DNA methylation for cancer diagnosis
Apart from genetic mutations, the instability of cancer cells is also defined by epigenetic alterations involving, among others, aberrant methylation of gene promoters. This occurs at specific sites known as CpG islands and compromises the physiological gene expression pattern, thereby contributing further to malignancy. To define and delineate the role of the epigenetic profile in colon cancer and leukaemia, the EU-funded project 'The use of methylated DNA immunoprecipitation MeDIP in cancer for better clinical management' (CANCERDIP) brought together leading European researchers in the field. The ultimate objective was to generate insight into the mechanisms of epigenetic regulation, focusing on DNA methylation. To this end, partners used state-of-the-art techniques to identify differentially methylated regions in cancer samples that could potentially serve as biomarkers or therapeutic targets. For such high-throughput analysis, the consortium developed the MethylCap method of capturing methylated DNA using a methyl-binding domain (MBD) followed by genomic sequencing. Bioinformatics analysis of the sequencing data verified the potential of this information to discriminate cancer from normal tissue. It also identified genes such as CSPG2/VCAN that are hypermethylated in colon cancer on a regular basis. By comparing the gene expression and DNA methylation profiles of leukaemia samples before treatment and after relapse, scientists were able to pinpoint candidate genes with a prognostic value. Regarding the mechanisms that regulate DNA methylation, scientists focused on the impact of polycomb genes and their association with DNA methyltransferases. Phosphorylation of these enzymes was discovered as a previously unrecognised mechanism for the regulation of methylation. Central to CANCERDIP project work was the development of tools for large-scale analysis of the DNA methylation pattern. With the use of magnetic beads for immunoprecipitation, the MeDIP kit accelerated the analysis of DNA methylation while at the same time improving its sensitivity. Furthermore, through the development of specialised software, the CANCERDIP consortium provided invaluable tools for validating DNA methylation biomarkers based on large-scale methylation data. Taken together, the accomplishments of the participants in the CANCERDIP project offered novel basic knowledge on cancer epigenetics. The identified biomarkers and genes have high prognostic significance and may be exploited for clinical stratification of cancer patients.
