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.

Re-writing the Manual of Life

A little while ago we talked about a fantastic triumph by a team at Great Ormond Street Hospital (Gosh! Wonderful GOSH) in using a form of immunotherapy to save a little girl. What they did was to take the T cells from a sample of her blood and use gene editing – molecular cutting and pasting – to remove some genes and add others before growing more of the cells and then putting them back into the patient.

Gene editing – genetic engineering that removes or inserts sections of DNA – uses engineered nucleases, enzymes that snip DNA but do so in a controlled way by homing in on a specific site (i.e. a defined sequence of As, Cs, Gs and Ts).

We mentioned that there are four main ways of doing this kind of engineering – the GOSH group used ‘transcription activator-like effectors’ (TALEs). However, the method that has made the biggest headlines is called CRISPR/Cas, and it has been very much in the news because a legal battle is underway to determine who did what in its development and who, therefore, will be first in line for a Nobel Prize.

Fortunately we can ignore such base pursuits and look instead at where this technology might be taking us.

What is CRISPR/Cas?

CRISPRs (pronounced crispers) are bits of DNA that contain short repetitions of base sequence, each next to a ‘spacer’ sequence. The spacers have accumulated in bacteria as a defence mechanism – they’re part of the bacterial immune system – and they’re identical to sequences found in viruses that infect microbes. In other words, the cunning bugs pick up bits of dangerous viruses to make a rogues gallery so they can recognize and attack those viruses next time they pop in.

Close to CRISPR sit genes encoding Cas proteins (enzymes that cut DNA, so they’re ‘nucleases’). When the CRISPR-spacer DNA is read by the machinery of the cell to make RNA, the spacer regions stick to Cas proteins and the whole complex, including the viral sequences, can roam the cell seeking a virus with genetic material that matches the CRISPR RNA. The CRISPR RNA sticks to the virus and Cas chops its DNA – end of virus. So Cas, by binding to CRISPR RNA, becomes an RNA-guided DNA cutter.

crispr-pic

CRISPR-CAS: Bug defence against invaders. Viruses can attack bacteria just as they can human cells. Over time bugs have evolved a cunning defence strategy: they insert short bits of viral DNA into their own genome (above). These contain repeated sequences of bases and each is followed by short segments of ‘spacer DNA’ (above). This happens next to DNA that encodes Cas proteins so that both are ‘read’ to make RNA (transcription). Cas proteins bind to spacer RNA, leaving the adjacent viral RNA free to attach to any complementary viral DNA it encounters. The Cas enzyme is thus guided to DNA that it can cleave. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats.

Why is CRISPR/Cas in the headlines?

We saw in Gosh! Wonderful GOSH how the Great Ormond Street Hospital team tinkered with DNA and in Self Help – Part 2 we summarized another way of doing this using viruses (notably a disabled form of the human immunodeficiency virus) to carry novel genes into cells.

A further arm of immunotherapy attempts to reverse an effect called checkpoint blockade whereby the immune system response to tumours is damped down – e.g. by using antibodies that target a protein called PD-1 (Self Help – Part 1).

Now comes news of a Chinese trial which will be the first time cells modified using CRISPR–Cas9 gene editing have been injected into people. The chap in charge is Lu You from Sichuan University’s West China Hospital in Chengdu and the plan is to take T cells from the blood patients with metastatic non-small cell lung cancer for whom chemotherapy, radiation therapy and other treatments have failed.

The target will be the PD-1 gene, the idea being that, if you want to stop PD-1 doing its stuff, far better than mucking about with antibodies is to just knock out its gene: no gene no protein! What could possibly go wrong?

Well, wonderful though CRISPR is, it doesn’t always hit the right target but in this trial the cells can be tested to make sure it’s the PD-1 gene that’s been zonked – so that shouldn’t be a problem. However, it’s a blockbuster in that all the multiplied T cells put back into the patient will be active – i.e. will have lost the PD-1 brake. Whilst that may be good for zonking tumours, goodness knows what it might do elsewhere.

The initial trial is on a small scale – just 10 people. If there are problems one possibility is to try to take the T cells from the site of the tumour, which might select those specifically targeting the tumour – not straightforward as lung cancers are difficult to get at.

Anyone for a DNA upgrade?

It’s hard to say where all this is leading. However, as Chinese scientists have already made the first CRISPR-edited human embryos and the first CRISPR-edited monkeys, the only safe bet is that China will be to the fore.

 

The Shocking Effect of Boiled Bugs

There’s never a dull moment in science – well, not many – and at the moment no field is fizzing more than immunotherapy. Just the other day in Outsourcing the Immune Response we talked about the astonishing finding that cells from healthy people could be used to boost the immune response – a variant on the idea of taking from patients cells that attack cancers, growing them in the lab and using genetic engineering to increase potency (generally called adoptive cell therapy).

