Same Again Please

 

It’s often said that every family has its secret — Uncle Fred’s fondness for the horses, Cousin Bertha’s promiscuity, etc. — whatever it is that ‘we don’t talk about.’ If that’s true the scientific community is no exception. For us the unutterable is reproducibility — meaning you’ve done an experiment, new in some way, but the key questions are: ‘Can you do it again with the same result?’ and, even more important: ‘Can someone else repeat it?’

Once upon a time in my lab we had a standing joke: whoever came bounding along shouting about a new result would be asked ‘How reproducible is it?’ Reply: ‘100%!’ Next question: ‘How often have you done the experiment?’ Reply: ‘Once!!’ Boom, boom!!!

Not a rib-tickler but it did point to the knottiest problem in biological science namely that, when you start tinkering with living systems, you’re never fully in control.

How big is the problem?

But, as dear old Bob once put it, The Times They Are a-Changin’. Our problem was highlighted in the cancer field by the Californian biotechnology company Amgen who announced in 2012 that, over a 10 year period, they’d selected 53 ‘landmark’ cancer papers — and failed to replicate 47 of them! Around the same time a study by Bayer HealthCare found that only about one in four of published studies on potential drug targets was sufficiently strong to be worth following up.

More recently the leading science journal Nature found that almost three quarters of over 1,500 research scientists surveyed had tried to replicate someone else’s experiment and failed. It gets worse! More than half of them owned up to having failed to repeat one of their own experiments! Hooray! We have a result!! If you can’t repeat your own experiment either you’re sloppy (i.e., you haven’t done exactly what you did the first time) or you’ve highlighted the biological variability in the system you’re studying.

If you want an example of biological variation you need look no further than human conception and live births. Somewhere in excess of 50% of fertilized human eggs don’t make it to birth. In other words, if you do a ‘thought experiment’ in which a group of women carry some sort of gadget that flags when one of their eggs is fertilized, only between one in two and one in five of those ‘flagged’ will actually produce an offspring.

However you look at it, whether it’s biological variation, incompetence or plain fraud, we have a problem and Nature’s survey revealed that, to their credit, the majority of scientists agreed that there was a ‘significant crisis.’

The results of the survey by Nature from Baker 2016.

Predictably, but disturbingly for us in the biomedical fields, the greatest confidence in published results was shown by the chemists and physicists whereas only 50% of data in medicine were thought to be reproducible. Oh dear!

Tackling the problem in cancer

The Reproducibility Project: Cancer Biology, launched in 2013, is a collaboration between the Center for Open Science and Science Exchange.

The idea was to take 50 cancer papers published in leading journals and to attempt to replicate their key findings in the most rigorous manner. The number was reduced from 50 to 29 papers due to financial constraints and other factors but the aim remains to find out what affects the robustness of experimental results in preclinical cancer research.

It is a formidable project. Before even starting an experiment, the replication teams devised detailed plans, based on the original reports and, as the result of many hours effort, came up with a strategy that both they and the original experimenters considered was the best they could carry out. The protocols were then peer reviewed and the replication plans were published before the studies began.

Just to give an idea of the effort involved, a typical replication plan comprises many pages of detailed protocols describing reagents, cells and (where appropriate) animals to be used, statistical analysis and any other relevant items, as well as incorporating the input from referees.

The whole endeavor is, in short, a demonstration of scientific practice at its best.

To date ten of these replication studies have been published.

How are we doing?

The critical numbers are that 6 of the 10 replications ‘substantially reproduced’ the original findings, although in 4 of these some results could not be replicated. In 4 of the 10 replications the original findings were not reproduced.

The first thing to say is that a 60% rate of ‘substantial’ successful replication is a major improvement on the 11% to 25% obtained by the biotech companies. The most obvious explanation is that the massive, collaborative effort to tighten up the experimental procedures paid dividends.

The second point to note is that even when a replication attempt fails it cannot be concluded that the original data were wrong. The discrepancy may merely have highlighted how fiendishly tricky biological experimentation can be. The problem is that with living systems, be they cells or animals, you never have complete control. Ask anyone who has a cat.

More likely, however, than biological variation as a cause of discrepancies between experiments is human variation, aka personal bias.

This may come as a surprise to some but, rather than being ‘black and white’ much of scientific interpretation is subjective. Try as I might, can I be sure that in, say, counting stained cells I don’t include some marginal ones because that fits my model? OK: the solution to that is get someone else to do the count ‘blind’ — but I suspect that quite often that’s not done. However, there are even trickier matters. I do half a dozen repeats of an experiment and one gives an odd result (i.e., differs from the other five). Only I can really go through everything involved (from length of coffee breaks to changes in reagent stocks) and decide if there are strong enough grounds to ignore it. I do my best to avoid personal bias but … scientists are only human (fact!).

A closer look at failure

One of the failed replications is a particularly useful illustration for this blog. The replication study tackled a 2012 report that bacterial infection (specifically a bacterium, Fusobacterium nucleatum, that occurs naturally in the human oral cavity) is present in human colon cancers but not in non-cancerous colon tissues. It hit the rocks. They couldn’t detect F. nucleatum in most tumour samples and, when they did, the number of bugs was not significantly different to that in adjacent normal tissue.

Quite by chance, a few months ago, I described some more recent research into this topic in Hitchhiker or Driver?

I thought this was interesting because it showed that not only was F. nucleatum part of the microbiome of bowel cancer but that when tumour cells spread to distant sites (i.e., underwent metastasis) the bugs went along for the ride — raising the key question of whether they actually helped the critical event of metastasis.

So this latest study was consistent with the earlier result and extended it — indeed they actually showed that antibiotic treatment to kill the bugs slowed the growth of human tumour cells in mice.

Where does that leave us?

Well, helpfully, the Reproducibility Project also solicits comments from independent experts to help us make sense of what’s going on. Step forward Cynthia Sears of The Johns Hopkins Hospital. She takes the view that, although the Replication Study didn’t reproduce the original results, the fact that numerous studies have already found an association between F. nucleatum and human colon cancer means there probably is one — consistent with the work described in Hitchhiker or Driver?

One possible explanation for the discrepancy is that the original report studied colon tissue pairs (i.e., tumour and tumour-adjacent tissues) from colon cancer patients but did not report possibly relevant factors like age, sex and ethnicity of patients. In contrast, the replication effort included samples from patients with cancer (tumour and adjacent tissue) and non-diseased control tissue samples from age, sex and ethnicity matched individuals.

So we now know, as Dr. Sears helpfully remarks, that the association between F. nucleatum bugs and human colon cancer is more complicated first appeared! Mmm. And, just in case you were in any doubt, she points out that we need to know more about the who (which Fusobacterium species: there are 12 of them known), the where (where in the colon, where in the world) and the how (the disease mechanisms).

Can we do better?

