And Now There Are Six!!

Scientists eh! What a drag they can be! Forever coming up with new things that the rest of us have to wrap our minds around (or at least feel we should try).

Readers of these pages will know I’m periodically apt to wax rhapsodic about ‘the secret of life’ – the fact that all living things arise from just four different chemical units, A, C, G and T. Well, from now on it seems I’ll need to watch my words – or at least my letters – though maybe for a while I can leave it on the back burner in the “things that have been but not yet” category, to use the melodic prose of Christopher Fry.

Who dunnit?

The problem is down to Floyd Romesberg and his team at the Scripps Research Institute in California.

Building on a lot of earlier work, they’ve made synthetic units that stick together to form pairs – just like A-T and C-G do in double-stranded DNA. But, as these novel chemicals (X & Y) are made in the lab, the bond they form is an unnatural base pair.

Left: Two intertwined strands of DNA are held together in part by hydrogen bonds. Right top: Two such bonds (dotted lines) link adenine (A) to thymine (T); three form between guanine (G) and cytosine (C). These bases attach to sugar units (ribose) and phosphate groups (P) to form DNA chains. Right bottom: Synthetic X and Y units can also stick together and, via ribose and phosphate, become part of DNA.

After much fiddling Romesberg’s group derived E. coli microbes that would take up X and Y when they were fed to the cells as part of their normal growth medium. The cells treat X and Y like the units they make themselves (A, C, G & T) and insert them in new DNA – so a stretch of genetic code may then read: A-C-G-T-X-T-A-C-Y-A-T-… And, once part of DNA, the novel units are passed on to the next generation.

Science fiction?
If this has you thinking creation and exploitation of entirely new life forms?!!’ you’re not alone. Seemingly Romesberg is frequently asked if he’s setting up Jurassic Park but, as he points out, the modified bugs he’s created survive only as long as they’re fed X and Y so if they ‘escape’ (being bugs this would probably be down the drain rather than over a fence), they die. Cunning eh?!!

Is this coming to a gene near you?
No. It is, however, clear that more synthetic bases will be made, expanding the power of the genetic code yet further. What isn’t yet known is what the cells will make of all this. In other words, the whole point of tinkering with DNA is to modify the code to make novel proteins. In the first instance the hope is that these might be useful in disease treatment. Rather longer-term is the notion that new organisms might emerge with specific functions – e.g., bugs that break down plastic waste materials.

At the moment all this is speculation. But what is now fact is amazing enough. After 4,000 million years since the first life-forms emerged, more than five billion different species have appeared (and mostly disappeared) on earth – all based on a genetic code of just four letters.

Now, in a small lab in southern California, Mother Nature has been given an upgrade. It’s going to be fascinating to see what she does with it!

Reference

Zhang, Y. et al. (2017). Proceedings of the National Academy of Sciences 114, 1317-1322.

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Cockles and Mussels, Alive, Alive-O!

And so they are across the globe, not forgetting clams, a term that can cover all bivalve molluscs – a huge number of species (over 15,000), all having a two-part, hinged shell. The body inside doesn’t have a backbone, making it soft and edible on a scale of keeping-you-alive to orgasmic, depending on the consumer – oysters and scallops are part of the family.

Bivalves are particularly common on rocky and sandy coasts where they potter happily along, generally burrowing into sediment although some of them, scallops for instance, can swim. By and large their only problem is that humans like to eat them.

Clamming up

However, it gradually emerged in the 1970s that there was another cloud hovering over some of these gastronomic delights. Their commercial importance had drawn attention to the fact that soft-shell clams living along the east coast of North America, together with mussels on the west coast and cockles in Ireland, were dying in large numbers. The cause was an unusual type of cancer in which leukemia-like cells reproduce until they turn the blood milky and the animals die, in effect, from asphyxiation. In soft-shell clams, also known as sand gapers and steamers, the disease has spread over 1,500 km from Chesapeake Bay to Prince Edward Island.

A 2009 study had shown that as the disease progresses there is a rise in the number of blood cells that have abnormally high amounts of DNA (in clams typically four times the normal number of chromosomes – i.e. they’re tetraploid). In parallel with this change the cells make increasing amounts of an enzyme called reverse transcriptase (RT).

That was pretty surprising as RT does what its name suggests: reverses part of the central dogma of molecular biology (DNA makes RNA makes protein) by using RNA as a template to make DNA. RT is usually carried by viruses whose hereditary material is RNA (rather than DNA – so they’re called retroviruses). As part of their life cycle they turn their genomes into DNA that inserts into the host’s genome – which gets reproduced (as RNA) to make more viruses.

But how did RT get into clams? Enter Michael Metzger and Stephen Goff from Columbia University in New York, together with Carol Reinisch and James Sherry from Environment Canada, who began to unravel the mystery.

Jumping genes

Using high throughput sequencing they showed that clam genomes contain stretches of about 5,000 bases that came about when the RNA of a virus was copied into DNA by RT (reverse transcriptase) and then inserted into the host chromosome. Normal clams have from two to ten copies of this ‘repetitive element’ that Metzger & Co dubbed Steamer. That wasn’t too surprising as we have repetitive DNA too – it makes up about half the human genome. Many of these repeated sequences can move around within the genome – they’re often called ‘jumping genes’ – and it’s easy to see how this can happen when RT uses RNA to make DNA that can then pop into new sites in the genome. And you might guess that this process could damage the host DNA in ways that might lead to disease.

A long jump?

It turned out that the diseased clams had suffered massive amplification of Steamer to the extent that they carry 150 to 300 copies of the sequence. So that’s about 30 times as many Steamer DNAs being scattered across the clam genome – but how could that cause the same disease all the way from New York to Prince Edward Island? The answer came from peering into the DNA sequences of the tumour cells: they were virtually identical to each other – but they were different to those of their hosts! Meaning? The damage that led to leukemia, caused by shoe-horning 100s of extra copies of Steamer into clam genomes, only occurred once. And the staggering implication of that finding is that the cancer spread from a single ‘founder’ clam throughout these marine-dwelling molluscs. The resemblance to the way the cancer spreads in Tasmanian devils is striking.

Fishier and fishier

Fast forward to June 2016 and the latest contribution from the Metzger group reporting four more examples of transmissible cancer in bivalves – in mussels from British Columbia, in golden carpet shell clams from the Spanish coast and two forms in cockles.

Each appears to cause the same type of leukemia previously found in clams. The disease appears to be transmitted ‘horizontally’, i.e. by living cancer cells, descended from a single common ancestor, passing directly from one animal to another. Indeed, if you transplant blood cells from infected animals into normal clams they get leukemia.

 Species hopping

All that is quite amazing but the genetic analysis came up with an even more bizarre finding. In the golden carpet shell clams DNA from cancer cells showed no match with normal DNA from this species. It was clearly derived from a different species, which turned out to be the pullet shell clam – a species that, by and large doesn’t get cancer. So they have presumably come up with a way of resisting a cancer that arose in them, whilst at the same time being able to pass live tumour cells on to another species!!clam-transfer-pic

Cancer cell transmission between different species of shellfish. Cancer cells can arise in one species (pullet shell clams) that do not themselves develop leukemia but are able to pass live cells to another species (golden carpet shell clams) that do get leukemia (Metzger et al. 2016).

We have no idea how the cancer cells survive transfer. It seems most likely that they are taken up through the siphons that molluscs use for feeding, respiration, etc. and then somehow get across the walls of the respiratory/digestive systems. In the first step they would have to survive exposure to sea water which contains a lot more salt than cells are happy in. The ‘isotonic’ saline used in drips to infuse patients contains 0.9% salt whereas seawater, with 3.5%, is ‘hypertonic’ – cells put in a hypertonic solution will shrink as water is drawn out of the cell into the surrounding solution. Presumably the cells shrivel up a bit but some at least take this in their stride and recover to reproduce in their new host. Equally obscure is how a species can protect itself from a cancer that it can pass to another species.

These amazing findings throw a different light on the care-free underwater life depicted in Disney’s The Little Mermaid, in which the popular song ‘Under the Sea’ fails to mention floating cancer.

Can this happen to us?!!

