Hypomethylation and Hypermethylation in Cancer: Impact on Genes

Chemical modifications to DNA, such as methylation, regulate gene expression. In cancer, these modifications become dysregulated, leading to hypomethylation or hypermethylation, both of which contribute to tumor development.

Understanding these changes is essential for uncovering cancer mechanisms and identifying therapeutic targets.

Mechanisms Of Abnormal Methylation

DNA methylation involves adding a methyl group to cytosine residues within CpG dinucleotides and is regulated by DNA methyltransferases (DNMTs), including DNMT1, DNMT3A, and DNMT3B. DNMT1 preserves methylation during replication, while DNMT3A and DNMT3B establish new methylation marks. In cancer, disruptions in these enzymes lead to either excessive methylation at specific loci or a global loss of methylation.

Genome-wide hypomethylation, often due to reduced DNMT activity or mutations, erodes methylation marks that suppress repetitive elements and transposable sequences. Hypomethylation of LINE-1 and Alu elements contributes to chromosomal instability, increasing structural aberrations such as deletions, amplifications, and translocations. Additionally, loss of methylation in normally silenced regions can activate oncogenes, fueling tumor progression.

Conversely, hypermethylation silences tumor suppressor genes, often mediated by an overactive DNMT3B enzyme, which is upregulated in colorectal, lung, and breast cancers. Promoter hypermethylation in CpG islands represses genes involved in cell cycle regulation, DNA repair, and apoptosis, removing critical barriers to tumor development.

Methylation dysregulation also involves TET enzymes, which facilitate DNA demethylation. Mutations in TET2, frequently observed in hematologic malignancies, impair methylation removal, leading to gene silencing. Similarly, mutations in IDH1 and IDH2, common in gliomas and acute myeloid leukemia, produce 2-hydroxyglutarate, an oncometabolite that inhibits TET activity, causing widespread DNA hypermethylation and reinforcing tumor suppressor gene silencing.

Influence On Genes That Promote Cell Proliferation

Disruptions in methylation significantly impact genes that drive cell division. Hypomethylation of oncogenes leads to their overexpression, tipping the balance toward uncontrolled proliferation. In normal cells, methylation regulates oncogenes like MYC, RAS, and CCND1, preventing excessive growth. When this control is lost, these genes become hyperactive, accelerating tumor expansion.

MYC, a transcription factor regulating the cell cycle, is frequently upregulated in cancers due to promoter hypomethylation. In colorectal and breast cancers, loss of methylation in MYC regulatory regions enhances its activity, increasing cyclin synthesis and accelerating the G1-to-S phase transition. This shortens the time available for DNA repair, increasing genomic errors. Similarly, RAS family genes, involved in growth factor signaling, are often activated through hypomethylation, sustaining mitogenic signaling even without external growth stimuli.

Global hypomethylation also affects enhancer regions regulating multiple proliferation-associated genes. Super-enhancers, clusters of highly active regulatory elements, become aberrantly activated, driving rapid cell division. In glioblastoma, hypomethylation of super-enhancers controlling CDK6 leads to excessive cyclin-dependent kinase activity, bypassing cell cycle checkpoints and promoting unchecked growth.

Hypermethylation of genes involved in negative feedback loops exacerbates oncogene-driven proliferation. Tumor suppressors such as CDKN2A, which encodes the p16 protein, normally counterbalance excessive growth signals. In pancreatic and lung adenocarcinomas, CDKN2A undergoes promoter hypermethylation, silencing its expression and disrupting regulatory brakes on the cell cycle.

Effects On Genes That Inhibit Tumor Growth

Methylation changes frequently silence tumor suppressor genes, which regulate apoptosis, DNA repair, and cell cycle arrest. Unlike genetic mutations that permanently disable these genes, methylation-based silencing is reversible, making it a promising therapeutic target.

One of the most well-documented examples is TP53, the “guardian of the genome.” While many cancers harbor TP53 mutations, others silence its expression through promoter hypermethylation, preventing p53 transcription. Without functional p53, cells with genomic abnormalities continue dividing unchecked, accumulating mutations that fuel tumor progression. In breast and lung cancers, TP53 hypermethylation correlates with worse prognoses, as tumors lacking p53-mediated surveillance resist conventional therapies.

