Integration of Single-Cell and Spatial Transcriptome Sequencing Identifies CDKN2A as a Senescent Biomarker in Endothelial Cells Implicating Hepatocellular Carcinoma Malignancy

Integration of Single-Cell and Spatial Transcriptome Sequencing Identifies CDKN2A as a Senescent Biomarker in Endothelial Cells Implicating Hepatocellular Carcinoma Malignancy | 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 Single-Cell and Spatial Transcriptome Sequencing Identifies CDKN2A as a Senescent Biomarker in Endothelial Cells Implicating Hepatocellular Carcinoma Malignancy Yue Ma, Chenhe Yi, Ning Cai, Jinhong Chen This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4207895/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 Purpose: Hepatocellular carcinoma (HCC) is one of the most malignant tumors worldwide, remaining difficult to manage. The role of cellular senescence in HCC has been gradually recognized. The present study aimed to comprehensively analyze the senescence-related features of HCC in single-cell and spatial dimension. Methods: Integration of single-cell RNA sequencing (scRNA-Seq) and spatial transcriptome sequencing (ST) data enabled identification of senescence-related genes (SRGs) for HCC. A novel prognostic model based on SRGs was constructed, and spatial distribution of senescent endothelial cells (ECs) within HCC tumors was analyzed. Then, the role of senescent ECs was verified through in vitro and in vivo experiments. Results: Significant heterogeneity in senescence profiles of ECs was observed, with specific regulatory alterations existing the communication between senescent ECs and other cell types. Spatial analysis revealed senescent ECs mainly located in the core region of HCC. The interaction of senescent ECs and immune cells implicated their role in tumor progression and immunotherapeutic response. In addition, CDKN2A was identified as an independent risk factor for HCC prognosis by constructing a prognostic model. CDKN2A promoted senescence of ECs which exhibited a secretory phenotype. Furthermore, senescent ECs with CDKN2A overexpression promote the malignancy of HCC both in vitro and in vivo. Conclusion: The present study advances understanding of senescent ECs in HCC pathogenesis, providing an insight into evaluation of ECs senescence as a therapeutic target for HCC. Hepatocellular carcinoma Senescence Endothelial cells CDKN2A Full Text Additional Declarations No competing interests reported. Supplementary Files Supplementaryfile.pdf 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-4207895","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":287811773,"identity":"0631b950-009a-4fc0-80e1-7ffb9751ed90","order_by":0,"name":"Yue Ma","email":"","orcid":"","institution":"Fudan University","correspondingAuthor":false,"prefix":"","firstName":"Yue","middleName":"","lastName":"Ma","suffix":""},{"id":287811775,"identity":"f47d183d-b50d-4928-8391-09e67306409b","order_by":1,"name":"Chenhe Yi","email":"","orcid":"","institution":"Fudan University","correspondingAuthor":false,"prefix":"","firstName":"Chenhe","middleName":"","lastName":"Yi","suffix":""},{"id":287811777,"identity":"07592478-e095-4f4e-9f48-28edd1286144","order_by":2,"name":"Ning Cai","email":"","orcid":"","institution":"Huazhong University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Ning","middleName":"","lastName":"Cai","suffix":""},{"id":287811778,"identity":"93abf84b-ebf9-4bfe-9510-d9522f383120","order_by":3,"name":"Jinhong Chen","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA1UlEQVRIiWNgGAWjYBACxmYGNjDDgL0HTPPwEa+F5wwDwwGgFjYiLIJqkcgBa2EgqIW5nffYg487auXNJd8efPwxx06GjYH54aMbeB3Gl24488xxw52z85INDm5LBjqMzdg4B68WHjNp3rZjCQa3c8wkDm5jBmrhYZMmTsvNMyAt9URrqUkwuMED0nKYOC2SM9sOGG44k2NscHbbcR42ZgJ+MewHuudjW528wfEzhg8qt1Xb87M3P3yMV0sDmDqMJMSMRzkIyEOoOgLKRsEoGAWjYEQDAAgURBy5drp3AAAAAElFTkSuQmCC","orcid":"","institution":"Fudan University","correspondingAuthor":true,"prefix":"","firstName":"Jinhong","middleName":"","lastName":"Chen","suffix":""}],"badges":[],"createdAt":"2024-04-02 16:05:30","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4207895/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4207895/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":58458373,"identity":"2a7b576a-372f-48e0-ba96-982d9df472ff","added_by":"auto","created_at":"2024-06-17 01:29:29","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":7514535,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4207895/v1_covered_a24f7512-5eb8-4182-aa8b-a3e9d9513ae5.pdf"},{"id":54452170,"identity":"e59e2bfa-5e3d-47e2-84ed-b8deafc65ac2","added_by":"auto","created_at":"2024-04-10 18:22:01","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":517698,"visible":true,"origin":"","legend":"","description":"","filename":"Supplementaryfile.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4207895/v1/65f1497fdd42b38569eff257.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Integration of Single-Cell and Spatial Transcriptome Sequencing Identifies CDKN2A as a Senescent Biomarker in Endothelial Cells Implicating Hepatocellular Carcinoma Malignancy","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":"Hepatocellular carcinoma, Senescence, Endothelial cells, CDKN2A","lastPublishedDoi":"10.21203/rs.3.rs-4207895/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4207895/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003ePurpose: Hepatocellular carcinoma (HCC) is one of the most malignant tumors worldwide, remaining difficult to manage. The role of cellular senescence in HCC has been gradually recognized. The present study aimed to comprehensively analyze the senescence-related features of HCC in single-cell and spatial dimension.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eMethods: Integration of single-cell RNA sequencing (scRNA-Seq) and spatial transcriptome sequencing (ST) data enabled identification of senescence-related genes (SRGs) for HCC. A novel prognostic model based on SRGs was constructed, and spatial distribution of senescent endothelial cells (ECs) within HCC tumors was analyzed. Then, the role of senescent ECs was verified through in vitro and in vivo experiments.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eResults: Significant heterogeneity in senescence profiles of ECs was observed, with specific regulatory alterations existing the communication between senescent ECs and other cell types. Spatial analysis revealed senescent ECs mainly located in the core region of HCC. 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