Well, not as far as we know. But the fact that the known number of cancers that can be passed from one animal to another has now risen to nine does make you wonder. However, there’s no evidence that it happens in humans in anything like the normal course of events. There are examples of person-to-person transfer, notably during organ transplantation, and there is one recent case of cancerous cells from a tapeworm colonising a human host. But these are very rare, the latter occurring in a patient with a severely weakened immune system, and there is no example of spread beyond two people.

Phew! What a relief! So now we can concentrate on following developments both in Tasmania and beneath the waves in the hope that, not only can we go on satisfying our lust for clam bakes and chowders, but that these incredible creatures will reveal secrets that will benefit mankind.

References

AboElkhair, M. et al. (2009). Reverse transcriptase activity associated with haemic neoplasia in the soft-shell clam Mya arenaria. Diseases of Aquatic Organisms 84, 57-63.

Arriagada, G. et al. (2014). Activation of transcription and retrotransposition of a novel retroelement, Steamer, in neoplastic hemocytes of the mollusk Mya arenaria. PNAS 2014 111 (39) 14175-14180; published ahead of print September 8, 2014, doi:10.1073/pnas.1409945111.

Metzger, M.J. et al. (2015). Horizontal Transmission of Clonal Cancer Cells Causes Leukemia in Soft-Shell Clams. Cell 161, 255–263.

Metzger, M.J. et al. (2016). Widespread transmission of independent cancer lineages within multiple bivalve species. Nature 534, 705–709.

Muehlenbachs, A. et al. (2015). Malignant Transformation of Hymenolepis nana in a Human Host. N Engl J Med 2015; 373:1845-1852.

Another Peek At The Poor Little Devils

A couple of years ago (July 2014) I wrote a piece called Heir of the Dog that featured Tasmanian devils. The size of a small dog, these iconic little chaps are the largest meat-eating marsupials in the world. I’d run into them at The Lone Pine Koala Sanctuary in Brisbane where they’re keeping company with the dozy, furry tree-climbers as part of a programme to save them – the devils, that is – from extinction by cancer.

animal-fact-guide

A Tasmanian devil. Photo: Animal Fact Guide

1024px-sarcophilus_harrisii_taranna

 

 

 

 

 

 

 

imgresTheir problem comes from their inclination to bite one another, thereby directly passing on living cancer cells (causing devil facial tumour disease – DFTD). At that time the only other known example of transmissible cancer was a rare disease in dogs (canine transmissible venereal tumour – CTVT).

Genetic archaeology

DNA sequencing (i.e. whole genome analysis) had shown that the sexually transmitted dog disease probably arose thousands of years ago in a wolf or East Asian breed of dog and that the descendants of those cells are now present in infected dogs around the world.

The same approach applied to the Tasmanian devil showed that the cancer first arose in a female. Cells derived from that original tumour have subsequently spread through the Tasmanian population, the clone evolving (i.e. genetically diverging) over time. In contrast to the canine disease, DFTD is probably not more than 20 years old. Nevertheless, it spread through the wild population to the extent that the species was listed as endangered in 2008 by the International Union for Conservation of Nature.

Which is why a lot of effort is going into saving them, one approach being a number of breeding programmes in mainland Australia, with the aim of transferring uninfected animals to Tasmania.

One good turn …?

We’re all in favour of saving the little fellows, even if you probably wouldn’t want one as a pet. But, smelly and ferocious as he is, the Tasmanian devil is turning out to be remarkable in ways that suggest they might repay our efforts to keep them going. Things have moved apace down under with Greg Woods, Ruth Pye, Elizabeth Murchison, Andrew Storfer and colleagues from the Universities of Tasmania, Cambridge, Southampton and Washington State making some remarkable discoveries.

Infected animals do indeed develop the most unpleasant, large tumours that are virtually 100% fatal – to the extent that DFTD has wiped out 80% of Tasmanian devils in just 20 years. But some animals survive, even though models of the epidemiology say they shouldn’t. Andrew Storfer’s group asked how they pulled off this trick by looking for genetic changes in almost 300 devils. Quite amazingly, they found that even in a period as short as 20 years there were seven different genes that appeared to have changed (i.e. mutated) in response to selection imposed by the disease. Five of these genes encode proteins known to be associated with cancer risk or the immune system in other mammals, including humans. It seems that the mutations help their immune system to adapt so that it can recognize and destroy tumour cells.

In parallel with those studies, Greg Woods and his team now have a vaccine that looks promising early in trials – in other words a way of boosting natural immunity. We are only just beginning to find ways of giving the human immune system a helping hand – hence the burgeoning field of immunotherapy – so anything that works in another animal might give some useful pointers for us.

sick-tasTasmanian devil facial tumour disease.

This has killed 80% of the wild Australian animals in just a few decades.

Photograph: Menna Jones.

As if that wasn’t enough, a second strain of cancer has been found in a small group of male Tasmanian devils. It causes fatal facial tumours that look much the same as the first DFTD. However, it has a completely different genetic cause – so different in fact that it carries a Y chromosome, clear indication that the two forms of the disease arose by quite distinct mechanisms – which makes this marsupial the only species known to be affected by two types of transmissible of cancer.

Milk and human kindness

On top of all that some brave souls at Sydney University, Emma Peel and Menna Jones, decided in that way that scientists do, to collect some milk from the ferocious furries, just to see if it was interesting. Astonishingly the marsupial milk contained small proteins (peptides) that could kill a variety of bugs. They’re called cathelicidins and one of the things they can target is methicillin-resistant Staphylococcus aureus – MRSA – one of the dreaded ‘superbugs’ that are resistant to penicillin and other antibiotics. It’s not clear whether these peptides help to protect the devils from cancer but if that’s how turns out it might be incredibly important for us. As for their antibiotic potential, well, as it’s predicted that by 2050 superbugs will be killing one of us every three seconds you could say that opportunity beckons.

So that’s all incredibly exciting – and not just for the Tassie devils. ­ But another reason for returning to this story is that the devils have recently been joined by another example of extraordinary cancer transmission – and this one comes from the last place on the planet that you’d look for it ….

References

Murchison, E.P. et al. (2012). Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer. Cell 148, 780–791.

Pye, R.J. et al. (2016). A second transmissible cancer in Tasmanian devils. Proceedings of the National Academy of Sciences USA, 113, 374–379.

Epstein, B. et al. (2016). Rapid evolutionary response to a transmissible cancer in Tasmanian devils. Nature Communications 7, Article number: 12684: doi:10.1038/ncomms12684.

Peel, E. et al. (2016). Cathelicidins in the Tasmanian devil (Sarcophilus harrisii). Scientific Reports 6, Article number: 35019. doi:10.1038/srep35019.

Dennis’s Pet Menace

As it happened, I’d already agreed to appear on Jeremy Sallis’ Lunchtime Live Show on BBC Radio Cambridgeshire – the plan being just to chat about cancery topics that might be of interest to listeners. Which would have been fine – if only The World Health Organization had left us in peace. But of course they chose last Tuesday to publish their lengthy cogitations on the subject of whether meat is bad for us – i.e. causes cancer.

Cue Press extremism: prime example The Times, quite predictably – they really aren’t great on biomedical science – who chucked kerosene on the barbie with the headline ‘Processed meats blamed for thousands of cancer deaths a year’.

But – to precise facts – and strictly it’s The International Agency for Research on Cancer, the cancer agency of the World Health Organization (WHO), that has ‘evaluated the carcinogenicity of the consumption of red meat and processed meat.’

But hang on … haven’t we been here before?

Indeed we have. As long ago as January 2012 in these pages we commented on the evidence that processed meat can cause pancreatic cancer and in May of the same year we reviewed the cogitations of the Harvard School of Public Health’s 28 year study of 120,000 people that concluded eating red meat contributes to cardiovascular disease, cancer and diabetes. To be fair, that history partially reflects why the WHO Working Group of 22 experts from 10 countries have taken so long to go public: they reviewed no fewer than 800 epidemiological studies! However, as the most frequent target for study was colorectal (bowel) cancer, that was the focus of their report released on 26th October 2015.

So what are we talking about?

Red meat, which means any unprocessed mammalian muscle meat, e.g., beef, veal, pork, lamb, mutton, horse or goat meat, that we usually cook before eating.

Processed meat: any meat not eaten fresh that has been salted, cured, smoked or whatever and commonly treated with chemicals to enhance flavour and colour and to prevent the growth of bacteria.

What did they say?

