A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

• Published in: Cell Vol. 166; no. 6; pp. 1500 - 1511.e9
• Main Authors: Singer, Meromit, Wang, Chao, Cong, Le, Marjanovic, Nemanja D., Kowalczyk, Monika S., Zhang, Huiyuan, Nyman, Jackson, Sakuishi, Kaori, Kurtulus, Sema, Gennert, David, Xia, Junrong, Kwon, John Y.H., Nevin, James, Herbst, Rebecca H., Yanai, Itai, Rozenblatt-Rosen, Orit, Kuchroo, Vijay K., Regev, Aviv, Anderson, Ana C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 08.09.2016
• Subjects: Animals; cancer; Carcinogenesis - genetics; Carcinogenesis - immunology; CD8; CD8-Positive T-Lymphocytes - immunology; CD8-Positive T-Lymphocytes - pathology; CRISPR-Cas Systems; CRISPR/Cas9; dysfunction; exhaustion; Female; Gata-3; GATA3 Transcription Factor - metabolism; Gene Expression Profiling; Gene Expression Regulation, Neoplastic - genetics; Humans; Lymphocyte Activation - genetics; Lymphocyte Activation - immunology; Lymphocytes, Tumor-Infiltrating - immunology; Lymphocytes, Tumor-Infiltrating - pathology; Melanoma - immunology; Melanoma - physiopathology; Metallothionein - deficiency; metallothioneins; Mice; Mice, Inbred BALB C; Mice, Inbred C57BL; single-cell; T cell; TILs; tumor; zinc; CRISPR/Cas9; CD8; T cell; tumor; exhaustion; single-cell; Gata-3; cancer; metallothioneins; TILs; zinc; dysfunction
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2016.08.052

Reversing the dysfunctional T cell state that arises in cancer and chronic viral infections is the focus of therapeutic interventions; however, current therapies are effective in only some patients and some tumor types. To gain a deeper molecular understanding of the dysfunctional T cell state, we analyzed population and single-cell RNA profiles of CD8+ tumor-infiltrating lymphocytes (TILs) and used genetic perturbations to identify a distinct gene module for T cell dysfunction that can be uncoupled from T cell activation. This distinct dysfunction module is downstream of intracellular metallothioneins that regulate zinc metabolism and can be identified at single-cell resolution. We further identify Gata-3, a zinc-finger transcription factor in the dysfunctional module, as a regulator of dysfunction, and we use CRISPR-Cas9 genome editing to show that it drives a dysfunctional phenotype in CD8+ TILs. Our results open novel avenues for targeting dysfunctional T cell states while leaving activation programs intact. [Display omitted] •Distinct gene modules for T cell dysfunction and activation can be uncoupled•Single-cell profiling of CD8 TILs shows that these modules are exclusive•Metallothioneins, zinc regulators, promote T cell dysfunction•CRISPR-Cas9 targeting shows Gata-3, a zinc-finger TF, promotes dysfunction Single-cell profiling of tumor-infiltrating lymphocytes identifies critical regulators of T cell dysfunction in cancer, opening new avenues for targeting dysfunctional T cell states while leaving activation programs intact.