Publications
Nature geneticsNov 2023 DOI:
10.1038/s41588-023-01554-0

Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens

McCutcheon, Sean R; Swartz, Adam M; Brown, Michael C; Barrera, Alejandro; McRoberts Amador, Christian; Siklenka, Keith; Humayun, Lucas; Ter Weele, Maria A; Isaacs, James M; Reddy, Timothy E; Allen, Andrew S; Nair, Smita K; Antonia, Scott J; Gersbach, Charles A
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Abstract
Clinical response to adoptive T cell therapies is associated with the transcriptional and epigenetic state of the cell product. Thus, discovery of regulators of T cell gene networks and their corresponding phenotypes has potential to improve T cell therapies. Here we developed pooled, epigenetic CRISPR screening approaches to systematically profile the effects of activating or repressing 120 transcriptional and epigenetic regulators on human CD8+ T cell state. We found that BATF3 overexpression promoted specific features of memory T cells and attenuated gene programs associated with cytotoxicity, regulatory T cell function, and exhaustion. Upon chronic antigen stimulation, BATF3 overexpression countered phenotypic and epigenetic signatures of T cell exhaustion. Moreover, BATF3 enhanced the potency of CAR T cells in both in vitro and in vivo tumor models and programmed a transcriptional profile that correlates with positive clinical response to adoptive T cell therapy. Finally, we performed CRISPR knockout screens that defined cofactors and downstream mediators of the BATF3 gene network.
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