A general prod

Just when you thought that was as smart as it could get, along comes Angus Dalgleish and chums from various centres in the UK and Spain with yet another way to give the immune system a shock. They used microorganisms (i.e. bugs) as a tweaker. The idea is that bacteria (that have been heat-killed) are injected, they interact with the host’s immune system and, by altering the proteins expressed on immune cells (macrophages, natural killer cells and T cells) can boost the immune response. That in turn can act to kill tumour cells. It’s a general ‘immunomodulatory’ effect. Dalgleish describes it as “rather like depth-charging the immune system which has been sent to sleep”. Well, giving it a prod at least.

bugs-pic

Inactivating bugs (bacteria) and waking up the immune system.

And a promising effect

The Anglo-Spanish effort used IMM-101 (a heat-killed suspension of a bacterium called Mycobacterium obuense) injected under the skin, which has no significant side-effects. The trial was carried out in patients with advanced pancreatic cancer, a disease with dismal prognosis, and IMM-101 immunotherapy was combined with the standard chemotherapy drug (gemcitabine). IMM-101increased survival from a median of 4.4 months to 7 months with some patients living for more than a year and one for nearly three years.

Although the trial numbers are small as yet, this is a very exciting advance because it looks as though immunotherapy may be able to control one of the most serious of cancers in which its incidence nearly matches its mortality.

References

Dalgleish, A. et al. (2016). Randomised, open-label, phase II study of gemcitabine with and without IMM-101 for advanced pancreatic cancer. British Journal of Cancer doi: 10.1038/bjc.2016.271.

 

Mutating into Gold

It’s probably just as well that few us are aware that the bodies we live in are a battlefield – the cells and molecules that make us are in constant strife to ensure our survival. The lid is lifted from time to time – when we get a cold or pick up some other infection and our immune response sorts it out but not without giving us a headache or a runny nose, just to let us know it’s on the job. By and large though, we plough our furrow in glorious ignorance.

Saving our cells

Perhaps the most important of all the running battles is to save our DNA – that is, to repair the damage continuously suffered by our genetic material so we can carry on. It’s an uphill struggle. The DNA in one of our cells can take up to a million hits every day – and the bombardment comes from every direction: from radiation, air pollution and carcinogens in some of the food we eat. And, of course, we don’t need to mention cigarette smoke.

Damaged chromosomes (blue arrows)

Damaged chromosomes    (blue arrows)

On top of all that cells have to make a new DNA copy every time they reproduce – and we do a lot of that: recall that you set sail on the journey of life as one single, fertilized egg cell and now look at you: a clump of ten trillion (1013) cells that, just to stay as you are, has to make one million new cells every second. What’s more some of your cells deliberately break their own DNA in a process called ‘gene shuffling’ that goes to make the finished product of your aforementioned immune system. The biochemical machinery that does these jobs is mighty efficient but nobody’s perfect – except, of course, for John Eales, Australia’s most successful rugby union captain, nicknamed “Nobody” because “Nobody’s perfect”. When the three thousand million base-pairs of DNA are stuck together for a new cell there’s a mistake about once in every million units added – but a kind of quality control check (mismatch repair) then fixes most of these, so that the overall error is about one in a thousand million. That’s one example of the nifty ways evolution has come up with to fix the damage suffered by our genetic material from all this replicating, assaulting and constructing.

Keeping the show on the road

The overall upshot of the repair machinery is that less than one mutation per day becomes fixed in our genomes – and thus passed on to succeeding generations of cells. The range of things that can damage DNA – and hence the different forms that damage can take – tells you that there must be several different repair systems and indeed we now know that about 200 genes and their protein products have a hand in some repair process or another. There’s so much to know that DNA damage and repair has its own data-base called, inevitably, REPAIRtoire. Much of what we know is, to a considerable extent, thanks to the labours of Tomas Lindahl, Paul Modrich and Aziz Sancar who have just been jointly awarded this year’s Nobel Prize in Chemistry. Because damage to DNA – aka mutations – drives the development of cancers you might suppose that in these pages we will have met these gentlemen before – and indeed we have, if not by name.

Tomas Lindahl Paul Modrich Aziz Sancar

Tomas Lindahl                      Paul Modrich                       Aziz Sancar

Winners of the 2015 Nobel Prize in Chemistry

Forty odd years ago much of the above would have bewildered cell biologists. Thirty years before then, in 1944, Oswald Avery, Colin MacLeod and Maclyn McCarty had shown for the first time that genes are composed of DNA, a finding confirmed in 1952 by Alfred Hershey and Martha Chase in a classic experiment using a virus that infects and replicates within a bacterium. But with the acceptance that, however improbable, our genetic material was indeed made of DNA there came the assumption that it must be very stable. After all, if it carried our most valuable possession then surely it had to be made of molecular granite, absolutely resistant to any kind of chemical change or degradation. Had the bewildered boffins been told that in the twenty-first century we would be sequencing woolly mammoth DNA from samples that are millions of years old they would have been confirmed in their view.

It was Tomas Lindahl in the early 1970s who demonstrated that, although DNA is indeed more stable than its close rello RNA (the intermediate in making proteins) it nevertheless decays quite rapidly under normal conditions – it’s only when sealed in permafrost or blobs of amber that it becomes frozen in time. Lindahl realized that for life based on DNA to have evolved there had to be repair systems that could sustain our genetic material in a functional state and he went on to resolve how one of these did it. Aziz Sancar has worked particularly on the circadian clock (discovering that CRY is a clock protein) and how cells repair ultraviolet radiation damage to DNA: people born with defects in this system develop skin cancer if they are exposed to sunlight. Paul Modrich has contributed mainly to our knowledge of mismatch repair.

