CANCERDIP

The use of Methylated DNA Immunoprecipitation MeDIP in cancer for better clinical management

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 Obiettivo del progetto (Objective)

'Aberrant DNA methylation is the most common molecular lesion of the cancer cell. Neither gene mutation nor cytogenetic abnormalities are as common in human tumours as DNA methylation alterations. The stability of our genome and correct gene expression is maintained to a great extent thanks to a perfectly preestablished pattern of DNA methylation and histone modifications. In cancer this idealistic scenario breaks down due to an interesting phenomenon whereby the regulatory regions (CpG islands) of certain tumour suppressor genes become hypermethylated, inactivating the gene as a consequence, whilst a wave of hypomethylation occurs in the genome. Indeed, CpG island promoter hypermethylation has a tumour-type-specific pattern, where each gene tends to be methylated in the cancer cells driven from a particular tissue, but not from others. It is also widely accepted that the multiprotein complex associated with the methylated DNA is also crucially involved in the repression of gene expression. Another aspect crucial for the interest of epigenetics in cancer is that promoter hypermethylation of the CpG island of tumours suppressor genes occurs early in tumorigenesis. Furthermore, it has been extensively reported that CpG promoter hypermethylation can be used as predictor of cancer behaviour and a predictor of response to treatment. This characteristic makes promoter hypermethylation combined with the epigenetic associated proteins profile, a potential biomarker for early detection of cancer and for the individualization of cancer treatment. We are going to use a novel technique based in chromatin immunoprecipitation, the Methylated DNA Immunoprecipitation (MeDIP) technique that will easily permit us to obtain an epigenomic profile which will be used to personalize cancer treatment and facilitate tumour diagnosis, prognosis and monitoring.'

Introduzione (Teaser)

The CANCERDIP initiative explored the use of the epigenetic profile of cancers as a predictor of cancer behaviour. Consortium members also developed molecular and bioinformatics tools that are expected to significantly aid the future analysis of DNA methylation.

Descrizione progetto (Article)

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.