Lineage identity governs oncogene dependence in murine NSCLC models of KRAS inhibitor resistance

Lineage identity governs oncogene dependence in murine NSCLC models of KRAS inhibitor resistance | 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 Lineage identity governs oncogene dependence in murine NSCLC models of KRAS inhibitor resistance Tyler Jacks, Nicolas Mathey-Andrews, Carrie Rodriguez, Bing Shui, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7058952/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 Primary and acquired resistance to targeted therapy represent significant challenges to durable treatment responses in cancer. In lung cancer and other cancer types, allele- specific and pan-KRAS inhibitors offer new promise, but these are hampered by incomplete responses as well as genetic and non-genetic mechanisms of acquired resistance. To model these mechanisms, we treat genetically engineered mouse models of KrasG12C-driven lung cancer with sotorasib, a KRASG12C inhibitor, until the emergence of drug resistance. The initial response to sotorasib was rapid, but incomplete. Residual tumor burden transcriptionally resembled the alveolar type II cell, phenocopying residual disease signatures identified in patients treated with EGFR inhibitors. After continued sotorasib treatment, we observed diverse mechanisms of drug resistance in vivo, including genetic MAPK reactivation and lineage transformation from adenocarcinoma to squamous histology. Focusing mechanistic studies on squamous transformation, we showed that expression of the basal transcription factor ∆Np63 is sufficient to rewire transformed alveolar organoids to a squamous state in vitro, conferring insensitivity to KRAS inhibition. In vivo, either ectopic expression of Sox2 or loss of Nkx2-1, which are tolerated during Kras-driven tumorigenesis, poised tumors for squamous lineage commitment upon KRAS inhibition. Squamous- transformed tumors did not exhibit evidence of KRAS/MAPK reactivation, underscoring the role for lineage transcription factors and histologic transformation in mediating oncogene independence. Biological sciences/Cancer/Lung cancer/Non-small-cell lung cancer Biological sciences/Cancer/Cancer therapy/Targeted therapies Full Text Additional Declarations Yes there is potential Competing Interest. N.M.A. has served as an Ad Hoc consultant for Longitude Capital on matters unrelated to the content of this manuscript. D.Y. is a co-founder and consultant for DEM Biopharma. T.J. is a member of the Board of Directors of Amgen and Thermo Fisher Scientific, a co-Founder of Dragonfly Therapeutics and T2 Biosystems. Amgen currently owns and markets sotorasib, the primary therapeutic compound used in this manuscript. Sotorasib was purchased from a third-party source, Selleck Chemicals, and the work was not performed as a sponsored research agreement. T.J. serves on the Scientific Advisory Board of Dragonfly Therapeutics, SQZ Biotech, and Skyhawk Therapeutics. T.J. is also the President of Break Through Cancer. His laboratory currently receives funding from the Lustgarten Foundation and Johnson & Johnson Lung Cancer Initiative, but this funding did not support the research described in this manuscript. The remaining authors declare no competing interests. Supplementary Files MASupplementaryTables.xlsx Supplementary Tables 1-7 MASFigscompressed.pdf Supplementary/Extended Data Figures 1-12 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-7058952","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":489728573,"identity":"c62cbe4f-0161-456c-99c9-e2fcbb528cc8","order_by":0,"name":"Tyler Jacks","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAsUlEQVRIiWNgGAWjYFCCAwyMDQw2DGwgNg8xGnggWtIY2NiI18IA0nKYgYFoLfaMhx9+nPHnfDSffAPjg7dtRNlyzFhyY9vt3DY2BmbDucRpOWDG+LABrIVNmpc4Lce/MT74cw6khf03kVrOmDFuYDsAtoWZOC0HzhRLzmxLBmpJbJacc44ILewzjm/82PPHLnd+8+GDH96UEaGFQeIAjAWMHuIAP7EKR8EoGAWjYOQCADY+NfrnVtZ2AAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0001-5785-8911","institution":"David H. Koch Institute for Integrative Cancer Research","correspondingAuthor":true,"prefix":"","firstName":"Tyler","middleName":"","lastName":"Jacks","suffix":""},{"id":489728574,"identity":"fda7e199-fd48-499a-9e00-01e011680f7f","order_by":1,"name":"Nicolas Mathey-Andrews","email":"","orcid":"","institution":"David H. Koch Institute for Integrative Cancer Research","correspondingAuthor":false,"prefix":"","firstName":"Nicolas","middleName":"","lastName":"Mathey-Andrews","suffix":""},{"id":489728575,"identity":"c9693790-82f6-4210-87ac-af9ddf03fe6f","order_by":2,"name":"Carrie Rodriguez","email":"","orcid":"","institution":"David H. Koch Institute for Integrative