H3K9me3 regulates IFNγlo Tex cell differentiation to promote colon tumor liver metastasis

Despite the breakthrough in immune checkpoint inhibitor (ICI) immunotherapy in human cancer, colon cancer, except for the small subset of microsatellite instable human colon cancer, does not respond to ICI immunotherapy. As liver metastasis accounts for over 90% of human colon cancer cases and mortality, ICI efficacy is primarily a measurement of liver metastasis suppression. Using a colon tumor liver metastasis syngeneic mouse model, we determined that mouse colon tumor liver metastases not only does not respond to anti-PD-1 immunotherapy but also exhibits no susceptibility to tumor-specific cytotoxic T lymphocyte (CTL) adoptive transfer immunotherapy. Analysis of human colon cancer liver metastases scRNA-seq datasets revealed that histone methyltransferases of histone 3 lysine 9 trimethylation (H3K9me3) are upregulated in colon tumor and expressed in subsets of T cells in liver metastases of human colon cancer patients. Targeted therapy with the H3K9me3-specific histone methyltransferase inhibitor F5446 suppresses colon tumor liver metastasis. scRNA-seq analysis revealed the accumulation of PD-1+Tim3+ Tex cells in mouse colon tumor liver metastases and F5446 treatment increased the level of IFNγhiPD-1lo Tex cells. Furthermore, F5446 therapy increased IFNγhi Tex-int cells in human colon cancer patient liver metastases-derived xenografts (PDX) and suppressed PDX growth in humanized mice. In human colon cancer patients, response to pembrolizumab is associated with tumor-infiltrating IFNγhi Tex cells. Our findings determine that H3K9me3 promotes differentiation of Tex cells and targeting H3K9me3 is an effective approach to increase IFNγhi Tex-int cells to reinvigorate CTL functionality to suppress colon cancer liver metastasis.