CAR19 therapy drives expansion of clonal hematopoiesis and associated cytopenias

CAR19 therapy drives expansion of clonal hematopoiesis and associated cytopenias | 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 CAR19 therapy drives expansion of clonal hematopoiesis and associated cytopenias Ash Alizadeh, Mark Hamilton, Nick Phillips, Troy Noordenbos, Jan Boegeholz, and 32 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7746241/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 CD19-directed chimeric antigen receptor T-cell therapy (CAR19) improves survival in patients with relapsed/refractory large B-cell lymphoma (rrLBCL) compared to immunochemotherapy with intent for autologous hematopoietic cell transplantation (HCT). However, major toxicities of CAR19 therapy include prolonged cytopenias, infection, and secondary hematologic malignancies. To investigate the mechanisms underlying these toxicities we studied a cohort of lymphoma patients receiving CAR19. CAR19-treated patients exhibited impaired immune reconstitution and increased infection compared to propensity-matched HCT-treated controls. Bone marrow analysis revealed prolonged post-CAR cytopenias is associated with clonal cytopenias of undetermined significance (CCUS) and is characterized by interferon-mediated inflammation. Despite durable lymphoma remissions, clonal hematopoiesis (CH) commonly expanded following CAR19 infusion and was associated with impaired immune reconstitution and the development of treatment related myeloid malignancy (tMN). The molecular composition and clinical outcomes of post-CAR tMN were comparable to those of post-HCT tMN. Single-cell DNA analysis revealed that most post-CAR CH clones harbored a single independent mutation and that CAR integration into T cells with CH mutations may drive persistence. These findings broadly implicate CH mutation burden and CH expansion in the development of post-CAR cytopenias and malignancies as well as mechanistically suggest these expansions occur in a background of marrow inflammation. Together, our results provide insight into the origins of key CAR19-associated toxicities, including infection and tMN. Health sciences/Diseases/Cancer/Haematological cancer/Lymphoma/Non-hodgkin lymphoma/B-cell lymphoma Biological sciences/Cancer/Cancer genomics Full Text Additional Declarations Yes there is potential Competing Interest. SKA: Foresight Diagnostics: Consulting; AstraZeneca: Advisory Board, speaker honoraria. MJF consults for Kite Pharma-Gilead, Adaptative Biotechnologies, Sobi, ADC Therapeutics, and Cargo Therapeutics; receives research support from Kite-Pharma-Gilead, Allogene Therapeutics, Cargo Therapeutics, PeproMene Bio, and Adaptative Biotechnologies. A.A.A. reports consultancy for Celgene, Chugai, Genentech, Gilead, Janssen, Pharmacyclics and Roche, scientific advisory board membership in the Lymphoma Research Foundation, and Professional Affiliations with the American Society of Hematology, American Society of Clinical Oncology, American Society of Clinical Investigation, Leukemia & Lymphoma Society, Research Funding from the National Cancer Institute, the National Heart, Lung, and Blood Institute, the US National Institutes of Health, Celgene, BMS and Pfizer, patent filings including patent issued, licensed and with royalties paid from FortySeven, a patent pending and Licensed to Foresight, a patent pending relating to MARIA, a patent issued and licensed to CiberMed, a patent issued and a patent pending to CiberMed, patents issued to Idiotype Vaccines, and a patent issued, licensed and with royalties paid from Roche, and equity ownership interests in CiberMed Inc., Foresight Diagnostics, FortySeven Inc. and CARGO Therapeutics. D.B.M. reports consultancy for Kite-Gilead, Novartis, Bristol Meyer Squib, Miltenyi Biotec, Adicet, Allogene, Janssen, Pharmacyclics, Precision Bio, Sana, Caribou, Regeneron (previously 2Seventy),and Appia Bio. Research funding from the NCI P01 CA049605, Leukemia & Lymphoma Society, Kite-Gilead, and Allogene. Supplementary Files SupplementV11submit.pdf Data Supplement 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-7746241","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":532233678,"identity":"fef19326-72a3-4bf4-824d-7f906d39189b","order_by":0,"name":"Ash 