PONE-D-24-37221Gene expression-based identification of prognostic markers in lung adenocarcinomaPLOS ONE

Dear Dr. Planck,

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Asmerom Tesfamariam Sengal, MD, PhD

Academic Editor

PLOS 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: 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: 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: The authors use publicly available microarray datasets to identify genes whose expression is associated with OS differences in lung adenocarcinoma and then tests clinical utility of select genes using IHC in Swedish cohorts. While correct statistical analysis was used and all conclusions are supported by the data, I had some minor concerns where further details or clarification are needed.

Reviewer #2: The research paper presents a comprehensive study on non-small cell lung cancer (NSCLC) data sets, where, via the means of finding strong statistical associations between gene expression and cancer patient overall survival data, the authors have extracted a list of genes serving as potential prognostic markers for adenocarcinoma-type lung cancer. These markers’ prognostic ability was then assessed on a protein level via immunohistochemistry (IHC), where protein expression was evaluated and its association with overall survival and recurrence-free interval in two patient cohorts was statistically tested.

Overall, the manuscript is well written and shows a strong methodology for predicting prognostic markers for NSCLC using gene expression data. The statistical analyses applied were appropriate for the research question and tested the data stringently. The negative findings (i.e. the results that did not reach statistical significance) were addressed in the discussion section, and the limitations of the study were acknowledged.

High-quality data sets were used for the discovery of prognostic markers and yielded excellent results, revealing a set of correlated genes involved in tumour proliferation. Further IHC experiments were designed with care and were able to demonstrate the promising potential of gene expression-based prognostic research, confirming some, but not all, of the associations with patient survival on the level of both gene and protein expression. Although the IHC validation data set has revealed few statistically significant results, using different expression level cut-offs, as noted by the authors, could potentially result in more positive findings. It also appears that multivariate Cox proportional hazards regression models were another high-impact factor that lowered the findings’ significance levels. It is possible that the size of the data set was too small relative to the number of predictor variables used, resulting in higher p-values; however, this may be subjective, as no standard cut-off for events per variable (EPV) has been defined in current literature.

With regard to manuscript revisions, I only have suggestions concerning a few minor points. I would recommend the authors to consider substituting the term “correlation” where it is not in the context of the actual correlation analyses. For example, on page 4, lines 31-32: “… to identify and validate markers with consistent correlation to overall survival (OS)”. The term “correlation”, although semantically correct, may be misleading here, as the relationship between OS and marker gene expression was established via a log-rank test. It would be better to replace the term “correlation” with “association” as it was already done in several parts of the text and within Figure 1.

Several minor typos and grammatical errors were spotted, therefore additional proofreading is recommended.

After these minor revisions are made, I recommend this manuscript for publication.

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Reviewer #1: No

Reviewer #2: No

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Submitted filename: PLOS ONE Review.docx

Gene expression-based identification of prognostic markers in lung adenocarcinoma

PONE-D-24-37221R1

Dear Dr. Planck,

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 in addition addressing the comments provided by the reviewer/s.

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Kind regards,

Asmerom Tesfamariam Sengal, MD, PhD

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: (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

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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

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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: 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: Authors have addressed all concerns and manuscript is ready for publication.

My only suggestion would be to update Supplementary Table 2 to include some kind of division between the three models (Ki67, MCM4, TYMS), such as through use of bold row borders.

Reviewer #2: The authors of this manuscript have addressed the comments thoroughly. The research is presented well and opens new avenues for future work. I recommend this manuscript for publication and wish the authors the best of luck.

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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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