SUV39H1 disruption imparts functional persistence to CD28-costimulated human CAR T cells

Abstract Retrovirally encoded CD19-specific CARs that incorporate CD28 and CD3z signaling motifs (Rv-1928z) have induced remarkable responses in patients with refractory leukemia and lymphoma. These CARs, however, induce a strong effector differentiation program in T cells that can limit their persistence and result in T cell dysfunction. Multiple studies have shown that effector differentiation and eventual dysfunction are associated with transcriptional and epigenetic changes. In this study, we examine the effect of disrupting the histone methyl transferase, SUV39H1 on the functional persistence of human Rv-1928z CAR T cells. SUV39H1 has recently been implicated in regulating memory to effector transition in murine T cells (Pace et al. 2018). To assess the impact of SUV39H1 in human Rv-1928z CAR T cells, we treated immune deficient mice bearing the human ALL cell line, NALM6, with limiting doses of SUV39H1-edited (SUV39H1etd) T cells. SUV39H1etd Rv-1928z CAR T cells have improved anti-tumor efficacy as compared to WT Rv-1928z CAR T cells, with 9/10 NALM6 bearing mice treated with SUV39H1etd Rv-1928z surviving as compared to 1/12 mice treated with WT Rv-1928z over the duration of observation (90 days). This enhanced tumor control in SUV39H1etd Rv-1928z CAR T cells was associated with improved CAR T cell persistence (> day 50). Paired genome accessibility (ATACseq) and transcriptional analysis on SUV39H1etd and WT Rv-1928z CAR T cells that have undergone multiple rounds of tumor rechallenges in vivo revealed epigenetic changes associated with SUV39H1 loss in Rv-1928z CAR T cells that promote expression of memory associated transcription factors and curtail T cell dysfunction in Rv-1928z CAR T cells.