Epigenetics of colorectal cancer: biomarker and therapeutic potential

Abstract

Colorectal cancer (CRC), a leading cause of cancer-related death worldwide, evolves as a result of the stepwise accumulation of a series of genetic and epigenetic alterations in the normal colonic epithelium, leading to the development of colorectal adenomas and invasive adenocarcinomas. Although genetic alterations have a major role in a subset of CRCs, the pathophysiological contribution of epigenetic aberrations in this malignancy has attracted considerable attention. Data from the past couple of decades has unequivocally illustrated that epigenetic marks are important molecular hallmarks of cancer, as they occur very early in disease pathogenesis, involve virtually all key cancer-associated pathways and, most importantly, can be exploited as clinically relevant disease biomarkers for diagnosis, prognostication and prediction of treatment response. In this Review, we summarize the current knowledge on the best-studied epigenetic modifications in CRC, including DNA methylation and histone modifications, as well as the role of non-coding RNAs as epigenetic regulators. We focus on the emerging potential for the bench-to-bedside translation of some of these epigenetic alterations into clinical practice and discuss the burgeoning evidence supporting the potential of emerging epigenetic therapies in CRC as we usher in the era of precision medicine.

Figure 1 |. Principles of epigenetics.

The main epigenetic modifications implicated in colorectal cancer (CRC) — including DNA methylation (1), histone modifications (2), long noncoding RNAs (lncRNAs) (3) and microRNAs (miRNAs; also known as miRs) (4) — are shown. Hypermethylation of CpG islands in promoter regions of tumour-suppressor genes placed by DNA-methyl transferases (DNMTs) inhibits gene expression and can favor tumorigenesis^, (1). If hypomethylation occurs in retrotransposable elements (such as LINE-1 elements), these are activated and insert themselves in distant fragile sites, leading to genomic instability. Hypomethylation of promoters or distant super-enhancers can enhance expression of proto-oncogenes. Acetyl-groups are placed by histone acetyl-transferases (HATs) and removed by histone deacetylases (HDACs); acetylation generally weakens the compaction status of the chromatin and makes the DNA accessible to transcription factors (2). Histone methylation is regulated by histone methyltransferases (HMTs) and histone demethylases (HDMs); methyl groups on histone tails create docking sites for proteins that can repress or increase gene expression (2). lncRNAs influence gene and protein expression through different molecular mechanisms (3). They can enhance transcription by recruiting transcription factors or repress transcription by decoying transcription factors and preventing their recruitment to transcriptional start sites. LncRNAs can also restore translation by ‘sponging’ miRNAs that would otherwise prevent translation of their corresponding mRNA. LncRNAs can also directly inhibit translation. The biogenesis of miRNAs starts with the transcription of the miRNA gene by RNA polymerase II (RNA Pol II) (4). The double-stranded, hairpin-formed pri-miRNA is processed to the pre-miRNA by Drosha/DGCR8 and then translocated to the cytoplasm by exportin-5. The RNAse III enzyme DICER cuts the hairpin loop, resulting in a double-stranded miRNA-miRNA molecule. The RNA-induced silencing complex (RISC) incorporates one of the strands and mediates its interaction with the target mRNA, leading either to translational inhibition or mRNA degradation.

Figure 2 |. Role of miRNAs and lncRNAs in CRC.

The roles of selected long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in regulating virtually all important signalling pathways relevant to colorectal cancer (CRC) are shown. Activation of the RAS-RAF-MEK pathway, which leads to enhanced proliferation and can modulate treatment responses, can occur via downregulation of miR-143 and/or upregulation of miR-31 (1). miR-21, the most frequently overexpressed miRNA in CRC, can favour cancer progression by targeting PTEN, preventing PIP3 dephosphorylation and resulting in hyperactivation of the PI3K-AKT pathway (2). In addition, miR-21 can target PDCD4, which is thought to be an important mediator in apoptosis effector pathways. (3) In the presence of DNA damage, p53 holds the cell cycle at the G1-S checkpoint to allow DNA repair or to induce apoptosis if repair is not possible. In a positive feedback loop, p53 increases the expression of miR-34a (which is frequently downregulated in CRC), resulting in enhanced p53 activity (4). Moreover, miR-34a directly targets SMAD4, a key effector in TGFβ signalling. Thus, downregulation of miR-34a enhances TGFβ signalling and results in enhanced epithelial-mesenchymal transition (EMT) and tumour cell invasion^, (5). Loss of E-cadherin in epithelial cells leads to a loss of contact inhibition, which favours cell growth, migration and invasion via β-catenin-TCF signalling (6). In CRC cells, miR-29a and the lncRNA HOTAIR have been described to decrease the expression of E-cadherin. miR-135 directly targets and downregulates APC, which, under normal conditions, degrades β-catenin, resulting in downstream activation of the WNT-β-catenin pathway (7). When tumours grow rapidly, hypoxia stimulates the formation of new blood vessels through angiogenesis, which is crucial for tumour survival and is regulated by the VEGF pathway. VEGF is a direct target of miR-126 and is also repressed by the lncRNA GAS5, and both are frequently downregulated in CRC^, (8).

Figure 3 |. Epigenetic biomarkers in CRC.

Given their emerging roles in colorectal cancer (CRC), epigenetic marks or regulators can be exploited as clinically relevant disease biomarkers for diagnosis, prognostication and prediction of treatment response. Blood-based biomarkers (serum or plasma) might have diagnostic, prognostic or predictive value in CRC. Tissue-based biomarkers in endoscopically resected lesions might also be used clinically to improve prediction of the risk of invasion of early lesions (carcinoma in situ or pT1) and guide treatment options and surveillance strategies. Stool-based biomarkers (from abraded carcinoma cells) have a number of potential diagnostic applications; for example, Cologuard (NDRG4 methylation, BMP3 methylation and KRAS mutation) for screening of adenomas and early-stage CRC. Endoscopic biopsies of normal rectal mucosa (which is less invasive than endoscopic resection) could be used to identify patients at a high risk of metachronous or synchronous lesions owing to ‘field defect’ in normal rectal mucosa; for example, methylation of miR-137 in endoscopic biopsy tissue is an independent risk factor for ulcerative colitis-associated CRC. Finally, tissue-based biomarkers in surgical specimens (primary metastatic or tumours) might also have prognostic or predictive roles.