Dissecting Regulatory Non-Coding GWAS Loci Reveals Fibroblast Causal Genes with Pathophysiological Relevance to Heart Failure

Dissecting Regulatory Non-Coding GWAS Loci Reveals Fibroblast Causal Genes with Pathophysiological Relevance to Heart Failure | 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 Dissecting Regulatory Non-Coding GWAS Loci Reveals Fibroblast Causal Genes with Pathophysiological Relevance to Heart Failure Chi-Ming Li, Richard Gill, Daniel Lu, Ittai Eres, Jiamiao Lu, and 12 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5837699/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 10 Oct, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Heart failure is caused in part by cardiac remodeling processes that include the death of cardiac myocytes and their replacement by cardiac fibroblasts. We hypothesized that these two cell types may harbor epigenetic contexts in which heart disease-associated non-coding SNPs perturb gene expression relevant to disease. Accordingly, we generated high-resolution Hi-C data layered with functional genomic information to annotate and link putative distal regulatory elements in heart disease-associated loci to gene promoters. Our analysis identified several target genes with established roles in cardiac fibrosis and/or heart disease (GJA1, TBC1D32, CXCL12, IL6R, and FURIN). Perturb-seq in cardiac fibroblasts to knock out putative regulatory elements confirmed regulatory relationships involving GJA1, CXCL12, and FURIN, as gene editing led to changes in transcriptomic signatures associated with fibroblasts in heart failure. Our results demonstrate how integrative multi-omic approaches can delineate pathophysiologically relevant regulatory circuits that connect protein-coding genes to non-coding genetic variants associated with disease. Health sciences/Cardiology/Cardiovascular biology/Cardiovascular genetics Biological sciences/Genetics/Genomics/Medical genomics Full Text Additional Declarations Yes there is potential Competing Interest. All of the authors except Dr. Kory Lavine were Amgen employees while performing experiment or analysis and owns Amgen stocks. Supplementary Files SupplementalNoteNatComm.docx Supplemental Notes Cite Share Download PDF Status: Published Journal Publication published 10 Oct, 2025 Read the published version in Nature Communications → 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-5837699","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":405125595,"identity":"a47d7f54-c516-42de-b7dc-0bd049ced6eb","order_by":0,"name":"Chi-Ming Li","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAw0lEQVRIiWNgGAWjYDACCcYGhgQGBhl+krXwSDYQrwVC8RgcIFYH/+zm1g0Pd9TyGB8/nfzi4w4GeX4xApol7hxsu5F45jiP2ZncbZYzzzAYzpydgF+LgUQiUEvbMR6zA7nbjHnbGBIMbhOrxbj/7TbjvyRoqeExkMjd/JiRGC0SN8BaDvBI3Hi7jbG3TYKwX/hnpD+7+bOtTo6/P3fzh59tNvL80gS0QMFhEMEmAY8mIkAdiGD+QLT6UTAKRsEoGFEAAJFpSSCwNg+QAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-2740-5652","institution":"Amgen Inc.","correspondingAuthor":true,"prefix":"","firstName":"Chi-Ming","middleName":"","lastName":"Li","suffix":""},{"id":405125596,"identity":"6d5cb4b2-469a-4512-a5b2-4a1d2f6a2c71","order_by":1,"name":"Richard Gill","email":"","orcid":"https://orcid.org/0000-0001-7057-7807","institution":"Amgen Inc","correspondingAuthor":false,"prefix":"","firstName":"Richard","middleName":"","lastName":"Gill","suffix":""},{"id":405125597,"identity":"666dc9c0-9803-4376-88bc-d3387fe6e03f","order_by":2,"name":"Daniel Lu","email":"","orcid":"","institution":"Amgen (United States)","correspondingAuthor":false,"prefix":"","firstName":"Daniel","middleName":"","lastName":"Lu","suffix":""},{"id":405125598,"identity":"a7853f65-d080-4ec2-ab8f-673150ff3a76","order_by":3,"name":"Ittai Eres","email":"","orcid":"https://orcid.org/0000-0002-0265-8194","institution":"Amgen