https://orcid.org/0000-0002-4986-055X
Peer Review History
| Original SubmissionAugust 21, 2025 |
|---|
|
PONE-D-25-45571 Combinatorial drug repurposing of Valproic acid and Zebularine regulates Krüppel-like factor 4 and β-catenin expression in colon cancer cells PLOS ONE Dear Dr. Kandhavelu, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript does not meet our criteria for publication and must therefore be rejected. Specifically, the reviewers and editors found that the manuscript lacks proper controls and statistical analysis to support the conclusions. We are sorry that we cannot be more positive on this occasion, but hope that you appreciate the reasons for this decision. Kind regards, Chunming Liu Academic Editor PLOS ONE [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: No ********** -->2. Has the statistical analysis been performed appropriately and rigorously? --> Reviewer #1: No ********** -->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 ********** -->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: No ********** -->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 manuscript reported a combination drug therapy by repurposing Valproic acid and Zebularine to regulate Krüppel-like factor 4 and β-catenin expression in colon cancer cells. However, it does not meet the publishing criteria of PLOS ONE. 1, Figure 1 shows no synergistic effects between Valproic acid and Zebularine in cell viability even though the authors claimed otherwise. 2, Figures 2,3,5 lack vehicle controls. 3, Figures 1,4,6 are missing statistical analysis. ********** -->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.] - - - - - For journal use only: PONEDEC3 |
| Revision 1 |
|
-->PONE-D-25-45571R1-->-->Combinatorial drug repurposing of Valproic acid and Zebularine regulates Krüppel-like factor 4 and β-catenin expression in colon cancer cells-->-->PLOS One Dear Dr. Kandhavelu, 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.-->--> -->--> Provide appropriate controls and inclusion of additional assays to attribute the tumour suppressive property of KLF4. A higher level of validation shall be provided for the observed changes in gene expression. Epigenetic changes observed shall be justified with additional experimentation using ChIP. Though novelty is not a prime concern to publish in PLoS ONE, it is essential to provide sufficient evidence on the claims made so that the study will contribute to the further advancement of the knowledge in this domain. Inconsistency in the expression of KLF4 with the drug dosage should be thoroughly addressed. Efforts have to be made to provide mechanistic insights to support the claims made. Please submit your revised manuscript by Jan 24 2026 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:-->
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, Suresh Yenugu 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 2. Thank you for stating in your Funding Statement: “We would like to acknowledge Natanya Moodley for manual support during the execution of research methodology. The study was supported by funding from the Cancer Association of South Africa (CANSA); and the Medical Research Council (MRC) of South Africa to the Wits/MRC Common Epithelial Cancer Research Centre. JK is grateful to the National Research Foundation (NRF) of South Africa, to the Griffin Trust Fund, University of the Witwatersrand and the Faculty of Health Sciences Research Committee (FRC) for funding. We also would like to thank Department of Internal Medicine, University of the Witwatersrand and all the funding agency.” Please provide an amended statement that declares all the funding or sources of support (whether external or internal to your organization) received during this study, as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now. Please also include the statement “There was no additional external funding received for this study.” in your updated Funding Statement. Please include your amended Funding Statement within your cover letter. We will change the online submission form on your behalf. 3. Thank you for stating the following financial disclosure: “We would like to acknowledge Natanya Moodley for manual support during the execution of research methodology. The study was supported by funding from the Cancer Association of South Africa (CANSA); and the Medical Research Council (MRC) of South Africa to the Wits/MRC Common Epithelial Cancer Research Centre. JK is grateful to the National Research Foundation (NRF) of South Africa, to the Griffin Trust Fund, University of the Witwatersrand and the Faculty of Health Sciences Research Committee (FRC) for funding. We also would like to thank Department of Internal Medicine, University of the Witwatersrand and all the funding agency.” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. We note that your Data Availability Statement is currently as follows: [All relevant data are within the manuscript and its Supporting Information files.] Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition). For example, authors should submit the following data: The values behind the means, standard deviations and other measures reported; The values used to build graphs; The points extracted from images for analysis. Authors do not need to submit their entire data set if only a portion of the data was used in the reported study. If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories. If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access. 