Single cell RNA-seq analysis of bone marrow (BM) samples of patients with B-Cell Acute Lymphoblastic Leukemia treated with anti CD19 CAR T cells

Single-cell RNA sequencing of BM resident immune cells of patients undergoing CAR T-cell infusion and their Infusion Product (IP). Data in this study were generated from a patients enrolled in the FT01CARCIK Phase I/IIb clinical trial (NCT03389035) and two patients treated with autologous commercial CAR T cells (tisagenlecleucel). BM samples have been collected before CAR T treatment (pre) and at early time points (1-2 months) after treatment (post). CD45+CD3+ T cells, and CD45+/lowCD3-, encompassing the hematopoietic immune niche of the TME cells, have been separated by flow cytometry-based cell sorting and compared to cells of the corresponding patient's BM before CAR T-cell treatment at the moment of relapse. In parallel, CAR T-cell infusion products (IP) have been sorted according to the surface CAR expression. Significance: This study highlights the critical role of the tumor microenvironment on CAR T-cell fate and endogenous immunity in B-cell acute lymphoblastic leukemia. We demonstrate that IFN response, hypoxia, and TGF-b signaling lead to general immune suppression, resulting in endogenous T-cell exhaustion and compromising CAR T-cell efficacy