Heavy water inhibits DNA double-strand break repairs and disturbs cellular transcription, presumably via quantum-level mechanisms of kinetic isotope effects on hydrolytic enzyme reactions

Takeshi Yasuda; Nakako Nakajima; Tomoo Ogi; Tomoko Yanaka; Izumi Tanaka; Takaya Gotoh; Wataru Kagawa; Kaoru Sugasawa; Katsushi Tajima

doi:10.1371/journal.pone.0309689

Peer Review History

Original SubmissionJune 6, 2024
24 Jul 2024 Decision Letter - A Ganesan, 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-24-22759Heavy water inhibits DNA double-strand break repairs and disturbs cellular transcription,presumably via quantum-level mechanisms of kinetic isotope effects on hydrolytic enzyme reactionsPLOS ONE Dear Dr. Yasuda, 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 Sep 07 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. 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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: We thank Dr. M. Jasin (Memorial Sloan-Kettering Cancer Center, NYC, USA) for the DR-GFP assay materials. We deeply appreciate Dr. S. Hirayama (Emeritus Professor, Kyoto Institute of Technology, Kyoto, Japan) and Dr. H. Kitoh-Nishioka (Kindai University, Osaka, Japan) for helpful instructions and discussions about quantum tunneling and kinetic isotope effects, and Dr. H. Kurumizaka and his laboratory members (The University of Tokyo, Tokyo, Japan) for purified histone proteins. This research was supported by Research Support Project for Life Science and Drug Discovery (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP22ama121009 (H. Kurumizaka). 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 study was funded by JSPS KAKENHI Grant Numbers 20K12177 (to T. Yasuda), 20K08071 (to K.T. and T. Yasuda), 22H03743 (to W.K. and T. Yasuda), and 22K08414 (to T.G. and T. Yasuda). This study was also funded by the joint research program of the Biosignal Research Center, Kobe University, Grant Numbers 281004 (to T. Yasuda and K.S.), and 201003 (to T. Yasuda and K.S.). The funders had no role in the study design, data collection, interpretation, or decision to submit the work for publication. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 3. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels. In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. 4. 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. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. 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Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: 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: General comments to the paper entitled: Heavy water inhibits DNA double-strand break repairs and disturbs cellular transcription, presumably via quantum-level mechanisms of kinetic isotope effects on hydrolytic enzyme reactions It is well known that the heavy hydrogen, the deuterium, is toxic in high concentrations. The author aimed to reveal the mechanism of deuterium, which is responsible for its toxic effect. To do that, the kinetic isotope effect on different enzymatic reactions was investigated in in vitro and in vivo systems. The study nicely presents the effect on several enzymatic reactions, such as deacetylation, DNA cleavage, and protein cleavage. This excellent study shows the importance of quantum mechanisms fundamentally determining the basis of life. The critical phenomenon of quantum tunneling involves comparing the behavior of the two stable hydrogen isotopes in the chemical reaction. Due to the 100% mass difference, the quantum tunneling effect is well documented in enzymes with hydrogen transfer. Congratulations to the authors on their excellent work relating to all the studies applying D2O in a wide range of concentrations. However, the last sentence of the “Quantum-level effects on life phenomena” paragraph suggests the authors missed something relating to deuterium research. The “D exists as hydrogen, which is essentially negligible on the Earth…” is in line with the concept accepted for 60 years after the discovery of D; we do not need to count on living organisms. Over 30 years ago, research started to investigate the biological effect of deuterium depletion, specifically the effect of D concentration below the natural level. Today, it is widely accepted that naturally occurring D has a central role in regulating cell growth, tumor development, and metabolism. I strongly encourage the authors to consider adding one more paragraph to the manuscript, citing papers on deuterium-depleted water (DDW) research. The tunneling effect is present in the cells even at a natural concentration of D. The potential impact of deuterium depletion on cell growth, gene expression, and metabolism suggests the tunneling effect's importance is even higher than the present manuscript suggests. Your research has the potential to give a clear explanation of the tunneling effect for the observed findings with DDW. ****** 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 ******** [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. Attachments Attachment Submitted filename: Heavy water inhibits DNA .....pdf https://doi.org/10.1371/journal.pone.0309689.r001
