PONE-D-24-01429Screening of potential regulatory genes in carotid atherosclerosis vascular immune microenvironment.PLOS ONE

Dear Dr. hou,

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PLOS ONE

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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: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: I Don't Know

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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?

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Reviewer #1: Yes

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: Zhang Y et al., studied potential regulatory genes in carotid atherosclerosis vascular immune microenvironment. Identifying potential genes that regulate the progression of carotid atherosclerosis is a demanding research topic. There is relevant published work so far (Zheng K et al., 2023, Dong R et al., 2022, Wang L et al., 2021). This study further extends the contemporary knowledge in carotid atherosclerosis immunology.

Previous studies used same database and identified same hub genes in some extent. For example, Liu C., 2021 identified RBM47, HCK, CD53, TYROBP, and HAVCR2 as Hub Genes using the same Gene Expression Omnibus database (GSE43292). In addition, Yao Yuan et al., 2024 analyzed GSE43292 database and identified hub genes such as AKTIP, ASPN, FAM26E, RAB23, PLS3, and PLSCR4. Ni Jiajun et al., 2023 and Chen M., et al., 2021 were used GSE28829 database and explored Go and KEGG pathways. Therefore, I am unsure how this study is novel compared to what is published so far.

Reviewer #2: In this research paper, the authors aim to uncover the changes in the immune microenvironment of vascular tissues at various stages during the progression of carotid atherosclerosis. Additionally, they seek to identify potential hub genes that regulate the immune microenvironment in this pathology.

It is an intersting work ; however, I have some comments and minor revisions :

1. This paper is founded on the data from two research papers (related to GSE43292 and GSE28829), which should be cited as references.

2. There is a mistyping in the results section. It should be corrected to "immune score" instead of "immune sore".

3. In the results section, the authors reported that "ACTN2 was positively correlated with most immune cell subtypes infiltration" and "PTPRC was negatively correlated with most immune cell subtypes infiltration." However, the discussion section contradicts these findings, stating that "ACTN2 is negatively correlated with most immune cell subtypes infiltration" and "PTPRC is positively correlated with most immune cell subtypes infiltration." To ensure consistency and coherence, the sentence should be corrected to align with the results and discussion.

4. In Figure 1C, “CAP” should be replaced by “CAS”.

5. The legend of Figure 1B and 2B should be corrected as follows: "The differences in immune score between the carotid atherosclerosis and control samples."

6. In the legend of Figure 5A and 5C, abbreviations such as BP (Biological Process) and CC (Cellular Component) should be added.

7. In the legend of Figures 5E and 5F, the significance of colors should be specified.

8. Genes such as ACTN2 and PTPRC should be written in italics.

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Reviewer #1: Yes: Md Mamun Al Amin, Ph.D.

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-24-01429_Review-comments_Mamun_20240217.docx

PONE-D-24-01429R1Screening of potential regulatory genes in carotid atherosclerosis vascular immune microenvironment.PLOS ONE

Dear Dr. hou,

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 Jul 29 2024 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,

Misbahuddin Rafeeq

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.

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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: All comments have been addressed

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: Partly

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: I Don't Know

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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: No

Reviewer #2: 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

Reviewer #2: No

**********

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: In the revised version, Zhang and colleagues have included three additional figures (Figure 9, 10 and 11). I am wondering, the authors have validated diagnostic efficiency on those two GSE cohorts. Models developed to identify diagnostic genes may be overly complex and tailored to the specific dataset, leading to poor performance when applied to new, unseen data. Regularization techniques and cross-validation are necessary to mitigate this type of risk. Despite this limitation, the authors have reported novel hub gene that may have a significant impact in the field.

Reviewer #2: Thank you for addressing all my concerns, however, the manuscript still needs to be revised:

1. First, there are several spelling and grammar errors, so the English must be proofread by a native English speaker.

2. There is a mistyping in the manuscript. It should be corrected to "GSE 28829" instead of "GSE 288292".

3. As suggested by the reviewer, previous studies used the same database and identified some hub genes, such as RBM47, HCK, CD53, AKTIP, ASPN, PLS3, and PLSCR4. In this regard, the results of these papers should be discussed in the manuscript to compare them with the present study and to suggest hypotheses that could explain the differences in hub genes found in these different studies.

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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

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[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.

Screening of potential regulatory genes in carotid atherosclerosis vascular immune microenvironment.

PONE-D-24-01429R2

Dear Dr. xianming hou,

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,

Misbahuddin Rafeeq

Academic Editor

PLOS ONE