The Epigenetics Revolution (30 page)
Read The Epigenetics Revolution Online
Authors: Nessa Carey
Tags: #Science/Life Sciences/Genetics and Genomics
Figure 10.4
A single base change which is in a part of the myostatin gene that does not code for protein nevertheless has a dramatic impact on the phenotype in the Texel sheep breed. The presence of an A base instead of a G in the myostatin mRNA leads to binding of two specific miRNAs. This alters myostatin expression, resulting in sheep with very pronounced muscle growth.
A single base change which is in a part of the myostatin gene that does not code for protein nevertheless has a dramatic impact on the phenotype in the Texel sheep breed. The presence of an A base instead of a G in the myostatin mRNA leads to binding of two specific miRNAs. This alters myostatin expression, resulting in sheep with very pronounced muscle growth.
There is a condition in humans called DiGeorge syndrome in which a region of about 3,000,000 bases has been lost from one of the two copies of chromosome 22
40
. This region contains more than 25 genes. It’s probably not surprising that many different organ systems may be affected in patients with this condition, including genito-urinary, cardiovascular and skeletal. Forty per cent of DiGeorge patients suffer seizures and 25 per cent of adults with this condition develop schizophrenia. Mild to moderate mental retardation is also common. Different genes in the 3,000,000 base-pair region probably contribute to different aspects of the disorder. One of the genes is called
DGCR8
and the DGCR8 protein is essential for the normal production of miRNAs. Genetically modified mice have been created with just one functional copy of
Dgcr8
. These mice develop cognitive problems, especially in learning and spatial processing
41
. This supports the idea that miRNA production may be important in neurological function.
40
. This region contains more than 25 genes. It’s probably not surprising that many different organ systems may be affected in patients with this condition, including genito-urinary, cardiovascular and skeletal. Forty per cent of DiGeorge patients suffer seizures and 25 per cent of adults with this condition develop schizophrenia. Mild to moderate mental retardation is also common. Different genes in the 3,000,000 base-pair region probably contribute to different aspects of the disorder. One of the genes is called
DGCR8
and the DGCR8 protein is essential for the normal production of miRNAs. Genetically modified mice have been created with just one functional copy of
Dgcr8
. These mice develop cognitive problems, especially in learning and spatial processing
41
. This supports the idea that miRNA production may be important in neurological function.
We know that ncRNAs are important in the control of cellular pluripotency and cellular differentiation. It’s not much of a leap from that to hypothesise that miRNAs may be important in cancer. Cancer is classically a disease in which cells can keep proliferating. This has parallels with stem cells. Additionally, in cancer, the tumours often look relatively undifferentiated and disorganised under the microscope. This is in contrast to the fully differentiated and well-organised appearance of normal, healthy tissues. There is now a strong body of evidence that ncRNAs play a role in cancer. This role may involve either loss of selected miRNAs or over-expression of other miRNAs, as shown in
Figure 10.5
.
Figure 10.5
.
Chronic lymphocytic leukaemia is the commonest human leukaemia. Approximately 70 per cent of cases of this type of cancer
42
have lost the ncRNAs called
miR-15a
and
miR-16-1
. Cancer is a multi-step disease and a lot of things need to go wrong in an individual cell before it becomes cancerous. The fact that so many cases of this type of leukaemia, the most common human leukaemia, lacked these particular miRNAs suggested that loss of these sequences happened early in the development of the disease.
42
have lost the ncRNAs called
miR-15a
and
miR-16-1
. Cancer is a multi-step disease and a lot of things need to go wrong in an individual cell before it becomes cancerous. The fact that so many cases of this type of leukaemia, the most common human leukaemia, lacked these particular miRNAs suggested that loss of these sequences happened early in the development of the disease.
An example of the alternative mechanism – over-expression of miRNAs in cancer – is the case of the
miR-17-92
cluster. This cluster is over-expressed in a range of cancers
43
. In fact, a considerable number of reports have now been published on abnormal expression of miRNAs in cancer
44
. In addition, a gene called
TARBP2
is mutated in some inherited cancer conditions
45
. The TARBP2 protein is involved in normal processing of miRNAs. This strengthens the case for a role of miRNAs in the initiation and development of certain human cancers.
miR-17-92
cluster. This cluster is over-expressed in a range of cancers
43
. In fact, a considerable number of reports have now been published on abnormal expression of miRNAs in cancer
44
. In addition, a gene called
TARBP2
is mutated in some inherited cancer conditions
45
. The TARBP2 protein is involved in normal processing of miRNAs. This strengthens the case for a role of miRNAs in the initiation and development of certain human cancers.
