Serial measurement of cytokines strongly predict COVID-19 outcome

Hasan Selcuk Ozger; Resul Karakus; Elif Nazli Kuscu; Umit Emin Bagriacik; Nihan Oruklu; Melek Yaman; Melda Turkoglu; Gonca Erbas; Aysegul Yucel Atak; Esin Senol

doi:10.1371/journal.pone.0260623

Peer Review History

Original SubmissionMay 28, 2021
1 Jul 2021 Decision Letter - Prasenjit Mitra, Editor PONE-D-21-17711 Serial measurement of cytokines strongly predict COVID-19 outcome PLOS ONE Dear Dr. Ozger, 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. ============================== ACADEMIC EDITOR: Please revise according to reviewers comments ============================== Please submit your revised manuscript by Aug 15 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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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 delete it from any other section. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No ****** 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 ****** 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 ****** 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 evaluated the predictive value of serially measured cytokines for 37 hospitalized COVID-19 cases and concluded that serially measured cytokines yield a better prediction for outcome of COVID-19 patients. Although the study appears interesting, there are a few issues that may have to be clarified/rectified. 1. The authors have stated their aim as to assess the value of change in cytokine levels in predicting COVID-19 mortality. To evaluate the same, ROC at different time points have been compared. However the comparison of ROC at different time points would enable the authors only to compare the predictive power of cytokines on one day compared to another. If the authors want to assess the value of change in cytokine levels, they may have to plot ROC with the change in the values. The authors may go through the following articles for reference: a. Yamaguchi, Kakuhiro MD, PhDa; Iwamoto, Hiroshi MD, PhDa,∗; Sakamoto, Shinjiro MD, PhDa; Horimasu, Yasushi MD, PhDa; Masuda, Takeshi MD, PhDa; Miyamoto, Shintaro MD, PhDa; Nakashima, Taku MD, PhDa; Ohshimo, Shinichiro MD, PhDb; Fujitaka, Kazunori MD, PhDa; Hamada, Hironobu MD, PhDc; Kohno, Nobuoki MD, PhDd; Hattori, Noboru MD, PhDa Serial measurements of KL-6 for monitoring activity and recurrence of interstitial pneumonia with anti-aminoacyl-tRNA synthetase antibody, Medicine: December 2018 - Volume 97 - Issue 49 - p e13542 doi: 10.1097/MD.0000000000013542 b. Kamarudin, A.N., Cox, T. & Kolamunnage-Dona, R. Time-dependent ROC curve analysis in medical research: current methods and applications. BMC Med Res Methodol 17, 53 (2017). https://doi.org/10.1186/s12874-017-0332-6 2. As the authors have mentioned in limitations, age and comorbidities are pronounced confounders of the study. Authors may have to explore the possibilities of regression analysis to account for the confounding effects of these factors. As different comorbodtites on its own can cause change in cytokine levels, it is imperative to delineate the role of cytokine in mortality independent of the influence of comorbidities. Further regression tools may help the authors in performing the analysis. Discussion also should include the possible role of these factors in altering the cytokine levels and leading to mortality. 3. I think Surviors and non- survivors would be a better terminology for the non-mortal and mortal groups. 4. Figures lack clarity. Better resolution figures to be included. ****** 6. 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Revision 1
11 Aug 2021 Author Response 08.03.2021 Thank you for your interest and valuable contribution to our article. We have revised our article according to your suggestions and made possible changes. We are resubmitting the article by making the changes suggested by the reviewers. New changes are marked in yellow in the manuscript. Best regards, Selcuk Journal requirements 1. Our manuscript re-edited according to PLOS ONE's style requirements. 2. Additional details on participant consent added to the method section. 3. The recommended statement added to the acknowledgment section of our article. The text on funding removed from the manuscript. 4. Ethics other than method section deleted. Answers to reviewer 1-Thank you very much for your suggestions. Our article is primarily based on the idea that single-measure cytokine analyzes with uncertain sampling time may be misleading due to the dynamic course of cytokines. For this reason, serial evaluations were planned. We think that the analysis on the change values you suggested will contribute to the objectives of the article. Therefore, the current analyzes have been reconsidered by taking into account the changes in cytokinin levels at day 0 and day 3, and necessary changes have been made in the article that we think will meet your recommendations. 2-We agree with you that regression analyzes are necessary to determine the role of cytokines in mortality, regardless of the influence of confounding factors such as, comorbidities, age, etc. However, we think that regression analyzes cannot be performed due to the current sample size especially in the non-survivors group. The number of patients included in the study was limited due to the low number of cases in our country during the study period, the fact that our study was conducted in a single center and central restrictions were imposed on multicenter studies related to COVID-19 in our country. Also, the high cost of financing due to the scope of the study, which aimed to evaluate many cytokines, caused the number of patients included in the study to be limited.This limitation is clearly stated in the limitation section of our article. 3-Based on your suggestions, the study groups were named survivors and non-survivors. 4-The figures in the study were evaluated and created in terms of re-resolution and clarity. Attachments Attachment Submitted filename: Answer to reviewers.docx https://doi.org/10.1371/journal.pone.0260623.r002