Research","correspondingAuthor":false,"prefix":"","firstName":"Ittai","middleName":"","lastName":"Eres","suffix":""},{"id":405125599,"identity":"5e63cdfd-b40c-4f26-9b11-d581c22b8e32","order_by":4,"name":"Jiamiao Lu","email":"","orcid":"","institution":"Amgen Inc.","correspondingAuthor":false,"prefix":"","firstName":"Jiamiao","middleName":"","lastName":"Lu","suffix":""},{"id":405125600,"identity":"62b4af12-545f-4454-ad84-d0b8bea348c6","order_by":5,"name":"Jixin Cui","email":"","orcid":"","institution":"Amgen Inc.","correspondingAuthor":false,"prefix":"","firstName":"Jixin","middleName":"","lastName":"Cui","suffix":""},{"id":405125601,"identity":"655963a9-0edf-4aaf-bcf8-63f2e249a701","order_by":6,"name":"Chen Wang","email":"","orcid":"","institution":"Amgen Inc","correspondingAuthor":false,"prefix":"","firstName":"Chen","middleName":"","lastName":"Wang","suffix":""},{"id":405125602,"identity":"a006ae25-aef3-4d6b-9eff-ec98901490ac","order_by":7,"name":"Zhongsheng Yu","email":"","orcid":"","institution":"Amgen Inc","correspondingAuthor":false,"prefix":"","firstName":"Zhongsheng","middleName":"","lastName":"Yu","suffix":""},{"id":405125603,"identity":"5477a013-f8fe-4012-b207-837692e6c0d9","order_by":8,"name":"Tracy Yamawaki","email":"","orcid":"https://orcid.org/0000-0002-7716-5650","institution":"Amgen","correspondingAuthor":false,"prefix":"","firstName":"Tracy","middleName":"","lastName":"Yamawaki","suffix":""},{"id":405125604,"identity":"4c191eab-abed-4f03-92cf-34c0f1ea6b93","order_by":9,"name":"Hong Zhou","email":"","orcid":"https://orcid.org/0000-0003-0120-3347","institution":"Amgen Inc.","correspondingAuthor":false,"prefix":"","firstName":"Hong","middleName":"","lastName":"Zhou","suffix":""},{"id":405125605,"identity":"cd09e288-73e1-41be-bebe-aecd1d4a41b1","order_by":10,"name":"Baikang Pei","email":"","orcid":"","institution":"Amgen Inc","correspondingAuthor":false,"prefix":"","firstName":"Baikang","middleName":"","lastName":"Pei","suffix":""},{"id":405125606,"identity":"00713b77-6779-4e14-b3ff-0fb096a0eb36","order_by":11,"name":"Junedh Amrute","email":"","orcid":"","institution":"Amgen Inc","correspondingAuthor":false,"prefix":"","firstName":"Junedh","middleName":"","lastName":"Amrute","suffix":""},{"id":405125607,"identity":"d04378eb-efe2-4f05-90b6-3ef1d48a2b5e","order_by":12,"name":"Yen-Sin Ang","email":"","orcid":"","institution":"Amgen Inc","correspondingAuthor":false,"prefix":"","firstName":"Yen-Sin","middleName":"","lastName":"Ang","suffix":""},{"id":405125608,"identity":"f92900b7-d35e-4b30-8aa7-656383c90a39","order_by":13,"name":"Songli Wang","email":"","orcid":"","institution":"Amgen Inc","correspondingAuthor":false,"prefix":"","firstName":"Songli","middleName":"","lastName":"Wang","suffix":""},{"id":405125609,"identity":"4178a3c6-ed3a-4ec1-9883-fdbb50271510","order_by":14,"name":"Kory Lavine","email":"","orcid":"https://orcid.org/0000-0003-1948-9945","institution":"Washington University School of Medicine","correspondingAuthor":false,"prefix":"","firstName":"Kory","middleName":"","lastName":"Lavine","suffix":""},{"id":405125610,"identity":"3538af95-abe9-46f7-a64e-9d608edfb911","order_by":15,"name":"Brandon Ason","email":"","orcid":"","institution":"Amgen Research","correspondingAuthor":false,"prefix":"","firstName":"Brandon","middleName":"","lastName":"Ason","suffix":""},{"id":405125611,"identity":"57169b4f-d0dc-46ab-8e31-4c6283109256","order_by":16,"name":"Yi-Hsiang Hsu","email":"","orcid":"","institution":"Beth Israel Deaconess Medical Center","correspondingAuthor":false,"prefix":"","firstName":"Yi-Hsiang","middleName":"","lastName":"Hsu","suffix":""}],"badges":[],"createdAt":"2025-01-16 01:05:10","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5837699/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5837699/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41467-025-64070-1","type":"published","date":"2025-10-10T04:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":93285037,"identity":"9affab1f-a634-400a-9540-a3d685d059c5","added_by":"auto","created_at":"2025-10-11 07:08:05","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2586944,"visible":true,"origin":"","legend":"Article File","description":"","filename":"GilletalHICHCMNHCFVHiCManuscriptNatComm.