Read The Epigenetics Revolution Online
Authors: Nessa Carey
Tags: #Science/Life Sciences/Genetics and Genomics
The Epigenetics Revolution (33 page)
Even within haematological tumours, there are differences between the DNMT and HDAC inhibitor drugs. Both DNMT inhibitors have been licensed for use in a condition called myelodysplastic syndrome
20
,
21
. This is a disorder of the bone marrow.
20
,
21
. This is a disorder of the bone marrow.
Both HDAC inhibitors have been licensed for a different kind of haematological tumour, called cutaneous T cell lymphoma
22
. In this disease, the skin becomes infiltrated with proliferating immunological cells called T cells, creating visible plaques and large lesions.
22
. In this disease, the skin becomes infiltrated with proliferating immunological cells called T cells, creating visible plaques and large lesions.
Not every patient with myelodysplastic syndrome or cutaneous T cell lymphoma gains a clinical benefit from taking these drugs. Even amongst the patients who do respond, none of these drugs really seem to cure the condition. If the patients stop taking the drugs, the cancer regains its hold. The DNMT1 inhibitors and the HDAC inhibitors seem to rein in the cancer cell growth, retarding and repressing it. They control rather than cure.
However, this often represents a significant improvement for the patients, bringing prolonged life expectancy and/or improved quality of life. For example, many patients with cutaneous T cell lymphoma suffer significant pain and distress because their lesions are constantly and excruciatingly itchy. The HDAC inhibitors are often very effective at calming this aspect of the cancer, even in patients whose survival times aren’t improved by these drugs.
Generally speaking, it’s often very difficult to know which patients will benefit from a specific new anti-cancer drug. This is one of the biggest problems facing the companies working on new epigenetic therapies for the treatment of cancer. Even now, several years after the first licences were granted by the FDA for 5-azacytidine and SAHA, we still don’t know why they work so much better in myelodysplastic syndrome and cutaneous T cell lymphoma than in other cancers. It just so happened that in the early clinical trials in humans, patients who had these conditions responded more strongly than patients with other types of cancers. Once the clinicians running the trials noticed this, later trials were designed that focused around these patient groups.
This may not sound like a major difficulty. It might seem straightforward for companies to develop drugs and then test them in all sorts of cancers and with all sorts of combinations of other cancer drugs, to work out how to use them best.
The problem with this is the expense. If we check out the web-site of the National Cancer Institute, we can look for the number of trials that are in progress for a specific drug. In February 2011, there were 88 trials to test SAHA
23
. It’s difficult to get definitive costs for how much clinical trials cost, but based on data from 2007, a value of $20,000 per patient is probably a conservative estimate
24
. Assuming each trial contains twenty patients, this would mean that the costs just for testing SAHA in the trials at the National Cancer Institute are over $35,000,000. And this is almost certainly an under-estimate of the overall cost.
23
. It’s difficult to get definitive costs for how much clinical trials cost, but based on data from 2007, a value of $20,000 per patient is probably a conservative estimate
24
. Assuming each trial contains twenty patients, this would mean that the costs just for testing SAHA in the trials at the National Cancer Institute are over $35,000,000. And this is almost certainly an under-estimate of the overall cost.
The researchers at Columbia University and Memorial Sloan-Kettering who first developed SAHA patented it. They then set up a company called Aton Pharma to develop SAHA as a drug. In 2004, after promising early results in cutaneous T cell lymphoma, Aton Pharma was bought by the giant pharmaceutical company Merck for over $120 million dollars. Aton Pharma had almost certainly spent millions of dollars to get SAHA to this stage. Drug discovery and development is an expensive business. The two companies that marketed the DNMT1 inhibitors have been bought relatively recently by larger pharmaceutical companies, in deals that totalled about $3 billion each
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. If a company has paid a huge amount of money to develop or buy in a new drug, it would much prefer not to carry on spending like a drunken sailor when it comes to clinical trials.
25
. If a company has paid a huge amount of money to develop or buy in a new drug, it would much prefer not to carry on spending like a drunken sailor when it comes to clinical trials.
Naturally, it would be a big improvement if we could run clinical trials with a much better idea of which patients will benefit, rather than having to take pot luck. Unfortunately, most researchers agree that many of the animal models used to test cancer drugs are very limited in their capacity to predict the most susceptible human cancer. To be fair, this isn’t just true of cancer drugs targeted at epigenetic enzymes, it’s also true of pretty much all oncology drug discovery.
In an attempt to get around this problem, researchers in both academia and industry are now looking for the next generation of epigenetic targets in oncology. DNMT1 is a relatively broad-acting enzyme. DNA methylation is rather all or nothing – a CpG is methylated or it isn’t. HDACs tend to be pretty non-discriminating too. If they can get access to an acetylated lysine on a histone tail, they’ll take that acetyl group off. There are a lot of lysines on a histone tail – there are are seven on histone H3, just for starters. There are at least ten different HDAC enzymes that SAHA can inhibit. It’s quite likely that each of these ten can deacetylate any of the seven lysines on the H3 tail. This is hardly what we would call fine-tuning.
No easy wins
This is why the field is now moving in the direction of assessing different epigenetic enzymes, which are much more limited in their actions, to see which are important players in different cancers. The rationale is that it will be easier to understand the cellular biology of enzymes with quite limited actions, and this will make it easier to determine which patients are likely to respond best to which drugs.
The first problem in doing this is rather a daunting one. Which proteins should we investigate? There are probably at least a hundred enzymes that add or remove histone modifications (writers and erasers of the epigenetic code). There are probably as many proteins that read the epigenetic code. To make matters worse, many of these writers, erasers and readers interact with each other. How can we begin to identify the most promising candidates for new drug discovery programmes?
We don’t have any useful compounds like 5-azacytidine and SAHA to guide us, so we have to rely on our relatively incomplete knowledge in cancer and in epigenetics. One area that is proving useful is considering how histone and DNA modifications work in tandem.
The most heavily repressed areas of the genome have high levels of DNA methylation and are extremely compacted. The DNA has become very tightly wound up, and is exceptionally inaccessible to enzymes that transcribe genes. But it’s the question of how these regions become so heavily repressed that is really important. The model is shown in
Figure 11.3
.
Figure 11.3
.
In this model, there is a vicious cycle of events that results in the generation of a more and more repressed state. One of the predictions from this model is that repressive histone modifications attract DNA methyltransferases, which deposit DNA methylation near those histones. This methylation in turn attracts more repressive histone modifying enzymes, creating a self-perpetuating cycle that leads to an increasingly hostile region for gene expression.
Figure 11.3
Schematic to illustrate how different types of epigenetic modifications act together to create an increasingly repressed and tightly condensed chromosome region, making it very difficult for the cell to express genes from this region.
Schematic to illustrate how different types of epigenetic modifications act together to create an increasingly repressed and tightly condensed chromosome region, making it very difficult for the cell to express genes from this region.
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
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,
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. 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.
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,
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. 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
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. 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.
28
. 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
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.
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.
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
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,
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. Basically, the more active these enzymes, the worse the prognosis for the patient.
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,
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. 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?
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
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. 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.
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. 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
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.
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