Peer Review History
| Original SubmissionJuly 24, 2020 |
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PONE-D-20-23009 MicroRNA characteristics in epithelial ovarian cancer. PLOS ONE Dear Dr. Prahm, 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. ============================== In addition to addressing the comments from the reviewers, please focus on the validation of the experiments and means of accessing rigor and reproducibility. ============================== Please submit your revised manuscript by Dec 11 2020 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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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. Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified whether consent was informed regarding the use of their tissue for the purposes of research. 3. Please note that PLOS does not permit references to “data not shown.” Authors should provide the relevant data within the manuscript, the Supporting Information files, or in a public repository. If the data are not a core part of the research study being presented, we ask that authors remove any references to these data. 4. To comply with PLOS ONE submission guidelines, in your Methods section, please provide additional information regarding your statistical analyses. For more information on PLOS ONE's expectations for statistical reporting, please see https://journals.plos.org/plosone/s/submission-guidelines.#loc-statistical-reporting. 5. In the Introduction section, please discuss how your study relates to and represents a scientific advance from your previous study in PLOS ONE (reference provided below): https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207319 Please provide a sound scientific rationale and justification for a separate publication on this topic. Thank you for your attention to this request. Additional Editor Comments (if provided): [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: 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 study performed by Prahm et al measured the expression levels of microRNAs in tumor samples from 197 patients with epithelial ovarian cancer using miRNA microarray. Data were normalized and analyzed for comparison between patients with different FIGO stages, tumor grades, histologic subtypes, and type I and type II tumors. The identified miRNAs with significantly altered expression levels between different groups of patients were further validated by analyzing external datasets where miRNA array expression profiles of ovarian cancer patients were described. The manuscript was well written and the data were presented in an intelligible fashion. However, the finding is not novel and the significance of the manuscript is compromised. Questions and criticism: 1. Most identified miRNAs with altered expression cannot be validated using the external datasets. Although this has been extensively discussed, it still brings concerns about the quality of the data. The microarray data are the only data created by this manuscript. The authors need to describe more about data processing, particularly how the raw data were normalized because miRNA arrays are usually spotted in low density due to low numbers and low expression of miRNAs. 2. The authors have not done any experiments to validate their array data except using the external datasets. But the external datasets failed to validate the changes of most miRNAs. Moreover, the fold changes of identified miRNAs are quite low, from 0.46 to 3.75 folds. A validation experiment using qRT-PCR is then highly needed. Other than confirming the changes of those identified miRNAs, the regulation of mRNA targets could be an alternative to validate the array data. 3. High-quality miRNA microarray data come from high-quality RNA samples. The authors have not mentioned anything about the quality control of their RNA isolation, particularly when RNA was isolated from formalin fixed and paraffin embedded tissues. But formalin fixation modifies nucleic acids and challenges the isolation of high-quality RNA for genetic profiling. Reviewer #2: I found this manuscript to be very well written and clear in it's presentation. There are a number of things that I will point out, and I feel that all are addressable to make this work acceptable for publication. The biggest issues are the validation failures, which in all honesty will make the very good work by the authors to have quite diminished interest to the readership. Can the data be approached using a multiple miRNA panel to address the question that they raise: to investigate if miRNA profiles could predict cytoreductive outcome in patients with FIGO stage IIIC and IV ovarian cancer? This could be a simple as constructing a polynomial predicting probability of cytoreductive outcomes based on ALL of the miRNAs described here that perform well and compare this with the performance of anatomical clinicopathological characteristics. The recent work by a large international group has taken this type of approach (DOI:https://doi.org/10.1016/j.annonc.2020.05.019) using a panel of select genes that they have identified. Using a combined miRNA panel may overcome the potential problems that could result from determinations by external cohorts outside the authors group. Using designations of Type I vs II ovarian cancers does not involve independent comparisons (see DOI: 10.3390/diagnostics10020056) because stage in addition to grade is a major determinant of aggressiveness. Let there be no mistaking my review: a very major issue is the validation failures. Additional points 1. While the origination of ovca in the fallopian tube has considerable momentum, the establishment that MOST ovarian cancers originate here is not well-established (line 55) 2. Lines 59-60 need to be adjusted in light of DOI: 10.3390/diagnostics10020056 3. Line 98 "are" change to "is" 4. Line 239 "differential" change to "differentially" 5. Line 295 "has" change to "have" 6. Line 362: "cloud" change to "could" 7. Reference 1 is outdated and should be replaced by https://doi.org/10.3322/caac.21590 8. A consideration of DOI:https://doi.org/10.1016/j.annonc.2020.05.019 should be included and referenced. 9. In Figure 1 the material below the figure is unclear to me. This should be explicitly explained in a figure legend. In addition, the colors chosen for the curves should be more distinct. For example, the 3rd and 4th curves from the top both appear black to me. This work could be morphed into an outstanding contribution deserving publication and I encourage the authors to do so. Otherwise the validation failures considerably reduce the importance of what they are reporting. ********** 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. |
| Revision 1 |
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MicroRNA characteristics in epithelial ovarian cancer. PONE-D-20-23009R1 Dear Dr. Prahm, 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, Shannon M. Hawkins, 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: 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: I appreciate the authors' efforts to make adjustments to the manuscript that reflect the points that I raised in review. I feel that it is ready for publication, having satisfied my review. ********** 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 |
| Formally Accepted |
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PONE-D-20-23009R1 MicroRNA characteristics in epithelial ovarian cancer. Dear Dr. Prahm: 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. Shannon M. Hawkins Academic Editor PLOS ONE |
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