Bioinformatic analysis of N6-methyladenosine, 5-methylcytosine, and N1-methyladenosine co-regulation patterns and validation of NSUN6 as a protective protein in colon cancer

Bioinformatic analysis of N6-methyladenosine, 5-methylcytosine, and N1-methyladenosine co-regulation patterns and validation of NSUN6 as a protective protein in colon cancer | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Bioinformatic analysis of N6-methyladenosine, 5-methylcytosine, and N1-methyladenosine co-regulation patterns and validation of NSUN6 as a protective protein in colon cancer WenJie Xie, Zhao Sun, Yang Fu This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3842256/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract BACKGROUND More than one hundred types of RNA modification involved in nearly all the biological processes. However, the crosstalk among these RNA methylations and their related regulators still remains mysterious in the development and progression of colon adenocarcinoma (COAD). OBJECTIVE This study aimed to explore the interactions and prognostic values of RNA methylation regulators in COAD. METHODS Subgroups of COAD patients from the TGCA database were determined by consensus clustering. GSVA and GSEA analyses were used to detect the different biological pathways. And algorithms including ssGSEA and ESTIMATE were performed for the immunological analysis. Moreover, the univariate and multivariate Cox analyses based on immunohistochemistry were applied to investigate the prognostic values. RESULTS COAD patients were divided into two groups: patients with the worse prognosis were identified with the dysregulated EMT, NF-κB and KRAS signaling pathways and higher stromal scores. NSUN6, the writer of m5C, was further confirmed as a protective protein by immunohistochemistry and multi-datasets analysis suggested that FBXW7 is co-expressed with NSUN6. CONCLUSIONS In COAD, interactions among the regulators of m6A, m5C and m1A could be used to distinguish the patients with different prognosis. And the m5C writer NSUN6 can be served as a prognostic biomarker. Biological sciences/Cancer Biological sciences/Computational biology and bioinformatics Colon cancer RNA methylation TCGA database NSUN6 FBXW7 Full Text Additional Declarations No competing interests reported. Supplementary Files FuyangFigS1.tif TableS1.xlsx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-3842256","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":267696236,"identity":"3e5d5ca7-6785-4f42-9299-aa1b09c00ba1","order_by":0,"name":"WenJie Xie","email":"","orcid":"","institution":"First Affiliated Hospital of Zhengzhou University","correspondingAuthor":false,"prefix":"","firstName":"WenJie","middleName":"","lastName":"Xie","suffix":""},{"id":267696237,"identity":"0a5c81f8-c3ee-478a-bbd3-0be3e6905877","order_by":1,"name":"Zhao Sun","email":"","orcid":"","institution":"First Affiliated Hospital of Zhengzhou University","correspondingAuthor":false,"prefix":"","firstName":"Zhao","middleName":"","lastName":"Sun","suffix":""},{"id":267696238,"identity":"71aa8501-c7cd-4dfd-a1ba-6c9d8b793f8c","order_by":2,"name":"Yang Fu","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAx0lEQVRIiWNgGAWjYBAC9gYwZQPh8RCjhecAmEojXcthUrRI5Bh+Lvh13l5+RgLjg7dtDPLmRGgxlp7Zd5uZcUYCs+HcNgbDnQ0EtNhL5BhI8/bcZmOWSGCT5m1jSDA4QIQtv3l7zvGwSSSw/yZWi5k0z48DEjxAW5iJ08LzrMyatyHZQILnYbPknHMShhsIamFP3nyb54+dvXx78sEPb8ps5AnawsDAYcDA2AZiMDYACQmC6oGA/QEDwx9iFI6CUTAKRsGIBQAetDa5XqkJgAAAAABJRU5ErkJggg==","orcid":"","institution":"First Affiliated Hospital of Zhengzhou University","correspondingAuthor":true,"prefix":"","firstName":"Yang","middleName":"","lastName":"Fu","suffix":""}],"badges":[],"createdAt":"2024-01-07 10:44:25","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3842256/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3842256/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":73379234,"identity":"491bc8a5-4c20-4570-9523-b2d32624fdda","added_by":"auto","created_at":"2025-01-09 