Urine metabolomic profiles of autism and autistic traits–A twin study

Abishek Arora; Francesca Mastropasqua; Sven Bölte; Kristiina Tammimies

doi:10.1371/journal.pone.0308224

Peer Review History

Original SubmissionDecember 6, 2023
15 Apr 2024 Decision Letter - Claudia Brogna, Editor PONE-D-23-39743Urine metabolomic profiles of autism and autistic traits – a twin studyPLOS ONE Dear Dr. Tammimies, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by May 30 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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In the online submission form, you indicated that the mass spectrometry data is accessible from the corresponding author after necessary clearances. The utilised code is available on GitHub (https://github.com/Tammimies- Lab/RATSS-Metabolomics) or available upon request from the corresponding author.. All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons on resubmission and your exemption request will be escalated for approval. 5. 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Revision 1
6 Jun 2024 Author Response Reviewer The metabolomic analysis in twin-cohort to discover urinary biomarker of autism is interesting and of significance. It is valuable to tease out many confounding factors, as gene and environment factors. Although no significant metabolic drivers for autism diagnosis were detected when controlling for other neurodevelopmental conditions. Some nominally changes were found within the twin pairs. Nevertheless, we have the following questions： 1. For PCA analysis, 9 individuals were outliers and excluded, but no better clustering and explained in further repeated PCA. What is the conceptual basis and meaning for excluding individual? As rightly stated, following PCA, 9 individuals were designated as outliers and excluded as they were outside the 95% confidence interval ellipses of the scatter plot for the most explanato-ry principal components (PC1 and PC2, Figure 1A). Further repeated PCAs did not improve clustering and were therefore not included. This rationale and our approach to handling outliers in this study is stated in the manuscript (lines 208 – 213). The removal of the outliers was done based on recommendations in the field (PMID: 38179935). Nevertheless, only 8.57% of the total study participants (N=105) were excluded, which would not have a statistical impact on our findings. 2. For untargeted metabolomics, features identified by the UPLC-MS should be listed and offer more details, as m/z, rt or fragmentation similarity, etc. It is important for ex-hibiting confidence in annotating metabolites. The 208 features identified following untargeted metabolomic using UHPLC-MS have been stated in Table S1 and Table S2. The UHPLC-MS analysis and annotation were performed by the Proteomics and Metabolomics Facility of the University of Tuscia, Italy, using their stand-ard established pipeline (lines 114 – 148). This analytical approach has also been utilised in previously published papers (PMIDs 32512190 and 27904735) by members of the core facili-ty. Unfortunately, we were not able to get the m/z, rt or fragmentation similarity from the core facility but only the standard annotated metabolites as reported. As the metabolomics analysis was performed on a clinical cohort, further data cannot be included in this manuscript in lieu of ethical considerations. 3. Urine is an unstable milieu, collection time and method may affect the results. While no information was given in the manuscript. Please explain your consideration of these factors. Thank you for noting, we have now included more information about how the urine was col-lected from the participants (lines 110 – 116). We additionally added a sentence about the col-lection of the urine samples and instability to the manuscript’s discussion (lines: 381 – 382). 4. As mentioned in the manuscript, indole-3-acetate is positive associated with autistic traits within the twin pairs. If it is possible to assess the potential of indole-3-acetate as a predictor? Although, indole-3-acetate is positively associated with autistic traits within the twin-pairs, it would not be appropriate to access its potential role as a predictor due to the confounding ef-fects of participant genetics. Academic Editor 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf The manuscript has been updated to meet the shared style requirements of PLOS ONE, includ-ing the naming of all uploaded files. 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. We have ensured that the grant information provided at the time of resubmission matches that which is included in the manuscript (lines 415 – 422). 3. Thank you for stating the following financial disclosure: "The project was supported by the Swedish Research Council (S.B., and K.T.), Swedish Foundation for Strategic Research (K.T.), the Swedish Brain Foundation – Hjärnfonden (K.T.), the Harald and Greta Jeanssons Foundations (K.T.), Åke Wiberg Foundation (K.T.), Strategic Research Area Neuroscience Stratneuro (K.T.), The Swedish Foundation for International Coop-eration in Research and Higher Education STINT (K.T.), and Board of Research at Ka-rolinska Institutet (K.T.). " 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 col-lection 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 amend-ed Role of Funder statement in your cover letter; we will change the online submission form on your behalf. The funders had no role in this study and this has been stated in the funding information (lines 420 – 422), as shared in the above-mentioned statement. 4. In the online submission form, you indicated that the mass spectrometry data is ac-cessible from the corresponding author after necessary clearances. The utilised code is available on GitHub (https://github.com/Tammimies-Lab/RATSS-Metabolomics) or available upon request from the corresponding author. All PLOS journals now require all data underlying the findings described in their man-uscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons on resubmission and your exemption re-quest will be escalated for approval. The data included in this manuscript pertains to clinical research and cannot be made publicly available for ethical and legal reasons as this would compromise patient privacy. 5. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please delete it from any other section. The ethics statement is included in the Materials and methods section (lines 86 – 88) and has been removed from any other section of the manuscript. 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 Sup-porting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. Captions for the Supporting information files have been included in the manuscript (lines 437 – 448) and match the in-text citations. Attachments Attachment Submitted filename: RATSS_Reviewer_Comments_Response.pdf https://doi.org/10.1371/journal.pone.0308224.r002
19 Jul 2024 Decision Letter - Claudia Brogna, Editor Urine metabolomic profiles of autism and autistic traits – a twin study PONE-D-23-39743R1 Dear Dr.Kristiina Tammimies, 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, Claudia Brogna Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0308224.r003
Formally Accepted
24 Jul 2024 Acceptance Letter - Claudia Brogna, Editor PONE-D-23-39743R1 PLOS ONE Dear Dr. Tammimies, 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 Dr. Claudia Brogna Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0308224.r004

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