5. Thank you for stating the following in your manuscript: “We would like to acknowledge Natanya Moodley for manual support during the execution of research methodology. The study was supported by funding from the Cancer Association of South Africa (CANSA); and the Medical Research Council (MRC) of South Africa to the Wits/MRC Common Epithelial Cancer Research Centre. JK is grateful to the National Research Foundation (NRF) of South Africa, to the Griffin Trust Fund, University of the Witwatersrand and the Faculty of Health Sciences Research Committee (FRC) for funding. We also would like to thank Department of Internal Medicine, University of the Witwatersrand and all the funding agency. “ We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. Please note that 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: “We would like to acknowledge Natanya Moodley for manual support during the execution of research methodology. The study was supported by funding from the Cancer Association of South Africa (CANSA); and the Medical Research Council (MRC) of South Africa to the Wits/MRC Common Epithelial Cancer Research Centre. JK is grateful to the National Research Foundation (NRF) of South Africa, to the Griffin Trust Fund, University of the Witwatersrand and the Faculty of Health Sciences Research Committee (FRC) for funding. We also would like to thank Department of Internal Medicine, University of the Witwatersrand and all the funding agency.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 6. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Additional Editor Comments (if provided): [Note: HTML markup is below. Please do not edit.] 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: (No Response) Reviewer #3: 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 #2: Partly Reviewer #3: No ********** -->3. Has the statistical analysis been performed appropriately and rigorously? --> Reviewer #2: Yes Reviewer #3: 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 #2: Yes Reviewer #3: 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 #2: Yes Reviewer #3: 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 #2: General Comments to the Authors: 1. The introduction is generally well structured; however, it would benefit from a more comprehensive discussion of the clinical symptoms, underlying causes, and major risk factors of colon cancer. Furthermore, a clearer linkage between these aspects and the rationale, objectives, and significance of the current study should be established to strengthen the contextual foundation of the manuscript. 2. The manuscript should maintain consistent scientific terminology throughout. In particular, β-catenin is referred to interchangeably as CTNNB1 and β-catenin, which may cause confusion and should be standardized. 3. The vehicle control images corresponding to the confocal microscopy experiments should be assembled and presented together in a single figure to improve clarity, organization, and comparative interpretation of the imaging data. 4. Vehicle control data appear to be missing from Figures 1D, 4, and 6. In the absence of these essential controls, the comparison of gene expression levels and treatment effects is scientifically inappropriate and weakens the reliability of the results. 5. In line 109 of the Introduction, the authors state that KLF4-overexpressing MCF-7 cells were used; however, there is no experimental evidence or methodological description confirming KLF4 overexpression. This inconsistency should be clarified and adequately supported. 6. The tumour-suppressive role attributed to KLF4 requires stronger experimental validation. Inclusion of apoptosis-specific assays, such as flow cytometry (FACS) analysis and Western blotting of apoptotic markers, is necessary because immunofluorescence alone is insufficient to conclusively demonstrate apoptotic induction. 7. The reported changes in gene expression should be supported by protein-level validation. Western blotting and relevant transfection-based functional assays are required to confirm that transcriptional changes translate into meaningful biological effects. 8. The reduction in cell proliferation does not appear to be proportionate to the reported increase in KLF4 expression. Given the modest decrease in cell viability relative to control, the claim that these effects are KLF4-dependent (as stated in lines 549–550) appears overstated and requires additional experimental justification. The use of the term “efficient” is also not adequately supported by the magnitude of the observed effects. 9. The proposed epigenetic effects of ZEB and VPA on histone modifications should be validated using chromatin immunoprecipitation (ChIP) assays to directly measure alterations in HDAC-associated histone marks. Reliance solely on qPCR data is insufficient to draw firm conclusions about the efficacy of the VPA+ZEB combination in colorectal cancer. 10. There appears to be a misrepresentation of concentration values in line 384, which should be carefully corrected to ensure the accuracy and reproducibility of the experimental conditions. 