In the light of all that the obvious question is: what can we do about the number of pre-clinical studies that are difficult if not impossible to reproduce? Answer, I think: not much. Rather than defeatist this seems to me a realistic response. There’s no way we could put in place the rigorous scrutiny of the Reproducibility Project across even a fraction of cancer research projects. The best we can do is make researchers as aware as possible of the problems and encourage them towards the very best practices — and assume that, in the end, the solid results will emerge and the rest will fall by the wayside.

Looking at the sharp end, it’s worth noting that, if you accept that some of the variability in pre-clinical experiments is down to the biological variation we mentioned above, it would at least be consistent with the wide range of patient responses to some cancer treatments. The reason for that, as Cynthia Sears didn’t quite put it, is that we just don’t know enough about how the humans we’re tinkering with actually work.

References

Baker, M. (2016). Is There a Reproducibility Crisis? Nature 533, 452-454.

Jarvis, G.E. (2017). Early embryo mortality in natural human reproduction: What the data say [version 2; referees: 1 approved, 2 approved with reservations] F1000Research 2017, 5:2765 (doi: 10.12688/f1000research.8937.2).

Monya Baker & Elie Dolgin (2017). Cancer reproducibility project releases first results. Nature 541, 269–270. doi:10.1038/541269a.

Begley, C.G. and Ellis, L.M. (2012). Drug development: Raise standards for preclinical cancer research. Nature 483, 531–533.

Prinz,F., Schlange,T. and Asadullah, K. (2011). Believe it or not: how much can we rely on published data on potential drug targets? NatureRev. Drug Discov. 10, 712.

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Caveat emptor

 

It must be unprecedented for publication of a scientific research paper to make a big impact on a significant sector of the stock market. But, in these days of ‘spin-off’ companies and the promise of unimaginable riches from the application of molecular biology to every facet of medicine and biology, perhaps it was only a matter of time. Well, the time came with a bang this June when the journal Nature Medicine published two papers from different groups describing essentially the same findings. Result: three companies (CRISPR Therapeutics, Editas Medicine and Intellia) lost about 10% of their stock market value.

I should say that a former student of mine, Anthony Davies, who runs the Californian company Dark Horse Consulting Inc., mentioned these papers to me before I’d spotted them.

What on earth had they found that so scared the punters?

Well, they’d looked in some detail at CRISPR/Cas9, a method for specifically altering genes within organisms (that we described in Re-writing the Manual of Life).

Over the last five years it’s become the most widely used form of gene editing (see, e.g., Seeing a New World and Making Movies in DNA) and, as one of the hottest potatoes in science, the subject of fierce feuding over legal rights, who did what and who’s going to get a Nobel Prize. Yes, scientists do squabbling as well as anyone when the stakes are high.

Nifty though CRISPR/Cas9 is, it has not worked well in stem cells — these are the cells that can keep on making more of themselves and can turn themselves in other types of cell (i.e., differentiate — which is why they’re sometimes called pluripotent stem cells). And that’s a bit of a stumbling block because, if you want to correct a genetic disease by replacing a defective gene with one that’s OK, stem cells are a very attractive target.

Robert Ihry and colleagues at the Novartis Institutes for Biomedical Research got over this problem by modifying the Cas9 DNA construct so that it was incorporated into over 80% of stem cells and, moreover, they could switch it on by the addition of a drug. Turning on the enzyme Cas9 to make double-strand breaks in DNA in such a high proportion of cells revealed very clearly that this killed most of them.

When cells start dying the prime suspect is always P53, a so-called tumour suppressor gene, switched on in response to DNA damage. The p53 protein can activate a programme of cell suicide if the DNA cannot be adequately repaired, thereby preventing the propagation of mutations and the development of cancer. Sure enough, Ihry et al. showed that in stem cells a single cut is enough to turn on P53 — in other words, these cells are extremely sensitive to DNA damage.

Gene editing by Cas9 turns on P53 expression. Left: control cells with no activation of double strand DNA breaks; right: P53 expression (green fluorescence) several days after switching on expression of the Cas9 enzyme. Scale bar = 100 micrometers. From Ihry et al., 2018.

In a corresponding study Emma Haapaniemi and colleagues from the Karolinska Institute and the University of Cambridge, using a different type of cell (a mutated line that keeps on proliferating), showed that blocking P53 (hence preventing the damage response) improves the efficiency of genome editing. Good if you want precision genome editing by risky as it leaves the cell vulnerable to tumour-promoting mutations.

Time to buy?!

As ever, “Let the buyer beware” and this certainly isn’t a suggestion that you get on the line to your stockbroker. These results may have hit share prices but they really aren’t a surprise. What would you expect when you charge uninvited into a cell with a molecular bomb — albeit one as smart as CRISPR/Cas9. The cell responds to the DNA damage as it’s evolved to do — and we’ve known for a long time that P53 activation is exquisitely sensitive: one double-strand break in DNA is enough to turn it on. If the damage can’t be repaired P53’s job is to drive the cell to suicide — a perfect system to prevent mutations accumulating that might lead to cancer. The high sensitivity of stem cells may have evolved because they can develop into every type of cell — thus any fault could be very serious for the organism.

It’s nearly 40 years since P53 was discovered but for all the effort (over 45,000 research papers with P53 in the title) we’re still remarkably ignorant of how this “Guardian of the Genome” really works. By comparison gene editing, and CRISPR/Cas9 in particular, is in its infancy. It’s a wonderful technique and it may yet be possible to get round the problem of the DNA damage response. It may even turn out that DNA can be edited without making double strand breaks.

So maybe don’t rush to buy gene therapy shares — or to sell them. As the Harvard geneticist George Church put it “The stock market isn’t a reflection of the future.” Mind you, as a founder of Editas Medicine he’d certainly hope not.

References

Ihry, R.J. et al. (2018). p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells. Nature Medicine, 1–8.

Haapaniemi, E. et al. (2018). CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response. Nature Medicine (2018) 11 June 2018.

Now You See It

 

In the pages of this blog we’ve often highlighted the power of fluorescent tags to track molecules and see what they’re up to. It’s a method largely pioneered by the late Roger Tsien and it has revolutionized cell biology over the last 20 years.

In parallel with molecular tagging has come genetic engineering that permits novel genes, usually carried by viruses, to be introduced to cells and animals. As we saw in Gosh! Wonderful GOSH and Blowing Up Cancer, various ‘virotherapy’ approaches have been used with some success to treat leukemias and skin cancers and a trial is underway in China treating metastatic non-small cell lung cancer.

A major aim of genetic engineering is to be able to control the expression of novel genes (i.e. protein production from the encoding DNA sequence) that have been introduced into an animal — in the jargon, to ‘switch’ on or off at will. That can be done but only by administering a drug or some other regulator, either in drinking water, by injection or squirting directly into the lungs. An ideal would be something that’s more controlled and less invasive. How about shining a light on the relevant spot?!

Wacky or what?

That may sound as though we’re veering towards science fiction but reflect for a moment that every animal with vision, however rudimentary, sees by transforming light entering the eyes into electrical signals that the brain turns into a picture of the world around them. This relies on photoreceptor proteins that span the membranes of retinal cells.

How vision works. Light passes through the lens and falls on the retina at the back of the eye. The photoreceptor cells it activates are rod cells (that respond to low light levels — there’s about 100 million of them) and cone cells (stimulated by bright light). Sitting across the membranes of these cells are photoreceptor proteins — rhodopsin in rods and photopsin in cones. Photoreceptor proteins change shape when light falls on them — the driver for this being a small chemical attached to the proteins called retinal, one of the many forms of vitamin A. This shape change allows the proteins to ‘talk’ to the inside of the cell, i.e. to interact with other proteins to switch on enzymes and change the level of ions (sodium and calcium). The upshot is that the signal is passed through neural cells in the optic nerve to the brain where the incoming light signals are processed into the images that we perceive.

The seemingly far-fetched notion of controlling genes by light was floated by Francis Crick in 1999. The field was launched in 2002 by Boris Zemelman and Gero Miesenböck who engineered neurons to express one form of rhodopsin. This gave birth to the subject of optogenetics — using light to control cells in living tissues that have been genetically modified to express light-sensitive ion channels such as rhodopsin. By 2010 optogenetics had advanced to being the ‘Method of the Year’ according to the research journal Nature Methods.

Dropping like flies

One of the most dramatic demonstrations of the power of optogenetics has come from Robert Kittel and colleagues in Würzburg and Göttingen who made a mutant form of a protein called channelrhodopsin-1 (found in green algae) and expressed it in fruit flies (Drosophila melanogaster). The mutant protein (ChR2-XXL) carries very large photocurrents of ions (critically sodium and calcium) with the result that photostimulation can drastically change the behaviour of freely moving flies.

Light-induced stimulation of motor neurons in adult flies expressing a mutant form of rhodopsin ChR2-XXL. Click to run movie.

Left hand tube: Activation of ChR2-XXL in motor neurons with white light LEDs caused reversible immobilization of adult flies. In contrast (right hand tube) flies expressing normal (wild-type) channelrhodopsin-2 showed no response. From Dawydow et al., 2014.

Other optogenetic experiments on flies can be viewed on You Tube, e.g., the TED talk of Gero Miesenböck and the Manchester Fly Facility video of fly maggots, engineered to have a channel protein (channelrhodopsin) in their neurons, responding to blue light.

Of flies … and mice … and men

This is stunning science and it’s opened a new vista in neurobiology. But what about the things we’re concerned with in these pages — treating diseases like diabetes and cancer?

Scheme showing how genetic engineering can make the release of insulin from cells controllable by light. Normally cells of the pancreas (beta cells) take up glucose when its level in the circulation rises (via a glucose transporter protein). The rise in glucose triggers ATP production in the cell. This in turn causes potassium channels in the membrane to close (called depolarization) and this opens calcium channels. The increase in calcium in the cell drives insulin secretion. From Kushibiki et al., 2015.

The left-hand scheme above shows how glucose triggers the pancreas to produce the hormone insulin. Diabetes occurs when either the pancreas doesn’t make enough insulin or when cells of the body don’t respond properly to insulin by taking up glucose.

As a first step to see whether optogenetic regulation of calcium levels in pancreatic cells could trigger insulin release, Toshihiro Kushibiki and colleagues at the National Defense Medical College in Saitama, Japan engineered the channelrhodopsin-1 protein into mouse cells and hit them with laser light of the appropriate frequency. An hour after a short burst of light (a few seconds) the insulin levels had doubled.

The photo below shows a clump of these cells: the nuclei are blue and the channel protein (yellow) can be seen sitting across the cell membranes.

 

Cells expressing a fluorescently tagged channelrhodopsin protein (yellow). Nuclei are blue. From Kushibiki et al., 2015.

 

 

To show that this could work in animals they suspended the engineered cells in a gel and inoculated blobs of the goo under the skin of diabetic mice. Laser burst again: blood glucose levels fell and they showed this was due to the irradiated, implanted cells producing insulin.

Fast forward three years

Those brilliant results highlighted the potential of optogenetic technology as a completely novel approach to a disease that afflicts over 300 million people worldwide.

Scheme showing a Smartphone can be used to regulate the release of insulin from engineered cells implanted in a mouse with diabetes. The key events in the cell are that the light-activated receptor turns on an enzyme (BphS) that in turn controls a transcription regulator (FRTA) that binds to a DNA construct to switch on the Gene Of Interest (GOI) — in this case encoding insulin. (shGLP1, short human glucagon-like peptide 1, is a hormone that has the opposite effect to insulin). From Shao et al., 2017.

In a remarkable confluence of technologies Jiawei Shao and colleagues from a number of institutes in Shanghai, including the Shanghai Academy of Spaceflight Technology, and from ETH Zürich have recently published work that takes the application of optogenetics well and truly into the twenty-first century.

They figured that, as these days nearly everyone lives with their smartphone, the world could use a diabetes app. Essentially they designed a home server SmartController to process wireless signals so that a smartphone could control insulin production by cells in gel capsules implanted in mice. There are differences in the genetic engineering of these cells from those used by Kushibiki’s group but the critical point is unchanged: laser light stimulates insulin release. The capsules carry wirelessly powered LEDs.

The only other thing needed is to know glucose levels. Because mice are only little and they’ve already got their gel capsule, rather than implanting a monitor they took a drop of blood from the tail and used a glucometer. However, looking ahead to human applications, continuous glucose monitors are now available that, placed under the skin, can transmit a radio signal to the controller and, ultimately, it will be possible for the gel capsules to have a built-in battery plus glucose sensor and the whole thing could work automatically.

Any chance of illuminating cancer?

This science is so breathtaking it seems cheeky to ask but, well, I’d say ‘yes but not just yet.’ So long as the ‘drug’ you wish to use can be made biologically (i.e. from DNA by the machinery of the cell), rather than by chemical synthesis, Shao’s Smartphone set-up can readily be adapted to deliver anti-cancer drugs. This might be hugely preferable to the procedures currently in use and would offer an additional advantage by administering drugs in short bursts of lower concentration — a regimen that in some mouse cancer models at least is more effective.

References

Dawydow, A., Kittel, R.J. et al., 2014. Channelrhodopsin-2–XXL, a powerful optogenetic tool for low-light applications. PNAS 111, 13972-13977.

Kushibiki et al., (2015). Optogenetic control of insulin secretion by pancreatic beta-cells in vitro and in vivo. Gene Therapy 22, 553-559.

