Zinc Regulators Drive a Dysfunction-Specific Gene Module

Chronic inflammation causes CD8+ T cells to become dysfunctional, or exhausted, and thus lose their effector function, express high levels of inhibitory receptors, and undergo transcriptional changes. To identify the molecular programs that drive the activation and dysfunction of CD8+ tumor-infiltrating lymphocytes (TIL), Singer, Wang, and colleagues generated bulk RNA profiles of activated, partially dysfunctional, and fully dysfunctional CD8+ TILs identified by their differential expression of inhibitory receptors. Cross–TIL subpopulation evaluation of the gene signature associated with fully dysfunctional CD8+ TILs revealed that metallothionein 1 (MT1), a zinc chaperone that regulates zinc metabolism, was the most differentially expressed gene across the TIL subpopulations. Depletion of metallothioneins in vivo restored CD8+ T-cell effector function and delayed tumor growth in a CD8+ T cell–dependent manner. Further, CD8+ T cells depleted of metallothioneins exhibited no change or a slight increase in expression of inhibitory receptors, suggesting uncoupling of dysfunctional phenotype and inhibitory receptor expression. Analysis of expression profiles generated from bulk activated, partially dysfunctional, and fully dysfunctional CD8+ TILs from tumor-bearing wild-type versus CD8+ TILs that do not exhibit dysfunction from MT knockout mice identified distinct transcriptional programs for CD8+T cell activation and dysfunction. Consistent with these findings, single-cell RNA sequencing of CD8+ TILs showed that the transcriptional programs of dysfunctional and activated CD8+ T-cell populations were uncoupled at the single-cell level. GATA binding protein 3 (GATA3)was the most overexpressed transcription factor in the dysfunctional CD8+ T-cell gene signature; CRISPR/Cas9-mediated targeting of GATA3 in naïve CD8+T cells increased T-cell effector function, caused no change in the expression of inhibitory receptors on CD8+ T cells, and delayed tumor growth in vivo. This comprehensive molecular characterization of activated and dysfunctional T cells may provide insights into the development of therapies targeting dysfunctional T cells.

Singer M, Wang C, Cong L, Marjanovic ND, Kowalczyk MS, Zhang H, et al. A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells. Cell 2016;166:1500–11.

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