Lindahl, Modrich, Sancar and their colleagues over many years haven’t come up with the philosopher’s stone – the chemists still can’t transmute base metals into gold without the aid of a particle accelerator. But what they have done is much more useful for mankind. Revealing the detail of how genome maintenance works has already lead to new cancer treatments and from this beginning will come greater benefits as time goes by. They should enjoy the proceeds of turning molecular knowledge if not to gold then into Swedish kronor (8 million of them) – for the rest of the world it’s a bargain.

References

Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature 362, 709-715.

Yang YG, Lindahl T, Barnes DE. (2007). Trex1 exonuclease degrades ssDNA to prevent chronic checkpoint activation and autoimmune disease. Cell 131, 873-886.

Shao, H, Baitinger, C, Soderblom, EJ, Burdett, V, and Modrich, P. (2014). Hydrolytic function of Exo1 in mammalian mismatch repair. Nucleic Acids Research 42, 7104-7112.

Tan C, Liu Z, Li J, Guo X, Wang L, Sancar A, Zhong D. (2015). The molecular origin of high DNA-repair efficiency by photolyase. Nat Commun. 6, 7302.

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.

Trouble With The Neighbours

It may seem odd to the point of negligence that a problem mankind has been grappling with since at least the time of the ancient Egyptians should, within the last ten years or so, be shown to have a whole new dimension, scarcely conceived hitherto. This hidden world, often now called the tumour microenvironment, is created as solid tumours develop and attract a variety of normal cells from the host to form a cellular cloud that envelops them and supports their growth (as we noted in Cooperative Cancer Groupies). We shouldn’t beat ourselves up for being slow to grasp its existence yet alone its importance – just take it as a reminder of the multi-faceted complexity that is cancer.

It’s true that over one hundred years ago the London physician Stephen Paget came up with his “seed and soil” idea – the notion that when cells escape from a primary tumour and spread to secondary sites (metastasis) they need to find a suitable spot that will nourish their growth, otherwise they perish – a fate that befalls most of them, fortunately for us.

But in the twenty-first century …

Perceptive though that idea was, it didn’t relate to the goings on in the vicinity of primary tumours – where the current picture is indeed of a cosmopolitan crowd of cellular groupies being recruited as the tumor starts to grow such that they infiltrate and closely interact with the cancer cells. The groupies are attracted by chemical messengers released by tumour cells – but it becomes a two-way communication, with messenger proteins shuttling to and fro between the different cell types.

Tumor uenvirThe tumour neighbourhood.

Two-way communication between host cells and tumor cells.

 White blood cells (e.g., lymphocytes and macrophages) are one group that succumbs to the magnetism of tumours. They’re part of the immune response that initially tries to eliminate the abnormal growth but, in an extraordinary transformation, when tumour cells manage to evade this defense the recruited cells change sides so to speak, switching their action to release signals that actively support tumor growth. The idea of boosting the initial anti-tumour response, thereby using the host defence system to increase the efficiency of tumour elimination, is the basis of immunotherapy, a popular research field at present to which we will return in a later piece.

Who’s who among the groupies

The finding that cells flooding into the ambience of a tumour can affect growth of the cancer has focussed attention on identifying all the constituents of the cellular cloud and unraveling their actions. Two recent studies by Claudio Isella from the University of Turin and Alexandre Calon from Barcelona, with their colleagues, have looked at a type of bowel cancer that has a particularly poor prognosis and used an ingenious ploy to lift the veil on who’s doing what to whom in the tumour milieu.

The tumours were initially classified on the basis of a genetic signature – that is, a snapshot of which genes are active in a tumour sample – ‘switched on’ or ‘expressed’ in the jargon – meaning that the information encoded in a stretch of DNA sequence is being used to make a functional gene product, usually a protein. They then used the crafty tactic of implanting human tumour cells into mice (the mice are ‘immunocompromised’ so that they don’t reject the human cells), separated the major types of cell in the tumours that grew and then looked at the genes expressed in those sub-sets. Remarkably, it emerged that, of the cell groupies that infiltrate into primary tumours, fibroblasts are particularly potent at driving tumour growth and metastasis. Fibroblasts are a cell type that makes the molecular scaffold that gives structure and shape to the various tissues and organs in animals – so it’s a surprise, to say the least, to find that cells with a rather mundane day job can play an important role in cancer progression. In this model system the sequence differences between corresponding human and mouse genes confirm that the predominant driver is mouse cells infiltrating the human tumours. Perhaps it shouldn’t be quite such a shock to find fibroblasts dabbling in cancer as we have met cancer-associated fibroblasts (CAFs) before as cells that, by releasing leptin, can promote the growth and invasion of breast cancer cells (in Isn’t Science Wonderful? Obesity Talks to Cancer).

How useful might this be?

