DNA hypomethylation restrains early antitumor immunity in prostate cancer [RNAseq]

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 characterize genomewide DNA methylation features of single metastatic prostate cancer cells, we processed blood specimens from five patients using microfluidic-based enrichment of CTCs, followed by individual cell micromanipulation of 44 CTCs for sequencing analysis. For comparison, 40 single cells were analyzed from four prostate cancer cell lines (LNCaP, VCaP, PC3 and 22Rv1) and from two non-transformed prostate cell lines (HPrEC and BPH-1), together with 13 microfluidic-processed single leukocytes from four age-matched healthy men. To confirm the identity of single CTCs isolated from blood specimens, we adapted single-cell multiomics sequencing to enable separation of nucleus from cytoplasm in individual cells, subjecting the former to single-cell whole genome bisulfite sequencing (scBS-seq) and the latter to single-cell RNA-seq (SMART-seq2). On average, we detected 9 million CpG sites for each single-cell DNA methylation sequencing sample, and 5,790 genes (RPM>0) for each single-cell RNA-seq library.