Beware of Greeks …

Finding the words

One of the pitfalls of writing is repetition. Be it book, blog or broadsheet, most authors must dread someone gleefully chirruping ‘You used that exact phrase in 1999.’ I wonder if The Immortal Bard suffered likewise – having to resort to ferreting through piles of dusty manuscripts, finally in desperation shouting ‘Anne, Anne – got this great new line If you prick us do we not bleed? – Heard it before?’

‘Yes, of course dear. You used it in that thing about the Italian moneylender.’

‘Damn. Thought it sounded familiar. Where would I be without your memory – make me immortal with a kiss.’

‘Give over you daft beggar – even you know that’s one of that Marlowe bloke’s lines!’

‘Doh!’

I’m something of a sitting duck here, partly through not being Shakespeare but also because of the habit of often talking about biology. Take one simple example, Will’s tiny pinprick of blood – in which there will be about fifty million cells. That’s fifty million separate little sacs swirling around in a bead you wouldn’t notice if it wasn’t bright red. Isn’t that stunning for starters? Indeed, but it’s when we turn to molecular cancer that nature’s capacity to amaze is unfettered, the remarkable becomes the norm and even the English language can seem inadequate.

Finding the exit

A study of a mouse model of one form of leukemia is the most recent contribution to have us sifting Shakespeare’s superlatives to do justice to the discovery. Blood cells start life within the bone marrow but, until they’ve matured, they’re corralled by a marrow–circulation barrier, also made of cells. Adult cells normally make proteins on their surface that attach to the barrier, and these help them to squeeze past into the freedom of the circulation. In leukemia abnormal levels of white blood cells are present in the circulation, which means that those cells have also found a way through the bone barrier. A Prague group have shown that one type of leukemic cell has come up with an astonishingly novel escape mechanism in which they release fragments of their own DNA. That’s pretty staggering because not only is DNA generally locked in the nucleus but it comes in large chunks called chromosomes. So two very unusual things have happened to get to this stage: (1) some of DNA has been shattered and (2) these pieces have crossed not only the membrane that encloses the nucleus but also the outer boundary of the cell itself.

DNA fragments from tumour cells enter barrier cells and kill them, releasing tumour cells into the circulation

But then something even more extraordinary happens: having tunneled their way out of the tumour cell, the escaped bits of DNA do a kind of reverse reprise by entering the cells that form the barrier between bone marrow and circulating blood. It’s as though the barrier cells see the passing packages of DNA as presents and gobble them up. Alas! They should have read their Virgil – or at least Dryden’s summary of the tale of the wooden horse of Troy: ‘Trust not their presents, nor admit the horse’ – for the barrier cells pay the ultimate price for their gluttony. The DNA fragments are sensed as something abnormal – as indeed they are – and this provokes a stress response – and a pretty extreme one at that – because the cells are so overwhelmed by the influx that they commit suicide.

The capacity for individual cells to switch on a death program is an important part of life – it’s essential in normal development and it’s also the best cancer defence we have. In other words, if things get out of control, kill the cell – because that eliminates the danger and cells can be replaced. But here we have an almost stupefying paradox: in the tumour cells this defence is neutralized – but they’ve come up with a way of turning it on in the normal cells they have to get past in order to spread around the organism.

It’s another astounding example of the plasticity of our genetic material and the incredible adaptability of cancer cells. Even Mr. S. might feel adjectivally challenged!

Reference

Dvořáková, M. et al., (2012). DNA released by leukemic cells contributes to the disruption of the bone marrow microenvironment. Oncogene 10 December 2012; doi: 10.1038/onc.2012.553

Water Street Press Speaks

Writing a pop science book (or more precisely, getting one published) has, to use the contemporary argot, been something of a life-changing experience. That simply means finding yourself doing strange things and meeting wonderful people that otherwise you would never have encountered. In the former category comes giving a stand-up routine on the stage of The Cambridge Union Society  as part of a Science Festival show compered by the comedian Robin Ince. In the latter comes Lynn Vannucci. An author herself, she was simply amazing in editing the final version of the book, and from this has blossomed a friendship that I treasure. She has since set up her own publishing company, Water Street Press, the aims of which promise a new world for authors. This review is from the WSP website.

