Finding faults in the BRAF gene

This entry is part 2 of 30 in the series Our milestones

Continuing Our Milestones series on Cancer Research UK-funded science that has made a big impact, we turn to BRAF – a gene that is faulty in more than half of all malignant melanomas and many other cancers. Our work paved the way for the development of the drug Zelboraf (vemurafenib), which is bringing precious extra time for people with advanced melanoma.

The research

“Mutations of the BRAF gene in human cancer” by Helen Davies, Graham Bignell and their colleagues in the UK, USA, Australia, Italy and Hong Kong, was published in the journal Nature in 2002. The research was funded by Cancer Research UK, the Wellcome Trust, The Institute of Cancer Research, Regione Autonoma della Sardegna and Breakthrough Breast Cancer, working together as part of the Cancer Genome Project.

This publication was the first major success for the Cancer Genome Project – an ambitious attempt to search for every human gene that stops working properly in cancer cells. The publication sparked a surge of interest in BRAF, which has thrown up exciting new leads for cancer drugs of the future.

To explain more about this research, we’ve put together a short film featuring Professor Richard Marais – one of the scientists involved in the original discovery – and Professor Caroline Springer, who is developing drugs to target BRAF.

Watch the video on YouTube

Read on to find out more about BRAF and its impact.

Background

The cells in our body constantly talk to each other using molecules, which tell them when to divide, when to die, and what sort of specialised cell to become. These signals are passed from protein to protein within the cell in an elaborate game of Chinese whispers that scientists refer to as a ‘signalling cascade’. The signals eventually reach the nucleus, where they switch genes on or off, telling the cell whether to multiply, die or specialise.

If any of the proteins in these cascades are faulty, the message might not get through, or it could be sent too many times. Either of these scenarios could lead to cancer if the cell doesn’t know that it should die, or starts to multiply out of control.

One of the key players in certain signalling cascades is BRAF, a protein produced from the instructions carried by the BRAF gene. BRAF is a kinase, a protein that sticks chemical ‘tags’ onto other proteins, activating them in order to pass on signals in the cell. And, as you might expect, faults in BRAF can have big implications for cells – and for cancer.

But a decade ago, BRAF wasn’t very interesting to cancer biologists. They were much more intrigued by a related protein called C-RAF, and thought that BRAF was mostly involved in brain development rather than cancer.

It wasn’t until Professor Mike Stratton and his colleagues decided to start the Cancer Genome Project – hunting for genetic faults in tumours – that the spotlight turned on BRAF.

What did they do and what did they find?

The scientists started by taking DNA from 15 samples of cancers – 6 breast cancers, one small cell lung cancer, 6 non-small cell lung cancer, one malignant melanoma, and one mesothelioma (a type of lung cancer). Crucially, the researchers also had access to healthy cells from the original patients as well.

They compared the DNA sequence of the BRAF gene in the samples and found three important occasions where the sequence in the cancer cells differed from that of the healthy cells by just one DNA ‘letter’ (base pair).

The BRAF gene is faulty in more than half of all melanoma skin cancer

Thinking that these differences could be important in cancer, the researchers widened their study to look at DNA taken from 530 samples of cancer cells that had been grown in the lab (called cell lines).

They found faults in BRAF in 43 of the cancer cell lines, including 20 out of 34 melanoma samples and 7 out of 40 bowel cancer samples, as well as a smaller proportion of other cancer types.

All the BRAF faults they had identified were clustered around two particular points within the gene. They homed in on these regions using a further 378 tumour samples from patients with a range of different cancer types. The results were striking – faults in BRAF were found in over two thirds of the melanoma samples, and a smaller proportion of bowel and ovarian cancers.

The final part of the puzzle was to figure out how the faults in BRAF might lead to cancer. Usually, faults in genes mean that the protein they produce is faulty and doesn’t work properly. But in this case, the scientists discovered that the BRAF faults they identified actually send the gene into overdrive. This means that it sends too many signals telling the cell to divide – a direct link to cancer.

In fact, one specific fault can increase the activity of BRAF by up to five hundred times, fuelling the runaway growth of cancer cells.

What impact has this work had?

At the end of their paper, the researchers themselves noted:

“The high frequency of BRAF mutations in melanoma and the relative lack of effective therapies for advanced stages of this disease suggest that inhibition of BRAF activity may be an important new strategy for the treatment of metastatic melanoma.”

In other words, designing drugs that specifically block BRAF could lead to urgently needed treatments for malignant melanoma, once it has spread. Researchers suggest that around 5,000 people die every year from different cancers with BRAF faults – and around 7 out of ten melanomas are caused by BRAF faults – so the stakes are high.

To this end, Cancer Research UK has continued to fund research into BRAF. In 2004, a team at the Institute of Cancer Research led by Professor Richard Marais analysed the structure of overactive BRAF from cancer cells, and compared it with BRAF taken from healthy cells (press release).

They found that faulty BRAF has a significantly different shape from the normal protein. This makes it an excellent candidate for drug targeting, as drugs designed specifically to lock onto the shape of BRAF would be less likely to affect the protein in healthy cells, helping to avoid side effects.

Professor Caroline Springer and colleagues at the Cancer Research UK Centre for Cancer Therapeutics at the Institute of Cancer Research are also making great progress in developing drugs to target faulty BRAF.

A paper published in 2006 described a new BRAF-blocking chemical with potential to go forward for further testing as a cancer drug. The chemical was found after testing 23,000 chemical compounds. More alternatives have since been discovered by the same team, (papers here and here, press release here) with more to come in the pipeline.

Other researchers around the world have also picked up the BRAF baton, investigating BRAF-blocking chemicals with a view to developing them into new cancer drugs. For example, scientists in the US have found an anti-BRAF chemical with potent activity against melanoma cells in the lab.

Furthermore, work by scientists at the Cancer Research UK Centre for Cell and Molecular Biology at The Institute of Cancer Research has shown that an exciting experimental cancer drug called 17-AAG can cause faulty BRAF in cancer cells to be broken down, while BRAF from healthy cells is less likely to be affected. Although more research is needed, this could be promising for treating cancer in the future.

~~We’re yet to see highly targeted BRAF-blocking drugs make it into clinical trials, but they certainly hold potential~~. As well as the impressive speed at which the international research community has moved from the initial discovery of BRAF faults in cancer to the development of promising drug candidates, this story is also a nice example of how research into cancer biology leads directly to new treatments for cancer.

Updated July 2011: Since we originally wrote this post, researchers have published results of clinical trials of the BRAF-blocking drug PLX4032 (vemurafenib), showing that it can bring significant benefits to people with advanced malignant melanoma. The development of this drug would not have been possible without the foundations laid by our scientists. Read more about these trials in the following posts:

Update 2012: Zelboraf (vemurafenib/PLX4032) was approved for melanoma patients by NICE (pdf) in December 2012, following successful large-scale trials.

Watch this animation about how these ‘targeted’ drugs work: