Another Brick in the Wall: Turning cancer’s strengths against it

A mutation that allows cells to grow out of control could also provide a new way to target and destroy cancer cells. This potential Achilles’ heel comes from a mutation in a gene called PTEN, which is found in a wide range of cancers.

PTEN is one of many tumour suppressor genes that we have to prevent our cells from growing out of control. If the PTEN gene stops working because of a mutation, it can cause tumours to develop – indeed many tumours have a mutated form of PTEN. However when a door closes, a window opens: the PTEN mutation helps the tumour to grow, but it could also mark it out as a target.

Researchers from the Institute of Cancer Research, London, found that switching off another gene known as NLK killed tumour cells that had the PTEN mutation. This makes NLK a good target for drug developers to create a new cancer treatment.

The difficult thing about cancer is that it is made of us – it is our own cells that have mutated and grow wildly out of control. That means it is unlikely there will ever be a quick fix. Antibiotics work efficiently because bacteria are so different to us that we can develop drugs that target their weaknesses yet barely affect our own cells. But how do you kill something that is the same as you? Current treatments for cancer cause a lot of side-effects in patients because as they try to kill the cancer they also do damage everything else in the body. This is why finding ways to target cancer specifically is so important.

There are several proteins which we cannot live without, and our cells die if the genes responsible for producing those proteins are mutated or switched off. Targeting these proteins and genes are rarely going to be useful for treatments, as they will kill the patient about as quickly as they kill the cancer. So Alan Ashworth and colleagues set out to find proteins that are not essential in healthy cells, but cells with the PTEN mutation cannot live without. This would pave the way for designing drugs that target the tumour and leave healthy cells alone.

The researchers took samples of tumour cells with and without the mutation, and switched off genes for important proteins that are used for regulating lots of processes in the cell. To do this they used small molecules of RNA (DNA’s less famous cousin) which interfere with the processes of specific genes. This is why these molecules are known as small interfering RNA (or siRNA). They block the chain of events that allow a gene to produce a protein, effectively switching it off. By switching off 779 genes individually, they could look for ones where cells with the PTEN mutation died and cells without the mutation survived.

This is how the researchers discovered the powerful effect of switching off the NLK gene. They are not certain how this works but it appears to protect a protein called FOXO1 that can act as a backup tumour suppressor and cause the cancer cell to die. When PTEN is mutated, the FOXO1 protein becomes vulnerable to a process called phosphorylation, which means it is ejected from the cell nucleus and destroyed. NLK is one of the proteins that phosphorylates FOXO1 and so by switching off the NLK gene, FOXO1 is able to do its job.

The phosphate group, shown at the top, consists of one phosphorus atom (in orange) and three oxygen atoms (in red). This can be added to certain amino acids to control the behaviour of the whole protein

Phosphorylation is the process of adding a phosphate group, shown at the top, to certain amino acids to control the behaviour of the whole protein. This group consists of one phosphorus atom (in orange) and three oxygen atoms (in red) and has a strong negative charge.

This is just the start of a long journey from the lab to (potentially) the hospital. The researchers have shown that targeting NLK is more likely to kill mutated cells than normal cells, but that does not mean it is safe. NLK still has a role to play in healthy cells and preventing it from working is likely to have side-effects, but it could be worthwhile if this approach can kill tumours. The next stage is to develop a drug to stop the NLK protein from working, so that it can be tested further in cells and in living organisms.

Promising leads against cancer appear often, yet very few ever make it as treatments. One big hurdle is making it through clinical trials; the new drug has to be better than currently available treatments. Targeting NLK would only work against cancers with the PTEN mutation, but now we can use the mutation as a marker to find out which patients that applies to. We are now in the age of personalised medicine, where we can have 100 different treatments for 100 different people with 100 different cancers. Gradually, we are finding ways to attack cancer in whichever form it appears and build up our range of treatments. The weaknesses that we find are not going to cure all cancers, but each one provides another brick in the wall.