10:56:01","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1771243,"visible":true,"origin":"","legend":"","description":"","filename":"FuyangManuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3842256/v1_covered_1d9225b6-d24c-459d-901f-a44386176b77.pdf"},{"id":49836505,"identity":"64fb5064-92e5-48a8-b4cb-54741214896e","added_by":"auto","created_at":"2024-01-18 18:58:40","extension":"tif","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":839658,"visible":true,"origin":"","legend":"","description":"","filename":"FuyangFigS1.tif","url":"https://assets-eu.researchsquare.com/files/rs-3842256/v1/7065cbd47d3d21e73b2b9de0.tif"},{"id":49836504,"identity":"7e548eaa-8db7-4854-bc58-0c4e0e558a9f","added_by":"auto","created_at":"2024-01-18 18:58:40","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":11303,"visible":true,"origin":"","legend":"","description":"","filename":"TableS1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3842256/v1/fc0aadbc8a45ab86ec5598e8.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Bioinformatic analysis of N6-methyladenosine, 5-methylcytosine, and N1-methyladenosine co-regulation patterns and validation of NSUN6 as a protective protein in colon cancer","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Colon cancer, RNA methylation, TCGA database, NSUN6, FBXW7","lastPublishedDoi":"10.21203/rs.3.rs-3842256/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3842256/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBACKGROUND\u003c/h2\u003e \u003cp\u003eMore than one hundred types of RNA modification involved in nearly all the biological processes. However, the crosstalk among these RNA methylations and their related regulators still remains mysterious in the development and progression of colon adenocarcinoma (COAD).\u003c/p\u003e\u003ch2\u003eOBJECTIVE\u003c/h2\u003e \u003cp\u003eThis study aimed to explore the interactions and prognostic values of RNA methylation regulators in COAD.\u003c/p\u003e\u003ch2\u003eMETHODS\u003c/h2\u003e \u003cp\u003eSubgroups of COAD patients from the TGCA database were determined by consensus clustering. GSVA and GSEA analyses were used to detect the different biological pathways. And algorithms including ssGSEA and ESTIMATE were performed for the immunological analysis. Moreover, the univariate and multivariate Cox analyses based on immunohistochemistry were applied to investigate the prognostic values.\u003c/p\u003e\u003ch2\u003eRESULTS\u003c/h2\u003e \u003cp\u003eCOAD patients were divided into two groups: patients with the worse prognosis were identified with the dysregulated EMT, NF-κB and KRAS signaling pathways and higher stromal scores. NSUN6, the writer of m5C, was further confirmed as a protective protein by immunohistochemistry and multi-datasets analysis suggested that FBXW7 is co-expressed with NSUN6.\u003c/p\u003e\u003ch2\u003eCONCLUSIONS\u003c/h2\u003e \u003cp\u003eIn COAD, interactions among the regulators of m6A, m5C and m1A could be used to distinguish the patients with different prognosis. And the m5C writer NSUN6 can be served as a prognostic biomarker.\u003c/p\u003e","manuscriptTitle":"Bioinformatic analysis of N6-methyladenosine, 5-methylcytosine, and N1-methyladenosine co-regulation patterns and validation of NSUN6 as a protective protein in colon cancer","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-01-18 18:58:35","doi":"10.21203/rs.3.rs-3842256/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"b006fa17-88b8-43c3-ab23-7c3c9ddc3af6","owner":[],"postedDate":"January 18th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":28206872,"name":"Biological sciences/Cancer"},{"id":28206873,"name":"Biological sciences/Computational biology and bioinformatics"}],"tags":[],"updatedAt":"2025-01-09T10:54:08+00:00","versionOfRecord":[],"versionCreatedAt":"2024-01-18 18:58:35","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-3842256","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3842256","identity":"rs-3842256","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}