As ever, this is just one more small step. However, the other key finding from this work is that a critical signal for the CAFs is a protein called transforming growth factor beta (TGFβ) and a small molecule that blocks its signal inhibits metastasis of human tumour cells in the mouse model. So yet again the cancer biologist’s best friend gives a glimmering of hope for human therapy.

References

Isella, C. et al. (2015). Stromal contribution to the colorectal cancer transcriptome. Nature Genet. http://dx.doi.org/10.1038/ng.3224

Calon, A. et al. (2015). Stromal gene expression defines poor-prognosis subtypes in colorectal cancer. Nature Genet. http://dx.doi.org/10.1038/ng.3225

Taking a Swiss Army Knife to Cancer

Murder is easy. You just need a weapon and a victim. And, I guess the police would add, opportunity. I hasten to point out that’s an observational note rather than an autobiographical aside. It’s relevant here because treating cancer is intentional homicide on a grand scale – the slaughter of millions of tumour cells. For individuals we cannot say whether the perfect murder is possible – how would we know – but on the mass scale history shows that even the most efficient machines for genocide have been, fortunately, less than perfect. In other words through incredible adaptability, ingenuity, determination and sheer will power, some folk will survive even the most extreme efforts of their fellow men to exterminate them. Cancers tend to mirror their carriers. With only rare exceptions, whatever we throw at them in attempts to eliminate their unwelcome presence, some of the little blighters will dodge the bullets, take a deep breath and start reproducing again. ‘What doesn’t kill you makes you stronger’ as the American chanteuse Kelly Clarkson has it – though to be fair I think she pinched the line from Nietzsche.

Multiple whammys

For cancer cells dodging extinction requires adaptability: using the flexibility of the human genetic code enshrined in DNA to change the pattern of gene expression or to develop new mutations that short-circuit the effects of drugs – finding many different ways to render useless drugs that worked initially. You might draw a parallel with the idea, correct as it turned out, of the prisoners who staged The Great Escape from Stalag Luft III in World War II that if they initially dug three tunnels simultaneously (Tom, Dick and Harry) the guards might find one but they’d probably not find all three.

An approach increasingly permeating cancer therapy is how to target several escape routes at once – can we at least give the tumour cell a serious headache in the hope that while it’s grappling with a molecular carpet bombing it might be more likely to drop dead. One way of doing this is simply to administer drug combinations and this has met with some success. However, for the most part, agents are not specific for tumour cells and their actions on normal cells give rise to the major problem of side effects.

Step forward Yongjun Liu and colleagues from Shandong University, Jinnan, People’s Republic of China and the sophisticated world of chemistry with efforts to fire a broad-shot that combines different ways of killing tumour cells with at least some degree of specific targeting.

Making the bullets

These chemists are clever chaps but, taken one step at a time, what they’ve done to make a very promising agent is simple. The game is molecular Lego – making a series of separate bits then hooking them together. The trendy name is click chemistry, a term coined in 1998 by Barry Sharpless and colleagues at The Scripps Research Institute, to describe reactions in which large, pre-formed molecules are linked to make even more complex multi-functional structures. You could describe proteins as a product of ‘click chemistry’ as cells join amino acid units to make huge chains – but you wouldn’t as it’s better to keep the name for synthetic reactions that make novel modules.

It might help to recall some school chemistry:

acid + base = salt + water (e.g., HCl + NaOH = NaCl + H2O)

Click chemistry is the same idea but the reactants are large molecules, rather than atoms of hydrogen, chlorine and sodium.

Anti-freeze to anti-cancer in a couple of clicks

The starting point here is remarkably familiar – it’s antifreeze, a chemical added to cooling systems to lower the freezing point of water (e.g., in motor engines). Antifreeze is ethylene glycol (two linked atoms of carbon with hydrogens: HO-CH2-CH2-OH): make a string of these molecules and you have a polymer – poly-ethylene glycol (PEG).

For click chemists it’s easy to tag things on to biologicial molecules, including PEG and most proteins. This study used biotin – a vitamin that works like a molecular glue by sticking strongly to another small molecule called avidin, found in egg white. Avidin can therefore be used to fish for anything tagged with biotin – it simply hooks two biotins together. The protein used here is an antibody that binds to a signaling molecule (VEGFR) present on the surface of most tumour cells and blood vessels. VEGFR helps tumour growth by providing a new blood supply – an effect blocked when the antibody binds to it.

Sounds familiar?

If chains of carbon atoms decorated with hydrogens seem familiar, so they should. They’re fats (the saturated fats you get in cream and butter are very similar to the chains of PEG). As anyone who’s done the washing up knows, fats and water don’t get on (which is why we have detergents). Put them in water and fats huddle together in blobs called micelles – sacs of fat. This gives them a useful property: if you mix something else in the water – a drug for instance – and then add PEG and separate the micelles that form, you’ve got drug trapped in a kind of carrier bag. Often called nanoparticles, these small, molecular bubbles made by chemists are packets of drug ready to be delivered.

Micelle Blog picA sac of poly-ethylene glycol (PEG) with entrapped drug (red dots) tagged in three different ways (Liu et al., 2014).

