Description

The Epigenetic Landscape of T Cell Exhaustion

Debattama R. Sen^1,2,*, James Kaminski^3,*, R. Anthony Barnitz¹, Makoto Kurachi⁴, Ulrike Gerdemann¹, Kathleen B. Yates¹, Hsiao-Wei Tsao¹, Jernej Godec^1,2, Martin W. LaFleur^1,2, Flavian D. Brown^1,2, Pierre Tonnerre⁵, Raymond T. Chung⁵, Damien C. Tully⁶, Todd M. Allen⁶, Nicole Frahm⁷, Georg M. Lauer⁵, E. John Wherry⁴, Nir Yosef^3,†, and W. Nicholas Haining^1,†

¹Dana-Farber Cancer Institute, Boston, MA; ²Harvard Medical School, Boston, MA; ³UC Berkeley, Berkeley, CA; ⁴University of Pennsylvania, Philadelphia, PA; ⁵Massachusetts General Hospital, Boston, MA; ⁶Ragon Institute of MGH, MIT, and Harvard, Boston, MA; ⁷Fred Hutchinson Cancer Research Center, Seattle, WA

*These authors contributed equally

^§These corresponding authors contributed equally

Exhausted T cells in cancer and chronic viral infection have distinctive patterns of gene expression, including sustained expression of the inhibitory receptor PD-1, but the regulation of gene expression in exhausted T cells is poorly understood. Here we define the accessible chromatin landscape in mouse and human exhausted CD8⁺ T cells and show that it is profoundly different from functional memory CD8⁺ T cells. Exhausted CD8⁺ T cells in a mouse model of chronic viral infection acquire an extensive, state-specific pattern of enhancers, which are organized into functional modules. One enhancer, -23.8kb from the Pdcd1 locus, is found only in exhausted T cells and other lymphocytes with sustained PD-1 expression. Genome editing shows it to be required for high PD-1 expression. Cas9-mediated in situ saturation mutagenesis of the enhancer pinpoints critical minimal sequences that correspond to bound transcription factor motifs for RAR, T-bet and Sox3 in exhausted CD8⁺ T cells. State-specific enhancer profiles identified in mouse exhausted CD8⁺ T cells are conserved in human exhausted antigen-specific CD8⁺ T cells responding to HIV and HCV infection. Detailed functional enhancer maps of T cell exhaustion reveal state-specific regulatory sequences and offer targets for genome editing that could alter gene expression preferentially in exhausted CD8⁺ T cells.