PONE-D-24-15574Transcriptomic analysis of cellular senescence induced by ectopic expression of ATF6α in human breast cancer cellsPLOS 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

Reviewer #3: Yes

Reviewer #4: Yes

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

Reviewer #1: N/A

Reviewer #2: I Don't Know

Reviewer #3: N/A

Reviewer #4: 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

Reviewer #3: Yes

Reviewer #4: 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

Reviewer #3: Yes

Reviewer #4: 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: This paper covers in great detail the research to study cellular senescence as triggered by various stressors. The paper also describes with ample clarity the entire sequence of steps performed to conduct the analysis. All the wet-lab methods employed for individual steps come with enough information to be able to replicate the study.

Overall, I am impressed by the authors’ approach and discussion to highlight the molecular mechnanisms underlying the ER stress0induced cellular senescence and the identification of key regulators like MAP2K 1/2 and GPAT4, and their downstream target DDIT3 in the induction of cellular senescence.

However, I would personally find it more reader-friendly and it would improve the chances of receiving more citations if the authors were to add more content specifically around the phenotypic manifestations of the 20 genes they found were significant in their time-series analysis and also find ways to weave a few lines on how their phenotypic manifestations might be inter-related. Such description can also be extended to offer the authors’ proposed strategies on how that might be used to provide more intuition around personalizing cancer therapies.

Overall, this is a good paper, and it would just add so much more value if the authors were to provide some additional content.

Also, I would much prefer the authors shared their NGS sequencing data files.

Reviewer #2: It requires little more details about the motivation of using 6h and 9h DEGs. It also lacks the details of how specifically MAP2K1/2-DDI3 axis influences cellular senescence via ATF6-alpha expression. The paper does not mention how other could have play some roles in linking the axis.

Reviewer #3: The authors address an important question on role of ATF6a in cellular senescence. However, the manuscript can be made robust by

1) Are the DEG the same if they work if a different cell line system?

2) The use ATF6a as a down stream O/E gene for their analysis. This is a little counterintuitive as they are over expressing the gene and hence this is to be expected.

3) Can they relate this to patient survival data between patients having high and low ATF6a expression levels? That will provide a nice translation link to their work.

4) The biological mechanism ATF6a ectopic expression is lacking and could be outside the scope of this work.

Reviewer #4: I think the article is well written, following are the comments to the authors:

1. Page 5: Line 62-64, please cite the study for the finding. If it is part of reference 1, please recite or reword the sentence as "our study also led us to discover that ATAF6_alpha..... senescence"

2. Line 68-70 : can the authors provide the rationale behind studying cell senescence in cancer cell lines and the broader impact of it ?

3. Lines 86-93 : introduces the importance of cell senescence in this study and should be discussed earlier . Either immediately after line 70 or the authors can briefly discuss why cell senescence is important to study in cancer cell in the paragraph of Line 59-70.

4. line 99-100 : Why did the authors pick MCF-7 cell line ? How did breast cancer subtype of ER+, PR+ , and glucocorticoid + factor into their analysis ?

5. Line 225 : Have any of these 6 genes been implicated in cell senescence before ?

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Reviewer #1: Yes: Sangeeta Shukla, PhD

Reviewer #2: No

Reviewer #3: No

Reviewer #4: No

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Attachments

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Submitted filename: PONE-D-24-15574.pdf

Transcriptomic analysis of cellular senescence induced by ectopic expression of ATF6α in human breast cancer cells

PONE-D-24-15574R1

Dear Dr. Sohn,

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,

Aniruddha Datta

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 #4: 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 #4: Yes

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

Reviewer #1: N/A

Reviewer #4: Yes

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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: Yes

Reviewer #4: 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 #4: 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: I closely compared the previous and recent versions of your submissions, and still find answers to the feedback/comments earlier not satisfying. However, the work described in the paper is undoubtedly novel and interesting, and I am willing to approve.

Reviewer #4: The authors have addressed my comments sufficiently and I do not have any further changes to recommend. Good Luck with the submission.

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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 #4: No

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