Identification and experimental validation of BMX as a crucial PANoptosis‑related gene for immune response in Spinal Cord Injury

Tianbao Feng; Jiating Hu; Mi Xie; Guodong Shi; Qi Wang; Jingyuan Yao; Xiaoqin Liu

doi:10.1371/journal.pone.0328002

Peer Review History

Original SubmissionFebruary 25, 2025
Decision Letter - Partha Mukhopadhyay, Editor PONE-D-25-09725Identification and experimental validation of BMX as a crucial PANoptosis‑related gene for immune response in Spinal Cord InjuryPLOS ONE Dear Dr. Liu, 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. Your manuscript was reviewed by two experts and both of them suggested many useful comments which should be addressed during revision. Please submit your revised manuscript by May 24 2025 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 . 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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: Partly Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 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: Yes ****** 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 used a Database of human patients some hours after spinal cord injury (SCI) to search for genes and/or pathways that could be important for this kind of lesion. I am only slightly familiar with bioinformatics, but I know that the results are as good as the database, and how it is analyzed and interpreted counts as much as the analysis itself. First, the dataset you are based on is, as you cited, white blood cells of peripheral blood. Although the authors mention justified limitations for this manuscript, I still think some caveats should be addressed. As it is not a dataset with samples from the injured tissue (which, for the nature of the lesion, is very hard to accomplish), an important approach would be selecting cell markers to trace an inflammatory profile of the subjects that could correspond to the changes in the genes you show. More importantly, I miss more in vivo data. The authors mention the heterogenicity of human samples. Here there was the chance to minimize such effects and to directly study how this lesion would affect individuals in a controlled environment. When we perform animal experiments, we must use the maximum out of them for ethics sake. Here you brought only one PCR result from the spinal cord of the animals. The very fact that you studied the injured neural tissue in the animals and peripheral WBC in your dataset should be used as a caveat. To ease such discrepancy, you could run some RT-qPCR for inflammatory cell markers and try to relate that to what you find in the human peripheral WBC dataset you used. If the authors still have samples of the injured tissue for histology, immunohistochemistry or in situ hybridization could add better knowledge to your data and a visualization of the cell infiltration. The in vivo experiments you bring here are not a proper validation of BMX as the authors claim in the title. Better validation of the importance of a single gene to make it worth publication alone could include experimental groups either treated with blockers/antagonists of the gene transcript or knockout animals. The authors mention other genes with possible importance on the way to get to BMX, like the CASP5. An alternative to this issue would be also to check the top 3, top 5 genes that are altered in the bioinformatics analysis. Nevertheless, I am also curious about why the authors chose to work with female rats. I suppose those were intact animals because you don’t mention any previous surgery. Was there any sort of estrus cycle control made to use the animals at the same time for all animals? Estrogen shows a protective effect on spinal cord injury (PMID: 36736846; 26461840), even therapeutically (PMID: 32680442; 12853305). This should be also raised as a limitation or a possible future direction, comparing males and females. Minor points: - Gene names, scientific names, and Latin terms such as in vivo should be in italics. - Supplementary Table 2 should be incorporated into the manuscript. Reviewer #2: My comments are uploaded as an attachment and I recommend some minor changes to be done before the final acceptance is made. The manuscript is well-written in terms of global scientific reporting standards but needs some revisions. ****** 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: No ******** [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 . Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: Review to PanOptosis.pdf https://doi.org/10.1371/journal.pone.0328002.r001
Revision 1