14 Sep 2021 Decision Letter - Prasenjit Mitra, Editor PONE-D-21-17711R1Serial measurement of cytokines strongly predict COVID-19 outcomePLOS ONE Dear Dr. Ozger, 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. ACADEMIC EDITOR: Please modify the manuscript Please submit your revised manuscript by Oct 29 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. 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, Prasenjit Mitra, MD, CBiol, MRSB, MIScT, FLS, FACSc, FAACC Academic 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: (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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: The reviewers have revised the manuscript adequately after addressing the comments and the efforts have to be appreciated. However, the following points may be noted: 1. For IL-1RA , the values are mentioned as 48 (7.1 to 9.1). Please do check once for typographical errors as median is less than the 75th percentile. 2. For PDGF-AA, the values are mentioned as 4857 ± 2411. From preliminary glance, the distribution appears to be normal. Please verify if the representation as mean ± SD is correct in this context or not. 3. In first line of discussion, it may have to be specifically mentioned that IL-6, IL-7, IL-10, IL-15, IL-27, IP-10, MCP-1, and GCSF cytokines on DAY OF ADMISSION could be used for prediction of mortality in COVID-19 patients. 4. The Figure 1 is not at all legible and is not acceptable in the current state . Figure 1 have to be redrawn. ****** 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 [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.0260623.r003
Revision 2
17 Sep 2021 Author Response 09.015.2021 Thank you for your interest and valuable contribution to our revised article. We have revised our article according to your suggestions and made possible changes. We are resubmitting the article by making the changes suggested by the reviewers. New changes are marked in yellow in the manuscript. Best regards, Selcuk Journal requirements 1.We've reviewed our reference list to make sure it's complete and accurate. References 23 and 24 ( [24] Costela-Ruiz VJ, Illescas-Montes R, Puerta-Puerta JM, Ruiz C, Melguizo-Rodriguez L. SARS-CoV-2 infection: The role of cytokines in COVID-19 disease. Cytokine Growth Factor Rev. 2020;54:62-75., [25] Petrey AC, Qeadan F, Middleton EA, Pinchuk IV, Campbell RA, Beswick EJ. Cytokine release syndrome in COVID-19: Innate immune, vascular, and platelet pathogenic factors differ in severity of disease and sex. J Leukoc Biol. 2021;109:55-66.) in the first manuscript were omitted from the first revision due to the reorganization of the discussion section. In the current revision, the references were checked and no change was made to the references. Answers to reviewer 1-Thank you very much for your suggestions. The values for IL-1RA in the non-survivor group were corrected to 48 (7.1 - 90.1). 2-You are right, the values for PDGF-AA show normal distribution. For this reason, instead of the median (IQR, 25-75%), it was preferred to presentation as mean ± SD. The error in this presentation was corrected and PDGF-AA values (5011 ± 2884 for non-survivors and 4283 ± 1979 for survivors) were shown. 3-'On the day of admission' was added in the first line of the discussion, according to your suggestion. 4- In our study, the GraphPad (version 9) program was used to create the graphs. Because Figure 1 is a multi-panel graph and many cytokine levels were compared, the desired image resolution could not be achieved. Figure 1 was revised based on your suggestions and your PLOS ONE figure preparation requirements. The pdf format of the graph was checked with the PACE PLOS and GIMP programs. We hope that sufficient quality and resolution have been achieved. But if the problem persists, we can rearrange the graphs by splitting (survivors, survivors, etc.). Attachments Attachment Submitted filename: Answer to reviewers.docx https://doi.org/10.1371/journal.pone.0260623.r004
15 Nov 2021 Decision Letter - Etsuro Ito, Editor Serial measurement of cytokines strongly predict COVID-19 outcome PONE-D-21-17711R2 Dear Dr. Ozger, 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, Etsuro Ito Academic Editor PLOS ONE 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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) ****** 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 https://doi.org/10.1371/journal.pone.0260623.r005
Formally Accepted
23 Nov 2021 Acceptance Letter - Etsuro Ito, Editor PONE-D-21-17711R2 Serial measurement of cytokines strongly predict COVID-19 outcome Dear Dr. Ozger: 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 Prof. Etsuro Ito Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0260623.r006

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