis is conducted to identify brain regions that represent illness-causal and mechanical-causal conditions differently, yielding results consistent with the univariate analyses. However, to test for the presence of a shared network, the authors only perform the Causal vs. Non-causal analysis. This analysis is not very informative because it includes all conditions mixed together and does not clarify whether both the illness-causal and mechanical-causal conditions contribute to these results.

      (2) To address this limitation, a useful additional step would be to use as ROIs the different regions that emerged in the Causal vs. Non-causal decoding analysis and to conduct four separate decoding analyses within these specific clusters:<br /> (a) Illness-Causal vs. Non-causal - Illness First;<br /> (b) Illness-Causal vs. Non-causal - Mechanical First;<br /> (c) Mechanical-Causal vs. Non-causal - Illness First;<br /> (d) Mechanical-Causal vs. Non-causal - Mechanical First.<br /> This approach would allow the authors to determine whether any of these ROIs can decode both the illness-causal and mechanical-causal conditions against at least one non-causal condition.

      (3) Another possible analysis to investigate the existence of a shared network would be to run the searchlight analysis for the mechanical-causal condition versus the two non-causal conditions, as was done for the illness-causal versus non-causal conditions, and then examine the conjunction between the two. Specifically, the goal would be to identify ROIs that show significant decoding accuracy in both analyses.

      (4) Along the same lines, for the ROI MVPA analysis, it would be useful not only to include the illness-causal vs. mechanical-causal decoding but also to examine the illness-causal vs. non-causal conditions and the mechanical-causal vs. non-causal conditions. Additionally, it would be beneficial to report these data not just in a table (where only the mean accuracy is shown) but also using dot plots, allowing the readers to see not only the mean values but also the accuracy for each individual subject.

      (5) The selection of Regions of Interest (ROIs) is not entirely straightforward:<br /> In the introduction, the authors mention that recent literature identifies the precuneus (PC) as a region that responds preferentially to images and words related to living things across various tasks. While this may be accurate, we can all agree that other regions within the ventral occipital-temporal cortex also exhibit such preferences, particularly areas like the fusiform face area, the occipital face area, and the extrastriate body area. I believe that at least some parts of this network (e.g., the fusiform gyrus) should be included as ROIs in this study. This inclusion would make sense, especially because a complementary portion of the ventral stream known to prefer non-living items (i.e., anterior medial VOTC) has been selected as a control ROI to process information about the mechanical-causal condition. Given the main hypothesis of the study - that causal inferences about illness might depend on content-specific semantic representations in the 'animacy network' - it would be worthwhile to investigate these ROIs alongside the precuneus, as they may also yield interesting results.

      (6) Visual representation of results:<br /> In all the figures related to ROI analyses, only mean group values are reported (e.g., Figure 1A, Figure 3, Figure 4A, Supplementary Figure 6, Figure 7, Figure 8). To better capture the complexity of fMRI data and provide readers with a more comprehensive view of the results, it would be beneficial to include a dot plot for a specific time point in each graph. This could be a fixed time point (e.g., a certain number of seconds after stimulus presentation) or the time point showing the maximum difference between the conditions of interest. Adding this would allow for a clearer understanding of how the effect is distributed across the full sample, such as whether it is consistently present in every subject or if there is greater variability across individuals.

      (7) Task selection:<br /> (a) To improve the clarity of the paper, it would be helpful to explain the rationale behind the choice of the selected task, specifically addressing: (i) why an implicit inference task was chosen instead of an explicit inference task, and (ii) why the "magic detection" task was used, as it might shift participants' attention more towards coherence, surprise, or unexpected elements rather than the inference process itself.<br /> (b) Additionally, the choice to include a large number of catch trials is unusual, especially since they are modeled as regressors of non-interest in the GLM. It would be beneficial to provide an explanation for this decision.

    3. Reviewer #2 (Public review):

      Summary:

      In this study, the authors hypothesize that "causal inferences about illness depend on content-specific semantic representations in the animacy network". They test this hypothesis in an fMRI task, by comparing brain activity elicited by participants' exposure to written situations suggesting a plausible cause of illness with brain activity in linguistically equivalent situations suggesting a plausible cause of mechanical failure or damage and non-causal situations. These contrasts identify PC as the main "culprit" in a whole-brain univariate analysis. Then the question arises of whether the content-specificity has to do with inferences about animates in general, or if there are some distinctions between reasoning about people's bodies versus mental states. To answer this question, the authors localize the mentalizing network and study the relation between brain activity elicited by Illness-Causal > Mech-Causal and Mentalizing > Physical stories. They conclude that inferring about the causes of illness partially differentiates from reasoning about people's states of mind. The authors finally test the alternative yet non-mutually exclusive hypothesis that both types of causal inferences (illness and mechanical) depend on shared neural machinery. Good candidates are language and logic, which justifies the use of a language/logic localizer. No evidence of commonalities across causal inferences versus non-causal situations is found.

      Strengths:

      (1) This study introduces a useful paradigm and well-designed set of stimuli to test for implicit causal inferences.

      (2) Another important methodological advance is the addition of physical stories to the original mentalizing protocol.

      (3) With these tools, or a variant of these tools, this study has the potential to pave the way for further investigation of naïve biology and causal inference.

      Weaknesses:

      (1) This study is missing a big-picture question. It is not clear whether the authors investigate the neural correlates of causal reasoning or of naïve biology. If the former, the choice of an orthogonal task, making causal reasoning implicit, is questionable. If the latter, the choice of mechanical and physical controls can be seen as reductive and problematic.

      (2) The rationale for focusing mostly on the precuneus is not clear and this choice could almost be seen as a post-hoc hypothesis.

      (3) The choice of an orthogonal 'magic detection' task has three problematic consequences in this study:<br /> (a) It differs in nature from the 'mentalizing' task that consists of evaluating a character's beliefs explicitly from the corresponding story, which complicates the study of the relation between both tasks. While the authors do not compare both tasks directly, it is unclear to what extent this intrinsic difference between implicit versus explicit judgments of people's body versus mental states could influence the results.<br /> (b) The extent to which the failure to find shared neural machinery between both types of inferences (illness and mechanical) can be attributed to the implicit character of the task is not clear.<br /> (c) The introduction of a category of non-interest that contains only 36 trials compared to 38 trials for all four categories of interest creates a design imbalance.

      (4) Another imbalance is present in the design of this study: the number of trials per category is not the same in each run of the main task. This imbalance does not seem to be accounted for in the 1st-level GLM and renders a bit problematic the subsequent use of MVPA.

      (5) The main claim of the authors, encapsulated by the title of the present manuscript, is not tested directly. While the authors included in their protocol independent localizers for mentalizing, language, and logic, they did not include an independent localizer for "animacy". As such, they cannot provide a within-subject evaluation of their claim, which is entirely based on the presence of a partial overlap in PC (which is also involved in a wide range of tasks) with previous results on animacy.

    4. Reviewer #3 (Public review):

      Summary:

      This study employed an implicit task, showing vignettes to participants while a bold signal was acquired. The aim was to capture automatic causal inferences that emerge during language processing and comprehension. In particular, the authors compared causal inferences about illness with two control conditions, causal inferences about mechanical failures and non-causal phrases related to illnesses. All phrases that were employed described contexts with people, to avoid animacy/inanimate confound in the results. The authors had a specific hypothesis concerning the role of the precuneus (PC) in being sensitive to causal inferences about illnesses.

      These findings indicate that implicit causal inferences are facilitated by semantic networks specialized for encoding causal knowledge.

      Strengths:

      The major strength of the study is the clever design of the stimuli (which are nicely matched for a number of features) which can tease apart the role of the type of causal inference (illness-causal or mechanical-causal) and the use of two localizers (logic/language and mentalizing) to investigate the hypothesis that the language and/or logical reasoning networks preferentially respond to causal inference regardless of the content domain being tested (illnesses or mechanical).

      Weaknesses:

      I have identified the following main weaknesses:

      (1) Precuneus (PC) and Temporo-Parietal junction (TPJ) show very similar patterns of results, and the manuscript is mostly focused on PC (also the abstract). To what extent does the fact that PC and TPJ show similar trends affect the inferences we can derive from the results of the paper? I wonder whether additional analyses (connectivity?) would help provide information about this network.

      (2) Results are mainly supported by an univariate ROI approach, and the MVPA ROI approach is performed on a subregion of one of the ROI regions (left precuneus). Results could then have a limited impact on our understanding of brain functioning.

      (3) In all figures: there are no measures of dispersion of the data across participants. The reader can only see aggregated (mean) data. E.g., percentage signal changes (PSC) do not report measures of dispersion of the data, nor do we have bold maps showing the overlap of the response across participants. Only in Figure 2, we see the data of 6 selected participants out of 20.

      (4) Sometimes acronyms are defined in the text after they appear for the first time.

    5. Author response:

      We thank the editors and reviewers for their comments on our manuscript. We found the comments of the reviewers helpful and plan to add new text, analyses, and figures to answer some of the outstanding questions.

      In response to the reviewers’ comments, we will clarify the goal of the paper in the introduction: to test the hypothesis that causal knowledge (i.e., an intuitive theory of biology) is embedded in domain-preferring semantic networks (i.e., semantic animacy network). This work links developmental psychology work on intuitive theories and cognitive neuroscience.

      As we will emphasize in the revised manuscript, the primary goal of the current paper is to test the claim that semantic networks encode causal knowledge, rather than to rule out the contribution of domain-general reasoning mechanisms to causal inference.

      In response to the reviewers’ suggestions, we will add multivariate and univariate whole-cortex analyses that provide further tests for domain-general causality responses. In particular, we will include new figures showing univariate responses to the mechanical inference condition over the non-causal control conditions as well as decoding between these conditions. The reviewers have also asked us to provide individual subject dispersion data. We appreciate this suggestion, and new figures will be added to display this information.

      We will also perform additional analysis in the precuneus (PC) to look for shared responses to illness and mechanical inferences. In accordance with our hypotheses, we have shown that the PC responds preferentially to illness inferences. To address the reviewers’ concerns about the selectivity of the PC to illness inferences, we will compare responses to i) illness inferences compared to the noncausal conditions and ii) mechanical inferences compared to the noncausal conditions in the PC to investigate the extent to which a shared response to causal inference across domains emerges in this region.

      Critically, we find that the cortical areas that distinguish between causal and non-causal conditions in a ‘domain general manner’ (i.e., for both illness and mechanical inferences) are driven by higher responses to the non-causal condition. Moreover, these responses in prefrontal cortex and elsewhere overlap an RT predictor of neural activity, suggesting that they may reflect difficulty effects.

      These results suggest that in the current task, signatures of causal inference are primarily found in domain-preferring semantic networks, rather than in domain-general fronto-parietal reasoning systems. We will provide additional discussion of the argument that the current results do not speak against the role of domain general systems across all types of causal reasoning. Instead, they suggest that the types of implicit causal inferences measured in the current study depend primarily on domain-preferring semantic networks.

      The reviewers have asked us to analyze responses to causal inferences about illness in the fusiform face area (FFA). We will perform this analysis. However, we note that univariate and multivariate whole-cortex analyses that are already included in the paper did not identify lateral ventral occipito-temporal cortex as a key region involved in causal inferences about illness. Further, we do not have FFA localizer data in the current participants; therefore, the results cannot be interpreted to reflect activity in functionally defined FFA.

      Two reviewers asked us to justify our choice of an implicit magic-detection task, which we will now do more clearly in the manuscript. This task was selected to ensure that participants were attending to the meaning of the vignettes. The goal of the current study was to investigate implicit causal inferences that routinely occur in language comprehension, e.g., when someone is reading a book. Past work has shown that explicitly judging the causality of causal and non-causal stimuli results in differences in response times across conditions (e.g., Kuperberg et al., 2006). In the current study, such judgments would also have introduced a confound between the behavioral decision and the condition of interest: the use of an explicit causal judgment task makes it impossible to know whether any observed neural differences between causal and non-causal conditions are simply due to differences in the selection of task responses. The selection of an orthogonal magic-detection task limits these confounds from complicating our interpretation of the neural data.

      One of the reviewers asked us to justify the number of catch trials that we decided to include in our paradigm. Approximately 20% of the vignettes were “magical” vignettes (the same proportion as each of the 4 experimental conditions) to encourage participants to remain attentive throughout the task. Since these catch trials are excluded from analysis, their proportion is unlikely to influence the results of the study. We will clarify this in the manuscript.

      A question was raised about the balance of trial numbers across conditions and across runs. To address this, we will include individual comparisons of each causal condition (n=36) with each non-causal condition (n=36; i.e., equal trial counts) where they are not already shown. With regard to runs, each condition is shown either 6 or 7 times per run (maximum difference of 1 trial between conditions), and the number of trials per condition is equal across the whole experiment: each condition is shown 7 times in two of the runs and 6 times four of the runs. This minor design imbalance is typical of fMRI experiments and is unlikely to impact the results. We will clarify this in the manuscript.

      We believe that our planned revisions will strengthen the paper and highlight its contributions to our understanding of the neural basis of implicit causal inference.

    1. eLife Assessment

      The authors examine the effect of cell-free chromatin particles (cfChPs) derived from human serum or from dying human cells on mouse cells in culture and propose that these cfChPs can serve as vehicles for cell-to-cell active transfer of foreign genetic elements. The work presented in this paper is intriguing and potentially important, but it is incomplete. At this stage, the claim that horizontal gene transfer can occur via cfChPs would strongly benefit from additional evidence emerging from multiple independent approaches. The evolutionary interpretations associated with the concept of "predatory genome" are premature based on the strength of evidence.

    2. Reviewer #1 (Public review):

      Summary:

      Horizontal gene transfer is the transmission of genetic material between organisms through ways other than reproduction. Frequent in prokaryotes, this mode of genetic exchange is scarcer in eukaryotes, especially in multicellular eukaryotes. Furthermore, the mechanisms involved in eukaryotic HGT are unknown. This article by Banerjee et al. claims that HGT occurs massively between cells of multicellular organisms. According to this study, the cell free chromatin particles (cfChPs) that are massively released by dying cells are incorporated in the nucleus of neighboring cells. These cfChPs are frequently rearranged and amplified to form concatemers, they are made of open chromatin, expressed, and capable of producing proteins. Furthermore, the study also suggests that cfChPs transmit transposable elements (TEs) between cells on a regular basis, and that these TEs can transpose, multiply, and invade receiving cells. These conclusions are based on a series of experiments consisting in releasing cfChPs isolated from various human sera into the culture medium of mouse cells, and using FISH and immunofluorescence to monitor the state and fate of cfChPs after several passages of the mouse cell line.