Water Street Press review of Betrayed by Nature: The War on Cancer:

“When one door closes another opens but we often look so long and regretfully upon the closed door that we do not see the one that has opened for us” – Alexander Graham Bell.

Lynn Vannucci, founder of Water Street Press

The fall of 2011 was a time of closing doors. Some of those doors I pulled shut myself. I was just starting to get a grip on both the enormous workload of, and the enormous opportunity in, becoming a publisher; clarity of purpose brought with it the need to clean house or clear paths or otherwise remove obstacles, and cleaning and clearing, while sometimes necessary, are time sucks and can be absolute spirit sappers.

Other doors felt as if they were being slammed in my face. A man named Daniel G. Reinhold—biologist, silversmith, computer genius, art collector, raconteur, crack shot, dog lover, father figure and (affectionately) Ogre—passed away, as did, in his absence, a part of my youth.

In the midst, then, of what was not a little bit of personal turmoil, I was asked to work on a book that was, at the time, called “Delinquent Genes,” about understanding cancer from the perspective of genetics—both the history of the disease and the strides that have been made in treating it. Now, if any of my old high school science teachers are reading this, they will be guffawing at the notion that I would be asked to work on such a book; none of them will remember me as their best student. But that’s exactly the value I bring to a book like this: I’m a filter. If I can understand the science, then the vast reading public, who are like me and not scientists, are going to understand it, too.

That doesn’t mean that biochemistry isn’t a stretch for me. But Robin Hesketh, the author of the book, has been a teacher in the Department of Biochemistry at the University of Cambridge and a fellow of Selwyn College for over twenty-five years; fortunately for me, and for his readers, he is a very, very good teacher.

The best part of working on the book, however—indeed, the best part of the book itself—is Robin, himself. The life of one out of every three people is going to be impacted by cancer; Robin was passionate about writing a book that would be of use to them—people who needed to understand the disease but who started out, as I had, with very little scientific background. When I didn’t understand a piece of the material, he was not only patient about explaining it yet again, his enthusiasm to do so never faltered. Cancer can be a devastating disease; Robin has spent his life studying it—has, like so many of us, suffered loss from it—and yet has not lost a charming, open optimism.

Optimism, like passion, is contagious. In the midst of a few tough months, working on a book about cancer was exactly the cure I needed. Betrayed by Nature is an important book—and it opened the door to a new and wonderful friendship.

Go here to buy Robin’s book, http://www.amazon.com/Betrayed-Nature-War-Cancer-Macsci/dp/0230338488, and go here, to his blog, for ever more information from this tireless and excellent teacher http://cancerforall.wordpress.com.

Dyslexic DNA

Writing in code

Did you notice a few months back that some boffins had written a book in DNA? No, that’s not a typo: what they did was to transcribe a 53,000 word book – plus pictures – into a synthetic DNA sequence. In essence, they re-wrote the book in binary by taking the four bases that make the genetic code of life and setting A and C to equal zero whilst G or T represented one. The result wasn’t without its typos: in the just over five million bits needed there were ten mistakes. So rather better than my touch-typing then. But there was a real commercial point behind this exercise, aside from showing, yet again, the astonishing coding capacity of our genetic material. One gram of DNA (you’ve got 500 grams) can store more than 100 billion DVDs, so not merely is it the ultimate in compacted data but it’s amazingly tough stuff – think of sequencing the woolly mammoth, in the freezer for thousands of years – by comparison with the latest software updates for my computer which usually mean I can’t read files 10 years old. And if I dig out my 20 year old 35 mm slides from the attic, chances are they’ll adorned by fungal growths.

