We are grateful to K. Murphy for the Batf3−/− mice, T. Hansen for providing MHC class I antibodies and the H-2Kb construct, D. Fremont for the human β2m construct, and the National Institutes of Health (NIH) Tetramer Core Facility for producing MHC class I tetramers. We also thank R. Ahmed and M. Hashimoto for the multiplex staining strategy used to define functional and dysfunctional T cells. We thank A. Bensimon, O. Schubert and P. Kouvonen for instrument maintenance and for technical support with the mass spectrometry measurements and R. Vanganipuram, M. Selby and J. Valle for generating and supplying anti-PD-1 and anti-CTLA-4 in endotoxin-free sterile form. We also thank K. Sheehan, P. Allen, G. Dunn and R. Chan for constructive criticisms and comments, all members of the Schreiber laboratory for discussions, and the many members of The Genome Institute at Washington University School of Medicine. We would also like to thank W. Song for his assistance with the bioinformatics approaches, P. Kvistborg for assistance with tetramer combinatorial coding, and Christopher Nelson for advice with peptide-MHC monomer purification. This work was supported by grants to R.D.S. from the National Cancer Institute (RO1 CA043059, U01 CA141541), the Cancer Research Institute and the WWW.W Foundation; to R.D.S. and W.E.G. from The Siteman Cancer Center/Barnes-Jewish Hospital (Cancer Frontier Fund); to W.E.G. from Susan G. Komen for the Cure (Promise grant); to E.R.M. from the National Human Genome Research Institute; to G.J.F. from the National Institute of Health (P50 CA101942, P01 AI054456, P50 CA101942); to A.H.S. from the National Institute of Health (P50 CA101942); and to T.N.S. from the Dutch Cancer Society (Queen Wilhelmina Research Award). E.C. is supported by a Marie Curie Intra-European Fellowship within the Seventh Framework Programme of the European Community for Research. M.M.G. was supported by a postdoctoral training grant (T32 CA00954729) from the National Cancer Institute and is currently supported by a postdoctoral training grant (Irvington Postdoctoral Fellowship) from the Cancer Research Institute. Aspects of studies at Washington University were performed with assistance by the Immunomonitoring Laboratory of the Center for Human Immunology and Immunotherapy Programs and the Siteman Comprehensive Cancer Center.