Shao, J. et al., 2017. Smartphone-controlled optogenetically engineered cells enable semiautomatic glucose homeostasis in diabetic mice. Science Translational Medicine 9, Issue 387, eaal2298.

Another Fine Mess

 

Did you guess from the title that this short piece is about the seeming inability of the British Government to run well, most things but especially IT programmes? Of course you did! Provoked by the latest National Health Service furore. In case you’ve been away with the fairies for a bit, a major cock-up in its computer system has just come to light whereby, between 2009 and 2018, it failed to invite 450,000 women between the ages of 68 and 71 for breast screening. Secretary of State for Health, Jeremy Hunt (our man usually on hand with a can of gasoline when there’s a fire), told Parliament that “there may be between 135 and 270 women who had their lives shortened”. Cue: uproar, headlines: HUNDREDS of British women have died of breast cancer (Daily Express), etc.

Logo credit: Breast Cancer Action

I’ve been reluctant to join in because I’ve said all I think is worth saying about breast cancer screening in two earlier pieces (Risk Assessment and Behind the Screen). Reading them again I thought they were a reasonable summary and I don’t think there’s anything new to add. However, this is  a cancer blog and it’s a story that’s made big headlines so I feel honour-bound to offer a brief comment — in addition to sympathizing with the women and families who have been caused much distress.

My reaction was that Hunt was misguided in mentioning specific numbers — not only because he was asking for trouble from the press but mainly because the evidence that screening itself saves lives is highly questionable. For an expert view on this my Cambridge colleague David Spiegelhalter, who is Professor for the Public Understanding of Risk, has analysed the facts behind breast screening with characteristic clarity in the New Scientist.

Anything to add?

I was relieved on re-reading Risk Assessment to see that I’d given considerable coverage to the report that had just come out (2014) from The Swiss Medical Board.  They’d reviewed the history of mammography screening, concluded that systematic screening might prevent about one breast cancer death for every 1000 women screened, noted that there was no evidence that overall mortality was affected and pointed out that false positive test results presented the risk of overdiagnosis.

In the USA, for example, over a 10-year course of annual screening beginning at 50 years of age, one breast-cancer death would have been prevented whilst between 490 and 670 women would have had a false positive mammogram calling for a repeat examination, 70 to 100 an unnecessary biopsy and between 3 and 14 would have been diagnosed with a cancer that would never have become a problem.

Needless to say, this landed the Swiss Big Cheeses in very hot water because there’s an awful lot of vested interests in screening and it’s sort of instinctive that it must be a good thing. But what’s great about science is that you can do experiments — here actually analysing the results of screening programmes — and quite often the results turn to be completely unexpected, as it did in this case where the bottom line was that mammography does more harm than good.

This has led to the recommendation that the current programmes in Switzerland should be phased out and not replaced.

So we’re all agreed then?

Of course not. In England the NHS recommendation remains that women aged 50 to 70 are offered mammography every three years — which is just as well or we’d have Hunt explaining the recent debacle as new initiative. The American Cancer Society “strongly” recommends regular screening mammography starting at age 45 and the National Cancer Institute refers to “experts” that recommend mammography every year starting at age 25 for women with mutations in their BRCA1 or BRCA2 genes.

The latter is really incredible because a study published in the British Medical Journal in 2012 found that these mutations made the carriers much more vulnerable to radiation-induced cancer. Specifically, women with BRCA 1/2 mutations who were exposed to diagnostic radiation (i.e. mammography) before the age of 30 were twice as likely to develop breast cancer, compared to those with normal BRCA genes.

They are susceptible to radiation that would not normally be considered dangerous because the two BRCA genes encode proteins involved in the repair of damaged DNA — and if that is defective you have a recipe for cancer.

Extraordinary.

So it’s probably true that the only undisputed fact is that we need much better ways for detecting cancers at an early stage of development. The best hope at the moment seems to be the liquid biopsy approach we described in Seeing the Invisible: A Cancer Early Warning System? but that’s still a long way from solving a general cancer problem, well illustrated by breast mammography.

No It Isn’t!

 

It’s great that newspapers carry the number of science items they do but, as regular readers will know, there’s nothing like the typical cancer headline to get me squawking ‘No it isn’t!” Step forward The Independent with the latest: “Major breakthrough in cancer care … groundbreaking international collaboration …”

Let’s be clear: the subject usually is interesting. In this case it certainly is and it deserves better headlines.

So what has happened?

A big flurry of research papers has just emerged from a joint project of the National Cancer Institute and the National Human Genome Research Institute to make something called The Cancer Genome Atlas (TCGA). This massive initiative is, of course, an offspring of the Human Genome Project, the first full sequencing of the 3,000 million base-pairs of human DNA, completed in 2003. The intervening 15 years have seen a technical revolution, perhaps unparalled in the history of science, such that now genomes can be sequenced in an hour or two for a few hundred dollars. TCGA began in 2006 with the aim of providing a genetic data-base for three cancer types: lung, ovarian, and glioblastoma. Such was its success that it soon expanded to a vast, comprehensive dataset of more than 11,000 cases across 33 tumor types, describing the variety of molecular changes that drive the cancers. The upshot is now being called the Pan-Cancer Atlas — PanCan Atlas, for short.

What do we need to know?

Fortunately not much of the humungous amounts of detail but the scheme below gives an inkling of the scale of this wonderful endeavour — it’s from a short, very readable summary by Carolyn Hutter and Jean Claude Zenklusen.

TCGA by numbers. The scale of the effort and output from The Cancer Genome Atlas. From Hutter and Zenklusen, 2018.

The first point is obvious: sequencing 11,000 paired tumour and normal tissue samples produced mind-boggling masses of data. 2.5 petabytes, in fact. If you have to think twice about your gigas and teras, 1 PB = 1,000,000,000,000,000 B, i.e. 1015 B or 1000 terabytes. A PB is sometimes called, apparently, a quadrillion — and, as the scheme helpfully notes, you’d need over 200,000 DVDs to store it.

The 33 different tumour types included all the common cancers (breast, bowel, lung, prostate, etc.) and 10 rare types.

The figure of seven data types refers to the variety of information accumulated in these studies (e.g., mutations that affect genes, epigenetic changes (DNA methylation), RNA and protein expression, duplication or deletion of stretches of DNA (copy number variation), etc.

After which it’s worth pausing for a moment to contemplate the effort and organization involved in collecting 11,000 paired samples, sequencing them and analyzing the output. It’s true that sequencing itself is now fairly routine, but that’s still an awful lot of experiments. But think for even longer about what’s gone into making some kind of sense of the monstrous amount of data generated.

And it’s important because?

The findings confirm a trend that has begun to emerge over the last few years, namely that the classification of cancers is being redefined. Traditionally they have been grouped on the basis of the tissue of origin (breast, bowel, etc.) but this will gradually be replaced by genetic grouping, reflecting the fact that seemingly unrelated cancers can be driven by common pathways.

