PONE-D-23-31014Identification of ADAMTSL2 as a potential prognosis biomarker associated with immune infiltrates and drug sensitivity in colorectal cancerPLOS ONE

Dear Dr. Huang,

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, especially in the results section.

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Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

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Reviewer #1: No

Reviewer #2: Yes

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

Reviewer #1: I Don't Know

Reviewer #2: N/A

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3. Have the authors made all data underlying the findings in their manuscript fully available?

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: No

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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: In the current manuscript the authors analyzed the prognostic roles of ADAMTSL2 in colorectal cancer.

below are my comment about this manuscript

1.The title of the manuscript is unclear. Please add detailed information about the patient group involved in the analysis. For example, include details about tumor stage and whether patients received any treatment before the analysis.

Abstract

1.The background is insufficient, and the study objective is not precisely described.

2.The study method is unclear; please provide a more detailed description.

3.The results are poorly written, and some are confusing, such as the statement, "ADAMTSL2 was associated with ECM-receptor interaction, basal cell carcinoma, dilated cardiomyopathy, TGF-beta signaling pathway, melanoma, arrhythmogenic right ventricular cardiomyopathy (ARVC), Olfactory transduction, complement and coagulation cascades, and hypertrophic cardiomyopathy (HCM)." Please summarize only the results directly related to the study objective.

4.The conclusion needs clarification.

Introduction and Method Section:

1.In section 2.5, subgroups were classified into two categories, 0-50 and 50-100. Please specify the criteria used to divide patients into these subgroups.

2.In section 2.7, the second paragraph lacks clarity and does not describe the method used to analyze the correlation between ADAMTSL2 and immune-related genes. Additionally, in section 2.8, the analysis method used to examine the correlation of ADAMTSL2 with TMB/MSI is not described.

3.Provide more explanation about the analysis used in section 2.9.

4.Clarify section 2.10 in more detail.

Results:

1.In section 3.1, the heading does not describe the findings clearly. The phrase "The results suggested that ADAMTSL2 was associated with tumorigenesis" needs clarification based on the data supporting this conclusion. Another conclusion, "indicating that ADAMTSL2 could be a new biomarker to differentiate CRC from non-tumor tissues," lacks sufficient data for such a claim.

2.In section 3.2, the description of the results in Figure 2 is not entirely correct and lacks clarity. Please rewrite this section.

3.In section 3.3, the results description is unclear and not entirely accurate. Additionally, there is a discrepancy between your above reported results that ADAMTSL2 is significantly low-expressed in CRC compared with normal colorectal tissue and in this section you stating that patients with high expression of ADAMTSL2 have significantly poor OS and DSS. This contradiction needs clarification.

4.In section 3.4, concentrate the analysis on pathways related to CRC and ignore unrelated pathways.

5.In section 3.5, explain the meaning of READ and COAD patients.

6.Clarify the main results in Sections 3.6, 3.7, and 3.8.

7.Rewrite section 3.9 for better clarity.

8.The results in section 3.11 contradict those in section 3.1. The expression of ADAMTSL2 is reported as lower in CRC compared to normal tissue in section 3.1, while section 3.11 you reports that ADAMTSL2 is highly expressed in CRC tissues. This discrepancy is unacceptable and requires attention.

Reviewer #2: In this study, Dr. Huang and their colleagues conducted a comprehensive analysis to evaluate the potential prognostic significance of the ADAMTS-like-2 (ADAMTSL2), as well as the correlation between ADAMTSL2 expression and immune infiltrates as well as drug sensitivity in colorectal cancer. Furthermore, they validated the elevated expression of ADAMTSL2 in colorectal cancer cell lines compared to normal cell line by Real-Time PCR. While the effort and perspective of this paper is interesting, there are several concerns and major revisions are expected.

1. In the introduction section, authors stated “The members of ADAMTSL (a disintegrin-like and metalloproteinase domain with thrombospondin type 1 motif-like) family that secrete glycoproteins are similar to ADAMTS proteases in structure”. This family members secrete glycoproteins? Or this family is kind of secreted glycoproteins. Please rewrite this sentence clearly.

