ABSTRACT
UHRF1 facilitates the establishment and maintenance of DNA methylation patterns in mammalian cells. The establishment domains are defined, including E3 ligase function, but the maintenance domains are poorly characterized. Here, we demonstrate that UHRF1 histone- and hemimethylated DNA binding functions, but not E3 ligase activity, maintain cancer-specific DNA methylation in human colorectal cancer (CRC) cells. Disrupting either chromatin reader activity reverses DNA hypermethylation, reactivates epigenetically silenced tumor suppressor genes (TSGs), and reduces CRC oncogenic properties. Moreover, an inverse correlation between high UHRF1 and low TSG expression tracks with CRC progression and reduced patient survival. Defining critical UHRF1 domain functions and its relationship with CRC prognosis suggests directions for, and value of, targeting this protein to develop therapeutic DNA demethylating agents.
Subject(s)
CCAAT-Enhancer-Binding Proteins/metabolism , Colorectal Neoplasms/enzymology , DNA Methylation , Epigenesis, Genetic , Ubiquitin-Protein Ligases/metabolism , Animals , CCAAT-Enhancer-Binding Proteins/genetics , Caco-2 Cells , Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , CpG Islands , Female , Gene Expression Regulation, Neoplastic , HCT116 Cells , HT29 Cells , Histones/genetics , Histones/metabolism , Humans , Male , Mice, Inbred BALB C , Mice, Inbred C57BL , Mice, Inbred NOD , Mice, Nude , Mice, SCID , Mutation , Neoplasm Metastasis , PHD Zinc Fingers , Prognosis , Time Factors , Ubiquitin-Protein Ligases/geneticsABSTRACT
We addressed the precursor role of aging-like spontaneous promoter DNA hypermethylation in initiating tumorigenesis. Using mouse colon-derived organoids, we show that promoter hypermethylation spontaneously arises in cells mimicking the human aging-like phenotype. The silenced genes activate the Wnt pathway, causing a stem-like state and differentiation defects. These changes render aged organoids profoundly more sensitive than young ones to transformation by BrafV600E, producing the typical human proximal BRAFV600E-driven colon adenocarcinomas characterized by extensive, abnormal gene-promoter CpG-island methylation, or the methylator phenotype (CIMP). Conversely, CRISPR-mediated simultaneous inactivation of a panel of the silenced genes markedly sensitizes to BrafV600E-induced transformation. Our studies tightly link aging-like epigenetic abnormalities to intestinal cell fate changes and predisposition to oncogene-driven colon tumorigenesis.
Subject(s)
Adenocarcinoma/genetics , Aging/genetics , Cell Transformation, Neoplastic/genetics , Colonic Neoplasms/genetics , DNA Methylation , Gene Silencing , Mutation , Proto-Oncogene Proteins B-raf/genetics , Stem Cells/enzymology , Wnt Signaling Pathway/genetics , Adenocarcinoma/enzymology , Adenocarcinoma/pathology , Age Factors , Aging/metabolism , Aging/pathology , Animals , Cell Transformation, Neoplastic/metabolism , Cell Transformation, Neoplastic/pathology , Colonic Neoplasms/enzymology , Colonic Neoplasms/pathology , Gene Expression Regulation, Neoplastic , Genetic Predisposition to Disease , Humans , Mice, Inbred NOD , Mice, Mutant Strains , Mice, SCID , Phenotype , Proto-Oncogene Proteins B-raf/metabolism , Stem Cells/pathology , Time Factors , Tissue Culture TechniquesABSTRACT
Overall shared DNA methylation patterns between senescence (Sen) and cancers have led to the model that tumor-promoting epigenetic patterns arise through senescence. We show that transformation-associated methylation changes arise stochastically and independently of programmatic changes during senescence. Promoter hypermethylation events in transformation involve primarily pro-survival and developmental genes, similarly modified in primary tumors. Senescence-associated hypermethylation mainly involves metabolic regulators and appears early in proliferating "near-senescent" cells, which can be immortalized but are refractory to transformation. Importantly, a subset of transformation-associated hypermethylated developmental genes exhibits highest methylation gains at all age-associated cancer risk states across tissue types. These epigenetic changes favoring cell self-renewal and survival, arising during tissue aging, are fundamentally important for stratifying cancer risk and concepts for cancer prevention.
