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Chimeric antigen receptor (CAR) T cells targeting CD19 induce durable responses in B-cell acute lymphoblastic leukemia (B-ALL). However, the contribution of the tumor microenvironment to the therapeutic response after CAR-T cell treatment remains incompletely understood. We performed single-cell RNA sequencing and spectral flow cytometry-based analyses of bone marrow-resident immune cells from B-ALL patients before and after CAR T-cell treatment. We observed profound changes in the microenvironment in response to CAR T cell-mediated inflammation, including an increase in myeloid cells. Significant induction of the IFN response, hypoxia, and TGF-β-signaling was associated with expansion of myeloid-derived suppressor cells (MDSCs) and endogenous exhausted CD8+ T cells. PD1 expression in endogenous T cells post-treatment was associated with a lack of durable response in the cohort of patients analyzed. Further, we revealed that HIF1α, VEGF, and TGFBR2 are key players in the intercellular communication between CAR T cells and the immune niche, driving widespread T-cell dysfunction. Infusion of anti-CD19 CAR T cells led to increased accumulation of human MDSCs, exacerbation of a hypoxic environment and T-cell exhaustion in HSPC-humanized mice bearing a human tumor. In conclusion, CAR T-cell-mediated myeloid activation is associated with pathways of immune dysregulation that may antagonize the effects of therapy.

Key points

• The tumor immune context post-treatment affects CAR T-cell fate and endogenous immunity in B-cell acute lymphoblastic leukemia.

• IFN response, hypoxia, and TGF-β-signaling result in endogenous T-cell exhaustion and compromise CAR T-cell efficacy.