Processed meat is now classified as carcinogenic to humans – that is it goes into the top group (Group 1) of agents that cause cancer.

Red meat is probably carcinogenic to humans (Group 2A). Group 2B is for things that are possibly carcinogenic to humans.

Why?

Because 12 of the 18 studies they reviewed showed a link between consumption of processed meat and bowel cancer and because it’s known that agents commonly added to processed meat (nitrates and nitrites) can, when we eat them, turn into chemicals that can directly damage DNA, i.e. cause mutations and hence promote cancers.

For red meat 7 out of 15 studies showed positive associations of high versus low consumption with bowel cancer and there is strong mechanistic evidence for a carcinogenic effect i.e. when meat is cooked genotoxic (i.e. DNA-damaging) chemicals can be generated. They put red meat in the probably group because several of the studies that the Working Group couldn’t fault – and therefore couldn’t leave out – showed no association.

Stop woffling

My laptop likes to turn ‘woffling’ into ‘wolfing’. Maybe it’s trying to tell me something.

But is The WHO trying to tell us something specific about wolfing? To be fair, they have a go by estimating that every 50 gram portion of processed meat (say a couple of slices of bacon) eaten daily increases the risk of bowel cancer by about 18%. For red meat the data ‘suggest’ that the risk of bowel cancer could increase by 17% for every 100 gram portion eaten daily.

And what might that mean?

In the UK about 6 people in 100 get bowel cancer: if you take The WHO maximum estimate and have everyone eat 50 grams of processed meat every day of their lives such that 18% more of them would get bowel cancer, the upshot would be 7 people in 100 rather than 6. So it’s a small rise in a relatively small risk.

As the report points out, the Global Burden of Disease Project reckons diets high in processed meat cause about 34,000 cancer deaths per year worldwide and, if the reported associations hold up, the figure for red meat would be 50,000. Compare those figures with smoking that increases the risk of lung cancer by 20-fold and The WHO’s estimate of up to 6 million cancer deaths per year globally caused by tobacco use and 600,000 per year by alcohol consumption.

All of which suggests that it isn’t very helpful to lump meat eating, tobacco and asbestos in the same cancer-causing category and that The WHO could do worse than come up with a new classification system.

And the message?

Unchanged. Remember mankind evolved into the most successful species on the planet as a meat eater. As the advert used to say: It looks good, it tastes good and by golly it does you good – not least as a source of protein, vitamins and other nutrients. Do some exercise and eat a balanced diet – just in case you’ve forgotten, that means limit the amount of red meat (The WHO suggests no more than 30 grams a day for men, 25 g for women) so try fish, poultry, etc. Stick with the ‘good carbs’ (vegetables, fruits, whole grains, etc.), cut out the ‘bad’ (sugar – see Biting the Bitter Bullet), eat fishy fats not saturated fats and, to end on a technical note, don’t pig out.

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‘The Divine Swine’ Castelnuovo Rangone, Italy

Meanwhile back on the Beeb

When the meat story broke I was a bit concerned that we might end up spending the whole of Lunchtime Live on how many bangers are lethal – especially as we were taking calls from listeners. Just in case things became a bit myopic I had Rasher up my sleeve. Rasher, you may recall, was Dennis the Menace‘s pet pig (in the The Beano‘s comic strip) who had a brother (Hamlet), a sister (Virginia Ham) and various other porky rellos. To bring it up to date we’d have introduced Sam Salami and Frank Furter and, of course, Rasher’s grandfather who was the model for the bronze statue named ‘The Divine Swine’ to be found in the little town of Castelnuovo Rangone in Pig Valley, Italy, the home of Parma ham.

But I shouldn’t have worried. All was well in the hands of Jeremy Sallis who, being a brilliant host, ensured that we mainly chatted about meatier matters than what to have for breakfast.

References

Press release: IARC Monographs evaluate consumption of red meat and processed meat.

Q&A on the carcinogenicity of the consumption of red meat and processed meat.

Carcinogenicity of consumption of red and processed meat. www.thelancet.com/oncology Published online October 26, 2015

Wonder of the World

Welcome back from our holidays on which, we trust, you had as much fun reading the four refresher pieces as I had writing them. Utter nonsense, of course. I’ve never found writing to be an orgasmic activity but, as they say about cod liver oil, it is good for you. However, whilst we were all improving ourselves on our deck-chairs and sun-loungers, the Tide of Science was waiting for no man: the waves of cancer biology have obliterated our sand castles and are fast approaching our toes. So let’s get on – albeit doing our best to make the segue from vacation to vocation as seamless as possible …..

So, on the subject of holidays, newspapers and magazines rather like the theme of ‘places to visit before you die’ – which is OK in that the world is wonderful and we should appreciate it. But there’s a problem in that one of the modern wonders is being able to see magnificent photos and movies of every far-flung nook, cranny and creature without leaving our sofa. So when we finally do get off our rear ends and chug past the Statue of Liberty on the Staten Island Ferry, zoom into Sydney or rock up to the Taj Mahal, the reaction is likely to be ‘That’s nice: looks just like on tv. Where next?’

Fortunately, being blasé has its limits. The only time I’ve made it to the Grand Canyon the mid-winter sun highlighted the colours of the rock striations so they were breathtaking in a way no photograph could quite capture. In the same vein, everyone should take the Trans-Siberian Railway we’re often told. And so you should but not because you will see houses and churches, rivers and trees that you can’t find on the Internet but because only borne by the train do you begin to sense the immensity of Mother Russia. The fact that the scenery is almost entirely birch trees minimizes distraction: all you can do is contemplate vastness – and the harshness that brings – an unvarying obbligato to Russian life.

A Provodnitsa looking after one of her passengers on The Trans-Siberian Railway

A Provodnitsa looking after one of her passengers on The Trans-Siberian Railway

The thrice-weekly freight at Grand Canyon Station, circa 1970

The thrice-weekly freight at Grand Canyon Station, circa 1970

 

 

 

 

 

 

Not Forgetting

All of which brings us to something else that is also truly a wonder of the world – cancer. If it seems a trifle weird to describe thus what’s usually classed as one of man’s greatest blights, consider this. The drive to control cancer has generated research on a scale unmatched in any other field of science. One upshot, not necessarily at the top of the list, is that we now have a breathtakingly detailed picture of the astonishing adaptability of life  – that is of our genetic material, DNA, and how its calisthenics can promote the most incredible behaviour on the part of individual cells. It’s true, you might point out, that we can see this by simply looking at the living world around us. The power of DNA to carry, in effect, limitless information produces the infinite cellular variety underpinning the staggering range of life that has evolved on earth. {Did you spot just the other day that a school field trip discovered 13 new species of spider in Queensland – yes, thirteen – inevitably headlined by The Sun as Creepy Hauly}

In the new world

But in focusing on cancers – what happens at the molecular level as they develop and how they evade our attempts to control them – the fine detail of this nigh-on incomprehensible power has been revealed as in no other way.

You’ll know what’s coming: the biggest single boost to this unveiling has been the arrival in the twenty-first century of methods for sequencing DNA and identifying which genes are expressed in cells at any given time. I know: in umpteen blogs I’ve gone on about its awe-inspiring power – but it is stunning and we’re at that stage when new developments leave one gasping almost on a monthly basis. The point here is that it’s not that the science keeps getting turned on its head. Far from it: the message remains that cells pick up changes to their DNA and, with time, these cumulative effects may drive them to make more of themselves than they should.

That’s cancer. But what is fantastic is the molecular detail that the ’omics revolution continues to lay bare. And that’s important because, as we have come to recognize that every cancer is unique, ideally we need to provide specifically tailored treatments, and we can only think of doing that when we know all the facts – even if taking them in demands a good deal of lying down in darkened rooms!

You could think of the fine molecular detail of cancers as corresponding to musical ornaments – flourishes that don’t change the overall tune but without which the piece would be unrecognizable. These include trills and turns – and all musicians will know their appoggiaturas from their acciaccaturas. They’re tiny embellishments – but just try removing them from almost any piece of music.

