Holiday Reading (2) – Poking the Blancmange

An evolutionary hiccup

It’s well known that tracing our family tree back 400 million years reveals a fishy past. This history is enshrined in our DNA in the pattern of nerves that control breathing. From time to time that control throws a wobbly in the form of involuntary spasms of the diaphragm manifested as a fit of hiccups – what the medics call singultus, which in Latin means sobbing – readily brought on by contemplating a comprehensive map of intracellular signalling pathways. Hiccups, however, are caused, as Neil Shubin, in his wonderful book Your Inner Fish has explained, by a mis-firing neuron in our brain stems that produces the type of electric signals that control the regular motion of amphibian gills. A genetic recipe hoarded in the nuclear loft is inadvertently recalled. For the most part this result of DIY evolution is no more than mildly embarrassing, although the poor fellow who made the Guinness Book of Records by hiccupping for 68 years may have used a stronger term.

As we’re really talking about cancer, we should mention that persistent spasms of hiccups and difficultly swallowing may be indicators of esophageal cancer, where a tumour in the gullet (the tube connecting the back of the mouth to the stomach) grows into the trachea and flips the hiccup switch by mechanical pressure.

Je pense, donc je suis un blanc-manger

Whilst the key feature of all these pathways is that they connect the outside world to the nucleus of a cell, it’s become clear that each pathway does not exist in isolation. Individual pathways can talk to each other – sometimes called cross-talk – individual domino runs intersecting, if you like. So evolution has cooked up thousands of proteins floating around in our cells that can be mapped into discrete signal pathways but, in the molecular jostle of the cell, each may affect any of the others – if not directly then via just a few intermediates. To avoid the Tokyo subway syndrome it’s easiest to think of the cell as a blancmange: poke it anywhere and the whole thing wobbles.

NetworkBlancmange

The complex network of signalling pathways in cells.

Left: the dots represent proteins that inter-communicate (lines) – best thought of as a blancmange.

Why is grasping this picture of what seems like a molecular madhouse important? Well, one thing we should bear in mind is that the set-up may look chaotic to us but our cells somehow make perfect sense of it all because they take clear decisions as to what to do. But the reason for grappling with it at all, other than to be humbled by our ignorance, is that these signal systems are a major target for anti-cancer drugs. To be more precise, it’s disruptions in these proliferation-controlling pathways, caused by mutations, at which we take aim with the contents of our drug cocktail cabinet.

What goes wrong in cancer?

If you want a three word definition of cancer ‘cells behaving badly’ will do fine. If you insist on being scientific ‘abnormal cell proliferation’ covers it nicely, meaning that control of cell replication has been overcome to the extent that cells reproduce more rapidly than they should or at an inappropriate time or in the wrong place. Underlying this abnormal behaviour is damage to DNA, that is, mutations. This remains true even if the initial cause does not directly affect DNA. It’s estimated that about 20% of the global cancer burden comes from infections, mainly in contaminated drinking water. These can cause chronic inflammation that eventually leads to mutations and thence to cancer. Other factors, for example, tobacco smoke and radiation, can directly damage DNA and about 10% of cancers are set off by what you might call a taxing inheritance – mutations already present in DNA at birth.

The capacity for high-throughput sequencing of complete human genomes has spawned ambitious projects that include Genomics England’s sequencing of 100,000 genomes by 2017 and The Cancer Genome Atlas that aims to provide a mutation data base for all the major cancers. One of the most mind-boggling facts that has already emerged from this revolution is the extent of disruption that can occur in the genomes of cancer cells: as many as one hundred thousand mutations within one cell. For the sake of completeness we should note that, cancer being cancer, the mutational spectrum is astonishing and, at the other end of the scale, there’s a childhood leukemia that results from just one change to DNA and there’s a type of central nervous system tumour that appears to develop without any mutations at all. For the most part, however, cancer cells carry a mind-boggling number of mutations and the assumption, nay hope, is that the vast majority of these changes are ‘passenger’ mutations that do not affect cellular behaviour: they’re a by-product of the genetic mayhem characterizing cancer cells. The ones that count are ‘driver’ mutations that can arise in any of several hundred of our 20,000 or so genes, changing the activity of the proteins they encode to contribute to cancer development. Only a small number (half a dozen or so), of these drivers, acting together, is required for cancer to emerge. Thus, although only a relatively small group of ‘drivers’ is needed, almost limitless combinations can arise.