Genetic switches

So DNA’s great for long-term information storage but this was by no means the first attempt to use biological molecules in ways we normally associate with electronic devices. When the code of DNA is ‘read’ to make an intermediate (RNA) from which, in turn, proteins can be made it’s acting as a biological transistor: a switch and amplifier that responds to an input signal. The DNA code ‘reader’ is a molecular machine called RNA polymerase (RNA pol) that moves step-wise along a strand of DNA, adding units one at a time to a growing molecule of RNA, complementary in sequence to the DNA template. This process is called ‘transcription’. In its wake another molecular machine can ‘translate’ the RNA codes into protein. RNA pol therefore ‘flows’ along a strand of DNA rather like a current of electrons through a transistor and, because RNA can makes lots of copies of a protein, the system has built-in amplification. Input control is via proteins that stick to segments of DNA called promoters and ‘switch on’ RNA pol (i.e., an analog input). After that the sequence of DNA itself can, in effect, say either ‘go’ or ‘stop’: short sequence motifs can wave RNA pol through or make it stall. The output signal is the protein made – and if you make green fluorescent protein (GFP) you can shine light on it and measure how much you’ve got from the fluorescence emitted.

Over the last few years a number of such gadgets have been made and inserted into bacterial cells to work as simple digital logic gates. In electronic-speak these have included DNA AND gates (giving a high output only if two inputs are high) and OR gates (a high output if one or both the inputs to the gate are high). They’re genetic transistors, processing signals like the logic gates built from transistors that, in combinations of billions, are the basis of computer memory and microprocessors.

Throwing a DNA switch

So what’s new?

For biological gates the problem has been that each needs its own construct (a DNA plasmid) and to make more complicated bits {e.g., EXCLUSIVE OR (XOR) gates (high output only if the inputs are different) or EXCLUSIVE NOR (XNOR) gates (output high only if inputs equal)} lots of constructs are required, each having to be persuaded to enter bacteria and to work in a stable fashion.

Step forward Drew Endy and colleagues from Stanford who, by dint of some very clever molecular biology, have combined multiple logic elements into a single construct – which they call a ‘transcriptor’. The switching capacity of their devices comes from integrases – enzymes made by viruses that infect bacteria – that can invert (flip) short stretches of DNA. These can be designed as switchable ‘go’ or ‘stop’ signals for RNA pol. Back in the 1940s Barbara McClintock, working on maize, discovered that stretches of DNA can be shifted around within the genome – they’re called ‘transposons’ – and integrases do the same thing as the enzymes that switch transposons around. McClintock remains, incidentally, the only lady to win a Nobel Prize for Medicine on her own. The great thing about integrases is that they can be turned on simply by adding the appropriate activator to the medium surrounding the cells.

This remarkable advance means that essentially any kind of gate can be built into a single, synthetically made genetic transistor, regulated by a range of integrases. The potential is somewhat mind-boggling but includes being able to monitor in real time the effects of drugs on the behavior of individual cells.

When John Bardeen, Walter Brattain and William Shockley (a Brit by origin but really another Stanford man) invented the transistor (they got the 1956 Nobel Prize in Physics) they can have had little idea of the impact it would have on mankind. But they really would have been staggered to know that, 60 years on, their successors would be shaping our genetic material to act as semiconductors in living cells.

Anything else?

So, as far as I can see, Drew Endy and his chums have done pretty well everything except build an EOR gate that responds to any input with “Don’t blame me”. But they’re such smart guys I bet they’ve got one of those in the fridge too – it was just that the journal editor lacked a sense of humour and wouldn’t publish it. Science editors have form in this department – recall the tale of Albert Szent-Gyorgyi who, whilst a member of my department back in the 1920s, isolated ascorbic acid (the vitamin that stops you getting scurvy) and, convinced it was a sugar (so it should have the suffix -ose – it’s actually made from glucose by oxidation) but not knowing the exact structure, sent his results to the Biochemical Journal calling it ‘ignose’. When the editor said ignose was silly Albert suggested ‘godnose’, getting a predictable response!

References

http://www.guardian.co.uk/science/2012/aug/16/book-written-dna-codehttp://www.huffingtonpost.com/2013/03/29/biological-computer_n_2981753.html

Bonnet, J., Yin, P., Ortiz, M.E., Subsoontorn, P. and Endy, D. (2013). Amplifying Genetic Logic Gates. Science 28 March 2013 / Page 1/ 10.1126/science.1232758http://www.sciencemag.org/content/early/recent

A Word From Down Under!