      Strengths:

      The results presented in this study are interesting because they may reveal unsuspected properties of some cell types that may be able to internalize free-circulating chromatin, leading to its chromosomal incorporation, expression, and unleashing of TEs. The authors propose that this phenomenon may have profound impacts in terms of diseases and genome evolution. They even suggest that this could occur in germ cells, leading to within-organism HGT with long-term consequences.

      Weaknesses:

      The claims of massive HGT between cells through internalization of cfChPs are not well supported because they are only based on evidence from one type of methodological approach: immunofluorescence and fluorescent in situ hybridization (FISH) using protein antibodies and DNA probes. Yet, such strong claims require validation by at least one, but preferably multiple, additional orthogonal approaches. This includes, for example, whole genome sequencing (to validate concatemerization, integration in receiving cells, transposition in receiving cells), RNA-seq (to validate expression), ChiP-seq (to validate chromatin state).

      Another weakness of this study is that it is performed only in one receiving cell type (NIH3T3 mouse cells). Thus, rather than a general phenomenon occurring on a massive scale in every multicellular organism, it could merely reflect aberrant properties of a cell line that for some reason became permeable to exogenous cfChPs. This begs the question of the relevance of this study for living organisms.

      Should HGT through internalization of circulating chromatin occur on a massive scale, as claimed in this study, and as illustrated by the many FISH foci observed in Fig 3 for example, one would expect that the level of somatic mosaicism may be so high that it would prevent assembling a contiguous genome for a given organism. Yet, telomere-to-telomere genomes have been produced for many eukaryote species, calling into question the conclusions of this study.

    3. Reviewer #2 (Public review):

      I must note that my comments pertain to the evolutionary interpretations rather than the study's technical results. The techniques appear to be appropriately applied and interpreted, but I do not feel sufficiently qualified to assess this aspect of the work in detail.

      I was repeatedly puzzled by the use of the term "function." Part of the issue may stem from slightly different interpretations of this word in different fields. In my understanding, "function" should denote not just what a structure does, but what it has been selected for. In this context, where it is unclear if cfChPs have been selected for in any way, the use of this term seems questionable.

      Similarly, the term "predatory genome," used in the title and throughout the paper, appears ambiguous and unjustified. At this stage, I am unconvinced that cfChPs provide any evolutionary advantage to the genome. It is entirely possible that these structures have no function whatsoever and could simply be byproducts of other processes. The findings presented in this study do not rule out this neutral hypothesis. Alternatively, some particular components of the genome could be driving the process and may have been selected to do so. This brings us to the hypothesis that cfChPs could serve as vehicles for transposable elements. While speculative, this idea seems to be compatible with the study's findings and merits further exploration.

      I also found some elements of the discussion unclear and speculative, particularly the final section on the evolution of mammals. If the intention is simply to highlight the evolutionary impact of horizontal transfer of transposable elements (e.g., as a source of new mutations), this should be explicitly stated. In any case, this part of the discussion requires further clarification and justification.

      In summary, this study presents important new findings on the behavior of cfChPs when introduced into a foreign cellular context. However, it overextends its evolutionary interpretations, often in an unclear and speculative manner. The concept of the "predatory genome" should be better defined and justified or removed altogether. Conversely, the suggestion that cfChPs may function at the level of transposable elements (rather than the entire genome or organism) could be given more emphasis.

    4. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Horizontal gene transfer is the transmission of genetic material between organisms through ways other than reproduction. Frequent in prokaryotes, this mode of genetic exchange is scarcer in eukaryotes, especially in multicellular eukaryotes. Furthermore, the mechanisms involved in eukaryotic HGT are unknown. This article by Banerjee et al. claims that HGT occurs massively between cells of multicellular organisms. According to this study, the cell free chromatin particles (cfChPs) that are massively released by dying cells are incorporated in the nucleus of neighboring cells. These cfChPs are frequently rearranged and amplified to form concatemers, they are made of open chromatin, expressed, and capable of producing proteins. Furthermore, the study also suggests that cfChPs transmit transposable elements (TEs) between cells on a regular basis, and that these TEs can transpose, multiply, and invade receiving cells. These conclusions are based on a series of experiments consisting in releasing cfChPs isolated from various human sera into the culture medium of mouse cells, and using FISH and immunofluorescence to monitor the state and fate of cfChPs after several passages of the mouse cell line.

      Strengths:

      The results presented in this study are interesting because they may reveal unsuspected properties of some cell types that may be able to internalize free-circulating chromatin, leading to its chromosomal incorporation, expression, and unleashing of TEs. The authors propose that this phenomenon may have profound impacts in terms of diseases and genome evolution. They even suggest that this could occur in germ cells, leading to within-organism HGT with long-term consequences.

      Weaknesses:

      The claims of massive HGT between cells through internalization of cfChPs are not well supported because they are only based on evidence from one type of methodological approach: immunofluorescence and fluorescent in situ hybridization (FISH) using protein antibodies and DNA probes. Yet, such strong claims require validation by at least one, but preferably multiple, additional orthogonal approaches. This includes, for example, whole genome sequencing (to validate concatemerization, integration in receiving cells, transposition in receiving cells), RNA-seq (to validate expression), ChiP-seq (to validate chromatin state).

      We agree with the reviewer’s suggestions. We propose to use RNA-seq using an orthogonal platform as a solution. This will allow us to answer multiple questions viz. validation of expression of human DNA in mouse cells, obtaining a detailed insight into genes and pathways driven by human cfChPs and enable us to identify chimeric human and mouse transcripts.

      Another weakness of this study is that it is performed only in one receiving cell type (NIH3T3 mouse cells). Thus, rather than a general phenomenon occurring on a massive scale in every multicellular organism, it could merely reflect aberrant properties of a cell line that for some reason became permeable to exogenous cfChPs. This begs the question of the relevance of this study for living organisms.

      We agree with the reviewer’s suggestion. We propose to show horizontal transfer of cfChPs using four different cell-lines representing four different species.

      Should HGT through internalization of circulating chromatin occur on a massive scale, as claimed in this study, and as illustrated by the many FISH foci observed in Fig 3 for example, one would expect that the level of somatic mosaicism may be so high that it would prevent assembling a contiguous genome for a given organism. Yet, telomere-to-telomere genomes have been produced for many eukaryote species, calling into question the conclusions of this study.

      The reviewer is right in expecting that the level of somatic mosaicism may be so high that it would prevent assembling a contiguous genome. This is indeed the case, and we find that beyond ~ 250 passages the genomes of the cfChPs treated NIH3T3 cells begin to die out apparently become their genomes have become too unstable for survival. This point will be highlighted in the revised version. It is likely that cell death resulting from large scale HGT creates a vicious cycle of more cell death induced by cfChPs thereby helping to explain the massive daily turnover of cells in the body (10<sup>9</sup> – 10<sup>12</sup> cells per day).  

      Reviewer #2 (Public review):

      I must note that my comments pertain to the evolutionary interpretations rather than the study's technical results. The techniques appear to be appropriately applied and interpreted, but I do not feel sufficiently qualified to assess this aspect of the work in detail.

      I was repeatedly puzzled by the use of the term "function." Part of the issue may stem from slightly different interpretations of this word in different fields. In my understanding, "function" should denote not just what a structure does, but what it has been selected for. In this context, where it is unclear if cfChPs have been selected for in any way, the use of this term seems questionable.

      We think this is a matter of semantics. We have used the term “function” since cfChPs that enter the cell are biologically active; they transcribe, translate, synthesize, proteins and proliferate. We, therefore feel that the term function is not inappropriate.

      Similarly, the term "predatory genome," used in the title and throughout the paper, appears ambiguous and unjustified. At this stage, I am unconvinced that cfChPs provide any evolutionary advantage to the genome. It is entirely possible that these structures have no function whatsoever and could simply be byproducts of other processes. The findings presented in this study do not rule out this neutral hypothesis. Alternatively, some particular components of the genome could be driving the process and may have been selected to do so. This brings us to the hypothesis that cfChPs could serve as vehicles for transposable elements. While speculative, this idea seems to be compatible with the study's findings and merits further exploration.

      We take the reviewer’s point. We will replace the term “predatory genome” with a more neutral and factual term “supernumerary genome” in the title and throughout the manuscript in the revised version.

      I also found some elements of the discussion unclear and speculative, particularly the final section on the evolution of mammals. If the intention is simply to highlight the evolutionary impact of horizontal transfer of transposable elements (e.g., as a source of new mutations), this should be explicitly stated. In any case, this part of the discussion requires further clarification and justification.

      We propose to revise the “discussion” section taking into account the issues raised by the reviewer and highlight the potential role of cfChPs in evolution by acting as vehicles of transposable elements.  

      In summary, this study presents important new findings on the behavior of cfChPs when introduced into a foreign cellular context. However, it overextends its evolutionary interpretations, often in an unclear and speculative manner. The concept of the "predatory genome" should be better defined and justified or removed altogether. Conversely, the suggestion that cfChPs may function at the level of transposable elements (rather than the entire genome or organism) could be given more emphasis.

      Our responses to this paragraph are given in the two above sections.

    1. eLife Assessment

      Valencia et al. combine elegant in vitro biochemical experiments with functional assays in cardiomyocytes to determine which properties of the FHOD3 formin are essential for sarcomere assembly. Using separation-of-function mutants, they show that FHOD3's elongation activity, rather than its nucleation, capping, or bundling activities, is key to its sarcomeric function. This is an important finding; most of the data presented in the manuscript are convincing, with the exception of two experiments (presence of FHOD3 at the barbed end of actin filaments in the TIRF elongation assays and characterization of the GS-FH1 mutant phenotype) that would merit few additional controls.

    2. Reviewer #1 (Public review):

      Summary:

      Formins are complex proteins with multiple effects on actin filament assembly, including nucleation, capping with processive elongation, and bundling. Determining which of these activities is important for a given biological process and normal cellular function is a major challenge.

      Here, the authors study the formin FHOD3L, which is essential for normal sarcomere assembly in muscle cells. They identify point mutants of FHOD3L in which formin nucleation and elongation/bundling activities are functionally separated. Expression of these mutants in neonatal rat ventricular myocytes shows that the control of actin filament elongation by formin is the major activity required for the normal assembly of functional sarcomeres.

      Strengths:

      The strength of this work is to combine sensitive biochemical assays with excellent work in neonatal rat ventricular myocytes. This combination of approaches is highly effective for analyzing the function of proteins with multiple activities in vitro.

      Weaknesses:

      FHOD3L does not seem to be the easiest formin to study because of its relatively weak nucleation activity and the short duration of capping events. This difficulty imposes rigorous biochemical analysis and careful interpretation of the data, which should be improved in this work.

    3. Reviewer #2 (Public review):

      This article elucidates the biochemical and cellular mechanisms by which the FHOD-family of formins, particularly FHOD3, contributes to sarcomere formation and contractility in cardiomyocytes. Formins are mainly known to nucleate and elongate actin filaments, with certain family members also exhibiting capping, severing, and bundling activities. Although FHOD3 has been well-established as essential for sarcomere assembly in cardiomyocytes, its precise biochemical functions and contributions to actin dynamics remain poorly understood.

      In this study, the authors combine in vitro biochemical assays with cellular experiments to dissect FHOD3's roles in actin assembly and sarcomere formation. They demonstrate that FHOD3 nucleates actin filaments and acts as a transient elongator, pausing elongation after an initial burst of filament growth. Using separation-of-function mutants, they show that FHOD3's elongation activity - rather than its nucleation, capping, or bundling capabilities - is key for its sarcomeric function.

      The experiments have been conducted rigorously and well-analyzed, and the paper is clearly written. The data presented support the authors' conclusions. I appreciate the detailed description and rationale behind the FHOD3 constructs used in this study.

      However, I was somewhat surprised and a bit disappointed that while the authors conducted single-color TIRF experiments to observe the effects of FHOD3 on single filaments, they did not use fluorescently labeled FHOD3 to directly visualize its behavior. Incorporating such experiments would significantly strengthen their conclusions regarding FHOD3's bursts of elongation interspersed with capping activity. While I understand this might require a few additional weeks of experiments, these data would add considerable value by directly testing the proposed mechanism.

      There is a typo in the word "required" in line number 30. The authors also use fit data to extract parameters in several panels (e.g., Figures 2b, 2d, 3a, and 3b). While these fit functions may be intuitive to actin experts, explicitly describing the fit functions in the figure legends or methods would greatly benefit the broader readership.

    4. Reviewer #3 (Public review):

      Valencia et al. aim to elucidate the biochemical and cellular mechanisms through which the human formin FHOD3 drives sarcomere assembly in cardiomyocytes. To do so, they combined rigorous in vitro biochemical assays with comprehensive in vivo characterizations, evaluating two wild-type FHOD3 isoforms and two function-separating mutants. Surprisingly, they found that both wild-type FHOD3 isoforms can nucleate new actin filaments, as well as elongate existing actin filaments in conjunction with profilin following barbed-end capping. This is in addition to FHOD3's proposed role as an actin bundler. Next, the authors asked whether FHOD3L promotes sarcomere assembly in cardiomyocytes through its activity in actin nucleation or rather elongation. With two function-separating mutants, the authors evaluated the numbers and morphology of sarcomeres, as well as their ability to beat and generate cardiac rhythm. The authors found that while the wild-type FHOD3L and the K1193L mutant can rescue sarcomere morphology and physiology, the GS-FH1 mutant fails to do so. Given that in GS-FH1 mainly elongation activity is compromised, the authors concluded that the elongation activity of FHOD3 is essential for its role in sarcomere assembly in cardiomyocytes, while its nucleator activity is dispensable. Overall, this important study provided a broadened view on the biochemical activities of FHOD3, and a pioneering view on a possible cellular mechanism of how FHOD3L drives sarcomere assembly. If further validated, this can lead to new mechanistic models of sarcomere assembly and potentially new therapeutic targets of cardiomyopathy.