Addressing the parcel

To turn PEG into a parcel two chemical tricks are needed. The first is to tag PEG with biotin. Now the nanoparticles will pick up VEGFR antibody labeled with avidin – and the antibody label can target the micelles to tumour cells and blood vessels.

Exploding the package

The second trick is the addition of another polymer (a chain of histidine amino acids) that triggers the disassembly of the nanoparticles when they find themselves close to or inside tumour cells – a more acidic environment than the circulation.

Seeing the results

The final twist is to include another modified PEG – this with a chemical group that binds gadolinium when it’s added to the water. Gadolinium is an ion (Gd3+) which shows up brightly in MRI scans – the idea being to highlight where the nanoparticles end up after injection into animals.

Does it work?

These multicomponent nanoparticles resemble a Swiss Army knife – all sorts of gadgets sticking out all over the place: PEG to make sacs that contain a drug, biotin hooked to VEGFR antibody to home in on tumour cells, an acidity sensor so the thing falls apart and releases its content on arrival and a contrast enhancer that shows up where this is happening in an MRI scan.

Injected into mice with liver tumours, these multi-functional nanoparticles do indeed home in on the tumours and their surroundings and drastically reduce tumour growth when they carry the drug sorafenib. Sorafenib is the only agent that has been shown to affect liver cancers, although its effects are brief. Compared to sorafenib alone, these new nanoparticles are about three times more potent – presumably because of their targeted delivery.

Where are we?

This wonderfully clever chemistry will not cure liver cancer. A good result when it reaches human trials would be six months remission by comparison with the current average of two months from treatment with sorafenib alone. But what it does show is that hitting cancers hard in multiple ways at least slows them down. We can only hope that more potent drugs and further ingenuity will progressively extend this capacity. The end is not in sight but brilliant technical advances such as that from Yongjun Liu’s lab may be spotlighting the way ahead.

Reference

Yongjun Liu et al., (2014). Multifunctional pH-sensitive polymeric nanoparticles for theranostics evaluated experimentally in cancer. Nanoscale 6, 3231-3242.

The Hay Festival

According to the Hay Festival  a recording of my talk ‘Demystifying Cancer’ on Wednesday 28th May should be available on their web site shortly and it can also be heard on the university site. However, I thought it might be helpful to post a version, not least for the for the rather breathless lady who arrived at the book signing session apologising for missing the lecture because she’d got stuck in mud. So for her and perhaps for many others I had the privilege of chatting to afterwards, read on …

 The Amazing World of Cells, Molecules … and CancerOpening pic

One of the biggest influences on my early years was the composer and conductor Antony Hopkins, who died a few days ago. Most of what I knew about music by the time I was 15 came from his wonderfully clear dissections of compositions in the series Talking About Music broadcast by the BBC Third Programme. When he was axed by the Beeb in 1992 for being ‘too elitist’ – yes, they talked that sort of drivel even then – Hopkins might have wished he’d been a biologist. After all, biology must be the easiest subject in the world to talk about. Your audience is hooked from the outset because they know it’s about them – if not directly then because all living things on the planet are interlinked – so even the BBC would struggle to make an ‘elitism’ charge stick. They know too that it’s beautiful, astonishing and often funny – both from what they see around them and also, of course, courtesy of David Attenborough. So it’s not a surprise when you show them that the micro-world of cells and molecules is every bit as wonderful.

The secret of life

What does come as a bit of a shock to most non-scientists is when you explain the secret of life. No, that’s not handing round pots of an immortalization elixir – much better, it’s outlining what’s sometimes rather ponderously called the central dogma of molecular biology – the fact that our genetic material (aka DNA) is made from only four basic units (most easily remembered by their initials: A, C, G and T – humans have over three thousand million of these stuck together). This is our ‘genome’ and the ‘genetic code’ enshrined in the DNA sequence makes us what we are – with small variations giving rise to the differences between individuals. The genetic code carries instructions for glueing together another set of small chemicals to make proteins. There are 20 of these (amino acids) and they can be assembled in any order to make proteins that can be thousands or even tens of thousands of amino acids long. These assemblies fold up into 3D shapes that give them specific activities. Proteins make living things what they are – they’re ‘the machines of life’ – and their infinite variety is responsible for all the different species to have appeared on earth. Can the basis of life really be so simple?

The paradox of cancer

Turning to cancer, a three word definition of ‘cells behaving badly’ would do fine. A more scientific version would be ‘cells proliferating abnormally.’ That is, cells reproducing either when they shouldn’t, or more rapidly than normal, or doing so in the wrong place. The cause of this unfriendly behavior is damaged DNA, that is, alteration in the genetic code – any such change being a ‘mutation’. If a mutation affects a protein so that it becomes, say, hyperactive at making cells proliferate (i.e. dividing to make more cells), you have a potential cancer ‘driver’. So at heart cancer’s very simple: it’s driven by mutations in DNA that affect proteins controlling proliferation. That’s true even of the 20% or so of cancers caused by chronic infection – because that provokes inflammation, which in turn leads to DNA damage.