The accumulation of mutations takes time, which is why cancers are largely diseases of old age: two thirds of them only appear in people over the age of sixty. The estimate is that if we lived to 140 everyone would get cancer but, pending that happy day, when or whether the disease manifests itself in an individual is indeed a matter of genetic roulette – genetic evolution within cancer cells. So wonderful has the technology become we can now inspect individual cells in tumours to reveal that driver mutations occur in single cells that can expand to form groups of cells, called clones. These multiple clones can modulate their mutational profile independently and, as a result, proliferate at different rates. So you can picture tumours as a complex patchwork of genetically related, competing clones. In other words, as we’ve suspected all along, cancers are a form of dynamic Darwinism.

The critical point is that key mutations drive cancer and they do so by upsetting the normal working of signal pathways that control whether cells proliferate or not. You could say it’s Nature poking the blancmange but these are delicately selected pokes – the product of the evolution of a cancer’s genetic signature – that just tweak signalling mechanisms enough to make cells a little more likely to multiply. In coming up with drugs that target specific mutations we’re giving the blancmange another poke – the aim being, of course, to prod it back to normality.

An obvious question

Having mentioned that, albeit very rarely, cancers emerge that don’t seem to be driven by changes in the sequence of DNA – how do they do that? The answer lies in epigenetic modifications – any modification of DNA, other than in the sequence of bases, that affects how an organism develops or functions. They’re brought about by tacking small chemical groups either on to some of the bases in DNA itself or on to the proteins (histones) that act like cotton reels around which DNA wraps itself. In effect this makes the DNA more difficult to get at for the molecular machines that turn the information in genes into proteins. So these small chemical additions act as a kind of ‘super switch’ that can, for example, block genes that act as brakes on cell proliferation – hence promoting cancer.

Reference

Neil Shubin Your Inner Fish, Random House, 2008.

Molecular Mosaics

Piazza Armerina is a little spot more or less in the centre of Sicily. It is in other words, with due respect to our Sicilian readers, pretty well the middle of nowhere. But you really should go there, off the beaten track though it is, because in the 4th century the local Roman landowner built himself a house. Unfortunately it was later buried by a landslide and remained thus until the 20th century when an excavation revealed that the villa contained the most extensive set of mosaics anywhere in the world. I should tell you that it takes a fair bit to get me excited about archaeological remains but I defy anyone not to be reduced to dropped jaws and softly exhaled ‘wows’ by the Villa Romana del Casale. The mosaics are vast and the scenes depicted span many aspects of the life of the times, from hunting to circuses and, although they won’t tell you who invented the bikini (and of course you’ve wondered!), the images of the ten ‘Bikini Girls’ reveal, so to speak, that such a garment, or lack of it, enlivened the Sicilian summer back in the days when Constantine & Co. were running the show.

Bikini girls

Bikini girls

How big is ‘vast’?

Mosaics seem to me unique among human creative endeavours because you may readily recognize the technical craft and bathe in the history or beauty displayed, as with other art forms, but after a bit you can’t ignore the feeling of sore knees and a twinge of back ache as your body goes into sympathetic spasms with the poor blighters who toiled away for decades to make the things. And how! In the Villa Romana there are 37 million colored tiles – each unique if examined closely enough, each set in position with loving care, each making its minute contributing to the whole.

Catching up – and overtaking – the Romans

It’s taken us seventeen centuries to come up with anything to match the complexity of such creations but the astonishing advances in sequencing our genetic code are now laying bare the mosaicism of tumours. The basic idea is simple to grasp: chip out little bits from different regions of a primary tumour and from secondary growths (metastases) that have seeded from the primary. Then throw the full power of DNA sequencing at them.

The picture that emerges is also simple to describe. Different regions of a tumour – as well as any secondary growths (formed when cells migrate through the circulation to lodge in other sites around the body, called metastases) – differ from each other. They have different ‘DNA signatures’. In other words, although the whole thing starts from a common ancestor (a starter cell if you like), tumours diverge as they grow. So you can think of them like evolving species – and draw family trees just like the ones that show how long it was since you were a chimp.

Kidney tumor muts.006Kidney Tumor tree

Dissecting a tumour (left) and its evolutionary tree.  R1-6: regions of a primary tumour; M: a secondary metastasis. The length of the lines between the kinks is proportional to the number of mutations picked up – thousands of them – on that stretch of the journey.

So tumours are a mosaic …

Indeed. Things are actually even more complicated than that because the sequence obtained for each bit is an average – it’s the predominant mutation pattern. That’s because even a small piece of tissue, say a millimetre in diameter, contains billions of cells (yes, that’s a thousand million) and, if you looked closely enough, you’d find that each individual cell has quirks in its DNA sequence that are all its own. Each is unique – like the tiles of the Villa Romana.

So what?

The molecular complexity, even within one tumour, is utterly mind boggling, but there are two good reasons why we should know what is being unearthed and make an effort to come to terms with it.

The first is that, although cancers are an aberration, the cellular variety they embody is a wonder to behold and the adaptability – mutability if you like – that they reveal gives us a new vantage point from which to contemplate the breathtaking variety of the natural world.

The second is more prosaic: if we’re going to reduce cancers to readily treatable conditions, we must understand the nature of the challenge – what makes a cancer cell tick. However stupefying the picture, that is what we are tackling and the more we know the more rational we can be in dealing with it.

So that’s good news?

Indeed. We’re approaching the point where it would be possible to offer this sort of screen to all new cancer patients and one benefit would be that we’d stop giving people drugs that won’t do any good – because they won’t hit the mutations carried by that individual. Such a programme would make a sizeable hole in the NHS budget but let’s follow the governmental example and not worry about money because we’ve got enough problems with the science. Although the huge number of mutations is daunting, a cheering point is that we can ignore most of them because we know that what’s important is a relatively small set of ‘driver’ mutations – the ones that force the abnormal cell proliferation that is the key feature of cancers – the rest are ‘passengers’, collateral DNA damage if you like, that surf along for the ride.

So we aren’t looking for drugs that can reverse all mutational effects – just enough to hit the drivers.

And the bad news?

We don’t have them. That is, there’s a huge number of drugs that are used against cancers but hardly any of them are ‘specific’ – actually target a molecular defect. Most are like a kind of shotgun that may affect cancer cells but does a lot of collateral damage. Cancers are driven by combinations of driver mutations, of which there are perhaps 20 or so that can come into play, and it’s the specific combinations of those in a given tumour that we need to target.

All of which means that there are two huge challenges: (1) to produce new drugs with good specificity that can hit the major drivers and (2) to be able to deploy them in combinations that give us a chance of outwitting the defences of cancer cells – namely mutating to use other drivers and getting rid of drugs by pumping them out. So, the biology is stunning but, despite the outrageous items that occasionally appear in our newspapers, it is difficult to be optimistic on anything other than a very long time-scale.

If, back in 330 AD, that Roman gent had said to his builder “So here’s the deal, chief: we’re aiming to decorate this place with about 40 million tiles” there would for sure have followed a good deal of stylus sucking as a prelude to “Can’t be done, Magister. Not with all the slaves in Rome” But it was. It just took a very long time and a lot of effort.

Reference

Gerlinger, M. et al., (2012). Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. The New England Journal of Medicine 366;10 nejm.org March 8.

http://www.telegraph.co.uk/health/healthnews/9832535/DNA-map-offers-hope-on-cancer-treatments.html