Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence

• Published in: Cancer cell 2022-07, Vol.40 (7), p.768-786.e7
• Main Authors: Belk, Julia A., Yao, Winnie, Ly, Nghi, Freitas, Katherine A., Chen, Yan-Ting, Shi, Quanming, Valencia, Alfredo M., Shifrut, Eric, Kale, Nupura, Yost, Kathryn E., Duffy, Connor V., Daniel, Bence, Hwee, Madeline A., Miao, Zhuang, Ashworth, Alan, Mackall, Crystal L., Marson, Alexander, Carnevale, Julia, Vardhana, Santosh A., Satpathy, Ansuman T.
• Format: Article
• Language: English
• Subjects: Animals; canonical BAF complex; Chromatin - genetics; Chromatin Assembly and Disassembly - genetics; chromatin remodeling; CRISPR; epigenetics; Epigenomics; genomics; Humans; immunology; in vivo Perturb-seq; Mice; Neoplasms - genetics; T cell exhaustion; T-Lymphocytes
• ISSN: 1535-6108; 1878-3686
• DOI: 10.1016/j.ccell.2022.06.001

T cell exhaustion limits antitumor immunity, but the molecular determinants of this process remain poorly understood. Using a chronic stimulation assay, we performed genome-wide CRISPR-Cas9 screens to systematically discover regulators of T cell exhaustion, which identified an enrichment of epigenetic factors. In vivo CRISPR screens in murine and human tumor models demonstrated that perturbation of the INO80 and BAF chromatin remodeling complexes improved T cell persistence in tumors. In vivo Perturb-seq revealed distinct transcriptional roles of each complex and that depletion of canonical BAF complex members, including Arid1a, resulted in the maintenance of an effector program and downregulation of exhaustion-related genes in tumor-infiltrating T cells. Finally, Arid1a depletion limited the acquisition of exhaustion-associated chromatin accessibility and led to improved antitumor immunity. In summary, we provide an atlas of the genetic regulators of T cell exhaustion and demonstrate that modulation of epigenetic state can improve T cell responses in cancer immunotherapy. [Display omitted] •In vitro T cell exhaustion assay enables genome-wide CRISPR-Cas9 screening•In vitro and in vivo genetic screens converge on cBAF and INO80 complex subunits•Arid1a-sgRNA T cells improve tumor control and enhance persistence of human T cells•Arid1a is required for acquisition of the epigenetic state of terminal exhaustion Belk et al. systematically dissect the genetic regulators of T cell exhaustion with a series of in vitro and in vivo CRISPR-Cas9 screens. The depletion of chromatin remodeling factors, in particular Arid1a, improves T cell function and reduces the transcriptional and epigenetic hallmarks of exhaustion.