PONE-D-21-39833Prediction of malignant transformation in oral epithelial dysplasia using infrared absorbance spectraPLOS ONE

Dear Dr. Shaw,

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 respond to the reviewers' comments. It sounds like an intriguing study but would gain from some clarification.

Please submit your revised manuscript by Mar 17 2022 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,

Patrick Ha

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

[This study was funded by Cancer Research UK C7738/A26196. BGE and CAW were supported by Engineering and Physical Sciences Research Council (EPSRC) PhD studentships.]

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: 

 [JMR, RJS, PW & SDB: Cancer Research UK grant number C7738/A26196. https://www.cancerresearchuk.org/ BGE & CAW were supported by Engineering and Physical Sciences Research Council (EPSRC) PhD studentships. https://epsrc.ukri.org/

The funders had no role in the 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.

3. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability.

Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized.

Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access.

We will update your Data Availability statement to reflect the information you provide in your cover letter.

[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: Partly

**********

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: This article describes a retrospective review of the use of Fourier-transform infrared (FTIR) absorbance spectra in predicting the transformation of oral epithelial dysplasia into oral carcinoma.

The authors compare spectroscopic data from 10 patients with oral epithelial dysplasia that underwent transformation into carcinoma to that from 7 patients with oral epithelial dysplasia that did not undergo transformation. The authors then use PCA-LDA (principal component analysis followed by linear discriminant analysis) to demonstrate that the FTIR data predicted malignant transformation with a sensitivity of 79% and specificity of 76%.

While I can’t comment on the validity of the methodology in this study due to my lack of expertise in IR spectroscopy, my impression is that this manuscript thoroughly describes a potentially compelling method of investigating oral epithelial dysplasia. This is of particular clinical relevance given that degree of dysplasia poorly predicts transformation. I therefore recommend acceptance.

Reviewer #2: In this study by Ellis et. al., the authors retrospectively review 17 patients with high risk oral epithelial dysplasia, 10 of which transformed to malignancy (T=transformed) and 7 of which did not (NT=non transformed), in order to determine whether Fourier-transformed IR microscopy and machine learning algorithm can predict malignant transformation.

The authors utilize PCA and k-means cluster analysis, with outliers removed by Hotellings T^2 summary statistic, to determine the spectral data to include in the development of the optimal machine learning algorithm. Having identified the data to include, the authors then use an unpublished optimization framework, PipeOpt, to test the performance of each pipeline using all possible combinations of pairs of T/NT samples as the test set, with the remaining samples as the training set. In total, 648 unique pipelines were tested. The PCA-LDA-derived linear discriminant score and weighting for different wavenumbers ultimately identified the 6 wavenumbers with the highest discriminatory power between T and NT groups. When applying this machine learning algorithm to infrared data collected by FTIR-microscopy, the sensitivity was 79%, specificity 76%, in identifying which lesions would undergo malignant transformation.

Overall, this study aims to address an important and difficult clinical scenario of which pre-malignant oral cavity lesions ultimately undergo malignant transformation with novel methodology. I am unable to comment on the mathematical soundness of the determination and implementation of the pipeline analysis. However, there are several areas of major concern, that if addressed, could eventually make this work suitable for publication.

1. From a clinical perspective, while it is helpful to understand which OED with severe histopathology undergo malignant transformation for counseling purposes, from an intervention standpoint, this is less relevant as most surgeons will excise forms of severe dysplasia. It would be of greater clinical utility to also include lesions that are mild and/or moderate dysplasia as a separate analysis, as there is more ambiguity in clinical decision making.

2. The authors do acknowledge that the small sample size is a limitation of this study. However, with testing of 648 different pipelines and 17 samples, there is a concern that the authors are overfitting their data, thereby making it difficult to interpret the utility of this algorithm. It would be helpful to see the predictive accuracy of this methodology replicated with a validation cohort.

3. Did all lesions undergo only incisional biopsy and then were followed? Or did some of these lesions undergo curative surgical excision?

4. Please clarify how the region of interest was determined.

**********

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.

Prediction of malignant transformation in oral epithelial dysplasia using infrared absorbance spectra

PONE-D-21-39833R1

Dear Dr. Shaw,

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,

Patrick Ha

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The authors have done a good job in responding to the reviewers' comments. This is a complex topic, and the algorithm(s) outlined are at the very least intriguing and warrant further study.

Reviewers' comments: