Circum-Mediterranean influence in the Y-chromosome lineages associated with prostate cancer in Mexican men: A Converso heritage founder effect?

Esmeralda Álvarez-Topete; Luisa E. Torres-Sánchez; Esther A. Hernández-Tobías; David Véliz; Jesús G. Hernández-Pérez; Ma. de Lourdes López-González; Marco Antonio Meraz-Ríos; Rocío Gómez

doi:10.1371/journal.pone.0308092

Peer Review History

Original SubmissionJanuary 8, 2024
17 Mar 2024 Decision Letter - Gyaneshwer Chaubey, Editor PONE-D-23-43139Circum-Mediterranean Influence in the Y-Chromosome Lineages Associated with Prostate Cancer in Mexican Men: A Converso Heritage Founder Effect?PLOS ONE Dear Dr. Gomez, 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 manuscript is interesting. However, many of the arguments are not justified. Please consider the questions from both of the reviewers and revised the manuscript accordingly. Please ensure that your decision is justified on PLOS ONE’s publication criteria and not, for example, on novelty or perceived impact. 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The following resources for replacing copyrighted map figures may be helpful: USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/ The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/ Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/ Landsat: http://landsat.visibleearth.nasa.gov/ USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/# Natural Earth (public domain): http://www.naturalearthdata.com/ [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: I Don't Know Reviewer #2: I Don't Know ****** 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: It is an interesting study. The paper need some improvement in the language. Although R1a haplogroup as per statistical tests used is claimed to contribute to prostate cancer (OR adjusted: 8.04, 95%CI 1.41 – 45.80) on perusing raw data an extremely small number of cases and controls are found in the study cohort. This makes it biologically less meaningful and the limitation should be discussed in the discussion and also indicated in the abstract - otherwise a wrong idea will be conveyed to the readers especially in view of high OR. Line 51 - Sentence not clear due to the word incidence Line 91 - replace the word statemented with a better word Line 168 - replace the word unknew with a better word Line 182 - correct the word avid Line 197 to 200 - write better - many uses of the word "those" Line 595 - correct the word technician Line 605 - replace the word disinterested with a more appropriate word Reviewer #2: In the manuscript “Circum-Mediterranean Influence in the Y-Chromosome Lineages Associated with Prostate Cancer in Mexican Men: A Converso Heritage Founder Effect?” the authors analyze the paternal origin of 152 patients with prostate cancer (cases) and 372 population (controls) from the Mexican Mestizo population. They focus on the influence of ethnicity in prostate cancer. The subject is the great interest for male health. The genetic factors highly contributes to the genesis of prostate cancer and ethnic may influence this contribution However to my point of view some issues may be improved. My main concern is regarding the low number of cases. It looks as the authors do not statistically analyzed the needed number to perform the study. They do not add this important information in the statistic section. Introduction section: Line 237 define CVM please Results In table 5, why it should be different risk between ethnicity and differences grades of prostate cancer? Is it a biological or cultural effect? I am concerned about the low number of prostate cancer Gleason <7 N=37 Discussion section It is an interesting description of ethnicity. I should suggest to focus on prostate cancer more than to the ethnicity, namely to focus in the aim of the work. Regarding other risk factors of prostate cancer, I agree with the authors (as they mentioned in the conclusion section) that is a limitation of the study, is it possible to obtain more data from the patients? Anyway it is an important limitation that should be discussed more deeply and it does not represent a conclusion of the study. Please explain “ The differences found between cases (23.5%) and controls 500 (13.1%) in the Central-East region could be explained by the exposed causes in prior paragraphs “ (line 500) How the exposed causes explain the differences in prostate cancer? . References section I could not find the reference Martinez- Cortes. ****** 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: Yes: Kamani Tennekoon Reviewer #2: Yes: Rossana Sapiro ******** [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. https://doi.org/10.1371/journal.pone.0308092.r001
Revision 1
23 May 2024 Author Response Response to Editor and Reviewer comments We would like to thank the Editor and Reviewers for the detailed review of our manuscript and the constructive feedback provided on it. We have carefully evaluated the points raised in the review and made the corresponding changes to the text. These changes have significantly improved the quality of the manuscript and appear highlighted in yellow in the main text. Our responses to the Editor and the Reviewer one appear in blue font below; Reviewer two appears in red font. Response to Editor We note that Figure 1 in your submission contain [map/satellite] images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission. We appreciate this suggestion. Nonetheless, the map used as Figure 1 of our manuscript is not a copyrighted map. Given that we need some specifications to depict particular features, I create totally this figure. In addition, we confirm that the map used in such figure has not been used or copyrighted, previously. On behalf of my co-authors, as well as on my behalf, we have included a letter confirming the sentences mentioned before. Response to Reviewers’ Reviewer #1 1. It is an interesting study. The paper needs some improvement in the language. Thank you for this observation. This new version has been proofread by an English Native. 2. Although R1a haplogroup as per statistical tests used is claimed to contribute to prostate cancer (OR adjusted: 8.04, 95%CI 1.41 – 45.80) on perusing raw data an extremely small number of cases and controls are found in the study cohort. This makes it biologically less meaningful, and the limitation should be discussed in the discussion and also indicated in the abstract - otherwise a wrong idea will be conveyed to the readers especially in view of high OR. We appreciate these suggestions, which have been attended at whole. The Discussion section includes the arguments about the effect of the sample size, a calculous of the statistical power, and the suggestion to confirm our findings. Similar arguments have been included in the Abstract section. 