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 4^th century the local Roman landowner built himself a house. Unfortunately it was later buried by a landslide and remained thus until the 20^th 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

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.

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

Getting your DNA in a twist

I have a good friend who has just emerged triumphant from a run-in with bowel cancer – she’s in complete remission! Almost as wonderful is the fact that colliding with cancer has converted her from a genuine non-scientist to one who devours biology like fish and chip suppers. Spotting a recent volley of media items about four-stranded ‘quadruple helix’ DNA in human cells, she was on Twitter in a flash: “Does this mean that people with cancer have lots more quadruplex DNA than normal?” As she knows I can’t stand the Tweet cult she was probably amazed to get a reply: short answer: “No.”

But as ever in science, there’s a long(er) response. So, if you’re interested in the gyrations and gymnastics of which your genetic code is capable, read on …

The DNA double helix

Beautiful DNA

As you know, DNA comes as a double helix – a 2-chain spiral of small units (called nucleotides) that stick together (the units contain bases, so they’re ‘base-paired’). The oft-reproduced double helix image is beautiful because it’s a repetitive structure and you can easily see how it can be ‘unzipped’ so that each half can be used as a template to make a copy and regions can be ‘read’ to make RNA and proteins – though it was really designed to enable biologists to make endless unzipping jokes about genes and jeans.

The two DNA molecules of the helix stick together because of a balance between three forces: (1) weak electronic attraction between some atoms in the bases (called hydrogen bonds), (2) a sort of glueyness between the bases because their chemical structure means they don’t like water much and they’d rather snuggle up together, and (3) a repulsion between the chains because of the repeated phosphate groups all the way along the backbone (these carry an electric charge and likes repel, as we know).

Ugly DNA

But with all these attractions and repulsions you might think there would be lots of ways nucleic acids could get tangled up with each other – and there is. So the common form of double helix (the beautiful shape) is B-DNA but there’s also A-DNA, C-DNA and Z-DNA. If you just change the conditions a bit (pinch of salt or whatever) you can tweak the interactions so bits of the bases that don’t interact in B-DNA will do so to give a slightly different shape (usually a bit distorted – ugly). As you can see from the structure, Z-DNA is more Homer Simpson than Watson and Crick.

B- and Z-DNA

B-DNA and Z-DNA

We can’t reproduce the environment of DNA in the nucleus so we don’t really have a clue but the betting is that short bits of DNA jink in and out of these odd structural formations – just as part of the continuous flexing of the molecules. There’s also a couple of other things that can happen that have been known for a long time – again just dependent on the precise conditions in which a piece of DNA finds itself.

Sexy modelling

The first is a variant on the hydrogen bonds that form between bases. One way to think of this is to imagine two circles of five people, each ring holding hands and facing outwards. Each person is an atom in the bases of DNA. Let’s think of base pairing as the two nearest in the circles getting close enough to kiss. That’s one hydrogen bond. But, of course, the two other pairs on either side will now be quite close: if one of them also manages to kiss (tongues may be used) now we have two hydrogen bonds – which is what holds the bases A and T together. But suppose that the pair on the other side (who must also be quite close with all this adjacent necking going on) decide they really fancy joining in and are so excited that they twist the circle out of shape to do so. That this can happen has been known for years (it’s called Hoogsteen base pairing after the voyeur what spotted it) and when it does it can distort the helix enough for a third DNA strand to wrap round the original two – so you get triple-stranded DNA.

A sexual need

Similarly, if you tweak the conditions you can get four strands of DNA to come together and indeed we’ve known for yonks that happens naturally during recombination (that’s when genetic material gets swapped between Mum and Dad chromosomes – the reason for sex). When that happens you can think of four DNA strands forming a cross, each quadrant contains DNA from one strand of a chromosome, base-paired to that in the next quadrant – which is how bits get swapped around.

Non-sexual hugging?

