Gene expression profiles of chimeric antigen receptor T cells with knockout of epigenetic genes

Persistence of infused antitumor T cells is one of the essential factors for durable therapeutic response. T cells undergo genome-wide alterations in epigenetic architecture upon repeated antigen encounter, which is inevitably accompanied by progressive T cell differentiation and loss of longevity. In this study, we explored key epigenetic factors associated with terminal T cell differentiation using CRISPR/Cas9-mediated knockout of epigenetic genes in chimeric antigen receptor (CAR)-engineered human T cells and identified multiple key epigenetic genes. We analyzed gene expression profiles of CAR-T cells that were knocked out with the specific epigenetic genes by RNA-sequencing. Overall design: Human CD8+ T cells derived from three different healthy donors were retrovirally transduced with an anti-CD19 CAR gene (FMC63-28z) and stimulated with the CD19+ B-cell acute lymphoblastic leukemia cell line NALM-6 for three times. RNA was collected after the third stimulation, and gene expression profiles were analyzed by RNA sequencing.