Revision 1
15 Aug 2024 Author Response Dear Editor: We are grateful to the academic editor and the reviewers for carefully reading our manuscript, and providing valuable comments that have helped us improve it. We have considered all of their comments, and incorporated the comments as much as possible in the revised version of our paper.　The revised parts of the manuscript are highlighted in red. We look forward to hearing from you regarding our submission and to responding to any future questions and comments you may have. Sincerely, Takeshi Yasuda Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan Tel: +81 43 206 3117 Fax: +81 43 206 4094 E-mail: yasuda.takeshi@qst.go.jp Response to the comments from the academic editor Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. 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 Thank you for your kind comment. The following corrections have been made in accordance with PLOS ONE's style requirements. The previous manuscript included a Full title and a Short title, but the Short title was removed in the revised manuscript. The ZIP codes and abbreviations were removed from the Affiliations. The information on the corresponding author was revised to include only the email address. As for the initials of the corresponding author after the e-mail address, we chose "Takeshi Y" to distinguish Takeshi Yasuda and Tomoko Yanaka, since they have the same TY initials. All major sections (Abstract, Introduction, Materials and methods, Results, Discussion, etc.) were changed to 18pt font. The PDF files of the main figure were changed to Tif files and renamed as "Fig1.tif", etc. Supporting information files are uploaded separately as individual files. The Supporting information file names were changed to "S1 Text.pdf", "S1 Fig.pdf", etc. The "Materials and Methods" section has been moved to the next section after the "Introduction". The numbering of the references has been corrected accordingly. We left the information about the two preprints on which this paper is based in the manuscript, because we could not determine whether it should be removed. Finally, we have replaced the KEGG permission file for PLOS Biology with the KEGG permission file for PLOS ONE. 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: We thank Dr. M. Jasin (Memorial Sloan-Kettering Cancer Center, NYC, USA) for the DR-GFP assay materials. We deeply appreciate Dr. S. Hirayama (Emeritus Professor, Kyoto Institute of Technology, Kyoto, Japan) and Dr. H. Kitoh-Nishioka (Kindai University, Osaka, Japan) for helpful instructions and discussions about quantum tunneling and kinetic isotope effects, and Dr. H. Kurumizaka and his laboratory members (The University of Tokyo, Tokyo, Japan) for purified histone proteins. This research was supported by Research Support Project for Life Science and Drug Discovery (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP22ama121009 (H. Kurumizaka). 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 study was funded by JSPS KAKENHI Grant Numbers 20K12177 (to T. Yasuda), 20K08071 (to K.T. and T. Yasuda), 22H03743 (to W.K. and T. Yasuda), and 22K08414 (to T.G. and T. Yasuda). This study was also funded by the joint research program of the Biosignal Research Center, Kobe University, Grant Numbers 281004 (to T. Yasuda and K.S.), and 201003 (to T. Yasuda and K.S.). The funders had no role in the study design, data collection, interpretation, or decision to submit the work for publication. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Thank you for pointing out the corrections. The histone proteins were provided by Dr. Kurumizaka through the support of the Research Support Project for Life Science and Drug Discovery (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)). The Grant (Grant Number JP22ama121009) was obtained by Dr. Kurumizaka, not by us. According to a statement from the BINDS office, BINDS-supported research must be mentioned in the acknowledgements as follows: "This research was supported by Research Support Project for Life Science and Drug Discovery (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP22ama121xxx". Therefore, we have included this sentence in the Acknowledgments Section instead of the Funding Statement. In consultation with the BINDS office, this sentence was moved to the Funding Statement. The Grant Number JP22ama121009 was changed to Grant Number JP23ama121009 at the request of the Kurumizaka Laboratory. Instead, in the Acknowledgments section, we removed the grant number information and revised the following sentence: "We also thank Dr. H. Kurumizaka and his laboratory members (The University of Tokyo, Tokyo, Japan) for providing purified histone proteins via Research Support Project for Life Science and Drug Discovery (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED." We removed any funding-related text from the manuscript, and updated our Funding Statement as follows: "This study was funded by JSPS KAKENHI Grant Numbers 20K12177 (to T. Yasuda), 20K08071 (to K.T. and T. Yasuda), 22H03743 (to W.K. and T. Yasuda), and 22K08414 (to T.G. and T. Yasuda). This study was also funded by the joint research program of the Biosignal Research Center, Kobe University, Grant Numbers 281004 (to T. Yasuda and K.S.), and 201003 (to T. Yasuda and K.S.). This research was supported by Research Support Project for Life Science and Drug Discovery (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP23ama121009 (H. Kurumizaka). The funders had no role in the study design, data collection, interpretation, or decision to submit the work for publication." 3. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels. In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. Thank you for pointing out the corrections. We added our original blot/gel image data (S1 Raw images.pdf) in the Supporting Information. Accordingly, the following sentences have been added to the legends of the Supporting information of the manuscript: "S1 Raw images. The original blot and gel images contained in the manuscript’s main figures and supplemental figures. The cropped areas used in the manuscript’s main figures and supplemental figures are surrounded by red lines." 4. 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. Thank you for your kind comment. We have verified that the reference list is complete and correct. Also, we did not cite any RETRACTED papers. Response to the comments from the reviewer #1 However, the last sentence of the “Quantum-level effects on life phenomena” paragraph suggests the authors missed something relating to deuterium research. The “D exists as hydrogen, which is essentially negligible on the Earth…” is in line with the concept accepted for 60 years after the discovery of D; we do not need to count on living organisms. Thank you for your kind comments. Your insights have highlighted the importance of the effects of naturally occurring deuterium concentrations. According to your comments, we have removed the following phrase: "which is essentially negligible on the Earth." Over 30 years ago, research started to investigate the biological effect of deuterium depletion, specifically the effect of D concentration below the natural level. Today, it is widely accepted that naturally occurring D has a central role in regulating cell growth, tumor development, and metabolism. I strongly encourage the authors to consider adding one more paragraph to the manuscript, citing papers on deuterium-depleted water (DDW) research. The tunneling effect is present in the cells even at a natural concentration of D. The potential impact of deuterium depletion on cell growth, gene expression, and metabolism suggests the tunneling effect's importance is even higher than the present manuscript suggests. Your research has the potential to give a clear explanation of the tunneling effect for the observed findings with DDW. Thank you for your understanding and appreciation of our research. We are particularly grateful that you pointed out the relevance of our results concerning the biological effects of deuterium-depleted water, which we had not previously considered. Your comments have greatly enhanced the significance of our findings. In line with your suggestions, we have added the following text to the end of the Discussion, citing the relevant papers (references 98-104) on DDW: "While the biological effects of high concentrations of heavy water are strong, there are also notable effects when the deuterium content in naturally occurring water is depleted [98-104]. Compared to normal water, deuterium-depleted water (DDW) reduces the growth rate of mammalian cells [98-100]. The inhibitory effect of DDW on cancer cell proliferation has attracted keen attention, from the perspective of cancer treatment [99-102]. DDW also alters gene expression [101, 104] and the amounts of intracellular metabolic products [102, 103]. Thus, like heavy water at high concentrations, DDW affects the same biological phenomena such as cell proliferation and transcription. Therefore, our study of quantum effects may provide a clear explanation for the observed biological effects of DDW, which could also result from quantum-level isotope effects on the numerous hydrolytic enzyme reactions within cells. Based on our findings and those of previous studies, it can be inferred that quantum-level mechanisms, including quantum tunneling, in hydrolytic enzyme reactions must have important effects on the fundamental life phenomena of organisms living on Earth." Attachments Attachment Submitted filename: Responses to Reviewers.docx https://doi.org/10.1371/journal.pone.0309689.r002
16 Aug 2024 Decision Letter - A Ganesan, Editor Heavy water inhibits DNA double-strand break repairs and disturbs cellular transcription,presumably via quantum-level mechanisms of kinetic isotope effects on hydrolytic enzyme reactions PONE-D-24-22759R1 Dear Dr. Yasuda, 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, A Ganesan Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0309689.r003
Formally Accepted
10 Sep 2024 Acceptance Letter - A Ganesan, Editor PONE-D-24-22759R1 PLOS ONE Dear Dr. Yasuda, 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 Prof. A Ganesan Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0309689.r004

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