In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer

Zeyu Chen; Eri Arai; Omar Khan; Zhen Zhang; Shin Foong Ngiow; Yuan He; Hua Huang; Sasikanth Manne; Zhendong Cao; Amy E Baxter; Zhangying Cai; Elizabeth Freilich; Mohammed A Ali; Josephine R Giles; Jennifer E Wu; Allison R Greenplate; Mohamed A Hakeem; Qingzhou Chen; Makoto Kurachi; Kito Nzingha; Viktoriya Ekshyyan; Divij Mathew; Zhuoyu Wen; Nancy A Speck; Alexis Battle; Shelley L Berger; E John Wherry; Junwei Shi

doi:10.1016/j.cell.2021.02.019

In vivo CD8⁺ T cell CRISPR screening reveals control by Fli1 in infection and cancer

Cell. 2021 Mar 4;184(5):1262-1280.e22. doi: 10.1016/j.cell.2021.02.019. Epub 2021 Feb 25.

Authors

Zeyu Chen¹, Eri Arai², Omar Khan³, Zhen Zhang⁴, Shin Foong Ngiow⁵, Yuan He⁶, Hua Huang⁷, Sasikanth Manne³, Zhendong Cao², Amy E Baxter³, Zhangying Cai³, Elizabeth Freilich⁸, Mohammed A Ali³, Josephine R Giles³, Jennifer E Wu³, Allison R Greenplate³, Mohamed A Hakeem³, Qingzhou Chen², Makoto Kurachi³, Kito Nzingha³, Viktoriya Ekshyyan³, Divij Mathew³, Zhuoyu Wen⁸, Nancy A Speck⁹, Alexis Battle¹⁰, Shelley L Berger⁴, E John Wherry¹¹, Junwei Shi¹²

Affiliations

¹ Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA.
² Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
³ Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁴ Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁵ Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA.
⁶ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
⁷ Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁸ Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁹ Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
¹⁰ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
¹¹ Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA. Electronic address: wherry@pennmedicine.upenn.edu.
¹² Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Electronic address: jushi@upenn.edu.

Abstract

Improving effector activity of antigen-specific T cells is a major goal in cancer immunotherapy. Despite the identification of several effector T cell (T_EFF)-driving transcription factors (TFs), the transcriptional coordination of T_EFF biology remains poorly understood. We developed an in vivo T cell CRISPR screening platform and identified a key mechanism restraining T_EFF biology through the ETS family TF, Fli1. Genetic deletion of Fli1 enhanced T_EFF responses without compromising memory or exhaustion precursors. Fli1 restrained T_EFF lineage differentiation by binding to cis-regulatory elements of effector-associated genes. Loss of Fli1 increased chromatin accessibility at ETS:RUNX motifs, allowing more efficient Runx3-driven T_EFF biology. CD8⁺ T cells lacking Fli1 provided substantially better protection against multiple infections and tumors. These data indicate that Fli1 safeguards the developing CD8⁺ T cell transcriptional landscape from excessive ETS:RUNX-driven T_EFF cell differentiation. Moreover, genetic deletion of Fli1 improves T_EFF differentiation and protective immunity in infections and cancer.

Keywords: CD8; CRISPR; Fli1; cancer; chronic infection; effector CD8 T cell; exhausted CD8 T cell; exhaustion; immunotherapy; protective immunity.

Publication types

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

MeSH terms

Animals
CD8-Positive T-Lymphocytes / cytology*
CD8-Positive T-Lymphocytes / immunology
CD8-Positive T-Lymphocytes / metabolism
CRISPR-Cas Systems
Cell Differentiation
Chronic Disease
Core Binding Factor Alpha 3 Subunit / metabolism
Epigenesis, Genetic
Gene Regulatory Networks
Infections / immunology
Mice
Neoplasms / immunology
Proto-Oncogene Protein c-fli-1 / metabolism*

Substances

Core Binding Factor Alpha 3 Subunit
Fli1 protein, mouse
Proto-Oncogene Protein c-fli-1
Runx3 protein, mouse

Abstract

Publication types

MeSH terms

Substances

Grants and funding