Lapping at your toes

So let’s look at three recent papers that have used these fabulous methods to unveil as never before the life history of cancers. The first is another masterful offering from The Sanger Institute on breast cancer: an in-depth analysis of 12 patients in which each tumor was sampled from 8 different locations. In the main the mutation patterns differed between regions of the same tumour. They extended this by looking at samples from four patients with multi-focal disease (‘foci’ being small clumps of tumour cells). As expected, individual foci turned out to be clearly genetically related to their neighbours but they also had many ‘private mutations’ – a term usually meaning a mutation found only in a single family or a small population. Here the ‘family’ are individual foci that must have arisen from a common ancestor, and you could think of them as a cellular diaspora – a localised spreading – which makes them a kind of metastasis. Quite often the mutations acquired in these focal sub-clones included major ‘driver’ genes (e.g., P53, PIK3CA and BRCA2). In general such potent mutations tend to be early events but in these foci they’ve appeared relatively late in tumour development. This doesn’t upend our basic picture: it’s just another example of ‘anything goes’ in cancer – but it does make the point that identifying therapeutic targets requires high-depth sequencing to track how individual cancers have evolved through continual acquisition of new mutations and the expansion of individual clones.

The authors used ‘coxcomb’ plots to portray these goings-on but they are quite tricky to make head or tail of. So, to avoid detail overload, I’ve converted some into genetic wallpaper, the non-repeating patterns illustrating the breathtaking variety that has evolved.

Wallpaper jpegDecorative DNA. The discs are ‘coxcomb’ plots – a variant of a pie chart. Here the colours and the wedge sizes represent mutations in different regions of four primary breast tumours. Every disc is different so that the message from this genetic wallpaper is of mutational variation not only between cancers but across the different samples taken from a single tumour. I trust that Lucy Yates, Peter Campbell and their colleagues will not be too upset at my turning their work into art (and greatly abbreviating the story): you can read the original in all its wondrous glory in Nature Medicine 21, 751–759.

The first person to come up with this very graphic way of conveying information was Florence Nightingale who, whilst working in Turkey during the Crimean War, realized that soldiers were dying in the hospitals not only from their wounds but, in much greater numbers, from preventable causes including infections, malnutrition and poor sanitation. Her meticulous recording and original presentation of hospital death tolls made her a pioneer in applied statistics and established the importance of sanitation in hospitals.

Something for the gentlemen

Two equally powerful onslaughts from Gunes Gundem, Peter Campbell and their colleagues at The Sanger Institute (again!) and Dan Robinson and pals from the University of Michigan Medical School have revealed the corresponding molecular detail of prostate cancer. Here too the picture is of each region of a tumour being unique in DNA terms. Moreover, they showed that metastasis-to-metastasis spread was common, either through the seeding of single clones or by the transfer of multiple tumour clones between metastatic sites.

Even that miserable old sod Lenin might have brightened at such fabulous science, before reverting to Eeyore mode with the inevitable “What’s to be done?” But it’s a good question. For example, as a general strategy should we try to kill the bulk of the tumour cells or aim for clones that, although small, carry very potent mutations.

Aside from the basic science, there is one quite bright ray of sunshine: about 90% of the mutations linked with the spread of prostate cancer are potentially treatable with existing drugs. And that really is encouraging, given that the disease kills 11,000 in the UK and over 30,000 in the USA every year.

prostate dogWe might also be heartened by the skills of German Shepherd dogs that can, apparently, be persuaded to apply one of their favourite pastimes – sniffing – to the detection of prostate cancer. Point them at a urine sample and 90% of the time they come up with the right answer. Given the well-known unreliability of the prostate-specific antigen blood test for prostate cancer, it’s nice to think that man’s best friend is on the job.

References

Yates, L.R., et al. (2015). Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nature Medicine 21, 751–759.

Robinson, D., et al. (2015). Integrative Clinical Genomics of Advanced Prostate Cancer. Cell 161, 1215–1228.

Gundem, G., et al. (2015). The evolutionary history of lethal metastatic prostate cancer. ICGC Prostate UK Group (2015). Nature 520, 353–357.

The Blink of an Eye

You might not have thought of it in quite this way but cancer biology is a bit like having kids. It seems you only have to turn your back and things have changed, not so as to be unrecognizable but enough to have you blinking in surprise, shock or horror. In the cancer field it’s true that, especially over the 12 years since human DNA was first completely sequenced, a fair bit of the jaw-dropping has been due to astonishing technical advances. Thus human genomes (i.e. their DNA sequence) can be laid bare in 24 hours – The International Cancer Genome Consortium now has over 10,000 cancer genomes in its database – and the power of the panoply of ’omics methods to probe ever deeper into the mind-boggling complexity of tumours is quite staggering (we risked a quick peep at just how tricky it is to disentangle a picture of the biology from the vast amounts of data in A Word From The Nerds).

Cancer’s simple

These revelations often leave us gasping at the variety and adaptability of nature and how that shows up time and again in the microworld of cancers. Of course, we’re used to the world being ever-changing but we like to think there are some things that are fixed. The Earth still rolled round the Sun even after the aeroplane was invented. When it comes to cancer the simple but fairly firm idea is that cells pick up changes in their genetic material (i.e. mutations in DNA) and if these affect an appropriate set of genes (i.e. encoded proteins) a cell starts misbehaving – multiplying when it shouldn’t or faster than normal. And that’s cancer. Of the twenty-odd thousand genes that make human beings, several hundred have this ability to be trouble-makers – and a handful at any one time (perhaps five to ten) is all it takes. Like any team, there are some high profile players: genes that crop up time and again in mutant form driving all sorts of different tumours. There’s maybe a dozen of these. The rest are bit part players: actors who can steal the show with a cameo role. In others words they’re low frequency cancer drivers, perfectly capable of doing the job but generally keeping a low profile.

All of which is fine: we can hang on to what we thought we knew. Cancers are caused by cumulative mutations – things are just complicated a bit because of the more or less infinite subtlety that the different combinations can cause. So cancer’s really pretty simple.

Oh no it’s not!

However, just once in a while – mercifully, or we’d all go potty – something comes along that has us, if not standing on our heads, at least wondering which way is up. Welcome Iñigo Martincorena, Peter Campbell and pals from The Sanger Institute in Cambridge – a regular source of wide-eyed wonder in genomics.

They’ve just done something that, on the face of it, was very odd. They carried out a thorough sequence analysis of samples of normal human skin, the skin in question being from eyelids. The plan was to try to get a picture of how cancers develop and eyelid skin is a good place to look because it gets a relatively high exposure to sun. Moreover, it’s easier to get hold of than you might think: there’s an age-related condition in which the skin loses its elasticity causing the eyelid to droop – which can be treated by surgery, i.e. cutting out some of the skin.

Fasten your seat belts: here comes the shaker. In 234 eyelid samples (biopsies) from four people the number of mutations was similar to that in many cancers! Yet more amazing, the mutated genes included most of the key ‘drivers’ of one of the major forms of skin cancer.

Putting numbers on it, they found about 140 driver mutations per square centimeter of skin.

The type of DNA damage was characteristic of the effect of ultraviolet light (e.g., changing C to T – i.e. the base cytosine is mutated to thymine) – so at least that wasn’t a surprise.

1 sq cm

Groups of mutant cells (clones) in a 1 square centimeter of normal eyelid skin.

The circles represent samples of skin that were sequenced. Their sizes and the representation of nested clones are based on the sequences obtained. The outermost layers of normal skin can therefore be viewed as “effectively a battlefield of hundreds of competing mutant clones in every square centimeter of skin.” (from Martincorena et al. 2015).

As Iñigo & Co put it ‘aged sun-exposed skin is a patchwork of thousands of evolving clones with over a quarter of cells carrying cancer-causing mutations.’ Notably, there were clones carrying two or three driver mutations – and yet the tissue showed no sign of cancer and functioned quite normally (apart from its wonky elastic).

Close your eyes: time for a re-think

So, there are thousands of mutations in each skin cell with hundreds of evolving clones per square centimeter and the profile of driver mutations varies between individuals. The obvious question, therefore, is ‘why isn’t this tissue cancerous?’ We don’t know but, given that key ‘drivers’ are present, it seems that these cells either have a kind of master ‘off switch’ that suppresses potent driver combinations or they need a further ‘on switch.’ There’s no evidence for either of these, nor is it clear whether other cell types can show this kind of restraint.

And there’s one more troubling point. Many cancer drugs are designed to target driver mutations and thus to kill the carrier cells. But if these mutations can crop up in normal cells, any such ‘cancer specific’ drugs might cause a good deal of what the military term collateral damage.

