Calculating and comparing codon usage values in rare disease genes highlights codon clustering with disease-and tissue- specific hierarchy

Rachele Rossi; Mingyan Fang; Lin Zhu; Chongyi Jiang; Cong Yu; Cristina Flesia; Chao Nie; Wenyan Li; Alessandra Ferlini

doi:10.1371/journal.pone.0265469

Peer Review History

Original SubmissionOctober 5, 2021
6 Dec 2021 Decision Letter - Yanbin Yin, Editor 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-21-32048Calculating and comparing codon usage values in rare disease genes highlights codon clustering with disease-and tissue- specific hierarchyPLOS ONE Dear Dr. Ferlini, 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 address both reviewers comments. ============================== Please submit your revised manuscript by Jan 20 2022 11:59PM. 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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: The manuscript is generally adequately well written. The authors structure it in a scientifically sound way, and the data are analysed adequately. The nature of the manuscript prohibits it from being broken down in more pieces so it can be more easily digested, therefore It is hard to suggest an improvement in terms of readability. The manuscript unfolds an important issue, and supports it in a thorough manner, providing some novel insights, perspective and future directions concerning disease related genes and codon usage bias. It should be accepted after minor revisions. Suggestions 1.Line 65, “genes casing human rare diseases” 2. Line 93 “an extreme CUB was identified in both human and chimpanzee compared to other mammals, suggesting its evolutionary meaning in processes plays an exclusive role in a specific eukaryotic lineage” : This part could be rephrased making it clearer 3. Concerning this part : 95 “A large consensus exists about the concept that the choice of a synonymous codon does affect… for all genes [8]”. - It is an important statement that is being made in the manuscript, about the consensus that exists around “choice of a synonymous codon does affect protein translation efficiency, expression level, structure, and function, a notion that has prompted”. -This statement, is not adequately represented by references, hence some more references would further develop it. 4. -At the results section “CUB fingerprint across mammals” it is stated from line 277 until line 284 that “…no clear tissue behavior or even specific gene-related clustering can be observed. This finding further supports that CU values show an mammals-related but with important gene-specific differences, which contribute to generate the CUB fingerprints” -Although this statement can stand on its own, if it could be commented along with the statement at lines 92-94 concerning chimps and humans… 92- “an extreme CUB was identified in both human and chimpanzee compared to other 93mammals, suggesting its evolutionary meaning in processes plays an exclusive role in a 94specific eukaryotic lineage” 5. In the discussion part, at lines 403 to 404, where a hypothesis is presented concerning the reason of CUB , it is stated that positive selection of specific codons could putatively be the reason for this fact. Since it is an aspect of the “story” the manuscript unfolds, maybe these codons should be mentioned along with a more specific hypothesis, as it is very nicely done at the following lines concerning muscle tissue and the stop codon. Reviewer #2: n the submitted manuscript , Dr. Rachele Ross et al try to use a new approach to analyze CUB in genes causing human disease-causing genes and non-disease-causing genes to understand connection between CUB and gene mutational diseases. In Particular, authors calculated CU values in tissue-specific and mostly expressed genes in three tissues and analyzed CU values between DC and NDC genes across 15 mammal species. In the end, they concluded that their approach described in this manuscript may be used to uncover connection between codon usage and rare diseases. Comments: 1. Authors only focused on tissue-specific genes. I'm wondering whether authors also calculated CU values in housekeeping genes related to disease( disease-causing genes) vs genes not related to disease ? 2. Why did authors analyze CU values in 15 mammalian species ? Do these species develop the same diseases ? What is the scientific background regarding it ? 3. Please add some background information into the abstract. ****** 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". 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Revision 1
