DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs

Cancer is characterized by hypomethylation-associated silencing of large chromatin domains, whose contribution to tumorigenesis is uncertain. Through high-resolution genome-wide single-cell DNA methylation sequencing, we identify 40 core domains that are uniformly hypomethylated from the earliest detectable stages of prostate malignancy through metastatic circulating tumor cells (CTCs). Nested among these repressive domains are smaller loci with preserved methylation that escape silencing and are enriched for cell proliferation genes. Transcriptionally silenced genes within the core hypomethylated domains are enriched for immune-related genes; prominent among these is a single 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. The re-expression of CD1 or IFI16 murine orthologs in immuno-competent mice abrogates tumorigenesis, accompanied by the activation of anti-tumor immunity. Thus, early epigenetic changes may shape tumorigenesis, targeting co-located genes within defined chromosomal loci. Hypomethylation domains are detectable in blood specimens enriched for CTCs. [Display omitted] •40 core hypomethylated domains, shared across prostate CTCs, arise early in tumorigenesis•Hypomethylation silences immune-related genes, sparing adjacent proliferation genes•The CD1A-IFI16 immune locus is consistently silenced by hypomethylation in cancer•Hypomethylated domains are detected in CTC-enriched blood in localized prostate cancer Analysis of primary prostate cancer and circulating tumor cells reveals how DNA hypomethylation during early prostate tumorigenesis silences immune surveillance genes while sparing proliferation-associated genes.