      The conclusions of this paper are mostly well supported by the comprehensive biochemical analyses performed by the authors. However, the sarcomere assembly defect phenotype in the GS-FH1 rescue condition requires further investigation, as the extremely low level of GS-FH1 signal in transfected cells in Figure 6A may reflect a failure of actin-binding by this construct in vivo, rather than its inability to drive elongation. Though the authors do show in Figure 6 that GS-FH1 can bind to normal-looking sarcomeres when they are present, this may be due to a lack of siRNA activity in these cells, such that endogenous FHOD3L is still present. In this possible scenario, GS-FH1 may dimerize with endogenous FHOD3L. The authors should demonstrate that GS-FH1 alone can indeed interact with existing actin filaments in vivo. While this has been clearly demonstrated in vitro, given the more complex biochemical environment in vivo where additional unknown binding partners may present, cautions should be made when extrapolating findings from the former to the latter.

    5. Author response:

      We thank the reviewers for their careful readings of our paper and their very positive assessment. Here we address the two major concerns they raised, referring to the revised version of the manuscript that will be submitted:

      (1) Important points were raised regarding the brief elongation events we reported. The time resolution and noise in our system reduce the accuracy of the burst velocity measurements. To address this, we have reached out to a colleague who is set up to repeat these measurements with microfluidics-assisted TIRF. The noise should be greatly reduced and the system is also optimal for directly visualizing labeled FHOD3, as suggested. We hope this experimental approach will provide new insights.

      In the meantime, we analyzed our data more closely. We were asked about the pauses we observe before bursts of elongation and how we know they are functionally relevant. The short answer is that we do not know. We reported them because they were so common:  in three independent experiments with wild type FHOD3L-CT we analyzed a total of 20 filaments. We detected 112 dim regions and 97 of these were pause/burst events (~87%). Among the cases lacking a pause we include instances of apparent "double bursts" with no time for capping in between (which may be a time resolution issue) and some cases where the burst was in progress when data collection started. In the latter case, we cannot determine whether or not a pause was missed. We cannot rule out that this pause reflects an interaction with the surface but might expect the frequency to be lower if it were. In fact, we did detect pauses in the profilin-actin negative control but only 4 pauses were detected across 21 filaments analyzed compared to 97 pauses observed in the presence of wild type FHOD3L across 20 filaments analyzed. We will revise the text to make our conclusions about pauses more circumspect.

      For comparison to our current data, we further analyzed the filaments in TIRF assays with no formin present. As the reviewers point out, inhomogeneities in filament intensity are normal. Thus, we examined any dim spots for pauses and/or bursts. We will report (future Figure 2G) that the velocity of growth of these dim spots was the same as the velocity of the rest of the filament. While our numbers may not be perfectly accurate due to the noise in our system, the difference of 3-4 fold increase versus no detectable change in rate is substantial and statistically different. In addition, we determined the number of dim spots per length of filament. We found a higher frequency of dim spots when FHOD3L-CT or FHOD3S-CT was present vs no formin, as will be shown in Figure 2 – figure supplement 1G and 2D.

      We are convinced that the brief dim events we observed in the presence of FHOD3L-CT do, in fact, reflect formin-mediated elongation and hope that the reviewers concur. This does not preclude our interest in the microfluidics and two-color assays, which we will pursue in the future.

      (2) The reviewers were concerned about the low protein levels in the GS-FH1 rescue experiments as reflected in the HA fluorescence intensity distributions shown in Fig. 5 – figure supplement 2A. While the scenario proposed could explain our observations with the GSFH1 rescues, it is quite complex and does not preclude the conclusion that the FH1 domain is critical. One limit of this scenario would be that the protein levels in the GS-FH1 cells reflect completely inactive protein, as opposed to FHOD3L that cannot elongate (by design). Given that the C-terminal half of the protein folds and functions and that the changes are made within an intrinsically disordered region, we do not favor this model. The reviewers suggest that the mutant protein detected in the few cells with (probably residual) sarcomeres could be stabilized, in part or entirely, by heterodimerization with residual endogenous wild type protein. We agree that heterodimerization is possible. The question becomes, how active is a heterodimer? If heterodimers have any activity, it seems far from sufficient to rescue sarcomere formation, suggesting that two functional FH1 domains are critical. To confirm this possibility, we would have to be able to determine whether the few sarcomeres present in these cases are residual and/or the new sarcomeres the low level of heterodimers could make. That said, we do not see evidence of correlation between protein levels and rescue at the level present in these cells (addressed below). Unfortunately, the proposed IP to test whether FHOD3L binds actin in vivo would only potentially report on filament side binding (both direct and indirect). It would not address whether the GS-FH1 mutant functions as a nucleator, elongator, bundler and/or capping protein in vivo.

      If we assume that the protein present is active, the critical question that we can address is whether the phenotype is due to low protein levels or if the phenotype is due to loss of elongation activity by FHOD3L. To address this question, we revisited our data.

      First, we plotted the distributions of the intensities of the cells we analyzed further, in addition to the automated readout of all the cells in the dish we originally presented (e.g. Fig. 4 – figure supplement 2A,B). These cells were selected randomly and, as should be the case, the distributions of their intensities agree well with the original distributions for the three different rescue constructs: FHOD3L, K1193L, and GS-FH1 (Fig. 6 – figure supplement 1A,B). We then asked whether there was any correlation between HA intensities with the sarcomere metrics. Consistent with in our pilot data, no correlation is evident in any of the three cases across the range of intensities we collected (400 – 2700 a.u.) (Fig. 6 – figure supplement 1C,D,E). We were originally satisfied with the GS-FH1 data, despite the low average intensity levels, because the intensities were well within the range that we established in pilot studies. These data reconfirm that the intensity levels are reasonable in a larger study.

      To more specifically address the question of whether low HA fluorescence intensity is likely to reflect sufficient protein levels to build sarcomeres, we re-examined two data sets from the FHOD3L WT rescue data. We found that, by chance, the first replicate of data from the wild type rescue has a comparable intensity distribution to that of the GSFH1 rescues (580 +/- 261 / cell vs. 548 +/- 105 / cell). In addition, we collected all of the data from cells with intensity levels <720, selected to mimic the distribution of the GS-FH1 cells (Fig. 6 – figure supplement 3A). We then compared the sarcomere metrics (sarcomere number, sarcomere length, sarcomere width) between the full data set and the two low intensity subsets using statistical tests as reported for the rest of the cell biology data set:

      · Sarcomere number is the only non-normal metric. We therefore used the Mann Whitney U test for each pairwise comparison, which shows no difference between all 3 WT distributions.

      · We compared Z-line lengths by Student’s two-sample, unpaired t-test for each pairwise comparison, again finding no significant difference for all distributions.

      · Sarcomere length shows a weakly significant difference (p=0.017 (compared to 0.033 for 3 treatment groups based on Bonferroni correction)) between the whole WT data set and bio rep 1, but no difference between the whole WT data set and the HA<720 group via Student’s two-sample, unpaired t-test.

      An alternate statistical analysis approach, one-way ANOVA and Tukey post hoc tests, gave similar results. Thus, cells expressing wild type FHOD3L at levels comparable to levels detected in GS-FH1 mutant rescues, are fully rescued. Based on these findings we conclude that the expression levels in the GS-FH1 are high enough to rescue the FHOD3 knock down, supporting our conclusion that the defect is due to loss of elongation activity. We will add this analysis and discussion to the revised manuscript.

      In future studies we will design less severe mutations to the FH1 domain. We hope to identify one with a strong effect on elongation and another with an intermediate effect. Once the best candidates are characterized in vitro, we will test them in our rescue experiments. If the strong mutant mimics the GS-FH1 rescue and the intermediate mutant is less severe, we will have strengthened our conclusion that elongation is a critical FHOD3L activity in sarcomere formation.

      Additional improvements will be made to the manuscript based on recommendations we received from the reviewers.

    1. eLife Assessment

      This important study investigates the role of vasopressin in modulating same-sex affiliative relationships in the context of linear dominance hierarchies. It provides convincing evidence that vasopressin signaling is involved in modulating aspects of affiliative behavior, although the evidence that affiliative relationships specifically arise from the triadic interaction study design is incomplete. Nevertheless, its focus on broadening the types of social relationships and species studied in this area makes it of interest to both neuroendocrinologists and colleagues studying the evolution and mechanisms underlying social affiliation.

    2. Reviewer #1 (Public review):

      Summary:

      The authors seek to establish whether triadic interaction can promote affiliative relationships in the context of strict dominance hierarchies, and whether the vasopressinergic system is involved in such affiliations. To address this, they experimentally examine how male same-sex affiliations form by testing triadic cohabitation in large-billed crows, a species where males are known to develop and maintain same-sex affiliative relationships within a strict linear social hierarchy. They show a reduction in aggressive behavior over time with cohabitation and the formation of affiliative relationships, as measured by reciprocal allopreening, between two members (dyad) of the triad. The authors then administer a V1aR antagonist to each member of the triad, finding that allopreening decreases and dominance/submissive behaviors reemerge only in the dyad that developed an affiliated relationship ("affiliated dyad") with blockade of V1aR, demonstrating that V1aR mediates maintenance of affiliative peer relationships. The questions of how peer affiliations form, particularly in the context of dominance hierarchies, and the role of V1aR in regulating these behaviors are impactful for the field of social behavior. While the experimental paradigm provides a new way of approaching these questions, we have outlined below our concerns regarding the collection and interpretation of the data that limit the impact of this particular study.

      Strengths:

      (1) The authors develop a behavioral paradigm and experimental sequence using large-billed crows that allows them to identify the formation of stable, affiliated dyads within triadic groups that are robust to subsequent testing and are sensitive to pharmacological manipulation.

      (2) The effects of V1aR antagonism on allopreening and respective dominance or submissive behaviors appear significant and specific to the affiliated dyad, which supports the view that V1aR plays a role in context-dependent, flexible regulation of aggressive behaviors across species. However, these results are difficult to interpret with respect to the authors' main claims given the weaknesses outlined below.

      Weaknesses:

      (1) The authors claim that the data demonstrates that a triadic social group facilitates the formation of affiliative dyads and go further to claim that these relationships have relevance to understanding coalition formation. It is difficult to say whether the triadic structure actually facilitates or promotes the formation of these affiliative interactions as stated without direct comparisons to alternately sized groupings. Further, the relevance to coalitions is weak without expanded behavioral testing.

      (2) Aspects of the experimental design introduce confounding factors that make it difficult to interpret the resulting data. In experiment 1, 6 of the 18 animals that are used for testing are part of multiple triads. This is not accounted for in either the experimental design (wash-out period prior to reuse of animals) or statistical analysis (including repeated testing as a factor in the model) or is not described. Further, while the authors do randomize and counterbalance the two dose trials for the antagonist, vehicle vs drug exposure is not randomized.

      (3) The re-emergence of dominance-related agonistic behaviors with V1aR antagonism specifically in the affiliated dyads is interesting, but difficult to interpret without further description and analysis of the dyadic behavior, particularly given the absence of dominance-related behaviors in either affiliated or unaffiliated dyads during the cohabitation period. In addition, the current data does not support the hypothesis that V1aR is also required to form affiliative relationships, as stated in the discussion (Lines 464-5, 472, 494), since the authors did not administer V1aR antagonist during the initial period of triadic cohabitation.

      (4) Sentences are often repetitive or duplicated (lines 424-426), and paragraphs should be condensed for easier reading, especially in the discussion. Further, some of the discussion might be better presented in an "Ideas and Speculation" subsection, which would help readers appropriately assess the validity of the conclusions based on the data vs the larger implications suggested by the authors.

    3. Reviewer #2 (Public review):

      Seguchi and Izawa provide robust evidence for the role of vasopressin in modulating same-sex affiliative relationships. Especially striking is that these effects appear to be selective to key relationships within a triadic social context. Overall, this is an interesting and rich dataset with compelling results. I largely have some clarifying questions.

      Experiment 1 Comments:

      (1) The primary argument/finding in this experiment is that a triadic situation/environment facilitates the development of male-male reciprocal social relationships. Overall, this effect appears striking in that male-male affiliative bonds (defined as reciprocal allopreening) formed in 6 of the 8 triads tested. However, there is no comparison group of dyads to determine whether co-housing for 2 weeks could also support the formation of male-male social bonds. This lack of a comparison group makes it unclear to what extent the triad is the key aspect of the environment that supports social bonding.

      (2) More specifically, the authors argue that it is not just that triads support affiliative male-male bonds, but that bonds form between the second "middle" (dominant/subordinate) and third "low" (subordinate/subordinate) individuals in each triad. However, it was difficult to assess this from the results.<br /> a) For example, in Figure 3B is each data point the average of two individuals, since in each triad there are two dominant and two subordinate individuals?<br /> b) For me, using more precise language beyond dominant and subordinate (e.g. middle and low), and more clearly displaying the results of allopreening for each pairwise dyad within a triad would improve the impact of the results and support the authors' argument.

      (3) Experiment 2 Comments:<br /> The results here are quite striking, despite the low sample size. In Figure 4, it appears that in every instance of administration V1aRA low and high administration decreased allopreening for both dominant and subordinate individuals.

      (4) Some methodological questions:<br /> a) Can you clarify whether the duration of the post-test was also 30 min?<br /> b) As in Experiment 1, how are individual birds represented in the triad? Was the second "Middle" bird (dominant/subordinate) tested as both a dominant and subordinate bird? My understanding is that the dominant and subordinate birds in Figure 4 are different individuals but that they are the same individuals represented between the affiliated dyad and unaffiliated dyad.

      (5) Throughout the manuscript (Lines 57-67; 557-566) the authors argue that the role of VP in regulating gregariousness can be extrapolated to understand the role of same-sex affiliative bonding. Importantly, gregariousness does not necessarily reflect affiliative bonding. While allopreening is specifically associated with social bonding (e.g. monogamous pair bonds) independent of broader social systems, gregariousness in general, and specifically as defined in many of the references cited, is independent of social bonds - in fact, it is assessed primarily in novel social contexts.

      (6) To clarify, adult prairie voles in the wild do not engage in same-sex affiliative behavior commonly. In fact one of the primary components of opposite-sex pair bonding is same-sex aggression. Thus, while mechanistic studies on the neurobiology of same-sex peer bonds are relevant for this work, I am less convinced that you can make comparisons between the ultimate function of same-sex affiliative relationships in prairie voles.

      (17) The results here are consistent with VP having an anxiolytic effect, as has been suggested in birds, with the consequences on social behaviors being directly or indirectly related. This may be a useful point to draw on in the discussion when considering your findings.

