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Watching cancers evolve using ‘liquid biopsies’

Just last year, Cancer Research UK scientists had reconstructed the evolution of a patient’s kidney tumour during treatment – one of many studies over the past few years illustrating cancer’s fearsome genetic complexity and adaptability.

This phenomenon, known as ‘intratumour heterogeneity’, led many to predict a long, hard slog to fully understand it – let alone get a handle on its implications for treatment.

One key concern was that patients would need to undergo a series of small operations (biopsies) to take repeated tissue samples to track how their cancer develops – and that this could be painful, costly and risky – especially for cancers deep in the body. And even then, because of the genetic variation within each patient’s cancer, there would be no guarantee that the biopsy results would represent an accurate picture.

Others also pointed out that such heterogeneity was a blow to the optimism around new-generation ‘targeted’ therapies, designed to treat cancer cells driven by individual mutations.

But recent discoveries have renewed this optimism. It turns out that tumours release DNA into the bloodstream, and that this seems to contain signals about what’s going on inside it. Consequently, there’s been a growing hope that analysing these DNA fingerprints could provide a quick, simple ‘liquid biopsy’ to track tumours’ progress.

And last month, researchers at Cancer Research’s Cambridge Institute published compelling evidence that circulating DNA could indeed be used to take a snapshot of the DNA errors (mutations) in a patient’s breast cancer.

Today they’ve gone one step further proving, in a beautifully detailed paper in the journal Nature, that blood samples can be used to monitor genetic changes in a patient’s disease over time.

This has the potential to be a game-changer, and rapidly accelerate research into what makes cancers tick, in real patients, in timeframes that can impact on clinical decision making.

Let’s look at what they found.

It’s in the blood

The research followed six patients – two with breast cancer, three with ovarian cancer and one with lung cancer. All of the patients’ cancers had spread to other parts of their bodies.

While they were undergoing treatment, these patients donated regular blood samples to a team of doctors and researchers led by three of Cancer Research’s leading experts – Professor Carlos Caldas, Dr James Brenton and Dr Nitzan Rosenfeld.

The research team analysed the samples using a technique called ‘exome sequencing’, which looks at the composition of each of our 20,000 genes (which make up a small fraction of the entire human genome).

Using this technique, the researchers were able to look at the proportion of the DNA in each patient’s blood that came from their tumour, and how the genes from the tumour differed from their normal DNA.

But crucially, since they had samples from before and after the patients had different treatments, the researchers were able to look at how the DNA from the tumour differed before and after treatment – including types of genetic differences it contained.
What did they find?

Genetic data on a screen

Gene sequencing can reveal why a cancer is resistant to a given drug

Each patient’s blood contained large numbers of mutated genes, coming from the cancer’s DNA. But the exact mutations, and their levels, subtly changed in response to treatment.

By comparing their findings to previous published studies on cancer drug resistance genes, the researchers were able to pinpoint the likely culprits. They highlighted several of these in their Nature paper.

One of the breast cancer patients was originally treated with a drug called epirubicin, then switched to a second drug called paclitaxel.

After paclitaxel treatment, the researchers spotted higher levels of a mutation in a gene called PIK3CA in the patient’s blood. Previous lab studies have implicated this mutation in paclitaxel resistance.

So it’s likely that the appearance of this mutation showed that the patient harboured cancer cells that were resistant to paclitaxel, which were now growing in response to the treatment.

The second breast cancer patient was treated with tamoxifen and trastuzumab (aka Herceptin). This resulted in increases in levels of a mutation in a gene called MED1, also previously linked to tamoxifen resistance. The patient was switched to a second drug combo – lapatinib and capecitabine – and very quickly, a second mutation in a gene called GAS6 became apparent as the cancer adapted to the treatment.

Again, this mutation has been previously linked to resistance to drugs like lapatinib.

Similar pheonomena were observed in the ovarian and lung cancer patients. For example, after she was treated with cisplatin, a mutation in a gene called RB1 became much more common in the blood of one of the ovarian cancer patients.

And studying the blood of the lung cancer patient, who was treated with gefitinib but didn’t respond, showed why: a new mutation had appeared in the EGFR gene (the target of gefitinib), causing the drug to stop working.
How does this help patients?

The search for ‘biomarkers’ – reliable ways to measure a tumour’s response to treatment – has been a long and tricky one – and has tended to look for proteins secreted by tumours.

This new research opens the door to using DNA – rather than proteins – as a much more reliable biomarker for a cancer’s growth. This has long been talked about, but never before demonstrated so elegantly. “It’s the missing piece of the jigsaw puzzle,” Professor Brenton told us. “We can now understand what happens during treatment, and how that affects the development of drug resistance.”

On top of this, its simplicity should allow the test to be used in a whole raft of clinical studies. “This is a test simple enough to be scaled up to 100s or 1000s of patients,” he said.

“There are, of course, still unanswered questions, and we don’t know 100 per cent whether this applies to every patient, but certainly for most of the main cancer types – breast, bowel, lung ovarian etc – there’s good evidence that monitoring tumour DNA is feasible.”

So… what happens next?

“We’re looking to get this out of the lab and into the clinic as soon as possible, and run clinical trials where we monitor patients’ DNA at the high quality levels in NHS hospitals – so-called CPA-standard testing. We want to work out how we can exploit changes in their tumour DNA to make solid clinical decisions that will help them,” he added.

The important leap forward, he says, is that DNA blood tests represent a test that won’t hurt or inconvenience the patients. “It’s a tremendously powerful technique.”

Professor Charlie Swanton, the London-based Cancer Research UK researcher whose kidney cancer heterogeneity study caused a big splash last year, is similarly excited.

“It’s a fabulous study,” he told us. “I have no doubt this is really game-changing for cancer biomarker development.” He thinks the paper will lead to a much deeper understanding of how different ‘sub-clones’ inside tumours evolve through treatment.

“Undoubtedly, this is a major step forward in overcoming the tumour sampling problems we are facing,” he says.

The Cambridge team are now working on a number of new studies to exploit the power of tumour DNA testing. There’s a long way to go before it becomes routine for all cancer patients, but given the resources being invested in gene testing, and the avalanche of molecular knowledge emerging from labs around the world, there are certain to be new advances before the year is out.

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