Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer

Peipei Zhou, Hao Shi, Hongling Huang, Xiang Sun, Sujing Yuan, Nicole M. Chapman, Jon P. Connelly, Seon Ah Lim, Jordy Saravia, Anil Kc, Shondra M. Pruett-Miller and Hongbo Chi ()
Additional contact information
Peipei Zhou: St. Jude Children’s Research Hospital
Hao Shi: St. Jude Children’s Research Hospital
Hongling Huang: St. Jude Children’s Research Hospital
Xiang Sun: St. Jude Children’s Research Hospital
Sujing Yuan: St. Jude Children’s Research Hospital
Nicole M. Chapman: St. Jude Children’s Research Hospital
Jon P. Connelly: St. Jude Children’s Research Hospital
Seon Ah Lim: St. Jude Children’s Research Hospital
Jordy Saravia: St. Jude Children’s Research Hospital
Anil Kc: St. Jude Children’s Research Hospital
Shondra M. Pruett-Miller: St. Jude Children’s Research Hospital
Hongbo Chi: St. Jude Children’s Research Hospital

Nature, 2023, vol. 624, issue 7990, 154-163

Abstract: Abstract CD8+ cytotoxic T cells (CTLs) orchestrate antitumour immunity and exhibit inherent heterogeneity1,2, with precursor exhausted T (Tpex) cells but not terminally exhausted T (Tex) cells capable of responding to existing immunotherapies3–7. The gene regulatory network that underlies CTL differentiation and whether Tex cell responses can be functionally reinvigorated are incompletely understood. Here we systematically mapped causal gene regulatory networks using single-cell CRISPR screens in vivo and discovered checkpoints for CTL differentiation. First, the exit from quiescence of Tpex cells initiated successive differentiation into intermediate Tex cells. This process is differentially regulated by IKAROS and ETS1, the deficiencies of which dampened and increased mTORC1-associated metabolic activities, respectively. IKAROS-deficient cells accumulated as a metabolically quiescent Tpex cell population with limited differentiation potential following immune checkpoint blockade (ICB). Conversely, targeting ETS1 improved antitumour immunity and ICB efficacy by boosting differentiation of Tpex to intermediate Tex cells and metabolic rewiring. Mechanistically, TCF-1 and BATF are the targets for IKAROS and ETS1, respectively. Second, the RBPJ–IRF1 axis promoted differentiation of intermediate Tex to terminal Tex cells. Accordingly, targeting RBPJ enhanced functional and epigenetic reprogramming of Tex cells towards the proliferative state and improved therapeutic effects and ICB efficacy. Collectively, our study reveals that promoting the exit from quiescence of Tpex cells and enriching the proliferative Tex cell state act as key modalities for antitumour effects and provides a systemic framework to integrate cell fate regulomes and reprogrammable functional determinants for cancer immunity.

Date: 2023
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DOI: 10.1038/s41586-023-06733-x

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