Figure 10.5
Decreased levels of certain types of microRNAs, or increased levels of others, may each ultimately have the same disruptive effect on gene expression. The end result may be increased expression of genes that drive cells into a highly proliferative state, increasing the likelihood of cancer development.
Decreased levels of certain types of microRNAs, or increased levels of others, may each ultimately have the same disruptive effect on gene expression. The end result may be increased expression of genes that drive cells into a highly proliferative state, increasing the likelihood of cancer development.
Hope or hype?
Given the increasing amounts of data suggesting a major role for miRNAs in cancer, it isn’t surprising that scientists began to get excited about the possibilities of using these molecules to treat cancer. The idea would be to replace ‘missing’ miRNAs or to inhibit ones that were over-expressed. The hope was that this could be achieved by dosing cancer patients with the miRNAs, or artificial variants of them. This could also have applications in other diseases where miRNA expression may have become abnormal.
Big pharmaceutical companies are certainly investing heavily in this area. Sanofi-Aventis and GlaxoSmithKline have each formed multi-million dollar collaborations with a company called Regulus Therapeutics in San Diego. They are exploring the development of miRNA replacements or inhibitors, to use in the treatment of diseases ranging from cancer to auto-immune disorders.
There are molecules very like miRNAs called siRNAs (
s
mall
i
nterfering RNAs). They use much the same processes as miRNA molecules to repress gene expression, especially degradation of mRNA. siRNAs have been used as tools very extensively in research, as they can be administered to cells in culture to switch off a gene for experimental investigations. In 2006, the scientists who first developed this technology, Andrew Fire and Craig Mello, were awarded the Nobel Prize for Physiology or Medicine.
s
mall
i
nterfering RNAs). They use much the same processes as miRNA molecules to repress gene expression, especially degradation of mRNA. siRNAs have been used as tools very extensively in research, as they can be administered to cells in culture to switch off a gene for experimental investigations. In 2006, the scientists who first developed this technology, Andrew Fire and Craig Mello, were awarded the Nobel Prize for Physiology or Medicine.
Pharmaceutical companies became very interested in using siRNAs as potential new drugs. Theoretically, siRNA molecules could be used to knock down expression of any protein that was believed to be harmful in a disease. In the same year that Fire and Mello were awarded their Nobel Prize, the giant pharmaceutical company Merck paid over one billion US dollars for a siRNA company in California called Sirna Therapeutics. Other large pharmaceutical companies have also invested heavily.
But in 2010 a bit of a chill breeze began to drift through the pharmaceutical industry. Roche, the giant Swiss company, announced that it was stopping its siRNA programmes, despite having spent more than $500 million on them over three years. Its neighbouring Swiss corporation, Novartis, pulled out of a collaboration with a siRNA company called Alnylam in Massachusetts. There are still plenty of other companies who have stayed in this particular game, but it would probably be fair to say there’s a bit more nervousness around this technology than in the past.
One of the major problems with using this kind of approach therapeutically may sound rather mundane. Nucleic acids, such as DNA and RNA, are just difficult to turn into good drugs. Most good existing drugs – ibuprofen, Viagra, anti-histamines – have certain characteristics in common. You can swallow them, they get across your gut wall, they get distributed around your body, they don’t get destroyed too quickly by your liver, they get taken up by cells, and they work their effects on the molecules in or on the cells. Those all sound like really simple things, but they’re often the most difficult things to get right when developing a new drug. Companies will spend tens of millions of dollars – at least – getting this bit right, and it is still a surprisingly hit-and-miss process.
It’s so much worse when trying to create drugs around nucleic acids. This is partly because of their size. An average siRNA molecule is over 50 times larger than a drug like ibuprofen. When creating drugs (especially ones to be taken orally rather than injected) the general rule is, the smaller the better. The larger a drug is, the greater the problems with getting high enough doses into patients, and keeping them in the body for long enough. This may be why a company like Roche has decided it can spend its money more effectively elsewhere. This doesn’t mean that siRNA won’t ever work in the treatment of illnesses, it’s just quite high risk as a business venture. miRNA essentially faces all the same problems, because the nucleic acids are so similar for both approaches.
Luckily, there is usually more than one way to treat a cat and in the next chapter, we’ll see how drugs targeting epigenetic enzymes are already treating patients with severe cancer conditions.
