Exhaustion-associated regulatory regions in CD8 + tumor-infiltrating T cells

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2776-E2785. doi: 10.1073/pnas.1620498114. Epub 2017 Mar 10.

Abstract

T-cell exhaustion is a progressive loss of effector function and memory potential due to persistent antigen exposure, which occurs in chronic viral infections and cancer. Here we investigate the relation between gene expression and chromatin accessibility in CD8+ tumor-infiltrating lymphocytes (TILs) that recognize a model tumor antigen and have features of both activation and functional exhaustion. By filtering out accessible regions observed in bystander, nonexhausted TILs and in acutely restimulated CD8+ T cells, we define a pattern of chromatin accessibility specific for T-cell exhaustion, characterized by enrichment for consensus binding motifs for Nr4a and NFAT transcription factors. Anti-PD-L1 treatment of tumor-bearing mice results in cessation of tumor growth and partial rescue of cytokine production by the dysfunctional TILs, with only limited changes in gene expression and chromatin accessibility. Our studies provide a valuable resource for the molecular understanding of T-cell exhaustion in cancer and other inflammatory settings.

Keywords: ATAC-seq; T-cell exhaustion; anti–PD-L1; checkpoint blockade therapy; chromatin accessibility.

Publication types

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

MeSH terms

  • Animals
  • Antigens, Neoplasm / genetics
  • Antigens, Neoplasm / immunology
  • CD8-Positive T-Lymphocytes / immunology*
  • Chromatin / immunology
  • Humans
  • Lymphocytes, Tumor-Infiltrating / immunology*
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Neoplasms / genetics
  • Neoplasms / immunology*
  • Nuclear Receptor Subfamily 4, Group A, Member 1 / genetics
  • Nuclear Receptor Subfamily 4, Group A, Member 1 / immunology
  • Regulatory Sequences, Nucleic Acid

Substances

  • Antigens, Neoplasm
  • Chromatin
  • Nr4a1 protein, mouse
  • Nuclear Receptor Subfamily 4, Group A, Member 1