Integration of Microbiome and Transcriptome information in helping Diagnosis of Colorectal Cancer

Integration of Microbiome and Transcriptome information in helping Diagnosis of Colorectal 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 Research Article Integration of Microbiome and Transcriptome information in helping Diagnosis of Colorectal Cancer Zhenyi He, Wenchuan Zhu, Yunjun Zeng, Sixian Li, Jun Ma, Zhiyan Yang, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7281730/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 11 You are reading this latest preprint version Abstract Background : Colorectal cancer (CRC) is a major global public health issue, with over 1.8 million new cases and 881,000 deaths in 2018. This study aims to explore the application of integrating microbiome and transcriptome analysis in the diagnosis of colorectal adenocarcinoma (COAD), focusing on its potential in identifying cancer biomarkers and predicting disease progression. Methods : By utilizing COAD transcriptome and microbiome data from TCGA, diversity and differential expression analyses were conducted to identify microbiome composition differences between primary tumors (PT) and solid tissue normal (STN) samples, and the role of mRNA in prognosis. Mediation analysis was used to identify interactions between microbiome, transcriptome, in COAD tumors. The Multi-Omics Graph convolutional NET works (MOGONET) framework was employed to combine these data for COAD tumor prediction. Results : Significant changes in microbiome composition and specific mRNA expression patterns were closely related to COAD development. It was observed that the Simplex virus genus can mediate the abundance of the BRAF transcripts, thereby affecting the risk of COAD. The MOGONET model demonstrated high accuracy in predicting COAD tumors, achieving 0.977 accuracy, 0.988 F1 score, and 1.0 AUROC. Conclusion : Integrating microbiome and transcriptome analysis shows significant potential in COAD diagnosis and prognostic assessment. These findings provide important insights for further clinical applications and cancer treatment strategies. COAD Microbiome mRNA Mediation analysis MOGONET Full Text Additional Declarations No competing interests reported. Supplementary Files table1.xlsx table2.xlsx table3.xlsx table4.xlsx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 09 Oct, 2025 Reviews received at journal 29 Sep, 2025 Reviews received at journal 28 Sep, 2025 Reviews received at journal 26 Sep, 2025 Reviewers agreed at journal 22 Sep, 2025 Reviewers agreed at journal 20 Sep, 2025 Reviewers agreed at journal 17 Sep, 2025 Reviewers invited by journal 13 Sep, 2025 Editor assigned by journal 01 Sep, 2025 Submission checks completed at journal 30 Aug, 2025 First submitted to journal 30 Aug, 2025 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. 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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-7281730","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":518081268,"identity":"f51ad29f-e832-4b41-9a70-f9afff86c4b7","order_by":0,"name":"Zhenyi He","email":"","orcid":"","institution":"Kunming University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Zhenyi","middleName":"","lastName":"He","suffix":""},{"id":518081269,"identity":"40868083-ff74-419d-aae1-eaed2d157703","order_by":1,"name":"Wenchuan Zhu","email":"","orcid":"","institution":"The First People’s Hospital of Yunnan 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Cancer","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"discover-oncology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"dion","sideBox":"Learn more about [Discover Oncology](https://www.springer.com/12672)","snPcode":"","submissionUrl":"","title":"Discover Oncology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Discover Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"COAD, Microbiome, mRNA, Mediation analysis, MOGONET","lastPublishedDoi":"10.21203/rs.3.rs-7281730/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7281730/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e: Colorectal cancer (CRC) is a major global public health issue, with over 1.8 million new cases and 881,000 deaths in 2018. This study aims to explore the application of integrating microbiome and transcriptome analysis in the diagnosis of colorectal adenocarcinoma (COAD), focusing on its potential in identifying cancer biomarkers and predicting disease progression.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods\u003c/strong\u003e: By utilizing COAD transcriptome and microbiome data from TCGA, diversity and differential expression analyses were conducted to identify microbiome composition differences between primary tumors (PT) and solid tissue normal (STN) samples, and the role of mRNA in prognosis. Mediation analysis was used to identify interactions between microbiome, transcriptome, in COAD tumors. The Multi-Omics Graph convolutional NET works (MOGONET) framework was employed to combine these data for COAD tumor prediction.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e: Significant changes in microbiome composition and specific mRNA expression patterns were closely related to COAD development. It was observed that the Simplex virus genus can mediate the abundance of the BRAF transcripts, thereby affecting the risk of COAD. The MOGONET model demonstrated high accuracy in predicting COAD tumors, achieving 0.977 accuracy, 0.988 F1 score, and 1.0 AUROC.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion\u003c/strong\u003e: Integrating microbiome and transcriptome analysis shows significant potential in COAD diagnosis and prognostic assessment. These findings provide important insights for further clinical applications and cancer treatment strategies.\u003c/p\u003e","manuscriptTitle":"Integration of Microbiome and Transcriptome information in helping Diagnosis of Colorectal Cancer","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-22 10:55:29","doi":"10.21203/rs.3.rs-7281730/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-09T14:59:18+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-29T23:11:40+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-28T15:39:50+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-26T04:13:43+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"82772761898122059788222326053094567483","date":"2025-09-23T01:23:23+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"322538220943550457718134826327193967056","date":"2025-09-20T16:05:49+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"150958596246309197482581235340274580365","date":"2025-09-17T15:39:58+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-09-13T07:45:26+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-09-01T05:38:16+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-08-30T14:30:48+00:00","index":"","fulltext":""},{"type":"submitted","content":"Discover Oncology","date":"2025-08-30T14:28:04+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"discover-oncology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"dion","sideBox":"Learn more about [Discover Oncology](https://www.springer.com/12672)","snPcode":"","submissionUrl":"","title":"Discover Oncology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Discover Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"8598bb70-d7b4-4512-b132-eff8924426a3","owner":[],"postedDate":"September 22nd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2025-11-05T16:39:17+00:00","versionOfRecord":[],"versionCreatedAt":"2025-09-22 10:55:29","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7281730","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7281730","identity":"rs-7281730","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}