This article was originally written for the Access to Understanding competition run by Europe PubMed Central

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…and this little piggy corrected genetic mutations

Scientists have come a step closer to being able to correct mistakes in our DNA, thanks to a new method for rewriting mutations in stem cells. This could be used to treat genetic diseases for which there are no treatments available.

The researchers made use of piggyBac, a ‘jumping gene‘ originally found in moths. These ‘jumping genes’, as their name suggests, move from place to place along the DNA and can be used to carry other genes with them. Acting as a genetic cut-and-paste, they can neatly insert a corrected gene with remarkable precision. “Our systems leave behind no trace of the genetic manipulation, save for the gene correction,” says Professor Allan Bradley of the Wellcome Trust Sanger Institute.

In the case described in Nature the team focused on a genetic liver disease.

Severe deficiency in the protein alpha 1-antitrypsin is caused by a mutation, which is found in 1 in 2000 North Europeans. This protein is produced in the liver, but is responsible for protecting the lungs. The mutation causes the protein to accumulate in the liver, leading to cirrhosis, and deplete in the lungs, causing emphysema.

The scientists converted samples of patients’ skin cells into stem cells and corrected the mutation, using piggyBac. These stem cells were then converted into liver cells, in test tubes and in mice, which were able to produce the correct form of the protein.

Despite advances in the technology, producing stem cells in this fashion introduces new mutations into the DNA. While most of these mutations are likely to be harmless, there can be potentially fatal side-effects. This risk will need to be minimized before the technique is brought forward to treating patients.

Currently the only cure for alpha 1-antitrypsin deficiency is a liver transplant, but with transplant waiting lists longer than ever, this new development can bring hope to thousands of sufferers.

Pearls of Wisdom: Oysters genome reveals hardy defences

The oyster genome has been sequenced, making it the first mollusc to have its whole DNA mapped out. Molluscs (more specifically the phylum Mollusca) are largest group of marine species, making up nearly a quarter of all known species, and naturally play an important part in maintaining the ecosystem. Analysis of the genome has revealed a highly developed response to environmental stresses.

Oysters tend to live in estuaries or by the seashore – both very changeable environments. Estuaries continuously vary in salinity, requiring a highly adaptable system for life there. The seashore, or intertidal region, also has varying salinity but also has the problem of exposure to air when the tide goes out. Although exposure to air might be the least of your concerns if you find yourself stuck in the full glare of the midday sun at low tide.

The Pacific Oyster (Crassostrea gigas) lives a difficult life, but has the tools to help it survive.
Credit: David.Monniaux

Protecting against heat is common concern and so we have specialised proteins to defend against damage, aptly known as heat shock proteins. These proteins are found in nearly all forms of life, that’s how important they are. Researchers found 88 HSP70 (heat shock protein 70) genes in the oyster genome, significantly more than the 17 genes found in humans. Not only are there many of these genes, but they are highly responsive; 14 times more Hsp70 was produced under heat stress overall, with some genes activating over 2000-fold.

Hsp70 is usually used in the cell to protect newly synthesized proteins. Proteins are often highly dependent on being folded properly to prevent them from aggregating. Aggregation not only means the protein is useless, but it may be damaging to the cell. As the protein leaves the ribosome it is in a vulnerable position until it has time to fold into shape. Hsp70 acts by cradling the protein strand and protecting it until it can be passed on for further processing.

Hsp70 is found in nearly all forms of life, that’s just how important it is

The protective ability of Hsp70 is also why it is known as a heat shock protein. When the temperature gets high, proteins begin to unfold and are again threatened by aggregation. Hsp70 recognises loose strands of protein and binds to them, protecting them in the same fashion. This may help to explain the oyster’s ability to survive at temperatures up to 49°C (120°F).

Heat is only one factor that oysters have to deal with and their genome shows just how hardy they are. They appear to have a high rate of mutations and a large number of transposons, both resulting in high genetic diversity. This has allowed them to accumulate many mechanisms to prevent apoptosis (programmed cell death) in times of stress. In fact, over 4000 genes (16% of the whole genome) responded to air exposure.

The paper in Nature detailing these results had 85 authors. This gives a good indication of how much work goes into whole genome sequencing and analysis. There is a lot to learn from studying the genomes of other organisms, but it is still difficult work.