As ever in science, an exciting new finding raises yet more questions. Answers will be forthcoming at some point. Just don’t blink!

Reference

Martincorena, I. et al. (2015). High burden and pervasive positive selection of somatic mutations in normal human skin. Science 348, 880-886.

Gentlemen! For goodness’ sake …

I reckon there should be a 21st century addition to the family etiquette handbook banning laptops at the breakfast table. It’s anti-social and indeed downright rude: at best you get to your emails ten minutes quicker but it’s also really stupid because computers do not thrive on a diet of milkdrops, cornflake fragments and bits of toast. I never appear without mine – and with it I bring another potential, disgraceful side-effect, manifested in our household on the second day of the New Year when, a few minutes after I’d sat down, booted up and started munching, the air gradually began to turn blue. “Oh dear” muttered youngest son: “he’s on to the science pages of the broadsheets: fingers in ears.” How shrewd. And what good advice.

Rattling my cage

So what was it that so wound me up when I was looking forward to a rather non-sciency, tranquil opening to the year? “Most cancers are caused by bad luck not genes or lifestyle, say scientists”, a headline trumpeted by The Telegraph was a great start, backed-up by much the same parroted in The Independent and The Guardian. The only good news was that, try as I did, I could find no equivalent coverage in The New York Times or The Sydney Morning Herald. Let’s hear it for the colonials – or at least their science editors!

What’s my problem?

Why is it that this sort of journalism so annoys and certainly did so on further reading of those new year contributions? Well, partly because it’s headline-driven rather than a thoughtful effort to inform the public. And then because what’s propagated isn’t totally wrong – that would be easy to deal with – but rather it’s a confused mish-mash of half-truths guaranteed to confuse utterly anyone who doesn’t have an assured grip on their molecular wits.

Let’s get things clear

First let’s get the basic picture clear, then see what “the scientists” really said in this new piece of work and finally illustrate how the Gentlemen (and Gentlewomen) of the Press get me so incensed.

Asked to sketch a current cancer portrait one might say: Cancers are caused by damage to DNA, i.e. mutations. Of our 20,000 or so genes several hundred can acquire mutations that change the activity of the proteins they encode to contribute to cancer development. Only a small number (half a dozen or so) of these ‘driver’ mutations, acting together, are required for cancer to emerge. Thus almost limitless combinations of drivers can arise. The effect of these cancer ‘drivers’ is to make cells proliferate (i.e. divide to make more cells) either at a faster rate than normal, or at the wrong time or in an abnormal place. Environmental factors (e.g., smoking) can increase the mutation rate and hence the chance that cancers will evolve. Most mutations accumulate during the lifetime of the individual (hence most cancers are ‘diseases of old age’). However, about 10% of cancers are started by inherited mutations (that the patient is born with), with further mutations being acquired after birth.

We should also bear in mind that collectively cancer comprise about 200 distinct diseases and that at the level of DNA sequence every tumour is unique.

Pancreatic cancer cells

 

Cancer cells dividing. Photograph: Visuals Unlimited, Inc./Dr. Stanley Flegler.

 

 

 

What’s new?

The work that the journalists caught on to didn’t describe any new experiments but instead looked at the long-standing puzzle of why cancers, although able to arise anywhere in the body, have a strong tissue bias. For example, tumours are twenty times more common in the large intestine than in the small intestine.

Noting that within many tissues most cells are short-lived and don’t give rise to progeny (and so are unlikely to initiate a tumour), the authors focused on the cells that can self-renew and are therefore responsible for the continued existence and repopulation of the tissue (often called stem cells). Searching the literature, they found 31 tissue types for which it was possible to work out how many stem cell divisions occur in an average human lifetime. Lo and behold, it turned out that the number of divisions correlated quite well with the lifetime risk for cancer in that tissue type i.e. the more replications of stem cells that a tissue requires over its lifetime to sustain its functional, the greater the risk of a tumour emerging in that tissue.

An interpretation of this is that the majority of cancers arise (i.e. are started) as a result of random mutations occurring during DNA replication in normal, non-cancerous cells. The underlying point here is that every time one cell makes two it must first duplicate its genetic material (i.e. replicate its DNA). This process is amazingly efficient but it’s not perfect (cells make a mistake once for every one thousand million coding units (i.e. bases) incorporated into new DNA). In the abstract of their paper the authors describe cancers initiated by these naturally occurring mutations as “bad luck” – unfortunately in my view, as the expression was a sure-fire red rag to the press bulls.

A really irritating example

From The Telegraph: “For years health experts have warned that tumours are driven by a bad diet, lack of exercise, or gene errors passed down from parents… But now a study has shown that most cancers are primarily caused by bad luck rather than poor lifestyle choices or defective DNA.”

NO IT HASN’T. Do you not read what you’ve written and consider how it might come across to readers who think they’ve grasped the basic picture, as summarized above under Let’s get things clear?

What the study confirms is that the major force behind cancers is the accumulation of mutations (defective DNA if you wish) as cells replicate during the lifetime of the individual. To the risk of getting cancers posed by this background to life may be added environmental factors that promote DNA damage and inherited variants in DNA (see A Taxing Inheritance for more about parental contributions).

Is this really anything new?

Well, it’s marginal and certainly not enough to merit the above headlines. The new work doesn’t alter in any way our summary. However, it’s interesting in that it offers an explanation for the wide variation in cancer incidence across different tissues and makes the point, for instance, that the relatively high rate of cell renewal in the lung makes this organ particularly susceptible to the mutagenic effects of cigarette smoke.

So, what about luck?

First we remain as we were: cancers are a fact of life – they’re hard-wired into the biology of life and they’ll come to all of us if we live long enough.

It is certainly true that there are many cancer patients who have had bad luck. They may have always eaten healthily, kept active and physically fit and been teetotal since birth and yet be stricken by, for example, a brain tumour or pancreatic cancer for which there are no known environmental risk factors that we can do anything about. They may have never smoked but nonetheless develop lung cancer (think of Roy Castle).

But it remains the case that for many cancers, it isn’t just about luck, it’s about choices, both for society and for individuals. Mention of environmental factors reminds us that mankind really isn’t doing very well on the self-help front. Eliminating smoking would reduce the global cancer burden (14 million new cases, over 8 million deaths per year) by about 22%. Infections, for example from contaminated drinking water, start about 20% of all cancers whilst alcohol consumption has a hand in about 4% and in the UK over 20% of bowel cancers are linked to eating red and processed meat.

Calm down!

I know that for all the effect my wittering about the quality of science journalism will have I might as well get on to the sports pages. I actually have some sympathy with the Gentlemen of the Press: writing about science is difficult – perhaps we should rejoice that there’s any national coverage. But there is a recurrent problem in the British press (see Not another ‘Great Cancer Breakthrough’!!!) that can easily be avoided. Just report evolving science stories as precisely and clearly as possible. They’re often sensational tales in their own right, so leave the sensationalism to the other pages and tell it as it is.

Rant over. Happy new year. Now, where’s the marmalade?

References

Tomasetti, C. and Vogelstein, B. (2015). Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Science 347, 78-81.

A Taxing Inheritance

The centenary of the beginning of the First World War prompted me, as perhaps many others, to reflect on how successive generations have done since then in terms of what they’ve bequeathed to their offspring. I didn’t need to think for too long though, to find myself muttering ‘Thank heavens for science’—because most of the rest is a pretty dismal chronicle. I know, not all technological advances in the past one hundred years have been a cause of unrestrained joy but many of them transformed life in the most wonderful ways. Would that we could point to such success in other fields.

Our best defence may be to aver: “Man cannot control the current of events. He can only float with them and steer”, a saying attributed to Otto von Bismarck. If the ‘Iron Chancellor’ actually did utter those words it seems to me he was being coy beyond belief. He is, after all, generally credited with unifying Germany, seeing off the last French monarch (Napoleon III) and establishing the peaceful domination of Europe by the German Empire that lasted until long after his death—and setting up the first welfare state along the way. “The main thing is to make history, not to write it” sounds much more like Bismarck in full and frank mode.

