Peer Review History
| Original SubmissionOctober 13, 2025 |
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Dear Dr. Lin, Please submit your revised manuscript by Jan 16 2026 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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Currently, your Funding Statement reads as follows: “This research was funded by Zhangzhou Affiliated Hospital of Fujian Medical University Doctoral Studio, Grant number: PDA202207.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. 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.] 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: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: I Don't Know ********** 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: No ********** Reviewer #1: Further detailed comments have been uploaded. This manuscript by Lin et al. describes the crucial role of macrophages in SSc-ILD. Using computational methods and a comprehensive array of bioinformatical analyses it identified 3 key genes contributing to inflammation driven fibrosis in SSc-ILD, namely ARG2, NKX2-1 and ELF3. Overall, a myriad of computational methods has been employed. These analytical methods are well described in the methods section. However, to make this work accessible to the non-bioinformatic audience, it would help to remind the reader of the aim of a particular analysis in the results section. The results section needs to be re-written, ensuing that figure legends and the main text contain the same information and that each figure with its legends can stand alone. Having identified the three key regulatory genes in SSc-ILD, the section on the drug identifications appears rather short and with less detail. This is, however, one of the most interesting results. Apart from the detailed requested corrections outlines below, my main criticism of the work is: 1. The number of images needs to be reduced to those more informative. Others should be included in the supplementary data. 2. Having identified the interaction of macrophages with alveolar type 2 cells in figure 2 this aspect in SSc-ILD development should have been further investigated. 3. Given the vast number of analyses, the limitations mentioned appear rather small. 4. Additionally, as fibrosis is the measurable outcome leading to SSc-ILD, the interaction of macrophages with fibroblasts should have been mentioned (and further interrogated). 5. This analysis should have been performed comparing SSc and SSc-ILD to identify which cell type / gene panel drives SSc-ILD in patients originally diagnosed with SSc (which is more manageable and has a better prognosis that the diagnosis of SSc-ILD). Please comment on this. 6. The lack of biological confirmation (although several studies are quoted suggesting the importance of the identified genes in the progression of fibrosis. (E.g., Knockout of the ARG2 gene can reduce age-related pulmonary fibrosis). Reviewer #2: The authors have carried out an important and complex evaluation of public single-cell transcriptomic datasets, which allowed them to identify genes associated with monocyte–macrophage function in SSc patients affected by ILD. Particularly noteworthy is the section linking these findings to potential drug targets, which in my view deserves greater emphasis, especially within the “Discussion” section. Although this is a highly valuable study from a biostatistical perspective, several key aspects require clarification. Major Comments 1. While the authors performed a significant biostatistical analysis using three public datasets and devoted much of the “Introduction” section to the role of macrophages in pulmonary fibrosis, the discussion appears lengthy and insufficiently focused on possible correlations and links between macrophages and differentially expressed genes, or on the results emerging from their analyses. In my opinion, this makes it difficult to fully appreciate the true value of the work. The discussion should therefore be substantially revised to highlight and interpret the results that are truly important—particularly those that may be useful for future translational and functional studies on macrophages (which, given the introduction, should be the primary cellular subset of interest), the pathways and signaling mechanisms involved, and the connections with pharmacological interventions. Indeed, the “Introduction” highlights the importance of macrophages, the results highlight distinct macrophage subsets (SPP1hi and FABP4hi), as well as differentially expressed genes and gene modules between SSc-ILD patients and healthy controls, along with differences in cell types. Yet, the discussion lacks a clear narrative thread that ties all these aspects together. The authors might consider streamlining the work, perhaps presenting fewer results, but ones that are more directly useful for understanding the study’s purpose and implications. 2. Although the authors refer to three major public datasets, it is unclear whether the reported findings derive from the analysis of all three datasets or primarily from GSE122960, which is the only dataset explicitly mentioned. This is a crucial point that must be clarified much more thoroughly. 3. The results indicate the presence of additional macrophage subgroups with varying abundance, yet these are neither reported nor discussed. Could the authors explain why this description was omitted? 4. The authors initially identified 50 candidate genes, but only 20 were ultimately evaluated. How and why was this reduction made? Are these genes specifically related to the disease? This discrepancy needs to be clarified. 5. In the “Introduction,” the authors describe the importance of macrophages in pulmonary fibrosis and SSc pathology. However, the literature cited should be updated, as several recent reviews have been published—for example: o Cutolo M. et al., Nature Reviews Rheumatology, 2025 Sep; 21(9):546–565. o Campitiello R. et al., Autoimmunity Reviews, 2024 Oct; 23(10):103637. doi: 10.1016/j.autrev.2024.103637. 6. In the “Results” section (lines 281 and 283), the authors write: “a relatively strong correlation.” Could they clarify what they mean by this? Is the correlation statistically significant or not? Minor comments. Please include the full-leigh name of molecules when cited for the first time in the manuscript (examples: TGFbeta1 and IL13 in the “Introduction” section). A full revision of the English style is needed. ********** 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: Dr Bettina C Schock 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.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.
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| Revision 1 |
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Identification of key genes related to macrophages in systemic sclerosis-associated interstitial lung disease based on single-cell and bulk transcriptomics data PONE-D-25-54894R1 Dear Dr. Lin, 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, Eric A. Shelden, Ph.D. Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #2: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #2: I Don't Know ********** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #2: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #2: Yes ********** Reviewer #2: I thank the authors for addressing the explanation to the single comments and for improving the manuscript. ********** 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 ********** |
| Formally Accepted |
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PONE-D-25-54894R1 PLOS One Dear Dr. Lin, 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. Eric A. Shelden Academic Editor PLOS One |
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