The complexity of cancer arises because, in contrast to several thousand other genetic diseases in which just a single gene is abnormal (e.g., cystic fibrosis), tumour cells accumulate lots of mutations. Within this genetic mayhem, relatively small groups of potent mutations (half a dozen or so) emerge that do the ‘driving’. Though only a few ‘driver mutations’ are required, an almost limitless number of combinations can arise.

Accumulating mutations takes time, which is why cancers are predominantly diseases of old age. Even so, we should be aware that life is a game of genetic roulette in which each individual has to deal with the dice thrown by their parents. The genetic cards we’re dealt at birth may combine with mutations that we pick up all the time (due to radiation from the sun and the ground, from some foods and as a result of chemical reactions going on inside us) to cause cancers and, albeit rarely, in unlucky individuals these can arise at an early age. However, aside from what Mother Nature endows, humans are prone to giving things a helping hand through self-destructive life-style choices – the major culprits, of course, being tobacco, alcohol and poor diets, the latter being linked to becoming overweight and obese. Despite these appalling habits we’re living longer (twice as long as at the beginning of the twentieth century) which means that cancer incidence will inevitably rise as we have more time to pick up the necessary mutations. Nevertheless, if we could ban cigarettes, drastically reduce alcohol consumption and eat sensibly we could reduce the incidence of cancers by well over a half.

How are we doing?

Some readers may recall that forty-odd years ago in 1971 President Nixon famously committed the intellectual and technological might of the USA to a ‘War on Cancer’ saying, in effect, let’s give the boffins pots of money to sort it out pronto. Amazing discoveries and improved treatments have emerged in the wake of that dramatic challenge (not all from Uncle Sam, by the way!) but, had we used the first grant money to make a time machine from which we were able to report back that in 2013 nearly six hundred thousand Americans died from cancer, that the global death toll was over eight million people a year and will rise to more than 13 million by 2030 (according to the Union for International Cancer Control), rather less cash might subsequently have been doled out. Don’t get me wrong: Tricky Dicky was spot on to do what he did and scientists are wonderful – clever, dedicated, incredibly hard-working, totally uninterested in personal gain and almost always handsome and charming. But the point here is that, well, sometimes scientific questions are a little bit more difficult than they look.

Notwithstanding, there have been fantastic advances. The five year survival rates for breast and prostate cancers have gone from below 50% to around 90% – improvements to which many factors have contributed including greater public awareness (increasing the take-up of screening services), improved surgical and radiology methods and, of course, new drugs. But for all the inspiration, perspiration and fiscal lubrication, cancer still kills over one third of all people in what we like to refer to as the “developed” world, globally breast cancer killed over half a million in 2012 and for many types of cancer almost no impact has been made on the survival figures. In the light of that rather gloomy summary we might ask whether there is any light at the end of the tunnel.

The Greatest Revolution

From one perspective it’s surprising we’ve made much progress at all because until just a few years ago we had little idea about the molecular events that drive cancers and most of the advances in drug treatment have come about empirically, as the scientists say – in plain language by trial and error. But in 2003 there occurred one of the great moments in science – arguably the most influential event in the entire history of medical science – the unveiling of the first complete DNA sequence of a human genome. This was the product of a miraculous feat of international collaboration called The Human Genome Project that determined the order of the four units (A, C, G and T) that make up human DNA (i.e. the sequence). Set up in 1990, the project was completed by 2003, two years ahead of schedule and under budget.

If the human genome project was one of the most sensational triumphs in the history of science what has happened in the ensuing 10 years is perhaps even more dazzling. Quite breathtaking technical advances now mean that DNA can be sequenced on a truly industrial scale and it is possible to obtain the complete sequence of a human genome in a day or so at a cost of about $1,000.

These developments represent the greatest revolution because they are already having an impact on every facet of biological science: food production, microbiology and pesticides, biofuels – and medicine. But no field has been more dramatically affected by this technological broadside than cancer and already thousands of genomes have been sequenced from a wide range of tumours. The most striking result has been to reveal the full detail of the astonishing genetic mayhem that characterizes cancer cells. Tens of thousands or even hundreds of thousands of mutations featuring every kind of molecular gymnastics imaginable occur in a typical tumour cell, creating a landscape of stunning complexity. At first sight this makes the therapeutic challenge seem daunting, but all may not be lost because the vast majority of this genetic damage plays no role in cancer development (they’re ‘passenger’ mutations) and the power of sequencing now means they can be sifted from the much smaller hand of ‘driver’ mutations. From this distillation have emerged sets of ‘mutational signatures’ for most of the major types of cancers. This is a seismic shift from the traditional method of assessing tumours – looking directly at the cells after treating them with markers to highlight particular features – and this genetic approach, providing for the first time a rigorous molecular basis for classifying tumours, is already affecting clinical practice through its prognostic potential and informing decisions about treatment.

