Interplay between the cancer genome and epigenome
Shen H, Laird PW. Interplay between the cancer genome and epigenome. Cell. 2013 Mar 28;153(1):38-55. doi: 10.1016/j.cell.2013.03.008. PMID: 23540689; PMCID: PMC3648790.
DNA methylation mechanism
While genetic mechanisms of oncogenesis are more easily seen and understood, epigenetic mechanisms can be powerful ones that can be transferred through cell divisions. Mutations in epigenetic regulators are important and lead to major changes in cancer cell epigenomes. Genetic mechanisms can inactivate tumor-suppressor genes or work with epigenetic mechanisms to make mutations and epigenetic dsyregulation more likely.
CpG cytosine-5 methylation
This is catalysed by DNMT3A and DNMT3B and maintained by DNAMT3B. Most of the mammalian genome is not methylated. The sparse methylated regions contain heavily methylated CpG dinucleotides and unmethylated CpG islands that are protected from DNA methylation by guanine-cytosine strand asymmetry and R loop formation. There may also be active demethylation by TET proteins. CpG islands are present on the start sites of half of human genes - genes that are actively expressed or about to be.
Methyl-CpG binding domains (MBD) or C2H2 zinc fingers recognize methylation DNA. MBDs and Kaiso (zinc finger) are involved in DNA methylation-mediated transcriptional repression of tumor suppressor genes with promoter DNA methylation.
Histone variants and modifications
Histone modifications are carried out by histone methyltransferases demethylases, acetyltransferases and deacetylases, and writers and erasers of phosphorylation and other modifications. They act in complexes like the Polycomb complex and counterbalance each other to regulate developmental genes, some of which are implicated in cancer. The Polycomb repressive complex 2 (PRC2) allows PRC1 to dock. PRC1 has a RING1B enzymatic core that monoubiquitinylates histone H2A at K119 and blocks RNA polymerase II elongation. The H3K4 methylation mark made by the Trithorax group complex counters Polycomb function. PRC2 targets embryonic stem cell transcription factors for differentiation and development regulators with the activating H3K4me3 and the repressive H3K27me3 marks. The Trithorax demethylase KDM6A can remove this repressive mark allowing for gene transcription for differentiation. Genes not needed for this process lose the activating mark and gain the repressive one.
Histone variants are found in different cell types and regions. Some like H2A.Z are found in regions requiring frequent changes and wide prevalence indicates prevalent chromatin exchange in embryonic stem cells.
Nucleosome positioning and remodelling
Nucleosome position can influence transcriptional activation and repression. There are chromatin remodelling complexes (SWI/SNF, chromodomain and helicase-like domain(CHD), ISWI and INO80) that can change nucleosome positions
Other epigenetic changes include:
- Hydroxylation
- Formylation
- Carboxylation
These changes are made by
initiators like lncRNAs,
writers establish marks, guided by sequence context, existing marks and bound proteins, ncRNAs, or nuclear architecture. Mutations to writers like DNMT3A are often found in cancers and
readers that interpret them,
erasers like TET that remove them,
remodelers that reposition nucleosomes and
Insulators
Insulators form boundaries between epigenetic domains and include the CCCTC-binding factor CTCF and CTCFL/BORIS. CTCF prevents enhancer interactions with unintended promoters. It also separates active and repressive chromatin domains.
Epigenetic state maintainance
The epigenome is copied between cell divisions by DNMT1 and H3K9 methyltransferase which are loaded into the replication fork and copy the marks. The Trithorax and Polycomb complexes are recruited during replication and distributed between the daughter cells to restore marks.
Epigenetic disruption in cancer
Studies have found contradictory changes in DNA methylation in cancer. Some find hypomethylation while others find hypermethylation of CpG islands. We know epigenetic changes can be causal in cancer since many tumor-supressor genes have been silenced by promoter CpG islands hypermethylation independent of mutational or structural inactivation of the gene. Further mouse models need epigenetic readers and writers for tumor development. Some methylation changes are essential for cancer cell survival.
Disruption of differentiation and development
Polycomb repressors mark differentiation and development regulator genes depending on that cells trajectory. These genes tend to be hypermethylated in their CpG islands during proliferation, ageing and malignant transformation. Cancer cells also show silencing of differentiation genes. This suggests a model where Polycomb target genes in stem cells acquire permanent silencing over time and lose their ability to differentiate, but are still able to proliferate. This would mean that it is an epigenetic modification rather than a genetic one that leads to malignant transformation.
CpG island methylator phenotypes
The CpG island methylator phenotype shows a high frequency of CpG island hypermethylation. There are distinct epigenetic subtypes for some cancers like CRC and glioblastoma, while others like ovarian cancer do not show such distinct subtypes.
Epigenetic influences on genomic integrity
Epigenetic mechanisms can affect the rates of lesion formation and repair. Methylated and unmethylated cytosine can both be deaminated. Unmethylated C forms uracil and 5mC forms thymine. Since uracil is not part of normal DNA is it more likely to be found and repaired than a change to thymine which leads to a 10-fold higher rate of C-to-T mutations in CpG dinucleotides that mostly contain MeC than other SNVs in the genome. The deamination of 5mC before replication leads to a normal T:A base that is not a repair candidate. About a quarter of TP53 mutations in cancer result from this epigenetic mark.
Regional effects of chromatic organization
Megabase regions of repressive chromatin (H3K9me3) are correlated with cancer SNVs. Genes resistant to cancer-associated hypermethylation tend to have retrotransposons near their transcription start sites compared to methylation-prone genes. Mouse models of DNMT deficiency tend to have chromosomal instability.
Epigenetic influences on DNA repair
Removal of DNA methyltransferases can lead to increased microsatellite instability (MSI), increased telomere lengths and telomeric recombination. The epigenetic silencing of DNA repair genes like MLH1 can lead to an increase in mutation rates and genomic instability in cancer cells.
Mutations of epigenetic regulator genes like writers and erasers can be mechanisms of oncogenesis. DNMT3A and TET2 mutations have been found in cancers.
Histone gene mutations can also be involved in cancer as they affect histone positioning and telomeres. Some like the K27M mutation mimic a Polycomb repressive mark. Histone methylation writer mutations like in MLL are found in leukemias. This may work by the inappropriate recruitment of epigenetic factors to MLL targets. Some writers like EZH2 have both gain-of-function and loss-of-function mutations in cancer. This may be part of a control system with different functions in different environments that are dysregulated when mutations occur in these genes.
Chromatin remodelling involves remodelling the structure and positioning of nucleosomes to enable access. Chromatin remodeler mutations are implicated in a number of different cancers. SWI/SNF complexes are remodelers with mutations in rhabdoid tumors.