Acquisition of an immunosuppressive microenvironment after anti-CD19 CAR T-cell therapy is associated with T-cell dysfunction and resistance

Background: 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. Methods: 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. Results: 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 interferon response, hypoxia, and TGF-β signaling was accompanied by expansion of myeloid-derived suppressor cells (MDSCs) and endogenous exhausted CD8+ T cells. PD-1 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 HIF-1α, VEGF, and TGFBR2 are key players in the intercellular communication between CAR T cells and the immune niche, potentially 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 hematopoietic stem/progenitor cell-humanized mice bearing a human tumor. Conclusions: In conclusion, CAR T-cell-mediated myeloid activation is associated with pathways of immune dysregulation that may antagonize the effects of therapy.