A new era

One of the first applications of genomics to cancer, was undertaken by a group at The Wellcome Trust Sanger Institute near Cambridge (where the UK part of the Human Genome Project had been carried out), who screened samples of the skin cancer known as malignant melanoma. This is now the fifth most common UK cancer – in young people (aged 15 to 34) it’s the second most common – and it killed over 2,200 in 2012. Remarkably, about half the tumours were found to have a hyperactivating mutation in a gene called BRAF, the effect being to switch on a signal pathway so that it drives cell proliferation continuously. It was a remarkable finding because up until then virtually nothing was known about the molecular biology of this cancer. Even more amazingly, within a few years it had lead to the development of drugs that caused substantial regression of melanomas that had spread to secondary sites (metastasized).

This was an early example of what has become known as personalized medicine – the concept that molecular analysis will permit treatment regimens to be tailored to the stage of development of an individual’s cancer. And maybe, at some distant time, the era of personalized medicine will truly come about. At the moment, however, we have very few drugs that are specific for cancer cells – and even when drugs work initially, patients almost invariably relapse as tumours become resistant and the cancer returns – one of the major challenges for cancer biology.

It behoves us therefore to think laterally, of impersonal medicine if you like, and one alternative approach to trying to hit the almost limitless range of targets revealed by genomics is to ask: do tumour cells have a molecular jugular – a master regulator through which all the signals telling it to proliferate have to pass. There’s an obvious candidate – a protein called MYC that is essential for cells to proliferate. The problem with stopping MYC working is that humans make about one million new cells a second, just to maintain the status quo – so informed opinion says that blocking MYC will kill so many cells the animal will die – which would certainly fix cancer but not quite in the way we’re aiming for. Astoundingly, it turns out in mice at least it doesn’t work like that. Normal cells tolerate attenuation of MYC activity pretty well but the tumour cells die. What a result!! We should, of course, bear in mind that the highway of cancer therapy is littered with successful mouse treatments that simply didn’t work in us – but maybe this time we’ll get lucky.

An Achilles’ heel?

In defining cancers we noted the possibility that tumour cells might proliferate in the wrong place. So important is this capacity that most cancer patients die as a result of tumour cells spreading around the body and founding secondary colonies at new sites – a phenomenon called metastasis. Well over 100 years ago a clever London physician by the name of Stephen Paget drew a parallel between the growth of tumours and plants: ‘When a plant goes to seed, its seeds are carried in all directions; but they can only live and grow if they fall on congenial soil.’ From this emerged the “seed and soil” theory as at least a step to explaining metastasis. Thus have things languished until very recent findings have begun to lift the metastatic veil. Quite unexpectedly, in mouse models, primary tumours dispatch chemical messengers into the blood stream long before any of their cells set sail. These protein news-bearers essentially tag a landing site within the circulatory system on which the tumour cells touch down. Which sites are tagged depends on the type of tumour – consistent with the fact that human cancers show different preferences in metastatic targets.

These revelations have been matched by stunning new video methods that permit tumour cells to be tracked inside live mice. For the first time this has shone a light on the mystery of how tumour cells get into the circulation – the first step in metastasis. Astonishingly tumour cells attach themselves to a type of normal cell, macrophages, whose usual job is to engulf and digest cellular debris and bugs. The upshot of this embrace is that the macrophages cause the cells that line blood vessels to lose contact with each other, creating gaps in the vessel wall through which tumour cells squeeze to make their escape. This extraordinary hijacking has prognostic value and is being used to develop a test for the risk of metastasis in breast cancers.

The very fact that cancers manifest their most devastating effects by spreading to other sites may lay bare an Achilles’ heel. Other remarkable technical developments mean that it’s now possible to fish out cancer cells (or DNA they’ve released) from a teaspoonful of circulating blood (that’s a pretty neat trick in itself, given we’re talking about fewer than 100 tumour cells in a sea of several billion cells for every cubic millimeter of blood). Coupling this to genome sequencing has already permitted the response of patients to drug therapy to be monitored but an even more exciting prospect is that through these methods we may be moving towards cancer detection perhaps years earlier than is possible by current techniques.

As we’ve seen, practically every aspect of cancer biology is now dominated by genomics. Last picIt’s so trendy that anyone can join in. Songs have been written about DNA and you can even make a musical of your own genetic code, French physicist Joel Sternheimer having come up with a new genre – protein music – in which sequence information is converted to musical notes. Antony Hopkins, ever receptive to new ideas, would have been enthralled and, with characteristic enthusiasm, been only too happy to devote an episode of Talking About Music to making tunes from nature.

it’s a small world

Once upon a time I went to Disneyland. My excuse is that it was a long time ago. So long, in fact, that I don’t need to specify where — it was before theme park cloning got going. Goodness knows why I went — given that if I was inclined to sticking pins in things, Mickey Mouse would be a prime target — though, logically, a model of Walt would come first. But one memory of that visit recurs unbidden to this day: the song ‘it’s a small world (after all).’ I know. I shouldn’t blame Disney as it was the Sherman Brothers greatest hit — and what with also writing the scores for Mary Poppins and Chitty Chitty Bang Bang, they’ve got a lot to answer for. Nevertheless and irritating though the jingle may be, it contains a rather profound line:

There’s so much that we share that it’s time we’re aware, It’s a small world after all’.

And that will do very well as our theme for the day.

