Department of Biomedical Engineering, Duke University, Durham, NC, USA.
Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
Nat Genet. 2023 Dec;55(12):2211-2223. doi: 10.1038/s41588-023-01554-0. Epub 2023 Nov 9.
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.
过继性 T 细胞疗法的临床应答与细胞产物的转录和表观遗传状态相关。因此,发现 T 细胞基因网络的调节剂及其相应表型有可能改善 T 细胞疗法。在此,我们开发了基于 CRISPR 的混合表观遗传筛选方法,系统地分析了 120 个激活或抑制转录因子和表观遗传因子对人 CD8 T 细胞状态的影响。我们发现,BATF3 的过表达促进了记忆 T 细胞的特定特征,并减弱了与细胞毒性、调节性 T 细胞功能和耗竭相关的基因程序。在慢性抗原刺激下,BATF3 的过表达逆转了 T 细胞耗竭的表型和表观遗传特征。此外,BATF3 增强了 CAR T 细胞在体外和体内肿瘤模型中的效力,并形成了与过继性 T 细胞治疗的阳性临床应答相关的转录特征。最后,我们进行了 CRISPR 敲除筛选,确定了 BATF3 基因网络的辅助因子和下游介质。
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