    4. Reviewer #3 (Public review):

      Summary:

      In this study, Seguchi & Izawa investigate the formation of male-male affiliative relationships within triads of large-billed crows. They then administered a vasopressin 1a receptor (V1aR) antagonist to either the dominant or subordinate individual within affiliative dyads, to examine whether blocking V1aR disrupts affiliative behavior. They discovered that affiliative dyads can be induced in large-billed crows by housing them in triads. They also found that blocking V1aRs significantly decreased allopreening (an affiliative behavior) within dyads. In addition, it increased aggression by dominant individuals and submissive calls by subordinate individuals.

      Strengths:

      This manuscript uses an especially interesting species - a highly intelligent and highly social corvid, with complex dominance hierarchies - to extend previous work into the effects of the oxytocin and vasopressin peptides hormones on social behaviors. The results are surprisingly clear, despite a small sample size. The authors use the correct statistical approaches to account for a complex, nested design. The introduction and discussion both reflect a strong understanding of the relevant literature, including the limitations of extrapolating from peripheral (intramuscular) versus central (into the brain) injections of the V1aR antagonist. In addition, the authors appear to have been transparent about the data and results, accounting for some of the challenges and limitations of the data and study.

      Weaknesses:

      There are two major concerns. First, the study has a very low sample size (8 triads for Experiment 1, and only 5 triads for Experiment 2). Despite the surprisingly convincing findings, the sample size is too small to support the claim that the vasopressin system "universally mediates same sex relationships. Secondly, the study does not account for the effects of V1aR on non-social behaviors. This is especially true because vasopressin/V1aR (and the particular antagonist used in this study) is known to have effects on osmotic balance, food intake, and stress, including in birds. My concern is that the behavioral effects could be accounted before by differences in general stress or activity levels. Allopreening is usually an activity performed in periods of relative inactivity with aggression being more characterized by high activity levels. The authors discuss these different effects of vasopressin/V1aR in the Discussion, but they do not account for these effects in the study design.

    1. eLife Assessment

      In their valuable study, Lee et al. explore a role for the Hippo signaling pathway, specifically wts-1/LATS and the downstream regulator yap, in age-dependent neurodegeneration and microtubule dynamics using C. elegans mechanosensory neurons as a model. The authors demonstrate that disruption of wts-1/LATS leads to age-associated morphological and functional neuronal abnormalities, linked to enhanced microtubule stabilization, and shows a genetic connection between yap and microtubule stability. Despite some mechanistic gaps, the study employs robust genetic and molecular approaches to reveal a convincing link between the Hippo pathway, microtubule dynamics, and neurodegeneration.

    2. Reviewer #1 (Public review):

      Summary:

      In this manuscript, the authors investigate the role of microtubule dynamics and its effects on neuronal aging. Using C. elegans as a model, the authors investigate the role of evolutionarily conserved Hippo pathway in microtubule dynamics of touch receptor neurons (TRNs) in an age-dependent manner. Using genetic, molecular, behavioral, and pharmacological approaches, the authors show that age-dependent loss of microtubule dynamics might underlie structural and functional aging of TRNs. Further, the authors show that the Hippo pathway specifically functions in these neurons to regulate microtubule dynamics. Specifically, authors show that hyperactivation of YAP-1, a downstream component of the Hippo pathway that is usually inhibited by the kinase activity of the upstream components of the pathway, results in microtubule stabilization and that might underlie the structural and functional decline of TRNs with age. However, how the Hippo pathway regulates microtubule dynamics and neuronal aging was not investigated by the authors.

      Strengths:

      This is a well-conducted and well-controlled study, and the authors have used multiple approaches to address different questions.

      Weaknesses:

      There are no major weaknesses identified, except that the effect of the Hippo pathway seems to be specific to only a subset of neurons. I would like the authors to address the specificity of the effect of the Hippo pathway in TRNs, in their resubmission.

    3. Reviewer #2 (Public review):

      Summary:

      This study examines a novel role of the Hpo signaling pathway, specifically of wts-1/LATS and the downstream regulator of gene expression, yap, in age-related neurodegeneration in C. elegans touch-responsive mechanosensory neurons, ALM and PLM. The study shows that knockdown or deletion of wts-1/LATS causes age-associated morphological abnormalities of these neurons, accompanied by functional loss of touch responsiveness. This is further associated with enhanced, abnormal, microtubule stabilization in these neurons.

      Strengths:

      This study examines a novel role of the Hpo signaling pathway, specifically of wts-1/LATS and the downstream regulator of gene expression, yap, in age-related neurodegeneration in C. elegans touch-responsive mechanosensory neurons, ALM and PLM. The study shows that knockdown or deletion of wts-1/LATS causes age-associated morphological abnormalities of these neurons, accompanied by functional loss of touch responsiveness. This is further associated with enhanced, abnormal, microtubule stabilization in these neurons. Strong pharmacological and especially genetic manipulations of MT-stabilizing or severing proteins show a strong genetic link between yap and regulation of MTs stability. The study is strong and uses robust approaches, especially strong genetics. The demonstrations on the aging-related roles of the Hpo signaling pathway, and the link to MTs, are novel and compelling. Nevertheless, the study also has mechanistic weaknesses (see below).

      Weaknesses:

      Specific comments:

      (1) The study demonstrates age-specific roles of the Hpo pathway, specifically of wts-1/LATS and yap, specifically in TRN mechanosensory neurons, without observing developmental defects in these neurons, or effects in other neurons. This is a strong demonstration. Nevertheless, the study does not address whether there is a correlation of Hpo signaling pathway activity decline specifically in these neurons, and not other neurons, and at the observed L4 stage and onwards (including the first day of adulthood, 1DA stage). Such demonstrations of spatio-temporal regulation of the Hpo signaling pathway and its activation seem important for linking the Hpo pathway with the observed age-related neurodegeneration. Can this age-related response be correlated to indeed a decline in Hpo signaling during adulthood? Especially at L4 and onwards? It will be informative to measure this by examining the decline in wts1 as well as yap levels and yap nuclear localization.

      (2) The Hpo pathway eventually activates gene expression via yap. Although the study uses robust genetic manipulations of yap and wts-1/LATS, it is not clear whether the observed effects are attributed to yap-mediated regulation of gene expression (see 3).

      (3) The observations on the abnormal MT stabilization, and the subsequent genetic examinations of MT-stability/severing genes, are a significant strength of the study. Nevertheless, despite the strong genetic links to yap and wts-1/LATS, it is not clear whether MT-regulatory genes are regulated by transcription downstream of the Hpo pathway, thus not enabling a strong causal link between MT regulation and Hpo-mediated gene expression, making this strong part of the study mechanistically circumstantial. Specifically, it will be good to examine whether the genes addressed herein, for example, Spastin, are transcriptionally regulated downstream of the Hpo pathway. This comment is augmented by the finding that in the wts-1/ yap-1 double mutants, MT abnormality, and subsequent neuronal morphology and touch responses are restored, clearly indicating that there is an associated transcriptional regulation

      Other comments:

      (1) The TRN-specific knockdown of wts-1 and yap-1 is a clear strength. Nevertheless, these do not necessarily show cell-autonomous effects, as the yap transcription factor may regulate the expression of external cues, secreted or otherwise, thus generating non-cell autonomous effects. For example, it is known that yap regulates TGF-beat expression and signaling.

      (2) Continuing from comment (3) above, it seems that many of the MT-regulators chosen here for genetic examinations were chosen based on demonstrated roles in neurodegeneration in other studies. It would be good to show whether these MT-associated genes are directly regulated by transcription by the Hpo pathway.

      (3) The impairment of the touch response may not be robust: it is only a 30-40% reduction at L4, and even less reduction at 1DA. It would be good to offer possible explanations for this finding.

    1. eLife Assessment

      This important work advances our understanding of parabrachial CGRP threat function. The evidence supporting CGRP aversive outcome signaling is solid, while the evidence for cue signaling and fear behavior generation is incomplete. The work will be of interest to neuroscientists studying defensive behaviors.

    2. Reviewer #1 (Public Review):

      Summary

      The authors asked if parabrachial CGRP neurons were only necessary for a threat alarm to promote freezing or were necessary for a threat alarm to promote a wider range of defensive behaviors, most prominently flight.

      Major Strengths of Methods and Results

      The authors performed careful single-unit recording and applied rigorous methodologies to optogenetically tag CGRP neurons within the PBN. Careful analyses show that single-units and the wider CGRP neuron population increases firing to a range of unconditioned stimuli. The optogenetic stimulation of experiment 2 was comparatively simpler but achieved its aim of determining the consequence of activating CGRP neurons in the absence of other stimuli. Experiment 3 used a very clever behavioral approach to reveal a setting in which both cue-evoked freezing and flight could be observed. This was done by having the unconditioned stimulus be a "robot" traveling along a circular path at a given speed. Subsequent cue presentation elicited mild flight in controls and optogenetic activation of CGRP neurons significantly boosted this flight response. This demonstrated for the first time that CGRP neuron activation does more than promote freezing. The authors conclude by demonstrating that bidirectional modulation of CGRP neuron activity bidirectionally affects freezing in a traditional fear conditioning setting and affects both freezing and flight in a setting in which the robot served as the unconditioned stimulus. Altogether, this is a very strong set of experiments that greatly expand the role of parabrachial CGRP neurons in threat alarm.

      Weaknesses

      In all of their conditioning studies the authors did not include a control cue. For example, a sound presented the same number of times but unrelated to US (shock or robot) presentation. This does not detract from their behavioral findings. However, it means the authors do not know if the observed behavior is a consequence of pairing. Or is a behavior that would be observed to any cue played in the setting? This is particularly important for the experiments using the robot US.

      The authors make claims about the contribution of CGRP neurons to freezing and fleeing behavior, however, all of the optogenetic manipulations are centered on the US presentation period. Presently, the experiments show a role for these neurons in processing aversive outcomes but show little role for these neurons in cue responding or behavior organizing. Claims of contributions to behavior should be substantiated by manipulations targeting the cue period.

      Appraisal

      The authors achieved their aims and have revealed a much greater role for parabrachial CGRP neurons in threat alarm.

      Discussion

      Understanding neural circuits for threat requires us (as a field) to examine diverse threat settings and behavioral outcomes. A commendable and rigorous aspect of this manuscript was the authors decision to use a new behavioral paradigm and measure multiple behavioral outcomes. Indeed, this manuscript would not have been nearly as impactful had they not done that. This novel behavior was combined with excellent recording and optogenetic manipulations - a standard the field should aspire to. Studies like this are the only way that we as a field will map complete neural circuits for threat.

    3. Reviewer #2 (Public Review):

      -Summary of the Authors' Aims:<br /> The authors aimed to investigate the role of calcitonin gene-related peptide (CGRP) neurons in the parabrachial nucleus (PBN) in modulating defensive behaviors in response to threats. They sought to determine whether these neurons, previously shown to be involved in passive freezing behavior, also play a role in active defensive behaviors, such as fleeing, when faced with imminent threats.

      -Major Strengths and Weaknesses of the Methods and Results:<br /> The authors utilized an innovative approach by employing a predator-like robot to create a naturalistic threat scenario. This method allowed for a detailed observation of both passive and active defensive behaviors in mice. The combination of electrophysiology, optogenetics, and behavioral analysis provided a comprehensive examination of CGRP neuron activity and its influence on defensive behaviors. The study's strengths lie in its robust methodology, clear results, and the multi-faceted approach that enhances the validity of the findings.

      No notable weakness found.

      -Appraisal of Aims and Results:<br /> The authors successfully achieved their aims by demonstrating that CGRP neurons in the PBN modulate both passive and active defensive behaviors. The results clearly show that activation of these neurons enhances fear memory and promotes conditioned fleeing behavior, while inhibition reduces these responses. The study provides strong evidence supporting the hypothesis that CGRP neurons act as a comprehensive alarm system in the brain.

      -Impact on the Field and Utility of Methods and Data:<br /> This work has significant implications for the field of neuroscience, particularly in understanding the neural mechanisms underlying adaptive defensive behaviors. The innovative use of a predator-like robot to simulate naturalistic threats adds ecological validity to the findings and may inspire future studies to adopt similar approaches. The comprehensive analysis of CGRP neuron activity and its role in defensive behaviors provides valuable data that could be useful for researchers studying fear conditioning, neural circuitry, and behavior modulation.

      -Additional Context:<br /> The study builds on previous research that primarily focused on the role of CGRP neurons in passive defensive responses, such as freezing. By extending this research to include active responses, the authors have provided a more complete picture of the role of these neurons in threat detection and response. The findings highlight the versatility of CGRP neurons in modulating different types of defensive behaviors based on the perceived intensity and immediacy of threats.

      Overall, this manuscript makes a significant contribution to our understanding of the neural basis of defensive behaviors and offers valuable methodological insights for future research in the field.

    4. Reviewer #3 (Public Review):

      Strengths:<br /> The study used optogenetics together with in vivo electrophysiology to monitor CGRP neuron activity in response to various aversive stimuli including robot chasing to determine whether they encode noxious stimuli differentially. The study used an interesting conditioning paradigm to investigate the role of CGRP neurons in the PBN in both freezing and flight behaviors.

      Weakness:<br /> The major weakness of this study is that the chasing robot threat conditioning model elicits weak unconditioned and conditioned flight responses, making it difficult to interpret the robustness of the findings. Furthermore, the conclusion that the CGRP neurons are capable of inducing flight is not substantiated by the data. No manipulations are made to influence the flight behavior of the mouse. Instead, the manipulations are designed to alter the intensity of the unconditioned stimulus.

    1. eLife Assessment

      This study presents a valuable advancement in antiviral research by applying SHAPE-Map to analyze the secondary structure of the Porcine Epidemic Diarrhoea Virus RNA genome in infected cells, identifying promising therapeutic targets within viral genomic RNA. The authors provide convincing evidence of potential antiviral targetable RNA regions through a wide array of data from different methods, supported by well-documented experimental design and data analysis, demonstrating how RNA structural probing can effectively discover RNA targets and enabling further discoveries in the field. The work will be of interest to researchers focused on RNA therapeutics and viral genome studies.

    2. Reviewer #1 (Public review):

      Summary:

      This study investigates the potential of targeting specific regions within the RNA genome of the Porcine Epidemic Diarrhea Virus (PEDV) for antiviral drug development. The authors used SHAPE-MaP to analyze the structure of the PEDV RNA genome in infected cells. They categorized different regions of the genome based on their structural characteristics, focusing on those that might be good targets for drugs or small interfering RNAs (siRNAs).

