Genomic insights into cancer-associated aberrant CpG island hypermethylation

Abstract

Carcinogenesis is thought to occur through a combination of mutational and epimutational events that disrupt key pathways regulating cellular growth and division. The DNA methylomes of cancer cells can exhibit two striking differences from normal cells; a global reduction of DNA methylation levels and the aberrant hypermethylation of some sequences, particularly CpG islands (CGIs). This aberrant hypermethylation is often invoked as a mechanism causing the transcriptional inactivation of tumour suppressor genes that directly drives the carcinogenic process. Here, we review our current understanding of this phenomenon, focusing on how global analysis of cancer methylomes indicates that most affected CGI genes are already silenced prior to aberrant hypermethylation during cancer development. We also discuss how genome-scale analyses of both normal and cancer cells have refined our understanding of the elusive mechanism(s) that may underpin aberrant CGI hypermethylation.

Keywords: CpG islands; DNA methylation; cancer; epigenetics; epigenomics.

Figure 1:

The methylation landscape of normal and cancerous cells. (A) The mammalian genome is depleted of CpGs and the majority of these are methylated (black lollipops). CGIs are rich in CpGs, frequently coincide with gene promoters and are generally unmethylated (white lollipops), irrespective of gene expression status. The bodies of active genes are enriched in hydroxymethylated CpGs (grey lollipops). (B) Both DNA methylation and hydroxymethylation are reduced in cancer genomes but some CGIs become aberrantly hypermethylated.

Figure 2:

Hypermethylation of driver and passenger genes in carcinogenesis. (A) Aberrant hypermethylation of CGIs is thought to cause the silencing of tumour suppressor genes and drive carcinogenesis. (B) The analysis of cancer methylomes demonstrates the majority of hypermethylated genes are repressed in preneoplastic cells. Hypermethylation of these, passenger, genes might be a surrogate of general epigenetic dysfunction that occasionally results in hypermethylation and repression of active driver genes. White lollipops - unmethylated CpGs, black lollipops - methylated CpGs.

Figure 3:

Models as to the consequences of widespread CGI hypermethylation in cancer. (A) Hypermethylation as a block to differentiation. This model predicts that key genes required for normal cellular differentiation become hypermethylated in cancer. The result is a block to their activation and thus normal differentiation processes within the cancer producing a more aggressive, stem-cell like phenotype. (B) Hypermethylation as a block to progression. Widespread hypermethylation of repressed CGI promoters might prevent their stochastic activation in individual cancer cells. If the activation of such genes facilitated survival in changing conditions, such as during metastasis to distant organs or treatment, widespread hypermethylation might restrict the potential for epigenetic adaptation and thus result in block to progression.

Figure 4:

Potential mechanisms of cancer-associated aberrant hypermethylation. CGIs bound are occupied by multiple factors that potentially play roles in aberrant CGI hypermethylation. (A) Nucleosomes incorporating the histone variant H2A.Z and with H3K4me3 marks, TFs, active transcription and TET enzymes may all help maintain the hypomethylated state of active CGIs in normal cells. TET enzyme function is most likely compromised in at least some cancers but this still leaves other protective factors at active CGIs. (B) Similarly, a number of factors are found at inactive CGIs that could potentially play a role in maintaining their normal hypomethylated state including TET enzymes, PRCs and stalled RNA polymerase. PRCs are thought to be lost, most likely along with stalled RNA polymerase, when CGIs become aberrantly hypermethylated, but it is unclear if this plays a mechanistic role in this cancer-associated epigenetic reprogramming. The role of DNMT recruitment in the process is also unclear. White lollipops - unmethylated CpGs, black lollipops - methylated CpGs.