Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells

Matthew B Dong; Guangchuan Wang; Ryan D Chow; Lupeng Ye; Lvyun Zhu; Xiaoyun Dai; Jonathan J Park; Hyunu R Kim; Youssef Errami; Christopher D Guzman; Xiaoyu Zhou; Krista Y Chen; Paul A Renauer; Yaying Du; Johanna Shen; Stanley Z Lam; Jingjia J Zhou; Donald R Lannin; Roy S Herbst; Sidi Chen

doi:10.1016/j.cell.2019.07.044

Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells

Cell. 2019 Aug 22;178(5):1189-1204.e23. doi: 10.1016/j.cell.2019.07.044.

Authors

Matthew B Dong¹, Guangchuan Wang², Ryan D Chow³, Lupeng Ye², Lvyun Zhu², Xiaoyun Dai², Jonathan J Park³, Hyunu R Kim², Youssef Errami², Christopher D Guzman⁴, Xiaoyu Zhou², Krista Y Chen⁵, Paul A Renauer⁶, Yaying Du², Johanna Shen⁵, Stanley Z Lam⁵, Jingjia J Zhou⁵, Donald R Lannin⁷, Roy S Herbst⁸, Sidi Chen⁹

Affiliations

¹ Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA; Immunobiology Program, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA.
² Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA.
³ Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA.
⁴ Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Immunobiology Program, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT 06510, USA.
⁵ Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA.
⁶ Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Combined Program in the Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT 06510, USA.
⁷ Department of Surgery, Yale University School of Medicine, New Haven, CT 06510, USA; Breast Cancer Program, Yale University School of Medicine, New Haven, CT06510, USA; Smilow Cancer Hospital, 35 Park Street, New Haven, CT 06510; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
⁸ Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA; Smilow Cancer Hospital, 35 Park Street, New Haven, CT 06510; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
⁹ Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA; Immunobiology Program, Yale University School of Medicine, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Liver Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT 06510, USA. Electronic address: sidi.chen@yale.edu.

Abstract

CD8 T cells play essential roles in anti-tumor immune responses. Here, we performed genome-scale CRISPR screens in CD8 T cells directly under cancer immunotherapy settings and identified regulators of tumor infiltration and degranulation. The in vivo screen robustly re-identified canonical immunotherapy targets such as PD-1 and Tim-3, along with genes that have not been characterized in T cells. The infiltration and degranulation screens converged on an RNA helicase Dhx37. Dhx37 knockout enhanced the efficacy of antigen-specific CD8 T cells against triple-negative breast cancer in vivo. Immunological characterization in mouse and human CD8 T cells revealed that DHX37 suppresses effector functions, cytokine production, and T cell activation. Transcriptomic profiling and biochemical interrogation revealed a role for DHX37 in modulating NF-κB. These data demonstrate high-throughput in vivo genetic screens for immunotherapy target discovery and establishes DHX37 as a functional regulator of CD8 T cells.

Keywords: CD8 T cell; DHX37; T cell effector function; adoptive transfer; breast cancer; immunotherapy; in vivo CRISPR screen; lentiCRISPR; target discovery; tumor infiltration.

Publication types

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

MeSH terms

Animals
Breast Neoplasms / pathology
Breast Neoplasms / therapy
CD8-Positive T-Lymphocytes / cytology
CD8-Positive T-Lymphocytes / immunology
CD8-Positive T-Lymphocytes / metabolism*
Cell Line, Tumor
Clustered Regularly Interspaced Short Palindromic Repeats / genetics
Cytokines / genetics
Cytokines / metabolism
Female
Humans
Immunologic Memory
Immunotherapy
Male
Mice
Mice, Knockout
NF-kappa B / metabolism
Programmed Cell Death 1 Receptor / metabolism
RNA Helicases / deficiency
RNA Helicases / genetics*
RNA, Guide, CRISPR-Cas Systems / metabolism
Transcriptome

Substances

Cytokines
NF-kappa B
Programmed Cell Death 1 Receptor
RNA, Guide, CRISPR-Cas Systems
Dhx37 protein, mouse
RNA Helicases

Abstract

Publication types

MeSH terms

Substances

Grants and funding