Peer Review History
| Original SubmissionAugust 26, 2022 |
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PONE-D-22-23915Lymphocyte deficiency alters the transcriptomes of oligodendrocytes, but not astrocytes or microgliaPLOS ONE Dear Dr. Zhang, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. As you can see from both reviewers' comments, there are concerns about the statistics and analysis of the results, and the relationship between the Rag2 and MHCII KOs, and importantly the lack of description of the most significant changes mentioned in the manuscript, regarding the oligodendrocytes. Please submit your revised manuscript by Nov 17 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
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Tsirka Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 3. Thank you for stating the following in the Competing Interests section: "I have read the journal's policy and the authors of this manuscript have the following competing interests: Ye Zhang consulted for Ono Pharmaceutical." 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Thank you for stating the following in the Acknowledgments Section of your manuscript: "This work is supported by the Achievement Rewards for College Scientists Foundation Los Angeles Founder Chapter and the National Institute of Mental Health of the National Institutes of Health (NIH) Award T32MH073526 to M.C.K, the National Institute of Neurological Disorders and Stroke of the National Institute of Health (NIH) R00NS089780, R01NS109025, the National Institute of Aging of the NIH R03AG065772, the National Institute of Child Health and Human Development P50HD103557, National Center for Advancing Translational Science UCLA CTSI Grant UL1TR001881, the W. M. Keck Foundation Junior Faculty Award, UCLA Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research (BSCRC) Innovation Award, the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program, and the Friends of the Semel Institute for Neuroscience & Human Behavior Friends Scholar Award to Y. Z" We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "This work is supported by the Achievement Rewards for College Scientists Foundation Los Angeles Founder Chapter and the National Institute of Mental Health of the National Institutes of Health (NIH) Award T32MH073526 to M.C.K, the National Institute of Neurological Disorders and Stroke of the National Institute of Health (NIH) R00NS089780, R01NS109025, the National Institute of Aging of the NIH R03AG065772, the National Institute of Child Health and Human Development P50HD103557, National Center for Advancing Translational Science UCLA CTSI Grant UL1TR001881, the W. M. Keck Foundation Junior Faculty Award, UCLA Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research (BSCRC) Innovation Award, the UCLA Jonsson Comprehensive Cancer Center and BSCRC Ablon Scholars Program, and the Friends of the Semel Institute for Neuroscience & Human Behavior Friends Scholar Award to Y. Z. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." Please include your amended statements within your cover letter; we will change the online submission form on your behalf. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: No ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors set out to investigate whether in the healthy brain, lymphocytes play a role in the transcriptomic phenotype of glial cells. The study has solid foundation in the idea that adaptive immune changes correlate with changes to glial cells in various disease states. To answer the question the authors use lymphocyte (Rag2-/-) deficient mice in naïve states as well as control mice and conduct RNA sequencing on acutely purified microglia, astrocytes, OPCs, and oligodendrocytes. The sequencing reveals that once lymphocytes are eliminated there are no transcriptomic differences in glia except for modest differences seen in the oligodendrocytes, though gross morphology of WM remains the same. Although there is space and need for a publication of this kind, as it stands the publication is lacking clarity as to the overall impact of the findings and the authors must expand on the topic. Reviewer #2: In this study, the authors sought to investigate whether lymphocytes are regulating the molecular phenotypes of glial cells (OPCs, oligodendrocytes, microglia, and astrocytes) in the healthy brain. They used a Rag2-/- mouse model (which results to the loss of all mature lymphocytes, including CD4+ T cells, CD8+ T cells, and B cells) to characterize the molecular phenotype of glial cells through RNA sequencing. The authors reported no changes in the molecular signatures of the majority of the glial cells, with the exception of oligodendrocytes. Considering the emerging interest on neuroimmune interactions (either innate or adaptive immune system) and the critical role they have upon the brain homeostasis and behavior, this study will help to further delve into potential connections between lymphocytes and glial cells in the CNS. However, there are some major concerns as well as minor suggestions about the study: 1. The authors in the introduction section (and specifically lines 44-52) focus on studies related