The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’ (I found it!) but ‘That’s funny …’
Isaac Asimov
There are multiple instances in science of a relatively chance event leading to a wonderful breakthrough. Probably the most famous example is Alexander Fleming’s observation that a particular mould, that had drifted by chance onto an experimental Petri dish, was able to kill the bacteria growing there. It was this random event that led to the discovery of penicillin and the development of the whole field of antibiotics. Millions of lives have been saved as a result of this apparently chance discovery.
Alexander Fleming won the Nobel Prize for Physiology or Medicine in 1945, along with Ernst Chain and Howard Florey who worked out how to make penicillin in large quantities so that it could be used to treat patients. Isaac Asimov’s famous statement at the top of this page flags up to us that Alexander Fleming wasn’t simply some fortunate man who struck lucky. His insight wasn’t a fluke. It’s very unlikely that Fleming was the first scientist whose bacterial cultures had become infected with mould. His achievement came in recognising that something unusual had happened, and appreciating its significance. Knowledge and training had prepared Fleming’s mind to make the most of the chance event. He saw what probably many others had seen before him but he thought what nobody else had thought.
Even if we accept the role that odd events have played in research, it would still be very comforting to think that science generally proceeds in a logical and ordered fashion. Here’s one way we could imagine such progress in epigenetics …
Epigenetic modifications control cell fate – it’s these processes by which liver cells, for example, stay as liver cells and don’t turn into other cell types. Cancer represents a breakdown in normal control of cell fate, because liver cells stop being liver cells and become cancer cells, suggesting that epigenetic regulation has become abnormal in cancer. We should therefore aim to develop drugs that influence this epigenetic mis-regulation. Such drugs may be useful for treating or controlling cancer.
That’s a neat and tidy process, and makes a lot of sense. In fact, hundreds of millions of dollars are being spent in the global pharmaceutical industry to develop epigenetic drugs for exactly this purpose. But the clear-cut thought process outlined above is not how this process of cancer drug discovery started.
There are already licensed drugs which treat cancer and which work by inhibiting epigenetic enzymes. These compounds were shown to be active against cancer cells
before
they were shown to work on epigenetic enzymes. In fact, it’s the success of these compounds that has really stirred up interest in epigenetic therapies, and in the whole field of epigenetics itself – so much for a neat narrative arc.
before
they were shown to work on epigenetic enzymes. In fact, it’s the success of these compounds that has really stirred up interest in epigenetic therapies, and in the whole field of epigenetics itself – so much for a neat narrative arc.
The accidental epigeneticist
Back in the early 1970s, a young South African scientist called Peter Jones was working with a compound called 5-azacytidine. This compound was already known to have anti-cancer effects because it could stop leukaemia cells from dividing, and had some beneficial effects when tested in childhood leukaemia patients
1
.
1
.
Peter Jones is now recognised as the founding father of epigenetic treatments for cancer. Tall, thin, tanned and with thick close-cropped white hair, he is an instantly recognisable presence at any conference. Like so many of the terrific scientists mentioned in this book, he has researched for decades in an ever-evolving field. He remains at the forefront of efforts to understand the impact of the epigenome on health. He is currently spearheading efforts to characterise all the epigenetic modifications present in a vast number of different cell types and diseases. These days he is able to call on technologies that allow his team to analyse millions of read-outs from highly specific and specialised equipment. Back in the early 1970s, he made his first breakthrough by being incredibly observant and thorough – a classic case of a prepared mind.
Forty years ago, nobody was quite sure how 5-azacytidine worked. It’s very similar in chemical structure to base C (cytidine) from DNA and RNA. It was assumed that 5-azacytidine got added into DNA and RNA chains. Once there, it somehow disrupted normal copying of DNA, and transcription or activity of RNA. Cancer cells such as the ones found in leukaemia are extremely active. They need to synthesise lots of proteins, which means they need to transcribe a lot of mRNA. Because they divide quickly they also need to replicate their DNA very efficiently. If 5-azacytidine was interfering with one or both of these processes, it would probably hamper the growth and division of the cancer cells.
Peter Jones and his colleagues were testing the effects of 5-azacytidine on a range of cells from mammals. It’s remarkably fiddly to get many types of cells to grow in the laboratory if you just take them straight out of a human or another animal. Even when you can get them to grow, they often stop dividing after a few cell divisions and die off. To get around this, Peter Jones worked with cell lines. Cell lines are derived originally from animals, including humans, but as a result of chance or experimental manipulation, they are able to grow indefinitely in culture, if given the right nutrients, temperature and environmental conditions. Cell lines are not exactly the same as cells in the body, but they are a useful experimental system.
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