Novel CRISPR-Cas9 BAP1 Knockout Pre-Clinical Tumor Model Recapitulates Human Melanoma Tumorigenesis and Immune Evolution

Novel CRISPR-Cas9 BAP1 Knockout Pre-Clinical Tumor Model Recapitulates Human Melanoma Tumorigenesis and Immune Evolution | 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 Novel CRISPR-Cas9 BAP1 Knockout Pre-Clinical Tumor Model Recapitulates Human Melanoma Tumorigenesis and Immune Evolution Mona Meng Wang, Yuanhan Li, Candice Ho, Willie Yu, Sarah Coupland, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6134890/v2 This work is licensed under a CC BY 4.0 License Status: Under Review Version 2 posted You are reading this latest preprint version Show more versions Abstract BAP1-deficient melanocytic tumors exhibit strong immunosuppressive features and poor prognosis. Currently, no immune-competent preclinical models exist to study their tumor-immune interactions or test new immunotherapies. This limitation hinders progress in understanding how BAP1 loss drives tumor aggressiveness and immune evasion. To address this, we generated a syngeneic BAP1 knockout melanocyte tumor line using CRISPR-Cas9. We then evaluated its functional and immunological impact in immune-competent mice, including its ability to recapitulate metabolic and immunosuppressive features of human BAP1-deficient melanomas. The selected knockout clone exhibited hallmarks of aggressive skin and intraocular melanomas, including epithelioid morphology, in vivo tumorigenic potential, rapid growth, and key immunosuppressive features, mirroring those observed in human BAP1-deficient melanomas. Cross-species single-cell transcriptome analysis demonstrated strong molecular overlap between BAP1 knockout mouse tumors and high-risk (class 2) human uveal melanomas, highlighting shared pathways in lipid metabolism, transmembrane receptor signaling, and immune modulation. Gene Set Enrichment Analysis confirmed that lipid metabolic reprogramming, previously described in human tumors, is also a key feature of our model, validating its ability to recapitulate human disease biology. This study introduces a syngeneic preclinical model that mimics the immunosuppressive landscape of BAP1-deficient melanocytic tumors, enabling the development and optimization of new combination immunotherapies. Biological sciences/Cancer/Cancer models Biological sciences/Molecular biology/CRISPR-Cas systems/CRISPR-Cas9 genome editing Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryTable1.pdf Supplementary Table 1 SupplementaryData2MelanaMutationProfile.xlsx Supplementary Dataset 2 supplementaryfig.1.tif Supplementary Fig 1 supplementaryfig.2.tif Supplementary Fig.2 supplementaryfig.3.pdf Supplementary Fig.3 supplementaryfig.4.pdf Supplementary Fig.4 supplementaryfig.5.tif Supplementary Fig.5 supplementaryfig.6.tif Supplementary Fig.6 SupplementaryData1OcularMelanocytesMutationProfile.xlsx Supplementary Dataset 1 SupplementaryData3B16F10MutationProfile.xlsx Supplementary Dataset 3 RS944.pdf Reporting Summary Cite Share Download PDF Status: Under Review Version 2 posted You are reading this latest preprint version Show more versions 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-6134890","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[{"code":1,"date":"2025-04-09 06:03:22","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"communications-biology","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"commsbio","sideBox":"Learn more about [Communications Biology](http://www.nature.com/commsbio/)","snPcode":"","submissionUrl":"","title":"Communications 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Evolution","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 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Currently, no immune-competent preclinical models exist to study their tumor-immune interactions or test new immunotherapies. This limitation hinders progress in understanding how BAP1 loss drives tumor aggressiveness and immune evasion. To address this, we generated a syngeneic BAP1 knockout melanocyte tumor line using CRISPR-Cas9. We then evaluated its functional and immunological impact in immune-competent mice, including its ability to recapitulate metabolic and immunosuppressive features of human BAP1-deficient melanomas. The selected knockout clone exhibited hallmarks of aggressive skin and intraocular melanomas, including epithelioid morphology, in vivo tumorigenic potential, rapid growth, and key immunosuppressive features, mirroring those observed in human BAP1-deficient melanomas. 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This study introduces a syngeneic preclinical model that mimics the immunosuppressive landscape of BAP1-deficient melanocytic tumors, enabling the development and optimization of new combination immunotherapies.","manuscriptTitle":"Novel CRISPR-Cas9 BAP1 Knockout Pre-Clinical Tumor Model Recapitulates Human Melanoma Tumorigenesis and Immune Evolution","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2025-04-15 04:41:37","doi":"10.21203/rs.3.rs-6134890/v2","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"communications-biology","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"commsbio","sideBox":"Learn more about [Communications Biology](http://www.nature.com/commsbio/)","snPcode":"","submissionUrl":"","title":"Communications Biology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Communications Series","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"98dc5de9-af25-4cee-a7a0-296ca64f0976","owner":[],"postedDate":"April 15th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":46696012,"name":"Biological sciences/Cancer/Cancer models"},{"id":46696013,"name":"Biological sciences/Molecular biology/CRISPR-Cas systems/CRISPR-Cas9 genome editing"}],"tags":[],"updatedAt":"2026-04-14T11:31:43+00:00","versionOfRecord":[],"versionCreatedAt":"2025-04-15 04:41:37","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-6134890","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6134890","identity":"rs-6134890","version":["v2"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}