Autologous anti-CD19 chimeric antigen receptor T cell (CAR T) therapy is highly effective in relapsed/refractory large B cell lymphoma (rrLBCL) but is associated with toxicities that delay recovery. While the biological mechanisms of cytokine release syndrome and neurotoxicity have been investigated, the pathophysiology is poorly understood for prolonged cytopenia, defined as grade ≥3 cytopenia lasting beyond 30 days after CAR T infusion. We performed single-cell RNA sequencing of bone marrow samples from healthy donors and rrLBCL patients with or without prolonged cytopenia and identified significantly increased frequencies of clonally expanded CX3CR1 hi cytotoxic T cells, expressing high interferon (IFN)-γ and cytokine signaling gene sets, associated with prolonged cytopenia. In line with this, we found that hematopoietic stem cells from these patients expressed IFN-γ response signatures. IFN-γ deregulates hematopoietic stem cell self-renewal and differentiation and can be targeted with thrombopoietin agonists or IFN-γ-neutralizing antibodies, highlighting a potential mechanism-based approach for the treatment of CAR T-associated prolonged cytopenia., Competing Interests: Declaration of interests M.R.G. reports research funding from Sanofi, Kite/Gilead, Abbvie, and Allogene; consulting for Abbvie; honoraria/consulting fees from Tessa Therapeutics, Monte Rosa Therapeutics, Daiichi Sankyo, and Abbvie; and stock ownership of KDAc Therapeutics. S.S.N. received research support from Kite/Gilead, BMS, Cellectis, Poseida, Allogene, Unum Therapeutics, Precision Biosciences, and Adicet Bio; served as Advisory Board Member/Consultant for Kite/Gilead, Merck, Novartis, Sellas Life Sciences, Athenex, Allogene, Incyte, Adicet Bio, BMS, Legend Biotech, Bluebird Bio, Fosun Kite, Sana Biotechnology, Caribou, Astellas Pharma, Morphosys, Janssen, Chimagen, ImmunoACT, and Orna Therapeutics; has received royalty income from Takeda Pharmaceuticals; has stock options from Longbow Immunotherapy, Inc; and has intellectual property related to cell therapy. P.S. received research support from Sobi, AstraZeneca/Acerta, ALX Oncology, and ADC Therapeutics; and served as Advisory Board Member/Consultant for Kite/Gilead, Roche/Genentech, Incyte/Morphosys, ADC Therapeutics, TG Therapeutics, Hutchinson/MediPharma, and AstraZeneca/Acerta. R.N. reports speakership for Incyte. J.R.W. reports consulting for Kite/Gilead, BMS, Novartis, Genentech/Roche, AstraZeneca, Morphosys/Incyte, Janssen, ADC Therapeutics, Calithera, Kymera, Merck, MonteRosa, SeaGen, and Abbvie; and research funding from Kite/Gilead, BMS, Novartis, Genentech/Roche, AstraZeneca, Morphosys/Incyte, Janssen, ADC Therapeutics, Calithera, and Kymera. S.A. reports research funding from Seattle Genetics, Merck, Xencor, Chimagen, and Tessa Therapeutics; advisory board membership or consulting for Tessa Therapeutic’s, Chimagen, ADC Therapeutics, and KITE/Gilead; and data safety monitoring board membership for Myeloid Therapeutics. L.J.N. reports honoraria for participation on advisory boards from ADC Therapeutics, Atara, BMS, Caribou Biosciences, Epizyme, Genentech, Genmab, Gilead/Kite, Janssen, Morphosys, Novartis, and Takeda; research support from BMS, Caribou Biosciences, Epizyme, Genentech, Genmab, Gilead/Kite, Janssen, IGM Biosciences, Novartis, and Takeda; and serves on a DSMB for DeNovo, Genentech, MEI, and Takeda. C.R.F. reports consulting for Abbvie, Bayer, BeiGene, Celgene, Denovo Biopharma, Foresight Diagnostics, Genentech/Roche, Genmab, Gilead, Karyopharm, N-Power Medicine, Pharmacyclics/Janssen, SeaGen, and Spectrum; research funding from 4D, Abbvie, Acerta, Adaptimmune, Allogene, Amgen, Bayer, Celgene, Cellectis EMD, Gilead, Genentech/Roche, Guardant, Iovance, Janssen Pharmaceutical, Kite, Morphosys, Nektar, Novartis, Pfizer, Pharmacyclics, Sanofi, Takeda, TG Therapeutics, Xencor, Ziopharm, Burroughs Wellcome Fund, Eastern Cooperative Oncology Group, National Cancer Institute, V Foundation, and Cancer Prevention and Research Institute of Texas: CPRIT Scholar in Cancer Research; and stock ownership in Foresight Diagnostics, N-Power Medicine. F.V. reports research funding from Allogene and Geron corporation; and honoraria from i3Health, Elsevier, America Registry of Pathology, Society of Hematology Oncology, and CRISP Therapeutics. K.T. reports consulting for Symbio Pharaceuticals and honoraria from Mission Bio. R.E.S. reports research funding from SeaGen, BMS, GSK, and Rafael Pharmaceuticals., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)