PONE-D-24-03827Comparative Analysis of Differentially Expressed Genes in Synovial Cells from Osteoarthritis and Rheumatoid Arthritis PatientsPLOS ONE

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Reviewers' comments:

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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

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

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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

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

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Reviewer #1: Yes

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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 expression patterns of particular genes within two autoimmune diseases, osteoarthritis (OA) and rheumatoid arthritis (RA), were investigated in a manuscript titled "Comparative Analysis of Differentially Expressed Genes in Synovial Cells from Osteoarthritis and Rheumatoid Arthritis Patients." The authors used one dataset for validation and three publically accessible datasets from the gene expression omnibus for analysis in order to accomplish this. They discovered common DEGs by a variety of statistical techniques and bioinformatics tools, which were then applied to gene ontology enrichment analysis, pathway analysis, transcription factor analysis, protein-protein interaction (PPI) network, and pathway analysis. Despite the authors' claims that they have validated their findings using a dataset, this work is merely screening and lacks validation trials. There is no mention of the validation outcome or specifics in the paper. However, I have some concerns that the authors need to resolve before the work is turned into a publishable format.

Major comments:

1. Details about the datasets are not presented in detail. Authors need to explain the type of dataset (Microarray/transcriptome), the number of samples, sample size (control and Disease), geographical origin of the dataset, Age group/gender information available, Keywords to extract dataset, etc.

2. On Page 11, between lines 4 and 8, it is stated as follows: "Finally, the differentially expressed genes (DEGs) identification package was used to perform differential expression analysis on the four annotated expression datasets (GSE821076 (OA), GSE77298 (RA), and GSE1919 divided into OA and RA)". The algorithms, tools, or packages utilized must be described clearly in the article.

3. From line 12 to 14 of page 11, it is mentioned “To eliminate batch effects12 arising from different platforms, a batch correction algorithm was employed. Limma13 ComBat used the transcriptional data from the four normalized”. What did you mean by transcriptional data? Is it transcriptomics data?

4. Lines 21–23 of Page 11 appear to be drafting the result. The author should not muck up the methodology or findings.

5. Biological pathways are stated on page 12, line 4. Gene ontology identifies biological processes, cellular components and Molecular Functions

6. Page 12, line 11, mentions hub gene identification using the Degree Algorithm. It must be accomplished by merging several topological parameters such as degree, closeness, betweenness, MCC, and so on. Determine which one meets the majority of the criteria. It is not justifiable to identify hub genes using a single network characteristic.

7. The introduction is too short with unnecessary details and at times loses the focus regarding the context of current study.

8. Page 12, Line 21 “Validation Analysis using the Validation Dataset”, Validation itself is an analysis.

9. Provide density plot to make sure that all data is evenly normalized.

10. In page 15, “among these, 15 were upregulated common DEGs including: STMN2, SDC1, PLXNC1, CDH11, IGJ, CXCL10, MARCKS, HK3, TNFSF11, IGHM, KDELR3, TNFRSF11A, CRIP1, ARHGAP5, and CD300C. The 15 downregulated common DEGs were: FASN, KLF9,ADH1A, ADIPOQ, FABP4, SHC3, APOD, TF, PRKAR2B, PLIN1, ADH1B, ZBTB16, SCD, SOX13, and P2RY14(figure 3). What is the significance of 15??

11. The venn diagram is not clear enough to convey the necessary information.

12. In page 16, it is stated that “ enrichment analysis revealed that the common DEGs were primarily enriched in the following aspects: Biological Pathway (BP): Major enrichment was observed in pathways related to myeloid cell differentiation, myeloid8 leukocyte differentiation, and temperature homeostasis, Cellular Component (CC)”. BP is Biological Process. If it is pathway, why the KEGG analysis is done again?

14. Network in page 18 is not clear. Make a better layout and mention the number of nodes and edges.

15. Figure legends in page 17, 21, 22 and 24 should be made short

16 The discussion is not well-presented. The results are mentioned again during the conversation. The authors must cite further research to back up their findings.

17. Authors claim in conclusion that the present study may “These findings not only reveal the commonalities at the molecular mechanism level between osteoarthritis (OA) and rheumatoid arthritis (RA), but also emphasize that these shared mechanisms provide new clues for therapeutic strategies. This study lays a valuable foundation for further understanding the shared and unique pathways of these two diseases, advancing the knowledge of potential therapeutic targets for OA genes and transcription factors during disease progression, thereby developing more targeted and efficient treatment methods.” The statement is poorly written in conclusion with lots of broken sentences and grammatical errors. Also justify this statement.

Minor Comment:

• Spelling mistake — "Founding" instead of "Funding" (page 26 line 22)

• For clarity, subfigure lettering should be within the graphic, not under it in the body text. (page 9, line 21; page 10 line 23; page 11 line 2; page 12 line 2; page 15 line 1; page 16 lines 7, 9)

• More clinical studies/case reports must be cited related to OA and RA association.

• Though the paper objective aims to describe a set of differentially expressed genes that could be used as a differential diagnosis between osteoarthritis and rheumatoid arthritis, it in fact does not find any such differential expression between OA and RA; instead only finding a common differential expression between either kind of arthritis and non-arthritis. A rephrasing of the objective to clarify the actual aim and finding of the research might be warranted. (page 1 lines 4 - 7)

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Reviewer #1: Yes: Dr. Deepa Madathil

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Analysis of Common Differential Gene Expression in Synovial Cells of Osteoarthritis and Rheumatoid Arthritis

PONE-D-24-03827R1

Dear Dr. han,

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.

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Kind regards,

Gurudeeban Selvaraj

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

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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

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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

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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

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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)

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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: Dr. Deepa Madathil

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