Cytotoxic bystander activation of endogenous CAR-negative T cells in response to CD19-CAR T cell therapy 3836

Description CD19-CAR T cell therapy has been FDA-approved for multiple indications including acute lymphoblastic leukemia (ALL) and lymphoma. While CD19-CAR T cells have been analyzed in detail pre and post infusion, endogenous (CAR-negative (neg)) T cells during the expansion and contraction phase of CAR T cell therapy have not been studied in detail. These could potentially enhance or limit the effectiveness of CAR T cells, for instance through bystander activation or eliminating CAR-positive (pos) T cells. We previously generated a single-cell gene expression (GEX) and paired T cell receptor (TCR) sequencing dataset of blood and bone marrow samples obtained within the first 3 months post CD19-CAR T cell therapy from 15 pediatric patients with ALL and had focused our analysis on CARpos T cells (Wilson et al, Cancer Discov 2022). The goal of this project is to characterize CARneg T cells. GEX analysis revealed populations of CARneg T cells characterized by putative cytotoxic bystander activation. Furthermore, analysis of TCR clonal diversity showed more clonal expansions among CD8+ bystander T cells compared to non-bystander T cells. By clustering CARneg TCR clonotypes based on their relative clonal size changes over time, we also identified a set of structurally similar TCRs that were persistently expanded after infusion, suggestive of an epitope-specific response. Our findings suggest that CARneg effector CD8+ T cells could play important roles during CAR T cell therapy.