SmallWorldFront83_wbYour inner self

A sobering thought about being human is that we’re mostly bugs – that’s to say on a cell to cell basis the microbes in our bodies outnumber us by ten to one. Ten to one: time for lunch, to recycle the old Goon Show gag, but first perhaps you should survey your microbiota – the 1000 or so assorted species of bacteria that have made you their home. Most of them (99%) reside in your digestive tract and we don’t notice them, of course, because they’re so much smaller than the cells of our body (they make up less than 3% of our mass). Sometimes called gut flora, they’re important in squeezing the last ounce of energy from what we eat by helping to digest sugars and they also make some vitamins that we need. You could, then, think of this unseen army of tiny cells as an organ in their own right. Unnoticed they may be but you upset them at your peril, as everyone knows who’s taken a course of antibiotics (e.g., penicillin) to get rid of unwanted bugs.

Bugs tummy

This vast force of bacteria, toiling away on our behalf in the dungeon of our innards, includes two major sub-families, Bacteroidetes and Firmicutes. Don’t worry about pronunciation: think of them as B & F. What’s important is that obese animals (including humans) have about half the number of Bs and double that of Fs, compared to normal. That’s a startling shift – the sort of result that gets scientists thinking: something fishy going on here. But what really gets their antennae twitching is the follow-up result. Each bug has its own genetic material (DNA) carrying a set of genes — different for each species. From faecal samples (i.e. stools) the total number of microbial genes can be estimated and — astonishingly — it turns out that there are several hundred times the number of our own genes. We have about 20,000, the bugs muster several million. But the really provocative result is that this total of microbial genes in our gut drops if we become obese:

Fewer genes = more body fat

More genes (a more diverse microbiome) = healthy status.

Cause or effect?

A good question — that can be answered by man’s best friend. Yes, I’m afraid it’s Mickey again. Mice born under aseptic conditions by Caesarean section don’t have any gut microbes — they’re ‘germ-free’ mice — and they grow up with less body fat than normal mice. However, give them the gut army from a normal mouse and they more than double their body fat in a couple of weeks. The microbiota from an obese mouse makes them gain twice as much fat. What happens if you colonise germ-free mice with human gut microbes? If they’re from someone who’s obese the mice also become obese, if fed a high-fat rather than a normal diet.

Because obesity is all about the balance between energy extracted from food and that expended, all this suggests that obesity-associated microbiomes increase the efficiency of extraction.

But if that’s the case maybe there are some slackers in the bug world – types that are pretty hopeless at food processing. Might they offset obesity? Well, at least one (by the name of Akkermansia muciniphila) does just that — again in mice — and its numbers are much reduced in obese people but go up after gastric bypass surgery that reduces the absorption of nutrients from food. This offers the seductive notion that some types of bug might help to reduce obesity.

Debugging

You may have spotted a bit of a cause for concern: if the make up of our gut bugs can affect how our bodies work — and especially whether we put on weight — what happens when we zap ourselves with antibiotics? The problem is, of course, that these drugs target a range of bacteria — they’re not particularly choosy — which is why you get diarrhœa when you take penicillin for a throat infection. And it’s not just you. In the UK we consume 30 million antibiotic prescriptions a year: Americans get through over 250 million and their children get an average of 15 courses of antibiotics in their early years.

The problem here is not about antibiotics being wonderful and saving millions of lives but the possibility that they might have long-term effects. Evidence for this has come from Martin Blaser’s group at New York University who showed that some antibiotics make mice put on weight and build up fat. What’s more, a high-fat diet adds to this effect. Remarkably, changes in the mice microbiota occur before they become obese — and the effects are for life. It seems extraordinary that a short drug pulse, such as we might give a child to cure an ear infection, can have permanent effects. The explanation may be that some gut bacteria are better at surviving the drug treatment resulting in a shift of microbiota balance to give more efficient digestion — i.e. greater energy provision.

It may not be coincidence that the escalation in antibiotic use since the 1940s has paralleled the obesity explosion. In 1989 no USA state had an obesity level above 14%; by 2010 none was below 20% — and the national average is now 30%.

Bugs and cancer: drivers or mirrors?

Those who follow this blog will know that where obesity lurks cancer looms. Indeed transferring microbiota to germ-free mice has been shown to promote a wide range of tumours and, conversely, depleting intestinal bacteria reduces the development of liver and colon cancers. It’s also worth noting that bowel cancer occurs more frequently in the large intestine than in the small — which may reflect the much higher microbial density.

Is it a small world after all?

All these findings suggest that our bug contingent can influence the onset of obesity and various cancers and that even brief drug treatments can have permanent effects on its make up. We have only the vaguest idea how this happens and most of the evidence so far comes from Mickey’s rellos. Even so, maybe in time we will be able to manipulate our personal gut micro-worlds to augment our defences against these potent foes.

Reference

Martin J. Blaser: Missing microbes, Henry Holt & Company 2014

http://www.amazon.com/Missing-Microbes-Overuse-Antibiotics-Fueling/dp/0805098100/ref=sr_1_1_ha?s=books&ie=UTF8&qid=1400478180&sr=1-1&keywords=missing+microbes