26 May 2025 Author Response Dear Reviewers, I would like to express my sincere gratitude for the time and effort you have dedicated to evaluating my manuscript titled "Identification and Experimental Validation of BMX as a Crucial PANoptosis-Related Gene for Immune Response in Spinal Cord Injury." I greatly appreciate the constructive comments and suggestions, which have significantly improved the quality of the paper. 1. ORCiD iD Validation: We will follow the steps outlined in your email to validate our ORCiD iD in the Editorial Manager system as required. We understand the importance of completing this validation and will ensure it is done promptly. 2. Animal Experiment Details: In response to your request, we have updated the SCI rat model establishment section to include additional information regarding the animal experiments. Specifically, the revised text is as follows: "At the end of the experiments, the animals were euthanized by administering an overdose of isoflurane for approximately 10 minutes, followed by exsanguination." This update addresses the details of euthanasia and the measures taken to alleviate suffering in accordance with PLOS ONE’s submission guidelines. In this revised version, I have addressed all the points raised by the reviewers. Below, I provide detailed responses to each comment, including the corresponding changes made to the manuscript. We have also addressed the reviewers’ comments in a separate document titled “Response to Reviewers.” For clarity, the reviewers' comments are included in italicized bold and our specific responses follow in Times New Roman font. Thank you once again for your valuable feedback and consideration. Sincerely, Xiaoqin Liu, PhD Yan’an Medical College of Yan’an University Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0328002.r002
Decision Letter - Partha Mukhopadhyay, Editor PONE-D-25-09725R1Identification and experimental validation of BMX as a crucial PANoptosis‑related gene for immune response in Spinal Cord InjuryPLOS ONE Dear Dr. Liu, 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. Your revised manuscript was reviewed same experts and one of them suggested a minor revision. Please address those comments and a quick editorial decision will be taken after satisfactory revision without sending to experts. Please submit your revised manuscript by Jul 30 2025 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Partha Mukhopadhyay, Ph.D. Section Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] 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 Reviewer #2: 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 Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: 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 Reviewer #2: 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: I appreciate the authors’ thorough and satisfactory responses to my previous concerns. I have only a few minor corrections to suggest regarding Figure 11. In subpanel 11B, a required symbol is missing. Additionally, the figure legend does not describe the significance symbol used. Lastly, I noted a likely error in the description of the IHC, where a reference is made to the “Lamc1 protein,” which appears to be unrelated or included by mistake. Please address these issues in the revised manuscript. Reviewer #2: The points and questions that were raised by me has been addressed. So do suggest acceptance of the manuscript. ****** 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 Reviewer #2: No ******** [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 . Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0328002.r003
Revision 2
16 Jun 2025 Author Response Reviewer #1: I appreciate the authors’ thorough and satisfactory responses to my previous concerns. I have only a few minor corrections to suggest regarding Figure 11. In subpanel 11B, a required symbol is missing. Additionally, the figure legend does not describe the significance symbol used. Lastly, I noted a likely error in the description of the IHC, where a reference is made to the “Lamc1 protein,” which appears to be unrelated or included by mistake. Please address these issues in the revised manuscript. Response to Reviewer #1: Response: We sincerely thank the reviewer for their careful evaluation of our manuscript and for acknowledging our thorough responses to previous concerns. We have addressed the minor issues raised as follows: Missing symbol in subpanel 11B of Figure 11: We have carefully reviewed Figure 11 and added the required symbol to subpanel 11B as suggested. The figure has been updated accordingly. Figure legend not describing the significance symbol: We have updated the figure legend to include a clear description of the significance symbol used in Figure 11. This change ensures that the figure legend fully corresponds with the content presented in the figure. Incorrect reference to “Lamc1 protein” in the IHC description: We appreciate the reviewer’s attention to this detail. After reviewing the manuscript, we found that the reference to the “Lamc1 protein” was an error. We have corrected this by changing it to “BMX protein” to accurately reflect the intended reference. The manuscript has been updated accordingly. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0328002.r004
Decision Letter - Partha Mukhopadhyay, Editor Identification and experimental validation of BMX as a crucial PANoptosis‑related gene for immune response in Spinal Cord Injury PONE-D-25-09725R2 Dear Dr. Liu, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Partha Mukhopadhyay, Ph.D. Section Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0328002.r005
Formally Accepted
Acceptance Letter - Partha Mukhopadhyay, Editor PONE-D-25-09725R2 PLOS ONE Dear Dr. Liu, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Partha Mukhopadhyay Section Editor PLOS ONE https://doi.org/10.1371/journal.pone.0328002.r006

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