      They found that dynamic single-stranded regions can be stabilized by compounds (e.g., to form G-quadruplexes), which inhibit viral proliferation. They demonstrated this by targeting a specific G4-forming sequence with a compound called Braco-19. The authors also describe stable (structured) single-stranded regions that they used to design siRNAs showing that they effectively inhibited viral replication.

      Strengths:

      There are a number of strengths to highlight in this manuscript.

      (1) The study uses a sophisticated technique (SHAPE-MaP) to analyze the PEDV RNA genome in situ, providing valuable insights into its structural features.

      (2) The authors provide a strong rationale for targeting specific RNA structures for antiviral development.

      (3) The study includes a range of experiments, including structural analysis, compound screening, siRNA design, and viral proliferation assays, to support their conclusions.

      (4) Finally, the findings have potential implications for the development of new antiviral therapies against PEDV and other RNA viruses.

      Overall, this interesting study highlights the importance of considering RNA structure when designing antiviral therapies and provides a compelling strategy for identifying promising RNA targets in viral genomes.

      Weaknesses:

      I have some concerns about the utility of the 3D analyses, the effects of their synonymous mutants on expression/proliferation, a potentially missed control for studies of mutants, and the therapeutic utility of the compound they tested vs. G-quadruplexes.

    3. Reviewer #2 (Public review):

      Summary:

      Luo et. al. use SHAPE-MaP to find suitable RNA targets in Porcine Epidemic Diarrhoea Virus. Results show that dynamic and transient structures are good targets for small molecules, and that exposed strand regions are adequate targets for siRNA. This work is important to segment the RNA targeting.

      Strengths:

      This work is well done and the data supports its findings and conclusions. When possible, more than one technique was used to confirm some of the findings.

      Weaknesses:

      The study uses a cell line that is not porcine (not the natural target of the virus).

    4. Reviewer #3 (Public review):

      Summary:

      This manuscript by Luo et al. applied SHAPE-Map to analyze the secondary structure of the Porcine Epidemic Diarrhoea Virus (PEDV) RNA genome in infected cells. By combining SHAPE reactivity and Shannon entropy, the study indicated that the folding of the PEDV genomic RNA was nonuniform, with the 5' and 3' untranslated regions being more compactly structured, which revealed potentially antiviral targetable RNA regions. Interestingly, the study also suggested that compounds bound to well-folded RNA structures in vitro did not necessarily exhibit antiviral activity in cells, because the binding of these compounds did not necessarily alter the functions of the well-folded RNA regions. Later in the manuscript, the authors focus on guanine-rich regions, which may form G-quadruplexes and be potential targets for small interfering RNA (siRNA). The manuscript shows the binding effect of Braco-19 (a G-quadruplex-binding ligand) to a predicted G4 region in vitro, along with the inhibition of PEDV proliferation in cells. This suggests that targeting high SHAPE-high Shannon G4 regions could be a promising approach against RNA viruses. Lastly, the manuscript identifies 73 single-stranded regions with high SHAPE and low Shannon entropy, which demonstrated high success in antiviral siRNA targeting.

      Strengths:

      The paper presents valuable data for the community. Additionally, the experimental design and data analysis are well documented.

      Weakness:

      The manuscript presents the effect of Braco-19 on PQS1, a single G4 region with high SHAPE and high Shannon entropy, to suggest that "the compound can selectively target the PQS1 of the high SHAPE-high Shannon region in cells" (lines 625-626). While the effect of Braco-19 on PQS1 is supported by strong evidence in the manuscript, the conclusion regarding the G4 region with high SHAPE and high Shannon entropy is based on a single target, PQS1.

    1. Author response:

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

      Reviewer #1 (Public review):

      Summary:

      In the manuscript "Intergenerational transport of double-stranded RNA limits heritable epigenetic changes," Shugarts and colleagues investigate intergenerational dsRNA transport in the nematode C. elegans. By inducing oxidative damage, they block dsRNA import into cells, which affects heritable gene regulation in the adult germline (Fig. 2). They identify a novel gene, sid-1-dependent gene-1 (sdg-1), upregulated upon SID-1 inhibition (Fig. 3). Both transient and genetic depletion of SID-1 lead to the upregulation of sdg-1 and a second gene, sdg-2 (Fig. 5). Interestingly, while sdg-1 expression suggests a potential role in dsRNA transport, neither its overexpression nor loss-of-function impacts dsRNA-mediated silencing in the germline (Fig. 7).

      Strengths:

      • The authors employ a robust neuronal stress model to systematically explore SID-1 dependent intergenerational dsRNA transport in C. elegans.

      • They discover two novel SID-1-dependent genes, sdg-1 and sdg-2.

      • The manuscript is well-written and addresses the compelling topic of dsRNA signaling in C. elegans.

      Weaknesses:

      • The molecular mechanism downstream of SDG-1 remains unclear. Testing whether sdg-2 functions redundantly with sdg-1could provide further insights.

      • SDG-1 dependent genes in other nematodes remain unknown.

      We thank the reviewer for highlighting the strengths of the work along with a couple of the interesting future directions inspired by the reported discoveries. The restricted presence of genes encoding SDG-1 and its paralogs within retrotransposons suggests intriguing evolutionary roles for these proteins. Future work could examine whether such fast-evolving or newly evolved proteins with potential roles in RNA regulation are more broadly associated with retrotransposons. Multiple SID-1-dependent proteins (including SDG-1 and SDG-2) could act together to mediate downstream effects. This possibility can be tested using combinatorial knockouts and overexpression strains. Both future directions have the potential to illuminate the evolutionarily selected roles of dsRNA-mediated signaling through SID-1, which remain a mystery.

      Reviewer #2 (Public review):

      Summary:

      RNAs can function across cell borders and animal generations as sources of epigenetic information for development and immunity. The specific mechanistic pathways how RNA travels between cells and progeny remains an open question. Here, Shugarts, et al. use molecular genetics, imaging, and genomics methods to dissect specific RNA transport and regulatory pathways in the C. elegans model system. Larvae ingesting double-stranded RNA is noted to not cause continuous gene silencing throughout adulthood. Damage of neuronal cells expressing double-stranded target RNA is observed to repress target gene expression in the germline. Exogenous short or long double-stranded RNA required different genes for entry into progeny. It was observed that the SID-1 double-stranded RNA transporter showed different expression over animal development. Removal of the sid-1 gene caused upregulation of two genes, the newly described sid-1-dependent gene sdg-1 and sdg-2. Both genes were observed to be negatively regulated by other small RNA regulatory pathways. Strikingly, loss then gain of sid-1 through breeding still caused variability of sdg-1 expression for many, many generations. SDG-2 protein co-localizes with germ granules, intracellular sites for heritable RNA silencing machinery. Collectively, sdg-1 presents a model to study how extracellular RNAs can buffer gene expression in germ cells and other tissues.

      Strengths:

      (1) Very cleaver molecular genetic methods and genomic analyses, paired with thorough genetics, were employed to discover insights into RNA transport, sdg-1 and sdg-2 as sid-1-dependent genes, and sdg-1's molecular phenotype.

      (2) The manuscript is well cited, and figures reasonably designed.

      (3) The discovery of the sdg genes being responsive to the extracellular RNA cell import machinery provides a model to study how exogenous somatic RNA is used to regulate gene expression in progeny. The discovery of genes within retrotransposons stimulates tantalizing models how regulatory loops may actually permit the genetic survival of harmful elements.

      Weaknesses:

      (1) The manuscript is broad, making it challenging to read and consider the data presented. Of note, since the original submission, the authors have improved the clarity of the writing and presentation.

      Comments on revised version:

      This reviewer thanks the authors for their efforts in revising the manuscript. In their rebuttal, the authors acknowledged the broad scope of their manuscript. I concur. While I still think the manuscript is a challenge to read due to its expansive nature, the current draft is substantially improved when compared to the previous one. This work will contribute to our general knowledge of RNA biology, small RNA regulatory pathways, and RNA inheritance.

      We thank the reviewer for highlighting the strengths of the manuscript and for helping us improve the presentation of our results and discussion.


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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In the manuscript "Intergenerational transport of double-stranded RNA limits heritable epigenetic changes" Shugarts and colleagues investigate intergenerational dsRNA transport in the nematode C. elegans. They induce oxidative damage in worms, blocking dsRNA import into cells (and potentially affecting the worms in other ways). Oxidative stress inhibits dsRNA import and the associated heritable regulation of gene expression in the adult germline (Fig. 2). The authors identify a novel gene, sid-1-dependent gene-1 (sdg-1), which is induced upon inhibition of SID-1 (Fig. 3). Both transient inhibition and genetic depletion of SID-1 lead to the upregulation of sdg-1 and a second gene, sdg-2 (Fig. 5). The expression of SDG-1 is variable, potentially indicating buffering regulation. While the expression of Sdg-1 could be consistent with a role in intergenerational transport of dsRNA, neither its overexpression nor loss-of-function impacts dsRNA-mediated silencing (Fig. 7) in the germline. It would be interesting to test if sdg-2 functions redundantly.

      In summary, the authors have identified a novel worm-specific protein (sdg-1) that is induced upon loss of dsRNA import via SID-1, but is not required to mediate SID-1 RNA regulatory effects.

      We thank the reviewer for highlighting our findings on SDG-1. We found that oxidative damage in neurons enhanced dsRNA transport into the germline and/or subsequent silencing.

      Remaining Questions:

      • The authors use an experimental system that induces oxidative damage specifically in neurons to release dsRNAs into the circulation. Would the same effect be observed if oxidative damage were induced in other cell types?

      It is possible that oxidative damage of other tissues using miniSOG (as demonstrated in Xu and Chisholm, 2016) could also enhance the release of dsRNA into the circulation from those tissues. However, future experiments would be needed to test this empirically because it is also possible that the release of dsRNA depends on physiological properties (e.g., the molecular machinery promoting specific secretion) that are particularly active in neurons. We chose to use neurons as the source of dsRNA because by expressing dsRNA in a variety of tissues, neurons appeared to be the most efficient at the export of dsRNA as measured using SID-1-dependent silencing in other tissues (Jose et al., PNAS, 2009).

      • Besides dsRNA, which other RNAs and cellular products (macromolecules and small signalling molecules) are released into the circulation that could affect the observed changes in germ cells?

      We do not yet know all the factors that could be released either in naive animals or upon oxidative damage of neurons that influence the uptake of dsRNA into other tissues. The dependence on SID-1 for the observed enhancement of silencing (Fig. 2) shows that dsRNA is necessary for silencing within the germline. Whether this import of dsRNA occurs in conjunction with other factors (e.g., the uptake of short dsRNA along with yolk into oocytes (Marré et al., PNAS, 2016)) before silencing within the germline will require further study. A possible approach could be the isolation of extracellular fluid (Banse and Hunter, J Vis Exp., 2012) followed by characterization of its contents. However, the limited material available using this approach and the difficulty in avoiding contamination from cellular damage by the needle used for isolating the material make it challenging.

      • SID-1 modifies RNA regulation within the germline (Fig. 7) and upregulates sdg-1 and sdg-2 (Fig. 5). However, SID-1's effects do not appear to be mediated via sdg-1. Testing the role of sdg-2 would be intriguing.

      We observe the accumulation of sdg-1 and sdg-2 RNA in two different mutants lacking SID-1, which led us to conservatively focus on the analysis of one of these proteins for this initial paper. We expect that more sensitive analyses of the RNA-seq data will likely reveal additional genes regulated by SID-1. With the ability to perform multiplexed genome-editing, we hope in future work to generate strains that have mutations in many SID-1-dependent genes to recapitulate the defects observed in sid-1(-) animals. Indeed, as surmised by the reviewer, we are focusing on sdg-2 as the first such SID-1-dependent gene to analyze using mutant combinations.

      • Are sdg-1 or sdg-2 conserved in other nematodes or potentially in other species?  appears to be encoded or captured by a retro-element in the C. elegans genome and exhibits stochastic expression in different isolates. Is this a recent adaptation in the C. elegans genome, or is it present in other nematodes? Does loss-of-function of sdg-1 or sdg-2 have any observable effect?

      Clear homologs of SDG-1 and SDG-2 are not detectable outside of C. elegans. Consistent with the location of the sdg-1 gene within a Cer9 retrotransposon that appears to have integrated only within the C. elegans genome, sequence conservation between the genomes of related species is only observed outside the region of the retrotransposon (see Author response image 1, screenshot from UCSC browser). There were no obvious defects detected in animals lacking sdg-1 (Fig. 7) or in animals lacking sdg-2 (data not shown). It is possible that further exploration of both mutants and mutant combinations lacking additional SID-1-dependent genes would reveal defects. We also plan to examine these mutants in sensitized genetic backgrounds where one or more members of the RNA silencing pathway have been compromised.

      Author response image 1.

      Clarification for Readability:

      To enhance readability and avoid misunderstandings, it is crucial to specify the model organism and its specific dsRNA pathways that are not conserved in vertebrates:

      We agree with the reviewer and thank the reviewer for the specific suggestions provided below. To take the spirit of the suggestion to heart we have instead changed the title of our paper to clearly signal that the entire study only uses C. elegans. We have titled the study ‘Intergenerational transport of double-stranded RNA in C. elegans can limit heritable epigenetic changes’

      • In the first sentence of the paragraph "Here, we dissect the intergenerational transport of extracellular dsRNA ...", the authors should specify "in the nematode C. elegans". Unlike vertebrates, which recognise dsRNA as a foreign threat, worms and other invertebrates pervasively use dsRNA for signalling. Additionally, worms, unlike vertebrates and insects, encode RNA-dependent RNA polymerases that generate dsRNA from ssRNA substrates, enabling amplification of small RNA production. Especially in dsRNA biology, specifying the model organism is essential to avoid confusion about potential effects in humans.

      We agree with most statements made by the reviewer, although whether dsRNA is exclusively recognized as a foreign threat by all vertebrates of all stages remains controversial. Our changed title now eliminates all ambiguity regarding the organism used in the study.

