Analysis of Promoter CpG Island Hypermethylation in Cancer: Location, Location, Location!

Abstract

The genetic and epigenetic alterations that underlie cancer pathogenesis are rapidly being identified. This provides novel insights in tumor biology as well as in potential cancer biomarkers. The somatic mutations in cancer genes that have been implemented in clinical practice are well defined and very specific. For epigenetic alterations, and more specifically aberrant methylation of promoter CpG islands, evidence is emerging that these markers could be used for the early detection of cancer as well as prediction of prognosis and response to therapy. However, the exact location of biologically and clinically relevant hypermethylation has not been identified for the majority of methylation markers. The most widely used approaches to analyze DNA methylation are based on primer-and probe-based assays that provide information for a limited number of CpG dinucleotides and thus for only part of the information available in a given CpG island. Validation of the current data and implementation of hypermethylation markers in clinical practice require a more comprehensive and critical evaluation of DNA methylation and limitations of the techniques currently used in methylation marker research. Here, we discuss the emerging evidence on the importance of the location of CpG dinucleotide hypermethylation in relation to gene expression and associations with clinicopathologic characteristics in cancer. Clin Cancer Res; 17(13); 4225-31. Ó2011 AACR.

Formalin-fixed, paraffin-embedded (FFPE) tissue epigenomics using Infinium HumanMethylation450 BeadChip assays

“…CpG methylation can be analysed after nucleic acid isolation from various cellular and cell-free sources. 7 Several techniques to analyse CpG methylation have been developed, encompassing locus-specific methods that interrogate single to few genes as well as genome-wide and whole genome methods capturing the epigenomic landscape in a high-throughput manner. For biomarker discovery studies, mostly genome-wide methods are applied as these enable comparisons of large parts of the DNA-methylome between different sample groups.…”

DNA methylation in germ cell tumour aetiology: current understanding and outstanding questions

“…Recent analyses of the spatial distribution of differentially methylated CpG sites have brought into question the relevance of previously reported methylation studies (Portela & Esteller 2010, van Vlodrop et al 2011. Unbiased global methylation analyses using immunocapturing techniques demonstrated that aberrantly methylated regions in colon cancer cells were not restricted to CpG islands (Weber et al 2005).…”

“…It is worth noting that C-DMRs displaying hypermethylation in cancer tend to associate with regions close to CpG islands (54% are situated within 500 bp of a CpG island) whereas those showing hypomethylation rarely associate closely with CpG R52 M Cusack and P Scotting islands (Irizarry et al 2009). Evidence that epigenetic silencing can occur over long distances (Frigola et al 2006, Tiwari et al 2008 and that gene silencing can depend on the methylation of specific sites within CpG islands (Zinn et al 2007, Sohn et al 2010 indicates that analysis of only a few CpG sites in a gene promoter region is likely to be insufficient to accurately reflect the methylation status of that gene (van Vlodrop et al 2011).…”

“…In particular, genome-wide bisulphite sequencing (Lister et al 2009) DNA methylation in germ cell tumour aetiology (Bibikova et al 2011) can now be used to comprehensively describe entire methylomes. Such data will hopefully allow us to fully describe the association between methylation, gene expression and clinical features (Cheung et al 2009, Esteller 2011, van Vlodrop et al 2011.…”

“…Technological advances now allow the analysis of individual CpG sites comprehensively covering the entire genome (Esteller 2011, van Vlodrop et al 2011. We have performed a preliminary study using Infinium HumanMethylation450 BeadChips to assay methylation in CpG islands, shores, shelves and intergenic regions at a high resolution in teratoma, YST, seminoma and EC cell lines.…”