Single cell genomics links targeted functional manipulations to efficacy-associated transcriptional signatures in anti-tumor T cells

Modifying CAR architecture or T cell differentiation state can enhance anti-tumor efficacy. However, pooled screening methods are often restricted to in vitro readouts of abundance or transcriptome, limiting projection of long-term T cell fates.

We implement barcoded scATAC-seq, tracking transcriptional fates of pooled murine or human CAR T cells with diverse functional modifications. We report stable and transient changes in transcription factor activity programmed by IL-2 concentration during in vitro expansion, and altered in vivo effector differentiation programs driven by combinatorial modifications in CAR antigen binding domain. These data establish use of genetic barcoding to tie targeted functional manipulations to single CAR T cell chromatin profiles in vitro and in vivo, providing insights toward augmented therapeutic efficacy.