The most encouraging thing to come out of the genetic changes driving these tumours is that for about half of them potential treatments are already available. That’s quite a surprise but it doesn’t mean that hitting those targets will actually work as anti-cancer strategies. Nevertheless, it’s a cheering point that the output of this phenomenal project may, as one of the papers noted, serve as a launching pad for real benefit in the not too distant future.

What should science journalists do to stop upsetting me?

Read the papers they comment on rather than simply relying on press releases, never use the words ‘breakthrough’ or ‘groundbreaking’ and grasp the point that science proceeds in very small steps, not always forward, governed by available methods. This work is quite staggering for it is on a scale that is close to unimaginable and, in the end, it will lead to treatments that will affect the lives of almost everyone — but it is just another example of science doing what science does.

References

Hutter, C. and Zenklusen, J.C. (2018). The Cancer Genome Atlas: Creating Lasting Value beyond Its Data. Cell 173, 283–285.

Hoadley, K.A. et al. (2018). Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell 173, 291–304.

Hoadley, K.A. et al. (2014). Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin. Cell 158, 929–944.

Hitchhiker Or Driver?

 

It’s a little while since we talked about what you might call our hidden self — the vast army of bugs that colonises our nooks and crannies, especially our intestines, and that is essential to our survival.

In Our Inner Self we noted that these little guys outnumber the human cells that make up the body by about ten to one. Actually that estimate has recently been revised — downwards you might be relieved to hear — to about 1.3 bacterial cells per human cell but it doesn’t really matter. They are a major part of what’s called the microbiome — a vast army of microorganisms that call our bodies home but on which we also depend for our very survival.

In our personal army there’s something like 700 different species of bacteria, with thirty or forty making up the majority. We upset them at our peril. Artificial sweeteners, widely used as food additives, can change the proportions of types of gut bacteria. Some antibiotics that kill off bacteria can make mice obese — and they probably do the same to us. Obese humans do indeed have reduced numbers of bugs and obesity itself is associated with increased cancer risk.

In it’s a small world we met two major bacterial sub-families, Bacteroidetes and Firmicutes, and noted that their levels appear to affect the development of liver and bowel cancers. Well, the Bs & Fs are still around you’ll be glad to know but in a recent piece of work the limelight has been taken by another bunch of Fs — a sub-group (i.e. related to the Bs & Fs) called Fusobacterium.

It’s been known for a few years that human colon cancers carry enriched levels of these bugs compared to non-cancerous colon tissues — suggesting, though not proving, that Fusobacteria may be pro-tumorigenic. In the latest, pretty amazing, installment Susan Bullman and colleagues from Harvard, Yale and Barcelona have shown that not merely is Fusobacterium part of the microbiome that colonises human colon cancers but that when these growths spread to distant sites (i.e. metastasise) the little Fs tag along for the ride! 

Bacteria in a primary human bowel tumour.  The arrows show tumour cells infected with Fusobacteria (red dots).

Bacteria in a liver metastasis of the same bowel tumour.  Though more difficult to see, the  red dot (arrow) marks the presence of bacteria from the original tumour. From Bullman et al., 2017.

In other words, when metastasis kicks in it’s not just the tumour cells that escape from the primary site but a whole community of host cells and bugs that sets sail on the high seas of the circulatory system.

But doesn’t that suggest that these bugs might be doing something to help the growth and spread of these tumours? And if so might that suggest that … of course it does and Bullman & Co did the experiment. They tried an antibiotic that kills Fusobacteria (metronidazole) to see if it had any effect on F–carrying tumours. Sure enough it reduced the number of bugs and slowed the growth of human tumour cells in mice.

Growth of human tumour cells in mice. The antibiotic metronidazole slows the growth of these tumour by about 30%. From Bullman et al., 2017.

We’re still a long way from a human therapy but it is quite a startling thought that antibiotics might one day find a place in the cancer drug cabinet.

Reference

Bullman, S. et al. (2017). Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science  358, 1443-1448. DOI: 10.1126/science.aal5240

One More Small Step

 

Back in the nineteenth century a chap called Augustus De Morgan came up with a set of laws that, when explained in English, sound like the lyrics of a Flanders & Swann song. Opaque to non-maths nerds they may be but they helped to build the mathematics of logic, so next time you meet AND / OR gates in electronics, spare him a thought.

In fact Augustus is rare — maybe unique — among mathematicians in that he’s not completely forgotten, for it was he who penned the lines:

Big fleas have little fleas upon their backs to bite ’em,
And little fleas have lesser fleas, and so, 
ad infinitum.

Given that we now know there’s over 2,500 species of fleas ranging in size from tiny to nearly one centimeter long, it may be literally true. But here, for once, the truth doesn’t matter. It’s a silly rhyme but nonsense verse it is not for it could well serve as a motto for biology because it really captures the essential truth of life: the exquisite choreography of living systems by which incomprehensible numbers of interactions come together to make them work.

Human fleas. Don’t worry: you’ll know if you have them.

Unbidden, De Morgan’s ditty came into my head as I was reading the latest research paper from David Lyden’s group, which he very kindly sent me ahead of publication this week. Avid readers will know the name for we have devoted several episodes (Keeping Cancer Catatonic, Scattering the Bad Seed and Holiday Reading (4) – Can We Make Resistance Futile) to the discoveries of his group in tackling one of the key questions in cancer — namely, how do tumour cells find their targets when they spread around the body? Key because it is this process of ‘metastasis’ that causes most (over 90%) of cancer deaths and if we knew how it worked maybe we could block it.

A succinct summary of those already condensed episodes would be: (1) cells in primary tumours release ‘messengers’ into the circulation that ‘tag’ metastatic sites before any cells actually leave the tumour, (2) the messengers that do the site-tagging are small sacs — mini cells — called exosomes, and (3) they find specific addresses by carrying protein labels (integrins) that home in to different organs — we represented that in the form of a tube train map in Lethal ZIP codes that pulled the whole story together.

The next small step

Now what the folks from Weill Cornell Medicine, New York, Sloan Kettering and a host of other places have done is adapt a flow system to look more closely at exosomes.

Separating small bodies. Particles are injected into a flowing liquid (left) and cross flow at right angles through a membrane (bottom) permits separation on the basis of effective size (called asymmetrical flow field-flow fractionation).

They found that a wide variety of tumour cell types secrete two distinct populations of exosomes — small (60-80 nanometres diameter) and large (90-120 nm). What’s more they found a third type of nanoparticle, smaller than exosomes (less than 50 nm) and without a membrane — so it’s a kind of blob of lipids and proteins (a micelle would be a more scientific term) — that they christened exomeres.

Is it real?