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5837699/v1_covered_874aa4ec-ba5b-4369-8050-45b9f7d3bee2.pdf"},{"id":74401528,"identity":"e8eadafb-a725-4d0c-ac4f-256bc8990fea","added_by":"auto","created_at":"2025-01-22 03:15:43","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":935232,"visible":true,"origin":"","legend":"Supplemental Notes","description":"","filename":"SupplementalNoteNatComm.docx","url":"https://assets-eu.researchsquare.com/files/rs-5837699/v1/00b5ca6fdf8676cb87e8a363.docx"}],"financialInterests":"\u003cb\u003eYes\u003c/b\u003e there is potential Competing Interest.\nAll of the authors except Dr. Kory Lavine were Amgen employees while performing experiment or analysis and owns Amgen stocks.","formattedTitle":"Dissecting Regulatory Non-Coding GWAS Loci Reveals Fibroblast Causal Genes with Pathophysiological Relevance to Heart Failure","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"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":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-5837699/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5837699/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Heart failure is caused in part by cardiac remodeling processes that include the death of cardiac myocytes and their replacement by cardiac fibroblasts. We hypothesized that these two cell types may harbor epigenetic contexts in which heart disease-associated non-coding SNPs perturb gene expression relevant to disease. Accordingly, we generated high-resolution Hi-C data layered with functional genomic information to annotate and link putative distal regulatory elements in heart disease-associated loci to gene promoters. Our analysis identified several target genes with established roles in cardiac fibrosis and/or heart disease (GJA1, TBC1D32, CXCL12, IL6R, and FURIN). Perturb-seq in cardiac fibroblasts to knock out putative regulatory elements confirmed regulatory relationships involving GJA1, CXCL12, and FURIN, as gene editing led to changes in transcriptomic signatures associated with fibroblasts in heart failure. Our results demonstrate how integrative multi-omic approaches can delineate pathophysiologically relevant regulatory circuits that connect protein-coding genes to non-coding genetic variants associated with disease.","manuscriptTitle":"Dissecting Regulatory Non-Coding GWAS Loci Reveals Fibroblast Causal Genes with Pathophysiological Relevance to Heart Failure","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-01-22 03:15:38","doi":"10.21203/rs.3.rs-5837699/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"64563e50-b510-4c84-9dd0-b96bec0f4de6","owner":[],"postedDate":"January 22nd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":43193551,"name":"Health sciences/Cardiology/Cardiovascular biology/Cardiovascular genetics"},{"id":43193552,"name":"Biological sciences/Genetics/Genomics/Medical genomics"}],"tags":[],"updatedAt":"2025-10-11T07:07:55+00:00","versionOfRecord":{"articleIdentity":"rs-5837699","link":"https://doi.org/10.1038/s41467-025-64070-1","journal":{"identity":"nature-communications","isVorOnly":false,"title":"Nature Communications"},"publishedOn":"2025-10-10 04:00:00","publishedOnDateReadable":"October 10th, 2025"},"versionCreatedAt":"2025-01-22 03:15:38","video":"","vorDoi":"10.1038/s41467-025-64070-1","vorDoiUrl":"https://doi.org/10.1038/s41467-025-64070-1","workflowStages":[]},"version":"v1","identity":"rs-5837699","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5837699","identity":"rs-5837699","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}