DNA Methylation Change Profiling of Colorectal Disease: Screening towards Clinical Use

Abstract

Colon cancer remains one of the leading causes of cancer-related deaths worldwide. Transformation of colon epithelial cells into invasive adenocarcinomas has been well known to be due to the accumulation of multiple genetic and epigenetic changes. In the past decade, the etiology of inflammatory bowel disease (IBD) which is characterized by chronic inflammation of the intestinal mucosa, was only partially explained by genetic studies providing susceptibility loci, but recently epigenetic studies have provided critical evidences affecting IBD pathogenesis. Over the past decade, A deep understanding of epigenetics along with technological advances have led to identifying numerous genes that are regulated by promoter DNA hypermethylation in colorectal diseases. Recent advances in our understanding of the role of DNA methylation in colorectal diseases could improve a multitude of powerful DNA methylation-based biomarkers, particularly for use as diagnosis, prognosis, and prediction for therapeutic approaches. This review focuses on the emerging potential for translational research of epigenetic alterations into clinical utility as molecular biomarkers. Moreover, this review discusses recent progress regarding the identification of unknown hypermethylated genes in colon cancers and IBD, as well as their possible role in clinical practice, which will have important clinical significance, particularly in the era of the personalized medicine.

Keywords: DNA methylation; biomarkers; colorectal cancer; epigenetic regulation; inflammatory bowel diseases (IBDs).

Figure 3

Identification of DNA hypermethylated genes in breast and colon cancers. (a) Heatmap cluster analysis of the 29 DNA hypermethylated genes shows three distinct gene groups (numbered blocks) identified by methylation frequency. A subset of genes was noted in our previous studies [32,35], and genes with blue letters were identified later [36]. (b) Multiple hypermethylated ECM genes in two primary colorectal cancers (CRC patients #1 and #2) (unpublished data).

Figure 1

Schematics of the main epigenetic mechanisms associated with gene transcriptional silencing. Histone modifications, DNA methylation, and non-coding RNA mediated gene silencing constitute three distinct mechanisms of epigenetic regulation. Abbreviations are following as TF (Transcription factor), H3K (Histon 3 Lysine), HMT (Histone methyltrasferase), HDM (Histone demethylase), and SAM (S-Adenosyl methionine).

Figure 2

Epigenetic mechanisms in cancers. (a) Transcriptional gene expression, particularly gene silencing, is mainly regulated by DNA methylation, histone modifications, and microRNAs. Representative enzymes that contribute to these modifications include DNA methyltransferases (DNMTs), the TET family, methyl-CpG-binding domains (MBDs), histone modifying enzymes (MLL1/2/3, SETD2, EZH2, LSD1, and UTX), histone methyltransferases (HMTs). The relationship among these processes establishes a heritable repressive state at the start site of genes resulting in transcriptional gene silencing (Adapted from You and Jones 2012). (b) Promoter DNA methylation patterns in normal and tumor cells. In normal cells, CpG dinucleotides are randomly methylated and not associated with CpG islands located in the promoter region. Thus, the unmethylated status of CpG islands in gene promoters permits active gene expression. In cancer cells, CpG islands in the gene promoter region become abnormally hypermethylated, causing transcriptional silencing of genes. Circles indicate CpG dinucleotides.

Figure 4

Schematic representation of extracellular matrix (ECM) pathway silencing by DNA hypermethylation in colon cancer. Six genes, namely, TIMP2, PLAU, TIMP3, Osteonectin, MMP9, and Nidogen, are regulated by promoter DNA hypermethylation in other cancer types and have been shown to be similarly altered in CRC in our previous study [36]. In addition, Yi et al. identified genes within the extracellular matrix, including 13 hypermethylated genes in CRC derived from our gene discovery approach (IGFBP3, HAPLN1, ICAM5, CD109, FLNC, GPNMB, NRCAM, EVL, NTNG1, MMP2, LAMA1, CPAMD8, and FBN2). Different colors indicate the locations of each gene. Yellow circles, green color and blue color indicate ECM, membrane, and cytoplasm, respectively. The functional gene ontology analysis was based on the MetaCore database (Adapted from Yi et al. 2011).