Tracing the evolutionary trajectory of CDK4/6 inhibitor resistance in oestrogen receptor positive breast cancer

Tracing the evolutionary trajectory of CDK4/6 inhibitor resistance in oestrogen receptor positive breast cancer | 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 Tracing the evolutionary trajectory of CDK4/6 inhibitor resistance in oestrogen receptor positive breast cancer Rachael Natrajan, Ioanna Mavrommati, Tabitha Branston, Fatemeh Ahmadi Moughari, and 13 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7488427/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 Understanding tumour evolution is key to overcoming resistance to CDK4/6 inhibitors (CDK4/6i) in oestrogen receptor positive breast cancer. While genetic changes contribute, many patients lack identifiable mutations, suggestive of non-genetic epigenetic reprogramming and transcriptional plasticity. Here, we integrate expressed barcode lineage tracing, single-cell and bulk profiling, together with mathematical modelling, to study the evolution of resistance to the clinically approved CDK4/6i; Abemaciclib and Palbociclib. Our findings show that the evolutionary path to resistance to CDK4/6i is dependent on both the specific drug and the cancer cell model and can be driven by heritable epigenetic changes, independent of other acquired genetic driver alterations. We identify epigenetically driven transcriptional cell states that pre-exist as minority sub-populations in parental cells that become enriched in CDK4/6i resistant cells and are characterised by increased enhancer accessibility despite resistant cells showing overall reduced global accessibility. These transcriptional states show open chromatin in parental cells, suggestive of the presence of pre-existing epigenetically ‘primed’ cells. Finally, we generate and validate a core set of genes predictive of neoadjuvant endocrine + CDK4/6i response. Functional genomic assessment of candidate genes from this signature highlights potential collateral vulnerabilities in resistant cells. Overall, our study highlights the functional role of epigenetic adaptation in driving CDK4/6i resistance. Biological sciences/Cancer/Breast cancer Biological sciences/Genetics/Epigenomics Biological sciences/Molecular biology/Transcriptomics Biological sciences/Cancer/Tumour biomarkers Full Text Additional Declarations Yes there is potential Competing Interest. R.N. receives and/or has received other academic research funding from Pfizer in the form of the Breast Cancer Now Catalyst academic grant scheme and academic consultancy fees from Ellipses Pharma unrelated to this work. T.A.G is named as a coinventor on patent applications that describe a method for TCR sequencing (GB2305655.9), a method to measure evolutionary dynamics in cancers using DNA methylation (GB2317139.0), and a method to infer drug resistance mechanisms from barcoding data (GB2501439.0). TG has received honorarium from Genentech and consultancy fees from DAiNA therapeutics. A.N.J.T. reports personal honoraria from Pfizer, Prime Oncology, MD Anderson, Medscape Education, EM Partners, GBCC conference, Cancer Panel, Research to Practise, Penn Medicine, and AZ; honoraria to either the ICR or King’s College research accounts from SABCS 2022, VJ oncology, GE healthcare, Gilead, AZ ESMO symposium 2021, AZ-Symposium at UKIBCS conference 2024, AZ Ad boards throughout 2021–2024 in the UK-Asia-Australia Canada, AZ at St Gallen Symposium-2023, Gilead, Aicme, AACR, Page Therapeutics, Ellipses SAB meetings from 2023- 2024, VHIO, Livingston Memorial, Tango Therapeutics, Guardant, Breast Cancer Trials 2024, FERO SAB member; Merck honoraria and stock in InBioMotion; honoraria and financial support for research from AZ, Medivation, Myriad Genetics, and Merck Serono; and grants for research from Breast Cancer Now, CRUK, and BCRF. A.N.J.T. also reports benefits from ICR’s Inventors Scheme associated with patents for PARP inhibitors in BRCA1/2 associated cancers, paid into research accounts at The ICR and to A.N.J.T.’s personal account. The remaining authors declare no conflicts of interest. Supplementary Files MavrommatiSuppTables.xlsx Extended Data Tables MavrommatiExtendedData.pdf Extended Data Figures 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. 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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-7488427","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":508165647,"identity":"15b69ab0-c19a-48ee-8da2-ce3844d61e8b","order_by":0,"name":"Rachael 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scheme and academic consultancy fees from Ellipses Pharma unrelated to this work. T.A.G is named as a coinventor on patent applications that describe a method for TCR sequencing (GB2305655.9), a method to measure evolutionary dynamics in cancers using DNA methylation (GB2317139.0), and a method to infer drug resistance mechanisms from barcoding data (GB2501439.0). TG has received honorarium from Genentech and consultancy fees from DAiNA therapeutics. A.N.J.T. reports personal honoraria from Pfizer, Prime Oncology, MD Anderson, Medscape Education, EM Partners, GBCC conference, Cancer Panel, Research to Practise, Penn Medicine, and AZ; honoraria to either the ICR or King’s College research accounts from SABCS 2022, VJ oncology, GE healthcare, Gilead, AZ ESMO symposium 2021, AZ-Symposium at UKIBCS conference 2024, AZ Ad boards throughout 2021–2024 in the UK-Asia-Australia Canada, AZ at St Gallen Symposium-2023, Gilead, Aicme, AACR, Page Therapeutics, Ellipses SAB meetings from 2023- 2024, VHIO, Livingston Memorial, Tango Therapeutics, Guardant, Breast Cancer Trials 2024, FERO SAB member; Merck honoraria and stock in InBioMotion; honoraria and financial support for research from AZ, Medivation, Myriad Genetics, and Merck Serono; and grants for research from Breast Cancer Now, CRUK, and BCRF. A.N.J.T. also reports benefits from ICR’s Inventors Scheme associated with patents for PARP inhibitors in BRCA1/2 associated cancers, paid into research accounts at The ICR and to A.N.J.T.’s personal account. The remaining authors declare no conflicts of interest.","formattedTitle":"Tracing the evolutionary trajectory of CDK4/6 inhibitor resistance in oestrogen receptor positive breast cancer","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-7488427/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7488427/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Understanding tumour evolution is key to overcoming resistance to CDK4/6 inhibitors (CDK4/6i) in oestrogen receptor positive breast cancer. While genetic changes contribute, many patients lack identifiable mutations, suggestive of non-genetic epigenetic reprogramming and transcriptional plasticity. Here, we integrate expressed barcode lineage tracing, single-cell and bulk profiling, together with mathematical modelling, to study the evolution of resistance to the clinically approved CDK4/6i; Abemaciclib and Palbociclib. Our findings show that the evolutionary path to resistance to CDK4/6i is dependent on both the specific drug and the cancer cell model and can be driven by heritable epigenetic changes, independent of other acquired genetic driver alterations. We identify epigenetically driven transcriptional cell states that pre-exist as minority sub-populations in parental cells that become enriched in CDK4/6i resistant cells and are characterised by increased enhancer accessibility despite resistant cells showing overall reduced global accessibility. These transcriptional states show open chromatin in parental cells, suggestive of the presence of pre-existing epigenetically ‘primed’ cells. Finally, we generate and validate a core set of genes predictive of neoadjuvant endocrine + CDK4/6i response. Functional genomic assessment of candidate genes from this signature highlights potential collateral vulnerabilities in resistant cells. 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