to meningeal lymphocyte roles in the brain. It is understandable that they should be distinguished from the peripherally recruited lymphocytes, however there is no other reference of the meningeal lymphocytes again in the manuscript and no distinction of them in the experiments they performed. Is there a specific reason the authors are underscoring this lymphocytic population? If not, then I would recommend using this space for the following suggestions (see end of comment 1). Moreover, in the next paragraph (lines 56-72), the authors provide a general background about functions of glial cells in health and disease. I agree that it is important to introduce the glial cells, since it is an important aspect of this study, however It should not be narrated as a glial section from a review paper. My recommendation would be to focus on the neuroimmune interactions and the effects they have on glial cells and brain homeostasis, and importantly provide more information about the roles of lymphocytes in CNS health and disease-since this is the central scope of the paper (should be significantly expanded more than just the 81-83 lines). Along the same lines the authors should provide more information about the Rag2-/- animal model in the introductory section, and specifically discuss previous findings regarding the cellular, molecular and behavioral mechanisms shown in the literature (i.e. refs 61-62). The reader should be able to understand the current gap in knowledge and how this paper seeks to contribute on that. 2. The authors mention in lines 92-94: «Overall, we find little evidence that lymphocytes influence CNS function by majorly contributing to the cellular states of glial cell types in the healthy brain». I find this inaccurate for 3 reasons: i) this study focuses only in tissue isolated from cerebral cortex (excluding the remaining brain areas), ii) the RNA sequencing analysis portrays molecular signatures and not cellular states of glial cells, and iii) the molecular changes found in the oligodendrocyte populations should have been further characterized to be able to conclude on that (as later will be discussed). 3. In the materials & methods section (line 116), the anti-CD45 also targets a small population of resident macrophages (~1-3%). This should be depicted in the manuscript. 4. With regard to Figure 1 data the authors: - Have not included information regarding either in figure legend or in the methods what z-score depicts and based on which control group the heatmap scale was made (increase or reduction of TPM compared to what control). - I would recommend including more marker genes (at least 4 more classic markers) for each glial cluster. - I would recommend the authors to provide a dot-plot analysis displaying the average expression levels (Change to avg. exp. scale), as well as the percentage of cells within each cell cluster expressing each marker gene (% Expression), split in groups of Rag2-/- vs Rag2+/+ mice. This information is needed to grasp the molecular signature of each group as well as whether the % of cells expressing the markers changes. 5. As in Figure 1, in Figure 2 more information about the volcano-plots should be included in the figure legend and the material & methods section. 6. The authors demonstrate an important finding depicting that lymphocyte deficiency dramatically affects the oligodendrocyte transcriptome. However, instead of focusing on this novel finding and try to strengthen their hypothesis with supplementary experiments, they only use one and a half panel [2A (Oligodendrocytes) and 2B] and they conclude in lines 244-245 that: «Despite the change in gene expression, gross patterns of myelin appear unchanged in Rag2-/- mice based on immunofluorescence of myelin basic protein (Fig 2B)». Therefore, there are some major points that the authors should improve for this section: i) Perform RNA expression analysis (i.e. RT-qPCR) to validate some things that showed up in their RNA sequencing analysis. ii) Then the next step would be to check protein expression (i.e. immunoblot analysis of some classic myelin or generally mature oligodendrocyte markers). iii) The authors provide 2 representative immunofluorescent staining for MBP, which brings up several issues: - There are no graphs or statistics to support their claims - These images actually depict a decrease in Rag2-/- mice - But even if the representative images are wrongly selected, there is no information which area of the cortex is this. The white matter can be dramatically different depending on the area and the bregma coordinates these sections are from. - The reader should be able to appreciate a larger cortical area (use lower magnification image and include insets with higher magnification) - I would strongly recommend quantification, if there has not been performed already, which should be normalized per area (or use integrated analysis). 