The Epigenetics Revolution

Jean-Pierre Issa has described the genes that are epigenetically silenced in colon cancer as the gatekeepers. They are frequently genes whose normal role is to move the cells away from self-renewal, and into fully differentiated cell types. Inactivation of these genes in cancer locks the cells in a self-renewing stem cell-like state. This creates a population of cells that are able to keep dividing, keep accumulating further epigenetic changes and mutations, and keep inching towards a full-blown cancer state[200].

When we visualise the cells in Waddington’s landscape, it’s quite difficult to visualise the ones that linger somewhere near the top. That’s because instinctively we know that that’s a really unstable place to be. A ball that has started rolling down a slope is always likely to keep going, unless something can hold it back. And even if such a ball does come to a halt, there’s always the chance it will start moving again, rolling on down that hill.

What holds cells in this teetering position? In 2006, a group headed by Eric Lander at the Broad Institute in Boston, found at least part of the answer. A key set of genes in ES cells, the pluripotent cells we have come to know so well, were found to have a really strange histone modification pattern. These were genes that were very important for controlling if an ES cell stayed pluripotent, or differentiated. Histone H3K4 was methylated at these genes, which normally is associated with switching on gene expression. H3K27 was also methylated. This is normally associated with switching off gene expression. So, which modification would turn out to be stronger? Would the genes be switched on or off?

The answer turned out to be both. Or neither, depending on which way we look at it. These genes were in a state called ‘poised’. Given the slightest encouragement – a change in culture conditions that pushed cells towards differentiation for example – one or other of these methylations was lost. The gene was fully switched on, or strongly repressed, depending on the epigenetic modification[201].

This is really important in cancer. Stephen Baylin is the third person, along with Peter Jones and Jean-Pierre Issa, who has done so much to make epigenetic therapies a reality. He has shown that these poised histone modifications are found in early cancer stem cells and are really significant for setting the DNA methylation patterns in cancer cells[202].

Of course, other events must also be taking place. Many people do not develop cancer, no matter what age they live to. Something must happen in the people who do develop cancer, which results in the normal stem cell pattern getting subverted and hardened so that the cells are locked into their aggressively and abnormally proliferative state. We know that environment can have a substantial impact on cancer risk (just think of the hugely increased risk of lung cancer in smokers) but we’re not clear on how or if the environment intersects with these epigenetic processes.

There may also be an aspect of pure bad luck in who develops cancer. We probably all have random fluctuations in the levels, activity or localisation of proteins that target, write, interpret and erase our epigenetic codes. And there are the non-coding RNAs too.

The 3′ UTRs of both DNMT3A and DNMT3B mRNA contain binding sites for a family of miRNAs called miR-29. Normally, these miRNAs will bind to the DNMT3A and DNMT3B mRNA molecules and down-regulate them. In lung cancer, the levels of these miRNAs drop and as a consequence DNMT3A and DNMT3B mRNA and subsequently protein expression is elevated. This is likely to increase the amount of de novo methylation of susceptible tumour suppressor promoters[203].

It is likely that there will also be feedback loops between miRNAs and the epigenetic enzymes they control, if one component of the pathway becomes mis-regulated. This will reinforce abnormal control mechanisms in the cell, leading to yet another vicious cycle, and is shown in Figure 11.4. In this example, a miRNA regulates a specific epigenetic enzyme, which itself modifies the promoter of the miRNA. In this case, the epigenetic enzyme creates a repressive modification.

^{Figure 11.4 A positive feedback loop which constantly drives down expression of a miRNA which would normally control expression of an epigenetic enzyme that creates a repressed chromatin state.}