Multi-omics analysis indicates an association between TAPBP and prostate cancer

Xinlong Wang; Aimin Jiang; Chao Li; Zhiyong Liu

doi:10.1371/journal.pone.0336438

Peer Review History

Original SubmissionNovember 20, 2024
15 May 2025 Decision Letter - Sarah Jose, Editor Dear Dr. Liu, Please submit your revised manuscript by Jun 28 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. 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, Sarah Jose, Ph.D. Staff 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Thank you for stating in your Funding Statement: [This work was supported by the 234 Panfeng Program at Changhai Hospital (No. 2020YXK030).]. Please provide an amended statement that declares all the funding or sources of support (whether external or internal to your organization) received during this study, as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now. Please also include the statement “There was no additional external funding received for this study.” in your updated Funding Statement. Please include your amended Funding Statement within your cover letter. We will change the online submission form on your behalf. 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. 4. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. 5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information . [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? Reviewer #1: Yes Reviewer #2: Partly ******** 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 Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: Relevant paper with high level of genomic-related in silico analyses. Authors showcased experience in the field of cancer genomics and modeling. However, I would recommend referring to the work of Rosalind Eeles, world expert in prostate cancer causing genes. I do not see even one of her many seminal papers cited here. So I urge the authors to amend this manuscript by referring to studies of RE, who identified prostate cancer susceptibility genes and led world-wide studies on thousands of both healthy men and individuals with prostate cancer. Reviewer #2: The manuscript titled “Multi-omics association study identifies potential prostate cancer-causing genes” presents a multi-omics approach to identify genes potentially associated with prostate cancer, with the aim of uncovering novel biomarkers. The study is well-executed, and the results are clearly presented. However, the discussion section is notably weak and requires substantial revision. It barely engages with the study’s own findings, limiting the interpretation and contextualization of the data. Additionally, the manuscript’s title is misleading, as the results do not fully support the strong claim implied. While the study shows promise, significant improvements—particularly in the discussion—are necessary to strengthen the manuscript. Additional suggestions are provided in the annotated PDF. ****** 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: PONE-D-24-53031_reviewer_PF.pdf https://doi.org/10.1371/journal.pone.0336438.r001
Revision 1
12 Jun 2025 Author Response Responses to editors’comments: Thank you for the editor’s kind suggestions. According to the editor’s requirements, we have endeavored to make the manuscript conform to the style of PLOS ONE and have included a funding statement in the new cover letter. Responses to reviewers’comments: Major points of Reviewer #1 Relevant paper with high level of genomic-related in silico analyses. Authors showcased experience in the field of cancer genomics and modeling. However, I would recommend referring to the work of Rosalind Eeles, world expert in prostate cancer causing genes. I do not see even one of her many seminal papers cited here. So I urge the authors to amend this manuscript by referring to studies of RE, who identified prostate cancer susceptibility genes and led world-wide studies on thousands of both healthy men and individuals with prostate cancer. Response: We thank the reviewer for this meaningful suggestion. In the introduction section of the manuscript, we mentioned the research of Rosalind Eeles (Reference 2). Following the reviewer's suggestion, we have added a discussion of the similarities and differences with the study of Rosalind Eeles in the discussion section and provided a citation (Conti DV, Darst BF, Moss LC, et al. Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction. Nature genetics. 2021 Jan;53(1):65-75). Major points of Reviewer #2 The manuscript titled “Multi-omics association study identifies potential prostate cancer-causing genes” presents a multi-omics approach to identify genes potentially associated with prostate cancer, with the aim of uncovering novel biomarkers. The study is well-executed, and the results are clearly presented. However, the discussion section is notably weak and requires substantial revision. It barely engages with the study’s own findings, limiting the interpretation and contextualization of the data. Additionally, the manuscript’s title is misleading, as the results do not fully support the strong claim implied. While the study shows promise, significant improvements—particularly in the discussion—are necessary to strengthen the manuscript. Additional suggestions are provided in the annotated PDF. Response: We thank the reviewer for this meaningful suggestion. In the revised manuscript, we have provided a more in-depth explanation and discussion of the genes ultimately identified. Additionally, we have changed the title of the manuscript to “Multi-omics analysis indicates an association between TAPBP and prostate cancer.” Attachments Attachment Submitted filename: Responses to reviewers.docx https://doi.org/10.1371/journal.pone.0336438.r002