      • Similarly, the authors should specify "in C. elegans" in the sentence "Therefore, we propose that the import of extracellular dsRNA into the germline tunes intracellular pathways that cause heritable RNA silencing." This is important because C. elegans small RNA pathways differ significantly from those in other organisms, particularly in the PIWI-interacting RNA (piRNA) pathways, which depend on dsRNA in C. elegans but uses ssRNA in vertebrates. Specification is crucial to prevent misinterpretation by the reader. It is well understood that mechanisms of transgenerational inheritance that operate in nematodes or plants are not conserved in mammals.

      The piRNAs of C. elegans are single-stranded but are encoded by numerous independent genes throughout the genome. The molecules used for transgenerational inheritance of epigenetic changes that have been identified thus far are indeed different in different organisms. However, the regulatory principles required for transgenerational inheritance are general (Jose, eLife, 2024). Nevertheless, we have modified the title to clearly state that the entire study is using C. elegans.  

      • The first sentence of the discussion, "Our analyses suggest a model for ...", would also benefit from specifying "in C. elegans". The same applies to the figure captions. Clarification of the model organism should be added to the first sentence, especially in Figure 1.

      With the clarification of the organism used in the title, we expect that all readers will be able to unambiguously interpret our results and the contexts where they apply. 

      Reviewer #2 (Public review):

      Summary:

      RNAs can function across cell borders and animal generations as sources of epigenetic information for development and immunity. The specific mechanistic pathways how RNA travels between cells and progeny remains an open question. Here, Shugarts, et al. use molecular genetics, imaging, and genomics methods to dissect specific RNA transport and regulatory pathways in the C. elegans model system. Larvae ingesting double stranded RNA is noted to not cause continuous gene silencing throughout adulthood. Damage of neuronal cells expressing double stranded target RNA is observed to repress target gene expression in the germline. Exogenous supply of short or long double stranded RNA required different genes for entry into progeny. It was observed that the SID-1 double-stranded RNA transporter showed different expression over animal development. Removal of the sid-1 gene caused upregulation of two genes, the newly described sid-1-dependent gene sdg-1 and sdg-2. Both genes were observed to also be negatively regulated by other small RNA regulatory pathways. Strikingly, loss then gain of sid-1 through breeding still caused variability of sdg-1 expression for many, many generations. SDG-2 protein co-localizes with a Z-granule marker, an intracellular site for heritable RNA silencing machinery. Collectively, sdg-1 presents a model to study how extracellular RNAs can buffer gene expression in germ cells and other tissues.

      We thank the reviewer for highlighting our findings and underscoring the striking nature of the discovery that mutating sid-1 using genome-editing resulted in a transgenerational change that could not be reversed by changing the sid-1 sequence back to wild-type.

      Strengths:

      (1) Very clever molecular genetic methods and genomic analyses, paired with thorough genetics, were employed to discover insights into RNA transport, sdg-1 and sdg-2 as sid-1-dependent genes, and sdg-1's molecular phenotype.

      (2) The manuscript is well cited, and figures reasonably designed.

      (3) The discovery of the sdg genes being responsive to the extracellular RNA cell import machinery provides a model to study how exogenous somatic RNA is used to regulate gene expression in progeny. The discovery of genes within retrotransposons stimulates tantalizing models how regulatory loops may actually permit the genetic survival of harmful elements.

      We thank the reviewer for the positive comments.

      Weaknesses:

      (1) As presented, the manuscript is incredibly broad, making it challenging to read and consider the data presented. This concern is exemplified in the model figure, that requires two diagrams to summarize the claims made by the manuscript.

      RNA interference (RNAi) by dsRNA is an organismal response where the delivery of dsRNA into the cytosol of some cell precedes the processing and ultimate silencing of the target gene within that cell. These two major steps are often not separately considered when explaining observations. Yet, the interpretation of every RNAi experiment is affected by both steps. To make the details that we have revealed in this work for both steps clearer, we presented the two models separated by scale - organismal vs. intracellular. We agree that this integrative manuscript appears very broad when the many different findings are each considered separately. The overall model revealed here forms the necessary foundation for the deep analysis of individual aspects in the future.

      (2) The large scope of the manuscript denies space to further probe some of the ideas proposed. The first part of the manuscript, particularly Figures 1 and 2, presents data that can be caused by multiple mechanisms, some of which the authors describe in the results but do not test further. Thus, portions of the results text come across as claims that are not supported by the data presented.

      We agree that one of the consequences of addressing the joint roles of transport and subsequent silencing during RNAi is that the scope of the manuscript appears large. We had suggested multiple interpretations for specific observations in keeping with the need for further work. To avoid any misunderstandings that our listing of possible interpretations be taken as claims by the reader, we have followed the instructions of the reviewer (see below) and moved some of the potential explanations we raised to the discussion section.

      (3) The manuscript focuses on the genetics of SDGs but not the proteins themselves. Few descriptions of the SDGs functions are provided nor is it clarified why only SDG-1 was pursued in imaging and genetic experiments. Additionally, the SDG-1 imaging experiments could use additional localization controls.

      We agree that more work on the SDG proteins will likely be informative, but are beyond the scope of this already expansive paper.  We began with the analysis of SDG-1 because it had the most support as a regulator of RNA silencing (Fig. 5f). Indeed, in other work (Lalit and Jose, bioRxiv, 2024), we find that AlphaFold 2 predicts the SDG-1 protein to be a regulator of RNA silencing that directly interacts with the dsRNA-editing enzyme ADR-2 and the endonuclease RDE-8. Furthermore, we expect that more sensitive analyses of the RNA-seq data are likely to reveal additional genes regulated by SID-1. Using multiplexed genome editing, we hope to generate mutant combinations lacking multiple sdg genes to reveal their function(s).

      We agree that given the recent discovery of many components of germ granules, our imaging data does not have sufficient resolution to discriminate between them. We have modified our statements and our model regarding the colocalization of SDG-1 with Z-granules to indicate that the overlapping enrichment of SDG-1 and ZNFX-1 in the perinuclear region is consistent with interactions with other nearby granule components.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      Major

      (1) As presented, the manuscript is almost two manuscripts combined into one. This point is highlighted in Figure 7h, which basically presents two separate models. The key questions addressed in the manuscript starts at Figure 3. Figures 1 and 2 are interesting observations but require more experiments to define further. For example, as the Results text describes for Figure 1, "These differences in the entry of ingested dsRNA into cells and/or subsequent silencing could be driven by a variety of changes during development. These include changes in the uptake of dsRNA into the intestine, distribution of dsRNA to other tissues from the intestine, import of dsRNA into the germline, and availability of RNA silencing factors within the germline." Presenting these (reasonable) mechanistic ideas detracted from the heritable RNA epigenetic mechanism explored in the later portion of the manuscript. There are many ways to address this issue, one being moving Figures 1 and 2 to the Supplement to focus on SID-1 related pathways.

      Since this manuscript addresses the interaction between intercellular transport of dsRNA and heritable epigenetic changes, it was necessary to establish the possible route(s) that dsRNA could take to the germline before any inference could be made regarding heritable epigenetic changes. As suggested below (pt. 2), we have now moved the alternatives we enumerated as possible explanations for some experimental results (e.g., for the differences quoted here) to the discussion section.

      (2) The manuscript includes detailed potential interpretations in the Results, making them seem like claims. Here is an example:

      "Thus, one possibility suggested by these observations is that reduction of sdg-1 RNA via SID-1 alters the amount of SDG-1 protein, which could interact with components of germ granules to mediate RNA regulation within the germline of wild-type animals."

      This mechanism is a possibility, but placing these ideas in the citable results makes it seem like an overinterpretation of imaging data. This text and others should be in the Discussion, where speculation is encouraged. Results sections like this example and others should be moved to the discussion.

      We have rephrased motivating connections between experiments like the one quoted above and also moved such text to the discussion section wherever possible.

      (3) A paragraph describing the SDG proteins will be helpful. Homologs? Conserved protein domains? mRNA and/or protein expression pattern across worm, not just the germline? Conservation across Caenorhabditis sp? These descriptions may help establish context why SDG-1 localizes to Z-granules.

      We have now added information about the conservation of the sdg-1 gene in the manuscript. AlphaFold predicts domains with low confidence for the SDG-1 protein, consistent with the lack of conservation of this protein (AlphaFold requires multiple sequence alignments to predict confidently). In the adult animal, the SDG-1 protein was only detectable in the germline. Future work focused on SDG-1, SDG-2 and other SDG proteins will further examine possible expression in other tissues and functional domains if any. Unfortunately, in multiple attempts of single-molecule FISH experiments using probes against the sdg-1 open reading frame, we were unable to detect a specific signal above background (data not shown). Additional experiments are needed for the sensitive detection of sdg-1 expression outside the germline, if any.  

      (4) Based on the images shown, SDG-1 could be in other nearby granules, such as P granules or mutator foci. Additional imaging controls to rule out these granules/condensates will greatly strengthen the argument that SDG-1 protein localizes to Z-granules specifically.

      We have modified the final model to indicate that the perinuclear colocalization is with germ granules broadly and we agree that we do not have the resolution to claim that the observed overlap of SDG-1::mCherry with GFP::ZNFX-1 that we detect using Airyscan microscopy is specifically with Z granules. Our initial emphasis of Z-granule was based on the prior report of SDG-1 being co-immunoprecipitated with the Z-granule surface protein PID-2/ZSP-1. However, through other work predicting possible direct interactions using AlphaFold (Lalit and Jose, bioRxiv, 2024), we were unable to detect any direct interactions between PID-2 and SDG-1. Indeed, many additional granules have been recently reported (Chen et al., Nat. Commun., 2024; Huang et al., bioRxiv 2024), making it possible that SDG-1 has specific interactions with a component of one of the other granules (P, Z, M, S, E, or D) or adjacent P bodies.

      Minor

      (1) "This entry into the cytosol is distinct from and can follow the uptake of dsRNA into cells, which can rely on other receptors." Awkard sentence. Please revise.

      We have now revised this sentence to read “This entry into the cytosol is distinct from the uptake of dsRNA into cells, which can rely on other receptors”

      (2) Presumably, the dsRNA percent of the in vitro transcribed RNA is different than the 50 bp oligos that can be reliably annealed by heating and cooling. Other RNA secondary structure possibilities warrant further discussion.

      We agree that in vitro transcribed RNA could include a variety of undefined secondary structures in addition to dsRNAs of mixed length. Such structures could recruit or titrate away RNA-binding proteins in addition to the dsRNA structures engaging the canonical RNAi pathway, resulting in mixed mechanisms of silencing. Future work identifying such structures and exploring their impact on the efficacy of RNAi could be informative. We have now added these considerations to the discussion and thank the reviewer for highlighting these possibilities.

    2. eLife Assessment

      In this report, the authors present valuable findings identifying a novel worm-specific protein (sdg-1) that is induced upon loss of dsRNA import via SID-1, but is not required to mediate SID-1 RNA regulatory effects. The genetic and genomic approaches are well-executed and the revision contain generally solid support for the central findings of the work. These findings will be of interest to those working in the germline epigenetic inheritance field.

    3. Reviewer #1 (Public review):

      Summary:<br /> In the manuscript "Intergenerational transport of double-stranded RNA limits heritable epigenetic changes," Shugarts and colleagues investigate intergenerational dsRNA transport in the nematode C. elegans. By inducing oxidative damage, they block dsRNA import into cells, which affects heritable gene regulation in the adult germline (Fig. 2). They identify a novel gene, sid-1-dependent gene-1 (sdg-1), upregulated upon SID-1 inhibition (Fig. 3). Both transient and genetic depletion of SID-1 lead to the upregulation of sdg-1 and a second gene, sdg-2 (Fig. 5). Interestingly, while sdg-1 expression suggests a potential role in dsRNA transport, neither its overexpression nor loss-of-function impacts dsRNA-mediated silencing in the germline (Fig. 7).

      Strengths:<br /> • The authors employ a robust neuronal stress model to systematically explore SID-1 dependent intergenerational dsRNA transport in C. elegans.<br /> • They discover two novel SID-1-dependent genes, sdg-1 and sdg-2.<br /> • The manuscript is well-written and addresses the compelling topic of dsRNA signaling in C. elegans.

      Weaknesses:<br /> • The molecular mechanism downstream of SDG-1 remains unclear. Testing whether sdg-2 functions redundantly with sdg-1could provide further insights.<br /> • SDG-1 dependent genes in other nematodes remain unknown.

    4. Reviewer #2 (Public review):

      Summary:

      RNAs can function across cell borders and animal generations as sources of epigenetic information for development and immunity. The specific mechanistic pathways how RNA travels between cells and progeny remains an open question. Here, Shugarts, et al. use molecular genetics, imaging, and genomics methods to dissect specific RNA transport and regulatory pathways in the C. elegans model system. Larvae ingesting double-stranded RNA is noted to not cause continuous gene silencing throughout adulthood. Damage of neuronal cells expressing double-stranded target RNA is observed to repress target gene expression in the germline. Exogenous short or long double-stranded RNA required different genes for entry into progeny. It was observed that the SID-1 double-stranded RNA transporter showed different expression over animal development. Removal of the sid-1 gene caused upregulation of two genes, the newly described sid-1-dependent gene sdg-1 and sdg-2. Both genes were observed to be negatively regulated by other small RNA regulatory pathways. Strikingly, loss then gain of sid-1 through breeding still caused variability of sdg-1 expression for many, many generations. SDG-2 protein co-localizes with germ granules, intracellular sites for heritable RNA silencing machinery. Collectively, sdg-1 presents a model to study how extracellular RNAs can buffer gene expression in germ cells and other tissues.

      Strengths:

      (1) Very cleaver molecular genetic methods and genomic analyses, paired with thorough genetics, were employed to discover insights into RNA transport, sdg-1 and sdg-2 as sid-1-dependent genes, and sdg-1's molecular phenotype.

      (2) The manuscript is well cited, and figures reasonably designed.

      (3) The discovery of the sdg genes being responsive to the extracellular RNA cell import machinery provides a model to study how exogenous somatic RNA is used to regulate gene expression in progeny. The discovery of genes within retrotransposons stimulates tantalizing models how regulatory loops may actually permit the genetic survival of harmful elements.

      Weaknesses:

      (1) The manuscript is broad, making it challenging to read and consider the data presented. Of note, since the original submission, the authors have improved the clarity of the writing and presentation.

      Comments on revised version:

      This reviewer thanks the authors for their efforts in revising the manuscript. In their rebuttal, the authors acknowledged the broad scope of their manuscript. I concur. While I still think the manuscript is a challenge to read due to its expansive nature, the current draft is substantially improved when compared to the previous one. This work will contribute to our general knowledge of RNA biology, small RNA regulatory pathways, and RNA inheritance.

