Is there something special about the tumour suppressor genes that get silenced using epigenetic modifications? There are two contrasting theories about this. The first is that there’s nothing special about these genes and the process is completely random. In this model, every once in a while a random tumour suppressor gets abnormally modified epigenetically. If this changes the expression of the gene, it may mean that cells with that epigenetic modification grow a bit faster or a bit better than their neighbours. This gives the cells a growth advantage and they keep outgrowing the cells around them, gradually accumulating more epigenetic and genetic changes that make them ever more cancerous.
The other theory is that the tumour suppressors that become repressed epigenetically are somehow targeted in this process. It’s not just random bad luck, these genes are actually at a higher than average risk of epigenetic silencing.
In recent years, as we’ve had the technology to profile the epigenetic modifications in more and more cell types, and at higher and higher resolutions, the field has shifted in favour of the second model. There are a set of genes that seem to be rather prone to getting themselves switched off epigenetically.
At first this seems incredibly counter-intuitive. Why on earth would billions of years of evolution leave us with cellular systems that render us prone to cancerous changes? Well, we have to put this in context. Most evolutionary pressures are connected with the drive to leave behind as many offspring as possible. For a human to reach reproductive age, it’s incredibly important that early development occur as efficiently as possible. After all, you can’t reproduce if you never make it past the embryo stage. Once we’ve reached reproductive age and had the opportunity to reproduce, there is little to be gained in evolutionary terms in us staying alive for several decades afterwards.
Evolution has favoured cellular mechanisms that promote effective early growth and development, including the production of multiple different tissue types. Many of these tissue types contain reservoirs of stem cells which are specific to that tissue. Our bodies need these for tissue growth as we mature, and for tissue regeneration following injury. The fates and identities of these tissue-specific stem cells are controlled by the precise patterns of epigenetic modifications. By using epigenetic modifications to control gene expression, the cells keep some flexibility. They have the potential to change into more specialised cells, for example. Perhaps even more importantly when considering cancer, the epigenetic modifications also allow cells to divide to form more stem cells. This is why we don’t run out of skin cells, or bone marrow cells, even if we live to be a hundred years old.
This requirement for gene expression patterns that aren’t completely set in stone is probably why epigenetic repression of tumour suppressor genes is not a random process. We can’t have things two ways. Regulatory systems that allow cells to be flexible are inevitably also systems that allow cells to go wrong. In evolutionary terms, it’s the price we have to pay for our Goldilocks scenario. Our epigenetic pathways make sure some of our cells aren’t completely pluripotent or completely differentiated. Instead, they are just right, hovering somewhere near the top of Waddington’s epigenetic landscape, but ready to roll down at any time.
Peter Laird, who like Peter Jones is based at the University of Southern California, has shown the knock-on effects of this system in cancer cells. His team analysed patterns of DNA methylation in cancer cells, especially focusing on the promoters of tumour suppressor genes. Tumour suppressor genes whose histones are methylated by the EZH2 complex in ES cells were twelve times as likely to have abnormally high levels of DNA methylation as those genes that aren’t targeted by EZH2. Peter Laird described this effect very elegantly, saying, ‘reversible gene repression is replaced by permanent silencing, locking the cell into a perpetual state of self-renewal and thereby predisposing to subsequent malignant transformation [sic].’[199] This is consistent with the idea that there is a stem cell aspect to cancer. If cells are locked into a stem cell-like state, where they can’t differentiate into cells at the bottom of the epigenetic landscape, they will be very dangerous because they will always be able to keep on dividing to form yet more cells like themselves.
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.