ABSTRACT
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.
Subject(s)
DNA Methylation , Prostatic Neoplasms , Animals , Humans , Male , Mice , Carcinogenesis/genetics , DNA , Epigenesis, Genetic , Prostatic Neoplasms/genetics , Neoplastic Cells, CirculatingABSTRACT
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.
Subject(s)
Breast Neoplasms/metabolism , Cell Proliferation , Immediate-Early Proteins/metabolism , Mitosis , Neoplastic Cells, Circulating/metabolism , Nuclear Receptor Subfamily 4, Group A, Member 1/metabolism , 3' Untranslated Regions , Animals , Antineoplastic Agents/pharmacology , Binding Sites , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Proliferation/drug effects , Chromatin Assembly and Disassembly , Female , Gene Expression Regulation, Neoplastic , Genomic Instability , HEK293 Cells , Humans , Immediate-Early Proteins/genetics , Indoles/pharmacology , MCF-7 Cells , Mice, Inbred NOD , Mice, SCID , Mitosis/drug effects , Neoplastic Cells, Circulating/drug effects , Neoplastic Cells, Circulating/pathology , Nuclear Receptor Subfamily 4, Group A, Member 1/antagonists & inhibitors , Nuclear Receptor Subfamily 4, Group A, Member 1/genetics , Phenylacetates/pharmacology , Proto-Oncogene Proteins c-fos/genetics , Proto-Oncogene Proteins c-fos/metabolism , R-Loop Structures , RNA Polymerase II/genetics , RNA Polymerase II/metabolism , Signal Transduction , Transcription Elongation, Genetic , Tumor Cells, Cultured , Xenograft Model Antitumor AssaysABSTRACT
Immune checkpoint blockade (ICB) has demonstrated efficacy in patients with melanoma, but many exhibit poor responses. Using single cell RNA sequencing of melanoma patient-derived circulating tumor cells (CTCs) and functional characterization using mouse melanoma models, we show that the KEAP1/NRF2 pathway modulates sensitivity to ICB, independently of tumorigenesis. The NRF2 negative regulator, KEAP1, shows intrinsic variation in expression, leading to tumor heterogeneity and subclonal resistance.