Debattama R. Sen1,2,*, James Kaminski3,*, R. Anthony Barnitz1, Makoto Kurachi4, Ulrike Gerdemann1, Kathleen B. Yates1, Hsiao-Wei Tsao1, Jernej Godec1,2, Martin W. LaFleur1,2, Flavian D. Brown1,2, Pierre Tonnerre5, Raymond T. Chung5, Damien C. Tully6, Todd M. Allen6, Nicole Frahm7, Georg M. Lauer5, E. John Wherry4, Nir Yosef3,†, and W. Nicholas Haining1,†
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.