Epigenetic profiles of chimeric antigen receptor T cells with knockout of PRDM1

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 PRDM1 as one of the key epigenetic genes regulating T cell differentiation. We compared epigenetic profiles of control and PRDM1-knockout CAR-T cells by ATAC-sequencing analysis. Human CD8+ T cells derived from two different healthy donors were retrovirally transduced with an anti-CD19 CAR gene (FMC63-28z) and the disrupted with PRDM1 using the CRISPR/Cas9 system. The control or PRDM1-knockout CAR-T cells were then stimulated with the CD19+ B-cell acute lymphoblastic leukemia cell line NALM-6 for three times. CD8+ CAR-T cells were isolated after the third stimulation, and epigenetic profiles were analyzed by ATAC sequencing.