19 Feb 2022 Author Response We thank the referee for the useful comments and here below we provided our replies: In response to Referee 1: 1.Line 65, “genes casing human rare diseases”: Amended in the manuscript text 2. Line 93 “an extreme CUB was identified in both human and chimpanzee compared to other mammals, suggesting its evolutionary meaning in processes plays an exclusive role in a specific eukaryotic lineage” : This part could be rephrased making it clearer: Amended in the manuscript text 3. Concerning this part : 95 “A large consensus exists about the concept that the choice of a synonymous codon does affect… for all genes [8]”. - It is an important statement that is being made in the manuscript, about the consensus that exists around “choice of a synonymous codon does affect protein translation efficiency, expression level, structure, and function, a notion that has prompted”.-This statement, is not adequately represented by references, hence some more references would further develop it. We added more reference to support the importance of the statement we reported in the manuscript. 4. -At the results section “CUB fingerprint across mammals” it is stated from line 277 until line 284 that“…no clear tissue behavior or even specific gene-related clustering can be observed. This finding further supports that CU values show an mammals-related but with important gene-specific differences, which contribute to generate the CUB fingerprints” Although this statement can stand on its own, if it could be commented along with the statement at lines 92-94 concerning chimps and humans… 92- “an extreme CUB was identified in both human and chimpanzee compared to other 93mammals, suggesting its evolutionary meaning in processes plays an exclusive role in a 94specific eukaryotic lineage” Amended in the manuscript text 5. In the discussion part, at lines 403 to 404, where a hypothesis is presented concerning the reason of CUB , it is stated that positive selection of specific codons could putatively be the reason for this fact. Since it is an aspect of the “story” the manuscript unfolds, maybe these codons should be mentioned along with a more specific hypothesis, as it is very nicely done at the following lines concerning muscle tissue and the stop codon. Amended in the manuscript text In response to Referee 2 1-Authors only focused on tissue-specific genes. I'm wondering whether authors also calculated CU values in housekeeping genes related to disease ( disease-causing genes) vs genes not related to disease We apologies to the reviewer for having not explained enough clearly our approach. Our rationale was to consider tissue-specific genes only, either for non-disease causing (“control”) and disease causing genes and to compare them. Therefore, in this proof-of-principle study, we did not include housekeeping genes. Indeed, we definitively believe that housekeeping genes, almost ubiquitously expressed, would deserve to be studied by the same approach. This is something we will certainly do in further studies. In this paper we were focused on tissue specificity, since having genes with same expression site/level facilitated CU values calculation and comparison between gene groups. Why did authors analyze CU values in 15 mammalian species ? Do these species develop the same diseases ? What is the scientific background regarding it ? Thanks for this question which allows to clarify the evolutionary analyses. In order to make more robust the identification of rare codons, we checked conservation of selected genes (both disease and non-disease causing) across mammals. We limited our selection to mammals to avoid to get i) too many bias due to the large specie variability, ii) to compare homo sapiens genes to species evolutionarily close (mammals and non-human primates). Regarding disease propensity, we disregarded wether species may develop human-like diseases, for two main reasons: this occurs very rarely (the so called natural animal disease models), and we were interested in comparing human genes only, since certainly related to diseases. Indeed, CUB was conserved among species, with however some difference in the heatmaps observed in disease-causing genes, especially those related to muscle diseases. Concluding, analyzing CU values across mammals provided a further support of the different CUB behavior (we found conserved among species) between disease and non-disease genes. We have modified and added a sentence (Introduction) to clarify this concept. Attachments Attachment Submitted filename: Answers ref 21.1.22.docx https://doi.org/10.1371/journal.pone.0265469.r002
3 Mar 2022 Decision Letter - Yanbin Yin, Editor Calculating and comparing codon usage values in rare disease genes highlights codon clustering with disease-and tissue- specific hierarchy PONE-D-21-32048R1 Dear Dr. Ferlini, 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, Yanbin Yin 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: The authors improved the manuscript implementing the suggestions/recommendations. Therefore my suggestion is that the manuscript be accepted. ****** 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 https://doi.org/10.1371/journal.pone.0265469.r003
Formally Accepted
17 Mar 2022 Acceptance Letter - Yanbin Yin, Editor PONE-D-21-32048R1 Calculating and comparing codon usage values in rare disease genes highlights codon clustering with disease-and tissue- specific hierarchy Dear Dr. Ferlini: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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 Dr. Yanbin Yin Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0265469.r004

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