11. The study currently lacks direct mechanistic evidence and relies heavily on previously published literature to support its conclusions. For a manuscript that claims novelty, original experimental validation of the proposed mechanisms is required rather than extrapolation from prior reports. Overall, while the study addresses an interesting and potentially relevant research question, the manuscript requires substantial revision. Critical methodological clarifications, inclusion of appropriate controls, and stronger mechanistic and protein-level validation are essential before the conclusions can be considered reliable. Reviewer #3: There are several critical inconsistencies between the mRNA data, protein-level observations, dosing rationale, and the mechanistic interpretation. These issues collectively undermine the reliability of the study’s conclusions. 1. Multiple discrepancies remain between qPCR data and confocal imaging results. • KLF4 mRNA is downregulated by VPA in both SW480 and DLD-1 cells (Fig. 1D), yet nuclear KLF4 protein staining increases markedly at 5 mM VPA (Fig. 2B). • Low-dose ZEB decreases KLF4 mRNA (Fig. 4, pages 15–16), but KLF4 protein intensity increases at both low and high ZEB doses (Fig. 5.I.A and 5.I.B, pages 17–18). • Under combinatorial treatment, SW480 cells show reduced KLF4 protein intensity at high dose (Fig. 7.I.B), while DLD-1 cells show substantial KLF4 upregulation at the mRNA level (Fig. 6, page 20). These contradictions are neither addressed nor explained. No mechanistic rationale, methodological clarification, or acknowledgment of potential post-transcriptional or post-translational regulation is provided. This creates fundamental uncertainty about the validity of the central conclusions. 2. Although the manuscript lists the doses used (1.5 mM / 5 mM VPA and 0.1 mM / 0.3 mM ZEB), the authors provide no scientific justification for selecting these concentrations. • No EC50/IC50 values are referenced. • No preliminary optimization or toxicity data are presented. • No supporting literature is cited. Without proper justification, it is unclear whether the chosen concentrations reflect physiologic relevance, mechanistic intent, or simply reflect cytotoxicity-driven effects. This remains a major methodological limitation. 3. The manuscript continues to assert mechanistic interactions that are not experimentally demonstrated: • Fig. 9 (page 27) is entirely conceptual and is not supported by any functional data generated in the study. • The Discussion (pages 23–26) repeatedly presents causal interpretations, particularly regarding Wnt signaling, apoptosis induction, and epigenetic regulation, that are not proven experimentally. • The proposed antagonistic relationship between KLF4 and CTNNB1 is not consistently supported by the gene expression data in Fig. 6 or the single-cell protein data in Fig. 8. • Crucially, no functional assays (e.g., KLF4 knockdown, β-catenin reporter assays, rescue experiments, chromatin studies) were performed to validate the proposed mechanism. ********** -->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 #2: No Reviewer #3: Yes: Abhijit Chakraborty ********** [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.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. |
| Revision 2 |
|
-->PONE-D-25-45571R2-->-->Combinatorial drug repurposing of Valproic acid and Zebularine regulates Krüppel-like factor 4 and β-catenin expression in colon cancer cells-->-->PLOS One Dear Dr. Kandhavelu, 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 Apr 29 2026 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:-->
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, Suresh Yenugu Academic Editor PLOS One Journal Requirements: If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Additional Editor Comments: Note that the suggestions of the reviewers have to be taken in all seriousness and modifications made, especially when claims are made on the mechanistic action in the absence of substantial data. Changes to the introduction, rationale and discussion should be made by citing appropriate references. [Note: HTML markup is below. Please do not edit.] 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: (No Response) Reviewer #3: 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 #2: Partly Reviewer #3: Partly ********** -->3. Has the statistical analysis been performed appropriately and rigorously? --> Reviewer #2: Yes Reviewer #3: I Don't Know ********** -->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 ********** -->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 ********** -->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: The revise manuscript does not still fully address the particular major comments mentioned in previous review which plays a significant role in proving the credibility of the study. Reviewer #3: The authors have made some effort to address my previous concerns, but several critical issues remain unresolved or insufficiently addressed. My overall assessment is that the manuscript still requires major revision before it can be considered for publication. Major Comments: 1. The authors added a paragraph to the Discussion invoking post-transcriptional and post-translational regulatory mechanisms to explain the discordances between KLF4 mRNA and protein levels. While this is a plausible general explanation, it remains entirely speculative and unsupported by any data generated in this study. No mRNA stability assays, polysome profiling, proteasome inhibition experiments, or microRNA data are presented. The response cites references 49-51 for these mechanisms, but these references do not appear in the manuscript's reference list this is a significant error that must be corrected. Furthermore, for the combinatorial treatment discordance (SW480 vs. DLD-1), the authors offer only a qualitative, cell-line-specific rationale without experimental substantiation. The discordances between mRNA and protein data remain a fundamental unresolved issue that meaningfully weakens the study's conclusions. 