    1. eLife Assessment

      This is a valuable study regarding the role of gasdesmin D in experimental psoriasis. The study contains solid evidence for such a role, involving neutrophils, from murine models of skin inflammation, as well as correlative data of elevated gasdermin D expression in human psoriatic skin. The findings will be of interest to researchers trying to unravel pathways of skin inflammation.

    2. Reviewer #1 (Public review):

      Summary:

      Recommendations for the authors In this study, Liu, Jiang, Diao et.al. investigated the role of GSDMD in psoriasis-like skin inflammation in mice. The authors have used full-body GSDMD knock-out mice and Gsdm floxed mice crossed with the S100A8- Cre. In both mice, the deficiency of GSDMD ameliorated the skin phenotype induced by the imiquimod. The authors also analyzed RNA sequencing data from the psoriatic patients to show an elevated expression of GSDMD in the psoriatic skin.

      Strengths:

      It has the potential to unravel the new role of neutrophils.

      Comments on revisions:

      The authors have addressed the majority of comments and concerns and highlighted the potential limitations wherever not possible.

    3. Reviewer #2 (Public review):

      Summary:

      The authors describe elevated GSDMD expression in psoriatic skin, and knock-out of GSDMD abrogates psoriasis-like inflammation.

      Strengths:

      The study is well conducted with transgenic mouse models. Using mouse-models with GSDMD knock-out showing abrogating inflammation, as well as GSDMD fl/fl mice without neutrophils having a reduced phenotype.

      My major concern would be the involvement of other inflammasome and GSDMD bearing cell types, esp. Keratinocytes (KC), which could be an explanation why the experiments in Fig 4 still show inflammation.

      Comments on revisions:

      The authors have sufficiently addressed my questions.

    4. Author response:

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

      eLife Assessment

      This is a potentially interesting study regarding the role of gasdesmin D in experimental psoriasis. The study contains useful data from murine models of skin inflammation, however the main claims (on neutrophil pyroptosis) are incompletely supported in its current form and require additional experimental support to justify the conclusions made.

      We sincerely appreciate the positive assessment regarding the significance of our study, as well as the valuable suggestions provided by the reviewers. We have included new data, further discussions and clarifications in the revised manuscript to adequately address all the concerns raised by the reviewers and better support our conclusions.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this study, Liu, Jiang, Diao et.al. investigated the role of GSDMD in psoriasis-like skin inflammation in mice. The authors have used full-body GSDMD knock-out mice and Gsdm floxed mice crossed with the S100A8- Cre. In both mice, the deficiency of GSDMD ameliorated the skin phenotype induced by the imiquimod. The authors also analyzed RNA sequencing data from the psoriatic patients to show an elevated expression of GSDMD in the psoriatic skin.

      Overall, this is a potentially interesting study, however, the manuscript in its current format is not completely a novel study.

      Strengths:

      It has the potential to unravel the new role of neutrophils.

      Weaknesses:

      The main claims are only partially supported and have scope to improve

      We thank the reviewer for the positive evaluation of the interest and potential of our work. In response to reviewers’ suggestions, we have added new content, including additional data and discussions, to further demonstrate the important role of GSDMD-mediated neutrophil pyroptosis in the pathogenesis of psoriasis, thereby enhancing the completeness of our research.

      Reviewer #2 (Public review):

      Summary:

      The authors describe elevated GSDMD expression in psoriatic skin, and knock-out of GSDMD abrogates psoriasis-like inflammation.

      Strengths:

      The study is well conducted with transgenic mouse models. Using mouse-models with GSDMD knock-out showing abrogating inflammation, as well as GSDMD fl/fl mice without neutrophils having a reduced phenotype.

      I fear that some of the conclusions cannot be drawn by the suggested experiments. My major concern would be the involvement of other inflammasome and GSDMD bearing cell types, esp. Keratinocytes (KC), which could be an explanation why the experiments in Fig 4 still show inflammation.

      Weaknesses:

      The experiments do not entirely support the conclusions towards neutrophils.

      We appreciate the reviewers’ positive evaluation regarding the application of our mouse models. We also thank the reviewers for insightful comments and suggestions that can improve the quality of our work. Addressing these issues has significantly strengthened our conclusions. Our responses to the above questions are as follows.

      Specific questions/comments:

      Fig 1b: mainly in KC and Neutrophils?

      In Figure 1b, we observed that GSDMD expression is higher in the psoriasis patient tissues compared to control samples. As the role of GSDMD in keratinocytes during the pathogenesis of psoriasis has already been explored[1], we focused our study on GSDMD in neutrophils. In response to the comments, we have added co-staining results of the neutrophil marker CD66b and GSDMD in the revised manuscript (see new Figure 3b in the revised manuscript). This addition further substantiates the expression of GSDMD in neutrophils within psoriasis tissue.

      Fig 2a: PASI includes erythema, scaling, thickness and area. Guess area could be trick, esp. in an artificial induced IMQ model (WT) vs. the knock-out mice.

      In our model, to accurately assess the disease condition in mice, we standardized the drug treatment area on the dorsal side (2*3 cm). Therefore, the area was not factored into the scoring process, and we have included a detailed description of this in the revised manuscript.

      Fig 2d: interesting finding. I thought that CASP-1 is cleaving GSDMD. Why would it be downregulated?

      Regarding the downregulation of CASP in GSDMD KO mouse skin tissue, existing studies indicate that GSDMD generates a feed-forward amplification cascade via the mitochondria-STING-Caspase axis [2]. We hypothesize that the absence of GSDMD attenuates STING signaling’s activation of Caspase.

      Line 313: as mentioned before (see Fig 1b). KC also show a stron GSDMD staining positivity and are known producers of IL-1b and inflammasome activation. Guess here the relevance of KC in the whole model needs to be evaluated.

      Our research primarily focuses on the role of neutrophil pyroptosis in psoriasis, this does not conflict with existing reports indicating that KC cell pyroptosis also contributes to disease progression[1]. Both studies underscore the significant role of GSDMD-mediated pyroptotic signaling in psoriasis, and the consistent involvement of KC cells and neutrophils further emphasizes the potential therapeutic value of targeting GSDMD signaling in psoriasis treatment. We have expanded upon this discussion in the revised manuscript.

      Fig 4i - guess here the conclusion would be that neutrophils are important for the pathogenesis in the IMQ model, which is true. This experiment does not support that this is done by pyroptosis.

      To address the question, we analyzed the publicly available single-cell transcriptomic data (GSE165021) and found that, compared to the control group, neutrophils infiltrating in IMQ-induced psoriasis-like tissue display a higher expression of pyroptosis-related genes (see new Figure 3e in the revised manuscript). These results strengthen our conclusions about the role of neutrophil pyroptosis in the progression of psoriasis.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Specific Comments:

      • Figure 1: Micro abscesses would already be dead, which would likely reflect as non-specific staining. Authors should consider double staining (e.g., GSDMD+Ly6G).

      We thank the reviewer for the useful suggestion. We have added co-staining results of the neutrophil marker CD66b and GSDMD in the revised manuscript (see new Figure 3b in the revised manuscript). This addition further substantiates the expression of GSDMD in neutrophils within psoriasis tissue.

      • Figures 1 b, c, and d do not have the n number for representative experiments and images.

      We apologize for our oversight. We have added the relevant information in the revised manuscript and have reviewed and corrected the entire text.

      • What is the difference between psoriasis patients in Figure 1 versus Figure 3 as the staining patterns are different? It is difficult to interpret from Figure 1 that expression is limited to neutrophils. Authors should consider double staining (e.g., GSDMD+Ly6G). How many samples were stained to draw this conclusion?

      We thank the reviewer for the suggestion. In Figure 1b, we observed that GSDMD expression is higher in the psoriasis patient tissues compared to control samples. We have added co-staining results of the neutrophil marker CD66b and GSDMD in the revised manuscript (see new Figure 3b in the revised manuscript). For each staining group, we examined samples from 3-5 patients to draw the conclusion.

      • Figure 2: GSDMD deficiency mitigates psoriasis-like inflammation in mice has been shown before (PMID#37673869). The paper showed that the GSDMD was mainly expressed in keratinocytes. What is the view of the authors on it and how does this data correlate with the data presented in this manuscript by the authors?

      Consistent with previous studies[1], we observed increased expression of pyroptosis-related proteins in psoriatic lesions. However, our research focused specifically on the role of neutrophil pyroptosis in psoriasis, this does not conflict with existing reports indicating that KC cell pyroptosis also contributes to disease progression. Both studies underscore the significant role of GSDMD-mediated pyroptotic signaling in psoriasis, and the consistent involvement of KC cells and neutrophils further emphasizes the potential therapeutic value of targeting GSDMD signaling in psoriasis treatment. We have expanded upon this discussion in the revised manuscript.

      • Figure 3d: It is unclear if the IF shows an epidermal or dermal area. As shown by authors in other figures (human psoriatic skin), do authors observe more GSDMD in the micro abscess, which is localized in the epidermis? The authors should also show the staining of GSDM/Ly6G in the whole skin sample.

      The region we presented for immunofluorescence staining corresponds to the dermis of the mice, as we did not observe typical neutrophil micro abscesses similar to those in human psoriasis in the epidermis of IMQ-induced classical psoriasis vulgaris (PV) model. Therefore, we have only shown the staining in the dermal area.

      • Figure 3e: PI staining also represents necrotic cells and TUNEL staining would not represent just apoptotic cells. It is unclear how the authors conclude an ongoing pyroptosis in neutrophils. A robust dataset is needed to provide evidence supporting neutrophil pyroptosis in the IMQ-challenged mice.

      We thank the reviewer for the valuable suggestion. GSDMD is the effector protein of pyroptosis. To further confirm that cells are undergoing pyroptosis, it is necessary to morphologically stain the GSDMD N-terminal protein. Although there is currently no GSDMD N-terminal fluorescent antibody available, we detected the cleaved N-terminus of GSDMD by WB in mouse psoriasis-like skin tissue, and its increased expression suggested increased cell pyroptosis (see new Figure 1d in the revised manuscript). Moreover, we analyzed the publicly available single-cell transcriptomic data (GSE165021) and found that, compared to the control group, neutrophils infiltrating in IMQ-induced psoriasis-like tissue display a higher expression of pyroptosis-related genes (see new Figure 3e in the revised manuscript). These results strengthen our conclusions about the role of neutrophil pyroptosis in the progression of psoriasis.

      • Figure 4: The authors did not clarify the reason for choosing D4 over the usual D7 for the imiquimod experiment. S100A8-Cre is also reported in monocytes and granulocytes/monocyte progenitors. And, the authors also show the expression in macrophages and neutrophils, but in the text, only neutrophils are mentioned. The authors should state the results in the text as well to avoid misrepresentation of the data.

      We thank the reviewer for the useful suggestion. We have repeated many times of experiments in our previous studies and observed that the IMQ-induced mouse psoriasis model showed the obvious signs of self-resolution after Day 4 even with continuing topical IMQ application, thus we chose 4 days over 7 days for the imiquimod experiment, which are consistent with many other studies[3, 4].

      Many studies use S100A8-Cre mice for neutrophil-specific gene knockout[5, 6]. Moreover, we used Ly6G antibody to eliminate neutrophils in GSDMD-cKO mice and control mice. It was found that the difference in lesions between the two groups was abolished after neutrophil depletion, indicating that neutrophil pyroptosis plays an important role in the pathogenesis of imiquimod-induced psoriasis-like lesions in mice. As the database analysis results showed that macrophages have slight expression of S100a8, according to the suggestion of the reviewer, we have added a more precise description in the revised manuscript.

      • Figure S2a: Ly6G antibody reduced the ly6G positive, but also negative cells compared to PBS. If this is correct, what is the explanation, and how this observation has been considered for concluding results?

      Neutrophils play an important role in regulating inflammatory responses, and their deletion can reduce the overall inflammatory level in the body, which also results in a decrease in other non-neutrophil cells. However, this change does not affect our conclusions. Our results show that after the deletion of neutrophils, there is no difference in the pathological manifestations between the cKO group and the control group. This further that GSDMD in neutrophil plays an important role in the pathogenesis of miquimod-induced psoriasis-like lesions in mice.

      • The conclusion in Figure 4i is incorrect as Ly6G administration had an effect on the wt, so it shows neutrophils play a role, but not neutrophil pyroptosis.

      - 321 "It was found that the difference in lesions between the

      - 321 two groups was abolished after neutrophil depletion (Fig4i, S2a), indicating that

      - 322 neutrophil pyroptosis plays an important role in the pathogenesis of

      - 323 imiquimod-induced psoriasis-like lesions in mice"

      Our results show that after the deletion of neutrophils, there is no difference in the pathological manifestations between the cKO group and the control group. This further indicates that the lower disease scores observed in cKO mice, in the absence of neutrophil deletion, depend on the presence of neutrophils. In the revised manuscript, we have changed the statement to “It was found that the difference in lesions between the two groups was abolished after neutrophil depletion (Fig4i, S2a), indicating that GSDMD in neutrophil plays an important role in the pathogenesis of miquimod-induced psoriasis-like lesions in mice”

      • The effect of LyG Ab: reduced PASI in the wt, but the effect on the ko remains the same. What are the other molecular changes observed? What was the level of neutrophils in the wt and the S1A008Cre GsdmDfl/fl mice under steady state and how are they change upon imiquimod challenge? A complete profiling of the immune cells is needed for all the experiments.

      As demonstrated by the results, the deletion of neutrophils did not significantly alter the pathological phenotype of cKO mice. We believe that this outcome precisely highlights the crucial role of GSDMD in regulating neutrophil inflammatory responses.

      • Figure S2b: The authors conclude that Il-1b in the imiquimod skin is mainly expressed by neutrophils, but the analysis presented in the figure does not support this conclusion. Both neutrophils and macrophages are majorly positive for I1-b, with some expression on Langerhans and fibroblasts. No n numbers are provided for the experiment

      As we discussed in the manuscript, we speculate that neutrophil pyroptosis may release cytokines, which in turn activate other cells to secrete cytokines, forming a complex inflammatory network in psoriasis. This may suggest that neutrophil pyroptosis may be involved in the pathogenesis of psoriasis by affecting the secretion of cytokines such as IL-1B and IL-6 by neutrophils, thereby affecting the function of other immune cells such as T cells and macrophages.