So there’s nothing new about odd DNA shapes but what has made the news is that for the first time, rather than looking at what can be made to happen in a test tube, Shankar Balasubramanian and his pals have looked in whole cells. To do this they made an antibody that sticks only to ‘quadruple helix’ DNA structures – G-quadruplexes. The upshot is that they detected quadruplexes scattered throughout chromosomes and they see more in cells that are rapidly dividing than in ones that are just sitting there (they looked in some cancer cells in culture that do divide quite rapidly – but bear in mind that in tumours cells aren’t diving all that fast). So the inference is that they might form as part of DNA replication and, if you can target them by their antibody, maybe you could do something similar with a drug that would stop cells dividing. And if you could target that to cancer cells you could stop them in their tracks.

And the catch …

Simple. But there are some problems. It’s possible the antibody helps the quadruplexes to form – so it could even be a cunning artifact. But if we assume it isn’t – then we come face to face with a really big problem. There are zillions of ways you can kill cancer cells. The difficulty is that there isn’t one that selects cancer cells from normals. It may be possible (though it’s not evident how) to target quadruplexes and block cell division – but there are lots of cells that we need to divide rapidly just to keep us going – and, if quadruplexes are real, presumably they have ’em. So non-specific killing is probably not a good idea. Twas ever thus.

References

Biffi, G., Tannahill, D., McCafferty, J. and Balasubramanian, S. (2013). Quantitative visualization of DNA G-quadruplex structures in human cells. Nature Chemistry published online: 20 January 2013 | doi: 10.1038/nchem.1548

http://www.cam.ac.uk/research/news/four-stranded-quadruple-helix-dna-structure-proven-to-exist-in-human-cells/

A few Choice words

The American Choice Reviews on line has this to say:

50-2688 RC275 2011-49931 CIP Science & Technology \ Health Sciences Hesketh, Robin.  Betrayed by nature: the war on cancer.  Palgrave Macmillan, 2012.  255p bibl index; ISBN 9780230338487, $28.00. Reviewed in 2013jan CHOICE. • New from Palgrave Macmillan • Reviewing a scientific treatise can be a routine task or occasionally an overall delight when the excellence of the approach, the writing style, and the scope and caliber of the subject coverage are of the degree found in this work by Hesketh (biochemistry, Univ. of Cambridge, UK). The comprehensive coverage of the many facets of cancer never leaves the reader feeling overburdened with too much information. The text flows smoothly from topic to topic, with chapters divided into four parts focusing on history and background information, genetics and cell changes, cancer cells, and diagnosis and therapy; coverage is adequate to indicate the relevance of each topic to the overall theme. The author writes in a somewhat personal and narrative style, with occasional well-placed tidbits in a lighter vein. Of the nine chapters, the last, “Where Are We? Where Are We Going?,” presents a well-thought-out synopsis of the current status of cancer and an assessment of what the future may hold for cancer victims. A glossary and a listing of cancer information resources support the text. Because of the overall excellence of this work, it is a “must read” for anyone who wishes to update his knowledge of this disease. Summing Up: Essential. All levels/libraries. – R. S. Kowalczyk, formerly, University of Michigan
More titles from Palgrave Macmillan
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Junk Store Opened: Millions of Bargains

Many moons ago, when I was nobbut a lad and sequencing the human genome was 30 years away, we nevertheless knew that there was something very odd about our genetic code. We knew there were three thousand million base pairs but that only a tiny fraction of that (a few percent) was necessary to encode all the proteins found in our bodies. What was the rest doing? As a sort of explanation two terms came into vogue: ‘selfish DNA’ (meaning stuff that just reproduced itself because it was there) and ‘junk DNA’ meaning everything that didn’t code for proteins.

One of the few predictions I’ve made that turned out to be right was embodied in a refusal to use either term – and if there’s anyone who can recall anything of my supervisions (that is, what the rest of the world calls tutorials) they might back me up on this. It’s true that, as time went by, we increasingly appreciated that non-coding DNA is important in controlling whether individual genes are switched on or off – that is, whether they make RNA and from that protein, according to sequences embedded in the DNA, or whether they make nothing.

However, getting a real grip on what all that seemingly spare DNA is doing has turned out to be so challenging that it is only now, 10 years after the first human sequence was produced, that we have hard data to go on. That unveiling has come from a follow-up called the ENCODE (Encyclopedia Of DNA Elements) programme – an international cooperative of extraordinary scale, with its heart at The Sanger Centre just outside Cambridge and with its head one Ewan Birney. Birney is a computational biologist – a new breed of scientist whose strength lies in bringing to bear methods that make sense of the vast amounts of data generated by current DNA sequencing techniques.