7. As mentioned in comment 6, the authors decided to not follow the innovative results they had from the RNA sequencing (Figs 1 and 2), but instead they used the whole Figure 3 to compare their findings on microglia with the previous publication of Pasciuto et al., Cell (2020). In my opinion the purpose and the flow of experiments in a study should not be determined by another study but on the hypothesis the authors have. On many occasions (lines 254-259) in the results section the authors compared their results with the previous study (it is more usual to do so in the discussion section), feeling as the sole purpose of this study was to prove the Pasciuto publication wrong. I would have been a lot more supportive on the narrative that the authors decided to take in Figure 3, if there was conclusive data of no effects of Lymphocytes upon the Oligodendrocytes (and as a consequence the authors sought investigate the microglia in more depth). However, the authors performed only a superficial characterization of Oligodendrocytes, and therefore decided to neglect the novel findings of their RNAseq study, making hard to follow the exact hypothesis of the study. 8. Regarding Figure 3, as previously mentioned in comment 6, the authors should also include either in the figure legend or the materials section, the following information: - How the quantification of RNAscope analysis was performed. - Which area of the cortex was analyzed - It should also be depicted on the y axis of the graphs that the mean fluorescent intensity was normalized to the area. 9. The authors in the first sentence of the discussion (lines 313-314): In this study, we find that microglia in adult Rag2-/- mice under homeostatic conditions are indistinguishable from microglia in immunocompetent mice. However, apart from the RNA sequencing data and the RNA expression of Tmem119 and C1qa, there is no other support for the “indistinguishable” phenotype the authors claim. I would recommend characterization of supplementary microglial markers not only on a RNA level (some classic markers for RT-qPCR: P2RY12, PTPRC, CX3CR1, CTSS, LPAR6, CD68, ARHGAP24, ITGAM, AIF1), but most importantly for protein expression experiments. In my point of view, what the authors depict on this study is that there is only an indication of no substantial molecular signature differences in microglia during lymphocyte deficiency, which remains to be further examined with the aforementioned experiments (especially when comparing these results with the Pasciuto et al. publication, which has dedicated a large palette of experimental approaches to conclude to their findings). 10. Furthermore, in Fig.3a-b based on the RNAscope in situ hybridization in Rag2-/- and Rag2+/+ brains, the authors conclude that the maturation of microglia is unaffected by the lymphocyte deficiency. However, again this cannot be concluded just by fluorescent quantification of just three RNA expression markers, and no protein analysis. I would at least request the authors to utilize their RNAseq expression dataset to complement these findings with a comparative transcriptional analysis using a wide range of microglial maturation genes from Rag2-/- vs the Rag2+/+ mice, in order to get a general score. 11. Of importance, a clarification is required for the Fig.3c. The authors took all the differentially expressed genes in microglia from the MHCII-knockout mice from the Pasciuto study and performed gene set enrichment analysis (GSEA) using their RNA-seq data. Based on that the authors found that the up- and down-regulated genes identified in this study did not show global enrichment in this dataset. The question is, was the whole cluster of microglia used for this GSEA analysis or just the microglial subcluster 3 that is mentioned in the Pasciuto study? 12. In the discussion the authors suggest possible explanations of the different results shown on this study compared to the Pasciuto et al., publication. To this end, it would be important to further describe the differences between the Rag2 KO mice and the MHCII KO used on the other study. This way the reader would be able to appreciate the findings of this study and the deviations between the studies. 13. The authors should include a statistics section in the methods. Also, summary statistics, the data points behind means, medians and variance measures should be available. ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: Yes: A.G. Kokkosis ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. 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| Revision 1 |
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Lymphocyte deficiency alters the transcriptomes of oligodendrocytes, but not astrocytes or microglia PONE-D-22-23915R1 Dear Dr. Zhang, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Stella E. Tsirka Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors adequately responded to all questions provided. The paper was scientifically sound to begin with, but required some clarifications in wording and a few extra experiments. ********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No ********** |
| Formally Accepted |
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PONE-D-22-23915R1 Lymphocyte deficiency alters the transcriptomes of oligodendrocytes, but not astrocytes or microglia Dear Dr. Zhang: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Stella E. Tsirka Academic Editor PLOS ONE |
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