Nature and Nurture

One form of history that we do write but indeed we cannot control comes in the form of the genetic material that we pass to the next generation. We’re all familiar with some of this legacy because we literally see it in physical resemblances and other attributes between parents and children (“He’s got his Mum’s eyes”) or shared by siblings (“Jack and Jill are wonderful musicians”). They’re shared because large chunks of the genetic code (i.e. DNA) are identical between the individuals concerned. But if conserved DNA makes for similarities, what of the differences—the fact that our parents and brothers look different to all the seven thousand million other people on the planet? Our unique features come from variations in the genetic code—odd changes in the units (bases) of DNA scattered through our genome. Called SNPs (pronounced ‘snips’ for single nucleotide polymorphisms), they’re what make the differences between us. In other words, a SNP is a difference in a single nucleotide—A, T, C or G—within a stretch of DNA sequence that is otherwise identical between two individuals. For example, you have AAGCCTA whereas I have AAGCTTA. These genetic variations that make individuals different are the basis of DNA fingerprinting.

There’s about three million SNPs scattered throughout the human genome (so, on average, you’d come across one in every 1,000 bases if you scanned your DNA from beginning to end) and they’re what makes each of us unique. Within ethnic groups common patterns of such variants confer characteristics (dark skin/light skin, tall/short, etc) and, with that in mind, you might guess that there will also be variants that make such groups more (or less) susceptible to diseases.

Of course, there’s an endless debate about the border between our genetic inheritance and how the world we experience makes us what we are—how much of Jack and Jill’s precocious talent is because Mum and Dad made them practice twelve hours a day from age five? Fortunately we can ignore nurture here and stick to genes because we’re trying to pin down the good and the bad of our genetic legacy.

What’s all this got to do with cancer?

A good bit is that we’re distinct from everyone else but still share family features. However, our genetic baggage may also contain some unwanted freebies—the most potent of which can give a helping hand to a variety of diseases, including cancers. Cancers are caused by damage to DNA—a build-up of changes, i.e. mutations, that affect the activity of proteins critically involved in controlling cell growth. For most cancers (90%) these mutations accumulate over the lifetime of the individual—they’re called “somatic mutations”—so you can’t blame anyone but yourself and Lady Luck. But about 10% get a kind of head start when someone is born with a key mutation. That is, the mutated gene came from either egg or sperm (so it’s a germline mutation). This effect gives rise to cancers that “run in families”: a critical mutation is passed from generation to generation so that children who inherit it have a greatly increased risk of developing cancer. Two of the most common cancers that can come in hereditary form are those of the breast and bowel.

Steeplechase

A mutational steeplechase leads to cancer. Of the tens of thousands of mutations that accumulate over time in a cancer cell, a small number of distinct “drivers” make the cancer develop (four are shown as Xs). Almost all mutations arise after birth, but about one in every ten cancers start because a person is unfortunate enough to be born with a mutation: they are already one jump ahead and are much more likely to get cancer than those born with a normal set of genes. The rate at which mutations arise is increased by exposure to carcinogens, e.g., in tobacco smoke.

Breast cancer is about twice as common in first-degree relatives of women with the disease as it is in the general population (you’re a first degree relative if you’re someone’s parent, offspring, or sibling). About 5% of all female breast cancers (men get the disease too but very rarely—about 1% of all breast cancers) arise from inherited mutations. In the 1990s two genes were identified that can carry such mutations. These are BRCA1 and BRCA2 and their abnormal versions can increase the lifetime risk of the disease to over 50%, compared with an average of about 10%. Since then heritable mutations in some other genes have also been shown to increase the risk.

Angelina Jolie

Angelina Jolie

A star turn

Breast cancer genetics came under the spotlight with the much-publicised saga of Angelina Jolie, the American film actress. Jolie’s mother and maternal grandmother had died of ovarian cancer and her maternal aunt from breast cancer—a family history that persuaded Jolie to opt for genetic testing that indeed revealed she was carrying a mutation in BRCA1 (BRCA1 and BRCA2 mutations account for about 10% of breast cancers and 15% of ovarian cancers). For Jolie the associated lifetime risk of breast cancer was estimated as 87%, prompting her to have a preventative double mastectomy, thereby reducing her risk to less than 5%. The months after she revealed her story saw the “Angelina effect”, a doubling in the number of women being referred for genetic testing for breast cancer mutations.

What’s all this got to do with SNPs?

The story so far is of the one in ten cancers that get kicked off by a powerful, inherited mutation that changes the action of the affected protein—the BRCAs being the best-known examples. However, the BRCAs and other known mutated genes account for only about 25% of familial breast cancers, meaning that for three quarters of cases the genetic cause remains unknown. And yet we know there is an inherited (genetic) cause simply because of the generational thread. Which brings us back to those other, more subtle tweaks to DNA that we mentioned—SNPs—alterations that don’t directly affect proteins, so they’re often called variants to distinguish them from mutations.

It seems very likely that the missing culprits are indeed SNPs—lots of them. These DNA variants each make a contribution so small that on its own would have no detectable effect on the chances that the carrier will get cancer. Their impact comes from a cumulative effect. They’re like pieces of straw, individually easily bent or broken but put a dozen of them together and you have a rope. Thus combinations of individually insignificant SNPs can raise the risk of cancer by, say, 10%—not a massive increase but not negligible either. Twins who are genetically identical have similar risks of developing breast cancer, consistent with the idea that many variants, each having a very small effect, can combine to give a substantial increase in risk. Very slowly, by sequencing lots of genomes, these rare variants are being identified. Given that clusters of appropriate variants confer risk, people with the “other” variant have, in effect, a degree of protection against cancer.

And in our more distant relatives?

All this comes from the huge effort that has gone into finding genetic variants linked to one of the most common cancers but, unsurprisingly, almost all the attention has focused on European women. Not before time, someone has got round to looking for breast cancer variants in East Asians who, after all, make up over one fifth of all the people in the world. Cai Qiuyin and his colleagues at the Vanderbilt University School of Medicine compared the genomes of over 20,000 cancer cases from China, Japan and South Korea with a similar number of disease-free controls. After much selecting and comparing of sequences, three particular DNA variants consistently associated with significant cancer risk. The variants were much less common in European women, suggesting that as the DNA keyboard has been strummed by evolution, distinct patterns associated with breast cancer have emerged in diverse populations.

Just two problems then. First it’s a huge task to assemble the lists of runners (and as the Asian results show, they will differ between ethnic groups). But the real challenge is yet to come. Almost all of these variants (99.9%) don’t change the sequence of proteins (i.e. how the proteins work). What they do is exert subtle effects on, for example, how much RNA or protein is made from a DNA gene at any time. At the moment we have little understanding of how this works, yet alone ideas on how to intervene to change the outcome.

Although identifying the BRCA genes that help to drive breast and ovarian cancers was a giant breakthrough, we still have no effective therapy for countering their malign influences. The intervening twenty-five years of effort have brought us to a new era of revealing the more subtle effects of variants. But the price we pay for unveiling the complete picture is perceiving just how tough is the therapeutic challenge.

Reference

Qiuyin Cai, et al. (2014). Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1. Nature Genetics 46, 886–890. doi:10.1038/ng.3041.

Heir of the Dog

I’ve probably in the past owned up to causing generations of students to do that raised eyebrow thing, familiar to all parents of teenagers, that, far more pointedly than words, says ‘The old boy’s finally lost it.’ Indeed I may well have a bit of a causative repertoire but one that unfailingly works is revealing that, even after a life in science, I still get ‘Wow’ moments every couple of months or so when I read or hear of some new discovery, method or insight that brings home yet again the wonder of Nature – or has you asking ‘Why didn’t I think of that?’ (The response to that one’s easy, by the way, so please don’t write in).

A common question

The most recent of these jaw-dropping events relates to a question often asked about cancer: ‘Can you catch it from someone else?’ In other words, can cancers be passed from one person to another by infection, much as happens with ’flu? The answer’s ‘No’ but, as usual in this field, even the firmest statement can do with a little explanation. The first point is that the ‘No’ is true even for 20% or so of cancers that are actually started by microbial infection – what you might call ‘bugs’ – bacteria, fungi, and viruses. One such, the bacterium Helicobacter pylori, can cause stomach ulcers that may lead to cancer. Those even smaller bugbears, viruses (typically one one-hundredth the size of a bacterium), are responsible for much of the cervical and liver cancer burden world-wide. Oh, and there’s a little, single-cell parasite (Trichomonas vaginalis), the most common non-viral, sexually transmitted infection in the world that, in men, can cause prostate cancer. But these infections are not cancers even though they may be an underlying cause – bacteria through prolonged inflammation and effects on the immune system and viruses by making proteins that affect how cells behave. Only when these perturbations cause genetic damage – i.e. DNA mutations – do you have a cancer. Which is why the answer to the original question is ‘No.’