2. The authors have added a paragraph to the Introduction justifying their concentration selections. This is an improvement. However, the justification cites references [24–28] that are not present in the reference list as numbered the numbering appears shifted and inconsistent with the manuscript body. This must be corrected. Additionally, the authors do not address whether VPA at 1.5–5 mM is clinically achievable in plasma or tissue — this is important context for a drug repurposing claim. 3. The authors replaced the schematic diagram (Fig. 9) with Table 2. While this is a positive step toward transparency, the core issue remains: causal mechanistic claims about Wnt signaling, apoptosis induction, and the KLF4-β-catenin antagonism continue to be made in the Discussion without any supporting functional data. No knockdown experiments, reporter assays, rescue experiments, or ChIP data have been added. The removal of the schematic is appreciated, but it does not resolve the problem of unsupported mechanistic language. The authors should clearly reframe the Discussion using appropriately hedged, correlative language, and distinguish firmly between what was observed versus what is speculated. Minor Comments: 1. The text still refers to "SYN 2 with 25 mM VPA" — this appears to be a persistent error (should be 5 mM VPA). The authors acknowledged this in their response but it must be verified as corrected in the final manuscript. 2. Line 359 refers to "HT29 and DLD-1 cells" when the study uses SW480 and DLD-1. This error remains uncorrected in the R2 manuscript and represents a serious inconsistency. 3. The abstract (line 36 of the R2 manuscript) still refers to "about one-fold" increase in DLD-1 cells in one place, while the body consistently reports a 22-fold increase. This needs reconciliation. 4. The single-cell quantification data in Figure 8 show that ZEB at 0.1 mM appears to stimulate CTNNB1 levels in both SW480 and DLD-1 cells, which is contradictory to the proposed anti-cancer mechanism. This is acknowledged briefly in the Results but not adequately discussed. 5. The Dunnett's test is appropriate for the comparisons described, but the manuscript continues to report some p-values inconsistently (e.g., "p > 0.0005" in section 3.4, which appears to be a typographical error and should likely be p < 0.0005). 6. The manuscript still contains grammatical errors and unclear phrasing throughout that impede scientific comprehension (e.g., "huge increase to about one-fold," "confrontational interaction," "injection of VPA and ZEB"). Professional English editing is still needed. The authors have made partial progress, but the manuscript continues to make mechanistic claims unsupported by functional data, contains unresolved discordances between mRNA and protein results, has uncorrected errors (including a cell line identification error in Section 3.8 and missing/incorrect references), and retains language issues. The study's conceptual contribution exploring VPA and ZEB combination effects on KLF4 and β-catenin in CRC remains of modest interest, but the conclusions must be more carefully aligned with the actual data, and the identified errors corrected before this work can be published. ********** -->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 #2: No Reviewer #3: Yes: Abhijit Chakraborty ********** [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.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.
|
| Revision 3 |
|
Combinatorial drug repurposing of Valproic acid and Zebularine regulates Krüppel-like factor 4 and β-catenin expression in colon cancer cells PONE-D-25-45571R3 Dear Dr. Kandhavelu, 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. For questions related to billing, please contact billing support. 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, Suresh Yenugu 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 #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 #2: Yes ********** -->3. Has the statistical analysis been performed appropriately and rigorously? --> 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 #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 #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 #2: Authors addressed several of my previous comments if not all. However the present data and revised manuscript may be sufficient to convince the audience on the concept and results. ********** -->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 #2: No ********** |
| Formally Accepted |
|
PONE-D-25-45571R3 PLOS One Dear Dr. Kandhavelu, 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 You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. 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 Dr. Suresh Yenugu Academic Editor PLOS One |
Open letter on the publication of peer review reports
PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.
We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.
Learn more at ASAPbio .