GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE345nnn/GSE345979/primaryOK200TranscriptomicsHomo sapiens OtherExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE345979GEOGSEfalseCellular and molecular mechanisms determining allogeneic CAR T cell rejection and expansion -- Submission 2 of 2 (scRNA/CITE-seq)Allogeneic CAR T cells could overcome limitations of autologous therapies but are limited by immune rejection. We evaluated 11 patients with large B-cell lymphoma treated with a single lot of cemacabtagene ansegedleucel (cema-cel), an allogeneic anti-CD19 CAR T product. Despite receiving identical infusion products, patients exhibited heterogeneous cema-cel expansion and clinical outcomes. Our integrated analyses using longitudinal TCRβ sequencing, single-cell molecular profiling, and mixed lymphocyte reaction assays revealed that high frequencies of pre-existing, recipient-derived alloreactive CD8+ T cells mediated rapid CAR T rejection in non-expanders. Furthermore, effector-like features, rather than stem/central memory programs, drove robust clonal CAR T expansion consistently across expanders. We confirmed similar expansion patterns in two independent cohorts treated with a separate lot of cema-cel or an allogeneic anti-BCMA CAR T product. These findings highlight distinct cell-extrinsic and cell-intrinsic mechanisms that influence allogeneic CAR T performance and provide insights to optimize donor selection, manufacturing, and product design.2026/09/23GSE345979GSM10020335GSM10020334GSM10020333GSM10020332GSM10020331GSM10020330GSM10020341GSM10020340GSM10020339GSM10020338GSM10020337GSM100203363017324676345979Homo sapiens[42788887]