There’s always one

Well, two in this case – and, given that we’re talking about cancer, you won’t be surprised that there are some oddities. They’re not exceptions to the ‘No’ answer because they occur in other animals – not in humans – but, in each, tumour cells are directly transferred from one creature to another – so it is cancer by infection. One such contagious tumour occurs in the Tasmanian devil. It’s transmitted by biting, an activity popular with these little chaps, and it gives rise to a particularly virulent facial tumor, eventually fatal because it prevents eating. To counter the probability that Tasmanian devils will become extinct in their native habitat, a number of Australian sanctuaries have breeding programmes aimed at setting up a disease-free colony on Kangaroo Island, South Australia.

TDs

Tas D

 

 

 

 

 

Tasmanian devils – cancer-free – Lone Pine Koala Sanctuary, Brisbane

A very similar condition in dogs known as canine transmissible venereal tumour (CTVT: also called Sticker’s sarcoma), mainly affects the external genitalia. First spotted in the nineteenth century by a Russian vet, it too is spread either by licking or biting and also through coitus. Dogs with CTVT can now be found on five continents and, from DNA analysis, we’ve known for some time that – remarkably – all their cancers are descended from a single, original tumour cell that appeared many years ago. They’re like one of those cell lines grown in labs all over the world, except they’ve been going far longer than any lab – with man’s best friend doing the cultivating.

So what is new?

Elizabeth Murchison and colleagues at The Wellcome Trust Sanger Institute, Cambridge have just produced the first whole-genome sequences of two of these tumours – from Australia and Brazil (an Aboriginal camp dog and a purebred American cocker spaniel). These confirmed that all CTVTs descend from a single ancestor who, they estimated, was trotting around about 11,000 years ago. The last common relative of the two dogs whose tumours were sequenced lived about 500 years ago, before his descendants went walkies to different continents.

And the ‘Wow’?

We already had a pretty good idea of how CTVTs have been handed down. In this paper the really amazing bit came in the detail. The authors estimated roughly how many mutations were present in each tumour. Answer: a staggering 1.9 million. And it’s staggering partly because it’s only slightly less than a change every 1,000 units (bases) in dog DNA but it’s truly awesome when you note that it’s several hundred times more than you find in most human cancers. We’re getting used to the idea of thousands or tens of thousands of mutations turning up in human cancer cells with associated gross disruptions of individual chromosomes. But these canine cancers display genetic mayhem on a massive scale – perhaps best visualized by comparing their chromosomes with those of a normal dog using a method that labels each with a different colour. A glance at the two pictures tells the story: all the cancer chromosomes from one of the tumour-bearing dogs (on the right) have been shuffled as if in some molecular card game. The full range of colours can still be seen, but of the normal pattern of 39 pairs of identical segments of DNA (left) there is no sign.

Two dogs chromos

Dog chromosomes. Left: normal; right: CTVT

(from Murchison, E.P. et al. (2014) Science 343, 437-440)

It seems incredible that cells can survive such a shattering of their genetic material – a state called ‘genetic instability’ because, once DNA damage sets in, mutations usually continue to accumulate. These cancers are uniquely bizarre, however, because although their genomes have been blown to smithereens, not only do the cells survive but they’ve continued suspended in this surreal state for centuries. They’re genetically stable – it really is the cellular equivalent of balancing an elephant on a pin.

‘Wow’ Indeed – but so what?

So like me you’ve been blown away by these discoveries but you may be asking, apart from the excitement, what’s in it for us humans? Well, there’s one other very strange thing about these dog cancers. Infected animals do indeed develop the most unpleasant, large tumours – but most of them are eventually rejected by the host dog. That is, its immune system gets to work to eliminate them – and after that the dog is immune to further infection. We are only just beginning to find ways of boosting the human immune system so that it can attack cancers and maybe, just maybe, we can extract from the stable chaos of the CTVT genome the secret of how they provoke rejection – and maybe that will guide human treatments.

Reference

Murchison, E.P. et al. (2014). Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage. Science 343, 437-440.

Scattering the Bad Seed

Cancers are very peculiar diseases. One of their fairly well-known oddities is that, by and large, it’s not the initial tumour that does the damage – rather that the vast majority of fatalities arise from its offshoots, secondary growths formed by cells escaping from the primary and spreading around the body, a diaspora called metastasis. That ‘vast majority’ is actually over 90% – so you might suppose most research effort would be focussed on how cells disseminate and what can be done to stop them in their tracks, whilst leaving the surgeons to deal with the primaries. But like many other things in life, logic plays a limited part in research strategy and to a great extent the boffins do what they fancy – or, to make it sound a bit more rigorous, what they feel is possible given the available tools. Which is perfectly reasonable: launching a project to build a radio would have been a bit perverse before Michael Faraday discovered electricity. In short, scientific research is all about practicalities – it’s what that great science communicator (and Nobel Prize winner) Peter Medawar called The Art of the Soluble.

Metastasis on the move

We recently recounted the emergence of the notion that cancers could spread around the body and how, by the end of the 19th century, this had led to the idea of ‘seed and soil’ – that cells cast off from primary tumours could drift around the circulation until they found somewhere congenial to drop anchor and set up a new home. That was in Keeping Cancer Catatonic and it was prompted by the fact that for rather more than 100 years metastasis seemed so difficult to get at, so impossible to model, there was virtually no progress and it is only now in the last few years that this critical cancer niche is once again on the move. The really exciting, and surprising, finding has been that, in mouse models, primary tumours dispatch chemical messengers into the blood stream long before any cells set sail. These protein news-bearers essentially tag a landing site within the circulatory system for the tumour cells to follow. And which sites are tagged depends on the type of tumour – consistent with the fact that human cancers show different preferences in metastatic targets.

A further twist is that even if tumour cells manage to follow this complicated guidance system and seed a new site, it’s not a disaster because their growth is suppressed by proteins released from nearby blood vessels. This presumably reflects the fact that tissues have systems to maintain the normal balance – to ensure that unusual things don’t happen – which means that everything is fine until that control is overwhelmed. When that happens other signals convert the dormant tumour into an expanding metastasis.

These very recent discoveries show that, at long last, our ignorance of how tumours spread is beginning to be chipped away and, because metastasis is the critical issue in cancer, this is a timely moment to do one of our crystal clear, simple summaries of what we know – which is relatively easy and will take much less time than if we reviewed our ignorance.

BOOKMARKING copy

Bookmarking cancer: Primary tumours mark sites around the body to which they will spread (metastasize) by sending out chemical signals that create sticky ‘landing sites’ (red protein A) on target cells. Cells released from the bone marrow carry proteins B and C. B attaches to A and tumour cells ‘land’ on C. Cells may remain quiescent in a new site for years or decades, their growth suppressed by signals (e.g., TSP-1) released from nearby blood vessels. Only when appropriate activating signals dominate (e.g., TGF beta) is secondary tumour growth switched on (see Keeping Cancer Catatonic for more details).

So what do we know?

Tumours arise from the accumulation of (essentially) random mutations and these drive the expansion of a family of cells to the point where they make their presence felt. From that, if the bearer is unlucky, emerges a sub-set of cells with the wanderlust. Cells in which the mutational hand they have acquired confer the ability to escape from the family bosom, chew through surrounding tissue, burrow into nearby blood vessels and thus voyage to distant places around the body. Some of these adventurous fellows may find landing sites where they can stick and, in effect, reverse their escape routine by squeezing through the vessel wall and chomping their way to a new niche in which to set up home. This process is sometimes called ‘colonization’ and it’s a pretty vivid description, evoking images of brave chaps taking on the elements to find a new world in which to prosper. The upshot is a malignant tumour.

I’m sorry for pulling a sciency trick back there by inserting ‘essentially’ – in brackets to persuade you to skim over it as if it was a mild hallucination. We’ll come back to the rivetting explanation of why I’d feel uncomfortable about just saying ‘random mutations’ another day but for the moment just stick with the idea that changes in DNA make cancers.

