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

Cell. 2016 Sep 8;166(6):1500-1511.e9. doi: 10.1016/j.cell.2016.08.052.

Abstract

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.

Keywords: CD8; CRISPR/Cas9; Gata-3; T cell; TILs; cancer; dysfunction; exhaustion; metallothioneins; single-cell; tumor; zinc.

Publication types

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

MeSH terms

  • Animals
  • CD8-Positive T-Lymphocytes / immunology
  • CD8-Positive T-Lymphocytes / pathology*
  • CRISPR-Cas Systems
  • Carcinogenesis / genetics
  • Carcinogenesis / immunology
  • Female
  • 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
  • Mice
  • Mice, Inbred BALB C
  • Mice, Inbred C57BL

Substances

  • GATA3 Transcription Factor
  • Metallothionein