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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. [ABSTRACT FROM AUTHOR]

Deregulation of oncogenic signals in cancer triggers replication stress. Immediate early genes (IEGs) are rapidly and transiently expressed following stressful signals, contributing to an integrated response. Here, we find that the orphan nuclear receptor NR4A1 localizes across the gene body and 3′ UTR of IEGs, where it inhibits transcriptional elongation by RNA Pol II, generating R-loops and accessible chromatin domains. Acute replication stress causes immediate dissociation of NR4A1 and a burst of transcriptionally poised IEG expression. Ectopic expression of NR4A1 enhances tumorigenesis by breast cancer cells, while its deletion leads to massive chromosomal instability and proliferative failure, driven by deregulated expression of its IEG target, FOS. Approximately half of breast and other primary cancers exhibit accessible chromatin domains at IEG gene bodies, consistent with this stress-regulatory pathway. Cancers that have retained this mechanism in adapting to oncogenic replication stress may be dependent on NR4A1 for their proliferation. [Display omitted] • NR4A1 specifically localizes to IEG gene bodies suppressing transcriptional elongation • Acute replication stress triggers NR4A1 release, triggering burst of IEG expression • NR4A1 deletion deregulates expression of the IEG FOS , triggering mitotic catastrophe • The NR4A1-IEG pathway denotes differentiated cancers with a favorable prognosis Studying tumorigenesis by patient-derived breast cancer cells, Guo et al. identify NR4A1 as a master regulator of replication stress-induced immediate early gene expression through a transcriptional processing checkpoint. Suppression of NR4A1 in cancer cells dependent on this pathway triggers mitotic catastrophe through unregulated expression of the IEG family member FOS. [ABSTRACT FROM AUTHOR]