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PeproMene Bio, and Adaptative Biotechnologies. \r\nA.A.A. reports consultancy for Celgene, Chugai, Genentech, Gilead, Janssen, Pharmacyclics and Roche, scientific advisory board membership in the Lymphoma Research Foundation, and Professional Affiliations with the American Society of Hematology, American Society of Clinical Oncology, American Society of Clinical Investigation, Leukemia \u0026 Lymphoma Society, Research Funding from the National Cancer Institute, the National Heart, Lung, and Blood Institute, the US National Institutes of Health, Celgene, BMS and Pfizer, patent filings including patent issued, licensed and with royalties paid from FortySeven, a patent pending and Licensed to Foresight, a patent pending relating to MARIA, a patent issued and licensed to CiberMed, a patent issued and a patent pending to CiberMed, patents issued to Idiotype Vaccines, and a patent issued, licensed and with royalties paid from Roche, and equity ownership interests in CiberMed Inc., Foresight Diagnostics, FortySeven Inc. and CARGO Therapeutics.\r\nD.B.M. reports consultancy for Kite-Gilead, Novartis, Bristol Meyer Squib, Miltenyi Biotec, Adicet, Allogene, Janssen, Pharmacyclics, Precision Bio, Sana, Caribou, Regeneron (previously 2Seventy),and Appia Bio. Research funding from the NCI P01 CA049605, Leukemia \u0026 Lymphoma Society, Kite-Gilead, and Allogene.","formattedTitle":"CAR19 therapy drives expansion of clonal hematopoiesis and associated cytopenias","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-7746241/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7746241/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"CD19-directed chimeric antigen receptor T-cell therapy (CAR19) improves survival in patients with relapsed/refractory large B-cell lymphoma (rrLBCL) compared to immunochemotherapy with intent for autologous hematopoietic cell transplantation (HCT). However, major toxicities of CAR19 therapy include prolonged cytopenias, infection, and secondary hematologic malignancies. To investigate the mechanisms underlying these toxicities we studied a cohort of lymphoma patients receiving CAR19. CAR19-treated patients exhibited impaired immune reconstitution and increased infection compared to propensity-matched HCT-treated controls. Bone marrow analysis revealed prolonged post-CAR cytopenias is associated with clonal cytopenias of undetermined significance (CCUS) and is characterized by interferon-mediated inflammation. Despite durable lymphoma remissions, clonal hematopoiesis (CH) commonly expanded following CAR19 infusion and was associated with impaired immune reconstitution and the development of treatment related myeloid malignancy (tMN). The molecular composition and clinical outcomes of post-CAR tMN were comparable to those of post-HCT tMN. Single-cell DNA analysis revealed that most post-CAR CH clones harbored a single independent mutation and that CAR integration into T cells with CH mutations may drive persistence. These findings broadly implicate CH mutation burden and CH expansion in the development of post-CAR cytopenias and malignancies as well as mechanistically suggest these expansions occur in a background of marrow inflammation. Together, our results provide insight into the origins of key CAR19-associated toxicities, including infection and tMN.","manuscriptTitle":"CAR19 therapy drives expansion of clonal hematopoiesis and associated cytopenias","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-10-21 06:58:04","doi":"10.21203/rs.3.rs-7746241/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":"2241a8e4-2eaf-4da1-a067-4dc9b95808ef","owner":[],"postedDate":"October 21st, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":56573591,"name":"Health sciences/Diseases/Cancer/Haematological cancer/Lymphoma/Non-hodgkin lymphoma/B-cell lymphoma"},{"id":56573592,"name":"Biological sciences/Cancer/Cancer genomics"}],"tags":[],"updatedAt":"2026-03-19T08:06:36+00:00","versionOfRecord":[],"versionCreatedAt":"2025-10-21 06:58:04","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7746241","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7746241","identity":"rs-7746241","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}