3. Line 51 - Sentence not clear due to the word incidence. We apologise for this mistake. Following your accurate observation, we have included the word “incidence” in the first sentence of the Introduction section. 4. Line 91 - replace the word statemented with a better word. We appreciate this suggestion. Thus, we have replaced “statement” with “suggested” to indicate that such population interaction was likely, diminishing the force of the pronouncement. 5. Line 168 - replace the word unknew with a better word. We thank the reviewer for this suggestion. We replaced “unknew” by “did not know”. 6. Line 182 - correct the word avid. We apologize for this typographic error; it has been corrected. 7. Line 197 to 200 - write better - many uses of the word "those". In full agreement with your comment. We have modified the redaction of this paragraph for accuracy and clarity in its reading. 8. Line 595 - correct the word technician. We agree with your comment; the word technician analyses was replaced by technical procedures. 9. Line 605 - replace the word disinterested with a more appropriate word. Thank you for this observation. We replaced disinterested by uninterested. Reviewer #2 In the manuscript “Circum-Mediterranean Influence in the Y-Chromosome Lineages Associated with Prostate Cancer in Mexican Men: A Converso Heritage Founder Effect?” the authors analyze the paternal origin of 152 patients with prostate cancer (cases) and 372 population (controls) from the Mexican Mestizo population. They focus on the influence of ethnicity in prostate cancer. The subject is the great interest for male health. The genetic factors highly contribute to the genesis of prostate cancer and ethnic may influence this contribution. However, to my point of view some issues may be improved. 1. My main concern is regarding the low number of cases. It looks as the authors do not statistically analyzed the needed number to perform the study. They do not add this important information in the statistic section. We appreciate your suggestions. We have replicated all your comments in the Discussion section, explaining the several arguments about your justified concerns. 2. Introduction section. Line 237 define CVM please. We appreciate this commentary. We have included the mean of the CVM acronym. 3. Results section In table 5, why it should be different risk between ethnicity and differences grades of prostate cancer? Is it a biological or cultural effect? I am concerned about the low number of prostate cancer Gleason <7 N=37 We thank the reviewer for this point. We have attended and replicated your comments in a Discussion section in a broad context. 4. Discussion section It is an interesting description of ethnicity. I should suggest to focus on prostate cancer more than to the ethnicity, namely to focus in the aim of the work. We thank the reviewer for this suggestion. As you mentioned we have focused on the influence of ethnicity in prostate cancer. In former reports our research group have discussed about the genetic contribution of several genes (PMID:32219892, 30774776, 27193223), the environmental pressure (PMID:34520388), and the concomitant diseases to prostate cancer development. In the present study, our goal was to determine whether paternal ancestral lineages have certain contribution to prostate cancer given that the family history is critical in its developed. Our findings obligate us to include the ethnicity as a cornerstone of the discussion. First at all, because the lineages found are not natives of the original populations of Mexico suggesting a possibly founder effect, which is novel in our research. Rather, is impossible to separate the study of uniparental markers such as Y-chromosome out of the historical, cultural and religious contexts. We acknowledge for its observation, but we think that in the literature exist many papers regarding with the genetic influence of cancer. Using the keyword of “prostate cancer” AND “genetics” there are 42,438 results. By contrast, using the keywords “prostate cancer” AND “Y-chromosome” there are 107 results. Of these, only seven were related to the influence haplogroups or lineages in the prostate cancer. Nonetheless, attending your commentary we have added a section (A medical context) explaining the possible mechanisms that could be involved in the possible contribution of patrilineages in the prostate cancer. This section is previous the Historical context. In addition, we have added some subheadings to be more clear in the Discussion. 5. Regarding other risk factors of prostate cancer, I agree with the authors (as they mentioned in the conclusion section) that is a limitation of the study, is it possible to obtain more data from the patients? Anyway it is an important limitation that should be discussed more deeply and it does not represent a conclusion of the study. Please, explain “The differences found between cases (23.5%) and controls 500 (13.1%) in the Central-East region could be explained by the exposed causes in prior paragraphs “(line 500) How the exposed causes explain the differences in prostate cancer? We acknowledge all your suggestions; we agree totally with your points. About the possibility to obtain more data from the patients, several papers have been published previously (PMID:32219892, 30774776, 27193223, 34520388). Regarding the limitations, these have been discussed broadly and we have modified the Conclusion. Also, we have explained the differences found in the Central-East region. 6. References section I could not find the reference Martinez- Cortes. You are right. Thank you for pointing out this omission. We have included this reference. Attachments Attachment Submitted filename: Alvarez-Topete et al-Rebuttal Letter-290424.docx https://doi.org/10.1371/journal.pone.0308092.r002
17 Jul 2024 Decision Letter - Gyaneshwer Chaubey, Editor Circum-Mediterranean Influence in the Y-Chromosome Lineages Associated with Prostate Cancer in Mexican Men: A Converso Heritage Founder Effect? PONE-D-23-43139R1 Dear Dr. Gomez, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Gyaneshwer Chaubey 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: Yes ****** 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 ****** 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 ****** 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: The authors have correctly addressed all my comments. The manuscript has been improved after the corrections. ****** 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 ******** https://doi.org/10.1371/journal.pone.0308092.r003
Formally Accepted
8 Aug 2024 Acceptance Letter - Gyaneshwer Chaubey, Editor PONE-D-23-43139R1 PLOS ONE Dear Dr. Gomez, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Gyaneshwer Chaubey Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0308092.r004

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