RB1, which encodes the retinoblastoma protein (pRB), also undergoes hypermethylation in cancers such as osteosarcoma and small cell lung cancer. Normally, pRB restricts cell cycle progression by inhibiting E2F transcription factors, keeping cells in G1 until appropriate growth signals are received. Loss of RB1 expression removes this checkpoint, allowing uncontrolled proliferation.

Hypermethylation also silences DNA repair genes, compounding genomic instability. BRCA1, essential for homologous recombination-mediated DNA repair, is often silenced via promoter methylation in sporadic breast and ovarian cancers. This alteration mimics BRCA1 germline mutations, impairing DNA repair and increasing sensitivity to DNA-damaging agents like platinum-based chemotherapy and PARP inhibitors.

Changes In Chromatin Structure

DNA methylation influences chromatin organization, dictating gene accessibility for transcription. DNA is packed around histone proteins to form nucleosomes, and methylation changes disrupt this structure, affecting gene expression.

Hypermethylation of promoter regions promotes heterochromatin formation, a tightly packed configuration that restricts transcription factor binding. Methyl-CpG-binding proteins like MeCP2 and MBD1 recruit histone-modifying enzymes, reinforcing repression. In breast and colon cancers, hypermethylated tumor suppressor promoters associate with histone deacetylases (HDACs), which remove acetyl groups from histones, compacting chromatin and silencing genes. Loss of active histone marks, such as H3K4 trimethylation, further reinforces this repressive state.

Global DNA hypomethylation, on the other hand, leads to chromatin relaxation, exposing regulatory elements that are typically inactive. This destabilizes genomic integrity by allowing transcription of normally silent regions, including repetitive sequences and endogenous retroviral elements. In hepatocellular carcinoma, genome-wide hypomethylation correlates with increased chromatin accessibility at loci promoting uncontrolled cell growth. The altered landscape shifts histone modifications toward activating marks like H3K9 acetylation, enhancing pro-proliferative gene expression.

Genomic Instability And Mutations

Aberrant DNA methylation contributes to genomic instability, a hallmark of cancer. Hypomethylation weakens chromosomal integrity, increasing susceptibility to breaks, translocations, and aneuploidy. Normally, methylation silences transposable elements like LINE-1 and Alu sequences, preventing their insertion into new genomic locations. When hypomethylation occurs, these elements become active, leading to random insertions that disrupt coding sequences or regulatory regions. In gastrointestinal and hematologic malignancies, hypomethylation-induced mobilization of these elements has been linked to chromosomal rearrangements driving oncogenesis.

Hypermethylation of DNA repair genes exacerbates mutation accumulation. MLH1, central to mismatch repair, is frequently silenced in colorectal cancer through promoter methylation, leading to microsatellite instability—a condition characterized by repetitive DNA sequence alterations. Similarly, MGMT, which encodes a DNA repair enzyme that removes alkylation damage, is often hypermethylated in glioblastomas. Loss of MGMT expression increases sensitivity to alkylating agents like temozolomide but also promotes mutation accumulation that drives tumor progression.

Interplay With Other Epigenetic Marks

DNA methylation interacts with other epigenetic modifications, such as histone modifications and non-coding RNAs, to regulate gene expression. Disruptions in these interactions amplify oncogenic signaling or reinforce tumor suppressor gene silencing.

Histone modifications dictate chromatin accessibility. DNA hypermethylation is often accompanied by histone deacetylation, further compacting chromatin and preventing transcription factor binding. HDACs recruited to hypermethylated promoters reinforce gene silencing, particularly in tumor suppressors like CDKN2A and RASSF1A. Conversely, global hypomethylation is associated with increased histone acetylation, leading to chromatin relaxation and oncogene activation.

Non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), also regulate DNA methylation. Some miRNAs target DNMTs, altering methylation patterns. For example, miR-29 inhibits DNMT3A and DNMT3B, leading to oncogene hypomethylation in chronic lymphocytic leukemia. Conversely, hypermethylation of miRNA promoters silences tumor-suppressive miRNAs, allowing oncogenes to evade regulation. Understanding these interactions highlights the potential for combination therapies targeting multiple layers of epigenetic control to restore normal gene expression.