Tumour cells are not very bright

This sequence is so convoluted that it sounds like the product of some devilish mastermind but in fact we know that the metastatic cell is incapable of thought because otherwise it would have stayed at home. Metastasis is a process so inefficient that it’s almost always fatal for the cell that tries it. Tumour cells that get into the circulation may be damaged in the rush-hour scrum that is cellular life in the bloodstream and be gobbled up by scavenger cells. Even if they do finally squeeze through a space in the wall – feeling they’ve made it – they may have suffered so much stress they’re just not up to producing a family in a new environment that mayn’t be entirely welcoming. So even after reaching a new home they may not survive any longer or just manage to form a small cluster of cells that hang on as a ‘dormant’ tumour – an indolent little outpost that represents no threat to the carrier, even though it may persist for decades. So, despite metastasis being the most life-threatening facet of cancer, the odds are strongly weighted against escaping tumour cells: even after they’ve made it into the circulation, only about one in every ten thousand makes it to a compatible site where it forms an embryonic colony.

How does it kick off?

Given that tumours are products of evolution – albeit on the hugely accelerated time-scale of an individual lifetime rather than the geological frame within which new species emerge – you might suppose that metastases are merely a potent end-product. A tumour cell continues to pick up mutations until eventually it has the required toolkit to burrow and squeeze, float and drift, touch down  on sticky patches, squeeze and burrow again and eventually thrive in a new home. In the best traditions of cancer, however, it turns out not to be like that – at least, as far as is known, no set of mutations defines cells as having acquired the tools of the spreading trade. In short, there’s no ‘genetic signature’ that uniquely marks a metastatic cell. Nevertheless, they are different: only a fraction of primary tumour cells acquire the ability to spread – so if it isn’t simply by picking up an escape kit of changes in DNA, how do they do it?

Making an escape kit

One of the things that does mark metastatic cells is a change in the genes expressed compared to their relatives in the rest of the tumour. That is they alter the pattern of proteins that they make. This switch reorganises the cell’s shape and helps it to move and, most notably, includes enzymes released into the environment that cut a path for the cell to invade its local surroundings en route to the circulation.  As you might guess, this switch in protein production appears to be reversed once a cell has found a new niche. But if this transition into an invasive (i.e. malignant) cell isn’t driven by specific mutations, how does it come about?

The answer seems to lie in a subtle fine-tuning of cell behaviour, rather than dramatic changes caused by mutations in DNA. In other words, cells emerge from the morass of mutations within a tumour with critical signal systems that are just that little bit more active than those of their companions. It’s less a tall poppy syndrome than the odd blade of grass that’s missed the mower and can see a wider world. If this still seems a bit far-fetched, recall that every cell is unique: however identical two cells may be, there will be tiny differences in the signals that control their level of response.  The minuscule edge that can give one cell over another is enough. Given time, it will reproduce to make a clone with the gymnastic ability and stamina required to embark on the fraught experience of founding a metastatic colony.

Spreading variety

One of the fascinating things about cancer is that there seems to be no absolute rules. For every generalization there’s a renegade – a piece of molecular or cellular jiggery-pokery that does it in a different way, often in a breath-taking example of Nature’s flexibility. So it is with metastasis in that, as we noted, different cancers show widely variable behaviour.  Some major types have usually spread by the time they are detected (lung, pancreatic) whereas generally breast and prostate tumours have not. Some forms of brain tumour usually invade locally and are rarely found at distant sites whilst others often metastasize. Sometimes secondary growths are found when the primary source can’t de detected at all – so they’re ‘cancers of unknown primary’ and they’re not uncommon, coming in the top 10% of diagnoses.

Equally bemusing is the range of favoured targets for dissemination. Prostate cancer cells commonly home in on bone whereas bone and muscle tumours often spread to the lungs. Others, however, are much more promiscuous and go for multiple sites (e.g., triple-negative breast cancer, skin melanoma and tumours originating in the lung and kidney). We have little idea what’s behind this variability though it may be a combination of different circulation patterns, capacity to slip through vessel walls and how well-equipped the cell is to survive in new terrain.

Making friends with the neighbours

In Cooperative Cancer Groupies we talked about one of the most recent evolutions in cancer thinking – the notion that tumours are not just made up of clumps of abnormal cells but that their locale becomes flooded with a variety of normal cells as the host mounts first an inflammatory response and then attempts to kill off the intruder through its immune system. When this defence fails and the tumour begins to develop it has succeeded in corrupting the groupies in the microenvironment so that now they send out signals that actively promote tumour growth. This type of local support is similarly critical in determining whether metastases take root, so to speak. Moreover, variation in the precise signals from normal cells between different tissues contributes to target preference for malignant cells.

Not like you see on t.v.

In the currently popular Danish political drama television series called Borgen there’s a scene in which a tabloid newspaper editor is offered a piece by a reputable journalist about the European Union that he rejects. “Don’t try to give me a story about the EU: it’s not sexy and it’s too complicated for our readers to understand.” We will have no truck with such patronising here, despite the fact that nobody ever accused metastasis of being sexy. Moreover, as no one ‘understands’ it, we take the view that we’re all in this together and, because it’s infinitely more important and fascinating than political stories, we have belaboured you with the foregoing! Just to make sure that the little we do know is clear, let us summarise in nine (more or less) one-liners:

  1. Tumor cells signal to potential secondary sites.
  2. They escape, burrow, circulate, lodge at landing sites and colonize.
  3. They change the pattern of proteins they make to permit escape.
  4. They change the pattern again when they colonize.
  5. No genetic signature (set of mutations) is known that indicates capacity to metastasize.
  6. The process is very inefficient – i.e. most tumor cells never form a colony.
  7. Despite the low success rate, metastasis is responsible for >90% of cancer deaths.
  8. Once colonization starts at secondary site, tumor cells recruit help from adjacent normal cells (as they do in primary tumors).
  9. Normal cells can also colonize – that is, non-tumour cells injected into the bloodstream of mice have been shown to form colonies in the lungs. 

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This beautiful picture taken by Bettina Weigelin and Peter Friedl, UMC St Radboud Nijmegen, shows the remarkable plasticity of cells. The tumour cells (green) are invading normal mouse skin (orange) that also contains nerve fibers (blue) and collagen (grey). Cells may invade singly or as clusters. Their flexibility in wiggling through skin is similar to what happens when they cross the walls of blood vessels. http://www.cell.com/Cell_Picture_Show

Perhaps the most surprising item is the one we slipped in at Number 9 – that metastasis, or at least the capacity to colonize secondary sites, is not an exclusively property of some tumour cells but that normal cells can do it too. For sure we assume tumour cells are better at it – not least because they can send out advance signals giving them a better chance of a happy landing. And, of course, once a colony has been founded, tumour cells already carry mutated genes that can act as ‘drivers’ for further expansion of the secondary growth. Even so, the fact that normal cells can pass from the blood to a niche in lung tissue shows that colony foundation is not a unique property of tumour cells. Lung colonization by normal cells may be down to mechanics. Your lungs, which of course fit inside your chest, resemble a sponge – a mass of fine tubes linked to 300 million air sacs (called alveoli): spread them out and they’d cover a tennis court. The alveoli are surrounded by the most intricate network of blood vessels (called capillaries) and it is here that oxygen is transferred to blood. The fine capillaries may simply be a very effective trap – cells may become stuck without the requirement for any specific markers.

And the outlook?

We have therefore a dim picture of what is involved in metastasis but the presumption is that it may rapidly brighten. It’s not hard to see why metastasis is the culprit in the overwhelming majority of cancer deaths. By spreading to new sites cancers increase enormously the difficulty of detecting them, they become almost impossible to treat by surgery and the only strategy remaining is to use drugs (chemotherapy). Currently there are hardly any treatment options available for tumours that have metastasized and even when drugs do work their effects are short lived and tumours recur. The unveiling of every new facet of the amazing puzzle that is metastasis refines our thinking about the problem and carries with it the possibility of new targets and strategies for its blockade. The end is nowhere in sight but we are, at long last, making a significant beginning.

References

Ghajar, C.M. et al. (2013). The perivascular niche regulates breast tumour dormancy. Nature Cell Biology 15, 807–817.

Brabletz, T., Lyden, D., Steeg, P.S. and Werb, Z. (2013). Roadblocks to translational advances on metastasis research. Nature Medicine 19, 1104-1109.