Cancer Research","correspondingAuthor":false,"prefix":"","firstName":"Carrie","middleName":"","lastName":"Rodriguez","suffix":""},{"id":489728576,"identity":"da5b5179-2d54-4c48-95fa-66668e7f6c25","order_by":3,"name":"Bing Shui","email":"","orcid":"https://orcid.org/0000-0002-5956-130X","institution":"David H. Koch Institute for Integrative Cancer Research","correspondingAuthor":false,"prefix":"","firstName":"Bing","middleName":"","lastName":"Shui","suffix":""},{"id":489728577,"identity":"47777ff2-e541-4c23-883b-75882f67c2cb","order_by":4,"name":"Agata Patriotis","email":"","orcid":"https://orcid.org/0000-0002-8237-975X","institution":"David H. Koch Institute for Integrative Cancer Research","correspondingAuthor":false,"prefix":"","firstName":"Agata","middleName":"","lastName":"Patriotis","suffix":""},{"id":489728578,"identity":"b9a06afb-0b9a-4216-b855-1f1359a7b62c","order_by":5,"name":"William Rideout","email":"","orcid":"","institution":"David H. Koch Institute for Integrative Cancer Research","correspondingAuthor":false,"prefix":"","firstName":"William","middleName":"","lastName":"Rideout","suffix":""},{"id":489728579,"identity":"b6d1f469-563b-4485-a626-2cac77418b8a","order_by":6,"name":"Victor Chen","email":"","orcid":"","institution":"Emory University","correspondingAuthor":false,"prefix":"","firstName":"Victor","middleName":"","lastName":"Chen","suffix":""},{"id":489728580,"identity":"b363c532-5bf2-4605-b554-a39779714c97","order_by":7,"name":"Ileana Murazzi","email":"","orcid":"","institution":"Herbert Irving Comprehensive Cancer Center, Columbia University","correspondingAuthor":false,"prefix":"","firstName":"Ileana","middleName":"","lastName":"Murazzi","suffix":""},{"id":489728581,"identity":"fce54413-d0dd-429b-8846-4443ea26e90e","order_by":8,"name":"Milton Cornwall-Brady","email":"","orcid":"https://orcid.org/0000-0002-7775-0606","institution":"David H. Koch Institute for Integrative Cancer Research","correspondingAuthor":false,"prefix":"","firstName":"Milton","middleName":"","lastName":"Cornwall-Brady","suffix":""},{"id":489728582,"identity":"e001a900-5a5e-4080-a1c3-e39b2a937e3c","order_by":9,"name":"Manyuan Liu","email":"","orcid":"","institution":"Herbert Irving Comprehensive Cancer Center, Columbia University","correspondingAuthor":false,"prefix":"","firstName":"Manyuan","middleName":"","lastName":"Liu","suffix":""},{"id":489728583,"identity":"a1f5bd20-41f5-452a-b59e-7bc6b585d0a9","order_by":10,"name":"Morgan Heileman","email":"","orcid":"","institution":"David H. Koch Institute for Integrative Cancer Research","correspondingAuthor":false,"prefix":"","firstName":"Morgan","middleName":"","lastName":"Heileman","suffix":""},{"id":489728584,"identity":"1bdd4dbd-58bc-4b75-bdb2-ab6fd2e99d63","order_by":11,"name":"Marianna Trakala","email":"","orcid":"","institution":"David H. Koch Institute for Integrative Cancer Research","correspondingAuthor":false,"prefix":"","firstName":"Marianna","middleName":"","lastName":"Trakala","suffix":""},{"id":489728585,"identity":"2e8187f8-c091-4c51-ad9c-a7209139a9af","order_by":12,"name":"Carla Concepcion","email":"","orcid":"","institution":"Herbert Irving Comprehensive Cancer Center, Columbia University","correspondingAuthor":false,"prefix":"","firstName":"Carla","middleName":"","lastName":"Concepcion","suffix":""},{"id":489728586,"identity":"bad8daa8-0876-4160-a1ed-f176340adc84","order_by":13,"name":"Dian Yang","email":"","orcid":"","institution":"Herbert Irving Comprehensive Cancer Center, Columbia University","correspondingAuthor":false,"prefix":"","firstName":"Dian","middleName":"","lastName":"Yang","suffix":""}],"badges":[],"createdAt":"2025-07-06 16:10:29","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7058952/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7058952/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":87465720,"identity":"d29eeeae-3100-456f-8d73-5b84921bcfc6","added_by":"auto","created_at":"2025-07-24 07:22:33","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":25392059,"visible":true,"origin":"","legend":"Article File","description":"","filename":"MatheyAndrewsetalv7.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7058952/v1_covered_36aca8b5-2011-4db8-9667-964124598ada.pdf"},{"id":87465311,"identity":"c53b8cb9-0a46-4b12-af31-82cb123e4656","added_by":"auto","created_at":"2025-07-24 07:13:29","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":4129990,"visible":true,"origin":"","legend":"Supplementary Tables 1-7","description":"","filename":"MASupplementaryTables.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7058952/v1/ef7d68839a635487ddc9ead7.xlsx"},{"id":87465300,"identity":"16c7242a-d710-4414-8d01-f982233e0588","added_by":"auto","created_at":"2025-07-24 07:13:26","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":42242696,"visible":true,"origin":"","legend":"Supplementary/Extended Data Figures 1-12","description":"","filename":"MASFigscompressed.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7058952/v1/7682e8ef8fa96ac2eab02440.pdf"}],"financialInterests":"\u003cb\u003eYes\u003c/b\u003e there is potential Competing Interest.\nN.M.A. has served as an Ad Hoc consultant for Longitude Capital on matters unrelated\r\nto the content of this manuscript. D.Y. is a co-founder and consultant for DEM\r\nBiopharma. T.J. is a member of the Board of Directors of Amgen and Thermo Fisher\r\nScientific, a co-Founder of Dragonfly Therapeutics and T2 Biosystems. Amgen currently\r\nowns and markets sotorasib, the primary therapeutic compound used in this manuscript.\r\nSotorasib was purchased from a third-party source, Selleck Chemicals, and the work\r\nwas not performed as a sponsored research agreement. T.J. serves on the Scientific\r\nAdvisory Board of Dragonfly Therapeutics, SQZ Biotech, and Skyhawk Therapeutics.\r\nT.J. is also the President of Break Through Cancer. His laboratory currently receives\r\nfunding from the Lustgarten Foundation and Johnson \u0026 Johnson Lung Cancer Initiative,\r\nbut this funding did not support the research described in this manuscript. The\r\nremaining authors declare no competing interests.","formattedTitle":"Lineage identity governs oncogene dependence in murine NSCLC models of KRAS inhibitor resistance","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"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":"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-7058952/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7058952/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Primary and acquired resistance to targeted therapy represent significant challenges to\r\ndurable treatment responses in cancer. In lung cancer and other cancer types, allele-\r\nspecific and pan-KRAS inhibitors offer new promise, but these are hampered by\r\nincomplete responses as well as genetic and non-genetic mechanisms of acquired\r\nresistance. To model these mechanisms, we treat genetically engineered mouse\r\nmodels of KrasG12C-driven lung cancer with sotorasib, a KRASG12C inhibitor, until the\r\nemergence of drug resistance. The initial response to sotorasib was rapid, but\r\nincomplete. Residual tumor burden transcriptionally resembled the alveolar type II cell,\r\nphenocopying residual disease signatures identified in patients treated with EGFR\r\ninhibitors. After continued sotorasib treatment, we observed diverse mechanisms of\r\ndrug resistance in vivo, including genetic MAPK reactivation and lineage transformation\r\nfrom adenocarcinoma to squamous histology. Focusing mechanistic studies on\r\nsquamous transformation, we showed that expression of the basal transcription factor\r\n∆Np63 is sufficient to rewire transformed alveolar organoids to a squamous state in\r\nvitro, conferring insensitivity to KRAS inhibition. In vivo, either ectopic expression of\r\nSox2 or loss of Nkx2-1, which are tolerated during Kras-driven tumorigenesis, poised\r\ntumors for squamous lineage commitment upon KRAS inhibition. Squamous-\r\ntransformed tumors did not exhibit evidence of KRAS/MAPK reactivation, underscoring\r\nthe role for lineage transcription factors and histologic transformation in mediating\r\noncogene independence.","manuscriptTitle":"Lineage identity governs oncogene dependence in murine NSCLC models of KRAS inhibitor resistance","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-07-24 07:13:21","doi":"10.21203/rs.3.rs-7058952/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-genetics","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"ng","sideBox":"Learn more about [Nature Genetics](http://www.nature.com/ng/)","snPcode":"","submissionUrl":"","title":"Nature Genetics","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Research","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"a9f0fcf2-543d-4319-8f86-24e4ac500e14","owner":[],"postedDate":"July 24th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":51993814,"name":"Biological sciences/Cancer/Lung cancer/Non-small-cell lung cancer"},{"id":51993815,"name":"Biological sciences/Cancer/Cancer therapy/Targeted therapies"}],"tags":[],"updatedAt":"2025-10-01T14:59:21+00:00","versionOfRecord":[],"versionCreatedAt":"2025-07-24 07:13:21","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7058952","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7058952","identity":"rs-7058952","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}