miR-455-3p has superior diagnostic potential to PSA in peripheral blood for prostate cancer

Yi Cen; Shourui Feng; Yuyu Xu; Churuo Zhang; Xiangjin Lin; Xuan Ye; Zeyu Zha; Haiyan Wang; Guangbin Zhu

doi:10.1371/journal.pone.0317385

Peer Review History

Original SubmissionApril 23, 2024
8 Nov 2024 Decision Letter - Gurudeeban Selvaraj, PhD, Editor PONE-D-24-12980miR-455-3p has superior diagnostic potential to PSA in peripheral blood for prostate cancerPLOS ONE Dear Dr. Zhu, 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 Dec 23 2024 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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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The manuscript evaluated miR-455-3p and PSA in the diagnosis of prostate cancer; it is well-designed; however, some flaws should be considered as follows: Please determine the internal control and housekeeping gene in the material method. Please use the reference for the Livak method (2-∆∆CT). It would be better to check urine Cell-Free MicroRNAs in prostate cancer patients, and compare it with serum concentration. Please explain the number of patients and healthy control in the material method, in sample collection the number of patients is not enough (PCa:8, healthy:4); however, in the result it was much more, so clarify the number of samples in the Clinical Sample Collection. Also, mention if qPCR was conducted on all the samples. It would better to estimate the correlation (r) between the concentration of PSA and the relative gene expression value in patients and healthy control. ****** 6. 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Revision 1
18 Nov 2024 Author Response Please determine the internal control and housekeeping gene in the material method. Thank you for your feedback. We have revised the manuscript accordingly. In the qPCR analysis, we have included U6 as the internal control gene to normalize the expression levels. This modification is now reflected in the materials and methods section. Please use the reference for the Livak method (2-∆∆CT). Thank you for your suggestion. We have now included the appropriate reference for the Livak method (2^-ΔΔCT) in the manuscript: Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3(6):1101-8. doi: 10.1038/nprot.2008.73. PMID: 18546601. It would be better to check urine Cell-Free MicroRNAs in prostate cancer patients and compare it with serum concentration. Thank you for the insightful suggestion. We have incorporated an analysis of urine cell-free miRNAs by adding GSE138740 dataset: Additionally, we included Figure S2, which presents correlation analyses of urinary cell-free miR-455-3p with clinical features in prostate cancer (PCa) patients. Specifically: Figure S2A shows a comparison of miR-455-3p expression between prostate cancer (P) and control (C) groups in the GSE138740 dataset. Figure S2B compares miR-455-3p expression between patients with Gleason scores (GS) < 8 and ≥ 8 in the GSE138740 dataset. Please explain the number of patients and healthy control in the material method, in sample collection the number of patients is not enough (PCa:8, healthy:4); however, in the result it was much more, so clarify the number of samples in the Clinical Sample Collection. Also, mention if qPCR was conducted on all the samples. Thank you for pointing this out. In the revised materials and methods section, we have clarified the number of samples used in our analysis: The results presented in Figures 1–3 and 5 are based on analyses of public datasets (GSE206793 and GSE112264). Figure 4 results reflect analyses conducted on clinical samples, which included qPCR validation. For the clinical sample collection, we used a total of 8 prostate cancer (PCa) samples and 4 healthy controls for qPCR analysis, as described. The qPCR was conducted on all clinical samples collected, and this has been clarified in the materials and methods section. It would better to estimate the correlation (r) between the concentration of PSA and the relative gene expression value in patients and healthy control. Thank you for the suggestion. We have conducted a correlation analysis between PSA concentration and miR-455-3p expression and presented the results in Figure S1, which shows the correlation in the GSE206793 dataset. Attachments Attachment Submitted filename: response.docx https://doi.org/10.1371/journal.pone.0317385.r002
27 Dec 2024 Decision Letter - Gurudeeban Selvaraj, PhD, Editor miR-455-3p has superior diagnostic potential to PSA in peripheral blood for prostate cancer PONE-D-24-12980R1 Dear Dr. Zhu, 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. 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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: (No Response) Reviewer #2: The detection of PSA, a commonly utilized tumor marker for prostate cancer (PCa), is often influenced by medications and various non-cancerous prostate lesions, highlighting the need for a novel marker to enhance diagnostic specificity and sensitivity. This study, leveraging bioinformatics techniques, has successfully identified miR-455-3p as a promising new marker. The article offers valuable insights into the advantages of utilizing miR-455-3p as an alternative PCa marker and delves into the intricate molecular mechanisms underlying its biological functions. The authors have thoughtfully addressed and revised the comments provided by previous reviewers. The overall structure and logic of the article are clear and coherent, making it a potential new tool for the precise diagnosis of clinical PCa. Therefore, I warmly recommend the acceptance of this 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: Yes: Elham Kazemirad Reviewer #2: No ******** https://doi.org/10.1371/journal.pone.0317385.r003
Formally Accepted
5 Jan 2025 Acceptance Letter - Gurudeeban Selvaraj, PhD, Editor PONE-D-24-12980R1 PLOS ONE Dear Dr. Zhu, 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 If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks 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. Gurudeeban Selvaraj, PhD Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0317385.r004

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