A perpetual problem in biology is reproducibility — that is, whether a new finding can be replicated independently by someone else. Or, put more crudely, do I believe this? This is such an important matter that it’s worth a separate blog but for the moment we’re OK because the results in this paper speak for themselves. First, by using electron microscopy, Lyden et al could actually look at what they’d isolated and indeed discerned three distinct nano-populations — which is how they were able to put the size limits on them.

Electron microscopy of (left) the input mixture (pre-fractionation) and separated fractions: exomere, small exosomes and large exosomes released by tumour cells.. Arrows indicate exomeres (red), small exosomes (blue) and large exosomes (green), from Zhang et al. 2018.

But what’s most exciting in terms of the potential of these results is what’s in the packets. Looking at the fats (lipids), proteins and nucleic acids (DNA and RNA) they contained it’s clear that these are three distinct entities — which makes it very likely they have different effects.

Given their previous finding it must have been a great relief when Lyden & Co identified integrin address proteins in the two exosome sub-populations. But what’s really astonishing is the range of proteins born by these little chaps: something like 400 in exomeres, about 1000 in small exosomes and a similar number in the big ones — and the fact that each contained unique sets of proteins. The new guys — exomeres — carry among other proteins, metabolic enzymes so it’s possible that when they deliver their cargo it might be able to change the metabolic profile of its target. That could be important as we know such changes happen in cancer.

It’s a bewildering picture and working out even the basics of what these little guys do and how it influences cancer is, as we say, challenging. But I think I know a good man for the job!

Augustus De Morgan looking down.

Mathematicians have a bit of a tendency to look down on us experimentalists thrashing around in the undergrowth and I suspect that up in the celestial library, as old Augustus De Morgan thumbed through this latest paper, a slight smile might have come over his face and he could have been heard to murmur: “See, I told you.”

References

Zhang, H. et al. (2018). Identification of distinct nanoparticles and subsets of extracellular vesicles by asymmetric flow field-flow fractionation. Nature Cell Biology 20, 332–343. doi:10.1038/s41556-018-0040-4

Sweet Love …

 

Sweet love, renew thy force; be it not said

Thy edge should blunter be than appetite,

Which but to-day by feeding is allay’d,

To-morrow sharpen’d in his former might:

No prize for knowing I didn’t write those lines — or even that they’re down to The Bard of Avon. What he was on about here is the distinction between genuine (sweet) love and lust (appetite), the problem being that the latter may be assuaged today but will surely return tomorrow. Had we, by some Star Trek-like device, been able to secure his services for this piece, Shakespeare, master of the double-entendre, would quickly have spotted an opportunity in his new role as pop-sci scribe. For sweet read sugar: for appetite addiction.

Gary Taubes considers sugar to be the root of most western illnesses. Photograph: Alamy

The combination can be toxic, as the estimable US journalist Gary Taubes has argued over the last 15 years. His latest book The Case Against Sugar has just come out and I’m keen to give it a plug. In so doing I should point out that we’ve also done our best in these pages to make the same case — particularly in relation to cancer. However, it’s a little while since we wrote specifically on sugar, diet and cancer, mainly because nothing really new has caught my eye. Reading again the most relevant of our blog stories I thought they did a pretty good job (as Shakespeare might have said, being a chap not known for modesty). Three I thought worth looking at again are:

Biting the Bitter Bullet: how obesity and cancer quite often come hand-in-hand and how it is that we’re seduced into eating more and more of something that can help us get fat and ill.

A Small Helping For Australia: makes the point that this is a global problem (even though Australia’s wonderful).

The Best Laid Plans in Mice and Men..: artificial sweeteners aren’t the solution – just another problem.

Actually, there is one recent result we might mention — from Ken Peeters, Johan Thevelein & colleagues at the University of Leuven. Bearing in mind the long-established ‘Warburg effect’ by which cancer cells switch the energy supply system that breaks down glucose from respiration (using oxygen) to fermentation (making lactate), they looked at yeast cells that grow fastest when they ferment — much as cancer cells grow quicker than normal cells. Rather remarkably, they discovered a hitherto unknown way in which fermentation links to a key pathway controlling cell proliferation. That pathway centres around a protein called RAS that we met in Mission Impossible.

This finding does not show that eating lots of sugar gives you cancer but what it does show is a way by which, if yeast cells ‘eat’ more sugar, they grow faster. It seems quite possible that the underlying mechanism might work in human cells (the human version of the protein that links sugar metabolism to RAS, called SOS1, works in yeast) — giving an explanation for the well-known fact that the more sugar you eat the fatter you are likely to become. And what we do know is that obesity does raise cancer risk.

I dare say Gary might reckon this result worth a footnote in the second edition of: The Case Against Sugar by Gary Taubes is published by Portobello Books (£14.99).

Reference

Peeters, K. et al., (2017). Fructose-1,6-bisphosphate couples glycolytic flux to activation of Ras. Nature Communications 8, Article number: 922 doi:10.1038/s41467-017-01019-z.

Lorenzo’s Oil for Nervous Breakdowns

 

A Happy New Year to all our readers – and indeed to anyone who isn’t a member of that merry band!

What better way to start than with a salute to the miracles of modern science by talking about how the lives of a group of young boys have been saved by one such miracle.

However, as is almost always the way in science, this miraculous moment is merely the latest step in a long journey. In retracing those steps we first meet a wonderful Belgian – so, when ‘name a famous Belgian’ comes up in your next pub quiz, you can triumphantly produce him as a variant on dear old Eddy Merckx (of bicycle fame) and César Franck (albeit born before Belgium was invented). As it happened, our star was born in Thames Ditton (in 1917: his parents were among the one quarter of a million Belgians who fled to Britain at the beginning of the First World War) but he grew up in Antwerp and the start of World War II found him on the point of becoming qualified as a doctor at the Catholic University of Leuven. Nonetheless, he joined the Belgian Army, was captured by the Germans, escaped, helped by his language skills, and completed his medical degree.

Not entirely down to luck

This set him off on a long scientific career in which he worked in major institutes in both Europe and America. He began by studying insulin (he was the first to suggest that insulin lowered blood sugar levels by prompting the liver to take up glucose), which led him to the wider problems of how cells are organized to carry out the myriad tasks of molecular breaking and making that keep us alive.

The notion of the cell as a kind of sac with an outer membrane that protects the inside from the world dates from Robert Hooke’s efforts with a microscope in the 1660s. By the end of the nineteenth century it had become clear that there were cells-within-cells: sub-compartments, also enclosed by membranes, where special events took place. Notably these included the nucleus (containing DNA of course) and mitochondria (sites of cellular respiration where the final stages of nutrient breakdown occurs and the energy released is transformed into adenosine triphosphate (ATP) with the consumption of oxygen).

In the light of that history it might seem a bit surprising that two more sub-compartments (‘organelles’) remained hidden until the 1950s. However, if you’re thinking that such a delay could only be down to boffins taking massive coffee breaks and long vacations, you’ve never tried purifying cell components and getting them to work in test-tubes. It’s a process called ‘cell fractionation’ and, even with today’s methods, it’s a nightmare (sub-text: if you have to do it, give it to a Ph.D. student!).