Above Genetics: How your behaviour can affect your DNA

It is now regarded as a simple fact of life that you are stuck with the genes your parents gave you. Genetic mutations from long ago have passed down from generation to generation, whether it is joined earlobes, knobbly knees or a higher risk of breast cancer. This is Darwinian inheritance in action.

But what if that isn’t the full story? What if your actions as a ten-year-old not only affected your genes, but those of your future children and grandchildren?

Darwin wasn’t the first to offer a theory on evolution; before him was Jean-Baptiste Lamarck, who suggested that traits developed by animals during their lifetime could be passed onto their children. The classic example is a giraffe, who, after years of stretching to reach higher leaves, would have offspring with longer necks. After several generations of stretching, giraffes would have necks as long as they are today.

This made intuitive sense and even Darwin was reluctant to dismiss it — he was not quite the Darwinist he is now made out to be. However, now that DNA is known to be responsible for passing on genetic information, it is hard to see how this could work. No amount of neck-straining will change your genes, so surely this cannot happen.

How could stretching your neck be passed on to the next generation?
Source: Brocken Inaglory

The Human Genome Project aimed to transcribe our DNA and find out what makes a human. Even after decoding all three billion ‘letters’, there was still not enough information to provide all the answers. One of the problems is that many genes can be switched off, or ‘silenced’, by the body. This occurs through methylation, where a small marker, just one carbon and three hydrogen atoms, is attached to a section of DNA and switches it off. Since this silences a gene without actually altering the genetic code, methylation is described as epigenetic, from the Greek ‘epi-’ for ‘above’. This system of silencing genes is another layer of information on top of the genetic code — an epigenetic code.

Methylation of DNA is a natural way that an organism regulates itself, but external factors can affect this dramatically. When a honey bee larva is fed on royal jelly its methylation levels fall, causing it to develop ovaries, grow larger and live longer, i.e. become a queen. However, it is not just food that is important; mice change their DNA methylation patterns depending on how much attention their mothers paid them as a pup.

Methylation of DNA is a very subtle change but its effects can be enormous.
Source: Christoph Bock

Epigenetic changes due to environment can happen even before birth. Studies of several famines, including the Dutch Hunger Winter of 1944 and the Great Chinese Famine of 1958–61, have shown that children conceived during these periods were underweight at birth. Now adults, they have increased rates of obesity, heart disease and schizophrenia, and have increased methylation of genes linked to these diseases. This makes clear the importance of epigenetics as not just an aside to genetics but a powerful force in its own right.

It was long thought that epigenetic changes could not be passed to our children, as sperm and egg cells undergo ‘reprogramming’ to wipe the slate clean. However, recent experiments have shown that mice are able to pass on epigenetic changes and historical records suggest that this may be happening in humans too.

As an isolated farming community in the early 1800s, Överkalix in north Sweden suffered from extreme fluctuation in food supply; some years would be plentiful while others would be ruinous. This variation encouraged Lars Olev Bygren, a preventative health specialist, to trace the ancestries of a hundred villagers and cross-reference them with harvest records. Remarkably, he found that boys who had survived a year of famine while aged 9–12 went on to have sons and grandsons who lived on average 32 years longer than those of boys who had enjoyed a year of feasting. This prepubescent stage is when the body is most susceptible to environmental changes; however it is remarkable that the repercussions can be seen two hundred years later in the lives of their grandchildren, who were never directly exposed to famine.

This seems very similar to Lamarck’s theory that the impact of an animal’s life is passed down to the next generation. However, epigenetics cannot replace Darwinian inheritance, where a genetic mutation is permanent, as epigenetic changes should only be temporary. But how long is temporary? We have seen effects passed down at least two generations in humans, while experiments with roundworms have shown epigenetic changes surviving over 40 generations.

Epigenetics gives us the flexibility that genetics could never provide, allowing us to adapt to our environment during our lifetime. However, it is not just our own lives being adjusted; we could be determining the lives of our future children. Take heed, the sins of the father may well be visited upon the son.