PONE-D-24-19973

Cuproptosis gene characterizes the immune microenvironment of diabetic nephropathy.

PLOS ONE

Dear Dr.  lu,

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.

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Kind regards,

Qi Zhao

Academic Editor

PLOS ONE

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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: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: 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

Reviewer #2: Yes

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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: No

Reviewer #2: 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: 1.English expressions need to be edited more careful and more native, in this manuscript, there are some mistakes.

2. I suggest the authors should add a flowchart in the manuscript to show the process very well.

3. I suggest the authors should elaborate their motivation in the discussion section, as they use several common bioinformatics analysis methods and online tools. What is the novelty and technicality of their work?

4. Advancements in computational capabilities have led to the widespread application of machine learning techniques, especially deep learning, across various bioinformatics fields. Important computational models in these fields should be cited. Some recommended studies are helpful (PMIDs: 36305458, 34232474, 35817399, 36584603, 37525507, 37660567, 38040204, and 37466194).

5. The authors should carefully check and unify the information of references. Some references lack the information of volume or contain the wrong page number.

6. Methods section is relatively simple because of no detail about the analysis. The analysis methods and statistical parameters must be clearly emphasized (i.e, reasons for selecting the algorithms used, threshold values used in statistical analysis, etc.).

7. The authors claim that HRSP12 and DCXR may be potential biological markers and renal protective factors. I think more validation should be adopted. Especially, I want to see some associations can be confirmed by other method or biological experiments.

8. Future work and limitations of the proposed algorithm should be addressed detailly in the manuscript for further research.

Reviewer #2: This study investigates the relationship between cuproptosis genes and the immune microenvironment in diabetic nephropathy (DN). RNA sequencing data from DN and normal renal tissues were analyzed for differential gene expression and immune cell subtype infiltration. NLRP3 and CDKN2A were positively correlated with immune scores, while NFE2L2 and other genes were negatively correlated. Consensus clustering based on cuproptosis genes identified two clusters: C1 (low cuproptosis gene expression, high immune cell infiltration) and C2 (opposite characteristics). Key genes DCXR and HRSP12 were identified and used to construct a nomogram with high diagnostic accuracy for DN. These genes may serve as potential biomarkers and renal protective factors. There are some issues that need to be addressed before the article can be accepted.

1.What do “NLRP3, CDKN2A, NFE2L2, LIAS, LIPT1, DLD, DBT and DLST” represent in the Abstract section? What are their full names? When first mentioned, the author should provide their full names to help readers better understand.

2.The authors should add a flowchart in the manuscript to show the process very well.

3.The Methods section in the text lacks corresponding literature references. The author did not provide sources and citations for the Methods mentioned.

4.The labeling of Figures in the paper is quite small. The contents within the figures are unclear. The author needs to carefully revise and modify the figure.

5.The authors should carefully check and unify the information of references. Some references lack the information of page number, such as ref [26].

6.The critique of current research limitations is somewhat lacking. The authors are encouraged to frame these deficiencies as directions for future research. Studies on gene/protein signaling networks using ODE-based theoretical modeling have played a crucial role in disease prediction (https://doi.org/10.1016/j.chaos.2023.114328, https://doi.org/10.1103/PhysRevE.108.064412, PMIDs: 33389663, 35958114). It would be beneficial if the authors could integrate and reference these four studies in this paper.

7.Besides, deep learning based algorithms offer valuable insights into diseases. It is essential to discuss and cite key computational models in these areas. Including some recommended studies would be beneficial (PMID: 38737196, doi:10.1016/j.swevo.2024.101567).

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Reviewer #1: No

Reviewer #2: No

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PONE-D-24-19973R1Cuproptosis gene characterizes the immune microenvironment of diabetic nephropathy.PLOS ONE

Dear Dr. lu,

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 Jan 31 2025 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,

Vinay Kumar, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

All comments from reviewer 1 needed to be answered

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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)

Reviewer #2: 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

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: No

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:  1. The authors didn't know how to write response letter. I always need to search for the revised content in the manuscript. You should list all the corresponding revisions in the letter.

2. The authors even write two “3” in the response to Reviewer #1.

3. The authors fail to elaborate their motivation in the discussion section. There are many papers on using machine learning to screen the core genes, so there is not as main innovation of the paper.

4. The authors should revise carefully corresponding to my previous comment #4. All the related paper should be cited.

5.The flowchart in Fig.1 is too simple to show the process of data collection and method implementation very well, please improve it.

6. Why the authors mention that HRSP12 and DCXR may be potential biomarkers and renal protective factors to my previous comment #7. If the authors can't get positive results, then what's the point of the experiment.

7. There are still some grammatical errors in the article, and the expression of some of the content is not clear enough. The authors need to check the manuscript carefully and make corresponding revision.

8. Why there are two new co-first authors in the revised manuscript?

Reviewer #2:  The author has addressed the reviewers' questions well. I recommend that the article be accepted for publication in this journal.

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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: 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.

Cuproptosis gene characterizes the immune microenvironment of diabetic nephropathy.

PONE-D-24-19973R2

Dear Dr. lu,

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.

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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,

Vinay Kumar, 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

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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

**********

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 author has already addressed all of the issues. I think the manuscript can be published in PLOS ONE.

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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: No

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