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

Julia A Belk; Winnie Yao; Nghi Ly; Katherine A Freitas; Yan-Ting Chen; Quanming Shi; Alfredo M Valencia; Eric Shifrut; Nupura Kale; Kathryn E Yost; Connor V Duffy; Bence Daniel; Madeline A Hwee; Zhuang Miao; Alan Ashworth; Crystal L Mackall; Alexander Marson; Julia Carnevale; Santosh A Vardhana; Ansuman T Satpathy

doi:10.1016/j.ccell.2022.06.001

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

Cancer Cell. 2022 Jul 11;40(7):768-786.e7. doi: 10.1016/j.ccell.2022.06.001. Epub 2022 Jun 23.

Authors

Julia A Belk¹, Winnie Yao², Nghi Ly², Katherine A Freitas³, Yan-Ting Chen⁴, Quanming Shi², Alfredo M Valencia⁵, Eric Shifrut⁶, Nupura Kale⁷, Kathryn E Yost⁸, Connor V Duffy⁹, Bence Daniel¹⁰, Madeline A Hwee⁴, Zhuang Miao⁹, Alan Ashworth¹¹, Crystal L Mackall¹², Alexander Marson¹³, Julia Carnevale¹⁴, Santosh A Vardhana¹⁵, Ansuman T Satpathy¹⁶

Affiliations

¹ Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
² Department of Pathology, Stanford University, Stanford, CA 94305, USA.
³ Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA 94035, USA; Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94035, USA.
⁴ Memorial Sloan Kettering Cancer Center, New York, NY, USA.
⁵ Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA.
⁶ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
⁷ UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
⁸ Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA.
⁹ Department of Genetics, Stanford University, Stanford, CA 94305, USA.
¹⁰ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA.
¹¹ UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
¹² Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA; Division of Pediatric Hematology/Oncology/Stem Cell Transplant and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94035, USA; Division of BMT and Cell Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94035, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
¹³ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
¹⁴ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
¹⁵ Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA.
¹⁶ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA 94035, USA; Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: satpathy@stanford.edu.

Abstract

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.

Keywords: CRISPR; T cell exhaustion; canonical BAF complex; chromatin remodeling; epigenetics; genomics; immunology; in vivo Perturb-seq.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chromatin / genetics
Chromatin Assembly and Disassembly* / genetics
Epigenomics
Humans
Mice
Neoplasms* / genetics
T-Lymphocytes

Substances

Chromatin

Abstract

Publication types

MeSH terms

Substances

Grants and funding