In vitro modeling of CD8+ T cell exhaustion enables CRISPR screening to reveal a role for BHLHE40

Jennifer E Wu; Sasikanth Manne; Shin Foong Ngiow; Amy E Baxter; Hua Huang; Elizabeth Freilich; Megan L Clark; Joanna H Lee; Zeyu Chen; Omar Khan; Ryan P Staupe; Yinghui J Huang; Junwei Shi; Josephine R Giles; E John Wherry

doi:10.1126/sciimmunol.ade3369

In vitro modeling of CD8⁺ T cell exhaustion enables CRISPR screening to reveal a role for BHLHE40

Sci Immunol. 2023 Aug 25;8(86):eade3369. doi: 10.1126/sciimmunol.ade3369. Epub 2023 Aug 18.

Authors

Jennifer E Wu^{1

2

3}, Sasikanth Manne^{1

2}, Shin Foong Ngiow^{1

2

3}, Amy E Baxter^{1

2}, Hua Huang^{1

2

4}, Elizabeth Freilich^{5

4}, Megan L Clark^{2

6}, Joanna H Lee^{1

2}, Zeyu Chen^{1

2}, Omar Khan^{1

2}, Ryan P Staupe^{1

2}, Yinghui J Huang^{1

2}, Junwei Shi^{2

5

4}, Josephine R Giles^{1

2

3}, E John Wherry^{1

2

3}

Affiliations

¹ Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
² Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
³ Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, USA.
⁴ Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁵ Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁶ Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

PMID: 37595022
DOI: 10.1126/sciimmunol.ade3369

Abstract

Identifying molecular mechanisms of exhausted CD8 T cells (T_ex) is a key goal of improving immunotherapy of cancer and other diseases. However, high-throughput interrogation of in vivo T_ex can be costly and inefficient. In vitro models of T_ex are easily customizable and quickly generate high cellular yield, enabling CRISPR screening and other high-throughput assays. We established an in vitro model of chronic stimulation and benchmarked key phenotypic, functional, transcriptional, and epigenetic features against bona fide in vivo T_ex. We leveraged this model of in vitro chronic stimulation in combination with CRISPR screening to identify transcriptional regulators of T cell exhaustion. This approach identified several transcription factors, including BHLHE40. In vitro and in vivo validation defined a role for BHLHE40 in regulating a key differentiation checkpoint between progenitor and intermediate T_ex subsets. By developing and benchmarking an in vitro model of T_ex, then applying high-throughput CRISPR screening, we demonstrate the utility of mechanistically annotated in vitro models of T_ex.

Publication types

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

MeSH terms

CD8-Positive T-Lymphocytes
Cell Differentiation
Clustered Regularly Interspaced Short Palindromic Repeats* / genetics
Epigenomics
T-Cell Exhaustion*

Abstract

Publication types

MeSH terms

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