So, we need to consider how is it that these global epigenetic alterations occur in the context of cancer? So, at the moment, we really don't have all of the answers, but we have some of the answers, and we think we know a little bit about this. So, it seems clear that there must be just some stochastic epigenetic alterations that occur by chance. But because some of these are then mitotically heritable and selected for because they might silence a tumor suppressor or activate an uncle gene you may have this accumulation of these epigenetic this particular epigenetic modification. But this really doesn't go to explain what happens with the long range epigenetic silencing that we see and particular epigenetic mistakes that occur. So, there's been discussion, as I mentioned, right back at the start. One of the hallmarks of cancer, or one of the emerging hallmarks of cancer, appears to be an increase or an influence of cellular stress. So, it's also been proposed that cellular stress may somehow alter the epigenetic makeup of the cell. We don't know too much more about each of these. But what has become clear in recent years is that there are essentially alterations to every class of every genetic modifier that we've discussed over the previous five weeks. So all of those enzymes or proteins that are involved in either laying down the epigenetic marks, removing the epigenetic marks or reading the epigenetic marks have some level of genetic aberration in them. So that is that they are mutated or over expressed or amplified. So they can be translocated, for example. And translocations can either inactivate a gene or activate a gene or mean that it's retargeted because it has another protein partner. It can be overexpressed or amplified in some way. So you can have multiple copies of the gene, and therefore get more of that protein product produced. That can actually be subject to CpG island hypermethylation and therefore silenced, so the genes that are involved in epigenetic control are no different to the others. Or more recently what's been found is that they can carry point mutations. And this seems to be extremely common that we have point mutations in the epigenetic modifier enzymes and others in the context of cancer. So interestingly, all of these different genetic changes to the epigenetic machinery appear to be very common and occur across all types or a broad spectrum of tumor types. So just to show you this in a more diagrammatic fashion. If you think about two nucleosomes that I'm showing you here, it's the same sort of notation lab views throughout. We know that the TET proteins, these are involved in DNA demethylation via hydroxylation. So they're removing DNA methylation as shown here. These are mutated in cancer. Chromatin remodelers which are opening up the chromatin or closing it up again are mutated in cancer. DNA methyl transferases are mutated in cancer. Of the proteins the methyl binding the main proteins that bind to methylated DNA are mutated in cancer. Histone deascetylases, histone acetylases and chromatin readers that can read an acetyl marker, in this case I'm showing you a methyl mark, are mutated. Histone methyl transferases, histone demethylases. So every class of these epigenetic machinery so every one of these epigenetic regulators are mutated in cancer. So you can imagine if you have mutations in the epigenetic machinery, then this is going to lead to downstream consequences in terms of the consequent epigenetic mistakes that are made because of these mutations. So we know if we take an example just here of a few histone methyltransferases and a few histone demethylases. In each case we know that the disruption type that we see, as I've mentioned before, can be many and varied. So we can have translocations leading to loss of function, amplifications leading to gain of function, mutations leading to gain of function or loss of function. Indeed CpGL and hypermethylation or deletion. So you can have lots of different ways that you can gain or lose the function of epigenetic modifiers. Even for just this restricted small number of genes I've put on this table, you can see that you've affected a broad range of genotypes. So you've got breast and prostate cancer. Different types of leukemias or blood cell disorders such as acute myeloid leukemia, or mylodysplastic syndrome, or lymphoma. You've got liver cancer, prostate cancer, bladder cancer, lung cancer, colon cancer. We really span the gamut of every single type of tumor type that's ever been observed. So, in all cases where sequencing has been performed to try and find the mutations in different disorders, you can essentially in any particular type of cancer you can find mutations in the epigenetic machinery. What's quite interesting is that if you then look at mutations in one gene, so rather than yes we're saying there are mutations all over the place, if you look at the mutations in one gene, just EZH2. So EZH2 is the enzymatic component of PRC2 that we've spoken about a lot. And it lays down H3K27 methylation. Again, we've spoken this repressive mark a lot and that it goes wrong in cancer. If you look in different tumor types, they can have either gain of function or loss of function, and this comes about by different mechanisms. In solid tumors, such as breast and prostrate, what's been known for quite a while is that they amplify EZH2 an this way, they have a gain of function of EZH2, they have additional EZH2 capacity if you like. Where as in hemetphoetic malignancies, there's this contrast between these two different types. In lymphoma then, or in a particular type of B cell lymphoma, you find that you have mutations, but these activate EZH2. Whereas in in Myelodysplastic syndrome, a different type of blood cell disorder found in the myeloid cells you have loss of EZH2 function. So why has this come about is telling you that EZH2's not universally, non-congenial and not universally a gene suppressor. And, really this is probably true for most epigenetic modifiers. So, it means that the way you should think about it is that really the function of each individual epigenetic modifier will depend on the cell type that you're looking at. This is true in cancer and in normal cells. So, if you think about the cell of origin of the cancer. For example, where the EZH2 mutation took place. Well, if that cell had a particular set of EZH2 and PIC2 target genes, then it will be those that are relevant to the outcome. Those that are relevant to us saying whether or not EZH2 is a tumor suppressor or an oncogene. But, in each different cell type, epigenetic modifiers may have different target genes. And it will be these different target genes, which will help to dictate whether or not that particular epigenetic modifier is a tumor suppressor or an oncogene in that particular case. And this is important to remember because we want to know, if we're thinking about being able to target these particular mutations or target the epigenetic machinery for therapeutics. Which I'll talk about in the next lecture. We need to know what the outcome would be. So we can't universally say inhibiting EZH2 would be a good thing. Inhibiting EZH2 might be a good thing in some solid malignancies and perhaps in the lymphomas but maybe a terrible thing in myelodysplastic syndrome for example. So we know that this actually is similar to what we said about DNA methylation. The role of DNA methylation was context dependent and dependent on the state of disease. And this may in fact be more universally true for other epigenetic modifiers as well. So to kind of wrap up what I've said about epigenetics in cancer but also this interplay with genetics. When I first show you this Yin Yang symbol I said that we know that genetic alterations can influence epigenetic alterations and epigenetic alterations can influence genetic alterations. So now I can show that we know that the genetic alterations can go through and alter the epigenetic aberrations. Because you can have mutations in the epigenetic modifiers themselves because mutations in the epigenetic modifiers lead to global changes in epigenetic state. But we also know that the epigenetic modifications can influence genetics because they will lead to increased genomic instability and even aberrant DNA repair when it happens in regions of heterochromatin. So in this way there is this complex interplay between the genetic and the epigenetic abnormalities that are found in cancer. And so we still don't necessarily know the cause and the consequence. We don't know that those mutations and epigenetic modifiers necessarily happened first. They may also have been epigenetic abnormalities such as the genome wide hypomethylation which led to genetic instability, which may have led to translocations in the epigenetic machinery. We don't yet know the answer, but it's going to be interesting in the coming years to be able to try to tease these apart. So in summary, we know that in the cancer cells we see CpG island hypermethylation, genome-wide hypomethylation, long-range epigenetic silencing or activation, and alterations to many other histone marks here. And in the DNA, the genetic changes, we know that we see all of these changes to the epigenetic machinery. Point mutations, translocations, amplifications, deletions, and copy number variations, these small insertions or deletions. And in concert, all of these things will result in the particular cancer phenotype. So in the next lecture I'd like to think about targeting the epigenetic machinery for therapeutic use.