By this point our famous Belgian had gathered a research group around him and they were trying to dissect how insulin worked in liver cells. To this end they (the Ph.D. students?!) were using cell fractionation and measuring the activity of an enzyme called acid phosphatase. Finding a very low level of activity one Friday afternoon, they stuck the samples in the fridge and went home. A few days later some dedicated soul pulled them out and re-measured the activity discovering, doubtless to their amazement, that it was now much higher!

In science you get odd results all the time – the thing is: can you repeat them? In this case they found the effect to be absolutely reproducible. Leave the samples a few days and you get more activity. Explanation: most of the enzyme they were measuring was contained within a membrane-like barrier that prevented the substrate (the chemical that the enzyme reacts with) getting to the enzyme. Over a few days the enzyme leaked through the barrier and, lo and behold, now when you measured activity there was more of it!

Thus was discovered the ‘lysosome’ – a cell-within-a cell that we now know is home to an array of some 40-odd enzymes that break down a range of biomolecules (proteinsnucleic acidssugars and lipids). Our self-effacing hero said it was down to ‘chance’ but in science, as in other fields of life, you make your own luck – often, as in this case, by spotting something abnormal, nailing it down and then coming up with an explanation.

In the last few years lysosomes have emerged as a major player in cancer because they help cells to escape death pathways. Furthermore, they can take up anti-cancer drugs, thereby reducing potency. For these reasons they are the focus of great interest as a therapeutic target.

Lysosomes in cells revealed by immunofluorescence.

Antibody molecules that stick to specific proteins are tagged with fluorescent labels. In these two cells protein filaments of F-actin that outline cell shape are labelled red. The green dots are lysosomes (picked out by an antibody that sticks to a lysosome protein, RAB9). Nuclei are blue (image: ThermoFisher Scientific).

Play it again Prof!

In something of a re-run of the lysosome story, the research team then found itself struggling with several other enzymes that also seemed to be shielded from the bulk of the cell – but the organelle these lived in wasn’t a lysosome – nor were they in mitochondria or anything else then known. Some 10 years after the lysosome the answer emerged as the ‘peroxisome’ – so called because some of their enzymes produce hydrogen peroxide. They’re also known as ‘microbodies’ – little sacs, present in virtually all cells, containing enzymatic goodies that break down molecules into smaller units. In short, they’re a variation on the lysosome theme and among their targets for catabolism are very long-chain fatty acids (for mitochondriacs the reaction is β-oxidation but by a different pathway to that in mitochondria).

Peroxisomes revealed by immunofluorescence.

As in the lysosome image, F-actin is red. The green spots here are from an antibody that binds to a peroxisome protein (PMP70). Nuclei are blue (image: Novus Biologicals)

Cell biology fans will by now have worked out that our first hero in this saga of heroes is Christian de Duve who shared the 1974 Nobel Prize in Physiology or Medicine with Albert Claude and George Palade.

A wonderful Belgian. Christian de Duve: physician and Nobel laureate.

Hooray!

Fascinating and important stuff – but nonetheless background to our main story which, as they used to say in The Goon Show, really starts here. It’s so exciting that, in 1992, they made a film about it! Who’d have believed it?! A movie about a fatty acid!! Cinema buffs may recall that in Lorenzo’s Oil Susan Sarandon and Nick Nolte played the parents of a little boy who’d been born with a desperate disease called adrenoleukodystrophy (ALD). There are several forms of ALD but in the childhood disease there is progression to a vegetative state and death occurs within 10 years. The severity of ALD arises from the destruction of myelin, the protective sheath that surrounds nerve fibres and is essential for transmission of messages between brain cells and the rest of the body. It occurs in about 1 in 20,000 people.

Electrical impulses (called action potentials) are transmitted along nerve and muscle fibres. Action potentials travel much faster (about 200 times) in myelinated nerve cells (right) than in (left) unmyelinated neurons (because of Saltatory conduction). Neurons (or nerve cells) transmit information using electrical and chemical signals.

The film traces the extraordinary effort and devotion of Lorenzo’s parents in seeking some form of treatment for their little boy and how, eventually, they lighted on a fatty acid found in lots of green plants – particularly in the oils from rapeseed and olives. It’s one of the dreaded omega mono-unsaturated fatty acids (if you’re interested, it can be denoted as 22:1ω9, meaning a chain of 22 carbon atoms with one double bond 9 carbons from the end – so it’s ‘unsaturated’). In a dietary combination with oleic acid  (another unsaturated fatty acid: 18:1ω9) it normalizes the accumulation of very long chain fatty acids in the brain and slows the progression of ALD. It did not reverse the neurological damage that had already been done to Lorenzo’s brain but, even so, he lived to the age of 30, some 22 years longer than predicted when he was diagnosed.

What’s going on?

It’s pretty obvious from the story of Lorenzo’s Oil that ALD is a genetic disease and you will have guessed that we wouldn’t have summarized the wonderful career of Christian de Duve had it not turned out that the fault lies in peroxisomes.

The culprit is a gene (called ABCD1) on the X chromosome (so ALD is an X-linked genetic disease). ABCD1 encodes part of the protein channel that carries very long chain fatty acids into peroxisomes. Mutations in ABCD1 (over 500 have been found) cause defective import of fatty acids, resulting in the accumulation of very long chain fatty acids in various tissues. This can lead to irreversible brain damage. In children the myelin sheath of neurons is damaged, causing neurological defects including impaired vision and speech disorders.

And the miracle?

It’s gene therapy of course and, helpfully, we’ve already seen it in action. Self Help – Part 2 described how novel genes can be inserted into the DNA of cells taken from a blood sample. The genetically modified cells (T lymphocytes) are grown in the laboratory and then infused into the patient – in that example the engineered cells carried an artificial T cell receptor that enabled them to target a leukemia.

In Gosh! Wonderful GOSH we saw how the folk at Great Ormond Street Hospital adapted that approach to treat a leukemia in a little girl.

Now David Williams, Florian Eichler, and colleagues from Harvard and many other centres around the world, including GOSH, have adapted these methods to tackle ALD. Again, from a blood sample they selected one type of cell (stem cells that give rise to all blood cell types) and then used genetic engineering to insert a complete, normal copy of the DNA that encodes ABCD1. These cells were then infused into patients. As in the earlier studies, they used a virus (or rather part of a viral genome) to get the new genetic material into cells. They choose a lentivirus for the job – these are a family of retroviruses (i.e. they have RNA genomes) that includes HIV. Specifically they used a commercial vector called Lenti-D. During the life cycle of RNA viruses their genomes are converted to DNA that becomes a permanent part of the host DNA. What’s more, lentiviruses can infect both non-dividing and actively dividing cells, so they’re ideal for the job.

