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

Giuliana P. Mognol; Roberto Spreafico; Victor Wong; James P. Scott-Browne; Susan Togher; Alexander Hoffmann; Patrick G. Hogan; Anjana Rao; Sara Trifari

doi:10.1073/pnas.1620498114

New Research In

Contributed by Anjana Rao, December 15, 2016 (sent for review November 28, 2016; reviewed by Jay Shendure and Warren Leonard)

Significance

Cancer cells can be recognized and attacked by CD8⁺ cytolytic T cells, but tumor-infiltrating T cells often become functionally incompetent (“exhausted”) and fail to destroy tumor cells. We show that T-cell exhaustion requires antigen recognition by tumor-infiltrating T cells. By examining the transcriptional and chromatin accessibility profiles of antigen-reactive and -unreactive tumor-infiltrating cells, we confirm our previous conclusion that the transcription factor NFAT promotes CD8⁺ T-cell exhaustion and we identify Nr4a transcription factors as new targets for future investigation. We show that anti–PD-L1 treatment, a clinically relevant checkpoint blockade therapy that counteracts T-cell exhaustion, has modest but functionally important effects on gene expression in exhausted cells, without causing major changes in patterns of chromatin accessibility.

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.

Footnotes

↵¹G.P.M., R.S., and V.W. contributed equally to this work.
↵²Present address: Department of Pediatric Hematology-Oncology, Rady Children's Hospital, San Diego, CA 92123.
↵³To whom correspondence should be addressed. Email: arao{at}lji.org.
↵⁴Present address: Sorrento Therapeutics, San Diego, CA 92121.

Author contributions: G.P.M., J.P.S.-B., A.H., P.G.H., A.R., and S. Trifari designed research; G.P.M., V.W., S. Togher, and S. Trifari performed research; G.P.M., R.S., V.W., J.P.S.-B., A.H., P.G.H., and S. Trifari analyzed data; R.S. provided computational and statistical analysis of next-generation sequencing data; and G.P.M., R.S., V.W., A.R., and S. Trifari wrote the paper.
Reviewers: J.S., University of Washington; and W.L., NIH.
The authors declare no conflict of interest.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession nos. GSE93014 and GSE88987).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1620498114/-/DCSupplemental.

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