The Epigenetics Revolution

Experimental data suggest that in many cases this model seems to be right. Repressive histone modifications can act as the bait to attract DNA methylation to the promoter of a tumour suppressor gene. A key example of this is an epigenetic enzyme we met in the previous chapter, called EZH2. The EZH2 protein adds methyl groups to the lysine amino acid at position 27 on histone H3. This amino acid is known as H3K27. K is the single letter code for lysine (L is the code for a different amino acid called leucine).

This H3K27 methylation itself tends to switch off gene expression. However, in at least some mammalian cell types, this histone methylation recruits DNA methyltransferases to the same region of chromatin[192][193]. The DNA methyltransferases include DNMT3A and DNMT3B. This is important because DNMT3A and DNMT3B can carry out the process known as de novo DNA methylation. That is, they can methylate virgin DNA, and create completely new regions of highly repressed chromatin. As a result, the cell can convert a relatively unstable repressive mark (H3K27 methylation) into the more stable DNA methylation.

Other enzymes are also important. An enzyme called LSD1 takes methyl groups off histones – it’s an eraser of epigenetic modifications[194]. It does this particularly strongly at position 4 on histone H3 (H3K4). H3K4 is the opposite of H3K27, because when H3K4 is clear of methyl groups, genes tend to be switched off.

Unmethylated H3K4 can bind proteins, and one of these is called DNMT3L. Perhaps not surprisingly, this is related to DNMT3A and DNMT3B. DNMT3L doesn’t methylate DNA itself, but it attracts DNMT3A and DNMT3B to the unmethylated H3K4. This provides another way to target stable DNA methylation to virgin territory[195].

In all likelihood, many histones positioned at the promoters of tumour suppressor genes carry both of these repressive histone marks – methylation of H3K27 and non-methylation of H3K4 – and these act together to target the DNA methyltransferases even more strongly.

Both EZH2 and LSD1 are up-regulated in certain cancer types, and their expression correlates with the aggressiveness of the cancer and with poor patient survival[196][197]. Basically, the more active these enzymes, the worse the prognosis for the patient.

So, histone modifications and DNA methylation pathways interact. This may explain, at least in part, one of the mysteries of existing epigenetic therapies. Why are compounds like 5-azacytidine and SAHA only controllers of cancer cells, rather than complete destroyers?

In our model, treatment with 5-azacytidine will drive down the DNA methylation for as long as the patients take the drug. Unfortunately, many cancer drugs have serious side-effects and the DNMT inhibitors are no exception. The side effects may eventually become such a problem that the patient has to stop taking the drug. However, the patient’s cancer cells probably still have histone modifications at the tumour suppressor genes. Once the patient stops taking 5-azacytidine, these histone modifications almost certainly start to attract the DNMT enzymes all over again, re-initiating stable repression of gene expression.

Some researchers are carrying out clinical trials using 5-azacytidine and SAHA together to try to interfere with this cycle, by disrupting both the DNA and histone components of epigenetic silencing. It’s not clear yet if these will be successful. If they aren’t, it might suggest that it’s not low levels of histone acetylation which are most important for re-establishing the DNA methylation. It might be that specific histone modifications, of the types just described, are more important. But we don’t yet have drugs to inhibit any of the other epigenetic enzymes, so we’re stuck with Hobson’s choice at the moment, that is, no choice at all.

In the future, we may not need to use DNMT inhibitors at all. The link between DNA methylation and histone modifications in cancer isn’t absolute. If a CpG island is methylated, the downstream gene is repressed. But there are tumour suppressor genes that are downstream of unmethylated CpG islands and tumour suppressor genes that don’t have a CpG island at all. These genes may still be repressed, but solely thanks to histone modifications[198]. This has been shown by Jean-Pierre Issa at the MD Anderson Cancer Center in Houston, who has been so instrumental in the implementation of epigenetic therapies in the clinic. In these instances, if we can find the right epigenetic enzymes to target with inhibitors, we may be able to drive re-expression of the tumour suppressors without needing to worry about DNA methylation.

An uneasy truce