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

• Published in: Nature (London) 2023-12, Vol.624 (7990), p.154-163
• Main Authors: Zhou, Peipei, Shi, Hao, Huang, Hongling, Sun, Xiang, Yuan, Sujing, Chapman, Nicole M., Connelly, Jon P., Lim, Seon Ah, Saravia, Jordy, KC, Anil, Pruett-Miller, Shondra M., Chi, Hongbo
• Format: Article
• Language: English
• Subjects: 38/47; 45/61; 45/91; 631/250/1619/554/1834/1269; 631/250/580; 96; 96/31; Anticancer properties; Cancer; CD8 antigen; CD8-Positive T-Lymphocytes; Cell differentiation; Cell Differentiation - genetics; Cell fate; Cells; Clustered Regularly Interspaced Short Palindromic Repeats; CRISPR; Cytotoxicity; Differentiation; Effectiveness; Epigenetics; Ets-1 protein; Gene expression; Hepatocyte nuclear factor 1; Humanities and Social Sciences; Humans; Ikaros protein; Immune checkpoint inhibitors; Immunity; Libraries; Lymphocytes; Lymphocytes T; Metabolism; multidisciplinary; Neoplasms; Science; Science (multidisciplinary); T-Lymphocytes, Cytotoxic
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-023-06733-x

CD8 + cytotoxic T cells (CTLs) orchestrate antitumour immunity and exhibit inherent heterogeneity 1 , 2 , with precursor exhausted T (T pex ) cells but not terminally exhausted T (T ex ) cells capable of responding to existing immunotherapies 3 – 7 . The gene regulatory network that underlies CTL differentiation and whether T ex 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 T pex cells initiated successive differentiation into intermediate T ex 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 T pex cell population with limited differentiation potential following immune checkpoint blockade (ICB). Conversely, targeting ETS1 improved antitumour immunity and ICB efficacy by boosting differentiation of T pex to intermediate T ex 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 T ex to terminal T ex cells. Accordingly, targeting RBPJ enhanced functional and epigenetic reprogramming of T ex cells towards the proliferative state and improved therapeutic effects and ICB efficacy. Collectively, our study reveals that promoting the exit from quiescence of T pex cells and enriching the proliferative T ex 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. Analyses of causal gene regulatory networks have identified key checkpoints mediating the progressive differentiation of CD8 + cytotoxic T cells, findings that have implications for anticancer immunotherapies such as adoptive cell therapy and immune checkpoint blockade.