Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapy [ATAC-seq]

Epigenetic reinforcement of T cell exhaustion is a major barrier limiting durability of T cell responses during immunotherapy, however the central epigenetic regulators restricting therapy-enabling T cell stemness in settings of prolonged antigen exposure remain to be fully resolved. Here we investigated DNMT3A, TET2, and ASXL1, the three most commonly mutated epigenetic regulators promoting clonal hematopoiesis (CH), to determine if they control the cardinal features of T cell stemness. Using a canonical murine model of exhaustion, we show that CD8 T cells lacking Dnmt3a, Tet2, or Asxl1 are able to preserve an immune checkpoint blockade (ICB) responsive progenitor-exhausted (Tpex) population for over a year during chronic antigen exposure without undergoing malignant transformation. Specific investigation into the lesser-studied regulator, Asxl1, revealed that this unprecedented maintenance of Tpex was achieved through preservation of the cell's self-renewal capacity with less terminal differentiation. Mechanistic investigation into the role of Asxl1 during CD8 T cell differentiation revealed epigenetic modification of the PR-DUB pathway involving H2AK119-ubiquitination. Extending this Tpex-preserving mechanism to immunotherapy, we report synergy between Asxl1 deficient T cells and anti-PDL1, resulting in heightened tumor control in murine tumor models and a survival advantage to the mutated T cells in treated patients. These data collectively define a core set of epigenetic regulators that control longevity of the stem-like T cell population responsible for clinical success during cancer immunotherapy. Overall design: 2 replicates of Rosa KO samples, 2 replicates of Asxl1 KO samples, 2 replicates of Rosa KO Ly108 subset, 2 replicates of Rosa KO Tim3 subset, 4 replicates of Asxl1 KO Ly108 subset, 4 replicates of Asxl1 KO Tim3 subset