A glance at the summary of what ENCODE involved suggests that, in the unlikely event of his getting bored with science, Birney would make a pretty good fist as Secretary-General of the United Nations. I’d like to try and persuade you that scientists are wonderful and lofty forms of our species but, alas, in fact they are generally ambitious, driven, self-centred, ruthless and intolerant. To make matters worse, quite a few are very smart. To get nearly 500 of the world’s best to sink self-interest and focus on one aim in a multi-national, multi-lingual, multi-racial collaboration that requires rigorous assessment of data and in which the scope for individual glory is almost negligible might well qualify as the greatest feat of man-management in the history of the human race.

So Birney’s a star but what did the world get for its money? The short answer is that we now know that, far from being ‘junk’, most of our DNA – over 80% – does something useful. Whilst only 1.6% carries protein-coding genes, much of the rest is important in regulating the activity of proteins generated from coding genes. The regulatory activity comes in the form of RNA: as we noted just now, DNA makes RNA makes protein – and the DNA sequences involved are called genes. But there’s a second class of genes, ones that transcribe DNA sequence into RNA – but then things stop. The RNA doesn’t go on to direct the making of proteins but rather goes off and regulates well, almost everything. So this second group are non-coding genes – because they don’t ‘make’ proteins.

How does the RNA of non-coding genes work? Well, in essence by sticking to other RNAs and to proteins themselves. What ENCODE has revealed is a panoply of types of RNA that comes in a wide range of sizes and has a finger in almost every bit of the cellular pie. So these varied RNAs act as cellular controllers at many levels and because cancers result from the subversion of normal control you would correctly guess that mutations in non-coding genes can be every bit as important as those that affect protein function directly.

Does this help in dealing with cancer and are there any bargains in the junk store? The short-term answers are ‘no’ and ‘lots – in theory’. As units of this army of RNAs help to control how we work normally, they also can go wrong – become mutated – so we have a new set of potential players in the cancer game. Detecting when individual RNAs join in won’t be so difficult: the real cancer challenge now is not target-spotting, it’s making the bullets to hit the targets.

Reference

Maher, B. (2012). ENCODE: The human encyclopaedia. Nature 489, 46-48.

Birney, E. (2012). The making of ENCODE: Lessons for big-data projects. Nature 489, 49-51.

No Surprise Here Then

The announcement that the 2012 Nobel Prize in Physiology or Medicine had gone to John Gurdon – jointly with Shinya Yamanaka – might well enter the Guinness Book of Records as the least surprising in history. Certainly in Cambridge, where Gurdon has worked since 1971, for as long as I can remember it has always been a matter of ‘when’ not ‘if.’ I guess having The Institute for Cell Biology and Cancer named after you, as it was in 2004, is a bit of a clue to his standing.

Sir John Gurdon, FRS

The work that launched Gurdon’s career in the 1960s showed, in effect, that the nucleus of every cell in the body contains the same genes – that is, the complete sequence of the individual’s DNA. The basic method was to use frogs, replacing the nucleus of an egg cell with that of a mature cell taken from the intestine. The fact that the modified egg turns into a normal tadpole shows that all the information needed to make the animal is retained in the DNA code of fully developed cells.

Frog eggs

Many years ago (over 30, I’m abashed to calculate) I was lucky enough to receive a personal demo of how to manipulate frog eggs in Gurdon’s lab from a friend who worked with him. As everyone knows, the eggs are quite big – about 1 mm in diameter – so you don’t need a microscope to see them – and in her hands fiddling with their nuclei looked pretty easy. It’s not, of course, which is why Gurdon’s early experiments caused controversy: not only were the results completely unexpected but quite a few people failed to reproduce them until sufficiently skilled hands had a go.

