The power and the promise of DNA methylation markers

Cytosine-5 DNA methylation occurs in mammals at CpG dinucleotides. About 70% of the CpG dinucleotides in the mammalian genome are methylated. The complexity of varying distributions of methylated cytosines across the approximately 50 million CpG dinucleotides of each mammalian genome in a DNA sample that is derived from a heterogenous tissue sample is a diagnostic dream and an analytical nightmare. A nomenclature for the three principal approaches to methylation analysis — methylation content, methylation levels and methylation patterns — is proposed. The latter two types of analysis can be performed at multiple sites in the genome to yield methylation profiles. In the past decade, DNA methylation analysis has been revolutionized by two technological advances — bisulphite modification of DNA and methylation-specific polymerase chain reaction (MSP). CpG islands are approximately 1-kb stretches of DNA-containing clusters of CpG dinucleotides that are usually unmethylated in normal cells and are often located near the 5′ ends of genes. Methylation of promoter CpG islands is associated with a closed chromatin structure and transcriptional silencing of the associated gene. Hypermethylation of CpG islands is a common event in carcinogenesis. The transcriptional silencing of tumour-suppressor genes by promoter CpG island hypermethylation can contribute to oncogenesis. DNA methylation profiles represent a more chemically and biologically stable source of molecular diagnostic information than RNA or most proteins. The diagnostic potential of DNA methylation profiles is still largely untapped. Cancer-specific DNA methylation patterns can be detected in tumour-derived free DNA in the bloodstream and in epithelial tumour cells shed into the lumen, offering a promising approach to the early detection of cancer. Clinical application will first require further validation and will ultimately be based on standardized MSP-based technologies, such as MethyLight, rather than on gel-based techniques. A distinction between the clinical and analytical sensitivities of DNA methylation biomarkers is proposed.