Targeting PTPN2 enhances human CAR T cell efficacy and the development of long-term memory [RNA-seq]

CAR T cells have been ineffective against solid tumors, where the hostile tumor microenvironment limits CAR T cell function and persistence. Here we have used CRISPR/Cas9 gene-editing, or a small molecule inhibitor to target protein tyrosine phosphatase N2 (PTPN2) in human CAR T cells specific for the Lewis Y (LeY) neo-antigen. Targeting PTPN2 increased CAR and cytokine signaling and enhanced the activation and cytotoxicity of anti-LeY CAR T cells. The deletion or the systemic inhibition of PTPN2 in human CAR T cells repressed the growth of human tumor xenografts or patient-derived xenografts in mice and prolonged survival. PTPN2 deletion or inhibition promoted the generation and intratumoral accumulation of stem cell memory CD8+ CAR T cells that are associated with persistent CAR T cell-mediated tumor repression and improved clinical outcomes in patients. These findings support the use of gene-editing or small molecule inhibitors for targeting PTPN2 in human CAR T cells to combat solid tumors. CAR T cells specific to Lewis Y antigen, derived from donor PBMCs, with or without CRISPR/Cas9-mediated deletion of PTPN2. stimulated with plate-coated anti-idiotype antibody (1 ?g/ml) to crosslink the LeY CAR for 6h. RNA-seq libraries were prepared from RNA using the Quant-seq 3 mRNA-seq Library Prep Kit for Illumina (Lexogen) as per the manufacturer’s instructions. NextSeq (Illumina, Inc., San Diego, CA) sequencing was performed to generate single-end, 75-bp RNA-seq short reads and subsequently CASAVA 1.8.2 was used for base calling. *************************************************************** there are privacy concerns regarding public access to the raw data ***************************************************************