Transfer Alert

This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present.

PONE-D-21-30926A framework for mutational signature analysis based on DNA shape parametersPLOS ONE

Dear Dr. Supek,

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.

While both reviews are favorable, there are multiple concerns about several aspects of statistical analysis, approach, interpretation and presentation. Please, address all reviewer's comments in a revised submission.

Please submit your revised manuscript by Dec 17 2021 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,

Sergey Korolev, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at 

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. 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.

3. Thank you for stating the following in the Acknowledgments Section of your manuscript: 

"This work has received funding from the European Union’s Framework Programme for Research and Innovation Horizon 2020 (2014-2020), under the Marie Skłodowska-Curie PROBIST grant agreement No. 754510 (to A.K. and J.L., PROBIST co-fund fellowship of the Barcelona Institute of Science and Technology) and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 757700, to F.S). F.S. is funded by the ICREA Research Professor program. A.K., J.L. and F.S. acknowledge support of the Severo Ochoa Centres of Excellence program of the Spanish Ministry of Economy and Competitiveness to the IRB Barcelona. Work in the laboratory of F.S. was supported by the ERDF/Spanish Ministry of Science, Innovation and Universities-Spanish Research State Agency/RegioMut project (grant agreement No. BFU2017-89833-P). "

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. 

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: 

"This work has received funding from the European Union’s Framework Programme for Research and Innovation Horizon 2020 (2014-2020), under the Marie Skłodowska-Curie PROBIST grant agreement No. 754510 (to A.K. and J.L., PROBIST co-fund fellowship of the Barcelona Institute of Science and Technology) and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 757700, to F.S). F.S. is funded by the ICREA 

Research Professor program. A.K., J.L. and F.S. acknowledge support of the Severo Ochoa Centres of Excellence program of the Spanish Ministry of Economy and Competitiveness to the IRB Barcelona. Work in the laboratory of F.S. was supported by the ERDF/Spanish Ministry of Science, Innovation and Universities-Spanish Research State Agency/RegioMut project (grant agreement No. BFU2017-89833-P).

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

[Note: HTML markup is below. Please do not edit.]

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

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

**********

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

**********

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: Mutational signatures represent different mutational processes underlying cancer initiation and development, and they are usually reported by the frequency of tri/penta-nucleotide contexts. This study considers structural features that may enhance the interpretation of sequence-based signature. Overall, this work is of high quality. Although the ability of shape parameters to predict mutation probability is not better than sequence context, the incorporation of trinucleotide-based mutation type with structural-based parameters could provide new insights for mechanisms of mutagenesis.

I have below comments.

1, The author should explain why only focus on these three shape parameters. They mentioned the affect of hairpin structure on mutation formation, but not actually include it as a parameter.

2, For Fig2 and Fig3, the author only used one sample to represent the typical mutational processes. It would be good to see if the trend still holds for additional individuals as there are a lot of such samples available from TCGA/ICGC. In addition, POLE mutants have different hotspots (like V411L and P286R) with differential spectrum (Fang et al, 2020, PLos Gene; Hodel et al, 2020, Mol Cell), the sample used in this study should be indicated.

3, Poisson regression to evaluate sequence-based variables and structural-based variables for mutation probability would be good to be presented by an equation in the method.

4, In page 34, I think the second paragraph is out of scope of this paper. Maybe it is better to discuss how the shape parameters incorporated-signature would benefit to personalized therapy.

Reviewer #2: In this study Karolak et al. described how data on DNA structure can predict mutation probability. They firstly analyzed the role of DNA structure and nucleotide context in mutation probability independently and then tried to extend the idea of standard mutational signatures (based on trinucleotide mutational spectrum) by including information about structural features. The idea itself looks very exciting. My main concern about it is prediction of structural features from DNA sequence and very strong correspondence between contexts and structures at such a small scale. Mutagenic processes in investigated cancers are highly context-dependent, so by definition you will have structure-dependence as well if each context corresponds to very specific structure. It would be informative to understand how much different contexts vary in described structural parameters. It would also be interesting to see whether different contexts with similar structure can have similar changes in mutation probability. Probably it would be helpful to investigate more large-scale structures to see whether there are differences in mutability of particular context in different structures? Similar to example with APOBEC in stem loops.

For investigated cancers, models with structural features performed similarly well to contexts. It would be interesting to investigate whether this is the case for cancers without such high context-specificity.

The most interesting part of the paper is prediction of new signatures that could not be extracted based only on nucleotide context. Although the method seems not to be ideal and the biological interpretation is quite limited, this work is a good start point in this direction.

Comments:

1. Figure 1 is not fully understandable. From the scheme, it seems that far right and far left nucleotides are not engaged in any parameter estimation that seems not to be true.

2. Is it correct that Poisson regressions do not take information about mutation type into account? I mean that coefficients on Figure 2 and Figure 3 show influence on mutation probability of central nucleotide independently of mutation type. In this case, they seem to be biased by the main mutation type in cancer.

3. Could you please discuss in text why 3nt-seq model always performs better than 5nt-seq model? (Table 1).

4. Page 13 “the structural DNA features compared favorably (pR2=0.81 for 7nt-str, Table 1) to the sequence DNA features (pR2=0.81 for 5nt-seq)”. Why do you call this comparison favorable if they have equal pR2?

5. Page 13 “The overall predictive accuracy was higher for the POLE tumor than for MSI tumor (Table 1), suggesting that mutational risk can be predicted from DNA shape to a variable degree across different mutational processes.” From Table 1 it is seen that context-model also performs better for PolE compared to MSI. As structural features were predicted from nucleotide sequence this fact can probably be explained by lower context-specificity of MMR compared to PolE.

6. Page 14 “Considered together with over- and under-twisting at positions -1 and +1, respectively, this suggests that DNA motifs experiencing APOBEC mutagenesis may be more prone to have flipped out bases”. It is interesting to investigate the co-occurrence and simultaneous influence of structures found significant in Poisson regression.

7. Figure 5. X-axis is impossible to read. Structural signatures seems to be very similar between different signatures in contrast to difference between context signatures. For example, structural elements for SBS1, SBS3L, SBS6, SBS7b seems very similar for C>T mutation but contexts differ extremely. Could you explain this? I lack the interpretation as I was not able to understand the correspondence of bars to structural features.

8. Figure 6 looks confusing. For example, SBS4 that you describe as tobacco smoking induced was not found in any lung cancer. For LUSC you determined high exposure to SBS8L/4L that is also similar to SBS4 but for luad you didn’t observe any of them. SBS7a,b,c are not pronounced in skcm.

Misprint

1. Page 19 “suggesting that both DNA sequence features and the and DNA structural features should be considered jointly…”

**********

6. 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.

A framework for mutational signature analysis based on DNA shape parameters

PONE-D-21-30926R1

Dear Dr. Supek,

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.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

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,

Sergey Korolev, 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

Reviewer #2: All comments have been addressed

**********

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: (No Response)

**********

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

Reviewer #1: Yes

Reviewer #2: (No Response)

**********

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: (No Response)

**********

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 Response)

**********

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)

Reviewer #2: (No Response)

**********

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