      We have added the n number in the revised manuscript.

      • For clarity and transparency, a list of antibodies with the associate clone and catalogue number should be provided or integrated into the method text.

      We thank the reviewer for the useful suggestion. We have added the associate clone and catalogue number of antibodies used in the method text of revised manuscript.

      Reviewer #2 (Recommendations for the authors):

      Fig 3b: psoriasis and pustular psoriasis have a different pathophysiology (autoimmune vs. autoinflammatory). Neutrophils are centrally important for GPP for the cleavage of IL-36. Guess as not further referred to pustular psoriasis in the paper, that comparison is rather deviating from the story.

      In Figure 3b, we stained for GSDMD and CD66b in both plaque psoriasis (PV) and generalized pustular psoriasis (GPP), not to compare the expression differences between the two types of psoriasis, but rather to demonstrate that significant GSDMD expression is present in neutrophils in different types of psoriasis. Unfortunately, due to the lack of a well-established animal model for GPP, we were only able to conduct studies using the established PV animal model. We acknowledge this limitation in our research. In our revised manuscript, we have added the following explanation in the discussion section: “Although we observed significantly increased GSDMD in neutrophils in pustular psoriasis, we were constrained to studying the established PV animal model due to the current absence of a mature GPP animal model. This represents a limitation of our study.”

      In summary, we appreciate the Reviewer’s comments and suggestions. We feel that the inclusion of new data addresses the concerns in a comprehensive manner and adds further support to our original conclusions. We hope you will now consider the revised manuscript worthy of publication in eLife.

      References:

      (1) Lian, N., et al., Gasdermin D-mediated keratinocyte pyroptosis as a key step in psoriasis pathogenesis. Cell Death & Disease, 2023. 14(9): p. 595.

      (2) Han, J., et al., GSDMD (gasdermin D) mediates pathological cardiac hypertrophy and generates a feed-forward amplification cascade via mitochondria-STING (stimulator of interferon genes) axis. Hypertension, 2022. 79(11): p. 2505-2518.

      (3) Lin, H., et al., Forsythoside A alleviates imiquimod-induced psoriasis-like dermatitis in mice by regulating Th17 cells and IL-17a expression. Journal of Personalized Medicine, 2022. 12(1): p. 62.

      (4) Emami, Z., et al., Evaluation of Kynu, Defb2, Camp, and Penk Expression Levels as Psoriasis Marker in the Imiquimod‐Induced Psoriasis Model. Mediators of Inflammation, 2024. 2024(1): p. 5821996.

      (5) Stackowicz, J., et al., Neutrophil-specific gain-of-function mutations in Nlrp3 promote development of cryopyrin-associated periodic syndrome. Journal of Experimental Medicine, 2021. 218(10): p. e20201466.

      (6) Abram, C.L., et al., Distinct roles for neutrophils and dendritic cells in inflammation and autoimmunity in motheaten mice. Immunity, 2013. 38(3): p. 489-501.

    1. eLife Assessment

      This important work is a versatile new addition to the chemical protein modifications and bioconjugation toolbox in synthetic biology. The technology developed cleverly uses Connectase to irreversibly fuse proteins of interest together so they can be studied in their native context, with convincing data showing the technique works for various protein partners. This work will help multiple fields to explore multi-function constructs in basic synthetic biology. This work will also be of interest to those studying fusion oncoproteins commonly expressed in various human pathologies.

    2. Reviewer #1 (Public review):

      Fuchs describes a novel method of enzymatic protein-protein conjugation using the enzyme Connectase. The author is able to make this process irreversible by screening different Connectase recognition sites to find an alternative sequence that is also accepted by the enzyme. They are then able to selectively render the byproduct of the reaction inactive, preventing the reverse reaction, and add the desired conjugate with the alternative recognition sequence to achieve near-complete conversion. I agree with the authors that this novel enzymatic protein fusion method has several applications in the field of bioconjugation, ranging from biophysical assay conduction to therapeutic development. Previously the author has published on the discovery of the Connectase enzymes and has shown its utility in tagging proteins and detecting them by in-gel fluorescence. They now extend their work to include the application of Connectase in creating protein-protein fusions, antibody-protein conjugates, and cyclic/polymerized proteins. As mentioned by the author, enzymatic protein conjugation methods can provide several benefits over other non-specific and click chemistry labeling methods. Connectase specifically can provide some benefits over the more widely used Sortase, depending on the nature of the species that is desired to be conjugated. However, due to a similar lengthy sequence between conjugation partners, the method described in this paper does not provide clear benefits over the existing SpyTag-SpyCatcher conjugation system. Additionally, specific disadvantages of the method described are not thoroughly investigated, such as difficulty in purifying and separating the desired product from the multiple proteins used. Overall, this method provides a novel, reproducible way to enzymatically create protein-protein conjugates.

      The manuscript is well-written and will be of interest to those who are specifically working on chemical protein modifications and bioconjugation.

    3. Reviewer #2 (Public review):

      Summary:

      Unlike previous traditional protein fusion protocols, the author claims their proposed new method is fast, simple, specific, reversible, and results in a complete 1:1 fusion. A multi-disciplinary approach from cloning and purification, biochemical analyses, and proteomic mass spec confirmation revealed fusion products were achieved.

      Strengths:

      The author provides convincing evidence that an alternative to traditional protein fusion synthesis is more efficient with 100% yields using connectase. The author optimized the protocol's efficiency with assays replacing a single amino acid and identification of a proline aminopeptidase, Bacilius coagulans (BcPAP), as a usable enzyme to use in the fusion reaction. Multiple examples including Ubiquitin, GST, and antibody fusion/conjugations reveal how this method can be applied to a diverse range of biological processes.

      Weaknesses:

      Though the ~100% ligation efficiency is an advancement, the long recognition linker may be the biggest drawback. For large native proteins that are challenging/cannot be synthesized and require multiple connectase ligation reactions to yield a complete continuous product, the multiple interruptions with long linkers will likely interfere with protein folding, resulting in non-native protein structures. This method will be a good alternative to traditional approaches as the author mentioned but limited to generating epitope/peptide/protein tagged proteins, and not for synthetic protein biology aimed at examining native/endogenous protein function in vitro.

    4. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Fuchs describes a novel method of enzymatic protein-protein conjugation using the enzyme Connectase. The author is able to make this process irreversible by screening different Connectase recognition sites to find an alternative sequence that is also accepted by the enzyme. They are then able to selectively render the byproduct of the reaction inactive, preventing the reverse reaction, and add the desired conjugate with the alternative recognition sequence to achieve near-complete conversion. I agree with the authors that this novel enzymatic protein fusion method has several applications in the field of bioconjugation, ranging from biophysical assay conduction to therapeutic development. Previously the author has published on the discovery of the Connectase enzymes and has shown its utility in tagging proteins and detecting them by in-gel fluorescence. They now extend their work to include the application of Connectase in creating protein-protein fusions, antibody-protein conjugates, and cyclic/polymerized proteins. As mentioned by the author, enzymatic protein conjugation methods can provide several benefits over other non-specific and click chemistry labeling methods. Connectase specifically can provide some benefits over the more widely used Sortase, depending on the nature of the species that is desired to be conjugated. However, due to a similar lengthy sequence between conjugation partners, the method described in this paper does not provide clear benefits over the existing SpyTag-SpyCatcher conjugation system.  Additionally, specific disadvantages of the method described are not thoroughly investigated, such as difficulty in purifying and separating the desired product from the multiple proteins used. Overall, this method provides a novel, reproducible way to enzymatically create protein-protein conjugates.

      The manuscript is well-written and will be of interest to those who are specifically working on chemical protein modifications and bioconjugation.

      Reviewer #2 (Public review):

      Summary:

      Unlike previous traditional protein fusion protocols, the author claims their proposed new method is fast, simple, specific, reversible, and results in a complete 1:1 fusion. A multi-disciplinary approach from cloning and purification, biochemical analyses, and proteomic mass spec confirmation revealed fusion products were achieved.

      Strengths:

      The author provides convincing evidence that an alternative to traditional protein fusion synthesis is more efficient with 100% yields using connectase. The author optimized the protocol's efficiency with assays replacing a single amino acid and identification of a proline aminopeptidase, Bacilius coagulans (BcPAP), as a usable enzyme to use in the fusion reaction. Multiple examples including Ubiquitin, GST, and antibody fusion/conjugations reveal how this method can be applied to a diverse range of biological processes.

      Weaknesses:

      Though the ~100% ligation efficiency is an advancement, the long recognition linker may be the biggest drawback. For large native proteins that are challenging/cannot be synthesized and require multiple connectase ligation reactions to yield a complete continuous product, the multiple interruptions with long linkers will likely interfere with protein folding, resulting in non-native protein structures. This method will be a good alternative to traditional approaches as the author mentioned but limited to generating epitope/peptide/protein tagged proteins, and not for synthetic protein biology aimed at examining native/endogenous protein function in vitro.

      I would like to sincerely thank both reviewers for their insightful and constructive feedback on the manuscript. I have addressed reviewer #1’s comments below:

      (1) The benefits over the SpyTag-SpyCatcher system. Here, the conjugation partners are fused via the 12.3 kDa SpyCatcher protein, which is considerably larger than the Connectase fusion sequence (20 aa). This is briefly mentioned in the introduction (p. 1 ln 24-25). In a related technology, the SpyTag-SpyCatcher system was split into three components, SpyLigase, SpyTag and KTag  (Fierer et al., PNAS 2014). The resulting method introduces a sequence between the fusion partners (SpyTag (13aa) + KTag (10aa)), which is similar in length to the Connectase fusion sequence. I mention this method in the discussion (p. 8, ln 296 - 297), but preferred not to comment on its efficiency. It appears to require more enzyme and longer incubation times, while yielding less fusion product (Fierer et al., Figure 2).

      (2) Purification of the fusion product. The method is actually advantageous in this respect, as described in the discussion (p. 8, ln 257-263). I plan to add a figure showing an example in the revised article.

    1. eLife Assessment

      This study investigated mitochondrial dysfunction and the impairment of the ciliary Sonic Hedgehog signaling in Lowe syndrome (LS), a timely topic given the limited research in this area. The data from patient iPSC-derived neurons and a mouse model were collected using solid methods, but the evidence supporting key claims is incomplete, and some technical aspects fall short of expectations. Despite these limitations, the study provides a useful foundation for exploring the relationship between mitochondrial defects and primary cilia in neural development.

    2. Reviewer #1 (Public review):

      Summary:

      This study by Lo et al. seeks to explain the cellular defects underlying the brain phenotypes of Lowe syndrome (LS). There have been limited studies on this topic and hence this is a timely study.

      Strengths:

      Studies such as these can contribute to an understanding of the cellular and developmental mechanisms of brain disorders.

      Weaknesses:

      This study by Lo et al. seeks to explain the cellular defects underlying the brain phenotypes of Lowe syndrome (LS). There have been limited studies on this topic and hence this is a timely study.

      The study uses two models: (1) an LS IOB knockout mouse and (2) neurons derived from iPSC lines from LS patients. These two models are used to present three separate findings: (1) altered mitochondria function, (2) altered numbers of neurons and glia in both models, and (3) some evidence of altered Sonic Hedgehog signaling projected as a defect in cilia.

      Conceptually, there are some problems of serious concern which must be carefully considered:<br /> (1) The IOB mouse was very extensively phenotyped when it was generated by Festa et.al HMM, 2019. It does not have any obvious phenotypes of brain deficits although the studies in this paper were very detailed indeed.<br /> (2) Reduced brain size is reported as a phenotype of the IOB mouse in this study. Yet over the many clinical studies of LS published over the years, altered brain size has not been noted, either in clinical examination or in the many MRI reports of LS patients.

      While reading through these results it is striking that the link between the three reported phenotypes is at least tenuous, and in fact may not exist at all. The link between mitochondria and neurogenesis is based on a single paper that has been cited incorrectly and out of context. There is no evidence presented for a link between the Shh signaling defect reported and the mitochondrial phenotype.

      General comments

      (1) The preparation of the manuscript requires improvement. There are many errors in the presentation of data.<br /> (2) The use of references needs to be re-considered. Sometimes a reference is used when in fact the results included in that paper are the opposite of what the authors intend.<br /> (3) The authors conclude the paper by claiming that mitochondrial dysfunction and impairments of the ciliary SHH contribute to abnormal neuronal differentiation in LS, but the mechanism by which this sequence of events might happen hasn't been shown.

      Final comments:

      (1) Phenotype of increased astrocytes:<br /> The phenotype of increased astrocytes in both the IOB mouse brain or iPSC-derived cultures iN cells requires clarification as one of the markers used as an astrocyte marker, BRN2, is commonly used as a neuronal marker. As LS is a neurodevelopmental disorder, and the phenotype in question is related to differentiation, it is crucial to shed light on the developmental timeline in which this phenotype is seen in the mouse brain.

      (2) Ciliary homeostasis:<br /> Mitochondrial dysfunction in astrocytes has been shown to induce a ciliogenic program. However, almost the opposite is shown in this paper, with regards to ciliation. Morphology of the cilia was not assessed either, which is an important feature of ciliary homeostasis. The improper ciliary homeostasis here appears to be the improper Shh signalling, which has not been shown to be related to mitochondrial dysfunction. This leaves one wondering how exactly the different phenotypes shown in this paper are connected.

      (3) This paper lacks a clear mechanistic approach. While the data validates the 3 broad phenotypes mentioned, there is a lack of connection between these phenotypes or an answer to why these phenotypes appear. While the discussion attempts to shed light on this by referencing previous studies, some of the referenced studies show contradicting results. Hence, it would be beneficial to clarify these gaps with further experiments and address the larger question of the connection between the mitochondria, Shh signalling, and astrocyte formation.

      (4) Most importantly, there is no mention of how the loss of OCRL, a 5-phosphatase enzyme, results in the appearance of the mentioned phenotypes. Since there are multiple studies in the field of Lowe Syndrome that shed light on the various functions of OCRL, both catalytic and non-catalytic, it is important to address the role of OCRL in resulting in these phenotypes.

      (5) There are numerous errors in the qPCR experiments performed with regard to the genes that were assayed. The genes mentioned in the text section do not match those indicated in the graphs or legends. This takes away the confidence of the reader in this data.