Antigen experience history directs distinct functional states of CD8+ CAR T cells during the anti-leukemia response

Abstract

Abstract Chimeric antigen receptor (CAR) T cells are highly effective in treating hematologic cancers, but patients can relapse due to downregulation of the CAR-targeted antigen, leading to the hypothesis that CAR T cells require high density of target antigen to be effective. Non-engineered CD8+ memory T cells generate more rapid and robust effector T cell responses upon secondary infection, relative to their naïve counterparts, and can display higher antigen sensitivity. Our objective was to characterize the role of prior CD8+ T cell antigen experience (AgEx) in dictating functional CAR-mediated anti-tumor responses. To study the effect of T cell AgEx history on CD8+ CAR T cell (CAR8) function in vivo, we used a vaccine model to control prior T cell AgEx history, and a syngeneic adoptive transfer model with murine anti-CD19 CAR8 targeting murine leukemia engineered to express a low or high level of CD19. We analyzed CAR8 expansion and leukemia burden using flow cytometry and performed ATACseq and RNAseq at timepoints pre- and post-CAR transduction and after reinfusion of CAR8 into leukemia-bearing mice to ask whether CAR8 function was determined by the epigenetic and/or transcriptomic state of the starting cell population. We found that starting cell state dictated in vivo CAR8 effector functions, expansion, and differential chromatin accessibility in regions containing binding motifs for AP-1, Runx, Tcf and other transcription factor (TF) families. Motif chromatin accessibility and gene expression of many TFs showed distinct patterns temporally. We conclude that CAR8 maintain functional traits epigenetically imprinted in the starting cell and predict these analyses could inform methods to transcriptionally modulate CAR T cell function.