SMARCB1 missense mutants disrupt SWI/SNF complex stability and remodeling activity

SMARCB1 missense mutants disrupt SWI/SNF complex stability and remodeling activity | 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 SMARCB1 missense mutants disrupt SWI/SNF complex stability and remodeling activity Garrett W. Cooper, Benjamin P. Lee, Won Jun Kim, Yongdong Su, and 16 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6018128/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Chromatin remodeling complexes, such as the SWItch/Sucrose Non-Fermentable (SWI/SNF) complex, play key roles in regulating gene expression by modulating nucleosome positioning. The core subunit SMARCB1 is essential for these functions, as it anchors the complex to the nucleosome acidic patch, enabling effective chromatin remodeling. While biallelic inactivation of SMARCB1 is a hallmark of several aggressive pediatric malignancies, the functional implication of missense mutations is not fully understood. Current diagnostic approaches focus on detecting the presence or absence of SMARCB1 by immunohistochemistry (IHC) often without consideration of mutation status as such data is lacking. Here, we present the first comprehensive deep mutational scanning (DMS) of SMARCB1, encompassing 8,418 amino acid substitutions, to systematically assess their functional impact. We show that missense mutations in the RPT2 domain of SMARCB1 disrupt SMARCB1 tumor suppressor function by destabilizing the SWI/SNF complex. Notably, we identify mutations in RPT2 that impair chromatin remodeling and transcriptional regulation to an extent comparable to nonsense mutations, despite maintaining detectable protein expression, thus challenging the conventional diagnostic reliance on IHC. Importantly, these mutations seem to act by disrupting winged-helix domain flexibility. These findings provide a deeper understanding of the role of SMARCB1 in chromatin remodeling and cancer biology, highlighting the limitations of current mutation classification approaches. By establishing a high-throughput functional framework, this study offers a critical resource for elucidating SMARCB1’s mutational landscape and its implications for cancer diagnostics. Biological sciences/Molecular biology/Chromatin/Chromatin remodelling Health sciences/Oncology/Cancer/Paediatric cancer Biological sciences/Genetics/Functional genomics/Mutagenesis Full Text Additional Declarations Yes there is potential Competing Interest. G.W.C. completed an internship with GRAIL, Inc in Summer 2024. R.E.L. is currently employed by RAN Biotechnologies. F.P. is a current employee of Merck Research Laboratories. D.E.R. receives research funding from members of the Functional Genomics Consortium (Abbvie, BMS, Jannsen, and Merck), and is a director of Addgene, Inc. W.C.H. is a consultant for Thermo Fischer, Solasta Ventures, KSQ Therapeutics, Frontier Medicines, Jubilant Therapeutics, RAPPTA Therapeutics, Serinus Biosciences, Kestral Therapeutics, Crane Biotherapeutics, Function Oncology, and Perceptive. Biotherapeutics, Function Oncology and Calyx. Supplementary Files SupplementaryVideo1.mp4 Supplementary Video Cite Share Download PDF Status: Under Review 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-6018128","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":433894291,"identity":"f92c42f8-8013-41c0-9465-7dfe855b072a","order_by":0,"name":"Garrett W. 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R.E.L. is currently employed by RAN Biotechnologies. F.P. is a current employee of Merck Research Laboratories. D.E.R. receives research funding from members of the Functional Genomics Consortium (Abbvie, BMS, Jannsen, and Merck), and is a director of Addgene, Inc. W.C.H. is a consultant for Thermo Fischer, Solasta Ventures, KSQ Therapeutics, Frontier Medicines, Jubilant Therapeutics, RAPPTA Therapeutics, Serinus Biosciences, Kestral Therapeutics, Crane Biotherapeutics, Function Oncology, and Perceptive. Biotherapeutics, Function Oncology and Calyx.","formattedTitle":"SMARCB1 missense mutants disrupt SWI/SNF complex stability and remodeling activity","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-6018128/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6018128/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Chromatin remodeling complexes, such as the SWItch/Sucrose Non-Fermentable (SWI/SNF) complex, play key roles in regulating gene expression by modulating nucleosome positioning. The core subunit SMARCB1 is essential for these functions, as it anchors the complex to the nucleosome acidic patch, enabling effective chromatin remodeling. While biallelic inactivation of SMARCB1 is a hallmark of several aggressive pediatric malignancies, the functional implication of missense mutations is not fully understood. Current diagnostic approaches focus on detecting the presence or absence of SMARCB1 by immunohistochemistry (IHC) often without consideration of mutation status as such data is lacking. Here, we present the first comprehensive deep mutational scanning (DMS) of SMARCB1, encompassing 8,418 amino acid substitutions, to systematically assess their functional impact. We show that missense mutations in the RPT2 domain of SMARCB1 disrupt SMARCB1 tumor suppressor function by destabilizing the SWI/SNF complex. Notably, we identify mutations in RPT2 that impair chromatin remodeling and transcriptional regulation to an extent comparable to nonsense mutations, despite maintaining detectable protein expression, thus challenging the conventional diagnostic reliance on IHC. Importantly, these mutations seem to act by disrupting winged-helix domain flexibility. These findings provide a deeper understanding of the role of SMARCB1 in chromatin remodeling and cancer biology, highlighting the limitations of current mutation classification approaches. By establishing a high-throughput functional framework, this study offers a critical resource for elucidating SMARCB1’s mutational landscape and its implications for cancer diagnostics.","manuscriptTitle":"SMARCB1 missense mutants disrupt SWI/SNF complex stability and remodeling activity","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-03-26 11:32:42","doi":"10.21203/rs.3.rs-6018128/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":"5e7d6287-4a02-4868-b77f-13dab201dfea","owner":[],"postedDate":"March 26th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":46202542,"name":"Biological sciences/Molecular biology/Chromatin/Chromatin remodelling"},{"id":46202543,"name":"Health sciences/Oncology/Cancer/Paediatric cancer"},{"id":46202544,"name":"Biological sciences/Genetics/Functional genomics/Mutagenesis"}],"tags":[],"updatedAt":"2026-03-23T14:50:33+00:00","versionOfRecord":[],"versionCreatedAt":"2025-03-26 11:32:42","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6018128","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6018128","identity":"rs-6018128","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}