9 Sep 2025 Decision Letter - Yang Shi, Editor Multi-omics analysis indicates an association between TAPBP and prostate cancer. PLOS ONE Dear Dr. Wang, Thank you for submitting your manuscript to PLOS ONE. First, we apologize again for the unusual delay in processing your submission, as the original Academic Editor who had agreed to handle it became unavailable. We have invited Dr. Yang Shi, who has agreed to serve as the new Academic Editor. Academic Editor Comments ============================== Academic Editor Comments Please submit your revised manuscript by Oct 23 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. 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, Dr. Yang Shi Academic Editor PLOS ONE Journal Requirements: If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. [Note: HTML markup is below. Please do not edit.] 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.0336438.r003
Revision 2
11 Sep 2025 Author Response Responses to editors’comments: Thank you for the editor’s kind suggestions. According to the editor’s requirements, we have endeavored to make the manuscript conform to the style of PLOS ONE and have included a funding statement in the new cover letter. Responses to editors’comments 2: Thank you for the editor’s kind suggestions. 1. The abstract on the submission page includes non-English text; this section needs to be translated into English. Response: We have corrected the abstract of the submission page 2. On the title page, please clearly identify the corresponding author (or state that the last two authors are joint corresponding authors, if that is what the asterisk * denotes) and provide the corresponding author’s email address. Response: We have identified the corresponding author and email address as required 3. The title of Section 1.4, “Single-cell data,” duplicates that of Section 1.3, and the content of Section 1.4 is not re\lated to single-cell data. Response: We have corrected the title of 1.4 to Ethics Statement Responses to reviewers’comments: Major points of Reviewer #1 Relevant paper with high level of genomic-related in silico analyses. Authors showcased experience in the field of cancer genomics and modeling. However, I would recommend referring to the work of Rosalind Eeles, world expert in prostate cancer causing genes. I do not see even one of her many seminal papers cited here. So I urge the authors to amend this manuscript by referring to studies of RE, who identified prostate cancer susceptibility genes and led world-wide studies on thousands of both healthy men and individuals with prostate cancer. Response: We thank the reviewer for this meaningful suggestion. In the introduction section of the manuscript, we mentioned the research of Rosalind Eeles (Reference 2). Following the reviewer's suggestion, we have added a discussion of the similarities and differences with the study of Rosalind Eeles in the discussion section and provided a citation (Conti DV, Darst BF, Moss LC, et al. Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction. Nature genetics. 2021 Jan;53(1):65-75). Major points of Reviewer #2 The manuscript titled “Multi-omics association study identifies potential prostate cancer-causing genes” presents a multi-omics approach to identify genes potentially associated with prostate cancer, with the aim of uncovering novel biomarkers. The study is well-executed, and the results are clearly presented. However, the discussion section is notably weak and requires substantial revision. It barely engages with the study’s own findings, limiting the interpretation and contextualization of the data. Additionally, the manuscript’s title is misleading, as the results do not fully support the strong claim implied. While the study shows promise, significant improvements—particularly in the discussion—are necessary to strengthen the manuscript. Additional suggestions are provided in the annotated PDF. Response: We thank the reviewer for this meaningful suggestion. In the revised manuscript, we have provided a more in-depth explanation and discussion of the genes ultimately identified. Additionally, we have changed the title of the manuscript to “Multi-omics analysis indicates an association between TAPBP and prostate cancer.” Attachments Attachment Submitted filename: Responses to reviewers1.docx https://doi.org/10.1371/journal.pone.0336438.r004
26 Oct 2025 Decision Letter - Yang Shi, Editor Multi-omics analysis indicates an association between TAPBP and prostate cancer. PONE-D-24-53031R2 Dear Dr. Wang, 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. For questions related to billing, please contact billing support . 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, Yang Shi, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): One minor issue is that some sections are numbered while others are not, which the authors are advised to correct during proofreading. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #2: All comments have been addressed Reviewer #3: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #2: Yes Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #2: Yes Reviewer #3: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #2: Yes Reviewer #3: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #2: Yes Reviewer #3: Yes ****** Reviewer #2: (No Response) Reviewer #3: The authors have satisfactorily addressed all prior concerns. I have no additional comments. Congratulations to the authors. ****** 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 #2: No Reviewer #3: No ******** https://doi.org/10.1371/journal.pone.0336438.r005
Formally Accepted
Acceptance Letter - Yang Shi, Editor PONE-D-24-53031R2 PLOS ONE Dear Dr. Wang, 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. 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. Yang Shi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0336438.r006

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