In vivo CRISPR screens identify key modifiers of human CAR T cell function [scRNA-seq]

Chimeric antigen receptor (CAR) T cells are highly effective in hematologic malignancies1. However, loss of CAR T cells contributes to relapse in many patients2–4. These limitations could be overcome using targeted gene editing to increase CAR T cell persistence. Here, we performed in vivo loss-of-function CRISPR screens in BCMA-targeting CAR T cells to investigate genes influencing CAR T cell persistence and function in a human multiple myeloma model. We tracked the expansion and persistence of CRISPR-library edited T cells in vitro and then at early and late timepoints in vivo to track the performance of gene modified CAR T cells from manufacturing to survival in tumors. The screens revealed several context-specific regulators of CAR T cell expansion and persistence. Ablation of RASA2 and SOCS1 enhanced T cell expansion in vitro, while loss of PTPN2, ZC3H12A, and RC3H1 conferred early selective growth advantages to CAR T cells in vivo. Strikingly, we identified cyclin-dependent kinase inhibitor 1B (CDKN1B), a cell cycle regulator, as the most important factor limiting CAR T cell fitness at late timepoints in vivo. CDKN1B ablation increased BCMA CAR T cell proliferation and effector function, significantly enhancing tumor clearance and overall survival. Thus, our findings reveal differing effects of gene-perturbation on CAR T cells over time and in different environments, highlight CDKN1B as a promising target to generate highly effective CAR T cells for multiple myeloma, and underscore the potential importance of in vivo screening as a tool for identifying genes to enhance CAR T cell efficacy. A small pool of CRISPR modified CAR T cells were isolated from the spine and femurs of mice 21 days after T cell transfer. Mice had been previously engrafter with MM1.S myeloma cells for 21 days prior to CAR T cell transfer.