Subject(s)
Cell Transformation, Neoplastic/genetics , CpG Islands/genetics , DNA Methylation/genetics , Epigenesis, Genetic/genetics , Animals , Cellular Senescence/genetics , Humans , Mice , Mice, SCID , Neoplasms/genetics , Promoter Regions, Genetic/genetics , RiskABSTRACT
An oncogenic role for CHD4, a NuRD component, is defined for initiating and supporting tumor suppressor gene (TSG) silencing in human colorectal cancer. CHD4 recruits repressive chromatin proteins to sites of DNA damage repair, including DNA methyltransferases where it imposes de novo DNA methylation. At TSGs, CHD4 retention helps maintain DNA hypermethylation-associated transcriptional silencing. CHD4 is recruited by the excision repair protein OGG1 for oxidative damage to interact with the damage-induced base 8-hydroxydeoxyguanosine (8-OHdG), while ZMYND8 recruits it to double-strand breaks. CHD4 knockdown activates silenced TSGs, revealing their role for blunting colorectal cancer cell proliferation, invasion, and metastases. High CHD4 and 8-OHdG levels plus low expression of TSGs strongly correlates with early disease recurrence and decreased overall survival.
Subject(s)
Autoantigens/genetics , Colorectal Neoplasms/genetics , DNA Methylation , Epigenetic Repression , Gene Expression Regulation, Neoplastic , Gene Silencing , Genes, Tumor Suppressor , Mi-2 Nucleosome Remodeling and Deacetylase Complex/genetics , 8-Hydroxy-2'-Deoxyguanosine , Animals , Autoantigens/metabolism , Cell Movement , Cell Proliferation , Clustered Regularly Interspaced Short Palindromic Repeats , Colorectal Neoplasms/enzymology , Colorectal Neoplasms/pathology , Colorectal Neoplasms/surgery , DNA (Cytosine-5-)-Methyltransferases/genetics , DNA (Cytosine-5-)-Methyltransferases/metabolism , DNA Damage , DNA Glycosylases/genetics , DNA Glycosylases/metabolism , Deoxyguanosine/analogs & derivatives , Deoxyguanosine/metabolism , Disease-Free Survival , Down-Regulation , Enhancer of Zeste Homolog 2 Protein/genetics , Enhancer of Zeste Homolog 2 Protein/metabolism , HCT116 Cells , Histocompatibility Antigens/genetics , Histocompatibility Antigens/metabolism , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Humans , Kaplan-Meier Estimate , Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism , Mice, Inbred BALB C , Mice, Nude , Neoplasm Metastasis , Oxidative Stress , Proportional Hazards Models , RNA Interference , Receptors for Activated C Kinase , Receptors, Cell Surface/genetics , Receptors, Cell Surface/metabolism , Time Factors , Transcription, Genetic , Transfection , Tumor Suppressor ProteinsABSTRACT
The gene hypermethylated in cancer-1 (HIC1) encodes a zinc-finger transcription factor that belongs to a group of proteins known as the POZ family. HIC1 is hypermethylated and transcriptionally silent in several types of human cancer. Homozygous disruption of Hic1 impairs development and results in embryonic and perinatal lethality in mice. Here we show that mice disrupted in the germ line for only one allele of Hic1 develop many different spontaneous malignant tumors, including a predominance of epithelial cancers in males and lymphomas and sarcomas in females. The complete loss of Hic1 function in the heterozygous mice seems to involve dense methylation of the promoter of the remaining wild-type allele. We conclude that HIC1 is a candidate tumor-suppressor gene for which loss of function in both mouse and human cancers is associated only with epigenetic modifications.