2. Which database or algorithm was used to evaluate the relationship between ADAMTSL2 and TMB/MSI?

3. Why did the authors include references for some parts of material method section that, in my opinion, it seems unnecessary (such as Ref [32]).

4. In the result section, 3.1. ADAMTSL2 is aberrantly expressed in pan cancer and CRC part, I think the authors have inaccurately written this paragraph. They stated “The expression of ADAMTSL2 were lower in CRC compared to normal tissue (2.670 ± 0.040 vs. 1.678 ± 0.063, p < 0.001) (Figure 1B). The expression of ADAMTSL2 were lower in CRC tissues compared to paired normal tissues” . But I think ADAMTSL2 expression is higher in CRC compared to normal tissue.

5. In the result section, 3.3. Association of ADAMTSL2 with survival in patients with CRC part, Table S3 shows the results of univariate and multivariate analyses, not the correlation between ADAMTSL2 expression and clinicopathologial characteristics. I think the authors have inaccurately written some parts of this paragraph (the results of univariate analysis).

6. Authors have stated that ADAMTSL2 is highly expressed in CRC tissues compared with normal colorectal tissues in “3.11. ADAMTSL2 was aberrantly expressed in CRC tissues and cell lines part”. However, they have not specified the characteristics of these tissues. Or which correlation was between ADAMTSL2 expression and clinicopathological features in these tissues.

7. The discussion part was inadequately written. The authors should interpret the results. For example, how this gene is related to the mentioned signaling pathways? Or how the authors interpret the relationship between ADAMTSL2 expression and TMB/MSI? Or the relationship of the ADAMTSL2 high expression group with higher stromal score?

8. In the present study, ADAMTSL2 expression is associated with different immune infiltration, some immune checkpoint genes, and signaling pathways. These are highly interesting results. One possible method would be to use siRNA to downregulate the ADAMTSL2 expression in the CRC cell lines or mouse model, assess the expression of some investigated genes, and confirm by experimental examination.

9. The figures presented have poor contrast, including Figures 1-8.

10. Abbreviations should be fully described the first time they appear, such as COAD, READ, IGLEC15, IDO1, CD274, HAVCR2, PDCD1, CTLA4, LAG3, and PDCD1LG2, …

11. There are some grammatical errors throughout, such as:

ADAMTSL2 were associated with

The occurrence and development of CRC is associated

The expression of ADAMTSL2 were lower in CRC tissues compared to paired normal tissues

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Reviewer #1: No

Reviewer #2: No

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PONE-D-23-31014R1ADAMTSL2 is associated with immune infiltration and predicts a poor prognosis in colorectal cancerPLOS ONE

Dear Dr. Huang,

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 May 16 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,

Shiki Fujino, M.D.

Academic Editor

PLOS ONE

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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 #2: All comments have been addressed

Reviewer #3: (No Response)

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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 #2: Yes

Reviewer #3: Partly

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

Reviewer #2: I Don't Know

Reviewer #3: 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 #2: Yes

Reviewer #3: 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 #2: Yes

Reviewer #3: (No Response)

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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 #2: (No Response)

Reviewer #3: (No Response)

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Reviewer #2: No

Reviewer #3: No

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Attachments

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PONE-D-23-31014R2ADAMTSL2 is a novel prognostic biomarker in colorectal cancerPLOS ONE

Dear Dr. Huang,

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.

The lack of validation in real samples is the weak point of your article. However, I think ADAMTSL2 should be investigated as a potential marker in immuno-oncology. Please reconsider the title (delete novel) and include some information that these are from dataset analysis.

Please submit your revised manuscript by May 24 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,

Shiki Fujino, M.D.

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.

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.

ADAMTSL2 is a potential prognostic biomarker and immunotherapeutic target for colorectal cancer: bioinformatic analysis and experimental verification

PONE-D-23-31014R3

Dear Dr. Huang,

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.

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Kind regards,

Shiki Fujino, M.D.

Academic Editor

PLOS ONE

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