ENAapplication/xmlftp://primaryOK200GenomicsCrystal L. Mackall, Sylvia K. Plevritis, Stanford Cancer Institute, Department of Biomedical Data Science, Stanford University School of Medicinehttps://www.ebi.ac.uk/ena/browser/view/PRJNA714638Homo sapiensPurpose: To compare cell states amoung three populations of interest among circulating CAR T cells in patients with lymphoma. Methods: Nine patients with large B-cell lymphoma (LBCL) were treated with axicabtagene ciloleucel (axi-cel), a commercial CD19-targeted CAR T-cell therapy. On day 7, fresh peripheral blood mononuclear cells were stained with an antibody panel for fluorescence-activated cell sorting (FACS), a panel for cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), and a viability dye. Single live CAR+ T cells were sorted from each patient, counted, processed for 5' single-cell RNA-sequencing with feature barcoding and TCR clonotype analysis on the 10X Genomics platform, and sequenced by the Stanford Genomics Facility (HighSeq 4000) or Novogene (NovaSeq 6000). Results: We found that circulating CD4+ and CD8+ CAR T cells that express CD57 and T-bet are clonally expanded and display features of effector T cells. In contrast, CD4+ CD57- CAR T cells that express Helios expand polyclonally and display features of T regulatory cells. Conclusions: This study provides insights into cell states of circulating CAR T cells on day 7 that associate with clinical response or toxicity in LBCL patients treated with axi-cel. Overall design: CAR T cells were sorted from blood of nine LBCL patients on day 7 following axi-cel infusion. Three populations of interest were identified within each CAR T-cell sample.xref:PubMed:36097223ENACMAR, d230, Thymus-Dependent Lymphocytes, CVB3-binding protein, Constitutive androstane receptor, SPG5C, dTAFII250, NSHPT, T-Lymphocyte, Germinoblastoma, Constitutive active response, EfW1, Malignant, Germinoblastic Sarcoma, GPRC2A, DLEU5, Cars, dmTAF[[II]]230, ADOHR, Automobile, Malignant Lymphomas, Client., T Lymphocyte, dmTAF1, AW553441, Taf230, actomyosin ring, RFP2, Rfp2, ESTM32, MCVADR, CAR4|6, MB67, PGN, CNC, Lymphomas, TAF250, Reticulolymphosarcoma, HCVADR, HHC, RNF77, Sarcomas, Taf200, AU016810, 3110001L12Rik, dTAF[[II]]250, TFIID TAF250, cel, cell, HCAR, T-Cells, Coxsackievirus B-adenovirus receptor, T, Taf1p, EIG8, dTAF250, MCAR, T Cells, Malignant Lymphoma, Sarcoma, TSE1, Clients, Gprc2a, ACRDYS1, HHC1, PPNAD1, cytokinetic ring, constriction ring, TAF, T Lymphocytes, Thymus Dependent Lymphocytes, hCAR, Lymphocyte, PKR1, data, dTAF[[II]]230, TAF[[II]]250, 2610206D03Rik, CAR-beta, TAF200, Orphan nuclear receptor MB67, l(3)84Ab, CaR, BG:DS00004.13, TAFII-250, TAF250/230, LEU5, Cell, dTAF230, Constitutive activator of retinoid response, TAFII250, Reticulolymphosarcomas, T-Cell, p230, TAF[[II]]250/230, TFIID, Germinoblastic Sarcomas, CAR, Car, Germinoblastic, Taf[[II]]250, TAF[[II]]230, FHH, PCAR1, AA209988, Thymus-Dependent, Lymphocytes, TAF[II]250, MLYM, Germinoblastomas, CG17603, TAF[[II]], PRKAR1, Thymus-Dependent Lymphocyte, CAR1, FIH, DmelCG17603, CNC1, contractile actomyosin ring, lymphoma, Taf250, CAR4/6, Patient, SR3-5, Lymphoma, Cells, T Cell, HYPOC1, AI551208, Care2, TAF230, lymphoid cancer, TAF1CMAR, d230, Thymus-Dependent Lymphocytes, CVB3-binding protein, Constitutive androstane receptor, SPG5C, dTAFII250, NSHPT, T-Lymphocyte, Germinoblastoma, Constitutive active response, EfW1, Malignant, Germinoblastic Sarcoma, GPRC2A, DLEU5, Cars, dmTAF[[II]]230, ADOHR, Automobile, Malignant Lymphomas, Client., T Lymphocyte, dmTAF1, AW553441, Taf230, actomyosin ring, RFP2, Rfp2, ESTM32, MCVADR, CAR4|6, MB67, PGN, CNC, Lymphomas, TAF250, Reticulolymphosarcoma, HCVADR, HHC, RNF77, Sarcomas, Taf200, AU016810, 3110001L12Rik, dTAF[[II]]250, TFIID TAF250, cel, cell, HCAR, T-Cells, Coxsackievirus B-adenovirus receptor, T, Taf1p, EIG8, dTAF250, MCAR, T Cells, Malignant Lymphoma, Sarcoma, TSE1, Clients, Gprc2a, ACRDYS1, HHC1, PPNAD1, cytokinetic ring, constriction ring, TAF, T Lymphocytes, Thymus Dependent Lymphocytes, hCAR, Lymphocyte, PKR1, data, dTAF[[II]]230, TAF[[II]]250, 2610206D03Rik, CAR-beta, TAF200, Orphan nuclear receptor MB67, l(3)84Ab, CaR, BG:DS00004.13, TAFII-250, TAF250/230, LEU5, Cell, dTAF230, Constitutive activator of retinoid response, TAFII250, Reticulolymphosarcomas, T-Cell, p230, TAF[[II]]250/230, TFIID, Germinoblastic Sarcomas, CAR, Car, Germinoblastic, Taf[[II]]250, TAF[[II]]230, FHH, PCAR1, AA209988, Thymus-Dependent, Lymphocytes, TAF[II]250, MLYM, Germinoblastomas, CG17603, TAF[[II]], PRKAR1, Thymus-Dependent Lymphocyte, CAR1, FIH, DmelCG17603, CNC1, contractile actomyosin ring, lymphoma, Taf250, CAR4/6, Patient, SR3-5, Lymphoma, Cells, T Cell, HYPOC1, AI551208, Care2, TAF230, lymphoid cancer, TAF1falseSingle-cell sequencing data for circulating CAR T cells in lymphoma patientsSingle-cell sequencing data for circulating CAR T cells in lymphoma patients2025-09-242022-10-07PRJNA714638GSE168940960636097223