Shinya Yamanaka, working in Kyoto, followed this up by unveiling the specific genes that are needed to make ‘pluripotent’ cells – cells that have the capacity to develop into any of the many cell types that make up a body. In a series of the most elegant molecular biology manipulations, he started with a large panel of genes previously implicated in controlling embryonic stem cells. From these he teased out four that, when ‘switched on’ to make their encoded proteins, can confer pluripotentcy.

Dr. Shinya Yamanaka

Their work has already had massive consequences. It’s founded a new branch of science – stem cell biology. Most famously, this has produced Dolly the Sheep – the first mammal to be cloned from an adult cell – but it has also led to skin being grown in the lab for use as grafts to repair burns and, even more astonishingly, to the creation of entire organs (e.g., bladder) from the patient’s own cells to provide a transplant that will not give rise to an immune response and hence rejection.

It has also had an impact on cancer – perhaps unsurprisingly given that the genes identified by Yamanaka can rejuvenate cell growth, and abnormal proliferation lies at the heart of the disease. Two of the pluripotent genes he identified are ‘oncogenes’, that is, they can help to drive tumour development (Myc and Klf4). This has generated the ‘cancer stem cell hypothesis’ that arises from the fact that some of the cells in tumours have features similar to those found in embryonic stem cells (e.g., they can be distinguished because they make the some of the same surface proteins). The significance, of course, is that working out how to control pluripotency may also reveal ways of targeting cancer cells.

So none would argue the award is overdue – Gurdon’s former schoolteacher, who wrote that ‘his ideas about becoming a Scientist’ are ‘on his present showing … quite ridiculous’ and whose report he still keeps, is presumably imparting his perception in the classroom in the sky.

But how has the Prize affected Sir John, you might wonder? Well, not detectably in that he has commented that‘It isn’t going to be particularly productive to clear off to some exotic place and I don’t have a yacht’ and indeed, most days you can still spot a tall, distinctive figure walking determinedly along Tennis Court Road, where The Gurdon Institute lives, usually with woolly hat pulled firmly down against the elements, at 79 years young the very embodiment of what science is really about.

References

Gurdon, J. B.; Elsdale, T. R.; Fischberg, M. (1958). “Sexually Mature Individuals of Xenopus laevis from the Transplantation of Single Somatic Nuclei”. Nature 182, 64–65.

Gurdon, J. B. (1962). “The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpoles”. Journal of Embryology and Experimental Morphology 10, 622–640.

http://www.nobelprize.org/nobel_prizes/

One Book Good, Two Books Better?

Well, from the author’s viewpoint it’s a no-brainer in the regrettable modern argot but, aside from that lone and far from impartial figure, it probably depends on who’s doing the reading. So let’s get the basics clear: this blog is about current topics related to cancer and the idea is to follow – albeit even more colloquially – the style and content of Betrayed by Nature (that’s Book 1, by the way).

Book 2 has just come out and it’s a textbook. The title tells all: Introduction to Cancer Biology – written to take students from high school/sixth form to degree level in cell & molecular biology and cancer – or indeed anyone else who moves into the field from what’s sometimes deferentially referred to as the ‘hard sciences’ (that means, for example, folk like physicists and maths whizzos who decide to take on the challenge of disentangling cancer).

So, of course, the Christmas message is “Read both” – but, being serious for a mo, only take on Book 2 if you are (or at least thinking of becoming), ‘a serious scientist’ and, contrary to what you may be told, there aren’t many of them – we really are jolly souls and labs resound to shrieks of mirth and girlish giggles (and that’s just the blokes).

So by the end of Book 2 we’ve met a lot of genes and much of the complexity of cancer is laid bare in grizzly detail, whereas in BbN the aim is to tell the essential story in entertaining style. Even so, both books were written with the same guiding principle: the way our cells behave – and misbehave – is a wonderful, compelling tale and they come together as a work of art – a human being. The challenge for the author is to convey all that through the words you put down on the page.

I’m not the first scientist to recognise the problem. Max Born (who won the 1954 Nobel prize in physics for his work on quantum mechanics – he was great mates with Werner Heisenberg – of uncertainty fame) wrote “To present a scientific subject in an attractive and stimulating manner is an artistic task, similar to that of a novelist or even a dramatic writer. The same holds for writing textbooks.” Couldn’t have put it better Max.