Development and validation of a set of novel and robust 4-lncRNA-based nomogram predicting prostate cancer survival by bioinformatics analysis

Peng Zhang; Xiaodong Tan; Daoqiang Zhang; Qi Gong; Xuefeng Zhang

doi:10.1371/journal.pone.0249951

Peer Review History

Original SubmissionSeptember 4, 2020
10 Dec 2020 Decision Letter - Hiromu Suzuki, Editor PONE-D-20-27863 Development and validation of a set of novel and robust 4-lncRNA-based nomogram predicting prostate cancer survival by bioinformatics analysis PLOS 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. Please submit your revised manuscript by Jan 17 2021 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. 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Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Hiromu Suzuki, M.D., Ph.D. Academic Editor PLOS ONE Additional Editor Comments: This manuscript was carefully reviewed by 2 experts, and both of them found several concerns which need to be addressed before acceptance. For instance, reviewer 1 suggested to discuss the limitation of this study. Reviewer 2 also suggested additional analysis using other datasets to validate the results. Please respond to each of the reviewer comments. 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. 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We will update your Data Availability statement to reflect the information you provide in your cover letter. 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. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ [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: No Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know 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 manuscript by Zhang, et al. uses the TCGA data to identify differentially expressed lncRNA between cancerous and non-cancerous tissues. In their analysis, they identified four lncRNA’s (2 protective and 2 harmful) that help improve stratification of overall survival from prostate cancer. Evaluating their data, it appears that there were only 9 deaths amongst the 397 patients who were included in the study. Therefore, since they are only evaluating overall survival, and not biochemical recurrence, distant metastasis, or progression of disease, how their results can be meaningful in making a clear utility of the four lncRNA’s. The limitations of their study are not discussed at all. They also make overstatements that their findings can be used to determine need for adjuvant therapy. However, without validation and evaluation of other parameters, besides overall survival, they cannot make such lofty claims. Reviewer #2: 1、The as-constructed lncRNAs-based signature in this study can serve as a novel tool and shed more lights on PCa diagnosis and treatment. The 4 lncRNAs–based signature is constructed to predict the OS for PCa through bioinformatic analysis. This prediction signature outstandingly improves the Gleason score performance in distinguishing PCa, and it can also be used to discriminate PCa (Gleason > 7). 2、It is better to add other databases analysis and related function experiments. 3、A few sentence typos，such as line78 4-lncrNA etc. ****** 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. https://doi.org/10.1371/journal.pone.0249951.r001
Revision 1
12 Mar 2021 Author Response Dear Dr. Hiromu Suzuki Thank you very much for your decision letter and advice on our manuscript (Manuscript PONE-D-20-27863) entitled “Development and validation of a set of novel and robust 4-lncRNA-based nomogram predicting prostate cancer survival by bioinformatics analysis”. We also thank the reviewers for the constructive comments and suggestions. We have revised the manuscript accordingly, and all amendments are indicated by red font in the revised manuscript. In addition, our point-by-point responses to the comments are listed below this letter. We hope that our revised manuscript is now acceptable for publication in your journal and look forward to hearing from you soon. With best wishes, Yours sincerely, Xuefeng Zhang First of all, we would like to express our sincere gratitude to the reviewers for their constructive and positive comments. Replies to Reviewer 1 Reviewer #1: The manuscript by Zhang, et al. uses the TCGA data to identify differentially expressed lncRNA between cancerous and non-cancerous tissues. In their analysis, they identified four lncRNA’s (2 protective and 2 harmful) that help improve stratification of overall survival from prostate cancer. Evaluating their data, it appears that there were only 9 deaths amongst the 397 patients who were included in the study. Therefore, since they are only evaluating overall survival, and not biochemical recurrence, distant metastasis, or progression of disease, how their results can be meaningful in making a clear utility of the four lncRNA’s. The limitations of their study are not discussed at all. They also make overstatements that their findings can be used to determine need for adjuvant therapy. However, without validation and evaluation of other parameters, besides overall survival, they cannot make such lofty claims. Response: We added gene sequencing and clinical data from ICGC database to conduct additional analysis and verification of the prediction performance of our prediction model. Because the mortality rate for prostate cancer in the United States is so low, only nine of the 397 Americans from the TCGA database previously included in the study died. Because this study evaluated overall survival, we added 378 patients from the ICGC database from China, 34 of whom died. Thus, the reliability of this study is further increased. We have added a discussion of the limitations of this study. Replies to Reviewer 2 Reviewer #2: 1、The as-constructed lncRNAs-based signature in this study can serve as a novel tool and shed more lights on PCa diagnosis and treatment. The 4 lncRNAs–based signature is constructed to predict the OS for PCa through bioinformatic analysis. This prediction signature outstandingly improves the Gleason score performance in distinguishing PCa, and it can also be used to discriminate PCa (Gleason > 7). 2、It is better to add other databases analysis and related function experiments. 3、A few sentence typos，such as line78 4-lncrNA etc. Response: 1. We added gene sequencing and clinical data from ICGC database to conduct additional analysis and verification of the prediction performance of our prediction model. 2. In view of the expression errors in our paper you proposed, we have also made corresponding modifications. 3. Correction has been made in the revised manuscript Attachments Attachment Submitted filename: Response to Reviewers_Feb15.docx https://doi.org/10.1371/journal.pone.0249951.r002
29 Mar 2021 Decision Letter - Hiromu Suzuki, Editor Development and validation of a set of novel and robust 4-lncRNA-based nomogram predicting prostate cancer survival by bioinformatics analysis PONE-D-20-27863R1 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, Hiromu Suzuki, M.D., Ph.D. 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 Reviewer #2: (No Response) ******** 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: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: (No Response) ****** 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: (No Response) ****** 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: (No Response) ****** 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: (No Response) Reviewer #2: (No Response) ****** 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 https://doi.org/10.1371/journal.pone.0249951.r003
Formally Accepted
19 Apr 2021 Acceptance Letter - Hiromu Suzuki, Editor PONE-D-20-27863R1 Development and validation of a set of novel and robust 4-lncRNA-based nomogram predicting prostate cancer survival by bioinformatics analysis 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. Hiromu Suzuki Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0249951.r004

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