DNA hypomethylation restrains early antitumor immunity in prostate cancer [ChIP-seq and CUT&RUN]

Cancer is characterized by hypomethylation-associated silencing of large chromatin domains, whose contribution to tumorigenesis is uncertain. Through high-resolution single cell DNA methylation sequencing in prostate cancer, we identify 40 core hypomethylation domains, consistently hypomethylated across tumor cells and arising at early stages of malignancy. Transcriptionally silenced genes within these domains are enriched for immune-related genes; nested among repressive domains are small loci with preserved methylation, encoding cell proliferation genes that escape silencing. Prominent among hypomethylation-silenced genes is a gene cluster harboring all five CD1 genes that present lipid antigens to NKT cells, and four IFI16-related interferon-inducible genes implicated in innate immunity. Re-expression of CD1 or IFI16 murine orthologs in immunocompetent mice abrogates prostate tumorigenesis, accompanied by activation of anti-tumor immunity. Thus, early epigenetic changes in cancer may shape tumorigenesis, targeting co-located genes within defined chromosomal loci. Hypomethylation domains are detectable in blood specimens enriched for circulating tumor cells. To assess the repressive histine mark enrichment in prostate cancer, we performed H3K27me3 and H3K9me3 Cut and Run assay in mutiple prostate cancer cell lines and normal prostate epithelial cell lines. In addtion, we applied ultra-low-input native ChIP-seq procedure to the purified nuclei from microdissected normal prostate and from GS6 or GS8 prostate tumor specimens.