In the first phase of this ongoing, multi-centre trial a total of 17 boys with ALD received Lenti-D gene therapy. After about 30 months, in results reported in October 2017, 15 of the 17 patients were alive and free of major functional disability, with minimal clinical symptoms. Two of the boys with advanced symptoms had died. The achievement of such high remission rates is a real triumph, albeit in a study that will continue for many years.

In tracing this extraordinary galaxy, one further hero merits special mention for he played a critical role in the story. In 1999 Jesse Gelsinger, a teenager, became the first person to receive viral gene therapy. This was for a metabolic defect and modified adenovirus was used as the gene carrier. Despite this method having been extensively tested in a range of animals (and the fact that most humans, without knowing it, are infected with some form of adenovirus), Gelsinger died after his body mounted a massive immune response to the viral vector that caused multiple organ failure and brain death.

This was, of course, a huge set-back for gene therapy. Despite this, the field has advanced significantly in the new century, both in methods of gene delivery (including over 400 adenovirus-based gene therapy trials) and in understanding how to deal with unexpected immune reactions. Even so, to this day the Jesse Gelsinger disaster weighs heavily with those involved in gene therapy for it reminds us all that the field is still in its infancy and that each new step is a venture into the unknown requiring skill, perseverance and bravery from all involved – scientists, doctors and patients. But what better encouragement could there be than the ALD story of young lives restored.

It’s taken us a while to piece together the main threads of this wonderful tale but it’s emerged as a brilliant example of how science proceeds: in tiny steps, usually with no sense of direction. And yet, despite setbacks, over much time, fragments of knowledge come together to find a place in the grand jigsaw of life.

In setting out to probe the recesses of metabolism, Christian de Duve cannot have had any inkling that he would build a foundation on which twenty-first century technology could devise a means of saving youngsters from a truly terrible fate but, my goodness, what a legacy!!!

References

Eichler, F. et al. (2017). Hematopoietic Stem-Cell Gene Therapy for Cerebral Adrenoleukodystrophy. The New England Journal of Medicine 377, 1630-1638.

 

Much Ado About … Some Things

Given that the ‘festive season’ is approaching, maybe we should try to find something joyous to say about cancer. It’s not difficult. Over the last 60 years (1950-2013) the 5-year Relative Survival Rates for white Americans for breast and prostate cancers have gone from about 50% to over 90% (99.6% in fact for prostate). A number of other types (e.g., testicular cancer) are now largely curable, if treated early enough. Similar trends have occurred in most developed countries – all this through advances in surgery and radiotherapy but, most of all, because of new drugs.

Big Pharma

It’s big business. According to the Financial Times, annual spending on cancer drugs hit $100 billion worldwide in 2014 and is projected to exceed $150 billion by 2020. As you would hope, this expenditure on drug development and production has resulted in a gradual rise in available cancer drugs, represented below by the number of new cancer drugs approved each year by the American Food and Drug Administration (FDA).

Number of new cancer drugs approved each year by the American Food and Drug Administration from 1949 to 2016 (from Hope Cristol, The American Cancer Society, 2016).

Data compiled from drugs@fda.gov, National Cancer Institute, FDA Orange Book, FDA.gov, and centerwatch.com. Reporting and analysis by Sabrina Singleton, ACS research historian.

We should note that the FDA equivalent on this side of the Atlantic is the European Medicines Agency (EMA) and they tend to follow similar licensing patterns. Thus in 2016 a total of 74 new drug approvals were granted by the FDA and the EMA — 19 by the EMA only, 19 by only the FDA, with 36 approved by both. Of the drugs approved by the EMA in 2016, 17 had received prior FDA approval (i.e. in 2015 or earlier). However, only six drugs registered in the US in 2016 had prior EMA approval, indicating that drug companies tend to apply for approval in the US first before registering their products in the EU.

So rejoice and be merry — and drink to the triumph of science!!

It’s not unbounded joy, of course, because global cancer incidence continues to rise and a number of cancers (e.g., lung, liver and pancreas) remain refractive to all approaches thus far with survival rates stuck below 20%.

A Winter’s Tale

But what’s this? A further, wintry blast of reality from The British Medical Journal no less. It comes from Courtney Davis and her friends at King’s College London and the London School of Economics and Political Science (LSE) who looked at the track record of cancer drugs approved by the EMA between 2009 and 2013. Over this period the EMA approved the use of 48 new cancer drugs.

Charge your glass

It might be a good idea to sit down with a stiff drink at this point and remind ourselves that there are only two aims for cancer drugs: they must either extend the life of the patient or improve their quality of life.

What Dr. D & chums found was — and here, to be absolutely clear, we should quote exactly what they said — “… that most drugs entered the market without evidence of benefit on survival or quality of life. At a minimum of 3.3 years after market entry, there was still no conclusive evidence that these drugs either extended or improved life for most cancer indications. When there were survival gains over existing treatment options or placebo, they were often marginal.”

To be precise, it was 57% (39 of the 68 drugs) that entered the market with no evidence that they improved survival or quality of life.

Cripes!

What does this mean – and how can it be?

Well, first up, clearly a lot of money has been spent by drug companies and health services for absolutely no benefit to patients. Unsurprisingly the authors of the study called on the EMA to “increase the evidence bar for the market authorisation of new cancer drugs.” Which I take to mean ‘get some meaningful data before you stick stuff out there.’ But here’s where things get tricky. If your aim is to extend life, how can you prove a drug works other than by giving it to a significant number of patients and waiting a long time to see what happens?

The way round this has been for clinical trials to use indirect or “surrogate” measures of drug efficacy. The idea is that these endpoints show whether a drug has biological activity and thus might be of clinical use. However, they are not reliable measures of improved quality of life or survival.

So this report leaves us with a long-standing problem. On the one hand there is the understandable drive to get new drugs to patients asap but, on the other, there is the fact that only human beings can model how well a drug works in us. However good your in vitro systems may be and however closely mice may resemble men, they’re not the real thing.

One thing we could do that the report suggests, is to integrate the development and commercialization of cancer drugs at least across the two biggest markets of America and Europe so that the FDA and the EMA don’t appear to be operating in parallel worlds.

All told then, perhaps we should supplant our earlier merriment with the chilling thought that, even after so many years of perspiration and inspiration, cancers still present an immense challenge.

References

Davis, C. et al. (2017). Availability of evidence of benefits on overall survival and quality of life of cancer drugs approved by European Medicines Agency: retrospective cohort study of drug approvals 2009-13. BMJ 2017;359:j4530 doi: 10.1136/bmj.j4530 (Published 2017 October 03).

SEER Cancer Statistics Review (CSR) 1975-2014, updated June 28, 2017.

Cristol, H. (2016). Evolution and Future of Cancer Treatments, The American Cancer Society.